Here are some definitions I put together. These are referenced from various articles on this site. These are brief explanations of some biological terms that were nevertheless too long to add to the articles without interrupting their flow.

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  • Allele
  • Single Nucleotide Polymorphism
  • Phylogenetics
  • Speciation

Allele

A snippet of DNA at a specified locus on a chromosome. Usually, the snippet of DNA equals one gene, but not always (people are now talking about alleles in junk DNA, where there are no genes that normally express themselves). Diploid organisms have paired homologous chromosomes; therefore each chromosome of the pair has a version of each allele. These versions may be identical, or different. When identical, the individual is homozygous, otherwise the individual is heterozygous.

Alleles may often be dominant or recessive, which refers to whether or not they express their traits in the phenotype. A dominant allele will always express itself in the phenotype, whereas a recessive allele will only express if no dominant allele is present (two recessive alleles present instead). However, many alleles are neither dominant or recessive. They can be incompletely dominant (traits of both alleles are blended, also known as blended inheritance), such as when crossing Antirrhinums — flowers with incompletely dominant red and white alleles for petal color — the resulting offspring have pink petals. Or they may be co-dominant, such as A and B human blood types, each of which is expressed, resulting in an AB blood type.

Note that it is not necessary that all genes will only have two possible alleles. For example, in human blood types there are 3 possible alleles: A, B, and i. Type A produces antigen A, type B produces antigen B, and type i does not produce any antigen at all, leading to condition O. This is why they are known as ABO blood types. While multiple alleles of a gene may exist in the wild (in a given population), any particular individual can only have 2 alleles since there are only 2 homologous chromosomes for a diploid organism. The alleles in any individual determine his phenotype, given the caveats that alleles can be dominant, co-dominant, incompletely dominant, or recessive. Also, not all traits are controlled by a specific gene. Some traits can be controlled by more than a single gene (therefore by more than 2 alleles). Such traits are called polygenic.

Relationship of alleles to phenotype in human blood groups
Allele 1
Allele 2
Genotype
Phenotype
A
A
AA
A
A
B
AB
AB
A
i
Ai
A
B
A
BA
AB
B
B
BB
B
B
i
Bi
B
i
A
iA
A
i
B
iB
B
i
i
ii
O

Note that there are 9 possible permutations of alleles, which lead to 6 possible genotypes (Ai = iA, Bi = iB, AB = BA) and 4 possible phenotypes (AA = A, BB = B).

Single Nucleotide Polymorphism

A Single Nucleotide Polymorphism, or SNP, is the variation of a single nucleotide pair (A-T replaced with C-G, or vice versa) within a defined DNA snippet. This DNA snippet might be a gene (both in coding and non-coding regions of the gene), or a non-gene (intergenic) part of the chromosome. As such, an SNP creates alleles. Most SNPs only have two versions of the allele, one with A-G and the other with C-T at the specified location.

Even SNPs within the coding region of a gene don’t necessarily create differences in the amino acids coded, because of the degeneracy of the genetic code. An SNP in which the amino acid is not changed is called synonymous, while an SNP in which the amino acid is changed as a result of the SNP is called non-synonymous. SNPs not in protein-coding regions may still have consequences for gene splicing, transcription factor binding, or the sequence of non-coding RNA.

SNPs are important in the study of population genetics. The minor allele frequency is the ratio of chromosomes in the population carrying the less common variant to those with the more common variant. Therefore, by definition it is always less than one (though some people now express them as a percentage instead). Since populations differ, the minor allele frequency can only be stated for a defined population.

Phylogenetics

There are probably somewhere between 5 million and 100 million species on Earth, of which about 1.75 million have been identified. Of these, only about 60 or 70,000 have been studied in any detail. Classifying these organisms into related groups is the field of taxonomy. Typically, organisms are classified into groups which form a tree-like structure, with broad divisions at the bottom (towards the trunk), branching into increasingly finer divisions towards the top. These divisions, or “ranks” thus follow a hierarchy, for example, the table on the right.

Taxonomic Classification of Humans
Domain Eukarya
Kingdom Animalia
Phylum Chordata
Class Mammalia
Order Primates
Family Hominidae
Genus Homo
Species H. sapiens

This is a “reversed” tree, with the trunk (the broadest groups) on top, and the progressively finer detailed branches as we go downwards. Various biology texts use either the top-down or the bottom-up representation; it doesn’t matter which is used, so long as it’s clear that one end represents the broadest divisions of life, while the other end narrows towards progressively finer sub-divisions.

The full biological name for a species consists of genus and species, for example, Homo sapiens. Because each name consists of two parts (genus and species), it is called binomial nomenclature. This nomenclature was first proposed by Carl Linnaeus in the early 18th century.

The taxonomy proposed by Carl Linnaeus and other biologists until very recently was based on appearance and ease of classification. “Ease of classification” in this case means using information that is readily available by looking at a specimen, such as morphology (the general size and shape of the organism) and anatomy (the internal structure of the organism). So, for example, you could form a category for “animals that walk on two hind legs and who have the two forelegs adapted into wings”, or birds.

Information about behavior or habits can also be used, for example carnivora or herbivora, depending on their dietary preference. In fact, almost any feature that differentiates one group from another can be used as a basis for biological classification, such as number of legs, warm blooded or cold blooded, egg laying or giving live birth, etc.

Because of the immense variation possible in this classification system, we end up with some very mixed categories. For example, cats, cows and crocodiles all belong to the category of “4 legged animals”. But cats and crocodiles are carnivores while cows are herbivores. So it would seem that “4 legged animals” is a broader group, which could be subdivided into “meat eating” (cats and crocs) and “plant eating” (cows). But cats and cows are warm blooded, while crocs are not, so now we have another category that groups dissimilar animals (herbivores and carnivores) into a single category “warm blooded”, while excluding crocs, who also have four legs.

In fact, this sort of mix-up: this and that plus this other, except that one” is pretty much the norm in taxonomy, which makes such divisions very complicated. Biologists have been trying to simplify them for centuries, by moving various species, genera, families, orders, etc. from one place on the tree to another, to minimize these sort of complications. The goal has been to find a system that:

  • is consistent and makes biological sense, that is, uses some fundamental biological property to classify organisms instead of by mixing and matching traits that themselves vary across the taxonomic tree (for example, dividing by warm/cold bloodedness on one branch of the tree, dividing by the presence/absence of feathers and wings on another branch)
  • does not contain exclusions and exceptions, for example “all animals having X, Y and Z traits belong to group A, except for this group of animals who have X, Y and Z traits, but we’ve decided not to group them with A for other reasons”.

Phylogenetics is one approach to classification that tries to do these two things. Phylogenetics classifies life based on evolutionary relationships. The consistent, unifying theme is evolution, or more particularly, how a given life form traces its ancestry from earlier life forms. Any two subdivisions are related by having a common ancestor. The closer the common ancestor, the more related they are. This is a very simple concept, very similar to how we understand being “related” in families. We are closely related to our siblings because we share a close common ancestor (our parents). We are less closely related to first cousins, because the common ancestor is farther back (our grandparents).

As the figure above shows, phylogenetics is very much like relationships between a family, except that it is not at the level of organisms, but rather at the level of groups of organisms. This is a very important distinction, and must be understood to make sense of the figure above.

The basic unit of a phylogenetic scheme is not an individual, but rather a group of individuals capable of interbreeding with each other – that is, a species. This may consist of thousands or millions of individuals. Phylogeny is based on tracing evolutionary relationships between species, which mean tracing back their ancestry to the last common ancestor. If the common ancestor is close to them in time, then the species are closely related. If the common ancestor is further back in time (meaning each species has separate lines of intermediate ancestral species, which ultimately converge at a common ancestor far back in time), then they are less closely related.

For example, there are two species of chimpanzees – the common chimpanzee (Pan troglodytes) and the bonobo (Pan paniscus). They share a common ancestor at the genus level, about 2.9 million years ago. This means that there existed some species 2.9 million years ago, whose progeny include both the common chimpanzee and the bonobo. Both these species belong to the same genus – Pan. On the other hand, chimpanzees share a common ancestor with humans about 6.4 million years ago. Again, this means that 6.4 million years ago there lived some species, whose progeny include humans, common chimpanzees and bonobos. This more distant relationship is past the level of genus, as humans (genus Homo) and chimpanzees (genus Pan) belong to different genera. Going back further, chimpanzees share a common ancestor with gorillas about 8.8 million years ago. There was some species that existed 8.8 million years ago, whose descendents include common chimpanzees, bonobos, humans, and at least 2 species of gorillas. At this point we are talking about the common ancestor of 3 different genera: PanHomo and Gorilla. These are united by the subfamily Homininae. Note that the classification system in the earlier table (species – genus – family – order – class) is much simplified, and there can be many additional divisions in between, by adding prefixes such as sub or infra or super, for example subfamily, superfamily, infraorder, etc.

Going back further, the last common ancestor between chimpanzees and orangutans was a species that lived about 15.7 million years ago. This common ancestor includes among its descendents everything listed above (common chimpanzees, humans, 2 species of gorilla) plus orangutans (genus Pongo, which consists of at least 2 species of orangutan). This is the level of family, according to the taxonomic scheme described above, and the name of this family is Hominidae.

In a similar fashion, we could widen the base of this tree, including more members, by going back further in time. At 20.4 million years we’d find a common ancestor to include gibbons into our collection. About 29.2 million years ago, we’d find a common ancestor with old world monkeys. We’re now at the superfamily level: Cercopithecoidea. We’d have to go back about 43 million years to find a common ancestor with new world monkeys. This would be the last common ancestor of all current and extinct monkeys and apes. We can go back further to about 65 million years to find a common ancestor with tarsiers, and about 75 million years to also include lemurs and lorises (tarsiers, lemurs and lorises are known as prosimians). This would bring us to the level of Order, which in this case is Primates.

Note that these dates of last common ancestors (dates of divergence) are approximate. Various kinds of evidence are used to deduce them. The oldest known primate from fossil evidence is Plesiadapis, which is only about 55 – 58 million years old. On the other hand, molecular genetics (based on calculations made from the degree of similarity of DNA) indicate that the primate tree first appeared about 85 million years ago. Of course, since the last common ancestor of all known primates is only about 75 million years old, it’s possible that other types of primates (aside from the prosimians, monkeys, apes and humans listed in the geneology above) branched off earlier, and are unknown to us. New fossil evidence will help us refine these estimates.

The purpose of this discussion was to show a new method of classification – phylogenetics – which is not based on variables such as who eats what, whether they fly or walk or crawl — but rather on evolutionary relationships between organisms, traced by common descent. Taxonomy is always in a state of flux, as old relationships are re-evaluated and re-sorted in ways that make more sense. However, because of the advent of phylogenetics, which is largely based on DNA sequencing, many of the old taxonomic divisions have become especially confusing.

Ideally, we would like to retain some of the old names and classifications, because many biologists are familiar with them, and also because they do in fact often show evolutionary relationships. In evolutionary terms, changes are relatively slow to happen, so if a group of organisms were previously categorized by certain anatomical/morphological similarities, the chances are good that these similarities have a close evolutionary origin. Similar structure often implies a close evolutionary relationship, but not always, as homologous structures can also evolve independently.

Cladistics

Cladistics is the chief methodology of phylogenetics – the classification of organisms into clades. A clade is simply a species, together with all species descended from it, whether living or extinct. It is simply a branch of the evolutionary tree. In its simplest form, it consists of two related species and their common ancestral species, for example, common chimpanzees plus bonobos plus their common ancestral species that lived 2.9 million years ago, plus any of its other descendents who are now extinct. The root of the clade is that common ancestral species from 2.9 million years ago, which gave rise to two existing species (common chimps and bonobos), plus any other species it may have produced that are now extinct.

Just like a real tree, you can pick a branch near the very tip, close to the leaves. Or you can pick a branch closer to the trunk, which subdivides into many other branches. So you could pick the last common ancestor of all primates, and its descendents would include all prosimians, monkeys, apes and humans, whether living or extinct. This is also a clade.

Cladistic

 

Clades can be nested inside other clades. For example, the clade consisting of the two species of chimpanzees plus their common ancestor can be nested inside the larger clade consisting of all species of humans (living and extinct) plus chimpanzees (living or extinct), plus the common ancestor of humans and chimpanzees. This clade in turn, can be nested inside the larger clade consisting of chimpanzees, humans and gorillas, plus their common ancestor. A clade is said to be basal to another clade if it contains the other clade as a subset within it.

In this sense, it is much like regular taxonomy, with its genera and families and orders. However, it’s based strictly on evolutionary relationships so it includes all descendents of a common ancestor (unlike regular taxonomy, which might exclude some descendents), and it doesn’t include anything not descended from that common ancestor (again unlike regular taxonomy, which might group together species not descended from a common ancestor).

Grouping organisms in this way so that all organisms in a group share the same last common ancestor is the ideal situation that biologists strive towards. However, this is not always possible. Because of uncertainty in evolutionary relationships and because of prior nomenclature which is still extensively in use, such grouping is not always possible. Uncertainty in evolutionary relationships comes from the fact that such relationships are usually determined by DNA sequencing, and only a tiny fraction of all species have been sequenced so far. Also, many species are extinct and their DNA is no longer available for sequencing. In such cases, they have to be classified based on the features of their fossil remains, where evolutionary relationships are not so clear.

So in practice, phylogenetic groups can be of several kinds, as seen in the diagram below.

phylogenetic groups

 

Monophyletic

A group derived from a common ancestor, which includes all species derived from that common ancestor and no species not derived from it. This group would constitute a clade, and is the basis for cladistics. The group with the brown fill in the figure above is monophyletic, including the last common ancestor for reptiles, with all of its descendents – testudines (turtles and tortoises), lepidosauria (all scaled reptiles such as lizards and snakes), crocodilia (all crocodiles, alligators, etc.), and aves (all birds). This includes all extinct species belonging to these subgroups as well, such as dinosaurs, mososaurs, pterosaurs, plesiosaurs, etc., which are part of the subfamily Diapsida.

Paraphyletic

A group derived from a common ancestor, which only includes species derived from that ancestor, but does not include all species derived from that ancestor. In effect, you start from one clade and include some subclades within it, but not all. This is shown in the diagram above enclosed in the bluish background. It’s identical to the monophyletic group above, except that is doesn’t include aves, or birds. The traditional classification does not include birds among the reptiles. This is therefore a paraphyletic group, which is monophyletic minus one clade.

There are many such paraphyletic groups. For example, the traditional term “apes” includes lesser apes (gibbons) plus greater apes (orangutans, gorillas and chimpanzees). However, it excludes humans. But if you look at this cladistically, the common ancestor of all apes was also the ancestor of humans, therefore lesser apes, greater apes and humans form a monophyletic group, or a clade. By excluding humans, the group has now become paraphyletic. The reasons for such exclusions usually have to do with traditional classifications, in this case the broad classification of primates into prosimians, new world monkeys, old world monkeys, lesser apes, greater apes, humans — in order of evolutionary distance from humans.

Polyphyletic

So far, these groups have included certains species plus their last common ancestor – monophyletic (ancestor species plus everything descended from it) and paraphyletic (ancestor species plus some species descended from it but not all). In contrast, a polyphyletic group does not include the common ancestor.

For example, in the diagram above, the group of warm blooded animals includes birds and mammals, and is a polyphyletic group. Their common ancestor belongs to the clade Amniota, in the superclass Tetrapoda (tetrapoda = vertebrates with four limbs, amniota = those tetrapods which evolved to lay eggs on land, with hard shells and other modifications that allowed the eggs to survive on land). This common ancestor of birds and mammals was not warm blooded, and was neither bird nor mammal. This is therefore a polyphyletic group, consisting of the clade of birds plus the clade of mammals. Warm bloodness in birds and mammals does not share an evolutionary origin, they did not both evolve from some warm blooded ancestor. Instead, warm bloodedness evolved separately in both clades – an example of convergent evolution.

Some final thoughts on phylogenetics

Taxonomy is an ongoing process. Species are subject to re-classification, as new data comes in and evolutionary relationships are better understood. Some of the most important data comes from DNA sequencing, which is generally considered more objective than trying to deduce relationships based on physical similarities and differences. As more species are sequenced, new clades will be added and old ones refined. In this process, species are often moved from one group to another, because it turns out that the superficial resemblance that prompted the original classification was accidental, and not related to evolutionary origin.

In this context, the following terms are used to describe the traits being compared:

Plesiomorphy

This term is used for an ancestral trait, present at the base of the tree, inherited from a common ancestor. This trait is not necessarily present in all descendents of that ancestor – some descendents may retain it, while others may lose it. For example, the common ancestor of birds and reptiles was cold blooded – so cold bloodedness is a plesiomorphic trait, inherited from the common ancestor. Some of the descendents have retained it (lizards, snakes, etc.), while others have lost it (birds). More generally, consider an ancestral species with a certain trait. This trait is retained in some of it descendents – groups A, C, D and F, while it is lost in descendents in groups B and E. Note that all groups, A to F are descended from the same ancestor.

The significance of this is that such plesiomorphic traits can’t be used to define evolutionary relationships between members of the same clade. So we shouldn’t separate out groups A,C,D and F into one subclade, and B and E into another subclade. Why not? Remember, cladistics means organizing groups of species by common descent. So if we observe that groups A, C, D and F have retained the trait in question, and on that basis put them in a separate subclade from groups B and E, we have in fact stated our belief that groups A,C,D and F had an ancestor in common which was not the ancestor of groups B and E. But this is probably wrong, since the trait in question is ancestral to all the groups, and therefore lineages that keep it or lose it may do so for completely unrelated reasons, not common ancestry.

In general, any trait that is ancestral to a clade (plesiomorphic to it) should not be used to form subclades within that clade.

Apomorphy

In contrast to plesiomorphies, an apomorphy is a trait that developed within a clade, and is not inherited from the common ancestor. As such, it can be used to distinguish subclades within the clade. For example, in the clade vertebrates, some vertebrates developed four limbs. These four limbed vertebrates can therefore be grouped together into the subclade TetrapodaAll tetropods have four limbs, and only tetrapods among all vertebrates have four limbs.

When an apomorphy is shared within a group, it’s called a synapomorphy within the group – a shared trait for the group.

Homoplasy

This is the reverse of plesiomorphy. A plesiomorphic trait is one present in the ancestral species. A homoplasy, on the other hand, is a trait shared by certain groups of descendents, but not present in the ancestor. To use the same example, warm bloodedness is a homoplasy. It was not present in the common ancestor of birds and mammals. So it must have evolved independently.

Homoplasies should not be used to group organisms. Thus “warm blooded animal” may be a useful term at times, but it has no place in taxonomy.

All of these terms are relative to an organism’s position within a clade. For example, an apomorphy of one clade (shared by all species within that clade) becomes a plesiomorphy of any subclade within it (meaning, it was inherited from a common ancestor). Among the clade of tetrapods, all species have four limbs – therefore, having four limbs is an apomorphy for that clade. However, if you look at a subclade within the clade of tetrapods, such as birds, then having four limbs is not an apomorphy for that subclade. Instead, it is a plesiomorphy, a trait inherited from the common ancestor of birds, which was itself a tetrapod. Therefore, the characteristic of having four limbs should not be used to distinguish one group of birds from another, but it can be used to distinguish tetrapods from all other vertebrates.

In practice, it’s often difficult to know which characteristics are apomorphies for a certain clade and which are homoplasies. Which charateristics can be used to define the clade, because they share common descent from an ancestor who had that characteristic, and which are simply examples of convergent evolution. In some cases the question cannot be resolved and has to wait for more data and further analysis. This is another contributor to the uncertainty and constant flux in taxonomy.

Modes of Speciation

There are several terms that describe how speciation occurs. All species arise from pre-existing species through a process of reproductive isolation. A number of individuals break off or subdivide from a population, and become reproductively isolated. They breed among themselves, but not with the rest of the population. Over time, differences accumulate, but these differences remain within the break-off group and are not transmitted to the rest of the population because of the breeding barrier. Similarly, differences develop in the larger population after the split, which are not transmitted to the break-off group because of the same breeding barrier. These differences eventually become significant enough to make cross-breeding impossible between the groups, even if it had been initially possible. The break-off group then become a new species.

The chart below shows some common ways in which this can happen.

Modes of Speciation

Allopatry

This happens when there is a geographical barrier between the subpopulation and the main population. A barrier can appear as a result of migration, for example, if a number of individuals migrate to a different location and there is a separation of many miles between them and the original population. Or it can happen when natural barriers appear, which subdivide the population. For example, a dry area of desert may appear in the middle of a population, separating it into two, a river might appear in the middle of a range. Or continents may split apart. Although such things can take some time (a few thousand years), in terms of the lifespan of a species, they are brief and rapid events. Typically, changes will happen much faster in the smaller subdivision, because of genetic drift and the founder effect.

Sympatry

This happens in populations that are not separated by what we typically understand as a “geographical barrier”. An example might be that a forest contains a patch of trees of a certain species, for unrelated reasons (perhaps it’s a clonal growth, could be any number of reasons). A leaf-eating population of insects inhabiting that forest become subdivided because certain members of that population exist in that patch of trees, and therefore only eat from its leaves. Over time, they may become specialized and prefer leaves from only those trees, even if other trees later become available. Such small changes can start a trend which becomes magnified over time. For example, these trees might come into flower at a specific time of the year, different from other trees around them. This will over time affect the lifestyle of the insects specialized to eat from them, perhaps changing their mating time to coincide with the flowering of their chief food source. They may thus not mate with the larger population even when they can, because their mating cycles have become desynchronized with the larger population.

Peripatry and Parapatry

These are similar to allopatry and sympatry, respectively. Peripatry is like allopatry in that there is geographical isolation, but there is no geographic barrier as such. Instead, it happens along the periphery (hence peri-patry) of the population’s range. Typically, population density is greater near the center and drops off towards the periphery. So gene flow might be very high among parts of the population near the center, but quite low at the periphery. In such cases, differences may develop between subpopulations at the center and at the periphery, leading to eventual speciation.

Parapatry is more like sympatry in that the original cause for the subdivision of the population is not geographical, but rather behavioral. Again, it may be a specialized food source which forces different foraging behaviors, different mating behaviors. However, this happens on the edge of range, not anywhere in the middle like for sympatry. The result is that the thin population density at the edge soon causes individuals to either adopt the new lifestyle or retreat to the main population, if they want to continue to mate. So a geographical isolation appears (again, in the absence of typical geographical barriers), but here the isolation begins with changes in behavior. Unlike peripatry, where isolation appears first, and then behavioral and genetic differences.

Dichopatry

This is sort of a catchall term that could apply to any kind of -patry, the difference being that the population is divided evenly into approximately equal halves. This is a special case, because normally the main population is much larger than any break-off group. It has relevance for speciation, in that genetic drift is slow in large populations, therefore the two subpopulations will drift apart very slowly.

Stasipatry

This happens in a limited number of species (some plants, some grasshoppers). Due to errors in reproduction, some individuals may have different ploidy than the main population from which they derive – that is, they may have double or triple the number of chromosomes. In many species, such a situation would kill the individuals containing these errors, or at least make them sterile. However, in some species, these individuals live, and while they are infertile with the main population, they are fertile with other individuals who have the same ploidy error. They can then mate and give rise to a subpopulation which can be exactly like the parent population in morphology or behavior, but are reproductively isolated from it.