TY  - JOUR
A1  - Kutschera, Verena Esther
A1  - Bidon, Tobias
A1  - Hailer, Frank
A1  - Rodi, Julia L.
A1  - Fain, Steven R.
A1  - Janke, Axel
T1  - Bears in a forest of gene trees : phylogenetic inference is complicated by incomplete lineage sorting and gene flow
T2  - Molecular biology and evolution
N2  - 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.
KW  - species tree
KW  - introgressive hybridization
KW  - Ursidae
KW  - phylogenetic network
KW  - coalescence
KW  - multi-locus analyses
Y1  - 2014
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/37176
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30:3-371767
SN  - 1537-1719
SN  - 0737-4038
N1  - Copyright © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
VL  - 31
IS  - 8
SP  - 2004
EP  - 2017
PB  - Oxford Univ. Press
CY  - Oxford
ER  -