Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis

• DOI: 10.1101/gr.125864.111
• Publication Date: 2011-12-30T03:45:21Z
• Authors: John E. McCormack; Brant C. Faircloth; Nicholas G. Crawford; Patricia Adair Go...; Robb T. Brumfield; Travis C. Glenn
• Keywords: Phylogenomics; Mammal; Tree (set theory); Supermatrix

Phylogenomics offers the potential to fully resolve Tree of Life, but increasing genomic coverage also reveals conflicting evolutionary histories among genes, demanding new analytical strategies for elucidating a single history life. Here, we outline phylogenomic approach using novel class phylogenetic markers derived from ultraconserved elements and flanking DNA. Using species-tree analysis that accounts discord hundreds independent loci, show this marker is useful recovering deep-level phylogeny in placental mammals. In broad outline, our agrees with recent studies mammals, including several formerly controversial relationships. Our results inform two outstanding questions mammal involving rapid speciation, where methods are particularly needed. Contrary most studies, study supports first-diverging lineage includes elephants tenrecs (Afrotheria). The level conflict gene consistent basal divergence occurring or near "anomaly zone" failure account coalescent stochasticity will mislead inference. Addressing long-standing mystery, find some support high data set traditional placement bats (Chiroptera) sister clade containing Perissodactyla, Cetartiodactyla, Carnivora, not nested within latter clade, as has been suggested recently, although other were conflicting. One remarkable findings their DNA rich source information strong application across Amniotes.