Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes

Abstract

The order Carnivora, which currently includes 296 species classified into 16 families, is distributed across all continents. The phylogeny and the timing of diversification of members of the order are still a matter of debate. Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence times among species of Carnivora. We assembled 51 new mitogenomes from 13 families, and aligned them with available mitogenomes by selecting only those showing more than 1% of nucleotide divergence and excluding those suspected to be of low-quality or from misidentified taxa. Our final alignment included 220 taxa representing 2,442 mitogenomes. Our analyses led to a robust resolution of suprafamilial and intrafamilial relationships. We identified 21 fossil calibration points to estimate a molecular timescale for carnivorans. According to our divergence time estimates, crown carnivorans appeared during or just after the Early Eocene Climatic Optimum; all major groups of Caniformia (Cynoidea/Arctoidea; Ursidae; Musteloidea/Pinnipedia) diverged from each other during the Eocene, while all major groups of Feliformia (Nandiniidae; Feloidea; Viverroidea) diversified more recently during the Oligocene, with a basal divergence of Nandinia at the Eocene/Oligocene transition; intrafamilial divergences occurred during the Miocene, except for the Procyonidae, as Potos separated from other genera during the Oligocene.

Correction: Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes

“…For comparison, the values in blue are mean ages estimated using a log normal prior distribution for fossil calibration points ("L approach"; see main text for details and discussion). Species names follow the classification of the IUCN [1]; the name of the taxa written in red have been changed following our results which suggest these taxonomic changes (see the discussion for details).…”

“…The two outgroup species are not shown. Species names follow the classification of the IUCN [1]; the taxa written in red highlight the taxonomic issues discussed in the main text. The accession numbers of the 42 mitogenomes of Carnivora specially sequenced for this study are indicated in red.…”

A mitochondrial genome phylogeny of voles and lemmings (Rodentia: Arvicolinae): Evolutionary and taxonomic implications

“…Complete mitochondrial genome datasets provide a robust phylogeny with highly resolved trees having strong branch support [40]. However, the mitochondrial genomes can conflict with a phylogeny estimated from the nuclear genome due to the replacement of organelle genomes from one species or populations with those of another mediated by hybridization and introgression [41][42][43][44]. The use of mitochondrial genome datasets may also provide evidences of adaptive radiations, as signatures of selection were detected during reconstructing mitochondrial genome phylogenies for the number of vertebrate taxa including deep-sea fishes [45,46], marine turtles [47,48], and mammals [49][50][51][52][53][54].…”

Geologically calibrated mammalian tree and the corresponding global events, including birth of human

“…The maximum age is inferred by an additional fossil age older than that speci c node (and the minimum age), i.e., the stem age (or the parent node age at an edge) is representative, although the de nition is sometimes unclear and controversial. Minimum ages are generally more accurate and reliable than maximum ages (Hassanin et al, 2021). In actual mammalian MCMCTree analyses (dos Reis et al, 2012(dos Reis et al, , 2018, a speci c node age (posterior divergence time) is estimated by prior divergence time applying minimum and maximum ages, although maximum age is only roughly estimated (named soft maximum bound).…”

“…Application of genome-scale sequence data may be better as dos Raise et al ( 2012) did so, but in the present case unrelated to the precision of node dating, calibration method is much more important. Hassanin et al (2021) applied a lognormal distribution on the calibrated node ages and compared it to the uniform distribution for the minimum and maximum age sets. In BEAST v.1 X, considering maximum ages, we tried to select lognormal for prior distribution to construct Fig.…”