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- 10.1: Discovering How Populations Change
- Evolution by natural selection arises from three conditions: individuals within a species vary, some of those variations are heritable, and organisms have more offspring than resources can support. The consequence is that individuals with relatively advantageous variations will be more likely to survive and have higher reproductive rates than those individuals with different traits. The advantageous traits will be passed on to offspring in greater proportion.
- 10.2: Mechanisms of Evolution
- Four factors that can change the allele frequencies of a population. Natural selection works by selecting for alleles that confer beneficial traits or behaviors, while selecting against those for deleterious qualities. Mutations introduce new alleles into a population. Genetic drift stems from the chance occurrence that some individuals have more offspring than others and results in changes in allele frequencies that are random in direction.
- 10.3: Evidence of Evolution
- The evidence for evolution is found at all levels of organization in living things and in the extinct species we know about through fossils. Fossils provide evidence for the evolutionary change through now extinct forms that led to modern species. For example, there is a rich fossil record that shows the evolutionary transitions from horse ancestors to modern horses that document intermediate forms and a gradual adaptation t changing ecosystems.
- 10.4: Speciation
- Speciation occurs along two main pathways: geographic separation (allopatric speciation) and through mechanisms that occur within a shared habitat (sympatric speciation). Both pathways force reproductive isolation between populations. Sympatric speciation can occur through errors in meiosis that form gametes with extra chromosomes, called polyploidy. Autopolyploidy occurs within a single species, whereas allopolyploidy occurs because of a mating between closely related species.
- 10.5: Common Misconceptions about Evolution
- Although the theory of evolution initially generated some controversy, by 20 years after the publication of On the Origin of Species it was almost universally accepted by biologists, particularly younger biologists. Nevertheless, the theory of evolution is a difficult concept and misconceptions about how it works abound. In addition, there are those that reject it as an explanation for the diversity of life.
Thumbnail: The hominoids are descendants of a common ancestor. (Public Domain; Huxley - Mans Place in Nature).
The Embryo Project Encyclopedia
In his essay "Evolution and Tinkering," published in Science in 1977, François Jacob argues that a common analogy between the process of evolution by natural selection and the methods of engineering is problematic. Instead, he proposes to describe the process of evolution with the concept of bricolage (tinkering). In this essay, Jacob does not deny the importance of the mechanism of natural selection in shaping complex adaptations. Instead, he maintains that the cumulative effects of history on the evolution of life, made evident by molecular data, provides an alternative account of the patterns depicting the history of life on earth. Jacob's essay contributed to genetic research in the late twentieth century that emphasized certain types of topics in evolutionary and developmental biology, such as genetic regulation, gene duplication events, and the genetic program of embryonic development. It also proposed why, in future research, biologists should expect to discover an underlying similarity in the molecular structure of genomes, and that they should expect to find many imperfections in evolutionary history despite the influence of natural selection.
The author of the article, François Jacob, studied enzyme expression and regulation in bacteria and bacteriophages at the Institut Pasteur in Paris, France. In 1965, Jacob won the Nobel Prize in Physiology or Medicine with André M. Lwoff and Jacques L. Monod for their work on the genetic control of enzyme and virus synthesis. At the Institut Pasteur, Jacob and his colleagues constructed a model of gene regulation according to which regulatory proteins in cells interact to switch on or off genes, and thus control physiological processes. They named this regulatory mechanism an operon, and hypothesized that it existed in the cells of all living organisms. Subsequent research confirmed their hypothesis. The ubiquity of regulation processes found at the molecular level led Jacob to consider its implications for evolutionary biology.
Jacob was also influenced by the work of Claude Lévi-Strauss, who was affiliated to Collège de France in Paris, France, and who applied the theoretical framework of structural linguistics to anthropology. Lévi-Strauss argued that researchers could analyze human communication through the various relations between the signifier and the signified and the changes in the relations between these units. In a similar way, Jacob said that the study of evolution could benefit from the analysis of the main units in molecular biology, such as the structural genes and the regulatory genes, and from the analysis of the changes in the relations between the units involved in the regulation of cell physiology. In his 1977 essay, "Evolution and Tinkering," Jacob assimilated his knowledge of molecular biology into his philosophical ideas about the nature of science and scientific method.
The essay has ten sections. Jacob begins with an outline of his conception of the scientific worldview and the relationship between the natural and social sciences. In the first two sections, Jacob states that science is a human product that consists of a series of cultural attempts to delimit the possible by framing explanatory systems and bestowing unity and coherence upon the world. Like mythology, science attempts to explain the actual by delineating the possible, including the unknown or the invisible. Science, Jacob claims, can be differentiated from other cultural myths by its commitment to experimentation, and its ongoing process of criticism and revision. As such, science aims to provide only partial and provisional answers to questions about the world. The history of science, according to Jacob, depicts a pattern in which scientific knowledge begins as isolated pieces of knowledge in particular scientific domains, and develops into a unified account of phenomena.
In the third section, "The Hierarchy of Object," Jacob addresses the challenges of studying objects, such as living organisms, human language and behaviour, and social and economic structures. Jacob argues against what he calls methodological reductionism, stating that it would be absurd to try to explain something complex, like democracy, by appealing to the structure and properties of its elementary physical particles. Nonetheless—Jacob notes—the laws that govern elementary physical particles constrain every higher level object of study, including political structures. Lower levels of the hierarchy of objects limit the range of possibilities for objects in higher levels.
In the fourth section, "Constraints and History," Jacob states that most objects of scientific study are complex organizations or systems influenced by a combination of constraints and history. For instance, he argues that emergent properties of a system can be explained by appealing to the components of the system, but they cannot be deduced from them. In other words, one can not predict the emergent properties of complex systems, like cells' and organisms' properties, from the properties of their components. The complex nature of the objects of study constrains predictions. Thus, such objects require examination at more than one level of analysis. Furthermore, Jacob argues that, because complex objects can result from evolutionary processes, they are also constrained by history. For example, scientists have shown that the structure of a cell relies on its molecular elements and composition. However, Jacob notes, any evidence of these molecular elements in prebiotic time is not sufficient to explain the origin of life on earth. Historical conditions, including highly contingent events, have played a role in the origin of life.
In the next two sections, Jacob introduces and develops the metaphor of tinkering to bring into focus the historical character of evolutionary theory. Jacob begins, in the fifth section, by describing the process of natural selection as an imposition of constraints on open systems, or organisms. Natural selection, according to Jacob, is both a negative and a positive force. It is negative in the sense that it works to eliminate less fit variants in a population, and it is positive in the sense that it works to integrate mutations that accumulate over time to produce adaptations. Jacob states that natural selection's creative force is evident in its ability to recombine old material into novelties new structures, new organs, and even new species.
In section six, "Evolution and Tinkering," Jacob dismisses a comparison between natural selection and engineering for three reasons. First, unlike natural selection, an engineer works according to a pre-conceived plan of the final product. Second, an engineer actively chooses her materials and has access to the best tools designed for accomplishing the task at hand. Natural selection, in contrast, affects the structurally and functionally imperfect parts of the biotic world and reconfigures existing systems into novel ones. Third, if the engineer is successful, the final product achieves a level of perfection. Evolution by natural selection, however, yields imperfect products. For these three reasons, Jacob rejects an analogy between natural selection and engineering, and instead he proposes the metaphor that natural selection is like a bricoleur (tinkerer). Like natural selection, a tinkerer works with no specific end in mind, collecting any materials at his disposal, and rearranges them into a workable object. Thus, contingency constitutes the main feature of evolutionary processes.
Jacob further elaborates this analogy in the seventh section, "Evolution as Tinkering." Different tinkerers, Jacob argues, likely develop different solutions to similar problems. For example, evolution has resulted in different types of eyes—pinhole, lens, and multiple tubes—to address the issue of how organisms use light to perceive the world. In these cases, natural selection used materials at its disposal to form differently-structured adaptations to similar problems. Here, Jacob underscores the claim that evolution never produces new forms from scratch.
Jacob argues that this tinkering characteristic of evolutionary processes is most evident at the molecular level. In section eight, "Molecular Tinkering," he explains that all living organisms, both unicellular and multicellular, exhibit an underlying unity in their chemical structures and functions. Jacob states that, because all life shares the same organic molecules and similar metabolic pathways, it is more probable that new functional proteins have arisen from a rearrangement of genetic elements than it is that those proteins appeared anew. As evidence, Jacob cites the discovery that similar DNA sequences from organisms as distantly related as fruit flies and pigs help cause structures as different as wings and legs to develop.
To support his analogy, Jacob appeals to a hypothesis of Susumu Ohno's, who worked at City of Hope Medical Center in Duarte, California. Ohno presented the hypothesis in 1970, and it is about the logic of gene duplication events in evolutionary history. When a gene gets copied or duplicated in a genome, the new gene lacks the functional constraints of the old gene. In such cases, the duplicated copy can accumulate beneficial or neutral mutations with little deleterious effect on the overall fitness of the organism. This accumulation can lead to the re-arrangement of genetic elements, so that existing structures can acquire new functions. This hypothesis of genomic change, Jacob argues, illustrates the process of tinkering.
According to Jacob, molecular biologists have shown that most morphological change in vertebrates has not resulted from new structural genes, but rather it is the consequence of a change in the regulation of genetic components, including events like heterotopy, a change in the spatial location of developmental events, and heterochrony, a change in the timing of developmental events. Jacob argues that these events occur in embryonic development according to the precise schedule of a genetic program, suggesting that gene regulation is the key factor in the generation of animals' forms and functions.
In the ninth section, Jacob outlines two consequences of the metaphor of evolution as a process of tinkering. First, if his analogy holds, then biologists should expect to find similarities in the underlying molecular elements of different species. For example, Jacob argues, biochemists have discovered hormone peptides that trigger a variety of chemical reactions in cells from organisms in different species. Second, biologists should expect to see many imperfections or redundancies in the design of organisms. For instance, Jacob explains, the human reproductive system illustrates a less than perfect mechanism in which almost half of the total number of conceptions result in no viable fetuses.
Jacob ends his essay with a final example of tinkering, arguing that the human brain is a product of highly contingent, historical events. Jacob contends that, in humans, the addition of the neo-cortex to the rhinencephalon, a primitive part of the brain responsible for the sense of smell and theorized to control instinct, has set the conditions for the evolution of the human brain. The human brain is thus the result of an imperfect patchwork of a structure controlling visceral or emotional drives, the rhinencephalon, and a structure controlling more sophisticated cognitive abilities, the neo-cortex. This case can be extrapolated, Jacob argues, to a general rule for evolution: evolution is the net result of a particular sequence of historical opportunities.
Jacob's essay had, at first, a mixed reception. Many biologists said that the description of evolution by natural selection as a process of tinkering was blatantly obvious. In 1983 Walter Gehring and his team at the University of Basel in Basel, Switzerland, discovered of a standard set of DNA sequences called the Homeobox in genes that controlled the embryonic development of body plans of animals. Scientists soon found the Homeobox in genes of diverse organisms from flies to humans. Given those results, scientists explicitly began referring to Jacob's essay and to his concept of tinkering.
In 1982, Jacob published a series of lectures given at the University of Washington in Seattle, Washington, under the title The Possible and the Actual, which includes a slightly modified version of his original essay, "Evolution and Tinkering," as well as some essays expounding his philosophy of science. In 2006, the Novartis Foundation in London, United Kingdom, held a symposium on the concept of tinkering in evolution and development. By the second decade of the twenty-first century, scientists had cited "Evolution and Tinkering" thousands of times.
Evolution is the central unifying concept in biology. Biology can be divided in various ways. One way is by the level of biological organization, from molecular to cell, organism to population. An earlier way is by perceived taxonomic group, with fields such as zoology, botany, and microbiology, reflecting what were once seen as the major divisions of life. A third way is by approach, such as field biology, theoretical biology, experimental evolution, and paleontology. These alternative ways of dividing up the subject can be combined with evolutionary biology to create subfields like evolutionary ecology and evolutionary developmental biology.
More recently, the merge between the biological science and applied sciences gave birth to new fields that are extensions of evolutionary biology, including evolutionary robotics, engineering,  algorithms,  economics,  and architecture.  The basic mechanisms of evolution are applied directly or indirectly to come up with novel designs or solve problems that are difficult to solve otherwise. The research generated in these applied fields in turn contribute to progress, especially thanks to work on evolution in computer science and engineering fields such as mechanical engineering. 
In evolutionary developmental biology the different processes of development can play a role in how a specific organism reaches its current body plan. The genetic regulation of ontogeny and phylogenetic process is what allows for this kind of understanding of biology to be possible. Looking at different processes during development, and going through the evolutionary tree, one can determine at which point a specific structure came about. For example, the three germ layers can be observed to not be present in cnidarians and ctenophores, which instead present in worms, being more or less developed depending on the kind of worm itself. Other structures like the development of Hox genes and sensory organs such as eyes can also be traced with this practice. 
The idea of evolution by natural selection was proposed by Charles Darwin in 1859, but evolutionary biology, as an academic discipline in its own right, emerged during the period of the modern synthesis in the 1930s and 1940s.  It was not until the 1980s that many universities had departments of evolutionary biology. In the United States, many universities have created departments of molecular and cell biology or ecology and evolutionary biology, in place of the older departments of botany and zoology. Palaeontology is often grouped with earth science.
Microbiology too is becoming an evolutionary discipline, now that microbial physiology and genomics are better understood. The quick generation time of bacteria and viruses such as bacteriophages makes it possible to explore evolutionary questions.
Many biologists have contributed to shaping the modern discipline of evolutionary biology. Theodosius Dobzhansky and E. B. Ford established an empirical research programme. Ronald Fisher, Sewall Wright and J. S. Haldane created a sound theoretical framework. Ernst Mayr in systematics, George Gaylord Simpson in paleontology and G. Ledyard Stebbins in botany helped to form the modern synthesis. James Crow,  Richard Lewontin,  Dan Hartl,  Marcus Feldman,   and Brian Charlesworth  trained a generation of evolutionary biologists.
Current research in evolutionary biology covers diverse topics and incorporates ideas from diverse areas, such as molecular genetics and computer science.
First, some fields of evolutionary research try to explain phenomena that were poorly accounted for in the modern evolutionary synthesis. These include speciation,   the evolution of sexual reproduction,   the evolution of cooperation, the evolution of ageing,  and evolvability. 
Second, biologists ask the most straightforward evolutionary question: "what happened and when?". This includes fields such as paleobiology, as well as systematics and phylogenetics.
Third, the modern evolutionary synthesis was devised at a time when nobody understood the molecular basis of genes. Today, evolutionary biologists try to determine the genetic architecture of interesting evolutionary phenomena such as adaptation and speciation. They seek answers to questions such as how many genes are involved, how large are the effects of each gene, how interdependent are the effects of different genes, what do the genes do, and what changes happen to them (e.g., point mutations vs. gene duplication or even genome duplication). They try to reconcile the high heritability seen in twin studies with the difficulty in finding which genes are responsible for this heritability using genome-wide association studies. 
One challenge in studying genetic architecture is that the classical population genetics that catalysed the modern evolutionary synthesis must be updated to take into account modern molecular knowledge. This requires a great deal of mathematical development to relate DNA sequence data to evolutionary theory as part of a theory of molecular evolution. For example, biologists try to infer which genes have been under strong selection by detecting selective sweeps. 
Fourth, the modern evolutionary synthesis involved agreement about which forces contribute to evolution, but not about their relative importance.  Current research seeks to determine this. Evolutionary forces include natural selection, sexual selection, genetic drift, genetic draft, developmental constraints, mutation bias and biogeography.
An evolutionary approach is key to much current research in organismal biology and ecology, such as in life history theory. Annotation of genes and their function relies heavily on comparative approaches. The field of evolutionary developmental biology ("evo-devo") investigates how developmental processes work, and compares them in different organisms to determine how they evolved.
Many physicians do not have enough background in evolutionary biology, making it difficult to use it in modern medicine. 
Evolution plays a role in resistance of drugs. For example, how HIV becomes resistant to medications and the body's immune system. The mutation of resistance of HIV is due to the natural selection of the survivors and their offspring. The one HIV that survived the immune system reproduced and had offspring that were also resistant to the immune system.  Drug resistance also causes many problems for patients such as a worsening sickness or the sickness can mutate into something that can no longer be cured with medication. Without the proper medicine a sickness can be the death of a patient. If their body has resistance to a certain number of drugs, then the right medicine will be harder and harder to find. Not finishing an antibiotic is also an example of resistance that will cause the bacteria or virus to evolve and continue to spread in the body.  When the full dosage of the medication does not enter the body and perform its proper job, the virus and bacteria that survive the initial dosage will continue to reproduce. This makes for another sickness later on that will be even harder to cure because this disease will be resistant to the first medication used. Finishing medicine that is prescribed is a vital step in avoiding antibiotic resistance. Also, those with chronic illnesses, illnesses that last throughout the lifetime, are at a greater risk to antibiotic resistance than others.  This is because overuse of a drug or too high of a dosage can cause a patient's immune system to weaken and the illness will evolve and grow stronger. For example, cancer patients will need a stronger and stronger dosage of medication because of their low functioning immune system. 
Some scientific journals specialise exclusively in evolutionary biology as a whole, including the journals Evolution, Journal of Evolutionary Biology, and BMC Evolutionary Biology. Some journals cover sub-specialties within evolutionary biology, such as the journals Systematic Biology, Molecular Biology and Evolution and its sister journal Genome Biology and Evolution, and Cladistics.
Other journals combine aspects of evolutionary biology with other related fields. For example, Molecular Ecology, Proceedings of the Royal Society of London Series B, The American Naturalist and Theoretical Population Biology have overlap with ecology and other aspects of organismal biology. Overlap with ecology is also prominent in the review journals Trends in Ecology and Evolution and Annual Review of Ecology, Evolution, and Systematics. The journals Genetics and PLoS Genetics overlap with molecular genetics questions that are not obviously evolutionary in nature.
Enzyme evolution: innovation is easy, optimization is complicated
Functional innovation by divergent evolution is easy.
Gene loss is also an important driver of enzyme evolution.
Evolutionary trajectories are governed by myriad biophysical and cellular factors.
New knowledge of ‘real world’ enzymes will inform engineering and synthetic biology.
Enzymes have been evolving to catalyze new chemical reactions for billions of years, and will continue to do so for billions more. Here, we review examples in which evolutionary biochemists have used big data and high-throughput experimental tools to shed new light on the enormous functional diversity of extant enzymes, and the evolutionary processes that gave rise to it. We discuss the role that gene loss has played in enzyme evolution, as well as the more familiar processes of gene duplication and divergence. We also review insightful studies that relate not only catalytic activity, but also a host of other biophysical and cellular parameters, to organismal fitness. Finally, we provide an updated perspective on protein engineering, based on our new-found appreciation that most enzymes are sloppy and mediocre.
Wild horses were known since prehistory from central Asia to Europe, with domestic horses and other equids being distributed more widely in the Old World, but no horses or equids of any type were found in the New World when European explorers reached the Americas. When the Spanish colonists brought domestic horses from Europe, beginning in 1493, escaped horses quickly established large feral herds. In the 1760s, the early naturalist Buffon suggested this was an indication of inferiority of the New World fauna, but later reconsidered this idea.  William Clark's 1807 expedition to Big Bone Lick found "leg and foot bones of the Horses", which were included with other fossils sent to Thomas Jefferson and evaluated by the anatomist Caspar Wistar, but neither commented on the significance of this find. 
The first Old World equid fossil was found in the gypsum quarries in Montmartre, Paris, in the 1820s. The tooth was sent to the Paris Conservatory, where it was identified by Georges Cuvier, who identified it as a browsing equine related to the tapir.  His sketch of the entire animal matched later skeletons found at the site. 
During the Beagle survey expedition, the young naturalist Charles Darwin had remarkable success with fossil hunting in Patagonia. On 10 October 1833, at Santa Fe, Argentina, he was "filled with astonishment" when he found a horse's tooth in the same stratum as fossil giant armadillos, and wondered if it might have been washed down from a later layer, but concluded this was "not very probable".  After the expedition returned in 1836, the anatomist Richard Owen confirmed the tooth was from an extinct species, which he subsequently named Equus curvidens, and remarked, "This evidence of the former existence of a genus, which, as regards South America, had become extinct, and has a second time been introduced into that Continent, is not one of the least interesting fruits of Mr. Darwin's palæontological discoveries."  
In 1848, a study On the fossil horses of America by Joseph Leidy systematically examined Pleistocene horse fossils from various collections, including that of the Academy of Natural Sciences, and concluded at least two ancient horse species had existed in North America: Equus curvidens and another, which he named Equus americanus. A decade later, however, he found the latter name had already been taken and renamed it Equus complicatus.  In the same year, he visited Europe and was introduced by Owen to Darwin. 
The original sequence of species believed to have evolved into the horse was based on fossils discovered in North America in 1879 by paleontologist Othniel Charles Marsh. The sequence, from Eohippus to the modern horse (Equus), was popularized by Thomas Huxley and became one of the most widely known examples of a clear evolutionary progression. The horse's evolutionary lineage became a common feature of biology textbooks, and the sequence of transitional fossils was assembled by the American Museum of Natural History into an exhibit that emphasized the gradual, "straight-line" evolution of the horse.
Since then, as the number of equid fossils has increased, the actual evolutionary progression from Eohippus to Equus has been discovered to be much more complex and multibranched than was initially supposed. The straight, direct progression from the former to the latter has been replaced by a more elaborate model with numerous branches in different directions, of which the modern horse is only one of many. George Gaylord Simpson in 1951  first recognized that the modern horse was not the "goal" of the entire lineage of equids,  but is simply the only genus of the many horse lineages to survive.
Detailed fossil information on the distribution and rate of change of new equid species has also revealed that the progression between species was not as smooth and consistent as was once believed. Although some transitions, such as that of Dinohippus to Equus, were indeed gradual progressions, a number of others, such as that of Epihippus to Mesohippus, were relatively abrupt in geologic time, taking place over only a few million years. Both anagenesis (gradual change in an entire population's gene frequency) and cladogenesis (a population "splitting" into two distinct evolutionary branches) occurred, and many species coexisted with "ancestor" species at various times. The change in equids' traits was also not always a "straight line" from Eohippus to Equus: some traits reversed themselves at various points in the evolution of new equid species, such as size and the presence of facial fossae, and only in retrospect can certain evolutionary trends be recognized. 
Phenacodontidae is the most recent family in the order Condylarthra believed to be the ancestral to the odd-toed ungulates. [ citation needed ] It contains the genera Almogaver, Copecion, Ectocion, Eodesmatodon, Meniscotherium, Ordathspidotherium, Phenacodus and Pleuraspidotherium. The family lived from the Early Paleocene to the Middle Eocene in Europe and were about the size of a sheep, with tails making slightly less than half of the length of their bodies and unlike their ancestors, good running skills for eluding predators. [ citation needed ]
Eohippus appeared in the Ypresian (early Eocene), about 52 mya (million years ago). It was an animal approximately the size of a fox (250–450 mm in height), with a relatively short head and neck and a springy, arched back. It had 44 low-crowned teeth, in the typical arrangement of an omnivorous, browsing mammal: three incisors, one canine, four premolars, and three molars on each side of the jaw. Its molars were uneven, dull, and bumpy, and used primarily for grinding foliage. The cusps of the molars were slightly connected in low crests. Eohippus browsed on soft foliage and fruit, probably scampering between thickets in the mode of a modern muntjac. It had a small brain, and possessed especially small frontal lobes. 
Its limbs were long relative to its body, already showing the beginnings of adaptations for running. However, all of the major leg bones were unfused, leaving the legs flexible and rotatable. Its wrist and hock joints were low to the ground. The forelimbs had developed five toes, of which four were equipped with small proto-hooves the large fifth "toe-thumb" was off the ground. The hind limbs had small hooves on three out of the five toes, while the vestigial first and fifth toes did not touch the ground. Its feet were padded, much like a dog's, but with the small hooves in place of claws. 
For a span of about 20 million years, Eohippus thrived with few significant evolutionary changes.  The most significant change was in the teeth, which began to adapt to its changing diet, as these early Equidae shifted from a mixed diet of fruits and foliage to one focused increasingly on browsing foods. During the Eocene, an Eohippus species (most likely Eohippus angustidens) branched out into various new types of Equidae. Thousands of complete, fossilized skeletons of these animals have been found in the Eocene layers of North American strata, mainly in the Wind River basin in Wyoming. Similar fossils have also been discovered in Europe, such as Propalaeotherium (which is not considered ancestral to the modern horse). 
Approximately 50 million years ago, in the early-to-middle Eocene, Eohippus smoothly transitioned into Orohippus through a gradual series of changes.  Although its name means "mountain horse", Orohippus was not a true horse and did not live in the mountains. It resembled Eohippus in size, but had a slimmer body, an elongated head, slimmer forelimbs, and longer hind legs, all of which are characteristics of a good jumper. Although Orohippus was still pad-footed, the vestigial outer toes of Eohippus were not present in Orohippus there were four toes on each fore leg, and three on each hind leg.
The most dramatic change between Eohippus and Orohippus was in the teeth: the first of the premolar teeth was dwarfed, the last premolar shifted in shape and function into a molar, and the crests on the teeth became more pronounced. Both of these factors gave the teeth of Orohippus greater grinding ability, suggesting Orohippus ate tougher plant material.
In the mid-Eocene, about 47 million years ago, Epihippus, a genus which continued the evolutionary trend of increasingly efficient grinding teeth, evolved from Orohippus. Epihippus had five grinding, low-crowned cheek teeth with well-formed crests. A late species of Epihippus, sometimes referred to as Duchesnehippus intermedius, had teeth similar to Oligocene equids, although slightly less developed. Whether Duchesnehippus was a subgenus of Epihippus or a distinct genus is disputed.  Epihippus was only 2 feet tall. 
In the late Eocene and the early stages of the Oligocene epoch (32–24 mya), the climate of North America became drier, and the earliest grasses began to evolve. The forests were yielding to flatlands, [ citation needed ] home to grasses and various kinds of brush. In a few areas, these plains were covered in sand, [ citation needed ] creating the type of environment resembling the present-day prairies.
In response to the changing environment, the then-living species of Equidae also began to change. In the late Eocene, they began developing tougher teeth and becoming slightly larger and leggier, allowing for faster running speeds in open areas, and thus for evading predators in nonwooded areas [ citation needed ] . About 40 mya, Mesohippus ("middle horse") suddenly developed in response to strong new selective pressures to adapt, beginning with the species Mesohippus celer and soon followed by Mesohippus westoni.
In the early Oligocene, Mesohippus was one of the more widespread mammals in North America. It walked on three toes on each of its front and hind feet (the first and fifth toes remained, but were small and not used in walking). The third toe was stronger than the outer ones, and thus more weighted the fourth front toe was diminished to a vestigial nub. Judging by its longer and slimmer limbs, Mesohippus was an agile animal.
Mesohippus was slightly larger than Epihippus, about 610 mm (24 in) at the shoulder. Its back was less arched, and its face, snout, and neck were somewhat longer. It had significantly larger cerebral hemispheres, and had a small, shallow depression on its skull called a fossa, which in modern horses is quite detailed. The fossa serves as a useful marker for identifying an equine fossil's species. Mesohippus had six grinding "cheek teeth", with a single premolar in front—a trait all descendant Equidae would retain. Mesohippus also had the sharp tooth crests of Epihippus, improving its ability to grind down tough vegetation.
Around 36 million years ago, soon after the development of Mesohippus, Miohippus ("lesser horse") emerged, the earliest species being Miohippus assiniboiensis. As with Mesohippus, the appearance of Miohippus was relatively abrupt, though a few transitional fossils linking the two genera have been found. Mesohippus was once believed to have anagenetically evolved into Miohippus by a gradual series of progressions, but new evidence has shown its evolution was cladogenetic: a Miohippus population split off from the main genus Mesohippus, coexisted with Mesohippus for around four million years, and then over time came to replace Mesohippus. 
Miohippus was significantly larger than its predecessors, and its ankle joints had subtly changed. Its facial fossa was larger and deeper, and it also began to show a variable extra crest in its upper cheek teeth, a trait that became a characteristic feature of equine teeth.
Miohippus ushered in a major new period of diversification in Equidae. 
The forest-suited form was Kalobatippus (or Miohippus intermedius, depending on whether it was a new genus or species), whose second and fourth front toes were long, well-suited to travel on the soft forest floors. Kalobatippus probably gave rise to Anchitherium, which travelled to Asia via the Bering Strait land bridge, and from there to Europe.  In both North America and Eurasia, larger-bodied genera evolved from Anchitherium: Sinohippus in Eurasia and Hypohippus and Megahippus in North America.  Hypohippus became extinct by the late Miocene. 
The Miohippus population that remained on the steppes is believed to be ancestral to Parahippus, a North American animal about the size of a small pony, with a prolonged skull and a facial structure resembling the horses of today. Its third toe was stronger and larger, and carried the main weight of the body. Its four premolars resembled the molar teeth the first were small and almost nonexistent. The incisor teeth, like those of its predecessors, had a crown (like human incisors) however, the top incisors had a trace of a shallow crease marking the beginning of the core/cup.
In the middle of the Miocene epoch, the grazer Merychippus flourished.  It had wider molars than its predecessors, which are believed to have been used for crunching the hard grasses of the steppes. The hind legs, which were relatively short, had side toes equipped with small hooves, but they probably only touched the ground when running.  Merychippus radiated into at least 19 additional grassland species.
Three lineages within Equidae are believed to be descended from the numerous varieties of Merychippus: Hipparion, Protohippus and Pliohippus. The most different from Merychippus was Hipparion, mainly in the structure of tooth enamel: in comparison with other Equidae, the inside, or tongue side, had a completely isolated parapet. A complete and well-preserved skeleton of the North American Hipparion shows an animal the size of a small pony. They were very slim, rather like antelopes, and were adapted to life on dry prairies. On its slim legs, Hipparion had three toes equipped with small hooves, but the side toes did not touch the ground.
In North America, Hipparion and its relatives (Cormohipparion, Nannippus, Neohipparion, and Pseudhipparion), proliferated into many kinds of equids, at least one of which managed to migrate to Asia and Europe during the Miocene epoch.  (European Hipparion differs from American Hipparion in its smaller body size – the best-known discovery of these fossils was near Athens.)
Pliohippus arose from Callippus in the middle Miocene, around 12 mya. It was very similar in appearance to Equus, though it had two long extra toes on both sides of the hoof, externally barely visible as callused stubs. The long and slim limbs of Pliohippus reveal a quick-footed steppe animal.
Until recently, Pliohippus was believed to be the ancestor of present-day horses because of its many anatomical similarities. However, though Pliohippus was clearly a close relative of Equus, its skull had deep facial fossae, whereas Equus had no fossae at all. Additionally, its teeth were strongly curved, unlike the very straight teeth of modern horses. Consequently, it is unlikely to be the ancestor of the modern horse instead, it is a likely candidate for the ancestor of Astrohippus. 
Dinohippus was the most common species of Equidae in North America during the late Pliocene. It was originally thought to be monodactyl, but a 1981 fossil find in Nebraska shows some were tridactyl.
Plesippus is often considered an intermediate stage between Dinohippus and the extant genus, Equus.
The famous fossils found near Hagerman, Idaho were originally thought to be a part of the genus Plesippus. Hagerman Fossil Beds (Idaho) is a Pliocene site, dating to about 3.5 mya. The fossilized remains were originally called Plesippus shoshonensis, but further study by paleontologists determined the fossils represented the oldest remains of the genus Equus.  Their estimated average weight was 425 kg, roughly the size of an Arabian horse.
At the end of the Pliocene, the climate in North America began to cool significantly and most of the animals were forced to move south. One population of Plesippus moved across the Bering land bridge into Eurasia around 2.5 mya. 
The genus Equus, which includes all extant equines, is believed to have evolved from Dinohippus, via the intermediate form Plesippus. One of the oldest species is Equus simplicidens, described as zebra-like with a donkey-shaped head. The oldest fossil to date is
3.5 million years old from Idaho, USA. The genus appears to have spread quickly into the Old World, with the similarly aged Equus livenzovensis documented from western Europe and Russia. 
Molecular phylogenies indicate the most recent common ancestor of all modern equids (members of the genus Equus) lived
5.6 (3.9–7.8) mya. Direct paleogenomic sequencing of a 700,000-year-old middle Pleistocene horse metapodial bone from Canada implies a more recent 4.07 Myr before present date for the most recent common ancestor (MRCA) within the range of 4.0 to 4.5 Myr BP.  The oldest divergencies are the Asian hemiones (subgenus E. (Asinus), including the kulan, onager, and kiang), followed by the African zebras (subgenera E. (Dolichohippus), and E. (Hippotigris)). All other modern forms including the domesticated horse (and many fossil Pliocene and Pleistocene forms) belong to the subgenus E. (Equus) which diverged
4.8 (3.2–6.5) million years ago. 
Pleistocene horse fossils have been assigned to a multitude of species, with over 50 species of equines described from the Pleistocene of North America alone, although the taxonomic validity of most of these has been called into question.  Recent genetic work on fossils has found evidence for only three genetically divergent equid lineages in Pleistocene North and South America.  These results suggest all North American fossils of caballine-type horses (which also include the domesticated horse and Przewalski's horse of Europe and Asia), as well as South American fossils traditionally placed in the subgenus E. (Amerhippus)  belong to the same species: E. ferus. Remains attributed to a variety of species and lumped as New World stilt-legged horses (including H. francisci, E. tau, E. quinni and potentially North American Pleistocene fossils previously attributed to E. cf. hemiones, and E. (Asinus) cf. kiang) probably all belong to a second species endemic to North America, which despite a superficial resemblance to species in the subgenus E. (Asinus) (and hence occasionally referred to as North American ass) is closely related to E. ferus.  Surprisingly, the third species, endemic to South America and traditionally referred to as Hippidion, originally believed to be descended from Pliohippus, was shown to be a third species in the genus Equus, closely related to the New World stilt-legged horse.  The temporal and regional variation in body size and morphological features within each lineage indicates extraordinary intraspecific plasticity. Such environment-driven adaptative changes would explain why the taxonomic diversity of Pleistocene equids has been overestimated on morphoanatomical grounds. 
According to these results, it appears the genus Equus evolved from a Dinohippus-like ancestor
4–7 mya. It rapidly spread into the Old World and there diversified into the various species of asses and zebras. A North American lineage of the subgenus E. (Equus) evolved into the New World stilt-legged horse (NWSLH). Subsequently, populations of this species entered South America as part of the Great American Interchange shortly after the formation of the Isthmus of Panama, and evolved into the form currently referred to as Hippidion
2.5 million years ago. Hippidion is thus only distantly related to the morphologically similar Pliohippus, which presumably became extinct during the Miocene. Both the NWSLH and Hippidium show adaptations to dry, barren ground, whereas the shortened legs of Hippidion may have been a response to sloped terrain.  In contrast, the geographic origin of the closely related modern E. ferus is not resolved. However, genetic results on extant and fossil material of Pleistocene age indicate two clades, potentially subspecies, one of which had a holarctic distribution spanning from Europe through Asia and across North America and would become the founding stock of the modern domesticated horse.   The other population appears to have been restricted to North America. However, one or more North American populations of E. ferus entered South America
1.0–1.5 million years ago, leading to the forms currently known as E. (Amerhippus), which represent an extinct geographic variant or race of E. ferus.
Genome sequencing Edit
Early sequencing studies of DNA revealed several genetic characteristics of Przewalski's horse that differ from what is seen in modern domestic horses, indicating neither is ancestor of the other, and supporting the status of Przewalski horses as a remnant wild population not derived from domestic horses.  The evolutionary divergence of the two populations was estimated to have occurred about 45,000 YBP,   while the archaeological record places the first horse domestication about 5,500 YBP by the ancient central-Asian Botai culture.   The two lineages thus split well before domestication, probably due to climate, topography, or other environmental changes. 
Several subsequent DNA studies produced partially contradictory results. A 2009 molecular analysis using ancient DNA recovered from archaeological sites placed Przewalski's horse in the middle of the domesticated horses,  but a 2011 mitochondrial DNA analysis suggested that Przewalski's and modern domestic horses diverged some 160,000 years ago.  An analysis based on whole genome sequencing and calibration with DNA from old horse bones gave a divergence date of 38–72 thousand years ago. 
In June 2013, a group of researchers announced that they had sequenced the DNA of a 560–780 thousand year old horse, using material extracted from a leg bone found buried in permafrost in Canada's Yukon territory.  Before this publication, the oldest nuclear genome that had been successfully sequenced was dated at 110–130 thousand years ago. For comparison, the researchers also sequenced the genomes of a 43,000-year-old Pleistocene horse, a Przewalski's horse, five modern horse breeds, and a donkey.  Analysis of differences between these genomes indicated that the last common ancestor of modern horses, donkeys, and zebras existed 4 to 4.5 million years ago.  The results also indicated that Przewalski's horse diverged from other modern types of horse about 43,000 years ago, and had never in its evolutionary history been domesticated. 
A new analysis in 2018 involved genomic sequencing of ancient DNA from mid-fourth-millennium B.C.E. Botai domestic horses, as well as domestic horses from more recent archaeological sites, and comparison of these genomes with those of modern domestic and Przewalski's horses. The study revealed that Przewalski's horses not only belong to the same genetic lineage as those from the Botai culture, but were the feral descendants of these ancient domestic animals, rather than representing a surviving population of never-domesticated horses.  The Botai horses were found to have made only negligible genetic contribution to any of the other ancient or modern domestic horses studied, which must then have arisen from an independent domestication involving a different wild horse population. 
The karyotype of Przewalski's horse differs from that of the domestic horse by an extra chromosome pair because of the fission of domestic horse chromosome 5 to produce the Przewalski's horse chromosomes 23 and 24. In comparison, the chromosomal differences between domestic horses and zebras include numerous translocations, fusions, inversions and centromere repositioning.  This gives Przewalski's horse the highest diploid chromosome number among all equine species. They can interbreed with the domestic horse and produce fertile offspring (65 chromosomes). 
Pleistocene extinctions Edit
Digs in western Canada have unearthed clear evidence horses existed in North America until about 12,000 years ago.  However, all Equidae in North America ultimately became extinct. The causes of this extinction (simultaneous with the extinctions of a variety of other American megafauna) have been a matter of debate. Given the suddenness of the event and because these mammals had been flourishing for millions of years previously, something quite unusual must have happened. The first main hypothesis attributes extinction to climate change. For example, in Alaska, beginning approximately 12,500 years ago, the grasses characteristic of a steppe ecosystem gave way to shrub tundra, which was covered with unpalatable plants.   The other hypothesis suggests extinction was linked to overexploitation by newly arrived humans of naive prey that were not habituated to their hunting methods. The extinctions were roughly simultaneous with the end of the most recent glacial advance and the appearance of the big game-hunting Clovis culture.   Several studies have indicated humans probably arrived in Alaska at the same time or shortly before the local extinction of horses.    Additionally, it has been proposed that the steppe-tundra vegetation transition in Beringia may have been a consequence, rather than a cause, of the extinction of megafaunal grazers. 
In Eurasia, horse fossils began occurring frequently again in archaeological sites in Kazakhstan and the southern Ukraine about 6,000 years ago.  From then on, domesticated horses, as well as the knowledge of capturing, taming, and rearing horses, probably spread relatively quickly, with wild mares from several wild populations being incorporated en route.  
Return to the Americas Edit
Horses only returned to the Americas with Christopher Columbus in 1493. These were Iberian horses first brought to Hispaniola and later to Panama, Mexico, Brazil, Peru, Argentina, and, in 1538, Florida.  The first horses to return to the main continent were 16 specifically identified [ clarification needed ] horses brought by Hernán Cortés. Subsequent explorers, such as Coronado and De Soto, brought ever-larger numbers, some from Spain and others from breeding establishments set up by the Spanish in the Caribbean. Later, as Spanish missions were founded on the mainland, horses would eventually be lost or stolen, and proliferated into large herds of feral horses that became known as mustangs. 
The indigenous peoples of the Americas did not have a specific word for horses, and came to refer to them in various languages as a type of dog or deer (in one case, "elk-dog", in other cases "big dog" or "seven dogs", referring to the weight each animal could pull). 
The ancestors of the horse came to walk only on the end of the third toe and both side (second and fourth) "toes". Skeletal remnants show obvious wear on the back of both sides of metacarpal and metatarsal bones, commonly called the "splint bones". They are the remnants of the second and the fourth toes. Modern horses retain the splint bones they are often believed to be useless attachments, but they in fact play an important role in supporting the carpal joints (front knees) and even the tarsal joints (hocks).
A 2018 study has found remnants of the remaining digits in the horse's hoof, suggesting a retention of all five digits (albeit in a "hourglass" arrangement where metacarpals/tarsals are present proximally and phalanges distally). 
Throughout the phylogenetic development, the teeth of the horse underwent significant changes. The type of the original omnivorous teeth with short, "bumpy" molars, with which the prime members of the evolutionary line distinguished themselves, gradually changed into the teeth common to herbivorous mammals. They became long (as much as 100 mm), roughly cubical molars equipped with flat grinding surfaces. In conjunction with the teeth, during the horse's evolution, the elongation of the facial part of the skull is apparent, and can also be observed in the backward-set eyeholes. In addition, the relatively short neck of the equine ancestors became longer, with equal elongation of the legs. Finally, the size of the body grew as well. [ citation needed ]
Coat color Edit
The ancestral coat color of E. ferus was possibly a uniform dun, consistent with modern populations of Przewalski's horses. Pre-domestication variants including black and spotted have been inferred from cave wall paintings and confirmed by genomic analysis.  Domestication may have also led to more varieties of coat colors. 
10: Evolution and Its Processes - Biology
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HB’s research is part of a project that has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, Grant Number 851145 WV’s research funded through Paul Griffith’s Australian Laureate Fellowship project “A Philosophy of Medicine for the 21st Century” [Ref: FL170100160].
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12 Elegant Examples of Evolution
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In preparation for Charles Darwin's upcoming 200th birthday, the editors of Nature compiled a selection of especially elegant and enlightening examples of evolution.
They describe it as a resource "for those wishing to spread awareness of evidence for evolution by natural selection." Given the continuing battles over evolution in America's public schools — and, for that matter, the Islamic world — such a resource is most welcome.
However, Iɽ like to suggest another way of looking at the findings below, which range from the moray eel's remarkable second jaw to the unexpected plumage of dinosaurs. They are, quite simply, wondrous — glimpses through an evolutionary frame of life's incredible narrative, expanding to fill every possible nook and cranny of Earth's biosphere.
After all, it's hard to stir passion about the scientific validity of evolution without first captivating minds and imaginations. And this is a fine place to start.
Almost, But Not Quite, a Whale. The fossil record suggests that whales evolved on land, and intermediate species have been identified. But what of their last terrestrial ancestor? In 2007, researchers showed that Indohyus — a 50 million-year-old, dog-sized member of the extinct raoellidae ungulate family — had ears, teeth and bones that resembled whales, not other raoellids.
Out of the Soup. Whales represented a mammalian return to the water, but an even more extraordinary transition was made by the first creature to venture onto land — and that was made possible by Tiktaalik, discovered in 2004 on Ellesmere Island. Tiktaalik had a flexible neck and limb-like fins suitable for shallow waters, and, before long, land.
Dinosaurs of a Feather. Archaeopteryx, found in 1861, was long thought to be the first bird. Then it was recognized as something closer to a dinosaur with feathers — but still unique for that. In the 1980's, however, paleontologists digging in deposits more than 65 million years old in northern China found feathered dinosaurs which very definitely did not fly. Some dinosaurs, it appeared, may have looked far different from our traditional conception — and feathers may first have served an insulating or aesthetic, rather than aerodynamic, purpose.
Image: Zhao Chuang & Xing Lida / Nature
A Toothy Finding. In 2007, University of Helsinki evolutionary biologist Kathryn Kavanagh showed that molars emerge from front to back, with each tooth smaller than its precedent. Fodder for geeked-out dentists? Far from it: Her model predicted tooth development of rodents with different diets — a perfect confluence of a small mechanical observation and observed evolutionary trajectories.
Image: Kathryn Kavanagh / Nature
The Beginnings of Bones. Neural crest cells originate in the spinal cord before diffusing through our developing bodies, forming face and neck bones as well as sense organs and skin.
The fossil record, nearly bereft of embryos, provides little direct insight into these critically important stages. But technologies that let researchers track cells during embryo development finally allowed them to watch the neural crest's development, culminating in the attachment of head to the body at its front, while the back attachment springs from the mesoderm tissue layer. With that established, scientists can decipher shared evolutionary histories from muscle attachments: the cleithrum, for example, a bony girdle found in fishes, lives on in humans as the shoulder blade.
Image: Wolfson Institute for Biomedical Research / Nature
Natural Selection in Speciation. That differing selection pressures will cleave one species into two is a simple principle expressed in complex ways. One of these is reproductive isolation — when, for example, one species of stickleback fish live in freshwater streams, and the other goes to sea. Scientists found that stream-bound sticklebacks prefer larger mates, and genetic analysis confirmed that their populations are indeed diverging.
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