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Evolution of the haplo-diplontic life cycle

Evolution of the haplo-diplontic life cycle


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From wikipedia > Biological Life Cycle:

  • haplontic life cycle - the haploid stage is multicellular and the diploid stage is a single cell, meiosis is "zygotic".
  • diplontic life cycle - the diploid stage is multicellular and haploid gametes are formed, meiosis is "gametic".
  • haplodiplontic life cycle [… ] - multicellular diploid and haploid stages occur, meiosis is "sporic".

To my knowledge, all mammal species are diplontic. It might even be true for all vertebrates (but I am not sure). In plants and in fungi, there is a much greater diversity of life cycle however. In many (all?) bryophytes for example, the sporophyte (the diploid phase) is multicellular and its life is completely dependent on the gametophyte. This diversity of life cycle lead to the following question:

What drives the evolution of the relative time an organism spend in the haploid vs in the diploid phase of the life cycle?


This post comes as a follow up to @JAD's comment here


I just want to report the finding of one paper here. I don't know much about the rest of the literature and can't comment on it.

Otto et al. (2015) investigate this question in sexually reproducing organisms. As I understand it, they assume that the amount of time spent in on phase of the life cycle is proportional to the amount of selection happening in this phase. With a theoretical model Otto et al. (2015) showed that there is a sexual conflict over the length of the haploid phase. Mothers favour a longer haploid phase while fathers favour a shorter haploid phase. The outcome of the model depends upon who is in control of the length of this phase.

For mothers, producing a baby is often costly (see Bateman's principle). As such, the mother might want to ensure that its baby has high fitness. In the haploid phase, deleterious recessive alleles are no masked by their dominant counterpart and hence can be purged out of the population. A long haploid phase, therefore allows purging of deleterious alleles and make the diploid phase more resistant which is in the mothers interest.

Among fathers, the evolutionary pressures are different. Fathers evolve to mask mutations carried by their haploid gametes (e.g., by provisioning with diploid gene products), causing their sperm to be more competitive. As such, a father has interest that the haploid phase is short.


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Gilbert SF. Developmental Biology. 6th edition. Sunderland (MA): Sinauer Associates 2000.

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Silicon drives the evolution of complex crystal morphology in calcifying algae

This article is a Commentary on Langer et al. ( 2021), doi: 10.1111/nph.17230.

Coccolithophores are oceanic microalgae that have influenced the global climate for millions of years because of their ability to calcify (e.g. Monteiro et al., 2016 ). Their life cycle is haplo–diplontic with significant differences in the structure and morphology of the calcium carbonate plates (coccoliths) between haploid and diploid life-cycle stages (e.g. de Vargas et al., 2007 Frada et al., 2019 De Vries et al., 2021 ) (see Box 1 for a Glossary of terms). Whereas coccoliths of haploid life-cycle stages (holococcoliths (HOLs)) are uniform in shape and size, diploid stages are characterized by intricately-shaped coccoliths (heterococcoliths (HETs)) of almost infinite morphology. As HOLs seem to be formed differently and only appear in the fossil record c. 30 million years ago (MA) after the first HETs, it has been suggested that HOL formation represents an independent process of calcification, evolving after the emergence of HETs (e.g. Bown et al., 2004 De Vargas et al., 2007 ). Yet, in the recently published article in New Phytologist, Langer et al. ( 2021 doi: 10.1111/nph.17230) have challenged this view by carefully analysing the process of HOL formation. Combining state-of-the-art microscopy tailored to preserve all subcellular structures, and experiments to reveal the role of silicon in the process of calcification, they show that HOLs are formed in intracellular compartments similar to HETs and that silicon is only required for the formation of intricately shaped coccoliths. These results suggest that HOLs might represent an ancestral form of calcification and that the ability to use silicon in the process of calcification evolved later and is responsible for the synthesis of the elaborately shaped HETs.

Box 1. Glossary

Calcite A polymorph of calcium carbonate
Calcification Formation of intracellular calcium carbonate
Coccolithophores Unicellular eukaryotic microalgae from the clade Haptophyta
Coccoliths Calcium carbonate plates attached to the surface of cells
Coccospheres Three-dimensional exoskeleton formed by coccoliths
Diatoms Unicellular eukaryotic microalgae from the phylum Ochrophyta
Diversifying selection Natural selection that favours extreme over intermediate traits
Genetic drift Change in the frequency of an existing gene variant (allele) in a population due to random sampling of organisms
Gene genealogies Evolutionary relationships among haplotypes with populations
Gene flow Transfer of genetic material from one population to another
Haplo–diplontic life cycle Life cycle that includes haploid and diploid life-cycle stages
Heterococcoliths Calcium carbonate plates formed of radial arrays of interlocking calcite crystal units usually with alternating vertical and radial crystallographic orientations
Holococcoliths Calcium carbonate plates formed of rhombohedral calcite crystallites
Silica Silicon dioxide formed from orthosilicic acid by polycondensation

Calcification is the most characteristic feature of coccolithophores, which belong to the group of prymnesiophytes and diverged from their noncalcifying ancestors c. 310 Ma (e.g. Liu et al., 2010 ). There are over 250 known species of coccolithophores in sunlit oceans, contributing up to 10% of annual marine primary production (e.g. Poulton et al., 2007 ). Some species, including Emiliania huxleyi, are so productive that their blooms can be seen from space (Fig. 1). Despite their significance for the global carbon cycle, most studies so far have only focussed on a limited number of diploid coccolithophores with the best studied likely to be E. huxleyi (e.g. Read et al., 2013 Gal et al., 2018 ). Intricately shaped coccoliths allow easier identification of diploid species, which is possibly why haploid life-cycle stages, many of which do not calcify (e.g. von Dassow et al., 2012 ), have largely been neglected, biasing our current knowledge on coccolithophore biology and evolution.

‘The formation of intricately shaped coccoliths from rudimentary calcite crystals requires the presence of silicon. This novel insight brings us closer to understanding the evolution of morphological diversity in algae which have shaped planet Earth.’

How and when the life phase transitions occur is not well known for most coccolithophore species although several drivers have been identified for E. huxleyi (e.g. Frada et al., 2019 ). For instance, viral infections can cause a switch from the diploid to the haploid life-cycle phase to increase survival rates in response to a virus infection (Frada et al., 2008 ). Typically, though, ploidy and the proliferation of life cycle-stages are decoupled, similar to macroalgae and some plants where gametes develop independent life-cycle stages that reproduce asexually, i.e. gametophytes (e.g. Taylor et al., 2005 Coelho & Cock, 2020 ). Thus, both life-cycle stages are exposed to evolutionary forces and therefore might even speciate independently. Generally, it can be assumed that haplo–diplontic life cycles are better at exploring the adaptive landscape of a species because of the larger allelic diversity. Indeed, there is some evidence that different oceanic environments appear to select for different life-cycle stages of coccolithophores (e.g. De Vries et al., 2021 ) however, our knowledge of the adaptive benefits is still very limited. Nevertheless, it is likely that calcification, which underpins the formation of distinct phenotypes, is under selection and therefore the molecular machinery driving it. Depending on the species, basic calcium carbonate crystals (calcite) can transform into nanopatterned and elaborate coccoliths of seemingly infinite shape and form. HETs are formed inside a specialized Golgi-derived vesicle (e.g. Brownlee et al., 2015 ). Before they are extruded, they are formed by an unknown mechanism that controls crystal morphology and the overall shape and form of HETs. Together they form the coccosphere, which can include various appendages and in which the cell resides. In contrast to well-studied HETs, HOLs have received little attention, but their crystals resemble the typical rhombohedral geometry of inorganic calcite (e.g. Young et al., 1999 ). Furthermore, the morphological diversity of HOLs is much more constrained.

In 2016, the same laboratory at the Marine Biological Association (MBA) in Plymouth, UK, discovered that calcifying coccolithophores have something in common with their silicifying cousins: diatoms (Durak et al., 2016 ). However, diatom shells are made of silica and therefore thought to represent a distinct mechanism of biomineralization. This concept was challenged by the discovery of silicon transporters (SITs) in calcifying diploid coccolithophores (Durak et al., 2016 ). Some of these species even appear to have an obligatory requirement for silicon, similar to diatoms. Although the cellular mechanism by which silicon contributes to the process of calcification is still unknown, studies in other organisms have suggested that silica might be essential for the formation of ordered calcite crystals as seen in HETs but not in HOLs (e.g. Gal et al., 2012 ).

The study by Langer et al. has tested the hypothesis that HOLs represent an ancestral state of calcification, which is contradictory to the fossil record. As support for their hypothesis, they combined knowledge on the role of silicon for the formation of HETs and applied advanced microscopy to re-assess the calcification processes in HOLs. By using scanning electron microscopy in combination with high pressure freezing and freeze substitutions to preserve both inorganic and organic structures, it was possible for the first time to reveal that HOLs are formed inside the cells in vesicles similar to the synthesis of HETs. Langer et al. argue that this result provides first evidence for the presence of a last common ancestor that was capable of producing both HOLs and HETs as they share not only the same chemical process of calcification but also the same cell biology required to produce calcite crystals. Thus, Langer et al. have provided an evolutionary link between both modes of calcification (Fig. 2). As HOLs are structurally more simplistic, it suggests that they have evolved first, which was already postulated a few years ago by Frada et al. ( 2019 ). To identify why the additional complexity observed in HETs evolved later, Langer et al. drew on their insights into the role of silicon for the formation of complex calcite crystal morphology. Remarkably, they found that HOLs do not require silicon for crystal formation. They also discovered the presence of rhombohedral HOL crystals in diploid coccolithophores after replacing silicon in the growth medium by germanium. These results suggest that silicon is required for the synthesis of different crystal shapes as both life-cycle stages develop rudimentary rhombohedral crystals but intricately shaped coccoliths are only formed with the help of silicon (Fig. 2).

Although these results seem to have resolved a long-standing paradigm in the evolution of calcification in microalgae (e.g. Bown et al., 2004 De Vargas et al., 2007 ), they raise interesting questions. For instance, not all diploid coccolithophores with HETs require silicon during formation including the model species E. huxleyi (Durak et al., 2016 ). Furthermore, although the requirement for silicon explains why there is complex calcite crystal morphology, it does not explain the almost infinite morphological diversity of coccospheres. I argue that answers to these questions can be found by applying evolutionary theory to silicon and calcium carbonate metabolism. Although phylogenetics has been applied to reveal relationships between individual genes involved in biomineralization, the field will benefit from revealing how the evolutionary forces of mutation, selection, genetic drift and gene flow shaped the genetic and morphological diversity of biomineralizing microalgae. Langer et al. speculate that high concentrations of silicon in the surface oceans c. 250 Ma were driving the evolution of HETs. A subsequent decline of silicon due to the rise of diatoms might have caused the loss of an obligate silicon requirement at least in some species such as E. huxleyi and therefore provided a fitness advantage under lower silicon concentrations. Thus, they argue that changes in the environment selected for the evolution of complex crystal morphology in calcifying algae.

Combining molecular markers and fossils from the geological record of coccolithophores with demographic inference such as coalescence theory (e.g. Rosenberg & Nordborg, 2002 ), which provides a view backwards in time, will provide evidence as to whether environmental change (e.g. silicon concentrations) coincides with the point where gene genealogies (e.g. SITs) come together (‘coalesce’). Furthermore, identifying signals of selection will inform biochemical studies because they reveal which genes and functional domains likely contribute to the evolution of morphological diversity, which potentially is the outcome of diversifying selection. As mutational and demographic models are available for coccolithophores (Bendif et al., 2019 Krasovec et al., 2020 ), I consider this an exciting avenue for providing further insights into what drives the evolution of complex crystal morphology in calcifying algae. If extended to other biomineralizers, it might even reveal a unifying concept on which the apparently distinctive processes of calcification and silicification coalesce.


Results

Strain origins and characteristics at time of harvesting

E. huxleyi strains RCC1216 (2N) and RCC1217 (1N) were both originally isolated into clonal culture less than 10 years prior to the collection of biological material in this study (Table 1). Repeated analyses of nuclear DNA content by flow cytometry have shown no detectable variation in the DNA contents (the ploidy) of these strains over several years ([20] and unpublished tests performed in 2006 to 2008). Axenic cultures of both 1N and 2N strains were successfully prepared.

The growth rates of the 2N and 1N cultures used for library construction were 0.843 ± 0.028 day -1 (n = 4) and 0.851 ± 0.004 day -1 (n = 2), respectively. These rates were not significantly different (P = 0.70). Two other 1N cultures experienced exposure to continuous light for one or two days prior to harvesting due to a failure of the lighting system. The growth rate of these 1N cultures was 0.893 ± 0.008 day -1 (n = 2). These cultures were not used for library construction but were included in RT-PCR tests. Flow cytometric profiles and microscopic examination taken during harvesting indicated that nearly 100% of 2N cells were highly calcified (indicated by high side scatter) and that no calcified cells were present in the 1N cultures [21] (Figure 1). No motile cells were seen in extensive microscopic examination of 2N cultures over a period of 3 months. 1N cells were highly motile, and displayed prominent phototaxis in culture vessels (not shown).

Flow cytometry plot showing conditions of cells in cultures on day of harvesting. (a) 1N and, (b) 2N cells (red) were identified by chlorophyll autofluorescence and their forward scatter (FSC) and side scatter (SSC) were compared to 1 μm bead standards (green).

Both 1N and 2N cultures maintained high photosynthetic efficiency measured by maximum quantum yield of photosytem II (Fv/Fm) throughout the day-night period of harvesting. The Fv/Fm of phased 1N cultures was 0.652 ± 0.009 over the whole 24-h period it was slightly higher during the dark (0.661 ± 0.003) than during the light period (0.644 ± 0.001 P = 9.14 × 10 -5 ). The Fv/Fm of 2N cells was 0.675 ± 0.007, with no significant variation between the light and dark periods. These data suggest that both the 1N and 2N cells were maintained in a healthy state throughout the entire period of harvesting.

Cell division was phased to the middle of the dark period both in 2N cultures and in the 1N cultures on the correct light-dark cycle (Figure S1 in Additional data file 1). The 1N cultures exposed to continuous light did not show phased cell division. Nuclear extraction from the phased 1N cultures showed that cells remained predominantly in G1 phase throughout the day, entered S phase 1 h after dusk (lights off), and reached the maximum in G2 phase at 3 to 4 h into the dark phase (Figure 2). A small G2 peak was present in the morning hours and disappeared in the late afternoon. These data show that we successfully captured all major changes in the diel and cell cycle of actively growing, physiologically healthy 1N and 2N cells for library construction (below).

Cell cycle changes during the day-night cycle of harvesting. Example DNA content histograms of nuclear extracts taken from 1N cultures at different times are shown. The time point at 15 h on day 1 is not shown but had a similar distribution to that at 19 h on day 1 and 15 h30 on day 2. RNA was not collected at 15 h30 on day 2, but nuclear extracts (shown here), flow cytometric profiles, and Fv/Fm confirmed cells had returned to the same state after a complete diel cycle. Extracted nuclei were stained with Sybr Green I and analyzed by flow cytometry.

Global characterization of haploid and diploid transcriptomes

General features, comparison to existing EST datasets, and analysis of transcriptome complexity and differentiation

High quality total RNA was obtained from eight time points in the diel cycle (Figure S2 in Additional data file 1) and pooled for cDNA construction. We performed two rounds of 5'-end sequencing. In the first round, 9,774 and 9,734 cDNA clones were sequenced from the 1N and 2N libraries, respectively. In the second round, additional 9,758 1N and 9,825 2N clones were selected for sequencing. Altogether our sequencing yielded 19,532 1N and 19,559 2N reads for a total of 39,091 reads (from 39,091 clones). Following quality control, we finally obtained 38,386 high quality EST sequences ≥ 50 nucleotides in length (19,198 for 1N and 19,188 for 2N). The average size of the trimmed ESTs was 582 nucleotides with a maximum of 897 nucleotides (Table 2). Their G+C content (65%) was identical to that observed for ESTs from E. huxleyi strain CCMP1516 [22], and was consistent with the high genomic G+C content (approximately 60%) of E. huxleyi.

Sequence similarity searches between the 1N and 2N EST libraries revealed that only approximately 60% of ESTs in one library were represented in the other library. More precisely, 56 to 59% of 1N ESTs had similar sequences (≥ 95% identity) in the 2N EST library, and 59 to 62% of the 2N ESTs had similar sequences in the 1N EST library, with the range depending on the minimum length of BLAT alignment (100 nucleotides or 50 nucleotides). To qualify this overlap between the 1N and 2N libraries, we constructed two artificial sets of ESTs by first pooling the ESTs from both libraries and then re-dividing them into two sets based on the time of sequencing (that is, the first and the second rounds). Based on the same similarity search criteria, a larger overlap (73 to 79%) was found between the two artificial sets than between the 1N and 2N EST sets. Given the fact that our cDNA libraries were normalized towards uniform sampling of cDNA species, this result already indicates the existence of substantial differences between the 1N and 2N transcriptomes in our culture conditions.

Sequence similarity search further revealed an even smaller overlap between the ESTs from RCC1216/RCC1217 and the ESTs from other diploid strains of different geographic origins (CCMP1516, B morphotype, originating from near the Pacific coast of South America, 72,513 ESTs CCMP371, originating from the Sargasso Sea, 14,006 ESTs). Only 38% of the RCC1216/RCC1217 ESTs had similar sequences in the ESTs from CCMP1516, and only 37% had similar sequences in the ESTs from CCMP371 (BLAT, identity ≥ 95%, alignment length ≥ 100 nucleotides Figure 3). Overall, 53% of the RCC1216/RCC1217 ESTs had BLAT matches in these previously determined EST data sets. Larger overlaps were observed for the ESTs from the diploid RCC1216 (47% with CCMP1516 and 45% with CCMP371) than for the haploid RCC1217 strain (37% with CCMP1516 and 36% with CCMP371), consistent with the predominantly diploid nature of the CCMP1516 and CCMP371 strains at the time of EST generation. When the best alignment was considered for each EST, the average sequence identity between strains was close to 100% (that is, 99.7% between RCC1216/RCC1217 and CCMP1516, 99.6% between RCC1216/RCC1217 and CCMP371, and 99.5% between CCMP1516 and CCMP371), being much higher than the similarity cutoff (≥ 95% identity) used in the BLAT searches. The average sequence identity between RCC1216 (2N) and RCC1217 (1N) was 99.9%. Thus, sequence divergence between strains (or alleles) was unlikely to be the major cause of the limited level of overlap between these EST sets. A large fraction of our EST datasets thus likely provides formerly inaccessible information on E. huxleyi transcriptomes.

Venn diagram showing the degree of overlap existing E. huxleyi EST libraries. Included are the libraries analyzed in this study (1N RCC1217 and 2N RCC1216, combined) and the two other publicly available EST libraries (CCMP 1516 and CCMP371). ESTs were considered matching based on BLAT criteria of an alignment length of ≥ 100 nucleotides and ≥ 95% identity. The degrees of overlap increased only very modestly when the BLAT criteria were relaxed to an alignment length of ≥ 50 nucleotides.

One of the primary objectives of this study was to estimate the extent to which the change in ploidy affects the transcriptome. Therefore, we utilized for the following analyses only the ESTs from RCC1216 (2N) and RCC1217 (1N), originating from cultures of pure ploidy state and identical physiological conditions. The 38,386 ESTs from 1N and 2N libraries were found to represent 16,470 consensus sequences (mini-clusters), which were further grouped into 13,056 clusters (Table 3 Additional data file 2 includes a list of all ESTs with the clusters and mini-clusters to which they are associated and their EMBL accession numbers). Of the 13,056 clusters, only 3,519 (26.9%) were represented by at least one EST from each of the two libraries, thus defining a tentative 'core set' of EST clusters expressed in both cell types. The remaining clusters were exclusively composed of EST(s) from either the 1N (4,368 clusters) or the 2N (5,169 clusters) library hereafter, we denote these clusters as '1N-unique' and '2N-unique' clusters, respectively. Cluster size (that is, the number of ESTs per cluster) varied from 1 (singletons) up to 43, and displayed a negative exponential rank-size distribution for both libraries (Figure S3 in Additional data file 1). The Shannon diversity indices were found close to the theoretical maximum for both libraries, indicating a high evenness in coverage and successful normalization in our cDNA library construction (Table 4). Crucially, the fact that the rank-size distributions of the two libraries were essentially identical also shows that the normalization process occurred comparably in both libraries (Figure S3 in Additional data file 1).

Interestingly, a larger number of singletons was obtained from the 2N library (3,704 singletons, 19% of 2N ESTs) than from the 1N library (2,651 singletons, 14% of 1N ESTs), suggesting that 2N cells may express more genes (that is, RNA species) than 1N cells. To test this hypothesis, we assessed transcriptome richness (that is, the total number of mRNA species) of 1N and 2N cells using a maximum likelihood (ML) estimate [23] and the Chao1 richness estimator [24]. These estimates indicated that 2N cells express 19 to 24% more genes than 1N cells under the culture conditions in this study, supporting the larger transcriptomic richness for 2N relative to 1N (Table 4). To assess the above-mentioned small overlap between the 1N and 2N EST sets, we computed the abundance-based Jaccard similarity index between the two samples based on our clustering data. This index provides an estimate for the true probability with which two randomly chosen transcripts, one from each of the two libraries, both correspond to genes expressed in both cell types (to take into account that further sampling of each library would likely increase the number of shared clusters because coverage is less than 100%). From our samples, this index was estimated to be 50.6 ± 0.9% and again statistically supports a large transcriptomic difference between the haploid and diploid life cycles.

Functional difference between life stages

In the NCBI eukarote orthologous group (KOG) database, 3,286 clusters (25.2%) had significant sequence similarity to protein sequence families (Additional data file 3 provides a list of all clusters with their top homologs identified in UniProt, Swiss-Prot, and KOG, and also the number of component mini-clusters and ESTs from each library). Of these KOG-matched clusters, 2,253 were associated with 1N ESTs (1,385 shared core clusters plus 868 1N-unique clusters), and 2,418 were associated with 2N ESTs (1,385 shared core clusters plus 1,033 2N-unique clusters). The distributions of the number of clusters across different KOG functional classes were generally similar among the 1N-unique, the 2N-unique and the shared core clusters, with exceptions in several KOG classes (Figure 4a). The 'signal transduction mechanisms' and 'cytoskeleton' classes were significantly over-represented (12.3% and 4.15%) in the 1N-unique clusters relative to the 2N-unique clusters (7.36% and 1.55%) (P < 0.002 Fisher's exact test, without correction for multiple tests). These classes were also less abundant in the shared clusters (6.06% and 2.02%) compared to the 1N-unique clusters (P = 3.49 × 10 -7 for 'signal transduction mechanisms' P = 0.00395 for 'cytoskeleton'). In contrast, the 'translation, ribosomal structure and biogenesis' class was significantly under-represented (3.69%) in the 1N-unique clusters compared to the 2N-unique (6.97%) and the shared clusters (7.58%). Similar differences were observed when the 1N-unique and 2N-unique sets were further restricted to clusters containing two or more ESTs (Figure S4 in Additional data file 1).

Distribution of clusters and reads by KOG functional class and library. Distributions of clusters over KOG class for clusters shared between the 1N and 2N libraries and clusters unique to each library. Fisher's exact test was used to determine significant differences in the distribution of clusters by KOG class between the 1N-unique and 2N-unique sets (asterisks indicate the KOG classes exhibiting significant differences between the 1N-unique and 2N-unique sets) P < 0.002 without correction for multiple tests). The same test was applied to determine differences in the distribution of clusters by KOG class between the set of shared clusters and both 1N-unique and 2N-unique clusters (the at symbol (@) indicates KOG classes exhibiting significant differences between the 1N-unique and shared sets P < 0.002 without correction for multiple tests).

We used Audic and Claverie's method [25] to rank individual EST clusters based on the significance of differential representation in 1N versus 2N libraries. An arbitrarily chosen threshold of P < 0.01 provided a list of 220 clusters predicted to be specific to 1N (Additional data file 4) and a list of 110 clusters predicted to be specific to 2N (Additional data file 5). A major caveat is that normalization tends to reduce the confidence in determining differentially expressed genes between cells. As a first step to examine the prediction, we were particularly interested in transcripts that may be effectively absent in one life phase but not the other. Namely, we focused on 198 (90.0%) that are specific and unique to 1N as well as 89 (80.9%) clusters that are specific and unique to 2N, which we termed 'highly 1N-specific' (Tables 5 and 6 Additional data file 4) and 'highly 2N-specific' clusters (Tables 7 and 8 Additional data file 5).

The most significantly differentially represented highly 1N-specific clusters (P = 10 -9

10 -4 ) included a homolog of histone H4 (cluster GS09138 1N ESTs = 13 versus 2N ESTs = 0), a homolog of cAMP-dependent protein kinase type II regulatory subunit (GS00910 1N = 14 versus 2N = 0), a transcript encoding a DNA-6-adenine-methyltransferase (Dam) domain (GS02990) and four other clusters of unknown functions. Other predicted highly 1N-specific clusters included several flagellar components, and three clusters showing homology to the Myb transcription factor superfamily (GS00117, GS00273, GS01762 1N = 8, 8, and 6 ESTs, respectively, and 2N = 0 in all cases). The most significantly differentially represented highly 2N-specific clusters (P = 10 -7

10 -4 ) included a cluster of unknown function (GS11002 1N = 0 and 2N = 16) and a weak homolog of a putative E. huxleyi arachidonate 15-lipoxygenase (E-value 2 × 10 -6 ). Of the 199 highly 1N-specific clusters, 40 had homologs in the KOG database, including 9 clusters (22.5%) assigned to the 'posttranslational modification, protein turnover, chaperones' class and 10 (25.0%) assigned to the 'signal transduction mechanisms' class. The KOG classes for the 22 2N-specific clusters with KOG matches appeared more evenly distributed, with slightly more abundance in the 'signal transduction mechanisms' class (4 clusters, 18.2%). As discussed in the 'Validation and exploration of the predicted differential expression of selected genes' section of the Results, RT-PCR tests validated these predictions of differential expression with a high rate of success.

Taxonomic distribution of transcript homology varies over the life cycle

To characterize the taxonomic distribution of the homologs of EST clusters, we performed BLASTX searches against a combined database, which includes the proteomes from 42 selected eukaryotic genomes taken from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database (see Additional data file 6 for a list of selected genomes from the KEGG database) as well as prokaryotic/viral sequences from the UniProt database. There were 4,055 clusters (31.1% 1,731 shared, 1,083 1N-unique and 1,241 2N-unique clusters) with significant homology in the database (E-value <1 × 10 -10 ), with Viridiplantae, stramenopiles, and metazoans receiving the largest numbers of hits (72.1%, 66.4%, and 60.9%, respectively, of all clusters with KEGG hits). These clusters were classified by the taxonomic group of their closest BLAST homolog (that is, 'best hit'). The distribution of the taxonomic group was found to substantially vary among the shared, 1N-unique and 2N-unique clusters. Shared clusters had a significantly higher proportion of best hits to stramenopiles compared to both 1N-unique and 2N-unique clusters, while 1N-unique clusters had a significantly lower percentage of best hits to stramenopiles than 2N-unique clusters. In contrast, metazoans received a significantly greater portion of best hits from 1N-unique than from 2N-unique and shared clusters. Consistent with the above functional analysis, the KOG class 'signal transduction mechanisms' was over-represented in clusters best-hitting to metazoans (11.0%) compared to all clusters with homologs in KEGG (5.0%) or clusters best-hitting to Viridiplantae (4.8%) (P = 2.9 × 10 -13 and 5.0 × 10 -6 , respectively Fishers exact test). There was no difference among 1N-unique, 2N-unique, and shared clusters in the proportion of clusters with best hits to Viridiplantae (Figure 5). However, among the Viridiplantae best hits, a significantly greater proportion of 1N-unique clusters was found to be best-hitting to Chlamydonomas reinhardtii (Figure 5), the only free-living motile, haploid genome from Viridiplantae represented in our database.

The taxonomic distribution of homology. Shown are the percentages of clusters with KEGG homologs that have the 'best hit' in each taxonomic group. Indicated are cases where the proportion of clusters best hitting to the taxonomic group differs between 1N-unique and 2N-unique (asterisks) or between 1N-unique and shared clusters (at symbol (@)), tested as above. The inset shows the proportion of all assigned clusters that are accounted for by best-hits to Chlamydomonas reinhardtii (a subset of those which are best-hits to Viridiplantae). The differences between 1N-unique and 2N-unique, and between 1N-unique and shared clusters were significant (P < 0.002).

Of all clusters best-hitting to either Viridiplantae, stramenopiles, or metazoans, the shared clusters had the highest percentage of clusters (53.6%) with homologs in all three groups, and the lowest percentage of clusters (3.1%) with homologs only in metazoans (Figure S5 in Additional data file 1). Clusters with homologs in stramenopiles were significantly over-represented among shared clusters and under-represented in 1N-unique clusters relative to 2N-unique clusters.

The vast majority (7,442 clusters 57.0%) of the total EST clusters were orphans (Figure 6a). One of the main causes of the high orphan proportion might be the presence of many short EST clusters with only one or a few ESTs. The non-orphan clusters (having matches in UniProt, KOG, or the conserved domains database (CDD)) exhibited a significantly higher average number of reads per cluster (3.67, combining reads from both libraries) than orphan clusters (2.39 P < 0.0001, Mann-Whitney test). In a similar way, the orphan proportion decreased to 39.4% for the shared core clusters (Figure 6b), which have an average of 6.25 ESTs per cluster. However, a more detailed analysis indicated that the size of clusters (that is, the number of ESTs in the cluster) may not be the sole reason for the abundance of the orphan clusters. For instance, 58.6% of 1N-unique clusters with two or more ESTs were orphan clusters (Figure 6c). Furthermore, an even higher orphan proportion (63.9%) was obtained when these 1N-unique clusters were limited to the 119 clusters represented by ≥ 7 ESTs. Similarly high orphan proportions were also obtained for the 2N-unique clusters (56.3% for the clusters with ≥ 2 ESTs (Figure 6d), and 55.0% for the 60 clusters with ≥ 7 ESTs.). Overall, these results suggest that our transcriptomic data include many new genes probably unique to haptophytes, coccolithophores or E. huxleyi, and that many of these unique genes may be preferentially expressed in one of the two life cycle phases.

The proportion of orphan clusters. Non-orphan clusters that do not have hits in the KOG database are also represented (Others). (a) All clusters. (b) Shared clusters composed of reads in both 1N and 2N libraries. (c) Potentially 1N-specific clusters composed of two or more reads in the 1N library but zero in the 2N library. (d) Potentially 2N-specific clusters composed of two or more reads in the 2N library but zero in the 1N library.

Validation and exploration of the predicted differential expression of selected genes

We examined how well our in silico comparison of the two normalized libraries successfully identified gene content differentiating the two transcriptomes based on in-depth sequence/bibliographic analysis and RT-PCR assays (summarized in Tables S1 and S2 in Additional data file 7). We began with homologs of eukaryotic flagellar-associated proteins. This large group of proteins is well-conserved across motile eukaryotes. Genes for proteins known to be exclusively present in flagellar or basal bodies are expected to be specifically expressed in the motile 1N stage of E. huxleyi, whereas those for proteins known to also serve functions in the cell body may also be expressed in non-motile cells. Thus, flagella-related genes serve as a particularly useful initial validation step. Next, we examined several other clusters with strong in silico signals for differential expression between the 1N and 2N libraries. Finally, we explored clusters homologous to known Ca 2+ and H + transporters, potentially involved in the calcification process of 2N cells, and histones, which might play roles in epigenetic control of 1N versus 2N differentiation. In total, we tested the predicted expression patterns of 39 clusters representing 38 different genes. The predicted expression pattern (1N-specific, 2N-specific, or shared) was confirmed for 37 clusters (36 genes), demonstrating a high rate of success of the in silico comparison of transcriptome content.

Motility-related clusters

A total of 156 E. huxleyi EST clusters were found to be homologous to 85 flagellar-related or basal body-related proteins from animals or C. reinhardtii, a unicellular green alga serving as a model organism for studies of eukaryotic flagella/cilia [26–28] (Tables 9 and 10). This analysis combined a systematic BLAST searche using 100 C. reinhardtii motility-related proteins identified by classic biochemical analysis [27] with additional homology searches (detailed analysis provided in Additional data files 8 and 9). Of the 100 C. reinhardtii proteins, 64 were found to have one or more similar sequences in the E. huxleyi EST dataset. We could also identify homologs for six of the nine Bardet-Biedl syndrome (BBS) proteins known to be basal body components [29, 30]. Excluding 64 clusters closely related to proteins known to play additional roles outside the flagellum/basal body (such as actin and calmodulin) and 10 clusters showing a relatively low level of sequence similarity to flagellar-related proteins, 82 of the 156 clusters were considered highly specific to motility. Remarkably, these clusters were found to be represented by 252 ESTs from the 1N but 0 ESTs from the 2N library (Table 9). In contrast, clusters related to proteins with known possible roles outside of flagella tended to be composed of ESTs from both 1N and 2N libraries, as expected (Table 10).

The abundance of 1N-unique EST clusters with the closest homolog in Metazoa (Figure 5) appears to be partially due to the expression of genes related to flagellar components in 1N cells. In fact, 58 (37.2%) of the 156 motility-related clusters had best-hits to Metazoa in the KEGG database, compared to only 789 (14.1%) of all 5,614 non-orphan clusters (P = 2.9 × 10 -13 ).

Six core structural components of the flagellar apparatus were chosen for RT-PCR tests (Figure 7). These included three flagellar dynein heavy chain (DHC) paralogs (GS00667, GS02579 and GS00012), a homolog of the outer dynein arm docking complex protein ODA-DC3 (GS04411), a homolog of FAP189 and FAP58/MBO2, highly conserved but poorly characterized coiled-coil proteins identified in the C. reinhardti flagellar proteome [27] (GS02724), and a homolog of the highly conserved basal body protein BBS5 (GS00844) [31]. All showed expression restricted to 1N cells no signal could be detected for these five clusters in any 2N RNA samples. Curiously, three non-overlapping primer sets designed to GS000844 (BBS5) all detected evidence of incompletely spliced transcript products, suggesting its regulation by alternative splicing.

RT-PCR confirmation of expression of selected flagellar-related genes only in 1N cells. All reactions were run with the same RT+ cDNA samples. The RT-PCR shown at the top used the elongation factor 1α (GS000217) as a positive (loading) control showing successful cDNA amplification occurred in all samples. RT- control reactions prepared from the same RNA were run for nine of the PCRs shown here and no contaminating genomic DNA (gDNA) was ever found (see examples with RT- reactions included in Figure S6 in Additional data file 1). For clarity, RT- control reactions run simultaneously have been cut out here. Positions of molecular weight markers on each side of the gel are shown. The sample identifiers are listed for each lane at the top of the gel. 11 h, harvested at 11 h (late morning) 21 h, harvested at 21 h (early evening, time of S-phase) 02 h, harvested at 02 h (after cell division) CL, cultures (1N only) exposed to continuous light.

GS05223, containing three ESTs from the 1N library and none from the 2N, showed a significant sequence similarity to C. reinhardtii minus and plus agglutinins (BLASTX, E-values 3 × 10 -5 and 8 × 10 -6 , respectively), flagellar associated proteins involved in sexual adhesion [32]. RT-PCR confirmed that expression of GS05223 was highly specific to 1N cells, being undetectable in 2N cells (Figure 7). However, inspection of the BLASTX alignment between GS05223 and C. reinhardtii agglutinins revealed that the sequence similarity was associated with the translation of the reverse-complement of GS05223. We also found that all of the three ESTs in GS05223 contained poly-A tails, so must be expressed in the forward direction. Therefore, we concluded that GS05223 represents an unknown haploid-specific gene product that may not be related to flagellar functions.

Next we investigated four clusters that are homologous to proteins known to often have additional, non-flagellar roles in the cytoplasm, but that were represented only in the 1N library. Two clusters (GS02889 and GS03135) displayed homology to cytoplasmic dynein heavy chain (DHC), which is associated with flagella/cilia due to its role in intraflagellar transport. In animals and amoebozoa, it also has non-flagellar functions such as intracellular transport and cell division [33] however, both clusters showed potential 1N-specific expression, being represented by two and five 1N ESTs and zero 2N ESTs, respectively, and RT-PCR confirmed the predicted highly 1N-specific expression pattern (Figure 7).

The flagellar-related clusters included five homologs of phototropin. In C. reinharditii, phototropin is found associated with the flagellum and plays a role in light-dependent gamete differentiation [34]. However, phototropin is a light sensor involved in the chloroplast-avoidance response in higher plants [35], so can have roles outside the flagellum. Clusters GS00132, GS01923, and GS00920 showed the highest similarities to the C. reinharditii phototoropin sequence (E-values 1 × 10 -22 , 1 × 10 -21 , and 1 × 10 -22 , respectively) and were all only represented in the 1N library (four, four, and three ESTs, respectively). In contrast, GS04170, which showed weaker homology to phototropins (E-value 3 × 10 -9 ), was represented by four ESTs in the 2N library and zero from the 1N library. These four clusters all aligned well over the highly conserved LOV2 (light, oxygen, or voltage) domains [35, 36] of C. reinhardtii and Arabidopsis thaliana phototropins (Figure S7 in Additional data file 1). The fifth phototropin homolog, GS01944, was represented by ESTs from both libraries. GS01944 did not correspond to the LOV2 domain. GS00132 and GS00920 were selected for RT-PCR validation, which confirmed that expression of these clusters was indeed highly restricted to 1N cells (Figure 7), as predicted by in silico comparison of the two libraries.

We found that several of the selected flagellar-related EST clusters (GS00012, GS04411, GS00844, GS00132 and GS00920) showed a strongly diminished RT-PCR signal in the samples collected during the time of S-phase (Figure 7). Because many genes tested in this study did not display this pattern (for example, GS00217, GS00508, and GS00234), it might be due to real differences in the circadian timing of flagellar gene expression.

Use of digital subtraction to identify other 1N- or 2N-specific transcripts

Fourteen of the 199 clusters predicted to be highly 1N-specific and 10 of the 89 clusters predicted to be highly 2N-specific were tested by RT-PCR (Tables 5, 6, 7 and 8 Tables S1 and S2 in Additional data file 7). Twenty-three out of these 24 clusters did show the predicted strong phase-specific expression pattern, confirming that in silico subtraction of the two libraries identifies true phase-specific transcripts with a high success rate. Two (the DHC homologs GS00667 and GS00012) were discussed previously and the remaining 22 are discussed in this and the following sections.

1N-specific conserved flagellar-related cluster and 1N-specific possible signal transduction clusters

GS00242 had a moderate level of sequence similarity to the C. reinhardtii predicted protein A8J798 (E-value 4 × 10 -14 ) and the human spermatogenesis-associated protein SPT17 (E-value 8 × 10 -11 ). Although A8J798 is not among the previously confirmed flagellar protein components listed in Table S3 of Pazour et al. [27], these authors identified peptides derived from A8J798 in the C. reinhardtii flagellar proteome (listed as C-6350001). GS00242 was composed of eight 1N ESTs and zero 2N ESTs. We confirmed by RT-PCR that GS00242 could be detected in 1N RNA samples, but not in 2N RNA samples (Figure 8). GS00910 was classed by KOG as related to cGMP-dependent protein kinases and had a top Swiss-Prot hit to the Drosophila melanogaster protein KAPR2, a cAMP-dependent protein kinase type II regularory subunit. It was represented by 14 1N ESTs and 0 2N ESTs and detected by RT-PCR only in 1N RNA samples (Figure 8). The predicted highly 1N-specific expression of two further signal transduction-related clusters (GS00184, a putative protein kinase, and GS00234, a putative calmodulin-dependent kinase) was also confirmed by RT-PCR (Figure S8 in Additional data file 1).

RT-PCR tests of expression patterns of selected genes chosen by digital subtraction. RT- control reactions prepared from the same RNA were run for six of the PCRs shown here and no contaminating genomic DNA (gDNA) was ever found. For clarity, RT- control reactions run simultaneously have been cut out here. Positions of molecular weight markers on each side of the gel are shown. The sample identifiers are listed for each lane at the top of the gel (as for Figure 7).

1N-specific Myb homologs

Myb transcription factors control cell differentiation in plants and animals [37–39]. Of the three Myb homologs predicted to be highly 1N-specific, GS00273 was chosen for validation because it had the highest homology to known Myb proteins (Gallus gallus c-Myb transcription factor E-value 3 × 10 -34 ). The amino acid sequence derived from GS00273 was readily aligned over the conserved R2-R3 DNA binding regions of Myb family members [37] (Figure S9 in Additional data file 1). RT-PCR confirmed that GS00273 was strongly differentially expressed in 1N cells (Figure 8).

1N-specific cluster GS02894

Cluster GS02894 displayed a sequence similarity to the E. huxleyi 'glutamic acid-proline-alanine' coccolith-associated glycoprotein (GPA) (E-value 7 × 10 -7 ) and was represented by six ESTs from the 1N library and zero from the 2N library. RT-PCR confirmed that GS02894 was highly differentially expressed in 1N cells (Figure 8). Through visual inspection of alignment, we found that GS02894 in fact was aligned poorly with the GPA sequence (Figure S10 in Additional data file 1) and that the alignment did not cover the Ca 2+ -binding loops of the EF-hand motifs previously identified in GPA. GS02894 thus represents a haploid-specific gene product of unknown function.

Orphan 1N clusters

GS01257 and GS01805 were orphan clusters highly represented in the 1N library by 25 and 16 ESTs and none in the 2N library in either case (P = 1.50 × 10 -8 and 7.66 × 10 -6 , respectively). RT-PCR confirmed that both showed highly 1N-specific expression patterns (Figure 8). Both of these clusters showed multiple stop codons in every reading frame, the longest open reading frames on the forward strand being 36 and 35 codons, respectively (not shown). They might represent long 3' untranslated regions (UTRs) of genes that could be successfully identified with full-length sequencing or they might represent transcripts that do not encode proteins.

Other highly 1N-specific clusters tested by RT-PCR

A putative β-carbonic anhydrase (GS00157) and a putative cyclin (GS00508) both showed the predicted highly 1N-specific pattern of expression (Figure S8 in Additional data file 1). Two other predicted highly 1N-specific clusters (GS01285 and GS02990) were also confirmed by RT-PCR and are discussed in a later section.

2N-specific SLC4 family homolog

GS05051 was a homolog of the Cl - /bicarbonate exchanger solute carrier family 4 proteins (SLC4) [40]. This cluster was represented by seven 2N ESTs and zero 1N ESTs, which comprised six separate mini-clusters that only partially overlapped these might represent alternative transcripts. Primers designed to separate putative alternative transcripts both detected the expected products from 2N RNA samples but no product from 1N RNA samples in RT-PCR tests (Figure 8), confirming strong differential expression and the existence of alternatively spliced transcripts.

2N-specific SNARE homolog

GS02941, represented by nine 2N ESTs and zero 1N ESTs, was homologous to the SNARE protein family syntaxin-1 involved in vesicle fusion during exocytosis [41]. GS02941 had a top UniProt hit to Dictyostelium discoidium Q54HM5, a t-SNARE family protein (E-value 3 × 10 -32 ) and a top Swiss-Prot hit to the Caenorhabditis elegans syntaxin-1 homolog STX1A (E-value 2 × 10 -19 ). RT-PCR confirmed that GS02941 expression was detectable exclusively in RNA from 2N cells using three independent primer sets (Figure 8). The cluster was composed of six different mini-clusters, representing possible different alternative transcripts. Primers designed to mini-cluster e02941.1, one potential alternative transcript form, successfully amplified the predicted 317-nucleotide product but also amplified at least one other product of approximately 400 nucleotides. Only a single approximately 1,500-nucleotide product was amplified from genomic DNA. This suggests that the gene encoding GS02941 contains several (or large) introns that might be subjected to alternative splicing.

Orphan 2N clusters

GS02507, GS01164, GS01802, and GS11002 were orphan clusters highly represented in the 2N library with no reads from the 1N library. The longest open reading frames were 171, 309, 236, and 87 amino acids, respectively. GS02507, GS01164, and GS01802 could only be detected from 2N RNA samples, and not at all in 1N RNA samples (Figure 8). In contrast, GS11002 was easily detected in both 1N and 2N RNA samples (Figure 8). PCR amplification of GS01802 from genomic DNA of 2N cells revealed two products, differing by about 50 nucleotides but both larger than the single 444 nucleotides product from cDNA. Only the larger band was visible from 1N genomic DNA. This suggests that two alleles of GS01802 exist in 2N cells, differentiated by the length of an intron, and that only the larger of these alleles was inherited by the clonal 1N cells.

Other highly 2N-specific clusters tested by RT-PCR

GS00451 represents a putative aquaporin-type transporter. GS03351 was weakly homologous to a putative arachidonate lipoxygenase previously identified in E. huxleyi but to no other proteins in the searched databases, so it may represent a protein of unknown function. Both clusters were confirmed by RT-PCR to be highly 2N-specific (Figure S8 in Additional data file 1). Two other predicted highly 2N-specific clusters, GS00463 and GS02435, are discussed in the next sections.

Ca 2+ and H + transport and potential biomineralization-related transcripts

We chose to specifically examine Ca 2+ and H + transporters that might play a role in calcification and to determine whether any of them might display highly 2N-specific expression (Table 11). Five clusters had homology to vacuolar-type Ca 2+ /H + antiporters (VCX1). Although these sequences were aligned with matching regions of known VCX1 proteins at the amino acid level (Figure S11 in Additional data file 1), these clusters could not be well aligned at the nucleotide level (not shown), indicating that they represent paralogs. Only one of these, GS00304, showed possible 2N-specific expression, being represented by four ESTs in the 2N library and zero in the 1N library. GS00304 had a top Swiss-Prot hit to the A. thaliana VCX1 homolog CAX2_ARATH (E-value 3 × 10 -60 ). We confirmed by RT-PCR that GS00304 was strongly over-expressed in 2N cells using two independent primer sets (Figure 9).

RT-PCR determination of expression patterns of selected genes potentially related to biomineralization. RT- control reactions prepared from the same RNA were run for all of the PCRs shown here and no contaminating genomic DNA (gDNA) was ever found. For clarity, these RT- control reactions run simultaneously have been cut out here. Positions of molecular weight markers on each side of the gel are shown. The sample identifiers are listed for each lane at the top of the gel (as for Figure 7).

Three clusters showed similarity to sarcoplasmic/endoplasmic membrane (SERCA)-type Ca 2+ -transporting ATPases (Table 11). However, none of these clusters showed strong evidence of differential expression by in silico comparison of the two libraries.

Six clusters displayed sequence similarities to the K + -dependent Na + /Ca 2+ exchanger (NCKX) family of Ca 2+ pumps. These clusters did not align well with each other at the nucleotide level, indicating that they are likely to be distant paralogs (and not alleles). Two of these (GS05506 and GS00463) were only present in the 2N library (two EST reads, P = 0.1249, and eight EST reads, P = 0.00195, respectively). 2N-specific expression of GS00463 was confirmed by RT-PCR with two independent primer sets (Figure 9).

Homologs of 11 out of the 14 subunits of vacuolar-type H + -ATPases were identified, comprising a total of 16 clusters. Seven of these clusters were represented by both 1N- and 2N-ESTs. Only two clusters showed potential differential expression. GS01501 (top Swiss-Prot hit to Saccharomyces cerevisiae V-ATPase V0 domain subunit c', E-value 4 × 10 -38 ) was present only in the 1N library (four ESTs, P = 0.03129) whereas GS09780 (top Swiss-Prot hit to A. thaliana V1 domain subunit F) was represented only in the 2N library (four ESTs, P = 0.03129). Five clusters were homologous to V0 domain subunit a, the presumed path for proton transport. These clusters did not align at the nucleotide level, thus likely representing distant paralogs (and not alleles). Of the V0 domain subunit a homologs, three shared the highly conserved 20 amino acid motif that contains the R735 residue critical for H + transport (Figure S12 in Additional data file 1). The other two clusters, each represented by a single EST, were short and did not cover this conserved region. Clusters GS03783 and GS01934 were closely homologous (E-values 7 × 10 -38 and 4 × 10 -38 , respectively) to the V0 domain proteolipid subunit (subunit c/c') previously identified as a single-copy gene in the coccolithophore Pleurochrysis carterae [42]. These two clusters aligned poorly at the nucleotide sequence level and showed divergence at the amino acid sequence level, thus probably representing paralogs.

The glycoprotein GPA was previously identified to be closely associated with E. huxleyi coccoliths by biochemical and immunolocalization studies [43]. Cluster GS09822 was aligned perfectly over its entire length with the amino-terminal 86 codons of the previously sequenced GPA (AAD01505 Figure S10 in Additional data file 1), with minor differences in the 3' UTR (not shown). Surprisingly, GS09822 was represented by one 1N EST and one 2N EST, suggesting expression in both non-calcified 1N cells and calcifying 2N cells, and RT-PCR confirmed that this transcript was abundantly expressed in both calcifying 2N and non-calcifying 1N cells (Figure 9), as predicted from inter-library comparisons.

A previous study identified 45 transcripts with potential roles in biomineralization using microarrays and quantitative RT-PCR comparing expression levels in strain CCMP1516 under phosphate-replete (non-calcifying) and phosphate-limited (weakly calcifying) conditions and in calcifying cells of strain B39 [44]. We attempted to determine whether any of these transcripts might show highly 2N-specific expression patterns (see analysis in Additional data file 10). Of the 45 transcripts in Table 3 of Quinn et al. [44], only 23 could be unambiguously identified in public databases based on the provided information and three were each associated with more than one unique EST sequence in GenBank. Fifteen of these transcripts had BLAST matches to clusters in our dataset ten of these clusters were represented by both 1N and 2N ESTs. Four of the remaining five were represented by only single ESTs from the 2N library. The last cluster, GS03082, similar to GenBank EST sequence DQ658351 from CCMP1516, was composed of two ESTs from the 2N library and zero from the 1N library. However, the transcript for GS03082 was easily detected in RNA from both 1N and 2N cells (Figure 9). Thus, we could not confirm 2N-specific expression of the transcripts described in [44].

Possible epigenetic regulation of 1N versus 2N differentiation by histones

We selected the KOG class 'chromatin structure and dynamics' for closer examination because chromatin packaging might differ between 2N cells and 1N cells as the cells are similar in size but contain different DNA quantities. Also, chromatin factors are known to regulate gene expression. Within this class, two clusters with homology to H4 histones were found to exhibit potential differential expression. GS02435 was composed of six ESTs from the 2N library and zero from the 1N library (P = 0.0078). In contrast, GS09138 was composed of 13 ESTs from the 1N library and 0 from the 2N library (P = 6 × 10 -5 ). A sequence alignment analysis of GS09138 and two other H4 histone homologs (GS07034 and GS07988) showed that these shared high nucleotide identity over the coding region and 100% amino acid sequence identity (Figure S13 in Additional data file 1), suggesting that 1N and 2N cells may preferentially utilize alternative genes for what appear to be the same functional gene product. The 2N-specific GS02435 differed from other H4 histone homologs in the predicted amino acid sequence. The other H4 histone homologs were almost identical along their 103 amino acid predicted length to H4 histones from other eukaryotes but the longest reading frame of GS02435 exhibited an additional ≥ 50 residues in its amino-terminal sequence and lacked 3 carboxy-terminal conserved residues, making this predicted protein at least 27 amino acids longer (by taking the most downstream starting methionine codon) than the typical 103 amino acid residue H4 histones (Figure S13 in Additional data file 1). We confirmed by RT-PCR that GS02435 was detectable only in 2N RNA samples (Figure 10). Surprisingly, genomic DNA-positive controls showed that GS02435 was detected only in 2N genomic DNA and not in 1N genomic DNA (Figure 10). All of the other clusters examined in this study were detected in both 1N and 2N genomic DNA (Figures 7, 8, 9 and 10). The absence of GS02435 from the 1N genome was confirmed by PCR using three independent, non-overlapping PCR primer sets.

RT-PCR determination of expression patterns of selected histone genes. Positions of molecular weight markers on each side of the gel are shown. The sample identifiers are listed for each lane at the top of the gel (as for Figure 7).

There were five clusters with homology to the H2A histone. Alignments of the predicted polypeptides with other eukaryotic H2A histones showed high conservation (Figure S14 in Additional data file 1). GS10455 and GS07154 were identical to each other across the predicted amino acid sequences, although they diverged in nucleotide sequence, particularly in the predicted 5' and 3' UTRs. GS06864 and GS07501 were also identical in predicted amino acid sequence but diverged in nucleotide sequence. GS06749 was divergent from all the other E. huxleyi predicted H2A homologs, yet it still grouped well within other eukaryotic histone H2As in preliminary phylogenetic analysis. In particular, it was grouped within the H2A variant class H2AV (Figure S15 in Additional data file 1). GS06749 was composed of four ESTs from the 1N library and three ESTs from the 2N library, and RT-PCR confirmed that it was well-expressed in both 1N and 2N RNA samples (Figure 10). Only one H2A histone homolog, GS10455, showed signs of differential transcription, albeit not statistically significant (two ESTs in the 1N library compared to zero in the 2N library, P = 0.1251). We confirmed by RT-PCR that GS10455 was highly expressed in 1N cells with no detection in 2N phase cells (Figure 10).

Two other possible factors in epigenetic control were predicted to be highly 1N-specific. GS01285 had top Swiss-Prot homology to mouse histone H3-K9 methyltransferase 3 (E-value 3 × 10 -13 ). However, GS01285 had modestly higher homology scores (1 × 10 -16 ) to bacterial ankyrin repeat-containing proteins, so its function is uncertain. Conserved Domains Database (CDD) homology identified a possible DNA N-6-adenine-methyltransferase domain (E-value 4 × 10 -9 ) in GS02990. RT-PCR confirmed the prediction that both GS01285 and GS02990 were highly 1N-specific (Figure S8 in Additional data file 1).


Ecology and the Evolution of Biphasic Life Cycles

Sexual eukaryotes undergo an alternation between haploid and diploid nuclear phases. In some organisms, both the haploid and diploid phases undergo somatic development and exist as independent entities. Despite recent attention, the mechanisms by which such biphasic life cycles evolve and persist remain obscure. One explanation that has received little theoretical attention is that haploid‐diploid organisms may exploit their environments more efficiently through niche differentiation of the two ploidy phases. Even in isomorphic species, in which adults are morphologically similar, slight differences in the adult phase or among juveniles may play an important ecological role and help maintain haploid‐diploidy. We develop a genetic model for the evolution of life cycles that incorporates density‐dependent growth. We find that ecological differences between haploid and diploid phases can lead to the evolution and maintenance of biphasic life cycles under a broad range of conditions. Parameter estimates derived from demographic data on a population of Gracilaria gracilis, a haploid‐diploid red alga with an isomorphic alternation of generations, are used to demonstrate that an ecological explanation for haploid‐diploidy is plausible even when there are only slight morphological differences among adults.


For more information on understanding complex biology terms, see:

Biology Word Dissections - Do you know what pneumonoultramicroscopicsilicovolcanoconiosis is?

Biology Prefixes and Suffixes: "Cyto-" and "-Cyte" - The prefix cyto- means of or relating to a cell. It is derived from the Greek kytos which means hollow receptacle.

Biology Suffix Definition: -otomy, -tomy - The suffix "-otomy," or "-tomy," refers to the act of cutting or making an incision. This word part is derived from the Greek -tomia, which means to cut.
Biology Prefixes and Suffixes: proto- - The prefix (proto-) is derived from the Greek prôtos meaning first.
Biology Prefixes and Suffixes: staphylo-, staphyl- - The prefix (staphylo- or staphyl-) refers to shapes that resemble clusters, as in a bunch of grapes.


Plant Life Cycles

In plants, both haploid and diploid cells can divide by mitosis. This ability leads to the formation of different plant bodies haploid and diploid. The haploid plant body produces gametes by mitosis.

This plant body represents a gametophyte. Following fetilisation the zygote also divides by mitosis to produce a diploid sporophytic plant body. Haploid spores are produced by this plant body by meiosis. These in turn, divide by mitosis to form a haploid plant body once again. Thus, during the life cycle of any sexually reproducing plant, there is an alternation of generations between, gamete producing haploid gametophyte and spore producing diploid sporophyte.

Different plant groups, as well as individuals, representing them, differ in the following patterns:

1. Sporophytic generation is represented only by the one-celled zygote, There are no free-living sporophytes, Meiosis in the. zygote results in the formation of haploid spores. The haploid spores divide mitotically and form the gametophyte. The dominant, photosynthetic phase in such plants is the free-living gametophyte. This kind of life cycle is termed as haplontic. Many algae such as Volvox, Spirogyra and some species of Chlamydomomas represent this pattern.

Fig: Life cycle of Haplontic

2. The type wherein the diploid sporophyte is the dominant, photosynthetic, independent phase of the plant. The gametophytic phase is represented by the single to few-celled haploid gametophyte. This kind of lifecycle is termed as diplontic. All seed-bearing plants i.e. gymnosperms and angiosperms, follow this pattern.

Fig: Life cycle of Diplontic

3. Bryophytes and pteridophytes, interestingly, exhibit an intermediate condition (Haplo-diplontic) both phases are multicellular and often free-living. However, they differ in their dominant phases. A dominant, independent, photosynthetic, thalloid or erect phase is, represented by a haploid, gametophyte and it alternates with the short lived multicelluler sporophyte totally or partially dependent on the gametophyte for its anchorage and nutrition. All bryophytes represent this pattern. The diploid sporophyte is represented by a dominant, independent, photosynthetic, vascular plant body. It alternates with multicellular, saprophytic autotrophic, independent but short­lived haploid gametophyte. Such a pattern is known as haplo-diplontic life cycle. All pteridophytes exhibit this pattern.

While most algal genera are haplontic, some of them such as Ectacarpus, Polysiphonia, kelps ate haplo­diplontic. Fucus, an alga is diplontic.


Contents

The study of reproduction and development in organisms was carried out by many botanists and zoologists.

Wilhelm Hofmeister demonstrated that alternation of generations is a feature that unites plants, and published this result in 1851 (see plant sexuality).

Some terms (haplobiont and diplobiont) used for the description of life cycles were proposed initially for algae by Nils Svedelius, and then became used for other organisms. [4] [5] Other terms (autogamy and gamontogamy) used in protist life cycles were introduced by Karl Gottlieb Grell. [6] The description of the complex life cycles of various organisms contributed to the disproof of the ideas of spontaneous generation in the 1840s and 1850s. [7]

A zygotic meiosis is a meiosis of a zygote immediately after karyogamy, which is the fusion of two cell nuclei. This way, the organism ends its diploid phase and produces several haploid cells. These cells divide mitotically to form either larger, multicellular individuals, or more haploid cells. Two opposite types of gametes (e.g., male and female) from these individuals or cells fuse to become a zygote.

In the whole cycle, zygotes are the only diploid cell mitosis occurs only in the haploid phase.

The individuals or cells as a result of mitosis are haplonts, hence this life cycle is also called haplontic life cycle. Haplonts are:

  • In archaeplastidans: some green algae (e.g., Chlamydomonas, Zygnema, Chara) [8]
  • In stramenopiles: some golden algae[8]
  • In alveolates: many dinoflagellates, e.g., Ceratium, Gymnodinium, some apicomplexans (e.g., Plasmodium) [9]
  • In rhizarians: some euglyphids, [10]ascetosporeans
  • In excavates: some parabasalids[11]
  • In amoebozoans: Dictyostelium[8]
  • In opisthokonts: most fungi (some chytrids, zygomycetes, some ascomycetes, basidiomycetes) [8][12] : 15

In gametic meiosis, instead of immediately dividing meiotically to produce haploid cells, the zygote divides mitotically to produce a multicellular diploid individual or a group of more unicellular diploid cells. Cells from the diploid individuals then undergo meiosis to produce haploid cells or gametes. Haploid cells may divide again (by mitosis) to form more haploid cells, as in many yeasts, but the haploid phase is not the predominant life cycle phase. In most diplonts, mitosis occurs only in the diploid phase, i.e. gametes usually form quickly and fuse to produce diploid zygotes.

In the whole cycle, gametes are usually the only haploid cells, and mitosis usually occurs only in the diploid phase.

The diploid multicellular individual is a diplont, hence a gametic meiosis is also called a diplontic life cycle. Diplonts are:

  • In archaeplastidans: some green algae (e.g., Cladophora glomerata, [13]Acetabularia[8] )
  • In stramenopiles: some brown algae (the Fucales, however, their life cycle can also be interpreted as strongly heteromorphic-diplohaplontic, with a highly reduced gametophyte phase, as in the flowering plants), [12] : 207 some xanthophytes (e.g., Vaucheria), [12] : 124 most diatoms, [11] some oomycetes (e.g., Saprolegnia, Plasmopara viticola), [8]opalines, [11] some "heliozoans" (e.g., Actinophrys, Actinosphaerium) [11][14]
  • In alveolates: ciliates[11]
  • In excavates: some parabasalids[11]
  • In opisthokonts: animals, some fungi (e.g., some ascomycetes) [8]

In sporic meiosis (also commonly known as intermediary meiosis), the zygote divides mitotically to produce a multicellular diploid sporophyte. The sporophyte creates spores via meiosis which also then divide mitotically producing haploid individuals called gametophytes. The gametophytes produce gametes via mitosis. In some plants the gametophyte is not only small-sized but also short-lived in other plants and many algae, the gametophyte is the "dominant" stage of the life cycle.

  • In archaeplastidans: red algae (which have two sporophyte generations), some green algae (e.g., Ulva), land plants[8]
  • In stramenopiles: most brown algae[8]
  • In rhizarians: many foraminiferans, [11]plasmodiophoromycetes[8]
  • In amoebozoa: myxogastrids
  • In opisthokonts: some fungi (some chytrids, some ascomycetes like the brewer's yeast) [8]
  • Other eukaryotes: haptophytes[11]

Some animals have a sex-determination system called haplodiploid, but this is not related to the haplodiplontic life cycle.

Some red algae (such as Bonnemaisonia [15] and Lemanea) and green algae (such as Prasiola) have vegetative meiosis, also called somatic meiosis, which is a rare phenomenon. [12] : 82 Vegetative meiosis can occur in haplodiplontic and also in diplontic life cycles. The gametophytes remain attached to and part of the sporophyte. Vegetative (non-reproductive) diploid cells undergo meiosis, generating vegetative haploid cells. These undergo many mitosis, and produces gametes.

A different phenomenon, called vegetative diploidization, a type of apomixis, occurs in some brown algae (e.g., Elachista stellaris). [16] Cells in a haploid part of the plant spontaneously duplicate their chromosomes to produce diploid tissue.

Parasites depend on the exploitation of one or more hosts. Those that must infect more than one host species to complete their life cycles are said to have complex or indirect life cycles. Dirofilaria immitis, or the heartworm, has an indirect life cycle, for example. The microfilariae must first be ingested by a female mosquito, where it develops into the infective larval stage. The mosquito then bites an animal and transmits the infective larvae into the animal, where they migrate to the pulmonary artery and mature into adults. [17]

Those parasites that infect a single species have direct life cycles. An example of a parasite with a direct life cycle is Ancylostoma caninum, or the canine hookworm. They develop to the infective larval stage in the environment, then penetrate the skin of the dog directly and mature to adults in the small intestine. [18]

If a parasite has to infect a given host in order to complete its life cycle, then it is said to be an obligate parasite of that host sometimes, infection is facultative—the parasite can survive and complete its life cycle without infecting that particular host species. Parasites sometimes infect hosts in which they cannot complete their life cycles these are accidental hosts.

A host in which parasites reproduce sexually is known as the definitive, final or primary host. In intermediate hosts, parasites either do not reproduce or do so asexually, but the parasite always develops to a new stage in this type of host. In some cases a parasite will infect a host, but not undergo any development, these hosts are known as paratenic [19] or transport hosts. The paratenic host can be useful in raising the chance that the parasite will be transmitted to the definitive host. For example, the cat lungworm (Aelurostrongylus abstrusus) uses a slug or snail as an intermediate host the first stage larva enters the mollusk and develops to the third stage larva, which is infectious to the definitive host—the cat. If a mouse eats the slug, the third stage larva will enter the mouse's tissues, but will not undergo any development.

The primitive type of life cycle probably had haploid individuals with asexual reproduction. [11] Bacteria and archaea exhibit a life cycle like this, and some eukaryotes apparently do too (e.g., Cryptophyta, Choanoflagellata, many Euglenozoa, many Amoebozoa, some red algae, some green algae, the imperfect fungi, some rotifers and many other groups, not necessarily haploid). [20] However, these eukaryotes probably are not primitively asexual, but have lost their sexual reproduction, or it just was not observed yet. [21] [22] Many eukaryotes (including animals and plants) exhibit asexual reproduction, which may be facultative or obligate in the life cycle, with sexual reproduction occurring more or less frequently. [23]

Individual organisms participating in a biological life cycle ordinarily age and die, while cells from these organisms that connect successive life cycle generations (germ line cells and their descendants) are potentially immortal. The basis for this difference is a fundamental problem in biology. The Russian biologist and historian Zhores A. Medvedev [24] considered that the accuracy of genome replicative and other synthetic systems alone cannot explain the immortality of germ lines. Rather Medvedev thought that known features of the biochemistry and genetics of sexual reproduction indicate the presence of unique information maintenance and restoration processes at the gametogenesis stage of the biological life cycle. In particular, Medvedev considered that the most important opportunities for information maintenance of germ cells are created by recombination during meiosis and DNA repair he saw these as processes within the germ line cells that were capable of restoring the integrity of DNA and chromosomes from the types of damage that cause irreversible ageing in non-germ line cells, e.g. somatic cells.

The ancestry of each present day cell presumably traces back, in an unbroken lineage for over 3 billion years to the origin of life. It is not actually cells that are immortal but multi-generational cell lineages. [25] The immortality of a cell lineage depends on the maintenance of cell division potential. This potential may be lost in any particular lineage because of cell damage, terminal differentiation as occurs in nerve cells, or programmed cell death (apoptosis) during development. Maintenance of cell division potential of the biological life cycle over successive generations depends on the avoidance and the accurate repair of cellular damage, particularly DNA damage. In sexual organisms, continuity of the germline over successive cell cycle generations depends on the effectiveness of processes for avoiding DNA damage and repairing those DNA damages that do occur. Sexual processes in eukaryotes, as well as in prokaryotes, provide an opportunity for effective repair of DNA damages in the germ line by homologous recombination. [25] [26]


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+2 BIOLOGY PART-I

Classification of Plant Kingdom I 43 divisions of sporogenous cells, the spores are dispersed from the capsule. The sporophyte is partially dependent on the gametophyte. The common examples of mosses are Funaria, Polytrichum, Sphagnum etc. (Fig. 3.4, 3.5). 3.5 PETRIDOPHYTA: The Pteridophyta (Gk: Pteris - feather, phyton - plant) commonly called the oldest, seedless, vascular cryptogams and are represented by about 400 genera (Fossil and Living) and more than 10000 species. They are the first vascular land (terrestrial) plants. They dominated the forests of the carboniferous period, about 300 million years ago. The main plant body is a sporophyte, the dominant phase of life cycle and differentiated into stem, root and leaf like organs. They are the highest evolved cryptogams. Some tree-ferns (Cyathia, Celeotium) may attain a height of 20 meters. Pteridophytes are commonly found in cool, damp and shady places, though some species grow well in sandy soil. They are found in tropical and temperate regions of the world. The leaves in these plants are of two types small called microphylls (e.g. Selaginella) and larger ones called macrophylls (e.g. ferns) (Fig. 3.6). The Sporophytes bear sporangia that are subtended by leaf like appendages called sporophylls. The sporophylls in some cases form distinct structures called strobilus (e.g., Selaginella) or compact cone (e.g., Equisetum) (Fig.3.6). The Sporangia produce spores by meiosis in spore mother cells. The spores develop into inconspicuous, small but multicellular gametophytic body called prothallus which is monoecious (bearing sex organs in the same prothallus). The prothallus is free living, mostly photosynthetic and thalloid in nature. The gametophytic bodies require cool, damp and shady places fortheir growth. Because of such restricted habitat requirement and need of water for fertilization, the living pteridophytes have spread to limited or restricted and narrow geographical regions. The gametophytes bear male and female sex organs called antheridia and archegonia respectively. The antherozoids (male gametes) released from antheridia with the help of water reach to the archegonium. A zygote (2n) is formed as a result of fusion of male (antherozoid) and female gametes (egg) and forms the first cell of the sporophytic generation. Zygote develops into multicellular well differentiated sporophyte which is the dominant phase of life cycle of pteridophytes. In majority of pteridophytes, the spores are of similar sizes. Such plants are called homosporous. In Selaginella and Salvia, two kinds of spores mega or macro (large) and micro (small) spores are formed and plants bearing such spores are called heterosporous. The mega spores and microspores germinate to form female and male gametophytes respectively. The female gametophytes are retained on the parent sporophytes for variable periods till the development of roots within the female gametophyte. The zygote develops into a young sporophyte. This is a tendency to form the seed and called seed habit. Seed habit leads to formation of seed plants.

44 I Bureau’s Higher Secondary (+2) BIOLOGY -1 The plants show clear alternation of generations in their life cycle. The sporophyte and gametophyte are autotrophic and independent of each other. A Odd leaflet r'> Pinnae Rachis Leaflets Rachis Petiole Persistent leaf base Young leaf with Petiole — circinate ptyxis roots Persistent 'Circinately coiled E leaf bases young leaf Rhizome - -Terminal bud Rhizome .. . Adventitious------------- roots D Fig. 3.6 : Some Pteridophytes. A. Selaginella (Club Moss), B. Equisetum (Horsetail), C. Pteris (Fern), D. Dryopteris (Fern), E. Adiantum (Fern).

Classification of Plant Kingdom I 45 Classification of Pteridophytes : The pteridophytes comprise of four classes. 1. Psilopsida (Psilophytes) Most of them are fossils except few living members, e.g. Psi lot um. 2. Lycopsida (Clubmosses) They grow as prostrate aggregates like mosses, e.g. Lycopodium, Selaginella (Fig. 3.6) 3. Sphenopsida (Horsetails) They have articulated stem with whorls of branches and scale- like leaves. The spore producing bodies borne at the ends of branches resemble the tail of the horse, hence the name ‘horsetails’ e.g. Equisetum. (Fig. 3.6) 4. Pteropsida (Ferns) Ferns are most conspicuous amphibian pteridophytes which have underground stem (rhizome), adventitious roots and aerial pinnately compound leaves called fronds, e.g. Dryopteris, Cyathia, Pteris, Adiantum, Marsilea (Fig. 3.6) Economic importance : Afew economic uses pteridophytes are given below : 1. Lycopodium clavatum Spores used in rheumatism and cramps. Leaves are chewed for arresting food poisoning. 2. Psilotum nudum Oily spores given to infants to cure diarrhoea. 3. Selaginella repande Root paste applied over white patches in Leprosy. 4. Equisetum The entire plant is used for cooiling gonorrhoea. The plant paste applied in bone fractures. 5. Dryopteris cochlea Whole plant extract taken orally for snake bite. The powdered rhizome in water is taken for rheumatism and Leprosy. 6. Dicranopteris Fronds are used in asthma. The young fronds grinded in milk given to remove sterility in women. 7. Adiantum Rhizome and fronds are used in wound healing, boils, glandular swellings dysentery, ulcers and scorpion bites. Fronds are diuretic and the decoction is given to reduce fever. 8. Marsilea It is very rich in minerals and commonly eaten as leafy vegetable.

46 I Bureau’s Higher Secondary (+2) BIOLOGY -1 3.6. GYMNOSPERMS : The word Gymnosperm was used in 300 B.C. by Theophrastus, a pupil of Aristotle in his book ‘Enquiry into plants’. He used this term to embrace all those plants whose seeds were unprotected. The Gymnosperms (gymnos-naked, sperma-seeds) are plants in which the ovules are not enclosed by any ovary wall. No ovary is present in Gymnosperms. So the seeds developed from ovules are naked (not covered) and remain exposed before and after fertilization. Gymnosperms and Angiosperms are grouped under Spermatophytes. . Cycas circinnalis (After Blume) and bipinnate compound leaves) (After Engler and Prantl). Young seedling of Pinus. B. Dwarf shoots of Pinus insularis , A twig of Gnetum gnemon bearing male strobili. (one shown entire, others are dissected! C. A Pinus tree. Fig. 3.7 : Some Gymnosperms

Classification of Plant Kingdom I 47 Gymnosperms are found throught the surface of the globe, mostly in high altitudes. They are evergreen, some are deciduous, woody, xerophytic and include medium size to very tall trees and shrubs. One of the tallest, a giant redwood tree is Sequoia gigantea which lives for 4000 years. Gymnosperms formed dominant vegetation on the earth about 200 million years ago and later replaced by the angiosperms. Some of them live for thousands of years. Gymnosperms, today are represented by nearly 70 living genera 725 species. The main plant body is a well differentiated sporophyte (dominant phase of life cycle) consisting of root, stem, leaves and flowers. The gametophyte is very much reduced and remains within the sporophyte. The gametophyte is fully dependent on the sporophyte. These perennial woody trees have stems, may be unbranched (Cycas) or profusely branched (Pinus, Cedrus) (Fig. 3.7). Leaves (foliage leaves and scale leaves) are well adapted to tolerate extreme temperature, water scarcity and wind. The pinnate leaves of Cycas persist for few years. The needle-like leaves of pines (reduced surface area), sunken stomata and thick cuticle help to reduce water loss. Roots are tap roots and in some genera (in Pinus) have fungal association in the form of mycorrhiza. In Cycas, small specialized roots called coralloid roots associated with nitrogen-fixing Cyanobacteria are present. The vascular tissues are arranged into bundles just like angiosperms. However xylem does not have vessels and phloem with no companion cells except in Gnetum. Gymnosperms are heterosporous. They produce two kinds of haploid spores (meiospores-as a product of meiosis), microspores and megaspores within two different types of sporangia called microsporangia and megasporangia respectively, Again all sporangia are borne on sprophylls (micro / or megasporophylls) which are arranged spirally along the axis to form lax strobili or compact cones. The male (microsporangiate) cone or strobilus bears microsporophylls and microsporangia (pollen sacs). The microspore develops into a male gametophyte during gametophytic generation which is highly reduced and confined to a limited number of cells, called a pollengrain. The pollen grains are released from microsporangia and move by air currents. The female cone (strobilus) consists of megasporophylls which bear the exposed megasporangia called ovules. The ovules are integumented (seed coat) with an opening called micropyle. The ovule initially is filled with nucellus (nuceller tissue). Near the micropyler end, one of the nuceller cells gets differentiated into megaspore mother cell (2n) which divides meiotically to form four megaspores (n). Usually one haploid megaspore develops into a multicellular female gametophyte that forms two or more archegonia, the female sex organs bearing female gametes (egg). The female gametophyte is completely retained within the megasporangium or ovule, which is also dependent on the sporophytic tissue. The pollen gains enter through the microphyle of ovule, produce pollen tubes which grow towards archegonia and discharge the two male gametes near mouth of neck of archegonia.

48 I Bureau’s Higher Secondary (+2) BIOLOGY -1 One male gamete reaches the egg inside the venter, fertilization is effected and a diploid zygote (2n) is formed. The formation of pollen tube by pollen grain during fertilization process is called siphonogamy. Fertilization of one male gamete with the egg inside venter of achegonium results in formation of a diploid zygote (2n). MALE GAMETE POLLINATION ARCHEGONIUM 3-CELLED STAGE SUSPENSOR OF POLLEN GRAIN FEMALE GAMETOPHYTE WING FREE NUCLEAR DIVISION* POLLEN GRA N MICROSPORE ft MICROSPOROPHYLL COTYLEDONS TETRAD MEGASPOROPHYLL functional MEGASPORE TETRAD OF MEGASPORES OVULIFEROUS MICRO WING SCALE SPORANGIA BRACT DISPERSAL SCALE OVULE MALE' MEGASPOROPHYLL CONE SEED GERMINATING FEMALE CONE PLANT Fig. 3.8 : Diagrammatic Life Cyle of a Gymnosperm, Pinus

Classification of Plant Kingdom I 49 The zygote develops into an embryo, the future sporophyte. The whole ovule develops into the seed. Formation of many embryos within one ovule, called polyembryony is common in pines. Seeds are not enclosed by any other outer covering like ovary wall as in case of angiosperms. In Gymnosperms, there is no ovary. So seeds are uncovered or naked, hence the name ‘gymnosperms’, the naked-seeded plants. They have epigeal mode of germination. Plants show distinct alternation of generations. Classification of Gymnosperms : Gymnosperms includes three classes 1. Cycadopsida (Cycads) - They are represented by both fossil and living members and constitute a small group of gymnoperms. The living members are xerophytic and look like palms having fern like leaves. Plants are dioecious, means the microporophylls and megasporophylls are borne in separate plants. Examples: Cycas, Zamia, Macrozamia, Bowenia. 2. Coniferopsida (Conifers) - Conifers having more than 500 living species are the most dominant gymnosperms, mostly occurring in colder regions. The plants with their conical canopy bear cones as their male and females reproductive structures. The plant body has resin canals containing an aromatic, antiseptic semifluid called resin. Examples : Pinus, Ginkkgo, Cedrus, Abies, Cupressus. 3. Gnetopsida (Gnetum and allied plants) - This group includes climbing shurbs, shurbs and small trees. The external and internal features of Gnetum resemble angiosperms. Reproductive organs are borne in whorls or inflorescence. They have vessels in the xylem. Examples : Genetum, Ephedra and Welwitschia. Economic imprtance of Gymnosperms : They are greatly valued in world because of their importance to human beings. 1. Wood - Most of the species provide wood or timber for construction works, furniture and house building. 2. Resins - Resins produced by mostly conifer are unaffected by water and protect against insects. Pine gum, oil of terpentine, varnishes forwood paining, laundry soap, greases, printing ink, printing driers, shoe polish and insecticides are manufactured from resins. 3. Essential oils and falty oil production- (i) A fatty oil from conifer wood pulp used in manufacture of paints, soap, linoleum and emulsifiers. (ii) Spruce oil obtained from Abies, Picea oil from Cryptoneria, Araucaria, Cedar wood oil from Thuja and various essential oils from gymnosperms (mostly pines) are used by us in various ways. 4. Paper and Board (Cellulose and Pulp) - In USA, 85% of pulp used for paper making come from conifers. Himalayan conifers produce excellent pulp for paper industry.

50 I Bureau’s Higher Secondary (+2) BIOLOGY -1 5. Food - Pine kernels preserved in honey are eaten, seeds all pines theoritically have high food value. 6. Tannins - Tannins utilized for tranforming hides to leather. In petroleum industry, tannins are used as dispersant to control mud during oil well drilling. Barks of many confers like Tsuga, Sequoia, Larix, Picea contain high concentration of tannins. 7. Decoration and ornamental use - Mostly the leaves of Thuja, Araucaria, Cycas, Cupressus are used for decoration purpose. Ginkgo is called ‘maiden hair tree’ planted in most of Budhist temples in India, Japan, and China as ornamental tree. 8. Medicinal use - Ephedrine used as pulmonary decongestant is extracted from Ephedra. 3.7. ANGIOSPERMS : The angiosperms are flowering plants in which seeds are enclosed with the ovary. The ovule develops into seed and the ovary into fruit. Angisperms are exceptionally a large group of plants consisting of 2,50,000 known species. They are most recent and highly developed plants appeared on earth surface about 130 million years ago. Today they are the most dominant plant group and found to grow in almost every kind of habitat. They range in size from tiny, almost microscopic Wolfia to large tall trees of Eucalyptus over 100 meters. They may be annual, biennial or perennial herbs, shrubs or trees. The plant body is differentiated into stem, root and leaves. At maturity plants bear flowers which produce fruits and seeds. The vascular tissue are arranged in the form of vascular bundles. The xylem contains vessels and phloem has companion cells in addition to other vascular elements. The flowers are reproductive organs having two or one accessory whorls, perianth or calyx and corolla and two essential whorls, androecium and gynoecium. The whorls, calyx, corolla, androecium and gynoecium are composed of sepals, petals, stamens and carpels respectively. (Fig. 3.9) A stamen, the male sex organ of the flower, consists of a slender filament and an anther at the tip. Anther contains single or more microporangia (inside the lobes). The sporogenous cells of microsporangium undergo meiotic cell division to form microspores or pollen grains (Fig.3.10). The carpel or pistil, the female sex organ of the flower,

Classification of Plant Kingdom I 51 Fig. 3.10 : A. T.S of Mature Anther of Angiosperm, Fig. 3.12 : V.S of Angiospermic Ovule B. Pollen grain (Microspore) and its germination (Megasporangium) showing Integuments, Nucellus, forming male gametophyte. Embryo sac and Funiculus consists of ovary, style and stigma (3.11). The ovary encloses one to many ovules. An ovule consists of nucellus surrounded by two integuments with a fine opening microphyle. Pollen grains enter into the ovule through the micropyle. Four megaspores are formed as a result of meiotic cell division of megaspore mother cell produced by necellus. One or all the four haploid megaspores are utilized to form a female gametophyte or embryo sac with the nucellus of ovule. So the embryo sac contains all haploid cells and consists of (i) a three-celled egg apparatus (one egg cell + two synergids), (ii) three antipodal cells and (iii) two polar nuclei. The two haplaid polar nuclei fuse to form a diploid secondary nucleus.

52 I Bureau’s Higher Secondary (+2) BIOLOGY -1 Pollen grains after pollination from the anthers are carried by wind or other agencies to the stigma of the pistil. This is called pollination. Pollen grains germinate on the sticky surface of the stigma and produce pollen tubes (siphonogamy) which grow through the tissues of stigma and style to reach the ovlue. The pollen nucleus divides to form two male gametes. Ultimately pollen tubes enter egg apparatus of the female gametophyte or embryo sac where two male gametes are discharged. One male gamete fuses with the egg cell called syngamy to form a diploid zygote and the other fuses with diploid secondary nucleus to form a triploid primary endosperm nucleus (PEN). Because there are two fusions, this event is termed as double fertitization, an event unique to angiosperms. The zygote develops into the embroys or future sporophyte. The embryo may develop a single or two cotyledons. The primary endosperm nucleus develops into endosperm which provides nutrition to the growing embryo inside the ovule. The synergids and antipodals degenerate after fertilization. During these events the ovules develop into seeds and the ovary develops into a fuit. Atypical lifecyle is given in Fig. 3.13. Classification : The angiosperms are divided into two classes, (i) dicotyledons and (ii) monocotyledons. The dicotyledons are characterized by having two cotyledons in their seeds while monocotyledons have only one cotyledon. Class I Dicotyledons : The members of this class have leaves with reticulate (net like) venation, which show alternate, spiral or whorled phyllotaxy (arrangement of leaves). The flowers are tetramerous or pentamerous having four or five members in the various

Classification of Plant Kingdom I 53 GYMNOSPERMS ANGIOSPERMS Integumemnti •V’ - Nucellus 7 \\I ■/i •’ • *<\\ II: —nL_ Arche- I f ,? I)j Gameto- .!» X\\ gonium X T\" phyte Aff//,/ ///. y I - Gameto- __ Z_ Nucellus 1 ■/ 1. ■ ‘TA? J phyte ?/ / Integu- I* m® ments Female cone Sporophyll Ovary — Micropyle ______ Ovule Ovule aa Anther —// Two lobed sac with pollen grains H ' 5.1 'fits fl *( IJ ** ’•/ / sacs / Filament -— Anther T.S. Microsporophyll Stamen Cluster of male cones .Prothallial cell - Antheridial cell / z4* g'i >?< A •J / ''W — iuoe nucleus i ft < • ■ '' 7 --------- \\\\ 1 - Winged pollen grains Pollen grains Fig. 3.14 : Reproductive organs of >Gf>Gymnosperms and Angiosperms floral whorls, respectively. The vas cular bundles are open. i.e. cambium is present between the xylem and phloem. The seeds have two cotyledons. Class II : Monocotyledons (Mono = one, cotyledons = cotyledons) : The leaves are simple with a parallel venation pattern. The vascular bundles are closed (cambium absent) and scattered in the parenchyma. The flowers are trimerous (having 3 mem-bers in each floral whorl). The seeds possess only one cotyledon. The monocotyledons have, seven series, on the basis of the nature of perianth and condition of the ovary. Economic importance of Angiosperms : The angiosperms provide with food, fodder, fuel, shelter, clothings, medicines and several other commercially important products.

54 I Bureau’s Higher Secondary (+2) BIOLOGY -1 3.8. LIFE CYCLES AND ALTERNATION OF GENERATIONS As we have studied in the above, it is learnt that during life cycle of any sexually reproducing plant, there is an alternation of generations between the gamete producing haploid gametophyte and spore producing diploid sporophyte. Three basic patterns of life cycles are (i) Haplontic, (ii) Diplontic and (iii) Haplo-diplontic. 1. Haplontic - The dominant photosynthetic (green) phase is a free-living gametophyte. The sporophytic generation is represented by the one celled diploid zygote. There is no free living sporophyte which is completely dependent on gametophyte. The diploid zygote undergoes meiosis and forms haploid spores which in turn divide mitotically to form the gametophyte. This is called haplontic type of life cycle. This pattern is seen in algae, such as Volvox, Spirogyra and many other algae. 2. Diplontic - Here the diploid sporophyte is the green or photosynthetic, dominant and independent phase of the life cycle. The gametophytic phase which is fully dependant on the sporophyte and is represented by the single to few celled haploid gametophyte. This pattern is called diplontic type of life cycle and seen in all seed bearing plants (gymnosperms and angiosperms. Fucus (an algae) has diplontic patter of life cycle. 3. Haplo-diplontic - This is an intermediate pattern of life cycle in which both the phases are multicelluar and visible structures. A dominant prostrate or erect photosynthetic thalloid haploid gametophyte alternates with the short-lived multicelluar sporophyte. Here the sporophyte is totally or partially dependent on the gametophyte for its anchorage and nutrition. All Bryophytes show this pattern of haplo- diplontic life cycle. In pteridophytes, the diploid green and vascular sporophyte is the dominant phse of life cycle. Here alternation of generation is between multicelluar sporophytic or autotrophic and short-lived independent haploid gametophyte. This is also haplo-diplontic pattern of life cyle. In addition to all pteridophytes, some algal genera such as Ectocarpus, Polysiphoria and kelps exhibit haplo-diplontic pattern.

Classification of Plant Kingdom I 55 3.9. SUMMARY OF SALIENT FEATURES OF ALL PLANT GROUPS OF KINGDOM PLANTAE ALGAE 1. Algae are chlorophyll bearing green simple, thalloid, autotrophic, eukaryotic organisms have dominant gametophytic haploid bodies and largely aquatic. 2. Algae usually reproduce vegetatively by fragmentation, asexually by formation of different spores (zoopores, aplanospares, hypnospores) and sexually by formation of gametes which may show isogemy, anisogamy or oogamy. 3. The zygote never develops into embryo and true visible alternation of generations is absent but the life cycle pattern usually falls under haplontic type. 4. Depending on the type of pigment possessed, type of storage food materials, the algae are divided into three major classes such as, chlorophyceae (green algae), phaeophycea (brown algae) and Rhodophyceae (red algae). These are many other minor classes of algae. 5. Algae are used as food (Sargassum, Macrocystis, Chlorella, Spirulina), production hydro colloids (algin from brown algae, carrageen form red algae) and for production of agar- agar, a gellifying substance (from red aWgae-Gelidium and Gracilaria) BRYOPHYTA 1. Bryophytes having nonvascular, prostrate or erect, small, thallose or foliose gametophytic bodies are the amphibians of the plant kingdom and considered as first land plants and first archegoniates in the plant kingdom. 2. The main thallus body is a multicelluar, many cells thick, fixed to soil where they usually grow by rhizoids or and scales and dependent on water for sexual reproduction. 3. During sexual reproduction, the male and female gametes formed in the sex organs, antheridia and archegonia respectively, fuse to form a zygote which develops into multicellular body, the sporophyte. It is usually consisting of foot, seta and capsule containing haploid spores. 4. There is an alternation of generations between a gametophyte, the dominant phase of life style and a fully dependent (on gametophyte) sporophyte which thus, exhibits a haplo-diplontic pattern of life cycle. 5. Bryophytes are classified into (i) Hepaticae (Liverworts having prostrate dorsiventral thallus) (ii) Anthocerotae (Hornworts, also having prostrate gametophytes with erect horn like sporophytes) and Musci (mosses having effect upright slender axes bearing spirally arranged leaves and sporophytes at tips)

56 I Bureau’s Higher Secondary (+2) BIOLOGY -1 6. Bryophytes are great land colonisers and used as peat (Sphagnum moss) medicinally to cure kidney or gall bladder stone (Polytrichum commune), pulmonary disorders (Marchantia polymorpha), skin diseases packaging materials (mosses) and for geochemical evaluation of metals. PTERIDOPHYTES 1. The petridophytes are the first vascular land plants with independent sporophyte, the main plant body, differentiated into stem, root and leaves with well defined vascular tissue. 2. They have haplo-diplontic life cyle pattern where sporophyte phase is the dominant phase of life cycle in contrast to the haploid gametophytic phase which is short lived and reduced. 3. The haploid spores produced by sporangia borne on the sporophyte, germinate in cool­ damp environment to form gametophyte and bear sex organs, the antheridia (male) and the archegonia (female). 4. Water is required for transfer a male gametes to the archegonium where zygote is formed after fertilization. 5. The zygote is retained in the archegonium and develops into multi-cellular embryo that grows into a sporophyte. 6. Many pteridophytes have economic importance and in addition to decorative use (Ferns), these have many medicinal uses, such as cure for diarrhoea (Psilotum nudum), asthma (Dryopteris) wound healing (Adiantum), rheumatism (Dryopteris) etc. GYMNOSPERMS 1. Gymnosperms are naked-seeded plants with well developed vascular system in which ovules are not enclosed by any ovary wall and after fertilization seeds remain exposed. 2. The main plant body is a long-lived sporophyte differentiated into stem, leaves and roots and alternates with the very reduced gametophytic phase, showing a diplontic type of life cycle pattern. 3. The individual male and female cones or strobili are formed by aggregation of spirally arranged micro and megasporophylls which develop micro sporogia and megasporangia that, in turn, produce haploid microspores and megaspores respectively. 4. The microspore or pollen grain germinates to form pollen tube through which male gametes are released into the ovule where it fuses egg cell present in archegonium. 5. Pollination is anemophilous and after the process of fertilization, the zygote develop into an embryo and the ovules into seeds.

Classification of Plant Kingdom I 57 6. They have great economic importance and provide us food (pine kernels), timber (pines), resins from pines (as varnishes, oil of terpentine, gums, greases, printing ink), tannins for converting hides into leather (Tsuga, sequoia, Larix) medicines (Ephedrine from Ephedra) and other very useful products. ANGIOSPERMS 1. The angiosperms are closed seeded, most advanced (sprophytes) with highly developed reproductive structures (stamens and carpele / pistils) and after fertilization the ovlues develop into the seed and the ovary which encloses ovules develops into fruits. 2. The anther of stamens produces haploids pollen grains (male gametophyte) after meiosis and ovules inside ovaries form the haploid female gametophyte or emboryo sac which contains egg cell. 3. The male gametes formed in the male gametophyte pass through the pollen tube formed by pollen grains entering the female gametophyte, one fuses with the egg cell (syngamy) and the other with secondary nucleus, hence effect double fertilization, and form diploid embryo and triploid endosperm (triple fusion) respectively. 4. Double fertilization and triple fusion are unique to angiosperms which are further classified into dicotyledons and monocotyledons depending upon the number of cotyledons present in the embryo. 5. The gametophytic phase is highly reduced and fully dependent on the dominant sporophytic plant and the life cycle pattern is diplontic. 6. Angiospermic plant provide us food, fodder, fuel, shelter, clothing, medicines and several other commercially important products. The angiosperms are classified into monocotyledons and dicotyledons.

58 Bureau’s Higher Secondary (+2) BIOLOGY -1 SAMPLE QUESTIONS 1. Choose the correct answer from the words given bracket: (i) One the following is a vascular cryptogam (Bryophytes, Pteridophytes, Gymnosperms, Angiosperms) (ii) One of the following features of Gymnosperms is seen among lower group of plants (Seed, Ovule, Archegonium, Nucellus) (iii) Haplontic life cycle pattern is seen in one the following plant groups. (Algae, Angiosperms, Gymnosperms, Bryophytes) (iv) In which of the following zygote does not give rise to embryo. (Pteridophyte, Gymnosperms, Algae, Angiosperms) (v) One of the following is a naked seeded plant (Angiosperms, Gymnosperm, Bryophyta, Algae) 2. Select the correct answer of the following : (i) Green algae possess (c) Chlorophyll a, Carotenes (a) Chlorophyll a, b (b) Chlorophyll a, c (d) Chlorophyll b, carotenes (ii) Agar is obtained from (c) Spirogyra (a) Gelidium (b) Riccia (d) Laminaria (iii) Colour of brown algae is due to- (c) Phycocyanin (a) Carotenodis (b) Phycoerythrin (d) Fucoxanthin (iv) The largest alga out of four of the following (a) Spirogyra (c) Macrocystis (b) Fucus (d) Sargassum (v) The land plants that lack vascular tissue (a) Bryophyta (c) Pteridophyta (b) Angiosperms (d) Cycads (vi) Sprophyte is fully dependent and parasitic on gametophytic body is (a) Bryophyta (c) Monocots (b) Gymnosperm (d) Di cots (vii) Seedless vascular plants are the (a) Liverworts (c) Ferns (b) Mosses (d) Monocots

Classification of Plant Kingdom I 59 (viii) Multicellular branched rhizoids and leafy gametophytes are found in (a) All pteridophytes (c) Some pteriidophytes (b) Bryophytes (d) Gymnosperms (ix) Smallest angiosperms is (a) Striga (c) Eucalyptus (c) Wolfia (d) Nicotiana (x) Which of the following algae is very rich in proteins. (a) Uolthrix (c) Gelidium (b) Chlorella (d) Oscillatoria (xi) A seed plant having a palm like habit is (a) Pinus (c) Cycas (b) Gnetum (d) Ginkgo (xii) Gymnosperms are characterized by (a) Small leaves (c) Fruits (b) Naked Ovules (d) Ciliated sperms (xiii) The thallus of Riccia is (a) Triploid (c) Diploid (b) Haploid (d) Polyploid (xiv) Peat is formed by (a) Riccia (c) Sphagnum (b) Anthoceros (d) Funaria (xv) The sporophyte consisting of foot, seta and capsule is seen in (a) Riccia (c) Selaginella (b) Cycas (d) Funaria 3. Fill in the blanks. (i) Bog moses is a common name of. (ii) is the tallest anigosperms. (iii) Ferns contain underground stem called. (iv) In red algae the reserved food is. (v) The gymnosperms areseeded plants (vi) The angiosperms areseeded plants. (vii) Spirally arrangedconstitute a cone. (viii) Production of spores of different sizes is called. (ix) There is a single cotyledon in the embryo ofclass of angiosperms. (x) Gametophytes and sporophyte are independent of each other in.

60 Bureau’s Higher Secondary (+2) BIOLOGY -1 4. Write notes on (explain briefly the following terms) : Heterospory, Archegonium, Antheridium, Haplontic, Diplontic, Sporophyll, Embryosac, Isogamy, Double fertilisation, Triple fusion, Protonema. 5. Differentiate between : (i) Red algae and Brown algae (ii) Liverworts and Moss (iii) Bryophytes and Pteridophytes (iv) Syngamy and Triple fusion (v) Monocots and Dicots (vi) Algae and Fungi Long answer-type questions : 1. Describe the basis of classification and general characters of algae. 2. Name plant group which bear archegonia and describe the characteristic feature of first achegoniate land plant. 3. If both Gymnosperms and Angiosperms bear seeds, then why they are classfied separately. 4. What are Gymnosperms? Describe their economic importance.

CLASSIFICATION OF ANIMAL CHAPTER KINGDOM Every day we come across with different kinds of animals surrounding us. We know few of them in our local language. They differ in their structures and forms. So far over a million species of animals have been described and they have been classified scientifically and many of them still remain to be explored. So the need for classification becomes all the more important to provide scientific names and to put them in right position in the animal kingdom. 4.1. METHOD OF CLASSIFICATION : Although the animals differ in structure and form, there are some basic features common to many in relation to the level of organization of cells body symmetry, types of coelom and patterns of digestive, circulatory, reproductive and nervous systems. These features are used as the basis of animal classification and some of them are discussed hereunder. 4.1.1. Levels of Body Organisation : All the animals in the animal kingdom are multicellular except protozoa. Since their body consist of many cells, they show three levels of body organization such as (i) cellular level, (ii) tissue level and (iii) organ and organ system level. For example, in sponges, the cells are arranged as loose cell aggregates, i.e., they exhibit cellular level of organisation because most of the life activities are performed by individual cells. On the contrary, in higher forms some division of labour occur among the cells.Similar or nearly similar types of cells, performing the same function are grouped into tissues. Animals possessing this feature are said to be in tissue level of organisation (e.g., coelenterates). A still higher level of organisation, i.e., organ and organ system level is exhibited by members of Platyhelminthes and other higher-phyla, where tissues are grouped together into organ, and organs into organ systems. In animals like annelids, arthropods, molluscs, echinoderms and chordates, organs have been associated to form functional systems and each system is concerned with a specific physiological function. This pattern is called organ system level of organisation. Organ systems in different groups of animals exhibit various patterns of complexities. For example, the digestive system in platyhelminths has only a single opening to the exterior that serves both as mouth and anus, and hence, is called incomplete. A complete digestive system has two openings, mouth and anus. Similarly, the circulatory system may be of two types: (i) open type in which the blood is pumped out of the heart into a cavity and the cells and tissues are directly bathed in it or (ii) closed type, in which the blood is circulated through a series of vessels of varying diameters (arteries, veins and capillaries).

62 I Bureau’s Higher Secondary (+2) BIOLOGY -1 Animals can be categorised on the basis of their symmetry. Sponges are mostly asymmetrical, i.e., any plane that passes through the centre does not divide them into equal halves. When the plane of division passing through the central axis of the body divides the organism into two identical halves, they are called symmetrical. The body symmetry is of two types i.e. radial and bilateral. In radial symmetry, any plane of division passing through the central axis of the body divides the organism into two identical halves. Coelenterates, ctenophores and echinoderms have this kind of body symmetry [Fig. 4.1 (a)]. In bilateral symmetry like those an annelids„arthropods, chordates, etc., only one plane of division passing through the central axis divides the animal into two identical halves the right and left [Fig. 4.1 (b)]. 4.1.2. Diploblastic and Triploblastic Organisation : In tissue grade of animals, the cells are arranged in two or three embryonic layers i.e. an external ectoderm, a middle mesoderm and an internal endoderm. Animals having two germ layers like ectoderm and endoderm are called diploblastic animals, e.g., coelenterates. Anon-cellular gelatinous layer, mesoglea, is present between the ectoderm and the endoderm [Fig. 4.2 (a)]. Further above the scale, there is a transition between diplobastic and triploblastic plans. Here, there is a third layer between ectoderm and endoderm, the mesnchyme. It contains free and wandering cells in a gelationous matrix (e.g., platyhelminths). In aschelminths, there is a third layer of muscle-like cells in between. However, this layer does not give rise to coelom. This group, too, is in the transition between diploblasic and triploblastic body plans. Triploblastic Fig. 4.2 : Germinal layers and body plans in animals, animals have all the three germinal (a) Diploblastic, (b) Triploblastic layers namely ectoderm mesoderm

Classification of Animal Kingdom I 63 and endoderm, arranged concentrically from outer to inner and further more, the mesoderm gives rise to coelom, the true body cavity, (e.g., annelids to mammals) 4.1.3. Coelom : Presence or absence of a cavity between the body wall and the gut wall is a very important criterion in classification. The body cavity, which is lined by mesoderm is called coelom [Fig. 4.3 (c)].The animals, in which the body cavity is absent are called acoelomates, e.g., platyhelminths [Fig. 4.3 (a)]. In some animals, the body cavity is not lined by mesoderm. Instead, a layer of muscle-like cells is present between the ectoderm and endoderm. Such a body cavity is called pseudocoelom and the animals possessing them are called pseudocoelomates, e.g., aschelminths [Fig. 4.3 (b)]. Animals possessing coelom are called coelomates, e.g., annelids, molluscs, arthropods, echinoderms, hemichordates and chordates. 4.1.4. Segmentation : In some animals, the body is externally and internally divided into segments with a serial repetition of most of the organs. For example in annelids (earthworm and leech), the body is metamerically segmented and the phenomenon is called as metamerism. However, in higher forms, metamerism is evident only in embryonic stages, which is secondarily lost in the adults. 4.1.5. Notochord : Notochord is a mesodermally derived solid and cylindrical rod-like structure formed on the dorsal side during embryonic development in some animals. Animals with notochord are called chordates and those animals which do not posses this structure are non-chordates, e.g., Porifera to Hemichordala.

64 I Bureau’s Higher Secondary (+2) BIOLOGY -1 4.2. CLASSIFICATION OF ANIMAL KINGDOM : The Kingdom Animalia is divided into two sub-kingdoms, parazoa and metazoa on the basis of cell aggregation in the body. 4.2.1. SUB-KINGDOM I, PARAZOA Phylum Porifera (Fig.4.4) 1. Animals of cellular grade of organization with incipient tissue formation. It includes the only phylum, Porifera (L., porus, pore ferre, to bear). 2. Sedentary and solitary or colonial. 3. No organ system, digestive tract and mouth. 4. Body is porous with many internal cavities or canals lined by flagellated cells, known as choanocytes. The canals constitute a canal system, through which a continuous current of water flows through the body. 5. The body wall consists of two layers: outer pinacoderm, made up of a layer of flat cells, known as pinacocytes and inner choanoderm made up of flask-shaped flagellated cells, known as choanocytes. 6. The two are cemented together by a mesenchyme containing a matrix and several types of free and wandering mesenchyme cells. 7. The embryonic undifferentiating cells of the mesenchyme are known as archaeocytes. These can differentiate into any of the adult cell types during exigency, particularly during regeneration. 8. Endoskeleton is made up of calcareous or silicious spicules and/or sponging fibers. 9. Respiratory, excretory and nervous systems and sense organs are absent. 10. Generally hermaphrodite. Reproduction occurs by both asexual and sexual methods. Asexual reproduction occurs by budding and gemmule formation. 11. Fertilization is internal and cross fertilization is the rule. 12. Development is direct or indirect through free swimming larvae, known as amphiblastula and parenchymula. 13. Most have remarkable power of regeneration. [e.g. Leucosolenia, Sycon, Spongilla (fresh water sponge), Euplectella (Venus’ flower basket), Hyalonema (Glass-rope sponge) and Euspongia and Hippospongia (Bath sponges)] Porifera is divided into three classes : Calcarea, Hexactinellida and Demospongiae.

Classification of Animal Kingdom I 65 PORIFERA CLASS I CLASS II CLASS III CALCAREA HEXACTI NELLI DA DEMOSPONGIAE e.g. Leucosolenia, e.g. Spongilla, Euplectella e.g. Euspongia and Hippospongia Syon and Grantia and Hyalonema (Bath sponges) Sycon oscula Euplectella substratum Fig.4.4 : Representative types from Porifera Euspongia 4.2.2. SUB-KINGDOM II, METAZOA 1. Animals of tissue or organ and organ system grade of organization. 2. Mouth and digestive tract are present. It is divided into two grades, such as Radiata and Bilateria based on the primary body symmetry

66 I Bureau’s Higher Secondary (+2) BIOLOGY -1 4.2.2.1. GRADE I, RADIATA : Phylum, Coelenterata (Fig.4.5) 1. Animals with tissue grade of organization. It includes only one phylum, Cnidaria or Coelenterata (Gr., koilos, hollow enteron, intestine). 2. Two types of forms, such as polyp and medusa exist. Some are exclusively polypoid, while others are medusoid. Still some others have both forms in their life cycle. 3. The primary body symmetry is radial or biradial. 4. Digestive cavity or coelenteron or gastro-vascular cavity is the only cavity in the body. Anus is absent. 5. Diploblastic animals i.e. body wall has two primary germ layers, outer ectoderm and inner endoderm cemented together by a non-cellular gelatinous mesogloea. 6. Interstitial cells are embryonic undifferentiated cells, present both in ectoderm and endoderm, among other cells. These cells can differentiate into any other kind of cell during exigency, especially during regeneration. 7. A coelenterate has a mouth encircled by tentacles, armed with stinging cells, nematoblasts or cnidoblasts. 8. Digestion is both intra- and extra-cellular. 9. Nervous system is primitive and diffuse. 10. Reproduction is both asexual and sexual. 11. Asexual reproduction takes place by budding. 12. Development is indirect through a planula larva. 13. Some exhibit the phenomenon of polymorphism. 14. Have a remarkable power of regeneration. [e.g. Hydra, Obelia, Physalia (Portuguese man of war), Aurelia (Jelly fish) Adamsia (Sea anemone), and a great variety of corals] Coelenterata is divided into three classes : Hydrozoa, Scyphozoa and Anthozoa or Actinozoa. COELENTERATA I CLASS I V CLASS III HYDROZOA ANTHOZOA OR ACTINOZOA e.g. Hydra Obelia and Physalia CLASS II e.g. Adamsia (Sea anemone) and (Portuguese Man of war) Corals SCYPHOZOA e.g. Aurelia (Jelly fish)

Classification of Animal Kingdom I 67 testis tentacles medusa buds tentacle mouth mouth gonotheca -gastrovascular cavity hypostome longitudinal section of longitudinal gonangium ‘\"section of ectoderm hydranth endoderm— mouth grown bud hydranth with hypostome basal disc tentacles contracted hydranth with tentacles gonotheca - spread developing M *** hydrothecae medusa buds * perisarc coenosarc blastostyle hydrorrhiza crest or sail pneumatophore perisarcajl Obelia or float annuli ** \\ cinclidal tubercles hydrocaulus g shell of gastropod hermit-crab / gonozooids WK smaller yv dactylozooids gastrozooids |l ||| tentacles^dH if1 A larger dactylozooids bearing f' nematocysts^ ||| Physalia exumbrellar surface gonads gastrovascular canals circular canal \\ anemones marginal thophalium tentacles velarium oral arms- Aurelia acontia pinnate tentacles Adamsia anthrocodia contiguous cups or thecae completely retracted polyp i coenenchyme^.- Corallium Fig.4.5 : Representative types from Coelenterata

68 I Bureau’s Higher Secondary (+2) BIOLOGY -1 Difference between Parazoa and Metazoa : Metazoa 1. Cells are specialized and exhibit cell­ Parazoa 1. Includes multicellular animals, but the cell cooperation among themselves. cells do not exhibit cell-cell 2. Tissue and organ system grade of cooperation. organization. 2. Cellular grade of organization. 3. Triploblastic. 3. Diploblastic. 4. Digestive cavity present. 4. Digestive cavity is absent. 5. Canal system is never present, 5. Canal system is present, (e.g. Animals belonging to the phyla, (e.g. Animals belonging to the Phylum Coelenterata and above in the Porifera) evolution scale) 4.2.2.2. GRADE II, BILATERIA : 1. Animals with organ system grade of organization. 2. The primary body symmetry is bilateral. 3. Anus is generally present. Bilateria is divided into Acoelomata, Pseudocoelomata and Coelomata on the basis of the absence or presence of a true body cavity, the coelom. We mention again that the coelom is a cavity present between the ectoderm and endoderm and derived from and lined by mesoderm. 1. Group I, Acoelomata : 1. Coelom is absent. The region between the digestive tract (endoderm) and body wall (ectoderm) is filled with mesenchyme. Mesenchyme contains free and wandering cells in a matrix. The mesenchyme cells are not organized into a germ layer. 2. Incipiently triploblastic, since mesenchyme is not organized into mesoderm. 3. Body is unsegmented and if segmented, the youngest segment is close to the head (e.g. Taenia). 4. Excretory system consists of protonephridia with flame cells. 5. Acoelomata includes one phylum, Platyleminthes.

Classification of Animal Kingdom I 69 Phylum, Platyhelminthes (Gr., platys, flat or broad helminthes, worm) (Fig.4.6): 1. Includes mostly endo-parasitic animals, commonly known as flat worms. 2. Bilaterally symmetrical acoelomate animals. 3. Two layers, ectoderm and endoderm are cemented by a mesenchyme. The mesenchyme has embryonic undifferentiated cells, known as neoblasts, among other cells. The neoblasts can differentiate into any other kind of cell during exigency, especially during regeneration. 4. Endo-parasitic animals have suckers and hooks for clinging and attachment. 5. Alimentary canal may be present in some free living forms or absent in parasitic forms. If alimentary canal is present, an anus is absent. 6. Respiratory and circulatory systems are absent. Respiration occurs by the general surface of the body by diffusion. 7. Excretory system consists of single or paired protonephridia with flame cells or solenocytes. 8. Nervous system is primitive with a nerve centre at the anterior end with one or three pairs of nerve cords. 9. Generally hermaphodites. Cross fertilization in Turbellaria and Trematoda and self fertization in Cestoda occur. 10. Development generally is indirect through one or a few larval forms. 11. Some exhibit remarkable power of regeneration. 12. Parasitic forms exhibit parasitic adaptations. [e.g. Planaria, Fasciola hepatica (Liver fluke), Schistosoma (Blood fluke) and Taenia solium (Tape worm)] Platyhelminthes is divided into three classes: Turbellaria, Trematoda and Cestoda. PLATYHELMINTHES V V CLASS III CLASS II CESTODA CLASS I TREMATODA e.g. Taenia solium TURBELLARIA e.g-fasciola and Schistosoma e.g. PI an aria

70 I mouth Bureau’s Higher Secondary (+2) BIOLOGY -1 anterior end scolex __neck or area of poliferation immature proglottids strobila Planaria excretory pore Fasciola repatica Fig.4.6 : Representative types from Platyhelminthes 2. Group II, Pseudocoelomata : 1. There is a cavity between the digestive tract and body wall, but it is not lined by mesoderm. Therefore, it is known as a pseudocoelom or pseudocoel. 2. Anus present. 3. It includes one phylum, Nemathelminthes or Aschelminthes. Phylum, Nemathelminthes (Gr. Nematos, thread eidos, form helminthes, worm) (Fig. 4.7): 1. Includes animals, possessing cylindrical body and hence, known as round worms. 2. The body is covered by a cuticle 3. The ectoderm is syncytial. 4. Longitudinal muscle fibers are present in four bands 5. Alimentary canal is more or less straight with mouth and anus present at two extreme ends. 6. Respiratory and circulatory systems are absent. Respiration occurs by diffusion through the general surface of the body. 7. Flame cells and nephridia are absent. Excretory system is in the form of English alphabet H’ with longitudinal excretory canals. 8. Nervous system consists of a distinct circumenteric nerve ring, from which arise anterior and posterior longitudinal nerves. 9. Sexes are separate, exhibiting sexual dimorphism. 10. Fertilization is internal and development is direct. The fertilized egg hatches into an embryo, which moults four times before becoming an adult. 11. Most are endoparasites, exhibiting remarkable parasitic adaptations.

Classification of Animal Kingdom I 71 [e.g. Ascaris lumbricoides, Ancylostoma duodenale (Hook worm), Enterobius vermicularis (Human pin worm or thread worm) and Wuchereria bancrofti (Filarial worm)]. Buccal Mouth mouth mouth capsule cephalic Mouth expansion , anterior pharynx -ABA oviduct end bulb in anterior vulva ovary cloacal vagina anterior opening intestine 4 uterus testis L- posterior ovary vas deferens posterior uterus Female genital posterior aperture anus oviduct Cloacal V seminal vesicle rectum aperture pointed tail Copulatory bursa (b) Female (a) Male (b) Female Anus (a) Male Ascaris lumbricoides Ancylostoma duodenale Enterobius vermicularis Fig.4.7: Representative types from Nemathelminthes There is no certain agreement about the classification of Nemathelminthes. However, some texts describe Nematoda as one single class of the phylum. 3. Group III, Coelomata: 1. Coelom is present. 2. Truly triploblastic animals. 3. Excretory organs are protonephridia with flame cells or metanephridia with or without nephrostomes. Coelomata is divided into Schizocoela (Protostomia) and Enterocoela (Deuterostomia), based on the nature and origin of the coelom. (a) Schizocoela (Protostomia): In some texts, this group has been described as Annelid superphylum, which includes three major phyla, Annelida, Arthropoda and Mollusca. It is characterized by: 1. The coelom is schizocoelic i.e. it originates as a cavity in the mesoderm. 2. Cleavage is spiral and determinate. 3. Blastopore becomes the mouth.

72 I Bureau’s Higher Secondary (+2) BIOLOGY -1 4. Skeleton, if any, is ectodermal. 5. Trochophore type of larva. Phylum, Annelida (L., annelus, ring Gr., eidos, ring) (Fig. 4.8): 1. Body generally elongated, cylindrical or flattened dorso-ventrally and worm-like. 2. Body is metamerically segmented. 3. There is a pre-oral muscular projection, known as the prostomium. It is not a true body segment. 4. The first true body segment is known as peristomium, which follows the prostomium. 5. In a majority, the locomotor structures, known as setae, are present. 6. The coelom is schizocoelic and spacious. It is filled with a coelomic fluid. 7. In aquatic forms, such as in Nereis, lateral paddle-like parapodia are present. 8. The alimentary canal is straight and simple with mouth and anus present at opposite extremities. 9. Circulatory system is of closed type. Blood is red due to the presence of red blood pigment dissolved in the plasma. 10. Excretion occurs by segmentally arranged nephriidia and chloragogen or yellow cells. 11. Nervous system consists of a pair of cerebral ganglia, a sub-pharyngeal ganglion and a ganglionated solid ventral nerve cord. 12. Usually hermaphrodites, but some are monoecious. 13. Development is direct or indirect through a trochophore larva. [e.g. Pheretima posthuma (Earthworm), Nereis (Clamworm or Sandworm) and Hirudinaria granulosa (Indian cattle leech)] Annelida is divided into three classes, Polychaeta, Oligochaeta and Hirudinea on two counts. The first is based on the presence or absence of locomotor structures (setae or chetae). Secondly, if setae are present, these are numerous or few. ANNELI DA V CLASS I POLYCHAETA e.g. Nereis

Classification of Animal Kingdom I 73 tentacle prostomial palp Genital 13th segment mouth x prostomium Nereis papillae anterior sucker Female genital pore velum Male genital 1st —-• pore nephridiopore male genital pore female genital pore Prostamium segmental < receptor organs 17th s 3 nephridiopore (b) Posterior sucker (a) Hirudinaria granulosa Pheretima posthuma (Cattle leech) (Earthworm) Fig.4.8 : Representative types from Annelida Differences between pseudocoelomata and coelomata : Pseudocoelomata Coelomata 1. Body cavity is a true coelom. 1. Body cavity is a pseudocoelom or false coelom 2. Coelom is lined by mesoderm on both sides. 2. Pseudocoelom is not lined by mesoderm. 3. It arises as a cavity in the embryonic mesoderm. 3. It is derived from blastocoel of the embryo. 4. Internal organs are suspended within this cavity. 4. Internal organs are not suspended (e.g. Animals belonging to the phyla, within this cavity. Annelida and above in the evolution scale) (e.g. Animals belonging to the Phylum, Nemathelminthes or Aschelminthes) Phylum, Arthropoda (Gr., arthros, jointed podos, foot) (Fig. 4.9): 1. The body is segmented and each segment bears paired jointed appendages. 2. The body is generally divided into head, thorax and abdomen. However, in some forms the head and thorax fuse forming a cephalothorax. 3. Jointed appendages are present.

74 I Bureau’s Higher Secondary (+2) BIOLOGY -1 4. The body is covered by a cuticle, made of chitin. 5. Coelom is reduced and a spacious blood-filled cavity, known as haemocoel is present. 6. Alimentary canal is divided into fore gut, mid gut and hind gut. The mouth is surrounded by many jointed appendages. These together constitute the mouth parts 7. Respiration occurs by gills in aquatic forms, trachea and book lungs in air breathing (terrestrial) forms., 8. Circulatory system is of open type with the heart being dorsal in position. 9. Excretion occurs by malpighian tubules or green glands or coxal glands. 10. Nervous system consists of a brain lying in the head that is followed by a ganglionated double ventral nerve cord. 11. Sexes are separate. The phenomenon of sexual dimorphism is often exhibited. 12. Reproduction is sexual and fertilization is internal. 13. Development is direct or indirect through one or a few larval stages. [e.g. Peripatus, Palaemon (Fresh water prawn), Pennaeus (Brackish water prawn), Lobster, Crab, Millipedes, Centipedes, Scorpion, Spider, Limulus (King crab) Lepisma (Silver fish), Periplaneta americana (Cockroach), Butterfly and Moth, Mosquito, House fly]. Phylum, Arthropoda is primarily divided into five classes: Onychophora, Crustacea, Myriapoda, Arachnida and Insecta. Class, Insecta is further divided into two sub-classes: Apterygota [includes wing-less insects, e.g. Lepisma (Silverfish)] and Pterygota (includes insects with wings). ARTHROPODA CLASS I V J' CLASS V CLASS III ONYCOPHORA MYRIAPODA INSECTA e.g. Peripatus e.g. Millipedesand V Centipedes V CLASS II CLASS IV CRUSTACEA ARACHNIDA e.g. Palaemon (Frsh water prawn), e.g. Scorpion, Spider and Pennaeus (Brackish water prawn), Lobster and Crab Limulus (King Crab) SUB - CLASS I SUB - CLASS II APTERYGOTA PTERYGOTA e.g. Primitive, wing -less insects e.g. Insects with wings (Cockroach, [ Lepisma (Silver fish)] Butterfly, Dragonfly, Mosquito and Housefly

Classification of Animal Kingdom I 75 Arthrodial Cephalothorax Antennal spine Cephalic shield membrane Hepatic spine Compound eye Rostrum Ocelli Antenna Poison claw Antennule Antenna Stigmata Walking Pleopods III maxillipede Claws Telson Non chelate legs II Chelate leg Uropods Trunk Palaemon (Fresh water prawn) Preantenna Tubercles Oral papilla Prothorax Mouth Claws Trunk appendages Antenna Peripatus Centipede Antenna A x Antennule Great chela Mesothorax Compound Metathorax eye Carapace Walking leg Abdomen Anal cercus 10th tergum- Thoracic Styles legs Periplaneta americana (Cockroach) Abdomen Crab Fig.4.9 : Representative types from Arthropoda Differences between pseudocoel and haemocoel Pseudocoel Haemocoel 1. Mesoderm-lined true body cavity, filled 1. False body cavity, not lined by mesoderm with haemolymph or blood. 2. It is derived from blastocoel of the 2. It arises as a cavity in the embryonic embryo. mesoderm. 3. It is not filled with blood. 3. It is filled with blood or haemolymph, (e.g. Animals belonging to the phylum, (e.g. Animals belonging to the Phylum, Arthropoda) Nemathelminthes or Aschelminthes)

76 I Bureau’s Higher Secondary (+2) BIOLOGY -1 Phylum, Mollusca (L., mollis or molluscs, soft) (Fig. 4.10): 1. Aquatic, mostly marine but a few fresh water forms. 2. Body is secondarily unsegmented and bilaterally symmetrical. A few, like Pila, are secondarily asymmetrical due to a phenomenon called torsion that occurs during the development. 3. The body is divided into head, foot and visceral mass. All visceral organs constitute the visceral mass that is covered by a fold of the body wall, known as mantle. 4. The mantle secretes a calcareous (calcium carbonate) shell. 5. The coelom is reduced to the cavities of the pericardium and the cavities, where gonads are present. 6. The digestive tract is simple and tubular with mouth and anus present at opposite ends. However, in gastropods, the tract twists due to torsion and consequently, the mouth and anus come close to each other at the anterior end. 7. Respiration, in aquatic forms, takes place by gills or ctenidia. In terrestrial forms it occurs by pulmonary sacs. 8. Excretion is performed by a pair of kidneys. 9. Nervous system is centralized with a brain in the head, which is followed by nerves to different parts of the visceral mass. 10. Sense organs are in the form of eyes, tentacles, osphradium and statocyst. 11. Sexes are generally separate, but some are hermaphrodites. 12. Development is direct or indirect through larval stages known as trochophore, velliger and glochidium. [e.g. Pila globosa (Fresh water snail / Apple snail), Unio (Fresh water mussel), Pinctada sps (Pearl oyester), Sepia (Cuttie fish), Loligo (Squid) and Octopus (Sea devil)] The phylum, Mollusca is divided into six classes: Monoplacophora, Amphineura, Scaphopoda, Gastropoda, Bivalvia or Pelecypoda and Cephalopoda. MOLLUSCA CLASS I CLASS III CLASS V MONOPLACOPHORA SCAPHOPODA PELECYPODA e.g. Dentalium e.g. Unio (Fresh e.g. Neopilina water mussel), CLASS II Pinctada sps, (Pearl AMPHINEURA oyster) e.g. Chiton CLASS IV CLASS VI GASTROPODA CEPHALOPODA e.g. Pila globosa e.g. Sepia (Cuttie (Apple snail) fish), Loligo (Squid) and Octopus (Sea devil / Devil fish).

Classification of Animal Kingdom I 77 penultimate apex visceral mass whorl varix mantle ommatophore body outer right eye whorl lip nuchal lobe gg| supramarginal umbilicus mouth or groove aperture columellar lip left nuchal lobe operculum Pila (shell with operculum) first tentacle head foot second tentacle A Hinge ligament Umbo Lines of growth Exhalent Pila (Body after removing the shell) siphon Shell •/ Protruded suckers oral arms foot Inhalent Mantle edge tentacle siphon Unio oral arms head collar suckers -O' trunk or visceral funnel body—l || hump it suckers lateral fin or parapodium hectocotyl Octopus Fig.4.10: Representative types from Mollusca (b) Enterocoela (Deuterostomia): In some texts this group has been described as the Echinoderm superphylum that includes three major phyla, Echinodermata, Hemichordata and Chordata. 1. The coelom is enterocoelic i.e. it originates as pouches from the endoderm. 2. Cleavage is radial and indeterminate. 3. Blastopore becomes the anus. 4. Skeleton is mesodermal. 5. Pluteus type of larva.

78 I Bureau’s Higher Secondary (+2) BIOLOGY -1 Phylum, Echinodermata (Gr., echinos, spiny derma, skin) (Fig.4.11): 1. Exclusively marine animals having pentamerous radial symmetry. This symmetry is considered as secondary. The primary symmetry refers to the symmetry of their larvae, which is bilateral. This fact justifies their inclusion in the grade, Bilateria. 2. Body shape is variable like star-shaped, globular, spherical, etc. 3. Body is with distinct oral and aboral sides. No definite head, however, is present. 4. The skin is tough and leathery bearing spines and calcareous dermal ossicles. 5. A characteristic water vascular system or ambulacral system is present with numerous tube feet, which help in locomotion. 6. Alimentary canal is a straight or coiled tube. 7. Respiration occurs by diffusion through the body wall. 8. Blood vascular system, also known as haemal system, is of open type. 9. Excretion occurs through the body surface. 10. Nervous system is primitive 11. Sense organs are poorly developed. 12. Sexes are separate and reproduction is sexual. 13. Fertilization is external and development is indirect through characteristic larval forms, such as bipinnaria auricularia pluteus, etc. [e.g. Antedon (Sea lily), Asterias (Star fish), Cucumaria (Sea cucumber), Echinus (Sea urchin), Ophioderma (Brittle star)] The phylum, Echinodermata is primarily divided into two sub-phyla, Pelmatozoa and Eleutherozoa, based on whether the form is sedentary or free-living. Pelmatozoa is divided into five classes, of which one, Crinoidae is living, while others are extinct. Eleutherozoa is divided into five classes, of which four are living and one is extinct. The living classes are : Asteroidae Ophiuroidae Echinoidae and Holothuroidae. ECHINODERMATA I I SUB-PHYLUM I SUB-PHYLUM II PELMATOZOA ELEUTHEROZOA ------ CLASS I CLASS II — ---------- CLASS I CRI NOIDEA OPHIUROIDEA ASTEROIDEA e.g. Brittle star e.g. Antedon (Sea lily) e.g. Asterias (Star fish> CLASS II -V ---------- CLASS III (All extinct) ECHINOIDEA e.g. Echinus (Sea urchin) CLASS IV------- CLASS V HOLOTHUROIDEA (Extinct) e.g. Cucumaria (Sea cucumber)

Classification of Animal Kingdom I 79 normal dendritic tentacles Asterias Antedon Echinus Brittle star Fig.4.11 : Representative types from Echinodermata Differences between schizocoelic coelom and enterocoelic coelom Schizocoelic coelom Enterocoelic coelom 1. The coelom is formed by the splitting of mesoderm bands. 1. The coelom is derived from the dorso­ lateral mesodermal pouches from the 2. The mesoderm is derived from a wall of the archenteron. source other than the archenteron. 2. The mesoderm is derived from the 3. The mesodermal cells separate off archenteric roof. from the endoderm early during devel­ opment. 3. The mesodermal cells remain associ­ ated with the endoderm and separate (e.g. Animals belonging to the phyla, off late during the embryonic develop­ Annelida, Arthropoda and Mollusca) ment. (e.g. Animals belonging to the phyla, Echinodermata Hemichordata and Chordata)

80 I Bureau’s Higher Secondary (+2) BIOLOGY -1 Phylum, Hemichordata (Gr., hemi, half chorda, string or cord) (Fig. 4.12): 1. Exclusively marine, solitary or colonial. 2. Triploblastic and bilaterally symmetrical. 3. Body is vermiform (worm-like), divided into proboscis, collar and trunk. 4. Coelom is enterocoelic, divided into single protocoel and paired mesocoel and metacoel. 5. A pre-oral muscular extension, the buccal diverticulum is present. It was considered as homologous to the notochord of chordates. However, due to its structural dissimilarity, it is no longer considered as a notochord homologue. It is simply termed as a stomochord. Based on this, Hemichordata is separated off from Chordata and assigned with a phylum status and placed among non- chordates. 6. Pharyngeal gill clefts are present in pairs in the trunk. 7. Digestive tract is well defined and the anus is terminal at the posterior end. 8. Respiration is branchial i.e. takes place by gill pouches. 9. Circulatory system is of closed type. A heart vesicle or pericardium is present in the proboscis. 10. Excretion by a proboscis gland or glomerulus. 11. Nervous system is primitive comprising of an intra-epidermal nerve plexus. 12. Sexes are separate and fertilization is external. 13. Development is either direct or indirect through a larval form, known as tornaria larva. [e.g. Balanoglossus (Tongue or Acorn worm), Saccoglossus, Cephalodiscus, Rhabdopleura] The phylum, Hemichordata is divided into two main classes : (1) Enteropneusta and (2) Pterobranchia. Phylum, Chordata : 1. The name of the phylum is so because of the presence of a notochord. 2. The notochord is a solid chord consisting of vacuolated cells surrounded by two connective tissue sheaths. 3. In a few chordate groups, the notochord persists as such, while in a majority, it is transformed into a vertebral column by ossification and segmentation.

Classification of Animal Kingdom I 81 i— proboscis HEMI CHORDATA collar CLASS I branchio- > ENTEROPNEUSTA e.g. Balanoglossus and genital region Saccoglossus ridge CLASS II PTEROBRANCHIA hepatic e.g. Cephalodiscus and caecae hepatic Rhabdopleura region abdominal region anus Balanoglossus Fig.4.12: Representative types from Hemichordata 4. The pharynx is perforated by pharyngeal gill slits or clefts, which help in respiration. In a majority of chordates, the pharyngeal gill slits are lost secondarily. 5. There is a dorsal tubular nerve cord just dorsal to the notochord. It is simple in primitive chordates, while in higher chordates, it specializes as a brain at its anterior end. The nervous system consists of three elements, central nervous system or CNS (brain and the spinal cord), peripheral nervous system or PNS (cranial and spinal nerves) and autonomic nervous system or ANS (sympathetic and para-sympathetic nerves innervating the visceral organs). 6. Blood vascular system is of closed type. The heart is ventral in position. Barring a few primitive chordates, the blood contains nucleated corpuscles and the red blood corpuscles contain the red coloured respiratory pigment, haemoglobin. 7. Barring a few primitive chordates,the excretory organs are pro-, meso- or metanephric kidneys. 8. Generally, the sexes are separate with defined sexual dimorphism. 9. Fertilization is external or internal. 10. A majority are oviparous, while some are viviparous. 11. There is a tail. A tail is a post-anal extension of the body and thus, the anus comes to lie on the ventral side. See Fig.4.13 for a generalized chordate plan.

82 I Bureau’s Higher Secondary (+2) BIOLOGY -1 Chordata is divided into three sub­ phyla: Urochordata, Cephalochordata and Craniata or Vertebrata The representatives of Urochordata and Cephalochordata are considered as primitive chordates and hence are grouped together as Protochordata or Acraniata. This classification is based on the absence or presence of a cranium and a vertebral column. Cranium and vertebral column are two elements of the endoskeleton of vertebrates and both always go together i.e. wherever there is a cranium, there is a vertebral column. Protochordates have notochord, but, the notochord does not transform into vertebral column and therefore, are not supposed to have a cranium. This logic is enough to assign the synonym, acraniata, to Protochordata. Sub-phylum, Urochordata (Gr., uras, tail chorda, string or cord) (Fig.4.14): 1. Body is sac-like, covered with a test of tunicin. Hence, the name of the group is also mentioned as Tunicata in some texts. 2. There are two apertures : banchial and atrial. Branchial aperture opens into a pharynx, while the atrial aperture leads from an atrial cavity or atrium. 3. The body has a peculiar symmetry i.e. the branchial aperture is considered as the anterior end, while the opposite end is posterior. The atrial aperture is the dorsal side, while its opposite side is ventral. 4. Notochord is absent in the adult. However, it is present in the larva and confined to the tail region. Hence, the name of the group is Urochordata, which literally means, tail notochord. 5. The nerve cord is also absent in the adult. The nervous system is represented by only a dorsal ganglion and a few nerves originating from it. A full-fledged nerve cord is present in the larva, which degenerates during metamorphosis. 6. The degeneration of both the notochord and nerve cord occurs during metamorphosis, which has been termed as retrogressive metamorphosis. 7. The pharynx is perforated by many gill slits or clefts. 8. The interior of the pharynx is furnished with two special structures, endostyle and dorsal lamina to facilitate ciliary or filter feeding. 9. Hermaphrodites. The male and female gonads are united into one structure. 10. Development is always indirect with a tadpole larva, known as ascidian tadpole larva.

Classification of Animal Kingdom I 83 ANTERIOR DORSAL UROCHORDATA atrial branchial CLASS I aperture aperture ---- > LARVACEA test e.g. Oikopleuraand VENTRAL POSTERIOR CLASS II —> ASCI DI ACEA foot Herdmania e.g. Herd mania and Ascidia CLASS III ---- > THALIACEA e.g. Salpa and Doliolum Fig. 4.14: Representative types from Urochordata 11. The larva possesses all the diagnostic chordate characters, out of which the notochord and the nerve cord degenerate during retrogressive metamorphosis, [e.g. Herdmania (Sea squirt), Ascidia, Botryllus, Salpa, Doliuolum, and Oikopleura] The sub-phylum is divided into three classes: Larvacea, Ascidiacea and Thaliacea. Sub-phylum, Cephalochordata (Gr., kephale, head chorda, string or cord) (Fig. 4.15): 1. Solitary, marine, burrowing in the sand or mud. 2. Body is fish-like with tapering ends. 3. Unpaired dorsal, ventral and caudal fins are present. 4. The notochord extends all along the length of the body i.e. up to the extreme anterior end of the head, rostrum. Normally, the notochord does not extend into the head in chordates. This is an exceptional character and this character gives the name of the group as Cephalochordata. 5. The pharynx is perforated by gill slits or clefts. 6. The interior of the pharynx is furnished with two special structures, endostyle and dorsal lamina to facilitate ciliary or filter feeding. 7. An ectoderm-lined atrial cavity is present, which opens to the exterior through an atrial opening or atriopore. 8. The body is with segmented muscle or myotomes. 9. Respiration is branchial. 10. Blood-vascular system is of closed type with no heart, blood corpuscles and blood pigment.

84 I Bureau’s Higher Secondary (+2) BIOLOGY -1 11. Excretion takes place by protonepridia. 12. Nervous system consists of an ill-developed brain at the anterior end which is followed by a tubular nerve cord. 13. Sexes are separate and development is direct. 14. The group is represented by two genera, Branchiostoma (= Amphioxus) and Asymmetron. notochord dorsal fin rays dorsal fin metapieurai atriopore fold Amphioxus Fig.4.15: Amphioxus, a representative type from Cepholochordata Sub-phylum, Vertebrata or Craniata (Gr., kranion, head) All chordates barring protochordates are grouped together as Vertebrata or Craniata. Vertebrates are characterized by the presence of the following : 1. An endoskeleton of cartilages and bones. 2. Endoskeleton is classed under: (i) axial and (ii) appendicular. 3. The axial endoskeleton is constituted by the skull (skeletal frame of the head), vertebral column, sternum and ribs. 4. Both form the basis of the formation of the taxon, Vertebrata. 5. The vertebral column is a modification of the notochord. 6. The appendicular skeleton consists of limb bones and girdles (except fishes) Vertebrata is divided into two super-classes : Agnatha and Gnathostomata. Super-class, Agnatha (Gr., a, no gnathos, jaw): 1. Fish-like marine animals. 2. Jaws are absent, hence, are known as jaw-less vertebrates. 3. Paired appendages (fins) are absent.

Classification of Animal Kingdom I 85 4. It is divided into two classes: Ostracodermi and Cyclostomata. 5. Ostracodermi includes extinct jaw-less vertebrates, while Cyclostomata represents the living jaw-less vertebrates. Class, Cyclostomata (Gr., cyclos, circular stoma, mouth) (Fig.4.16): 1. Marine jaw-less vertebrates, which generally migrate to fresh water of rivers for spawning. 2. The body is eel-like, devoid of scales. 3. Mouth is circular and remains open throughout life. 4. Paired fins are absent. However, median fins, such as dorsal, ventral and caudal fins are present. 5. Paired naked gill openings (1-16 pairs) are present on the lateral side of the body. 6. There is a single median nostril, hence, the name of the group is also Monorrhina. 7. Endoskeleton is cartilaginous. 8. The notochord is persistent. 9. The skull is cartilaginous and poorly developed. It is followed by a branchial basket. 10. Sexes are separate. Gonads are singular and without gonoduct. 11. Development is direct or indirect through a characteristic larval stage, ammocoetes. [e.g. Petromyzon marinus (Lamprey), Myxine glutinosa and Bdellostoma (Hag fishes)] head trunk first dorsal fin second dorsal fin tail Petromyzon eye caudal fin tentacles single external mucous pores anus tail gill opening Myxine Fig.4.16 : Representative types from Cyclostomata

86 I Bureau’s Higher Secondary (+2) BIOLOGY -1 Super-class, Gnathostomata (Gr., gnathos, jaw stoma, mouth): 1. Mouth is guarded by upper and lower jaws. 2. Endoskeleton is made up of both cartilages and bones. 3. The notochord is transformed into a vertebral column that is constituted by several vertebrae. 4. Paired appendages (fins or limbs) are present. Differences between Agnatha and Gnathostomata Agnatha Gnathostomata 1. Defined jaws are present. 1. Jaws are absent. 2. Mouth can be closed by the jaws. 2. Mouth is circular in outline and can 3. Paired appendages (paired fins or not be closed. limbs) are present. 3. Paired appendages (paired fins) are 4. Cranium and vertebral column are well absent. developed. 4. Cranium and vertebral column are not 5. A pair of external nostrils. well developed. 6. Internal ear with three semicircular 5. Single external nostril. canals. (e.g. Animals belonging to Classes, 6. Internal ear with two semicircular Pisces to Mammalia) canals. [e.g. Animals belonging to the Class, Cyclostomata (Petromyzon and Myxine)] Gnathostomata is divided into two series: Pisces and Tetrapoda. Series, Pisces pisces, fishes) (Fig. 4.17): 1. Aquatic animals having streamlined body. 2. Body is covered by dermal scales. Scales are of several types : placoid, cycloid, ctenoid and cosmoid. 3. Internal gills, open to outside through paired gill openings. The gill openings are naked or covered by opercula (singular, operculum). 4. Respiration is branchial. However, in some forms (lung fishes) respiration is pulmonary i.e. occurs by lungs in addition to being branchial. 5. Some air-brerathing fishes possess accessory respiratory organs for aerial respiration. 6. Both median (unpaired) and paired fins are present. 7. Two pairs of paired fins, the pectoral and pelvic, characterize fishes. 8. The median fins include the dorsal, ventral and caudal fins. 9. The endoskeleton is cartilaginous or bony.

Classification of Animal Kingdom I 87 10. Lateral line system is well developed. This system functions as a rheoreceptor i.e. it detects the direction of the water current by perceiving vibrations. 11. The heart is two chambered consisting of an atrium and a ventricle. It is venous i.e. only deoxygenated blood circulates through it. 12. Single circulation. 13. Only the internal ear is present. 14. Kidney is mesonephros. 15. Sexes are separate. Development is indirect. [e.g. Scoliodon (Shark) Raja (Skate) Torpedo (Electric ray) Chimaera (Cat fish) Neoceratodus, Protopterus and Lepidosiren (Lunf fishes) Latimeria chalumnae', Labeorohita (Rohu) Catla catla (Bhakura) and Anabas testudineus (Climbing perch)] The series, Pisces is divided into seven classes : Pterychthys, Coccostei, Acanthodii, Elasmobranchii, Holocephali, Dipnoi and Teleostomi. The first three classes are extinct and often classed together as Placodermi. The latter four classes are living. Elasmobranchii includes all cartilaginous fishes. Holocephali is a small class and includes rat fish. It combines the characters of both cartilaginous and bony fishes. Therefore, it is considered as a connecting link between the two. The class Dipnoi includes lung or air-breathing fishes. There are only three discontinuously distributed representatives of this class. Teleostomi is divided into two sub-classes : Crossopterygii and Actinopterygii. The sub-class, Crossopterygii is very significant from the fact that it includes fishes possessing lobed fins or archipterygeal fins. These fishes are considered as the ancestors of the present-day land dwellers. All, except Latimeria chalumnae, are extinct. This representative has survived millions of years without any significant evolutionary change. Therefore, it is considered as a living fossil. In another classification, the cartilaginous fishes and bony fishes are grouped together as Chondrichthyes and Osteichthyes, respectively. PISCES 1 T“ CLASS I CLASS III CLASS V v PTERYCHTHYS ACANTHODII HOLOCEPHALI CLASS VII (Extinct) (Extinct) e.g. Chimaera TELEOSTOMI (Cat fish) v v CLASS II CLASS IV CLASS VI COCCOSTEI ELASMOBRANCHII DIPNOI e.g. Scoliodon (Shark), (Extinct) Raja (Skate), Torpedo e.g. Neoceratodus, Protopterus and (Electric ray) Lepidosiren. SUB-CLASS I v CROSSOPTERYGII (Lobed fin fishes) SUB-CLASS II e.g. Latimeria chalumnae, ACTINOPTERYGII Coelacanthus and Osteolepis (both Or TELEOSTOMI e.g. All present-day extinct) bony fishes.

88 I Bureau’s Higher Secondary (+2) BIOLOGY -1 caudal second dorsal fin first dorsal fin lateral line snout caudal fin anal fin . gill clefts \\external median ventral fin Pelvlc flnpectoral fin nostril Scoliodon (1 - 5) mouth nostril eye scales trunk dorsal fin tail spiracle electric mouth caudal fin organ pectoral fin pelvic fin pectoral fin pelvic fin Neoceratodus (Lung fish) first dorsal fin second dorsal fin caudal fin Torpedo (Electric ray) snout branchial (tubular) aperture nostril pectoral fin mouth operculum Dorsal fin dorsal fin Mouth brood pouch prehensile tail Caudal fin Pectoral fin Operculum Hippocampus (sea horse) Pelvic fin sansory Catlacatla (Rohu) frontal eye clasper dorsal fin lateral line mouth caudal fin operculum gill slit pectoral fin tail pelvic fin claspers Fig. 4.17: Representative types from Pisces Chimaera (Rat fish)

Classification of Animal Kingdom I 89 Series, Tetrapoda (Gr., tetra, four podos, foot): 1. Possess two pairs of appendages or limbs: a pair of fore limbs and a pair of hind limbs. 2. The limbs are pentadactyl i.e. each possesses five digits or fingers. However, in some tetrapods, limbs may bear less than five fingers. This is a secondary reduction in the normal number. Difference between Pisces and Tetrapoda : Pisces Tetrapoda 1. Aquatic vertebrates. 1. Aquatic, terrestrial, arboreal or aerial 2. Presence of paired fins (pectoral and vertebrates. pelvic fins). 2. Presence of paired pentadactyl limbs 3. Respiration, generally, takes place by (fore and hind limbs). gills. 3. Respiration, generally, takes place by 4. Generally oviparous. lungs. (e.g. All fishes) 4. Oviparous or ovoviviparous or viviparous. (e.g. Animals belonging to Classes, Amphibia to Mammalia) Tetrapoda is primarily divided into Anamniota and Amniota based on the absence or presence of extra-embryonic membranes (amnion, chorion, yolk sac and allantois). Anamniota includes the only class, Amphibia. Amniota includes three classes: Reptilia, Aves and Mammalia. Class, Amphibia (Gr., amphi, double or both bios, life) (Fig. 4.18): 1. The skin is smooth and moist with mucous glands. It is naked without scales. 2. Body is divided into head, trunk and tail. There is no neck between the head and the trunk. 3. Two pairs of pentadactyl limbs are present. 4. A pair of tympanum is present. 5. Respiration is of three types: cutaneous, bucco-pharyngeal and pulmonary. 6. Heart is three chambered with two auricles and a single ventricle. 7. The excretory organ is a pair of opisthonephric kidneys. 8. There is a cloaca, the converging chamber of the rectum and the urino-genital ducts. The cloaca discharges out through a cloacal aperture. 9. There are ten pairs of cranial nerves.

90 I Bureau’s Higher Secondary (+2) BIOLOGY -1 10. Poikilothermal or cold blooded vertebrates. 11. All undergo aestivation during summer and hibernation during winter. 12. Skull is dicondylic i.e., with two occipital condyles. 13. Sexes are separate. Oviparous. 14. Eggs are without shell and laid in water. 15. Fertilization is external. 16. Development is indirect with aquatic tadpole larvae of anurans or axolotl or the like larvae of urodeles. An aquatic larva undergoes a remarkable metamorphosis into a terrestrial adult. Thus, amphibians spend a part of their life cycle on land and the other in water. 17. Most amphibians exhibit the phenomenon of parental care. 18. Most urodeles exhibit the phenomenon of neoteny and paedogenesis. Neoteny is a prolongation of the larval life and paedogenesis is the attainment of sexual maturity during the larval life. 19. A few urodeles are permanently neotenic i.e. they fail to metamorphose and live with larval features. [e.g. Ichthyophis (Blind worm), Bufo melanostictus (Common toad), Hoplobatrachus tigerinus (=Rana tigerina) (Indian bull frog), Polypedates maculatus (Jumping frog), Ambystoma tigrinum (Tiger salamander), Salamandra (Terrestrial salamander), Amphiuma (Congo eel), Triton (European salamander), Necturus (Mud puppy)] Amphibia is primarily divided into two sub-classes : Stegocephalia and Lissamphibia. Stegocephalia includes all extinct amphibians belonging to three orders : Labyrinthodontia, Phylospondyli and Lepospondyli. Lissamphibia includes living amphibians belonging to three living orders : Gymnophiona or Apoda (limb-less amphibians), Anura or Salientia (tail-less amphibians) and Urodela or Caudata (tailed amphibians). AMPHIBIA SUB-CLASS I SUB-CLASS II STEGOCEPHALIA LISSAMPHIBIA (Extinct) (Living) ORDER I ORDER III ORDER II LABYRINTHODONTIA LEPOSPONDYLI ANURA or SALIENTIA (Tail-less amphibians) e.g. Fogs abd Toads VV ORDER II ORDER I ORDER III PHYLOSPONDYLI GYMNOPHIONA or APODA URODELA or CAUDATA (Limb-less amphibians) (Tailed amphibians) e.g. Icthyophis (Blind worm) e.g. Newts and Salamanders)

Classification of Animal Kingdom I 91 nostril mouth -nostril fore limb Salamandra external gills fore limb trunk hind limb caudal fin nostril Axolotle Larva eye tympanum adhesive pads or discs anus nostril fore limb Ichthyophis (Male) eggs Polypedates maculatus (Jumping frog) nostril nostril Ichthyophis (Female) fore limb Ambystoma tigrinum nostril mouth snout mid dorsal line warts nostril tympanum dorsal mouth parotoid gland surface ictitating membrane eye tympenum fore limb fingers thumb vent Hoplobatrachus tigerinus (Indian bull frog) Bufo melanostictus (Toad) Fig.4.18 : Representative types from Amphibia


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