5.1. The Isthmus of Panama emerged approximately 3 million years ago. Sequence divergence = 23/750 = 0.0307 = 3.1 per cent per 3 million years, or approximately 1 per cent per million years.
• That cytochrome b evolves at the same rate in the fish species for which the clock was calibrated and the species that are the subjects of the other studies.
• That the evolutionary rate of cytochrome b is constant along the entire gene (relevant if a non-homologous region of cytochrome b is being compared).
• That the cytochrome b clock has been constant over time (relevant if the species in the other studies had diverged substantially more or less than 3 million years ago).
5.2. The expected time until all gene copies coalesce is a) 4Ne = 4(200) = 800, and b) 200. These calculations are based on a number of assumptions including constant population size, no natural selection, and random mating.
5.3. The most parsimonious network, i.e. the one that requires the fewest mutation steps, is:
The bars over the connecting lines represent the number of mutations that are required between each haplotype. Haplotype 1 is most likely to be the ancestral haplotype because it is central to the network and has the largest number of connections.
5.4. The two processes are:
• Retention of ancestral polymorphism. If two populations or species have recently diverged, lineage sorting will not yet have resulted in monophyly and therefore alleles will be shared because they were present in the common ancestor.
• Hybridization -- alleles may introgress from one species to another.
5.5. (i) Haldane's rule states that these are more likely to be birds than mammals, because in birds the males are the homogametic sex.
(ii) This is more likely to be a tension zone, because female hybrids apparently have extremely low fitness levels.
(iii) Although nuclear DNA may introgress, mitochondrial DNA is unlikely to be exchanged between species to any extent because it is transmitted maternally and very few female hybrids survive.
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