Using genomic data to unravel the root of the placental mammal phylogeny

Abstract

The phylogeny of placental mammals is a critical framework for choosing future genome sequencing targets and for resolving the ancestral mammalian genome at the nucleotide level. Despite considerable recent progress defining superordinal relationships, several branches remain poorly resolved, including the root of the placental tree. Here we analyzed the genome sequence assemblies of human, armadillo, elephant, and opossum to identify informative coding indels that would serve as rare genomic changes to infer early events in placental mammal phylogeny. We also expanded our species sampling by including sequence data from >30 ongoing genome projects, followed by PCR and sequencing validation of each indel in additional taxa. Our data provide support for a sister-group relationship between Afrotheria and Xenarthra (the Atlantogenata hypothesis), which is in turn the sister-taxon to Boreoeutheria. We failed to recover any indels in support of a basal position for Xenarthra (Epitheria), which is suggested by morphology and a recent retroposon analysis, or a hypothesis with Afrotheria basal (Exafricoplacentalia), which is favored by phylogenetic analysis of large nuclear gene data sets. In addition, we identified two retroposon insertions that also support Atlantogenata and none for the alternative hypotheses. A revised molecular timescale based on these phylogenetic inferences suggests Afrotheria and Xenarthra diverged from other placental mammals ∼103 (95-114) million years ago. We discuss the impacts of this topology on earlier phylogenetic reconstructions and repeat-based inferences of phylogeny.

Genome analysis of the platypus reveals unique signatures of evolution

“…Genome landscape. To establish phylogeny we extended the basic data sampling approach described previously 73 to protein-coding genes, and used established techniques to analyse protein-coding indels 74 and retrotransposon insertions 75 ( Supplementary Notes 19).…”

Parallel signatures of sequence evolution among hearing genes in echolocating mammals: an emerging model of genetic convergence

“…In this method, posterior probabilities of all possible amino-acid substitutions were calculated along each branch under a JTT+F+G model of amino-acid substitution. We used tree topologies based on published data (Csorba et al, 2003;Nishihara et al, 2006;Miller-Butterworth et al, 2007;Murphy et al, 2007;McGowen et al, 2009;Khan et al, 2010) and we estimated branch lengths using MrBayes v3.1.2. For all pair-wise branch comparisons where both branches followed divergent paths, the sum of the joint probabilities of all possible pairs of convergent substitutions (same amino acid) and divergent substitutions were calculated.…”

Mammal madness: is the mammal tree of life not yet resolved?

“…These initial studies, which included representatives from all recognized mammalian orders, were based on large multigene datasets comprised of both nuclear and mitochondrial markers and provided support for four superordinal clades of placental mammals that are still recognized today: Afrotheria, Xenarthra, Euarchontoglires and Laurasiatheria [15,16,[26][27][28][29]. Subsequent studies of retrotransposed elements and indels provided confirmatory support for these four superordinal clades [13,15,16,26,29,41,42] [41] and others supporting Atlantogenata versus Boreoeutheria [52]. The most comprehensive study based on retroposon insertions provides commensurate levels of support for each of the three competing hypotheses [64].…”