ArticleMolecular biology and evolution2014
Bears in a forest of gene trees: phylogenetic inference is complicated by incomplete lineage sorting and gene flow.
Article in Molecular biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed.
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- Effects of the Ecuadorian Andes on genetic structure of the spectacled bear with new genetic datasets.Scientific reports · 2025Article
- A Tale of Too Many Trees: A Conundrum for Phylogenetic Regression.Molecular biology and evolution · 2025Article
- Trans-Specific Polymorphisms Between Cryptic Daphnia Species Affect Fitness and Behavior.Molecular ecology · 2025Article
- Genomic patterns in the dwarf kingfishers of northern Melanesia reveal a mechanistic framework explaining the paradox of the great speciators.Evolution letters · 2024Article
- Phylogenomics and Pervasive Genome-Wide Phylogenetic Discordance Among Fin Whales (Balaenoptera physalus).Systematic biology · 2024Article
- Balancing selection and the functional effects of shared polymorphism in crypticbioRxiv : the preprint server for biology · 2024Article
- Ursids evolved dietary diversity without major alterations in metabolic rates.Scientific reports · 2024Article
- A New Assessment of Robust Capuchin Monkey (Genes · 2023Article
- Ursids evolved early and continuously to be low-protein macronutrient omnivores.Scientific reports · 2022Article
- Uncovering the enigmatic evolution of bears in greater depth: The hybrid origin of the Asiatic black bear.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Phylogenomics and Diversification of the Schistosomatidae Based on Targeted Sequence Capture of Ultra-Conserved Elements.Pathogens (Basel, Switzerland) · 2022Article
- Genomic insights into zokors' phylogeny and speciation in China.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Sympatric speciation of the spiny mouse from Evolution Canyon in Israel substantiated genomically and methylomically.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Candidate-species delimitation inEcology and evolution · 2022Article
- Multispecies facial detection for individual identification of wildlife: a case study across ursids.Mammalian biology = Zeitschrift fur Saugetierkunde · 2022Article
- The genic view of hybridization in the Anthropocene.Evolutionary applications · 2021Article
- PhyloWGA: chromosome-aware phylogenetic interrogation of whole genome alignments.Bioinformatics (Oxford, England) · 2021Article
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6 authors.
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No grant is acknowledged in the PubMed record.
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.
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