Abstract
Mutation–selection phylogenetic codon models are grounded on population genetics first principles and represent a principled approach for investigating the intricate interplay between mutation, selection, and drift. In their current form, mutation–selection codon models are entirely characterized by the collection of site-specific amino-acid fitness profiles. However, thus far, they have relied on the assumption of a constant genetic drift, translating into a unique effective population size () across the phylogeny, clearly an unrealistic assumption. This assumption can be alleviated by introducing variation in between lineages. In addition to , the mutation rate (μ) is susceptible to vary between lineages, and both should covary with life-history traits (LHTs). This suggests that the model should more globally account for the joint evolutionary process followed by all of these lineage-specific variables (, μ, and LHTs). In this direction, we introduce an extended mutation–selection model jointly reconstructing in a Bayesian Monte Carlo framework the fitness landscape across sites and long-term trends in , μ, and LHTs along the phylogeny, from an alignment of DNA coding sequences and a matrix of observed LHTs in extant species. The model was tested against simulated data and applied to empirical data in mammals, isopods, and primates. The reconstructed history of in these groups appears to correlate with LHTs or ecological variables in a way that suggests that the reconstruction is reasonable, at least in its global trends. On the other hand, the range of variation in inferred across species is surprisingly narrow. This last point suggests that some of the assumptions of the model, in particular concerning the assumed absence of epistatic interactions between sites, are potentially problematic.
Highlights
Since the realization by Zuckerkandl and Pauling (1965) that genetic sequences are informative about the evolutionary history of the species, molecular phylogenetics has developed into a mature and very active field
The substitution patterns that can be reconstructed along phylogenies are modulated by the underlying population-genetic parameters, suggesting the possibility to infer the past variation of these parameters over the phylogeny
Here we introduce a variant of the mutation–selection codon model, in which selection is modulated along the sequence, whereas the mutation rate (l), the effective population size (Ne), and life-history traits (LHTs) are allowed to vary along the phylogeny
Summary
Since the realization by Zuckerkandl and Pauling (1965) that genetic sequences are informative about the evolutionary history of the species, molecular phylogenetics has developed into a mature and very active field. The substitution patterns that can be reconstructed along phylogenies are modulated by the underlying population-genetic parameters (mutation biases, selective landscapes, effective population size), suggesting the possibility to infer the past variation of these parameters over the phylogeny. Ecological properties, such as phenotypic characters or life-history traits (LHTs) can be observed in extinct or in present-day species. Genetic and phenotypic ancestral reconstructions can be used to unravel the interplay between evolutionary and ecological mechanisms
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have