Abstract
Reconstructing ancestral characters on a phylogeny is an arduous task because the observed states at the tips of the tree correspond to a single realization of the underlying evolutionary process. Recently, it was proposed that ancestral traits can be indirectly estimated with the help of molecular data, based on the fact that life history traits influence substitution rates. Here we challenge these new approaches in the Cetartiodactyla, a clade of large mammals which, according to paleontology, derive from small ancestors. Analysing transcriptome data in 41 species, of which 22 were newly sequenced, we provide a dated phylogeny of the Cetartiodactyla and report a significant effect of body mass on the overall substitution rate, the synonymous vs. non-synonymous substitution rate and the dynamics of GC-content. Our molecular comparative analysis points toward relatively small Cetartiodactyla ancestors, in agreement with the fossil record, even though our data set almost exclusively consists of large species. This analysis demonstrates the potential of phylogenomic methods for ancestral trait reconstruction and gives credit to recent suggestions that the ancestor to placental mammals was a relatively large and long-lived animal.
Highlights
Peer Community Journal is a member of the Centre Mersenne for Open Scientific Publishing http:// www.centre-mersenne.org/
Our goal in this study was to test the ability of molecular-aided method for ancestral trait reconstruction in a difficult case study – the Cetartiodactyla
Our analyses indicate that the per year synonymous substitution rate, the dN /dS ratio and GC-content dynamics all carry some signal regarding ancestral traits in cetartiodactyls
Summary
Peer Community Journal is a member of the Centre Mersenne for Open Scientific Publishing http:// www.centre-mersenne.org/. Using hundreds of nuclear genes, Romiguier, Ranwez, et al (2013) reported that the estimated dN /dS ratio and GC content dynamics during early divergence in placental mammals were comparable to those of current long-lived mammals, and very different from those of current short-lived mammals They concluded that placental ancestors were probably long-lived (>20 years) animals, in sharp contrast with the classical view of tiny early mammals diversifying after the massive extinction of large reptiles (e.g. Feldhamer et al, 2007). Lartillot and Delsuc (2012) analysed a smaller data set using a more sophisticated method in which the correlation between molecular rates and LHT was explicitly modelled (Lartillot and Poujol, 2011) Their results were largely consistent with those of Romiguier, Ranwez, et al (2013), rejecting the hypothesis of mouse-like placental ancestors, even though point estimates for ancestral traits differed between the two studies. It is widely admitted that body mass in cetartiodactyls has been convergently increasing in a number of independent lineages during the evolution of this group
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