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Sunday, March 29, 2015

Species


From Wikipedia, the free encyclopedia

Life Domain Kingdom Phylum Class Order Family Genus Species
The hierarchy of biological classification's eight major taxonomic ranks. A genus contains one or more species. Intermediate minor rankings are not shown.

In biology, a species (abbreviated sp., with the plural form species abbreviated spp.) is one of the basic units of biological classification and a taxonomic rank. A species is often defined as the largest group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, the difficulty of defining species is known as the species problem. Differing measures are often used, such as similarity of DNA, morphology, or ecological niche. Presence of specific locally adapted traits may further subdivide species into "infraspecific taxa" such as subspecies (and in botany other taxa are used, such as varieties, subvarieties, and formae).

Species hypothesized to have the same ancestors are placed in one genus, based on similarities. The similarity of species is judged based on comparison of physical attributes, and where available, their DNA sequences. All species are given a two-part name, a "binomial name", or just "binomial". The first part of a binomial is the generic name, the genus to which the species belongs. The second part is either called the specific name (a term used only in zoology) or the specific epithet (the term used in botany, which can also be used in zoology). For example, Boa constrictor is one of four species of the Boa genus. While the genus gets capitalized, the species name does not. The binomial is written in italics when printed and underlined when handwritten.

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, though other taxonomic levels such as families may be considered in broad-scale studies.[1] Extinct species known only from fossils are generally difficult to assign precise taxonomic rankings, which is why higher taxonomic levels such as families are often used for fossil-based studies.[1][2]

The total number of non-bacterial and non-archaeal species in the world has been estimated at 8.7 million,[3][4] with previous estimates ranging from two million to 100 million.[5]

History and development of the concept


John Ray

Carl Linnaeus believed in the fixity of species.

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).

John Ray (1686), an English naturalist, was the first to give a biological definition of the term species.[6]
In the 18th century Swedish scientist Carl Linnaeus classified organisms according to shared physical characteristics, and not simply based upon differences.[7] He is also established the idea of a taxonomic hierarchy of classification based upon observable characteristics and intended to reflect natural relationships.[8][9] At the time, however, it was still widely believed that there was no organic connection between species, no matter how similar they appeared. This view was influenced by European scholarly and religious education at the time, which held that the categories of life are dictated by God, in a hierarchical scheme. Although there are always differences (although sometimes minute) between individual organisms, Linnaeus strove to identify individual organisms that were exemplary of the species, and considered other non-exemplary organisms to be deviant and imperfect.[citation needed]

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. he attributed the giraffe's long neck to generations of giraffes stretching to reach the leaves of higher treetops). 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 traits will tend to be eliminated.

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 of both sexes, 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 of both sexes with a second population, and members of the second population can produce fertile offspring of both sexes with members of a third population, but members of the first and third population cannot produce fertile offspring, or can only produce fertile offspring of the homozygous sex. 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 taxonomists would disagree.[citation needed] For example, in many amphibians, most notably in New Zealand's Leiopelma frogs, the genome consists of "core" chromosomes that 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 DNA-DNA hybridization 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 SkuaGreat Skua phenomenon being a famous example.[10][11] 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.

Biologists' working definition

A usable definition of the word "species" and reliable methods of identifying particular species is 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. It is generally difficult to give precise taxonomic rankings to extinct species known only from fossils.

Some biologists may view species as statistical phenomena, as opposed to the traditional idea, with a species seen as a class of organisms. In that case, a species is defined as a separately evolving lineage that forms a single gene pool. Although properties such as DNA-sequences and morphology are used to help separate closely related lineages,[12] this definition has fuzzy boundaries.[13] However, the exact definition of the term "species" is still controversial, particularly in prokaryotes,[14] and this is called the species problem.[15] Biologists have proposed a range of more precise definitions, but the definition used is a pragmatic choice that depends on the particularities of the species of concern.[15]

Common names and species

The commonly used names for plant and animal taxa sometimes correspond to species:[16] 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 Elk (as the use in American English meaning Wapiti, not the use in British English meaning moose). The last two species were once considered a single species, illustrating how species boundaries may change with increased scientific knowledge.

Placement within genera

Ideally, a species is given a formal, scientific name, although in practice there are very many unnamed species (which have only been described, not named). When a species is named, it is placed within a genus. From a scientific point of view this can be regarded as a hypothesis that the species is more closely related to other species within its genus (if any) than to species of other genera. Species and genus are usually defined as part of a larger taxonomic hierarchy. The best-known taxonomic ranks are, in order: life, domain, kingdom, phylum, class, order, family, genus, and species. This assignment to a genus is not immutable; later a different (or the same) taxonomist may assign it to a different genus, in which case the name will also change.

In biological nomenclature, the name for a species is a two-part name (a binomial name), treated as Latin, although roots from any language can be used as well as names of locales or individuals. The generic name is listed first (with its leading letter capitalized), followed by a second term. The terminology used for the second term differs between zoological and botanical nomenclature.
  • In zoological nomenclature, the second part of the name can be called the specific name or the specific epithet. 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). For the gray wolf, the genus name is Canis, the specific name or specific epithet is lupus, and the binomen, the name of the species, is Canis lupus.
  • In botanical nomenclature, the second part of the name can only be called the specific epithet. The 'specific name' in botany is always the combination of genus name and specific epithet. For example, the species commonly known as the longleaf pine is Pinus palustris; the genus name is Pinus, the specific epithet is palustris, the specific name is Pinus palustris.
This binomial naming convention, later formalized in the biological codes of nomenclature, was first used by Leonhart Fuchs and introduced as the standard by Carolus Linnaeus in his 1753 Species Plantarum (followed by his 1758 Systema Naturae, 10th edition).

Abbreviated names

Books and articles sometimes intentionally do not identify species fully and use the abbreviation "sp." in the singular or "spp." (Species pluralis, Latin abbreviation for multiple species) in the plural in place of the specific epithet (e.g. Canis sp.) This commonly occurs in the following situations:
  • 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 within a genus, they use the genus name without the specific epithet.
Sometimes, the aforementioned plural is rendered as "sps.", which may lead to confusion with "ssp.", this one standing for subspecies instead. In books and articles, genus and species names are usually printed in italics. Abbreviations such as "sp.", "spp.", "sps.", "ssp.", "subsp.", etc. should not be italicized.[17][better source needed]

Identification codes

Various codes have been devised for identifying particular species. For example:

Difficulty defining or identifying species

It is surprisingly difficult to define the word "species" in a way that applies to all naturally occurring organisms,[21] and the debate among biologists about how to define "species" and how to identify actual species is called the species problem. Over two dozen distinct definitions of "species" are in use amongst biologists.[22][better source needed]This problem dates as early as to the writings of Charles Darwin. While Darwin wrote the following in On the Origin of Species, Chapter II:
No one definition has satisfied all naturalists; yet every naturalist knows vaguely what he means when he speaks of a species. Generally the term includes the unknown element of a distinct act of creation.[23]
He readdressed the question in The Descent of Man, specifically discussing the "question whether mankind consists of one or several species," where he revised his opinion, writing:
it is a hopeless endeavour to decide this point on sound grounds, until some definition of the term "species" is generally accepted; and the definition must not include an element that cannot possibly be ascertained, such as an act of creation.[24]
Most modern textbooks follow Ernst Mayr's definition, known as the Biological Species Concept (BSC) of a species as "groups of actually or potentially interbreeding natural populations, which are reproductively isolated from other such groups".[15] It has been argued that this definition of species is not only a useful formulation, but is also a natural consequence of the effect of sexual reproduction on the dynamics of natural selection.[25][26][27][28] (Also see Speciation.)

Various parts of this definition serve to exclude some unusual or artificial matings:[citation needed]
  • Those that as a result of deliberate human action, or occur only in captivity (when the animal's normal mating partners may not be available)
  • Those that involve animals that may be physically and physiologically capable of mating but, for various reasons, do not normally do so in the wild
The typical textbook definition above works well for most multi-celled organisms, but there are several types of situations in which it breaks down:
Among microorganisms, in particular, the problem of species identification is made difficult by discordance between molecular and morphological investigations; these can be categorized as two types: (i) one morphology, multiple lineages (e.g. morphological convergence, cryptic species) and (ii) one lineage, multiple morphologies (e.g. phenotypic plasticity, multiple life-cycle stages).[30] In addition, in these and other organisms, horizontal gene transfer (HGT) makes it difficult to define the term species.[citation needed] All species definitions assume that an organism acquires its genes from one or two parents very like the "daughter" organism, but HGT makes that assumption false.[citation needed] There is strong evidence of HGT between very dissimilar groups of prokaryotes, and at least occasionally between dissimilar groups of eukaryotes.[citation needed] Williamson argues that there is also evidence for HGT in some crustaceans and echinoderms.[31]

Definitions of species

Prior to Darwin, naturalists viewed species as ideal or general types, which could be exemplified by an ideal specimen bearing all the traits general to the species. Darwin's theories shifted attention from uniformity to variation and from the general to the particular. According to intellectual historian Louis Menand,
Once our attention is redirected to the individual, we need another way of making generalizations. We are no longer interested in the conformity of an individual to an ideal type; we are now interested in the relation of an individual to the other individuals with which it interacts. To generalize about groups of interacting individuals, we need to drop the language of types and essences, which is prescriptive (telling us what finches should be), and adopt the language of statistics and probability, which is predictive (telling us what the average finch, under specified conditions, is likely to do). Relations will be more important than categories; functions, which are variable, will be more important than purposes; transitions will be more important than boundaries; sequences will be more important than hierarchies.[32]
This shift results in a new approach to "species"; Darwin concluded that species are what they appear to be: ideas, which are provisionally useful for naming groups of interacting individuals. "I look at the term species", he wrote, "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 word variety, which is given to less distinct and more fluctuating forms. The term variety, again, in comparison with mere individual differences, is also applied arbitrarily, and for convenience sake."[32]

Practically, biologists define species as populations of organisms that have a high level of genetic similarity. This may reflect an adaptation to the same niche, and the transfer of genetic material from one individual to others, through a variety of possible means. The exact level of similarity used in such a definition is arbitrary, but this is the most common definition used for organisms that reproduce asexually (asexual reproduction), such as some plants and microorganisms.

This lack of any clear species concept in microbiology has led to some authors arguing that the term "species" is not useful when studying bacterial evolution.[who?] Instead they see genes as moving freely between even distantly related bacteria, with the entire bacterial domain being a single gene pool. Nevertheless, a kind of rule of thumb has been established, saying that species of Bacteria or Archaea with 16S rRNA gene sequences more similar than 97% to each other need to be checked by DNA-DNA Hybridization if they belong to the same species or not.[33] This concept has been updated recently, saying that the border of 97% was too low and can be raised to 98.7%.[34]

In the study of sexually reproducing organisms, where genetic material is shared through the process of reproduction, the ability of two organisms to interbreed and produce fertile offspring of both sexes is generally accepted as a simple indicator that the organisms share enough genes to be considered members of the same species. Thus a "species" is a group of interbreeding organisms.

This definition can be extended to say that a species is a group of organisms that could potentially interbreed—fish could still be classed as the same species even if they live in different lakes, as long as they could still interbreed were they ever to come into contact with each other. On the other hand, there are many examples of series of three or more distinct populations, where individuals of the population in the middle can interbreed with the populations to either side, but individuals of the populations on either side cannot interbreed. Thus, one could argue that these populations constitute a single species, or two distinct species. This is not a paradox; it is evidence that species are defined by gene frequencies, and thus have fuzzy boundaries.

Consequently, any single, universal definition of "species" is necessarily arbitrary. Instead, biologists have proposed a range of definitions; which definition a biologists uses is a pragmatic choice, depending on the particularities of that biologist's research.

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.

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).

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 or 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 four-winged Drosophila born to a 2-winged mother is not a different species). Species named in this manner are called morphospecies.[35][36]

Evolutionary species

A single evolutionary lineage of organisms within which genes can be shared, and that maintains its integrity with respect to other lineages through both time and space. At some point in the evolution of such a group, some members may diverge from the main population and evolve into a subspecies, a process that may eventually lead to the formation of a new species if isolation (geographical or ecological) is maintained. The process through which species are formed by evolution is called speciation. A species that gives rise to another species is a paraphyletic species, or paraspecies.[37]

Phylogenetic (cladistic) species

A phylogenetic or cladistic species is a group of organisms that shares an ancestor—a lineage that maintains its hereditary integrity with respect to other lineages through both time and space.[vague] At some point in the evolution of such a group, members may diverge from one another: when such a divergence becomes sufficiently clear,[vague] the two populations are regarded as separate species.[citation needed] This category of species definition differs from evolutionary species in that the parent of the phylogenetic species goes extinct taxonomically when a new species evolves; the mother and daughter populations now forming two new species.[citation needed] Subspecies as such are not recognized under this definition; either a population is a phylogenetic species or it is not taxonomically distinguishable.[citation needed]

It has been argued,[weasel words] that operation of the phylogenetic species concept (PSC) will lead to taxonomic inflation,[clarification needed] since smaller and smaller units of its population can be distinguished—even down to individuals.[citation needed] Species of bovine (i.e., cattle) for example, could be split up into any number of species based on this concept.[38]

Other species concepts

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.[39]
Reproductive species
Two organisms that are able to reproduce naturally to produce fertile offspring of both sexes. Organisms that can reproduce but almost always make infertile hybrids of at least one sex, such as a mule, hinny or F1 male cattalo are not considered to be the same species.[citation needed]
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 more problematic for organisms that do not reproduce sexually. 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.[citation needed]
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).[citation needed]

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.[citation needed]
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.[citation needed]
Phenetic species
Based on phenetics.
Microspecies
A species with very little genetic variability, usually one that reproduces by apomixis.
Recognition species
Based on shared reproductive systems, including mating behavior. The Recognition concept of species has been introduced by Hugh E. H. Paterson, after earlier work by Wilhelm Petersen.[citation needed]
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.[citation needed]

Numbers of species


An estimate of the number of some undiscovered and discovered eukaryotic species.[verification needed][citation needed]

Bearing in mind the aforementioned problems with categorizing species, the following numbers are only a guide. Based on various discussions from the first decade of the new millennium, counts can roughly be broken down as follows:[40]

Number of prokaryotic species, domain Bacteria

This number is very difficult to assess, but the discussed range varies from tens of thousands to billions;[41][42][43][44] most recent approaches and studies appear to favor the larger magnitude number.[45][46][47] Smaller numbers arise from assumptions based on a plateauing of identification of new species (which has technical explanations other than that fewer species remain to be identified).[41] Larger numbers address the fact that success in culturing bacteria has only been achieved in half of identified Bacterial phyla (where lack of success in attempts to culture a bacterial isolate limits abilities to study and delineate new species),[48] and address the difficulty of applying traditional botanic and zoologic definitions of species to asexually reproducing bacteria (where more modern sequencing and molecular approaches support higher species tallies).[43][49]

Number of prokaryotic species, domain Archaea

As a further microbial domain, the issues and difficulties of domain Bacteria also pertain to any counting of species of Archaea, all the more given their various extreme habitats. The classification of archaea into species is also controversial, as they also reproduce asexually (likewise eliminating applicability of species definitions based on interbreeding),[50] and face the same difficulties associated with organism isolation and culturing (see citations for Bacteria, above).[48][49][51] Archaebacteria have been shown to exhibit high rates of horizontal gene transfer (resulting from a bacterial cognate of sex), including between organisms quite separate based on genomic analysis.[52] As the Archaea article notes, "[c]urrent knowledge on genetic diversity is fragmentary and the total number of archaean species cannot be estimated with any accuracy" ... though like domain Bacteria, the number of cultured and studied phyla relative to the total is low (as of 2005, less than 50% of known phyla cultured).[53] Taken together, very high numbers of unique archaebacterial types are likely, as in the case of domain Bacteria.

Number of eukaryotic species

This number has historically varied from a few million to about 100 millions. However these higher numbers, which were based on the potential deep marine and arthropod diversity, are now considered unlikely. The total number of eukaryotic species is likely to be 5 ± 3 million of which about 1.5 million have been already named.[54] Some older estimates for various eukaryote phyla are:[citation needed]
At present, organisations such as the Global Taxonomy Initiative, the European Distributed Institute of Taxonomy and the Census of Marine Life (the last of these only for marine organisms) are trying to improve taxonomy and add previously undiscovered species to the taxonomy system.[60] Current knowledge covers only a portion of the organisms in the biosphere and thus does not enable a complete understanding of the workings of the environment.
Humankind is also currently wiping out undiscovered species at an unprecedented rate,[61] which means that even before a new species has had the chance of being studied and classified, it may already be extinct.

Lumping and splitting of taxa

The naming of a particular species may 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 colloquially, 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.[62][63]
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 formerly regarded as separate species are now considered 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 define either species or smaller distinct population segments. Identifying and naming species is the providence of alpha taxonomy.

Species problem


From Wikipedia, the free encyclopedia
The species problem is a mixture of difficult related questions that often come up when biologists define the word "species". Definitions are usually based on how individual organisms reproduce, but biological reality means that a definition that works well for some organisms (e.g., birds) will be useless for others (e.g., bacteria).

One common, but sometimes difficult, question is how best to decide which species an organism belongs to, because reproductively isolated groups may not be readily recognizable; cryptic species may be present.

Another common problem is how to define reproductive isolation, because some separately evolving groups may continue to interbreed to some extent, and it can be a difficult matter to discover whether this hybridization affects the long-term genetic make-up of the groups.

Many of the debates on species touch on philosophical issues, such as nominalism and realism, as well as on issues of language and cognition.

The current meaning of the phrase "species problem" is quite different from what Charles Darwin and others meant by it during the 19th and early 20th centuries.[2] For Darwin, the species problem was the question of how new species arose: speciation.

Confusion on the meaning of "Species"

Species is one of several ranks in the hierarchical system of scientific classification, called taxonomic ranks.

Even though it is not disputed that species is a taxonomic rank, this does not prevent disagreements when particular species are discussed. In the case of the Baltimore Oriole (Icterus galbula) and Bullock's Oriole (I. bullockii), two similar species of birds have sometimes in the past been considered to be one single species, the Northern Oriole (I. galbula). Currently, biologists agree that these are actually two separate species,[3] but in the past this was not the case.[4]

Disagreements and confusion happen over just what the best criteria are for identifying new species. In 1942, Ernst Mayr wrote that, because biologists have different ways of identifying species, they actually have different species concepts.[5] Mayr listed five different species concepts, and since then many more have been added.[6][7][8] The question of which species concept is best has occupied many printed pages and many hours of discussion.[9]

The debates are philosophical in nature. One common disagreement is over whether a species should be defined by the characteristics that biologists use to identify the species, or whether a species is an evolving entity in nature. Every named species has been formally described as a type of organism with particular defining characteristics. These defining traits are used to identify which species an organism belongs to. For many species, all of the individuals that fit the defining criteria also make up a single evolving unit, but it might not be known whether that is the case. These two different ways of thinking about species, as a category or as an evolving population, may be quite different from each other.

History

Before Darwin

The idea that one organism reproduces by giving birth to a similar organism, or producing seeds that grow to a similar organism, goes back to the earliest days of farming. While people tended to think of this as a relatively stable process, many thought that change was possible. The term species was just used as a term for a sort or kind of organism, until in 1686 John Ray introduced the biological concept that species were distinguished by always producing the same species, and this was fixed and permanent, though considerable variation was possible within a species.[10][11] Carolus Linnaeus (1707–1778) formalized the taxonomic rank of species, and devised the two part naming system of binomial nomenclature that we use today. However, this did not prevent disagreements on the best way to identify species.

The history of definitions of the term "species"[12][13] reveal that the seeds of the modern species debate were alive and growing long before Darwin.
"The traditional view, which was developed by Cain, Mayr and Hull in the mid-twentieth century, claims that until the ‘Origin of species’ by Charles Darwin both philosophy and biology considered species as invariable natural kinds with essential features. This ‘essentialism story’ was adopted by many authors, but questioned from the beginning by a minority … when Aristotle and the early naturalists wrote about the essences of species, they meant essential ‘functions’, not essential ‘properties’. Richards pointed out [Richard A. Richards, The Species Problem: A Philosophical Analysis, Cambridge University Press, 2010] that Linnaeus saw species as eternally fixed in his very first publication from 1735, but only a few years later he discovered hybridization as a modus for speciation.[14]

From Darwin to Mayr

Charles Darwin's famous book On the Origin of Species (1859) offered an explanation as to how species changed over time (evolution). Although Darwin did not provide details on how one species splits into two, he viewed speciation as a gradual process. If Darwin was correct, then, when new incipient species are forming, there must be a period of time when they are not yet distinct enough to be recognized as species. Darwin's theory suggested that there was often not going to be an objective fact of the matter, on whether there were one or two species.

Darwin's book triggered a crisis of uncertainty for some biologists over the objectivity of species, and some came to wonder whether individual species could be objectively real — i.e. have an existence that is independent of the human observer.[15][16]

In the 1920s and 1930s, Mendel's theory of inheritance and Darwin's theory of evolution by natural selection were joined in what was called the modern evolutionary synthesis. This conjunction of theories also had a large impact on how biologists think about species. Edward Poulton anticipated many ideas on species that today are well accepted, and that were later more fully developed by Theodosius Dobzhansky and Ernst Mayr, two of the architects of the modern synthesis.[17] Dobzhansky's 1937 book[18] articulated the genetic processes that occur when incipient species are beginning to diverge. In particular, Dobzhansky described the critical role, for the formation of new species, of the evolution of reproductive isolation.

Biological species concept

Ernst Mayr's 1942 book was a turning point for the species problem.[5] In it, he wrote about how different investigators approach species identification, and he characterized these different approaches as different species concepts. He also argued strongly for what came to be called a Biological Species Concept (BSC), which is that a species consists of populations of organisms that can reproduce with one another and that are reproductively isolated from other such populations.

Mayr was not the first to define "species" on the basis of reproductive compatibility, as Mayr makes clear in his book on the history of biology.[13] For example Mayr discusses how Buffon proposed this kind of definition of "species" in 1753.

Theodosius Dobzhansky was a close contemporary of Mayr and the author of a classic book about the evolutionary origins of reproductive barriers between species, which was published a few years before Mayr's.[18] Many biologists credit Dobzhansky and Mayr jointly for emphasizing the need to consider reproductive isolation when studying species and speciation.[19][20]

Mayr was persuasive in many respects and from 1942 until his death in 2005, both he and the Biological Species Concept played a central role in nearly all debates on the species problem. For many, the Biological Species Concept was a useful theoretical idea because it leads to a focus on the evolutionary origins of barriers to reproduction between species. But the BSC has been criticized for not being very useful for deciding when to identify new species. It is also true that there are many cases where members of different species will hybridize and produce fertile offspring when they are under confined conditions, such as in zoos. One fairly extreme example is that lions and tigers will hybridize in captivity, and at least some of the offspring have been reported to be fertile. Mayr's response to cases like these is that the reproductive barriers that are important for species are the ones that occur in the wild. But even so, it is also the case that there are many cases of different species that are known to hybridize and produce fertile offspring in nature.

After Mayr's 1942 book, many more species concepts were introduced. Some, such as the Phylogenetic Species Concept (PSC), were designed to be more useful than the BSC for actually deciding when a new species should be described. However, not all of the new species concepts were about identifying species, and some concepts were mostly conceptual or philosophical.

About two dozen species concepts have been identified or proposed since Mayr's 1942 book, and many articles and several books have been written on the species problem. At some point, it became common for articles to profess to "solve" or "dissolve" the species problem.[21][22][23][24][25][26][27]

Some have argued that the species problem is too multidimensional to be "solved" by one definition of species or one species concept.[28][29] Since the 1990s, articles have appeared that make the case that species concepts, particularly those that specify how species should be identified, have not been very helpful in resolving the species problem.[28][30][31][32][33]

Although Mayr promoted the biological species concept for use in systematics, the concept has been criticized as not being useful for those who do research in systematics. Some systematists have criticized the BSC as not being operational.[9][34][35][36] However, for many others, the BSC is the preferred description of species. For example, many geneticists who work on the process of species formation prefer the BSC because it emphasizes the role of barriers to reproduction between species.[37]

It has also been argued that the BSC, based on reproductive isolation, is not only a useful preferred description of species, but is also a natural consequence of the effect of sexual reproduction on the dynamics of natural selection.[38][39][40][41] (Also see speciation.)

Philosophical aspects

Realism and nominalism

Realism and Nominalism are philosophical subjects that come up in debates over whether species literally exist.
From one perspective, each species is a kind of organism and each species is based on a set of characteristics that are shared by all the organisms in the species. This usage of "species" refers to the taxonomic sense of the word, and under this kind of meaning a species is a category, or a type, or a natural kind. For example, the species that we call giraffe is a category of things that people have recognized have a lot in common with each other and to which we have given the name "giraffe". This is a category in the same sense that the words "mountain" and "snowflake" identify categories of things in nature.

This view of a species as a type, or natural kind, raises the question of whether such things are real. The question is not whether the organisms exist, but whether the kinds of organisms exist. There is a school of philosophical thought, called realism that says that natural kinds and other so called universals do exist. But what kind of existence would this be? It is one thing to say that a particular giraffe exists, but in what way does the giraffe category exist? This question is the opening for Nominalism which is a philosophical view that types and kinds, and universals in general, do not literally exist.

If the nominalist view is correct, then kinds of things that people have given names to, do not literally exist. It would then follow that species do not literally exist, because species are named types of organisms. This can be a troubling idea, particularly to a biologist who studies species. If species are not real, then it would not be sensible to talk about "the origin of a species" or the "evolution of a species". As recently at least as the 1950s, some authors adopted this view and wrote of species as not being real.[42][43]

A useful counterpoint to the nominalist view, in regard to species, was raised by Michael Ghiselin who argued that an individual species is not a type, but rather an actual individual, an actual entity.[22][44] This idea comes from thinking of a species as an evolving dynamic population. As an entity, a species exists quite regardless of whether or not people have observed it and whether or not it has been given a name based on traits shared by the organisms in the species.

Language and the role of human investigators

The nominalist critique of the view that kinds of things exist, raises for consideration the role that humans play in the species problem. For example, Haldane suggested that species are just mental abstractions.[45]

Several authors have noted the similarity between "species", as a word of ambiguous meaning, and points made by Wittgenstein on family resemblance concepts and the indeterminacy of language.[21][46][47]

Jody Hey described the species problem as a result of two conflicting motivations by biologists:[28][48]
  1. to categorize and identify organisms;
  2. to understand the evolutionary processes that give rise to species.
Under the first view, species appear to us as typical natural kinds, but when biologists turn to understand species evolutionarily they are revealed as changeable and without sharp boundaries. Hey argued that it is unrealistic to expect that one definition of "species" is going to serve the need for categorization and still reflect the changeable realities of evolving species.

Pluralism and monism

Usually, it is assumed that biologists approach the species problem with the idea that it would be useful to develop one common viewpoint of species – one single common conception of what species are and of how they should be identified. It is thought that, if such a monistic description of species could be developed and agreed upon, then the species problem would be solved.

In contrast, some authors have argued for pluralism, claiming that biologists cannot have just one shared concept of species, and that they should accept multiple, seemingly incompatible ideas about species.[49][50][51]

David Hull argued that pluralist proposals were unlikely to actually solve the species problem.[33]

Quotations on the species problem

"... I was much struck how entirely vague and arbitrary is the distinction between species and varieties" Darwin 1859 (p. 48)[1]

"No term is more difficult to define than "species," and on no point are zoologists more divided than as to what should be understood by this word". Nicholson (1872) p. 20[52]

"Of late, the futility of attempts to find a universally valid criterion for distinguishing species has come to be fairly generally, if reluctantly, recognized" Dobzhansky (1937) p. 310[18]

"The concept of a species is a concession to our linguistic habits and neurological mechanisms" Haldane (1956)[45]

"The species problem is the long-standing failure of biologists to agree on how we should identify species and how we should define the word 'species'." Hey (2001)[48]

"First, the species problem is not primarily an empirical one, but it is rather fraught with philosophical questions that require - but cannot be settled by - empirical evidence." Pigliucci (2003)[21]

"An important aspect of any species definition whether in neontology or palaeontology is that any statement that particular individuals (or fragmentary specimens) belong to a certain species is an hypothesis (not a fact)"[53]

"We show that although discrete phenotypic clusters exist in most [plant] genera (>80%), the correspondence of taxonomic species to these clusters is poor (<60%) and no different between plants and animals. ... Contrary to conventional wisdom, plant species are more likely than animal species to represent reproductively independent lineages."[54]

Introduction to entropy

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