D9 Phylogeography, molecular clocks, and phylogenies | 40 | v4

ABSTRACT

Key Notes https://www.niso.org/standards/z39-96/ns/oasis-exchange/table">

Evolution by divergence

Evolution occurs by changes in allele frequencies over time. Species form when populations diverge genetically to the extent that they cannot interbreed. They then continue to evolve and diverge independently. Degree of divergence for unselected characters is a measure of time since separation. Shared characteristics which evolved in a common ancestor are said to be homologous (e.g. mammals' back legs). Structures that have evolved similar functions separately are analogous (e.g. bats' wings and birds' wings). Evolving to be more similar from different starting points is called convergent evolution (e.g. whales and fish). Related species share homologous structures from their common ancestors, but do not share characters arising after separation.

Populations

Differences between populations within a species can show patterns of migration and colonization, and indicate degrees of divergence preceding speciation. Divergence may be selected. Dark skin in humans from equatorial regions may reduce damage from sunlight, and pale skin aids photosynthesis of vitamin D by sunlight in northern lands. There are large differences in blood group frequencies in different human populations, which may be due to selection by disease or to a drift and founder effect in small colonizing tribes.

Ring species

A ring species has an extended continuous range around an obstacle, but the populations at the extreme ends of the range are sufficiently diverged to be different species where they meet. An example is a boreal gull whose global range overlaps in Europe as the herring gull Laurus argentatus and the lesser black-backed gull L. fuscus. This shows that distance alone is an effective isolating mechanism.

Molecular clocks

The rate at which amino acid changing mutations accumulate in genes for specific proteins tends to be constant over time. Similarly, changes in ribosomal RNA sequence, synonymous changes in coding sequences (silent mutations), and changes in noncoding sequences all have particular rates. These can all be used as molecular clocks, faster diverging sequences for more recent events.

The degree of divergence between two species reflects the duration in time of their independent evolution. There is debate about whether the clock rate is faster at times of rapid evolution (adaptive radiations) and slower during stasis, and also about the effects of generation time and number of germline cell divisions.

Phylogenetics

Arranging species in order of increasing divergence gives a phylogenetic tree which represents evolutionary history. Species within a group are compared with a distantly related outgroup to provide an ancestral root to the tree. Animal mitochondrial DNA evolves rapidly and does not recombine, so is excellent for relatively recent divergences. Conserved proteins (e.g. cytochrome c) and ribosomal RNA are useful for studying the whole period of life on earth. Mitochondria and Y chromosomes do not recombine, and, in mammals, follow the maternal and paternal lines respectively. Each could be traced back to a single ancestor, yet many different versions exist in the population. Multiple alleles of nuclear genes exist and recombine, so the phylogeny of a species is the sum of the phylogenies of the DNA within it.