Incomplete Lineage Sorting in Mammalian Phylogenomics

Celine Scornavacca (1) , Nicolas Galtier (1, 2, 3, 4, 5)

1 UMR ISEM - Institut des Sciences de l'Evolution de Montpellier
2 CNRS - Centre National de la Recherche Scientifique
3 UM - Université de Montpellier
4 IRD - Institut de Recherche pour le Développement
5 EPHE - École Pratique des Hautes Études

—The impact of incomplete lineage sorting (ILS) on phylogenetic conflicts among genes, and the related issue of whether to account for ILS in species tree reconstruction, are matters of intense controversy. Here, focusing on full-genome data in placental mammals, we empirically test two assumptions underlying current usage of tree-building methods that account for ILS. We show that in this data set (i) distinct exons from a common gene do not share a common genealogy, and (ii) ILS is only a minor determinant of the existing phylogenetic conflict. These results shed new light on the relevance and conditions of applicability of ILS-aware methods in phylogenomic analyses of protein coding sequences. [Coalescence; exon; Supertree; phylogeny; placental.]

Domaines: Génétique des populations [q-bio.PE]; Systématique, phylogénie et taxonomie; Génomique, Transcriptomique et Protéomique [q-bio.GN]

Celine Scornavacca, Nicolas Galtier. Incomplete Lineage Sorting in Mammalian Phylogenomics. Systematic Biology, 2016, 66, pp.112 - 120. ⟨10.1093/sysbio/syw082⟩. ⟨hal-01815360⟩