4.6 - Classification and molecular phylogeny

Species and nested groups

A useful classification lets biologists identify an organism, communicate about it and investigate its relationships with other organisms. Taxonomy is the naming and classification of organisms. A named group at any rank is a taxon; the plural is taxa. Classification is built around species, but recognising a species is a biological problem, not simply a decision about which organisms look alike.

The important idea is a shared reproductive population. It does not mean every individual must reproduce: a juvenile or an infertile individual can still belong to the same species. Nor does looking different necessarily identify different species. Age, sex and environmental conditions can produce large differences within one species.

Reproductive isolation helps maintain separate gene pools. If populations no longer exchange alleles through reproduction, genetic differences can accumulate, as you met in 4.5. However, the interbreeding criterion has limits:

• Asexual organisms do not interbreed, so this test cannot delimit their species. Biologists instead use evidence such as genetic similarity, distinctive traits and separately evolving lineages.
• Fossil organisms cannot be tested for interbreeding. Their preserved structures and geological context provide evidence, but soft tissues, behaviour and DNA are often unavailable.
• Geographically separated populations may never meet, so their potential to interbreed can be difficult to establish. Occasional hybridisation also makes some boundaries less clear than a simple rule suggests.

Different lines of evidence therefore help biologists delimit species. The existence of difficult cases does not make species names useless; it means the evidence and the criterion being used must be clear. de Queiroz's discussion of species delimitation explains why several forms of evidence can matter.

Species are arranged in a nested hierarchy: domain → kingdom → phylum → class → order → family → genus → species. A genus contains related species, a family contains related genera, and so on. Groups become more inclusive towards domain. For example, humans belong to genus Homo and species Homo sapiens. A scientific binomial name has a capitalised genus followed by a lower-case specific name, both italicised in print. The complete two-word name identifies the species; “sapiens” alone does not. Naming makes communication consistent, while evidence determines which organisms should be grouped together.

Phenotype and genotype evidence

Biologists compare both similarities and differences when deciding how organisms are related. A phenotype consists of observable or measurable characteristics, including anatomy, physiology and behaviour. A genotype is an organism's genetic constitution; comparisons of DNA base sequences provide evidence about genetic similarities and differences.

Phenotype depends on genotype and on environmental influences. Related organisms may share inherited structures because they inherited the underlying developmental information from a common ancestor. For example, the same basic arrangement of limb bones in different mammals can support common ancestry even where those limbs have different functions. Comparing detailed structures is more informative than deciding that two animals have a similar outline.

Two cautions prevent a misleading classification. First, different phenotypes can arise within one species: plants of the same species can grow to different heights in different conditions. A visible difference alone therefore does not establish reproductive isolation. Second, unrelated lineages can independently evolve similar adaptations under similar selection pressures. This is convergent evolution. A streamlined body in a shark and a dolphin suits movement through water, but does not make the dolphin a fish. Shared superficial function or appearance can conceal different ancestry.

Genetic comparisons add many characters that may be invisible externally. Similar-looking organisms can have substantial sequence differences; organisms that look very different can retain many inherited sequences in common. A difference in height caused by growing conditions need not involve a difference in DNA sequence. Sequence comparisons can therefore help distinguish inherited differences from such environmental effects, although mutation and selection can change genetic variation across generations. Phenotypic and genotypic evidence should be considered together, with differences investigated rather than dismissed.

Suppose two flowering-plant populations differ in leaf size. If they grow under different light conditions, the difference might be an environmental response. Comparing plants grown under matched conditions helps test that explanation. Persistent inherited differences, evidence of reproductive isolation and consistent differences across several DNA regions would provide a stronger basis for recognising separate species than leaf size alone. None of these observations should be invented when they have not been measured.

Molecular sequence comparisons

Molecular phylogeny uses molecular comparisons to infer evolutionary relationships. A phylogeny is the evolutionary history and relationships of organisms or groups. DNA, RNA and amino acid sequences can provide evidence because they are inherited and can change over generations.

When comparing organisms, scientists first identify corresponding sequences inherited from the same ancestral sequence, rather than comparing unrelated genes merely because both occur in DNA. They align the sequences so that corresponding positions can be compared. Mutations since lineages separated can produce differences. Other things being comparable, fewer differences across suitable homologous sequences support a more recent common ancestor. Shared derived changes can also help identify a lineage. This is an inference about ancestry, not a statement that one living species changed into another living species.

For example, consider this deliberately short, invented DNA alignment. Each letter occupies a corresponding position; these are illustrative taxa and data, not results from a named study.

P and Q differ at one position, Q and R at three, and P and R at four. P and Q are therefore the closest pair in this fragment. The shared sequence can be explained by inheritance, with changes accumulating after lineages diverged. Eight bases are too little evidence for a secure whole-organism classification: agreement across longer sequences and several independent genes would increase confidence.

Molecular evidence has limitations. Different genes and lineages can change at different rates; a sequence may be too conserved to separate close relatives, or may have changed repeatedly so that some past changes are hidden. Gene transfer between lineages, particularly in microorganisms, can make one gene's history differ from the history of the organisms carrying it. Contamination, sequencing errors and poor alignment can also mislead. Scientists therefore compare suitable markers, wider samples and alternative analyses. There is no universal percentage similarity that automatically defines every species or gives an exact date of divergence.

Reading phylogenetic trees

A phylogenetic tree represents a hypothesis of common ancestry, with branching points connecting ancestral and descendant lineages. The root represents the common ancestor of all the taxa shown. An internal node represents a common ancestor where lineages diverged; terminal branches end in the taxa being compared. The closest relatives share the most recent common ancestor, found by tracing their branches back to the first node they share.