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. 2012 Jan;61(1):150-64.
doi: 10.1093/sysbio/syr089. Epub 2011 Sep 7.

Phylogenomic analysis resolves the interordinal relationships and rapid diversification of the laurasiatherian mammals

Xuming Zhou  1 , Shixia Xu, Junxiao Xu, Bingyao Chen, Kaiya Zhou, Guang Yang
Affiliations

Phylogenomic analysis resolves the interordinal relationships and rapid diversification of the laurasiatherian mammals

Xuming Zhou et al. Syst Biol. 2012 Jan.

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.

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Figures

F<sc>IGURE</sc> 1.
FIGURE 1.
Alternative hypotheses for the interorder relationships of major Laurasiatherian lineages based on molecular sequences data (a–e) and retroposon analysis (f). Clade support values and the size of the data sets used are available in Table 1.
F<sc>IGURE</sc> 2.
FIGURE 2.
Phylogenetic trees reconstructed using BI and ML methods based on two different data sets. Integers associated with branches are BP support values from ML analyses, whereas values of 1 or less are Bayesian PPs. Dash denotes BP support values that are <50%. Codon 1+2 and RY coding refer to the concatenated sequences combined with the first and second codon positions and combined with RY recoding, respectively. A consensus tree based on a majority rule of 97 BI trees from the 97-gene data set is shown in (b). Numbers associated with each branch represent the proportion of universally distributed input trees that contain that particular split.
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