title: Bears in a forest of gene trees: phylogenetic inference is complicated by incomplete lineage sorting and gene flow.
abstract: Ursine bears are a mammalian subfamily that comprises six morphologically and ecologically distinct extant species. Previous phylogenetic analyses of concatenated nuclear genes could not resolve all relationships among bears, and appeared to conflict with the mitochondrial phylogeny. Evolutionary processes such as incomplete lineage sorting and introgression can cause gene tree discordance and complicate phylogenetic inferences, but are not accounted for in phylogenetic analyses of concatenated data. We generated a high-resolution data set of autosomal introns from several individuals per species and of Y-chromosomal markers. Incorporating intraspecific variability in coalescence-based phylogenetic and gene flow estimation approaches, we traced the genealogical history of individual alleles. Considerable heterogeneity among nuclear loci and discordance between nuclear and mitochondrial phylogenies were found. A species tree with divergence time estimates indicated that ursine bears diversified within less than 2 My. Consistent with a complex branching order within a clade of Asian bear species, we identified unidirectional gene flow from Asian black into sloth bears. Moreover, gene flow detected from brown into American black bears can explain the conflicting placement of the American black bear in mitochondrial and nuclear phylogenies. These results highlight that both incomplete lineage sorting and introgression are prominent evolutionary forces even on time scales up to several million years. Complex evolutionary patterns are not adequately captured by strictly bifurcating models, and can only be fully understood when analyzing multiple independently inherited loci in a coalescence framework. Phylogenetic incongruence among gene trees hence needs to be recognized as a biologically meaningful signal.
authors.affiliation: Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany v.kutschera@gmx.net axel.janke@senckenberg.de.
authors.forename: Verena E
authors.initials: VE
authors.lastname: Kutschera
authors.affiliation: Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany.
authors.forename: Tobias
authors.initials: T
authors.lastname: Bidon
authors.affiliation: Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany.
authors.forename: Frank
authors.initials: F
authors.lastname: Hailer
authors.affiliation: Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany.
authors.forename: Julia L
authors.initials: JL
authors.lastname: Rodi
authors.affiliation: National Fish and Wildlife Forensic Laboratory, Ashland, OR.
authors.forename: Steven R
authors.initials: SR
authors.lastname: Fain
authors.affiliation: Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, GermanyInstitute for Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany v.kutschera@gmx.net axel.janke@senckenberg.de.
authors.forename: Axel
authors.initials: A
authors.lastname: Janke
mesh_terms: D000818:Animals; D002467:Cell Nucleus / Q000235:genetics; D019143:Evolution, Molecular; D051456:Gene Flow; D049810:Genetic Speciation; D007438:Introns; D008297:Male; D008928:Mitochondria / Q000235:genetics; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*; D001503:Ursidae / Q000145:classification / Q000235:genetics*; D014998:Y Chromosome / Q000235:genetics*
keywords: Ursidae; coalescence; introgressive hybridization; multi-locus analyses; phylogenetic network; species tree