2007
DOI: 10.1101/gr.5918807
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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 … Show more

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Cited by 405 publications
(372 citation statements)
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“…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).…”
Section: Methodsmentioning
confidence: 99%
“…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).…”
Section: Methodsmentioning
confidence: 99%
“…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.…”
Section: Discussionmentioning
confidence: 99%
“…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].…”
Section: Shaking the Morphological Treementioning
confidence: 99%