Introduction to genetics

From Wikipedia, the free encyclopedia

Genetics is the study of genes — what they are and how they work. Genes are units inside a cell that control how living organisms inherit features from their ancestors; for example, children usually look like their parents because they have inherited their parents' genes. Genetics tries to identify which features are inherited, and explain how these features pass from generation to generation.

In genetics, a feature of a living thing is called a "phenotypic trait", or simply "trait". Some traits are part of an organism's morphology, its form and structure; such as a person's eye-color, height or weight. Other sorts of traits are not easily seen and include blood types or resistance to diseases. The way our genes and environment interact to produce a trait can be complicated. For example, the general design of a tiger's stripes is inherited, whereas the actual stripe pattern on an individual tiger is influenced by environmental factors that are difficult to determine.

Genes are made from a long molecule called DNA, which is copied and inherited across generations. DNA is made of nucleotide, simple units that line up in a particular order within this long molecule. The order of these units carries genetic information, similar to how the order of letters on a page of text carries information. The language used by DNA is called the genetic code, which allows the genetic machinery to read the information in the genes in triplet sets of codons. This information is the instructions for constructing and operating a living organism.

The information within a particular gene is not always exactly the same between one organism and another, so different copies of a gene do not always give exactly the same instructions. Each unique form of a single gene is called an allele. As an example, one allele for the gene for hair color could instruct the body to produce a lot of pigment, producing black hair, while a different allele of the same gene might give garbled instructions that fail to produce any pigment, giving white hair. Mutations are random changes in genes, and can create new alleles. Mutations can also produce new traits, such as when mutations to an allele for black hair produce a new allele for white hair. This appearance of new traits is important in evolution.

Inheritance in biology

Genes and inheritance

A section of DNA; the sequence of the plate-like units (nucleotides) in the center carries information.

Red hair is a recessive trait.

Genes are pieces of DNA that contain information for synthesis of ribonuceic acids(RNAs) or polypeptides. Genes are inherited as units, with two parents dividing out copies of their genes to their offspring. This process can be compared with mixing two hands of cards, shuffling them, and then dealing them out again. Humans have two copies of each of their genes, and make copies that are found in eggs or sperm—but they only include one copy of each type of gene. An egg and sperm join to form a complete set of genes. The eventually resulting child has the same number of genes as their parents, but for any gene one of their two copies comes from their father, and one from their mother.^[1]

The effects of this mixing depend on the types (the alleles) of the gene. If the father has two copies of an allele for red hair, and the mother has two copies for brown hair, all their children get the two alleles that give different instructions, one for red hair and one for brown. The hair color of these children depends on how these alleles work together. If one allele overrides the instructions from another, it is called the dominant allele, and the allele that is overridden is called the recessive allele. In the case of a daughter with alleles for both red and brown hair, brown is dominant and she ends up with brown hair.^[2]

Although the red color allele is still there in this brown-haired girl, it doesn't show. This is a difference between what you see on the surface (the traits of an organism, called its phenotype) and the genes within the organism (its genotype). In this example you can call the allele for brown "B" and the allele for red "b". (It is normal to write dominant alleles with capital letters and recessive ones with lower-case letters.) The brown hair daughter has the "brown hair phenotype" but her genotype is Bb, with one copy of the B allele, and one of the b allele.

Now imagine that this woman grows up and has children with a brown hair man who also has a Bb genotype. Her eggs will be a mixture of two types, one sort containing the B allele, and one sort the b allele. Similarly, her partner will produce a mix of two types of sperm containing one or the other of these two alleles. When the transmitted genes are joined up in their offspring, these children have a chance of getting either brown or red hair, since they could get a genotype of BB = brown hair, Bb = brown hair or bb = red hair. In this generation, there is therefore a chance of the recessive allele showing itself in the phenotype of the children - some of them may have red hair like their grandfather.^[2]

Many traits are inherited in a more complicated way than the example above. This can happen when there are several genes involved, each contributing a small part to the end result. Tall people tend to have tall children because their children get a package of many alleles that each contribute a bit to how much they grow. However, there are not clear groups of "short people" and "tall people", like there are groups of people with brown or red hair. This is because of the large number of genes involved; this makes the trait very variable and people are of many different heights.^[3] Despite a common misconception, the green/blue eye traits are also inherited in this complex inheritance model.^[4] Inheritance can also be complicated when the trait depends on interaction between genetics and environment. For example, malnutrition does not change traits like eye color, but can stunt growth.^[5]

Inherited diseases

Some diseases are hereditary and run in families; others, such as infectious diseases, are caused by the environment. Other diseases come from a combination of genes and the environment.^[6] Genetic disorders are diseases that are caused by a single allele of a gene and are inherited in families. These include Huntington's disease, Cystic fibrosis or Duchenne muscular dystrophy. Cystic fibrosis, for example, is caused by mutations in a single gene called CFTR and is inherited as a recessive trait.^[7]

Other diseases are influenced by genetics, but the genes a person gets from their parents only change their risk of getting a disease. Most of these diseases are inherited in a complex way, with either multiple genes involved, or coming from both genes and the environment. As an example, the risk of breast cancer is 50 times higher in the families most at risk, compared to the families least at risk. This variation is probably due to a large number of alleles, each changing the risk a little bit.^[8] Several of the genes have been identified, such as BRCA1 and BRCA2, but not all of them. However, although some of the risk is genetic, the risk of this cancer is also increased by being overweight, drinking a lot of alcohol and not exercising.^[9] A woman's risk of breast cancer therefore comes from a large number of alleles interacting with her environment, so it is very hard to predict.

How genes work

Genes make proteins

The function of genes is to provide the information needed to make molecules called proteins in cells.^[1] Cells are the smallest independent parts of organisms: the human body contains about 100 trillion cells, while very small organisms like bacteria are just one single cell. A cell is like a miniature and very complex factory that can make all the parts needed to produce a copy of itself, which happens when cells divide. There is a simple division of labor in cells - genes give instructions and proteins carry out these instructions, tasks like building a new copy of a cell, or repairing damage.^[10] Each type of protein is a specialist that only does one job, so if a cell needs to do something new, it must make a new protein to do this job. Similarly, if a cell needs to do something faster or slower than before, it makes more or less of the protein responsible. Genes tell cells what to do by telling them which proteins to make and in what amounts.

Genes are expressed by being transcribed into RNA, and this RNA then translated into protein.

Proteins are made of a chain of 20 different types of amino acid molecules. This chain folds up into a compact shape, rather like an untidy ball of string. The shape of the protein is determined by the sequence of amino acids along its chain and it is this shape that, in turn, determines what the protein does.^[10] For example, some proteins have parts of their surface that perfectly match the shape of another molecule, allowing the protein to bind to this molecule very tightly. Other proteins are enzymes, which are like tiny machines that alter other molecules.^[11]

The information in DNA is held in the sequence of the repeating units along the DNA chain.^[12] These units are four types of nucleotides (A,T,G and C) and the sequence of nucleotides stores information in an alphabet called the genetic code. When a gene is read by a cell the DNA sequence is copied into a very similar molecule called RNA (this process is called transcription). Transcription is controlled by other DNA sequences (such as promoters), which show a cell where genes are, and control how often they are copied. The RNA copy made from a gene is then fed through a structure called a ribosome, which translates the sequence of nucleotides in the RNA into the correct sequence of amino acids and joins these amino acids together to make a complete protein chain. The new protein then folds up into its active form. The process of moving information from the language of RNA into the language of amino acids is called translation.^[13]

DNA replication. DNA is unwound and nucleotides are matched to make two new strands.

If the sequence of the nucleotides in a gene changes, the sequence of the amino acids in the protein it produces may also change - if part of a gene is deleted, the protein produced is shorter and may not work any more.^[10] This is the reason why different alleles of a gene can have different effects in an organism. As an example, hair color depends on how much of a dark substance called melanin is put into the hair as it grows. If a person has a normal set of the genes involved in making melanin, they make all the proteins needed and they grow dark hair. However, if the alleles for a particular protein have different sequences and produce proteins that can't do their jobs, no melanin is produced and the person has white skin and hair (albinism).^[14]

Genes are copied

Genes are copied each time a cell divides into two new cells. The process that copies DNA is called DNA replication.^[12] It is through a similar process that a child inherits genes from its parents, when a copy from the mother is mixed with a copy from the father.
DNA can be copied very easily and accurately because each piece of DNA can direct the creation of a new copy of its information. This is because DNA is made of two strands that pair together like the two sides of a zipper. The nucleotides are in the center, like the teeth in the zipper, and pair up to hold the two strands together. Importantly, the four different sorts of nucleotides are different shapes, so for the strands to close up properly, an A nucleotide must go opposite a T nucleotide, and a G opposite a C. This exact pairing is called base pairing.^[12]

When DNA is copied, the two strands of the old DNA are pulled apart by enzymes; then they pair up with new nucleotides and then close. This produces two new pieces of DNA, each containing one strand from the old DNA and one newly made strand. This process is not predictably perfect as proteins attach to a nucleotide while they are building and cause a change in the sequence of that gene. These changes in DNA sequence are called mutations.^[15] Mutations produce new alleles of genes. Sometimes these changes stop the functioning of that gene or make it serve another advantageous function, such as the melanin genes discussed above. These mutations and their effects on the traits of organisms are one of the causes of evolution.^[16]

Genes and evolution

Mice with different coat colors.

A population of organisms evolves when an inherited trait becomes more common or less common over time.^[16] For instance, all the mice living on an island would be a single population of mice. If over a few generations, white mice went from being rare, to being a large part of this population, then the coat color of these mice would be evolving. In terms of genetics, this is called a change in allele frequency—such as an increase in the frequency of the allele for white fur.

Alleles become more or less common either just by chance (in a process called genetic drift), or through natural selection.^[17] In natural selection, if an allele makes it more likely for an organism to survive and reproduce, then over time this allele becomes more common. But if an allele is harmful, natural selection makes it less common. For example, if the island was getting colder each year and was covered with snow for much of the time, then the allele for white fur would become useful for the mice, since it would make them harder to see against the snow. Fewer of the white mice would be eaten by predators, so over time white mice would out-compete mice with dark fur. White fur alleles would become more common, and dark fur alleles would become more rare.

Mutations create new alleles. These alleles have new DNA sequences and can produce proteins with new properties.^[18] So if an island was populated entirely by black mice, mutations could happen creating alleles for white fur. The combination of mutations creating new alleles at random, and natural selection picking out those that are useful, causes adaptation. This is when organisms change in ways that help them to survive and reproduce.

Genetic engineering

Since traits come from the genes in a cell, putting a new piece of DNA into a cell can produce a new trait. This is how genetic engineering works. For example, rice can be given genes from a maize and a soil bacteria so the rice produces beta-carotene, which the body converts to Vitamin A.^[19] This can help children suffering from Vitamin A deficiency. Another gene being put into some crops comes from the bacterium Bacillus thuringiensis; the gene makes a protein that is an insecticide. The insecticide kills insects that eat the plants, but is harmless to people.^[20] In these plants, the new genes are put into the plant before it is grown, so the genes are in every part of the plant, including its seeds.^[21] The plant's offspring inherit the new genes, which has led to concern about the spread of new traits into wild plants.^[22]
The kind of technology used in genetic engineering is also being developed to treat people with genetic disorders in an experimental medical technique called gene therapy.^[23] However, here the new gene is put in after the person has grown up and become ill, so any new gene is not inherited by their children. Gene therapy works by trying to replace the allele that causes the disease with an allele that works properly.

Species

From Wikipedia, the free encyclopedia

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 Skua – Great 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:

• National Center for Biotechnology Information (NCBI) employs a numeric 'taxid' or Taxonomy identifier, a "stable unique identifier", e.g. the taxid of H. sapiens is 9606.^[18]
• Kyoto Encyclopedia of Genes and Genomes (KEGG) employs a three- or four-letter code for a limited number of organisms; in this code, for example, H. sapiens is simply hsa.^[19]
• UniProt employs an "organism mnemonic" of not more than five alphanumeric characters, e.g. HUMAN for H. sapiens.^[20]
• Integrated Taxonomic Information System (ITIS) provides a unique number for each species.

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:

• By definition it applies only to organisms that reproduce sexually. So it does not work for asexually reproducing single-celled organisms and for the relatively few parthenogenetic or apomictic multi-celled organisms.^[29] The term "phylotype" is often applied to such organisms.
• Biologists frequently do not know whether two morphologically similar groups of organisms are "potentially" capable of interbreeding.^{[citation needed]}
• There is considerable variation in the degree to which hybridization may succeed under natural conditions, or even in the degree to which some organisms use sexual reproduction between individuals to breed.^{[citation needed]}
• In ring species, members of adjacent populations interbreed successfully but members of some non-adjacent populations do not.^{[ambiguous][citation needed]}

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]}

• As many as 1.5 million fungi^[55]
• 3,067 brown algae
• 17,000 lichens
• 321,212 plants, including:
  • 10,134 red and green algae
  • 16,236 mosses
  • 12,000 ferns and horsetails
  • 1,021 gymnosperms
  • 281,821 angiosperms
• 1,367,555 non-insect animals, including:
  • 1,305,250 invertebrates
    • 2,175 corals
    • 85,000 mollusks
    • As many as 1.1 million arachnids, including ~1 million mites and ~100,000 other arachnids^[56]
    • 47,000 crustaceans
    • 68,827 other invertebrates
  • 63,649 vertebrates
    • 31,300 fish
    • 7,093 amphibians^[57]
    • 9,768 reptiles^[58]
    • 9,998 birds
    • 5,490 mammals
• As many as 10–30 million insects^[59]

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.