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Pseudoextinction

Pseudoextinction

Pseudoextinction of a species occurs where there are no more living members of that species, but members of a daughter species or subspecies remain alive. Much of evolution is believed to occur through pseudoextinction, and many prehistoric extinct species have evolved into new species; for example the extinct Hyracotherium (an ancient horse-like animal) was the ancestor of several extant species including the horse, the zebra and the donkey. The Hyracotherium itself is no more, but because its descendants live on, it has suffered pseudoextinction. Pseudoextinction, also called phyletic extinction, can sometimes apply to wider taxons than the species level. For instance, the entire Superorder Dinosauria is believed to have become pseudoextinct by many paleontologists, who argue that the feathered dinosaurs are the ancestors of modern day birds. Some neoeugenicists, such as Gregory Stock argue that genetically engineered “designer babies” will ultimately lead to human pseudoextinction.

References

- Stock, G., 2003, Redesigning Humans: Choosing our genes, changing our future, Mariner Books ISBN 0618340831

External links

- [http://research.arc2.ucla.edu/pmts/rexcerpt.htm The Last Human] - Excerpt from Redesigning HUMANS by Gregory Stock, envisaging the engineered evolution of modern humans into a posthuman form, and saying: "Such an occurrence would more aptly be termed a pseudoextinction, since it would not end our lineage. Unlike the saber-toothed tiger and other large mammals that left no descendants when our ancestors drove them to extinction, Homo sapiens would spawn its own successors by fast-forwarding its evolution."
- [http://trc.ucdavis.edu/djbegun/Lect_paleo&homo.html The difficulty of differentiating extinction from pseudoextinction in the fossil record]
- [http://extinct.petermaas.nl The Extinction Website]
- [http://extinctanimals.proboards22.com The Extinction Forum], part of The Extinction Website. Category:Extinction Category:Evolutionary biology Category:Paleontology

Species

In biology, a species is the basic unit of biodiversity. In scientific classification, a species is assigned a two-part name in Latin. The genus is listed first (and capitalized), followed by a specific epithet. For example, humans belong to the genus Homo, and are in the species Homo sapiens. The name of the species is the whole binomial not just the second term (the specific epithet). The binomial, and most other purely formal aspects of the biological codes of nomenclature, were formalized by Carolus Linnaeus in the 1700's and as a result are called the "Linnaean system". At that time, species were thought to represent independent acts of creation by God, and were therefore considered objectively real and immutable. Since the advent of the theory of evolution, the conception of species has undergone vast changes in biology, however no consensus on the definition of the word has yet been reached. The most commonly cited definition of "species" was first coined by Ernst Mayr. By this definition, called the biological species concept or isolation species concept, species are "groups of actually or potentially interbreeding natural populations which are reproductively isolated from other such groups". However, many other species concepts are also used (see other definitions of species below). The scientific name of a species is properly typeset in italics. When an unknown species is being referred to this may be done by using the abbreviation "sp." in the singular or "spp." in the plural in the place of the second part of the scientific name. Note that the word "specie" is not the singular of "species". It refers to coined money.

Definitions of species

The definition of a species given above as taken from Mayr, is somewhat idealistic. Since it assumes sexual reproduction, it leaves the term undefined for a large class of organisms that reproduce asexually. Biologists frequently do not know whether two morphologically similar groups of organisms are "potentially" capable of interbreeding. Further, there is considerable variation in the degree to which hybridization may succeed under natural and experimental conditions, or even in the degree to which some organisms use sexual reproduction between individuals to breed. Consequently, several lines of thought in the definition of species exist: ; Typological species : A group of organisms in which individuals are members of the species if they sufficiently conform to certain fixed properties. The clusters of variations or phenotypes within specimens (ie: longer and shorter tails) would differentiate the species. This method was used as a "classical" method of determining species, such as with Linnaeus early in evolutionary theory. However, we now know that different phenotypes do not always constitute different species (e.g.: a 4-winged Drosophila born to a 2-winged mother is not a different species). Species named in this manner are called morphospecies. ; Morphological species : A population or group of populations that differs morphologically from other populations. For example, we can distinguish between a chicken and a duck because they have different shaped bills and the duck has webbed feet. Species have been defined in this way since well before the beginning of recorded history. This species concept is much criticised because more recent genetic data reveals that genetically distinct populations may look very similar and, contrarily, large morphological differences sometimes exist between very closely-related populations. Nonetheless, most species known have been described solely from morphology. ; Biological / Isolation species : A set of actually or potentially interbreeding populations. This is generally the most useful formulation for scientists working with living examples of the higher taxa like mammals, fish, and birds, but meaningless for organisms that do not reproduce sexually. It does not distinguish between the theoretical possibility of interbreeding and the actual likelihood of gene flow between populations and is thus impractical in instances of allopatric (geographically isolated) populations. The results of breeding experiments done in artificial conditions may or may not reflect what would happen if the same organisms encountered each other in the wild, making it difficult to gauge whether or not the results of such experiments are meaningful in reference to natural populations. ; Mate-recognition species : A group of organisms that are known to recognise one another as potential mates. Like the isolation species concept above, it applies only to organisms that reproduce sexually. Unlike the isolation species concept, it focuses specifically on pre-mating reproductive isolation. ; Phylogenetic / Evolutionary / Darwinian species : A group of organisms that shares an ancestor; a lineage that maintains its integrity with respect to other lineages through both time and space. At some point in the progress of such a group, members may diverge from one another: when such a divergence becomes sufficiently clear, the two populations are regarded as separate species. ; Microspecies : Species that reproduce without meiosis or mitosis so that each generation is genetically identical to the previous generation. See also apomixis. In practice, these definitions often coincide, and the differences between them are more a matter of emphasis than of outright contradiction. Nevertheless, no species concept yet proposed is entirely objective, or can be applied in all cases without resorting to judgement. Given the complexity of life, some have argued that such an objective definition is in all likelihood impossible, and biologists should settle for the most practical definition. For most vertebrates, this is the biological species concept, and to a lesser extent (or for different purposes) the phylogenetic species concept. Many BSC subspecies are considered species under the PSC; the difference between the BSC and the PSC can be summed up insofar as that the BSC defines a species as a consequence of manifest evolutionary history, while the PSC defines a species as a consequence of manifest evolutionary potential. Thus, a PSC species is "made" as soon as an evolutionary lineage has started to separate, while a BSC species starts to exist only when the lineage separation is complete.

Importance in biological classification

The idea of species has a long history. It is one of the most important levels of classification, for several reasons:
- It often corresponds to what lay people treat as the different basic kinds of organism - dogs are one species, cats another.
- It is the standard binomial nomenclature (or trinomial nomenclature) by which scientists typically refer to organisms.
- It is the only taxonomic level which has empirical content, in the sense that asserting that two animals are of different species is saying something more than classificatory about them. After thousands of years of use, the concept remains central to biology and a host of related fields, and yet also remains at times ill-defined and controversial.

Implications of assignment of species status

The naming of a particular species should be regarded as a hypothesis about the evolutionary relationships and distinguishability of that group of organisms. As further information comes to hand, the hypothesis may be confirmed or refuted. Sometimes, especially in the past when communication was more difficult, taxonomists working in isolation have given two distinct names to individual organisms later identified as the same species. When two named species are discovered to be of the same species, the older species name is usually retained, and the newer species name dropped, a process called synonymization, or convivially, as lumping. Dividing a taxon into multiple, often new, taxons is called splitting. Taxonomists are often referred to as "lumpers" or "splitters" by their colleagues, depending on their personal approach to recognizing differences or commonalities between organisms (see lumpers and splitters). Traditionally, researchers relied on observations of anatomical differences, and on observations of whether different populations were able to interbreed successfully, to distinguish species; both anatomy and breeding behavior are still important to assigning species status. As a result of the revolutionary (and still ongoing) advance in microbiological research techniques, including DNA analysis, in the last few decades, a great deal of additional knowledge about the differences and similarities between species has become available. Many populations which were formerly regarded as separate species are now considered to be a single taxon, and many formerly grouped populations have been split. Any taxonomic level (species, genus, family, etc.) can be synonymized or split, and at higher taxonomic levels, these revisions have been still more profound. From a taxonomical point of view, groups within a species can be defined as being of a taxon hierarchically lower than a species. In zoology only the subspecies is used, while in botany the variety, subvariety, and form are used as well.

The isolation species concept in more detail

In general, for large, complex, organisms that reproduce sexually (such as mammals and birds), one of several variations on the isolation or biological species concept is employed. Often, the distinction between different species, even quite closely related ones, is simple. Horses (Equus caballus) and donkeys (Equus asinus) are easily told apart even without study or training, and yet are so closely related that they can interbreed after a fashion. Because the result, a mule or hinny, is not usually fertile, they are clearly separate species. But many cases are more difficult to decide. This is where the isolation species concept diverges from the evolutionary species concept. Both agree that a species is a lineage that maintains its integrity over time, that is diagnosably different to other lineages (else we could not recognise it), is reproductively isolated (else the lineage would merge into others, given the chance to do so), and has a working intra-species recognition system (without which it could not continue). In practice, both also agree that a species must have its own independent evolutionary history—otherwise the characteristics just mentioned would not apply. The species concepts differ in that the evolutionary species concept does not make predictions about the future of the population: it simply records that which is already known. In contrast, the isolation species concept refuses to assign the rank of species to populations that, in the best judgement of the researcher, would recombine with other populations if given the chance to do so.

The isolation question

There are, essentially, two questions to resolve. First, is the proposed species consistently and reliably distinguishable from other species? Secondly, is it likely to remain so in the future? To take the second question first, there are several broad geographic possibilities.
- The proposed species are sympatric—they occupy the same habitat. Observation of many species over the years has failed to establish even a single instance of two diagnostically different populations that exist in sympatry and have then merged to form one united population. Without reproductive isolation, population differences cannot develop, and given reproductive isolation, gene flow between the populations cannot merge the differences. This is not to say that cross breeding does not take place at all, simply that it has become negligible. Generally, the hybrid individuals are less capable of successful breeding than pure-bred individuals of either species.
- The proposed species are allopatric—they occupy different geographical areas. Obviously, it is not possible to observe reproductive isolation in allopatric groups directly. Often it is not possible to achieve certainty by experimental means either: even if the two proposed species interbreed in captivity, this does not demonstrate that they would freely interbreed in the wild, nor does it always provide much information about the evolutionary fitness of hybrid individuals. A certain amount can be inferred from other experimental methods: for example, do the members of population A respond appropriately to playback of the recorded mating calls of population B? Sometimes, experiments can provide firm answers. For example, there are seven pairs of apparently almost identical marine snapping shrimp (Altheus) populations on either side of the Isthmus of Panama, which did not exist until about 3 million years ago. Until then, it is assumed, they were members of the same seven species. But when males and females from opposite sides of the isthmus are placed together, they fight instead of mating. Even if the isthmus were to sink under the waves again, the populations would remain genetically isolated: therefore they are now different species. In many cases, however, neither observation nor experiment can produce certain answers, and the determination of species rank must be made on a 'best guess' basis from a general knowledge of other related organisms.
- The proposed species are parapatric—they have breeding ranges that abut but do not overlap. This is fairly rare, particularly in temperate regions. The dividing line is often a sudden change in habitat (an ecotone) like the edge of a forest or the snow line on a mountain, but can sometimes be remarkably trivial. The parapatry itself indicates that the two populations occupy such similar ecological roles that they cannot coexist in the same area. Because they do not crossbreed, it is safe to assume that there is a mechanism, often behavioral, that is preventing gene flow between the populations, and that therefore they should be classified as separate species.
- There is a hybrid zone where the two populations mix. Typically, the hybrid zone will include representatives of one or both of the 'pure' populations, plus first-generation and back-crossing hybrids. The strength of the barrier to genetic transmission between the two pure groups can be assessed by the width of the hybrid zone relative to the typical dispersal distance of the organisms in question. The dispersal distance of oaks, for example, is the distance that a bird or squirrel can be expected to carry an acorn; the dispersal distance of Numbats is about 15 kilometres, as this is as far as young Numbats will normally travel in search of vacant territory to occupy after leaving the nest. The narrower the hybrid zone relative to the dispersal distance, the less gene flow there is between the population groups, and the more likely it is that they will continue on separate evolutionary paths. Nevertheless, it can be very difficult to predict the future course of a hybrid zone; the decision to define the two hybridizing populations as either the same species or as separate species is difficult and potentially controversial.
- The variation in the population is clinal; at either extreme of the population's geographic distribution, typical individuals are clearly different, but the transition between them is seamless and gradual. For example, the Koalas of northern Australia are clearly smaller and lighter in colour than those of the south, but there is no particular dividing line: the further south an individual Koala is found, the larger and darker it is likely to be; Koalas in intermediate regions are intermediate in weight and colour. In contrast, over the same geographic range, black-backed (northern) and white-backed (southern) Australian Magpies do not blend from one type to another: northern populations have black backs, southern populations white backs, and there is an extensive hybrid zone where both 'pure' types are common, as are crossbreeds. The variation in Koalas is clinal (a smooth transition from north to south, with populations in any given small area having a uniform appearance), but the variation in magpies is not clinal. In both cases, there is some uncertainty regarding correct classification, but the consensus view is that species rank is not justified in either. The gene flow between northern and southern magpie populations is judged to be sufficiently restricted to justify terming them subspecies (not full species); but the seamless way that local Koala populations blend one into another shows that there is substantial gene flow between north and south. As a result, experts tend to reject even subspecies rank in this case.

The difference question

Obviously, when defining a species, the geographic circumstances become meaningful only if the populations groups in question are clearly different: if they are not consistently and reliably distinguishable from one another, then we have no grounds for believing that they might be different species. The key question in this context, is "how different is different?" and the answer is usually "it all depends". In theory, it would be possible to recognise even the tiniest of differences as sufficient to delineate a separate species, provided only that the difference is clear and consistent (and that other criteria are met). There is no universal rule to state the smallest allowable difference between two species, but in general, very trivial differences are ignored on the twin grounds of simple practicality, and genetic similarity: if two population groups are so close that the distinction between them rests on an obscure and microscopic difference in morphology, or a single base substitution in a DNA sequence, then a demonstration of restricted gene flow between the populations will probably be difficult in any case. More typically, one or other of the following requirements must be met:
- It is possible to reliably measure a quantitative difference between the two groups that does not overlap. A population has, for example, thicker fur, rougher bark, longer ears, or larger seeds than another population, and although this characteristic may vary within each population, the two do not grade into one another, and given a reasonably large sample size, there is a definite discontinuity between them. Note that this applies to populations, not individual organisms, and that a small number of exceptional individuals within a population may 'break the rule' without invalidating it. The less a quantitative difference varies within a population and the more it varies between populations, the better the case for making a distinction. Nevertheless, borderline situations can only be resolved by making a 'best-guess' judgement.
- It is possible to distinguish a qualitative difference between the populations; a feature that does not vary continuously but is either entirely present or entirely absent. This might be a distinctively shaped seed pod, an extra primary feather, a particular courting behaviour, or a clearly different DNA sequence. Sometimes it is not possible to isolate a single difference between species, and several factors must be taken in combination. This is often the case with plants in particular. In eucalypts, for example, Corymbia ficifolia cannot be reliably distinguished from its close relative Corymbia calophylla by any single measure (and sometimes individual trees cannot be definitely assigned to either species), but populations of Corymbia can be clearly told apart by comparing the colour of flowers, bark, and buds, number of flowers for a given size of tree, and the shape of the leaves and fruit. When using a combination of characteristics to distinguish between populations, it is necessary to use a reasonably small number of factors (if more than a handful are needed, the genetic difference between the populations is likely to be insignificant and is unlikely to endure into the future), and to choose factors that are functionally independent (height and weight, for example, should usually be considered as one factor, not two).

Historical development of the species concept

In the earliest works of science, a species was simply an individual organism that represented a group of similar or nearly identical organisms. No other relationships beyond that group were implied. Aristotle used the words genus and species to mean generic and specific categories. Aristotle and other pre-Darwinian scientists took the species to be distinct and unchanging, with an "essence", like the chemical elements. When early observers began to develop systems of organization for living things, they began to place formerly isolated species into a context. To the modern mind, many of the schemes delineated are whimsical at best, such as those that determined consanguinity based on color (all plants with yellow flowers) or behavior (snakes, scorpions and certain biting ants). In the 18th century Carolus Linnaeus classified organisms according to differences in the form of reproductive apparatus. Although his system of classification sorts organisms according to degrees of similarity, it made no claims about the relationship between similar species. At the time, it was still widely believed that there is no organic connection between species, no matter how similar they appear; every species was individually created by God, a view today called creationism. This approach also suggested a type of idealism: the notion that each species exists as an "ideal form". Although there are always differences (although sometimes minute) between individual organisms, Linnaeus considered such variation problematic. He strove to identify individual organisms that were exemplary of the species, and considered other non-exemplary organisms to be deviant and imperfect. By the 19th century most naturalists understood that species could change form over time, and that the history of the planet provided enough time for major changes. As such, the new emphasis was on determining how a species could change over time. Jean-Baptiste Lamarck suggested that an organism could pass on an acquired trait to its offspring, i.e., the giraffe's long neck was attributed to generations of giraffes stretching to reach the leaves of higher treetops (this well-known and simplistic example, however, does not do justice to the breadth and subtlety of Lamarck's ideas). Lamarck's most important insight may have been that species can be extraordinarily fluid; his 1809 Zoological Philosophy contained one of the first logical refutations of creationism. With the acceptance of the work of Charles Darwin in the 1860s, Lamarck's view of evolution was quickly eclipsed. It was not until the late 20th century that his work began to be reexamined, and took its place as a fundamental stepping stone to the modern theory of adaptive mutation. Lamarck's long-discarded ideas of the goal-oriented evolution of species, also known the teleological process, have also received renewed attention, particularly by proponents of artificial selection. Charles Darwin and Alfred Wallace provided what scientists now consider the most powerful and compelling theory of evolution. Basically, Darwin argued that it is populations that evolve, not individuals. His argument relies on a radical shift in perspective from Linnaeus: rather than defining species in ideal terms (and searching for an ideal representative and rejecting deviations), Darwin considered variation among individuals to be natural. He further argued that variation, far from being problematic, actually provides the explanation for the existence of distinct species. Darwin's work drew on Thomas Malthus' insight that the rate of growth of a biological population will always outpace the rate of growth of the resources in the environment, such as the food supply. As a result, Darwin argued, not all the members of a population will be able to survive and reproduce. Those that did will, on average, be the ones possessing variations—however slight—that make them slightly better adapted to the environment. If these variable traits are heritable, then the offspring of the survivors will also possess them. Thus, over many generations, adaptive variations will accumulate in the population, while counter-adaptive will be eliminated. It should be emphasized that whether a variation is adaptive or non-adaptive depends on the environment: different environments favor different traits. Since the environment effectively selects which organisms live to reproduce, it is the environment (the "fight for existence") that selects the traits to be passed on. This is the theory of evolution by natural selection. In this model, the length of a giraffe's neck would be explained by positing that proto-giraffes with longer necks would have had a significant reproductive advantage to those with shorter necks. Over many generations, the entire population would be a species of long-necked animals. In 1859, when Darwin published his theory of natural selection, the mechanism behind the inheritance of individual traits was unknown. Although Darwin made some speculations on how traits are inherited (pangenesis), his theory relies only on the fact that inheritable traits exist, and are variable (which makes his accomplishment even more remarkable.) Although Gregor Mendel's paper on genetics was published in 1866, its significance was not recognized. It was not until 1900 that his work was rediscovered by Hugo de Vries, Carl Correns and Erich von Tschermak, who realised that the "inheritable traits" in Darwin's theory are genes. The theory of the evolution of species through natural selection has two important implications for discussions of species -- consequences that fundamentally challenge the assumptions behind Linnaeus' taxonomy. First, it suggests that species are not just similar, they may actually be related. Some students of Darwin argue that all species are descended from a common ancestor. Second, it supposes that "species" are not homogeneous, fixed, permanent things; members of a species are all different, and over time species change. This suggests that species do not have any clear boundaries but are rather momentary statistical effects of constantly changing gene-frequencies. One may still use Linnaeus' taxonomy to identify individual plants and animals, but one can no longer think of species as independent and immutable. The rise of a new species from a parental line is called speciation. There is no clear line demarcating the ancestral species from the descendant species. Although the current scientific understanding of species suggests there is no rigorous and comprehensive way to distinguish between different species in all cases, biologists continue to seek concrete ways to operationalize the idea. One of the most popular biological definitions of species is in terms of reproductive isolation; if two creatures cannot reproduce to produce fertile offspring, then they are in different species. This definition captures a number of intuitive species boundaries, but nonetheless has some problems, however. It has nothing to say about species that reproduce asexually, for example, and it is very difficult to apply to extinct species. Moreover, boundaries between species are often fuzzy: there are examples where members of one population can produce fertile offspring with a second population, and members of the second population can produce fertile offspring with members of a third population, but members of the first and third population cannot produces fertile offspring. Consequently, some people reject this notion of species. In recent years we have witnessed the drastic reduction in the size of breeding populations and the geographical range of many physically large mammals. In earlier times it was assumed that every species existed in at least a few thousand living individuals, except very rare relic, isolated groups. In the present, many well know mammal & bird species are so stressed by habitat loss, and other effects of the modern world, that only a very few breeding males may contribute the genetic material to a small number of breeding females. In these highly stressed conditions, the likelihood of change is very much greater. Mammals may become smaller, have darker fur, more stripes, more cautious behavior, even over time learn to co-exist with the human world. Very likely, evolution is radically accelerated, and we are only beginning to notice it. Species in transition before our eyes. It is possible that this severe stress is essential to the creation of new species, and may have been a prime factor throughout biological history, from other population reducing influences. Richard Dawkins defines two organisms as conspecific if and only if they have the same number of chromosomes and, for each chromosome, both organisms have the same number of nucleotides (The Blind Watchmaker, p. 118). However, most if not all taxonomists would strongly disagree. For example, in many amphibians, most notably in New Zealand's Leiopelma frogs, the genome consists of "core" chromosomes which are mostly invariable and accessory chromosomes, of which exist a number of possible combinations. Even though the chromosome numbers are highly variable between populations, these can interbreed successfully and form a single evolutionary unit. In plants, polyploidy is extremely commonplace with few restrictions on interbreeding; as individuals with an odd number of chromosome sets are usually sterile, depending on the actual number of chromosome sets present, this results in the odd situation where some individuals of the same evolutionary unit can interbreed with certain others and some cannot, with all populations being eventually linked as to form a common gene pool. The classification of species has been profoundly affected by technological advances that have allowed researchers to determine relatedness based on molecular markers, starting with the comparatively crude blood plasma precipitation assays in the mid-20th century and coming into full swing with Charles Sibley's ground-breaking DNA-DNA hybridisation studies in the 1970s. The results of the technique caused revolutionary changes in the higher taxonomic categories (such as phyla and classes), resulting in the reordering of many branches of the phylogenetic tree (see also: molecular phylogeny). For taxonomic categories below genera, the results have been mixed so far; the pace of evolutionary change on the molecular level is rather slow, yielding clear differences only after considerable periods of reproductive separation. Instances of hybridization can result in misleading molecular data, the Pomarine Skua - Great Skua phenomenon being a famous example. Turtles have been determined to evolve with just one-eighth of the speed of other reptiles on the molecular level, and the rate of molecular evolution in albatrosses is half of what is found in the rather closely related storm-petrels. The hybridization technique is however no longer considered a good technique and more reliable computational techniques for sequence comparison are now used for. Molecular taxonomy does not directly measure the evolutionary processes, but rather the overall change brought upon by these processes. The processes that lead to the generation and maintenance of variation such as mutation, crossover and selection are not uniform (see also molecular clock). DNA is only extremely rarely a direct target of natural selection rather than changes in the DNA sequence enduring over generations being a result of the latter; for example, silent transition-transversion combinations would alter the melting point of the DNA sequence, but not the sequence of the encoded proteins and thus are a possible example where, for example in microorganisms, a mutation confers a change in fitness all by itself.

External links

- http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/S/Speciation.html
- [http://www.sciencedaily.com/releases/2003/12/031231082553.htm 2003-12-31, ScienceDaily: Working On The 'Porsche Of Its Time': New Model For Species Determination Offered] Quote: "...two species of dinosaur that are members of the same genera varied from each other by just 2.2 percent. Translation of the percentage into an actual number results in an average of just three skeletal differences out of the total 338 bones in the body. Amazingly, 58 percent of these differences occurred in the skull alone. "This is a lot less variation than I'd expected", said Novak..."
- [http://www.sciencedaily.com/releases/2003/08/030808081854.htm 2003-08-08, ScienceDaily: Cross-species Mating May Be Evolutionarily Important And Lead To Rapid Change, Say Indiana University Researchers] Quote: "...the sudden mixing of closely related species may occasionally provide the energy to impel rapid evolutionary change..."
- [http://www.sciencedaily.com/releases/2004/01/040109064407.htm 2004-01-09 ScienceDaily: Mayo Researchers Observe Genetic Fusion Of Human, Animal Cells; May Help Explain Origin Of AIDS] Quote: "...The researchers have discovered conditions in which pig cells and human cells can fuse together in the body to yield hybrid cells that contain genetic material from both species... "What we found was completely unexpected", says Jeffrey Platt, M.D."
- [http://www.sciencedaily.com/releases/2000/09/000913211733.htm 2000-09-18, ScienceDaily: Scientists Unravel Ancient Evolutionary History Of Photosynthesis] Quote: "...gene-swapping was common among ancient bacteria early in evolution..."
- [http://plato.stanford.edu/entries/species/ Stanford Encyclopedia of Philosophy entry]
- [http://www.barcodinglife.org/ Barcoding of species] rank22 rank22 ms:Spesies ja:種 (生物) th:สปีชีส์

Evolution

, based on rRNA gene data, showing the separation of the three domains, bacteria, archaea, and eukaryotes, as described initially by Carl Woese.]] In biology, evolution is the process by which populations of organisms acquire and pass on novel traits from generation to generation, affecting the overall makeup of the population and even leading to the emergence of new species. The terms organic evolution or biological evolution are often used to distinguish this meaning from other usages. The development of the modern theory of evolution began with the introduction of the concept of natural selection in a joint 1858 paper by Charles Darwin and Alfred Russel Wallace. This theory achieved a wider readership in Darwin's 1859 book, The Origin of Species. Darwin and Wallace proposed that evolution occurs because a heritable trait that increases an individual's chance of successfully reproducing will become more common, by inheritance, from one generation to the next, and likewise a heritable trait that decreases an individual's chance of reproducing will become rarer. This work was groundbreaking, and overturned other evolutionary theories, such as that advanced by Jean Baptiste Lamarck. Because of its potential implications for the origins of humankind, the theory has been at the center of many social and religious controversies since its first inception (see Creation-evolution controversy). In the 1930s, scientists combined Darwinian natural selection with the re-discovered theory of Mendelian heredity to create the modern synthesis, now one of the fundamental scientific theories of biology. In the modern synthesis, "evolution" is defined as a change in the frequency of alleles within a population from one generation to the next. The basic mechanisms that produce these changes are natural selection, genetic drift, and genetic variation. The primary sources of genetic variation are mutation, sex, and gene flow.

Overview of evolution

Evidence of evolution

The process of evolution has left behind numerous records which reveal the history of species. While the best-known of these are the fossils, fossils are only a small part of the overall physical record of evolution. Fossils, taken together with the comparative anatomy of present-day plants and animals, constitute the morphological record. By comparing the anatomies of both modern and extinct species, biologists can reconstruct the lineages of those species with some accuracy. Using fossil evidence, for instance, the connection between dinosaurs and birds has been established by way of so-called "transitional" species such as Archaeopteryx. The development of genetics has allowed biologists to study the genetic record of evolution as well. Although we cannot obtain the DNA sequences of most extinct species, the degree of similarity and difference among modern species allows geneticists to reconstruct lineages with greater accuracy. It is from genetic comparisons that claims such as the 98-99% similarity between humans and chimpanzees come from, for instance. Other evidence used to demonstrate evolutionary lineages includes the geographical distribution of species. For instance, monotremes and most marsupials are found only in Australia, showing that their common ancestor with placental mammals lived before the submerging of the ancient land bridge between Australia and Asia. Scientists correlate all of the above evidence – drawn from paleontology, anatomy, genetics, and geography – with other information about the history of the earth. For instance, paleoclimatology attests to periodic ice ages during which the climate was much cooler; and these are found to match up with the spread of species such as the woolly mammoth which are better-equipped to deal with cold.

Morphological evidence

Fossils are important for estimating when various lineages developed. As fossilization on an organism is an uncommon occurrence, usually requiring hard parts (like bone) and death near a site where sediments are being deposited, the fossil record only provides sparse and intermittent information about the evolution of life. Fossil evidence of organisms without hard body parts, such as shell, bone, and teeth, is sparse but exists in the form of ancient microfossils and the fossilization of ancient burrows and a few soft-bodied organisms. Fossil evidence of prehistoric organisms has been found all over the Earth. The age of fossils can often be deduced from the geologic context in which they are found; and their absolute age can be verified with radiometric dating. Some fossils bear a resemblance to organisms alive today, while others are radically different. Fossils have been used to determine at what time a lineage developed, and transitional fossils can be used to demonstrate continuity between two different lineages. Paleontologists investigate evolution largely through analysis of fossils. Phylogeny, the study of the ancestry of species, has revealed that structures with similar internal organization may perform divergent functions. Vertebrate limbs are a common example of such homologous structures. Bat wings, for example, are very similar to hands. A vestigial organ or structure may exist with little or no purpose in one organism, though they have a clear purpose in other species. The human wisdom teeth and appendix are common examples.

Genetic sequence evidence

Comparison of the genetic sequence of organisms reveals that phylogenetically close organisms have a higher degree of sequence similarity than organisms that are phylogenetically distant. For example, neutral human DNA sequences are approximately 1.2% divergent (based on substitutions) from those of their nearest genetic relative, the chimpanzee, 1.6% from gorillas, and 6.6% from baboons. Sequence comparison is considered a measure robust enough to be used to correct erroneous assumptions in the phylogenetic tree in instances where other evidence is scarce. Further evidence for common descent comes from genetic detritus such as pseudogenes, regions of DNA which are orthologous to a gene in a related organism, but are no longer active and appear to be undergoing a steady process of degeneration. Since metabolic processes do not leave fossils, research into the evolution of the basic cellular processes is done largely by comparison of existing organisms. Many lineages diverged when new metabolic processes appeared, and it is theoretically possible to determine when certain metabolic processes appeared by comparing the traits of the descendants of a common ancestor.

History of evolutionary thought

metabolic.]] The idea of biological evolution has existed since ancient times, notably among Hellenists such as Epicurus and Anaximander, but the modern theory was not established until the 18th and 19th centuries, by scientists such as Jean-Baptiste Lamarck and Charles Darwin. While transmutation of species was accepted by a sizeable number of scientists before 1859, it was the publication of Charles Darwin's The Origin of Species by Means of Natural Selection which provided the first cogent mechanism by which evolutionary change could occur: his theory of natural selection. Darwin was motivated to publish his work on evolution after receiving a letter from Alfred Russel Wallace, in which Wallace revealed his own discovery of natural selection. As such, Wallace is sometimes given shared credit for the theory of evolution. Darwin's theory, though it succeeded in profoundly shaking scientific opinion regarding the development of life, could not explain the source of variation in traits within a species, and Darwin's proposal of a hereditary mechanism (pangenesis) was not compelling to most biologists. It was not until the late 19th and early 20th centuries that these mechanisms were established. pangenesis, proposed the theory of punctuated equilibrium in 1972.]] When Gregor Mendel's work regarding the nature of inheritance in the late 19th century was "rediscovered" in 1900, it led to a storm of conflict between Mendelians (Charles Benedict Davenport) and biometricians (Walter Frank Raphael Weldon and Karl Pearson), who insisted that the great majority of traits important to evolution must show continuous variation that was not explainable by Mendelian analysis. Eventually, the two models were reconciled and merged, primarily through the work of the biologist and statistician R.A. Fisher. This combined approach, applying a rigorous statistical model to Mendel's theories of inheritance via genes, became known in the 1930s and 1940s as the modern evolutionary synthesis. In the 1940s, following up on Griffith's experiment, Avery, McCleod and McCarty definitively identified deoxyribonucleic acid (DNA) as the "transforming principle" responsible for transmitting genetic information. In 1953, Francis Crick and James Watson published their famous paper on the structure of DNA, based on the research of Rosalind Franklin and Maurice Wilkins. These developments ignited the era of molecular biology and transformed the understanding of evolution into a molecular process: the mutation of segments of DNA (see molecular evolution). George C. Williams' 1966 Adaptation and natural selection: A Critique of some Current Evolutionary Thought marked a departure from the idea of group selection towards the modern notion of the gene as the unit of selection. In the mid-1970s, Motoo Kimura formulated the neutral theory of molecular evolution, firmly establishing the importance of genetic drift as a major mechanism of evolution. Debates have continued within the field. One of the most prominent public debates was over the theory of punctuated equilibrium, proposed in 1972 by paleontologists Niles Eldredge and Stephen Jay Gould to explain the paucity of transitional forms between phyla in the fossil record.

Social and religious controversies

Stephen Jay Gould from 1871 reflects part of the social controversy over whether humans and apes share a common lineage.]] There has been constant controversy surrounding the ideas presented by The Origin of Species since it was first printed in 1859. Since the early twentieth century, however, the idea that biological evolution of some form occurred and is responsible for speciation has been almost completely uncontested within the scientific community. Most controversy over the theory has come because of its philosophical, cosmological, and religious implications, and supporters as well as detractors have interpreted it as generally indicating that human beings are, like all animals, evolved, and that this account of the origins of humankind is squarely at odds with many religious interpretations. The idea that humans are "merely" animals, and are genetically very closely related to primates, have been independently argued as repellent notions by generations of detractors. Others also intepreted the truth of the theory to imply varying types of social changes — one prominent example is the idea of eugenics, formulated by Darwin's cousin Francis Galton, which argues for the improvement of human heredity by means of political policies. Others have found different political interpretations which have been used as arguments both for and against the theory. The questions raised about the relation of evolution to the origins of humans has made it an especially tenacious issue with religious traditions. It has prominently been seen as opposing a "literal" interpretation of the account of the origins of humankind as described in Genesis, the first book of the Bible. In many countries — notably in the United States — this has led to what has been called the Creation-evolution controversy, which has focused primarily on struggles over teaching curriculum.

Science of evolution

Science: fact and theory

The word "evolution" has been used to refer both to a fact and a theory, and it is important to understand both these different meanings of evolution, and the relationship between fact and theory in science.

Evolution as fact and theory

When "evolution" is used to describe a fact, it refers to the observations that populations of one species of organism do, over time change into new, or several new, species. In this sense, evolution occurs whenever a new strain of bacterium evolves that is resistant to antibodies that had been lethal to prior strains. Another clear case of evolution as fact involves the hawthorn fly, Rhagoletis pomonella. Different populations of hawthorn fly feed on different fruits. A new population spontaneously emerged in North America in the 19th century some time after apples, a non-native species, were introduced. The apple feeding population normally feeds only on apples and not on the historically preferred fruit of hawthorns. Likewise the current hawthorn feeding population does not normally feed on apples. A current area of scientific research is the investigation of whether or not the apple feeding race may further evolve into a new species. Some evidence, such as the fact that six out of thirteen alozyme loci are different, that hawthorn flies mature later in the season, and take longer to mature, than apple flies, and that there is little evidence of interbreeding (researchers have documented a 4-6%hybridization rate) suggests that this is indeed ocurring. (see Berlocher and Bush 1982, Berlocher and Feder 2002, Bush 1969, McPheron et. al. 1988, Prokopy et. al. 1988, Smith 1988) When "evolution" is used to describe a theory, it refers to an explanation for why and how evolution (for example, in the sense of "speciation") occurs. An example of evolution as theory is the modern synthesis of Darwin and Wallace's theory of natural selection and Mendel's principles of genetics. This theory has three major aspects: # Common descent of all organisms from a single ancestor or ancestral gene pool. # Manifestation of novel traits in a lineage. # Mechanisms that cause some traits to persist while others perish. When people provide evidence for evolution, in some cases they are providing evidence that evolution occurs; in other cases they are providing evidence that a given theory is the best explanation yet as to why and how evolution occurs.

The meaning of, and relationship between, fact and theory in science

:Main article: Theory The modern synthesis, like its Mendelian and Darwinian antecedents, is a scientific theory. In plain English, people use the word "theory" to signify "conjecture", "speculation", or "opinion". In this popular sense, "theories" are opposed to "facts" — parts of the world, or claims about the world, that are real or true regardless of what people think. In scientific terminology however, a theory is a model of the world (or some portion of it) from which falsifiable hypotheses can be generated and tested through controlled experiments, or be verified through empirical observation. In this scientific sense, "facts" are parts of theories – they are things, or relationships between things, that theories must take for granted in order to make predictions, or that theories predict. In other words, for scientists "theory" and "fact" do not stand in opposition, but rather exist in a reciprocal relationship – for example, it is a "fact" that every apple ever dropped on earth (under normal, controlled conditions) has been observed to fall towards the center of the planet in a straight line, and the "theory" which explains these observations is the current theory of gravitation. In this same sense evolution is a fact and modern synthesis is currently the most powerful theory explaining evolution, variation and speciation. Within the science of biology, modern synthesis has completely replaced earlier accepted explanations for the origin of species, including Lamarckism and creationism.
Who studies evolution?
Scholars in a number of academic disciplines and subdisciplines document the fact of evolution, and contribute to the theory of evolution.
Physical anthropology
Physical anthropology emerged in the late 1800s as the study of human osteology, and the fossilized skeletal remains of other hominids. At that time anthropologists debated whether their evidence supported Darwin's claims, because skeletal remains revelaed temporal and spacial variation among hominids, but Darwin had not offered an explanation of the mechanisms that produce variation. With the recognition of Mendelian genetics and the rise of the modern synthesis, however, evolution became both the fundamental conceptual framework for, and object of study of, physical anthropologists. In addition to studying skeletal remains, they began to study genetic variation among human populations (i.e. population genetics; thus, some physical anthropologists began calling themselves biological anthropologists.
Evolutionary biology
Evolutionary biology is a subfield of biology concerned with the origin and descent of species, as well as their change over time. At first it was an interdisciplinarity field including scientists from many traditional taxonomically oriented disciplines. For example, it generally includes scientists who may have a specialist training in particular organisms such as mammalogy, ornithology, or herpetology but use those organisms as systems to answer general questions in evolution. Evolutionary biology as an academic discipline in its own right emerged as a result of the modern evolutionary synthesis in the 1930s and 1940s. It was not until the 1970s and 1980s, however, that a significant number of universities had departments that specifically included the term evolutionary biology in their titles.
Evolutionary developmental biology
Evolutionary developmental biology is an emergent subfield of evolutionary biology that looks at genes of related and unrelated organisms. By comparing the explicit nucleotide sequences of DNA/RNA, it is possible to experimentally determine and trace timelines of species development. For example, gene sequences support the conclusion that chimpanzees are the closest primate ancestor to humans, and that arthropods (e.g., insects) and vertebrates (e.g., humans) have a common biological ancestor.
Ancestry of organisms
vertebrates In biology, the theory of universal common descent proposes that all organisms on Earth are descended from a common ancestor or ancestral gene pool (which is called having "common descent"). Evidence for common descent may be found in traits shared between all living organisms. In Darwin's day, the evidence of shared traits was based solely on visible observation of morphologic similarities, such as the fact that all birds — even those which do not fly — have wings. Today, the theory of evolution has been strongly confirmed by genetics. For example, every living cell makes use of nucleic acids as its genetic material, and uses the same twenty amino acids as the building blocks for proteins. All organisms use the same genetic code (with some extremely rare and minor deviations) to translate nucleic acid sequences into proteins. The universality of these traits strongly suggests common ancestry, because the selection of these traits seems somewhat arbitrary, . The evolutionary process can be exceedingly slow. Fossil evidence indicates that the diversity and complexity of modern life has developed over much of the age of the earth. Geological evidence indicates that the Earth is approximately 4.6 billion years old. (See Timeline of evolution.) Studies on guppies by David Reznick at the University of California, Riverside, however, have shown that the rate of evolution through natural selection can proceed 10 thousand to 10 million times faster than what is indicated in the fossil record. Information about the early development of life includes input from the fields of geology and planetary science. These sciences provide information about the history of the Earth and the changes produced by life. A great deal of information about the early Earth has been destroyed by geological processes over the course of time.
History of life
planetary sciences in the Siyeh Formation, Glacier National Park. In 2002, William Schopf of UCLA published a controversial paper in the journal Nature arguing that formations such as this possess 3.5 billion year old fossilized algae microbes. If true, they would be the earliest known life on earth.]] The chemical evolution from self-catalytic chemicals to life (see Origin of life) is not a part of biological evolution. Not much is known about the earliest developments in life. However, all existing organisms share certain traits, including cellular structure, and genetic code. Most scientists interpret this to mean all existing organisms share a common ancestor, which had already developed the most fundamental cellular processes, but there is no scientific consensus on the relationship of the three domains of life (Archea, Bacteria, Eukaryota) or the origin of life. Attempts to shed light on the earliest history of life generally focus on the behavior of macromolecules, particularly RNA, and the behavior of complex systems. The emergence of oxygenic photosynthesis (around 3 billion years ago) and the subsequent emergence of an oxygen-rich, non-reducing atmosphere can be traced through the formation of banded iron deposits, and later red beds of iron oxides. This was a necessary prerequisite for the development of aerobic cellular respiration, believed to have emerged around 2 billion years ago. In the last billion years, simple multicellular plants and animals began to appear in the oceans. Soon after the emergence of the first animals, the Cambrian explosion (a period of unrivaled and remarkable, but brief, organismal diversity documented in the fossils found at the Burgess Shale) saw the creation of all the major body plans, or phyla, of modern animals. This event is now believed to have been triggered by the development of the Hox genes. About 500 million years ago, plants and fungi colonized the land, and were soon followed by arthropods and other animals, leading to the development of land ecosystems with which we are familiar.
The Modern Synthesis
The current understanding of the mechanistics of evolution differs considerably from the theory first outlined by Charles Darwin. Importantly, advances in genetics pioneered by Gregor Mendel led to a sophisticated understanding of the basis of variation and the mechanisms of inheritance. In addition natural selection has come to be seen as only one of a number of forces acting in evolution. A notable milestone in this regard was the formulation of the neutral theory of molecular evolution by Motoo Kimura.
Heredity
Gregor Mendel first proposed a gene-based theory of inheritance, discretizing the elements responsible for heritable traints into the fundamental units we now call genes, and laying out a mathematical framework for the segregation and inheritance of variants of a gene, which we now refer to as alleles. Later research identified the molecule DNA as the genetic material, through which traits are passed from parent to offspring, and identified genes as discrete elements within DNA. Though largely faithfully maintained within organisms, DNA is both variable across individuals and subject to a process of change or mutation. Non-DNA based forms of heritable variation exist, which may change the way in which genes are expressed or maintained. The processes that produce these variations leave the genetic information intact and are often reversible. This is called epigenetic inheritance and may include phenomena such as DNA methylation, prions, and structural inheritance. Investigations continue into whether these mechanisms allow for the production of specific beneficial heritable variation in response to environmental signals. If this were shown to be the case, then some instances of evolution would lie outside of the typical Darwinian framework, which avoids any connection between environmental signals and the production of heritable variation.
Sexual reproduction
In addition to passing genetic material from parent to offspring, nearly all organisms employ sex to exchange genetic material. This, combined with meiotic recombination, allows genetic variation to be propagated through an interbreeding population. These mechanisms allow individual variations to be propagated more or less independently, so that the population as a whole can retain beneficial variation and eliminate harmful variation (rather than both of these effects competing within a single asexual organism). However, these mechanisms are not perfect, and so some variation is co-propagated as a result of linkage, producing some odd effects (see Muller's ratchet).
Mechanisms of evolution
Evolution consists of two basic types of processes: those that introduce new genetic variation into a population, and those that affect the frequencies of existing variation. There are three known processes that affect the survival of a characteristic (or, more specifically, the frequency of an allele):
- Natural selection
- Changes in population structure
- Genetic drift These basic mechanisms of evolution have all been observed in the present and in evidence of their existence in the past. Their study is being used to guide the development of new medicines and other health aids such as the current effort to prevent a H5N1 (i.e. bird flu) pandemic
Variation
Without genetic variation, populations cannot evolve. The two principle sources of genetic variation are mutations and gene flow. Other forms of genetic variation due to gene transfer include horizontal gene transfer, antigenic shift, and reassortment. Viruses can transfer genes between species [http://66.102.7.104/search?q=cache:tpICVNWaTbgJ:non.fiction.org/lj/community/ref_courses/3484/enmicro.pdf+sex+evolution+%22Horizontal+gene+transfer%22+-human+Conjugation+RNA+DNA&hl=en]. Bacteria can incorporate genes from other dead bacteria, exchange genes with living bacteria, and can have plasmids "set up residence seperate from the host's genome" [http://www2.nau.edu/~bah/BIO471/Reader/Pennisi_2003.pdf]. "Genes that move between species play by rules that microbial experts are just beginning to discern" [http://66.102.7.104/search?q=cache:gto6eXfbGIEJ:www.niagara.edu/eli/Science%252016%2520July%25202004.GeneSwap.doc+sex+evolution+%22Horizontal+gene+transfer%22+-human+Conjugation+RNA+DNA&hl=en].
Mutation
The ultimate source of all genetic variation is mutations. They are permanent, transmissible changes to the genetic material (usually DNA or RNA) of a cell, and can be caused by "copying errors" in the genetic material during cell division and by exposure to radiation, chemicals, or viruses. In multicellular organisms, mutations can be subdivided into germline mutations that occur in the gametes and thus can be passed on to progeny, and somatic mutations that often lead to the malfunction or death of a cell and can cause cancer. Mutations that are not affected by natural selection are called neutral mutations. Their frequency in the population is governed entirely by genetic drift and gene flow. It is understood that a species' genome, in the absence of selection, undergoes a steady accumulation of neutral mutations. The probable mutation effect is the proposition that a gene that is not under selection will be destroyed by accumulated mutations. This is an aspect of genome degradation. Not all mutations are created equal; simple point mutations (substitutions), which comprise the vast majority of genetic variation, usually can only alter the function or level of expression of existing genes. Gene duplications, which may occur via a number of mechanisms, are believed to be the major mechanism for the introduction of new genes; most genes belong to larger "families" of genes derived from a common ancestral gene (two genes from a species that are in the same family are dubbed "paralogs"). Finally, large chromosomal rearrangements (like the fusion of two chromosomes in the chimp/human common ancestor that produced human chromosome 2) almost invariably result in a speciation event.
Gene flow
Gene flow (or gene admixture) is introduction of variation into a population from an outside population. It is the only mechanism whereby two populations can become closer genetically while increasing their variation. Migration of one population into an area occupied by a second population can result in gene flow. Gene flow operates when geography and culture are not obstacles. When gene flow is impeded by non-geographic obstacles, the situation is termed reproductive isolation and is considered to be the hallmark of speciation.
Drift
Genetic drift describes changes in allele frequency from one generation to the next due to sampling variance. The frequency of an allele in the offspring generation will vary according to a probability distribution of the frequency of the allele in the parent generation. Thus, over time, allele frequencies will tend to "drift" upward or downward, eventually becoming "fixed" - that is, going to 0% or 100% frequency. Fluctuations in allele frequency between successive generations may result in some alleles disappearing from the population. Two separate populations that begin with the same allele frequencies therefore might drift by random fluctuation into two divergent populations with different allele sets (for example, alleles that are present in one have been lost in the other). Many aspects of genetic drift depend on the size of the population (generally abbreviated as N). This is especially important in small mating populations, where chance fluctuations from generation to generation can be large. The relative importance of natural selection and genetic drift in determining the fate of new mutations also depends on the population size and the strength of selection: when N times s (population size times strength of selection) is small, genetic drift predominates. When N times s is large, selection predominates. Thus, natural selection is 'more efficient' in large populations, or equivalently, genetic drift is stronger in small populations. Finally, the time for an allele to become fixed in the population by genetic drift (that is, for all individuals in the population to carry that allele) depends on population size, with smaller populations requiring a shorter time to fixation.
Population structure
An important facet of evolution occurs through changes in population structure. The movement of populations and changes in their size can have profound impacts on evolution over and above those governed by selection and drift. Migration can result in admixture leading to the introduction of new genetic variation, or it may result in geographic isolation which may in turn lead to reproductive isolation or speciation. Populations may also shrink or grow over time, producing "bottlenecks" or "explosions" respectively. Since population size has a profound effect on the relative strengths of genetic drift and natural selection, changes in population size can alter the dynamics of these processes considerably. Such changes may also produce dramatic and dangerous crashes in the level of genetic variation in the population, or allow rapid increases in standing genetic variation. The free movement of alleles through a population may also be impeded by population structure. For example, most real-world populations are not actually fully interbreeding; geographic proximity has a strong influence on the movement of alleles within the population. Many models of evolution rely on simplifying assumptions of constant population size and fully interbreeding populations for mathematical convenience. An example of the effect of population structure is the so-called founder effect, resulting from a migration and population bottleneck. In this case, a single, rare allele may suddenly increase very rapidly in frequency if it happened to be prevalent in a small number of "founder" individuals. The frequency of the allele in the resulting population can be much higher than otherwise expected, especially for deleterious, disease-causing alleles.
Selection and adaptation

Natural selection
Natural selection comes from differences in survival and reproduction as a result of the environment. Differential mortality is the survival rate of individuals to their reproductive age. Differential fertility is the total genetic contribution to the next generation. Note that, whereas mutations and genetic drift are random, natural selection is not, as it preferentially selects for different mutations based on differential fitnesses. For example, rolling dice is random, but always picking the higher number on two rolled dice is not random. The central role of natural selection in evolutionary theory has given rise to a strong connection between that field and the study of ecology. Natural selection can be subdivided into two categories:
- Ecological selection occurs when organisms that survive and reproduce increase the frequency of their genes in the gene pool over those that do not survive.
- Sexual selection occurs when organisms which are more attractive to the opposite sex because of their features reproduce more and thus increase the frequency of those features in the gene pool. Natural selection also operates on mutations in several different ways:
- Purifying or background selection eliminates deleterious mutations from a population.
- Directional selection increases the frequency of a beneficial mutation.
- Balancing selection maintains variation within a population through a number of mechanisms, including:
- Heterozygote advantage or overdominance, where the heterozygote is more fit than either of the homozygous forms (exemplified by human sickle cell anemia conferring resistance to malaria)
- Frequency-dependent selection, where rare variants have a higher fitness, because of thier rarity.
- Stabilizing selection favors average characteristics in a population, thus reducing gene variation but retaining the mean.
- Disruptive selection favors both extremes, and results in a bimodal distribution of gene frequency. The mean may or may not shift.
Adaptation
Through the process of natural selection, species become better adapted to their environments. Adaptation is any evolutionary process that increases the fitness of the individual, or sometimes the trait that confers increased fitness, e.g. a stronger prehensile tail or greater visual acuity. Note that adaptation is context-sensitive; a trait that increases fitness in one environment may decrease it in another. Evolution does not act in a linear direction towards a pre-defined "goal" — it only responds to various types of adaptionary changes. The belief in a telelogical evolution of this sort is known as orthogenesis, and is not supported by the scientific theory of evolution. One example of this misconception is the erroneous belief humans will evolve more fingers in the future on account of their increased use of machines such as computers. In reality, this would only occur if more fingers offered a significantly higher rate of reproductive success than those not having them, which seems very unlikely at the current time. Most biologists believe that adaptation occurs through the accumulation of many mutations of small effect. However, macromutation is an alternative process for adaptation that involves a single, very large scale mutation.
Speciation and extinction
macromutation Speciation is the creation of two or more species from one. This may take place by various mechanisms. Allopatric speciation occurs in populations that become isolated geographically, such as by habitat fragmentation or migration. Sympatric speciation occurs when new species emerge in the same geographic area. Ernst Mayr's peripatric speciation is a type of speciation that exists in between the extremes of allopatry and sympatry. Peripatric speciation is a critical underpinning of the theory of punctuated equilibrium. Extinction is the disappearance of species (i.e. gene pools). The moment of extinction generally occurs at the death of the last individual of that species. Extinction is not an unusual event in geological time — species are created by speciation, and disappear through extinction. The Permian-Triassic extinction event was the Earth's most severe extinction event, rendering extinct 90% of all marine species and 70% of terrestrial vertebrate species. In the Cretaceous-Tertiary extinction event many forms of life perished (including approximately 50% of all genera), the most often mentioned among them being the extinction of the non-avian dinosaurs (See Image 5).
See also

Notes and references
# "Ancient microfossils from Western Australia are again the subject of heated scientific argument: are they the oldest sign of life on Earth, or just a flaw in the rock?" "[http://www.abc.net.au/science/news/space/SpaceRepublish_497964.htm]" # Understanding Evolution, from California's Berkeley University. "[http://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_17] [http://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_16] # Li WH, Saunders MA (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69–87. Britten RJ (2002) Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels. Proc Natl Acad Sci U S A 99: 13633–13635. # Two sources: 'Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees'. and 'Quantitative Estimates of Sequence Divergence for Comparative Analyses of Mammalian Genomes' "[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11170892] [http://www.genome.org/cgi/content/full/13/5/813]" # Pseudogene evolution and natural selection for a compact genome. "[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10833048]" # Reference for emergence of new race of apple maggot flies http://www.nd.edu/~aforbes/ # Evaluation of the Rate of Evolution in Natural Populations of Guppies (Poecilia reticulata) "[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9072971&query_hl=2]" # The use of evolutionary principles to guide disease diagnosis and drug development with respect to bird flu (i.e. H5N1 virus) [http://www.cdc.gov/ncidod/EID/vol11no10/05-0644.htm] # Understanding Evolution, from California's Berkeley University: "Sex can introduce new gene combinations into a population. This genetic shuffling is another important source of genetic variation."[http://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_17]
- Berlocher, S.H. and G.L. Bush. 1982. An electrophoretic analysis of Rhagoletis (Diptera: Tephritidae) phylogeny. Systematic Zoology 31:136-155.
- Berlocher, S.H. and J.L. Feder. 2002. Sympatric speciation in phytophagous insects: moving beyond controversy? Annual Review of Entomology 47:773-815.
- Bush, G.L. 1969. Sympatric host race formation and speciation in frugivorous flies of the genus Rhagoletis (Diptera: Tephritidae). Evolution 23:237-251.
- Darwin, Charles November 24 1859. On the Origin of Species by means of Natural Selection or the Preservation of Favoured Races in the Struggle for Life. London: John Murray, Albemarle Street. 502 pages. Reprinted: Gramercy (May 22, 1995). ISBN 0517123207
- Prokopy, R.J., S.R. Diehl and S.S. Cooley. 1988. Behavioral evidence for host races in Rhagoletis pomonella flies. Oecologia 76:138-147.
- Zimmer, Carl. Evolution: The Triumph of an Idea. Perennial (October 1, 2002). ISBN 0060958502
- Larson, Edward J. Evolution: The Remarkable History of a Scientific Theory (Modern Library Chronicles). Modern Library (May 4, 2004). ISBN 0679642889
- Mayr, Ernst. What Evolution Is. Basic Books (October, 2002). ISBN 0465044263
- McPheron, B. A., D. C. Smith and S. H. Berlocher. 1988. Genetic differentiation between host races of Rhagoletis pomonella. Nature. 336:64-66.
- Gigerenzer, Gerd, et al., The empire of chance: how probability changed science and everyday life (New York: Cambridge University Press, 1989).
- Smith, D. C. 1988. Heritable divergence of Rhagoletis pomonella host races by seasonal asynchrony. Nature. 336:66-67.
- Williams, G.C. (1966). Adaptation and Natural Selection: A Critique of some Current Evolutionary Thought . Princeton, N.J.: Princeton University Press.
- Sean B. Carroll, 2005, Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom, W. W. Norton & Company. ISBN 0393060160
- Bill Bryson, A Short History of Nearly Everything, Black Swan Books (2004), ISBN 0-552-99704-8
External links

- [http://www.talkorigins.org Talk.Origins Archive] — see also talk.origins
- [http://evolution.berkeley.edu/ Understanding Evolution] @ [http://berkeley.edu Berkeley]
- [http://nationalacademies.org/evolution/ National Academies Evolution Resources]
- [http://www.evowiki.org/index.php/Main_Page EvoWiki] — A wiki whose goal is to promote general evolution education, and provide mainstream scientific responses to the arguments of antievolutionists.
- [http://www.chains-of-reason.org/chains/evolution-by-natural-selection/introduction.htm Evolution by Natural Selection] — An introduction to the logic of the theory of evolution by natural selection
- [http://www.pbs.org/wgbh/evolution/index.html Evolution] — Provided by PBS.
- [http://www.newscientist.com/channel/life/evolution Everything you wanted to know about evolution] — Provided by New Scientist.
- [http://evol.allenpress.com/evolonline/?request=index-html International Journal of Organic Evolution]
- [http://science.howstuffworks.com/evolution.htm/printable Howstuffworks.com — How Evolution Works]
- [http://pages.britishlibrary.net/charles.darwin/ Charles Darwin's writings]
- [http://www.genomenewsnetwork.org/categories/index/genome/evolution.php Evolution News from Genome News Network (GNN)]
- [http://www.nap.edu/books/0309063647/html/ National Academy Press: Teaching About Evolution and the Nature of Science]
- [http://www.evolution.mbdojo.com/evolution-for-beginners.html Evolution for beginners]
- [http://www.rmcybernetics.com/science/cybernetics/ai.htm RMCybernetics - AI] Evolution can create emergent behavior in a computer program.
- [http://www.sciencefriday.com/pages/2005/Nov/hour2_111805.html NPR - Science Friday: links to museums, articles and books.]
Evolution Simulators

- [http://www.truthtree.com/evolve.shtml Isolated species evolves to interact more efficiently with its environment (java applet)]
- [http://obermuhlner.com/public/Projects/Applets/Blobs/index.html Evolution in a predator-prey relationship (java applet)] Category:Evolutionary biology Category:Theories ko:진화 ja:進化 th:วิวัฒนาการ

Prehistory

- The term prehistory (Greek words προ = before and ιστορία = history) is usually used to describe the period before written history became available. Paul Tournal originally coined the term Pré-historique in describing the finds he had made in the caves of southern France, and was used in French since the 1830s to describe the time before writing, then introduced into English by Daniel Wilson in 1851.
- The term became less meaningful in the 20th century as the boundary between history (strictly the written record) and other disciplines became less rigid and defined. Indeed today most historians rely on evidence from multiple sources and the notion of limiting historical study to a 5000 year span, out of a possible few million years of human existence, and of only those few world cultures that left written records, is no longer taken seriously. For example historians study the Celts, African civilizations and North American civilizations, even though they are by definition "prehistory".
- Prehistory can be said to date back to the beginning of the universe itself, although the term is most often used to describe periods when there was life on Earth; dinosaurs can be described as prehistoric animals and cavemen are described as prehistoric people.
- Because, by definition, there are no written records from prehistoric times, the information we know about the time period is informed by the fields of palaeontology, astronomy, biology, geology, anthropology, archaeology, indeed all the natural sciences.
- Human prehistory differs from history not only in terms of chronology but in the way it deals with the activities of archaeological cultures rather than named nations or individuals. Restricted to material remains rather than written records (and indeed only those remains that have survived), prehistory is anonymous. Because of this, the cultural terms used by prehistorians such as Neanderthal or Iron Age are modern, arbitrary labels, the precise definition of which are often subject to discussion and argument.
- The date marking the end of prehistory, that is the date when written historical records become a useful academic resource, varies from region to region. In Egypt it is generally accepted that prehistory ended around 3500 BC whereas in New Guinea the end of the prehistoric era is set much more recently, AD 1900.

Age systems

- Until the arrival of humans, a geologic time scale defines periods in prehistory. Archaeology has augmented this record and provided more precise divisions during later, human, prehistory.
- Human prehistory in the Old World is often subdivided by the three-age system. This system of classifying human prehistory creates three consecutive time periods, named for their respective predominant tool-making technologies. In the New World other naming schemes have been defined such as that listed in Archeology of the Americas.
- These very general systems of dividing up prehistory are being found to be increasingly inapplicable as archaeological discoveries suggest a much more complex view of prehistory.

External links

- The Neanderthal site at [http://www.geocities.com/patrickbringmans/veldwezelt-hezerwater.html Veldwezelt-Hezerwater], Belgium

Hyracotherium

Hyracotherium ("mole beast") is the earliest known horse. It was dog-sized and four-toed. It lived between 60 and 45 million years ago in the Eocene. The first fossils of this tiny horse were found in England by the famous paleontologist Richard Owen in 1841. He did not have a full specimen, didn't realise what he had, and called it "mole beast". When a full specimen was discovered later it was given the more fitting name Eohippus ("dawn horse"). It wasn't realised until later that the two finds were the same species. The first published name has priority as the official name. Hyracotherium averaged only 2 feet (60 cm) in length and averaged 8 to 9 inches (20 cm) high at the shoulder. It had 4 hoofed toes on the front feet and 3 hoofed toes on each hind foot. The skull was long, having 44 long-crowned teeth. Hyracotherium is believed to have been a grazing herbivore that ate soft leaves and plant shoots. In elementary level textbooks, hyracotherium is commonly described as being "the size of a small fox terrier." This arcane analogy was so curious that Stephen Jay Gould wrote an essay about it ("The Case of the Creeping Fox Terrier Clone") in which he exposed shameless textbook plagiarism. They lived in the Northern Hemisphere (in Asia, Europe, and North America). Category:Prehistoric horses Category:Eocene

Horse

The Horse (Equus caballus) is a sizeable ungulate mammal, one of the seven modern species of the genus Equus. It has long played an important role in transport, whether ridden or used for pulling vehicles. They are also used for food. Though horses may have been domesticated in one isolated locale in 4500 BC, the unequivocal date of (1) domestication and (2) use as a means of transport dates to no earlier than circa 2000 BC, evidenced by the Sintashta chariot burials (see Domestication of the horse). Nevertheless, a close cousin of the horse, the donkey, was likely domesticated and used for transport circa 3000 BC (see discussions at Donkey and [http://nefertiti.iwebland.com/timelines/topics/means_of_transportation.htm]). Until the mid 20th century, armies used horses extensively in warfare: soldiers still call the groups of machines that now take the place of the horse on the battlefield "cavalry" units, sometimes keeping traditional names (Lord Strathcona's Horse, et cetera).

Domestication of the horse and surviving wild species

The earliest evidence for the domestication of the horse comes from Central Asia and dates to about 4,000 BCE. Competing theories exist about the time and place of domestication. However, wild species continued into historic times, including the Forest Horse, Equus caballus silvaticus (also called the Diluvial Horse); it is thought to have evolved into Equus caballus germanicus, and may have contributed to the development of the heavy horses of northern Europe, such as the Ardennais. The Tarpan, Equus caballus gmelini, became extinct in 1880. Its genetic line is lost, but a substitute has been recreated by "breeding back", crossing living domesticated horses that had features selected as primitive, thanks to the efforts of the brothers Lutz Heck (director of the Berlin zoo) and Heinz Heck (director of Tierpark Munich Hellabrunn). The resulting animal is more properly called the Wild Polish Horse or Konik. Konik] Only one true wild-horse species survives: Przewalski's Horse, Equus caballus przewalskii, a rare Asian species. Mongolians know it as the taki, while the Kirghiz people call it a kirtag. Wild populations exist in Mongolia; see: http://www.treemail.nl/takh/.

Wild vs. feral horses

One can distinguish between wild animals, whose ancestors have never undergone domestication, and feral animals, who had domesticated ancestors but who now live in the wild. Several populations of feral horses exist, including those in the West of the United States and Canada (often called "mustangs") and in parts of Australia (called brumbies) and in New Zealand (called "Kaimanawa horses"). These feral horses may provide useful insights into the behavior of their ancestral wild horses. The Icelandic horse (pony-sized but called a horse) provides an opportunity to compare contemporary and historical breed appearances and behaviour. Introduced by the Vikings into Iceland, Icelandic horses did not subsequently undergo the intensive selective breeding that took place in the rest of Europe from the middle ages onwards, and so they consequently bear a closer resemblance to pre-medieval breeds. The Icelandic horse has a four-beat gait called the "tölt", which equates to the rack exhibited by several American gaited breeds.

Other equids

Other members of the horse family include zebras, donkeys, and hemionids. The Donkey, Burro or Domestic Ass, Equus asinus, like the horse, has many breeds. A mule is a hybrid of a male ass and a mare and is infertile. A hinny is the less common hybrid of a female ass and a stallion. Recently breeders have begun crossing various species of zebra with mares or female asses to produce "zebra mules"—zorses and zonkeys (also called zedonks). This will probably remain a novelty hybrid as these individuals tend to inherit some of the nervous, difficult nature of their zebra parent. Full species list:
- Domesticated Horse (Equus caballus)
- Tarpan (Equus caballus gmelini)
- Przewalski's Horse (Equus caballus przewalskii)
- Donkey (Equus asinus)
- Onager (Equus hemionus)
- Kiang (Equus kiang)
- Mountain Zebra (Equus zebra)
- Plains Zebra (Equus quagga)
- Grevy's Zebra (Equus grevyi)

Evolution

All equids are part of the family Equidae, which dates back more than 50 million years. One of the first species was the tiny Hyracotherium. In the course of the million years, the horses evolved from leaf-eating forest-dwellers into grass-eating fast-running inhabitants of the open plains. The Evolution of the Horse lead to a reduction of the number of toes: from 5 per foot, to 3 per foot, to only 1 toe per foot. The genus Equus, to which all living equids belong, evolved a few million years ago. Examples of extinct horse genera include: Propalaeotherium, Mesohippus, Miohippus, Orohippus, Pliohippus, Anchitherium, Merychippus, Parahippus, Hipparion and Hippidion.

Natural History of the horse

Hippidion] In nature, horses function as prey animals. They have a natural tendency to flee from danger, though they will fight if cornered. Their eyes lie to the side of the head, giving them a wide view while grazing (slightly less than 180 degrees to each side, overlapped in front and leaving a blind spot in the rear). Even domesticated horses startle easily and must, for the safety of riders, undergo careful introductions to strange objects and situations. Horses live in family groups in primarily grassland habitats. These normally consist of a mature stallion, his harem of about one to ten mares, and the mares' offspring. Once young males reach breeding age and begin to attempt to breed with mares or to challenge the herd stallion, the latter drives them out of the herd to form "bachelor bands" with other young stallions. Usually not until a stallion reaches 7 or 8 years old does he stand a real chance of acquiring mares, eventually becoming, if successful in the attempt, a "band stallion", i.e. having a harem of his own, having separated female equids from another stallion's band. harem An alpha mare dictates the direction in which a family herd travels, while the stallion brings up the rear, "herding" his family. Recently, researchers have observed that a form of democracy appears to exist among horses. For instance, if the majority of the herd wants to stop and eat, the whole herd follows suit and stops.

Specialized vocabulary

The English-speaking world measures the height of horses in hands. One hand is defined in British law as 101.6 mm and is derived from a previous definition of 4 inches. Adult horses can range in size from 5 hands (0.5 m) (a very small miniature horse or falabella) to over 19 hands (1.8 m). By convention, 15.2 hh means 15 hands, 2 inches (1.57 m) in height, measured at the highest point of the withers. Usually, size alone marks the difference between horses and ponies. The threshold is 14.2 hh (1.47 m) for an adult. Below the threshold it is a pony, above the threshold it is a horse. Thus normal variations can mean that a horse stallion and horse mare can become the parents of an adult pony. However, a distinct set of characteristic pony traits, developed in northwest Europe and further evolved in the British Isles, muddies the issue of whether we use the word "pony" to describe a size or a type. Many people consider the Shetland pony as the archetypical pony, with its proportions very different from horses. Several small breeds appear as "horses" or "ponies" interchangeably, including the Icelandic, Fjord, and Caspian. Breeders of miniature horses favor that name because they strive to reproduce horse-like conformation in a very small size, even though their animals undeniably descend from ponies.

Words for gaits

All horses move naturally in four basic gaits, the walk, trot, canter/lope ("canter" in English riding, "lope" in Western), and the gallop.
- the walk - a "four beat" lateral gait in which a horse must have three feet on the ground and only one foot in the air at any time. The walking horse will lift first a hind leg, then the foreleg on the same side, then the remaining hind leg, then the foreleg on the same side. To get a horse into walk from halt, one must gently squeeze the sides of the horse and release the pressure on the reins. To get a horse to walk from trot, one must take sitting trot and gently apply pressure on the reins.
- the trot/jog - a "two beat" diagonal gait in which a foreleg and opposite hindleg (often called "diagonals") touch the ground at the same time. In this gait, each leg bears weight separately, making it ideal to check for lameness or for stiffness in the joints. To get a horse to trot fom walk you must soften your reins and apply more pressure with the leg. There are two types of trot a rider can do. Rising trot, where the rider stands up slightly in the saddle each time the horses outside front leg goes forward, and sitting trot, where the rider sits in the saddle and goes with the horse's movement.
- the canter/lope - A "three beat" gait in which a foreleg and opposite hindleg strike the ground together, and the other two legs strike separately. A cantering horse will first stride off with the outside hind leg, then then inside hind and outside fore together, then the inside front leg, and finally a period of suspension in which all four legs are off the ground. the rhythm should be 1-2-3, 1-2-3, etc. When cantering in a straight line, it does not usually matter which foreleg (or leading leg) goes first, but both leads should receive equal practice time, as otherwise the horse may become "one-sided" or develop a reluctance to canter on a specific lead. In the arena, the horse should canter on the inside lead. In making a fairly tight turn, the inside leg (the one nearest to the center of the turn) should lead, as this prevents the horse from "falling in". to get a horse to canter on the correct leg from trot, one must go into sitting trot, place their outside leg slightly behind the girth and squeeze with the inside leg. To get a horse to canter from gallop, one must alter the position of the body slightly back in the saddle, then yo