The evolutionary history of bears is characterized by gene flow across species
Vikas Kumar, Fritjof Lammers, Tobias Bidon, Markus Pfenninger, Lydia Kolter, Maria A. Nilsson & Axel Janke
Scientific Reports 7, Article number: 46487 (2017)
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Computational biology and bioinformaticsEvolutionEvolutionary genetics
Received: 23 November 2016 Accepted: 17 March 2017
Published online: 19 April 2017
Figure 2: A coalescent species tree and a split network analysis from 18,621 GF ML trees.
Abstract
Bears are iconic mammals with a complex evolutionary history. Natural bear hybrids and studies of few nuclear genes indicate that gene flow among bears may be more common than expected and not limited to polar and brown bears. Here we present a genome analysis of the bear family with representatives of all living species. Phylogenomic analyses of 869 mega base pairs divided into 18,621 genome fragments yielded a well-resolved coalescent species tree despite signals for extensive gene flow across species. However, genome analyses using different statistical methods show that gene flow is not limited to closely related species pairs. Strong ancestral gene flow between the Asiatic black bear and the ancestor to polar, brown and American black bear explains uncertainties in reconstructing the bear phylogeny. Gene flow across the bear clade may be mediated by intermediate species such as the geographically wide-spread brown bears leading to large amounts of phylogenetic conflict. Genome-scale analyses lead to a more complete understanding of complex evolutionary processes. Evidence for extensive inter-specific gene flow, found also in other animal species, necessitates shifting the attention from speciation processes achieving genome-wide reproductive isolation to the selective processes that maintain species divergence in the face of gene flow.
Acknowledgements
We are grateful to Luay Nakhleh (Rice University) for expert help with Phylo-Net analyses, Yichen Zheng for valuable comments on the manuscript and to Jon Baldur Hlidberg (www.fauna.is), and Aidin Niamir for artwork. Blood samples were kindly provided by Carsten Ludwig (Allwetter Zoo Münster), Tim Schikora (Zoo Schwerin), Christian Wenker (Basel Zoo) and Eva Martinez Nevado (Zoo Madrid). This study was supported by Hesse’s funding program LOEWE (Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz) and the Leibniz Society.
Author information
Affiliations
Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
Vikas Kumar, Fritjof Lammers, Tobias Bidon, Markus Pfenninger, Maria A. Nilsson & Axel Janke
Goethe University Frankfurt, Institute for Ecology, Evolution & Diversity, Biologicum, Max-von-Laue-Str. 13, D-60439 Frankfurt am Main, Germany
Vikas Kumar, Fritjof Lammers, Tobias Bidon, Markus Pfenninger & Axel Janke
AG Zoologischer Garten Cologne, Riehler Straße 173, 50735 Cologne, Germany
Lydia Kolter
Contributions
A.J. designed the research and obtained funding. A.J. and T.B. collected the data; V.K. and F.L. conducted the analyses; L.K. provided pedigrees and located samples; A.J., V.K., M.P., M.N., F.L., and T.B. interpreted the results; A.J. and V.K. wrote the paper with the help of all authors.
Competing interests
The authors declare no competing financial interests.
Corresponding author
Correspondence to Axel Janke.
