Data from: Reconstructing the phylogenetic history of long-term effective population size and life-history traits using patterns of amino acid replacement in mitochondrial genomes of mammals and birds

The nearly neutral theory, which proposes that most mutations are
deleterious or close to neutral, predicts that the ratio of nonsynonymous
over synonymous substitution rates (dN/dS), and potentially also the ratio
of radical over conservative amino acid replacement rates (Kr/Kc), are
negatively correlated with effective population size. Previous empirical
tests, using life-history traits (LHT) such as body-size or
generation-time as proxies for population size, have been consistent with
these predictions. This suggests that large-scale phylogenetic
reconstructions of dN/dS or Kr/Kc might reveal interesting
macroevolutionary patterns in the variation in effective population size
among lineages. In this work, we further develop an integrative
probabilistic framework for phylogenetic covariance analysis introduced
previously, so as to estimate the correlation patterns between dN/dS,
Kr/Kc, and three LHT, in mitochondrial genomes of birds and mammals. Kr/Kc
displays stronger and more stable correlations with LHT than does dN/dS,
which we interpret as a greater robustness of Kr/Kc, compared with dN/dS,
the latter being confounded by the high saturation of the synonymous
substitution rate in mitochondrial genomes. The correlation of Kr/Kc with
LHT was robust when controlling for the potentially confounding effects of
nucleotide compositional variation between taxa. The positive correlation
of the mitochondrial Kr/Kc with LHT is compatible with previous reports,
and with a nearly neutral interpretation, although alternative
explanations are also possible. The Kr/Kc model was finally used for
reconstructing life-history evolution in birds and mammals. This analysis
suggests a fairly large-bodied ancestor in both groups. In birds,
life-history evolution seems to have occurred mainly through size
reduction in Neoavian birds, whereas in placental mammals, body mass
evolution shows disparate trends across subclades. Altogether, our work
represents a further step toward a more comprehensive phylogenetic
reconstruction of the evolution of life-history and of the
population-genetics environment.