Phylogenomic Analysis Resolves the Interordinal Relationships and Rapid Diversification of the Laurasiatherian Mammals

Abstract

Although great progress has been made in resolving the relationships of placental mammals, the position of several clades in Laurasiatheria remain controversial. In this study, we performed a phylogenetic analysis of 97 orthologs (46,152 bp) for 15 taxa, representing all laurasiatherian orders. Additionally, phylogenetic trees of laurasiatherian mammals with draft genome sequences were reconstructed based on 1608 exons (2,175,102 bp). Our reconstructions resolve the interordinal relationships within Laurasiatheria and corroborate the clades Scrotifera, Fereuungulata, and Cetartiodactyla. Furthermore, we tested alternative topologies within Laurasiatheria, and among alternatives for the phylogenetic position of Perissodactyla, a sister-group relationship with Cetartiodactyla receives the highest support. Thus, Pegasoferae (Perissodactyla + Carnivora + Pholidota + Chiroptera) does not appear to be a natural group. Divergence time estimates from these genes were compared with published estimates for splits within Laurasiatheria. Our estimates were similar to those of several studies and suggest that the divergences among these orders occurred within just a few million years.

Importance of synonymous substitutions under dense taxon sampling and appropriate modeling in reconstructing the mitogenomic tree of Eutheria

“…We did not include Erinaceidae in our analysis, because the position of Erinaceidae has not been settled, as noted in the Supplementary text. Although Erinaceidae was placed as the most basal lineage among eutherian mammals on the basis of the mitgenome analysis (Supplementary text), this phylogenetic position is unlikely from nuclear evidence (Murphy et al, 2001;Douady et al, 2002;Hallström et al, 2011;Zhou et al, 2012). The aberrant placement of Erinaceidae was attributed to their distinct nucleotide compositions and rapid rate of mitogenome evolutoion, particularly in hedgehogs (Lin et al, 2002;Nikaido et al, 2003;Gibson et al, 2005).…”

Summary of Laurasiatheria (Mammalia) Phylogeny

“…Subsequently, Zhou et al (2011b) investigated Laurasiatheria phylogeny based on 97 orthologous genes (~46 kb) from six orders. Regardless of datasets and analytic methods used, they obtained an identical tree topology of (Eulipotyphla, (Chiroptera, ((Carnivora, Pholidota), (Cetartiodactyla, Perissodactyla)))) ( Figure 1H, Table 1).…”

“…However, the phylogeny and evolution of Laurasiatheria remain subjects of heated debate and are not yet well-established. The origins of Laurasiatheria have been dated to the Cretaceous, ranging from 100 to 78.5−93 mya according to several molecular estimates (Cao et al, 2000;Hallström & Janke 2008Hallström et al, 2011;Hasegawa et al, 2003;Ji et al, 2002;Kitazoe et al, 2007;Meredith et al, 2011;Murphy et al, 2004;Zhou et al, 2011b). However, most morphological studies place the origins of this super-order in the Paleocene (Asher et al, 2003;Wible et al, 2007Wible et al, , 2009Luo et al, 2011).…”

“…However, most morphological studies place the origins of this super-order in the Paleocene (Asher et al, 2003;Wible et al, 2007Wible et al, , 2009Luo et al, 2011). The diversification of mammalian species within Laurasiatherian orders appear to have radiated within 1−4 mya in the Eocene (Hallström & Janke 2008Zhou et al, 2011b). So, attempts to clarify relationships among the six Laurasiatheria orders from a variety of studies have encountered serious challenges due to the rapid evolutionary radiations and recent speciation events.…”

“…G: Madsen et al, 2001Meredith et al, 2011. H: Murphy et al, 2001aWaddell et al, 2001;Beck et al, 2006;Bininda-Emonds et al, 2007;Zhou et al, 2011b. I: Madsen et al, 2002.…”