Trends in Ecology & Evolution
Measurably evolving populations
Section snippets
Theoretical concepts
Most statistical methods in phylogenetics and population genetics have been developed to analyze isochronous sequences; for example, tree-building methods, such as UPGMA, phylogenetic tests of the molecular clock hypothesis [3] and population genetic methods based on coalescent theory 8, 9, 10, 11. However, such approaches should not be directly applied to MEPs for two important reasons: (1) methods that fail to incorporate the temporal structure in heterochronous sequences will suffer from
Measuring evolution with ancient DNA
The amplification of mitochondrial DNA (mtDNA) from subfossil bone material at least 60 000 years old 27, 28 has become increasingly reliable, provided that the cold conditions that are a requirement for long-term DNA survival are met 27, 29, 30. With the success of mtDNA recovery from late Pleistocene subfossil material, researchers are now embarking on the recovery of DNA sequences from similarly aged nuclear loci [31]. This increasing abundance of ancient DNA sequences provides an
Measuring the evolution of RNA viruses
As a group, RNA viruses encompass such well known pathogens as HIV, influenza and foot and mouth disease, and are characterized by populations that continuously generate huge numbers of mutations owing to their large numbers, very short generation times and the error-prone nature of their replication machinery 39, 40. Some of these mutations are carried to fixation by random genetic drift or by the strong directional selection exerted by host immune responses, resulting in a very fast rate of
Prospects
Measurably evolving populations provide an opportunity to ask questions about population dynamics and molecular evolution that are otherwise inaccessible using isochronous sequences. All populations accumulate mutations over time, but whether we treat a population as a MEP will depend on the amount of temporally related information in the data obtained. Given knowledge about the biological properties of a population, the MEP concept can guide us in designing sampling strategies suitable for a
Acknowledgements
This work was funded by EPSRC and MRC (A.J.D., R.F.), grant 21–02–0206 from the Danish Natural Science Research Council (R.F.), The Wellcome Trust (O.G.P.) and The Royal Society (A.R.). The authors acknowledge helpful comments from Geoff Nicholls and two anonymous referees.
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2023, Trends in ParasitologyCitation Excerpt :Although we focus on Plasmodium, the concepts apply to a broader range of sexually recombining pathogens. Both mutation and recombination generate genetic variation [11,12]: mutation creates differences, while recombination creates new combinations of those differences. Mutational differences, δ, can be modeled simply as a linear function of time t, the rate of mutation per locus per time μ, and the number of loci l: δ = μlt [12].