Species
INTRODUCTION
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. Because genetic incapability to interbreed is an essetial break between species, some argue that a more precise or differentiating measure would be based on similarity of DNA. Morphology was once considered evidence for intermediate stages of speciation, however, because an organism's form may be the product of convergent evolution, morphology is not evidence of common class or phyla. Speciation is often misused to distinguish populations separated by geographic impediments, pathological preferences, or even morphological impediments who may yet remain genetically compatible to interbreed. Study of the Drosophila species of Hawaii is considered by many as a dramatic case of sequential genetic speciation providing evidence that new species do arise from pre-existing species in nature, however, if these populations are genetically capable of interbreeding, then no true speciation has occurred. Presence of specific locally adapted traits are considered by some to further subdivide species into subspecies, however, locally adapted traits would include variations within a species as inconsequential as hair color or size and do not constitute speciation at all. "Subspecies" in such a context is an oxymoron. "Species" was defined long before the discovery of DNA, but with the discovery of DNA, there is conflict in its usage that must be resolved. The term must be refined to exclude irrelevancies like morphological similarities and more persistent reference to genetic composition which is now known to BE the difference between "species". Misuse of the term "species" confuses relevant with irrelevnt distinctions among species and inhibits resolution of long outstanding issues of philosophical, religious and biological importance.
The commonly used names for plant and animal taxa sometimes correspond to species: for example, "lion," "walrus," and "Camphor tree" – each refers to a species. In other cases common names do not: for example, "deer" refers to a family of 34 species, including Eld's Deer, Red Deer and Wapiti (Elk). The last two species were once considered a single species, illustrating how species boundaries may change with increased scientific knowledge.
Each species is placed within a single genus. This is a hypothesis that the species is more closely related to other species within its genus than to species of other genera. All species are given a binomial name consisting of the generic name and specific name (or specific epithet). For example, Pinus palustris (commonly known as the Longleaf Pine).
A usable definition of the word "species" and reliable methods of identifying particular species are essential for stating and testing biological theories and for measuring biodiversity. Traditionally, multiple examples of a proposed species must be studied for unifying characters before it can be regarded as a species. Extinct species known only from fossils are generally difficult to give precise taxonomic rankings to. A species which has been described scientifically can be referred to by its binomial names.
Nevertheless, as Charles Darwin remarked,
- I look at the term species as one arbitrarily given for the sake of convenience to a set of individuals closely resembling each other .... it does not essentially differ from the term variety, which is given to less distinct and more fluxtuating forms. The term variety, again in comparison with mere individual difference, is also applied arbitrarily, and for mere convenience sake.[1]
Because of the difficulties with both defining and tallying the total numbers of different species in the world, it is estimated that there are anywhere between 2 and 100 million different species.[2]
Binomial convention for naming species
In scientific classification, a species is assigned a two-part name, treated as Latin, although roots from any language can be used as well as names of locales or individuals. The genus is listed first (with its leading letter capitalized), followed by a second term: for example, gray wolves belong to the species Canis lupus, coyotes to Canis latrans, golden jackals to Canis aureus, etc., and all of those belong to the genus Canis (which also contains many other species). The name of the species is the whole binomial, not just the second term (which may be called specific name for animals).
The binomial naming convention that is used, later formalized in the biological codes of nomenclature, was first used by Leonhart Fuchs and introduced as the standard by Carolus Linnaeus in his 1758 classical work Systema Naturae 10th edition. As a result, it is sometimes called the "binomial nomenclature." At that time, the chief biological theory was that species represented independent acts of creation by God and were therefore considered objectively real and immutable.
Abbreviation
Books and articles sometimes intentionally do not identify species fully and use the abbreviation "sp." in the singular or "spp." in the plural in place of the specific epithet: for example, Canis sp. This commonly occurs in the following types of situation:
- The authors are confident that some individuals belong to a particular genus but are not sure to which exact species they belong. This is particularly common in paleontology.
- The authors use "spp." as a short way of saying that something applies to many species within a genus, but do not wish to say that it applies to all species within that genus. If scientists mean that something applies to all species with a genus, they use the genus name without the specific epithet.
In books and articles that use the genus and species names are usually printed in italics. If using "sp." and "spp.," these should not be italicized.
Difficulty of defining "species" and identifying particular species
It is surprisingly difficult to define the word "species" in a way that applies to all naturally occurring organisms, and the debate among biologists about how to define "species" and how to identify actual species is called the species problem.
Most textbooks define a species as all the individual organisms of a natural population that generally interbreed at maturity in the wild and whose interbreeding produces fertile offspring. Various parts of this definition are there to exclude some unusual or artificial matings:
- Those which occur only in captivity (when the animal's normal mating partners may not be available) or as a result of deliberate human action.
- Animals which may be physically and physiologically capable of mating but do not normally do so in the wild, for whatever reason.
- Animals whose offspring are normally sterile. For example, mules and hinnies have rarely produced further offspring (only one documented case for hinnies, and seven for mules) when mated with a creature of the same type (a mule with a mule, or a hinny with a hinny).
Living organisms
The typical textbook definition (above) works well for most multi-celled organisms, but there are several types of situations in which it breaks down:
- By definition it applies only to organisms which reproduce sexually. So it does not work for asexually reproducing single-celled organisms and for the relatively few parthenogenetic multi-celled organisms. The term "phylotype" is often applied to such organisms.
- Some hybrids, e.g., mules, hinnies, ligers and tigons, apparently cannot produce offspring when mated with one of their own kind (e.g. a mule with a mule), but sometimes do produce offspring when mated with members of one of the parent species (e.g. a liger with a lion). Usually in such hybrids the males are sterile, so one could improve the basic textbook definition by changing "... whose interbreeding produces fertile offspring" to "... whose interbreeding produces offspring in which both sexes are normally fertile".
- In ring species, members of adjacent populations interbreed successfully but members of widely-separated populations do not.
- In a few cases it may be physically impossible for animals which are members of the same species to mate, for example a Great Dane and a Chihuahua are both dogs and therefore members of the same species, but cannot mate because of the great difference in size and weight (physical build).
Horizontal gene transfer makes it even more difficult to define the word "species". There is strong evidence of horizontal gene transfer between very dissimilar groups of procaryotes, and possibly between dissimilar groups of single-celled eucaryotes; and Williamson[3] argues that there is evidence for it in some crustaceans and echinoderms. All definitions of the word "species" assume that an organism gets all its genes from one or two parents which are very like that organism, but horizontal gene transfer makes that assumption false.
Extinct organisms
Many extinct organisms are known only from fossils, which generally only preserve hard features. Fossils have not (so far) shown us what bred with what, and cannot tell us whether any resulting offspring would have been fertile. So paleontologists generally use either the morphological or the evolutionary definition of species (see below).
Paleontologists also have to cope with another difficulty: one species may gradually evolve into one or more others after a few million years; the original type of organism and the final one are so different that one could not regard the ancestors and the descendants as members of the same species if they existed at the same time; but the intermediate types are so similar to the next and previous types that one cannot say exactly where species A changed into species B. Paleontologists devised the concept of chronospecies to describe the simplest case, where at the end of the process there is only one descendant type of organism and there are no longer any individuals of the ancestral type. But even this refinement does not work in cases where several descendant types are alive at the same time or where the ancestral type and at least one descendant type are alive at the same time - and both of these situations are common in the evolution of life on Earth. Human evolution may offer a striking example: some geneticists have suggested that for about 1 million years there was some interbreeding between the early ancestors of humans and the early ancestors of chimpanzees (James Mallet and other MIT and Harvard scientists, as quoted in the news magazine This Week, June 9, 2006).
Definitions of species
The question of how best to define "species" is one that has occupied biologists for centuries, and the debate itself has become known as the species problem. One definition that is widely used is that a species is a group of actually or potentially interbreeding populations that are reproductively isolated from other such groups.[4]
The definition of a species given above is derived from the behavioral biologist Ernst Mayr, and is somewhat unrealistic. 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 (i.e. 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 reveal 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 a 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.
- Biological / reproductive species
- Two organisms that are able to reproduce naturally to produce fertile offspring. Organisms that can reproduce but almost always make infertile hybrids, such as a mule or hinny, are not considered to be the same species.
- Mate-recognition species
- A group of organisms that are known to recognize 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 (Cladistic)/ Evolutionary / Darwinian species[verification needed]
- 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. Subspecies as such are not recognized under this approach; either a population is a phylogenetic species or it is not taxonomically distinguishable.
- Ecological species
- A set of organisms adapted to a particular set of resources, called a niche, in the environment. According to this concept, populations form the discrete phenetic clusters that we recognize as species because the ecological and evolutionary processes controlling how resources are divided up tend to produce those clusters
- Genetic species
- based on similarity of DNA of individuals or populations. Techniques to compare similarity of DNA include DNA-DNA hybridization, and genetic fingerprinting (or DNA barcoding).
- Phenetic species
- based on phenotypes
- Recognition species
- based on shared reproductive systems, including mating behavior
- Microspecies
- Species that reproduce without meiosis or fertilization so that each generation is genetically identical to the previous generation. See also apomixis.
- Cohesion species
- Most inclusive population of individuals having the potential for phenotypic cohesion through intrinsic cohesion mechanisms. This is an expansion of the mate-recognition species concept to allow for post-mating isolation mechanisms; no matter whether populations can hybridize successfully, they are still distinct cohesion species if the amount of hybridization is insufficient to completely mix their respective gene pools.
- Evolutionarily Significant Unit (ESU)
- An evolutionarily significant unit is a population of organisms that is considered distinct for purposes of conservation. Often referred to as a species or a wildlife species, an ESU also has several possible definitions, which coincide with definitions of species.
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 judgment. 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 (BSC), and to a lesser extent (or for different purposes) the phylogenetic species concept (PSC). 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. Accordingly, there can be considerable conflict between alternative classifications based upon the PSC versus BSC, as they differ completely in their treatment of taxa that would be considered subspecies under the latter model (e.g., the numerous subspecies of honey bees).
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 highest taxonomic level which mostly cannot be made more or less inclusionary.
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.
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. In conservation biology, the concept of evolutionary significant units (ESU) is used, which may be define either species or smaller distinct population segments.
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 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 from 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? Second, 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 (Alpheus) 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. Many of these early delineation schemes would now be considered whimsical and these included 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 that time, it was still widely believed that there was no organic connection between species, no matter how similar they appeared. This approach also suggested a type of idealism: the notion that each species existed 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. Jean-Baptiste Lamarck, in his 1809 Zoological Philosophy, offered one of the first logical arguments against creationism. The new emphasis was on determining how a species could change over time. 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). With the acceptance of the natural selection idea of Charles Darwin in the 1860s, however, Lamarck's view of goal-oriented evolution, also known as a teleological process, was eclipsed. Recent interest in inheritance of acquired characteristics centers around epigenetic processes, e.g. methylation, that do not affect DNA sequences, but instead alter expression in an inheritable manner. Thus, neo-lamarckism, as it is sometimes termed, is not a challenge to the theory of evolution by natural selection.
Charles Darwin and Alfred Wallace provided what scientists now consider as the most powerful and compelling theory of evolution. Darwin argued that it was populations that evolved, not individuals. His argument relied on a radical shift in perspective from that of 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 that 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 it remains imperfect. 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 definition of a species.
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 to Charles Sibley's ground-breaking DNA-DNA hybridisation studies in the 1970s leading to DNA sequencing techniques. The results of these techniques 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. DNA-DNA hybridization results have led to misleading conclusions, 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 now obsolete and is replaced by more reliable computational approaches for sequence comparison. Molecular taxonomy is not directly based on the evolutionary processes, but rather on 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.
