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Citation for Study 11662

Citation title: "Recurrent Introgression of Mitochondrial DNA Among Hares (Lepus spp.) revealed by Species-tree Inference and Coalescent Simulations".

Study name: "Recurrent Introgression of Mitochondrial DNA Among Hares (Lepus spp.) revealed by Species-tree Inference and Coalescent Simulations".

This study is part of submission 11652 (Status: Published).

Citation

Melo-ferreira J., Boursot P., Carneiro M., Esteves P.J., Farelo L., & Alves P.C. 2011. Recurrent Introgression of Mitochondrial DNA Among Hares (Lepus spp.) revealed by Species-tree Inference and Coalescent Simulations. Systematic Biology, .

Authors

• Melo-ferreira J. (submitter) 00351 252 660 415
• Boursot P.
• Carneiro M.
• Esteves P.J.
• Farelo L.
• Alves P.C.

Abstract

Understanding recent speciation history requires merging phylogenetic and population genetics approaches, taking into account the persistence of ancestral polymorphism and possible introgression. The emergence of a clear phylogeny of hares (genus Lepus) has been hampered by poor genomic sampling and possible occurrence of mitochondrial DNA introgression from the arctic/boreal Lepus timidus into several European temperate and American boreal species. However, no formal test of introgression, taking also incomplete lineage sorting into account, has been done. Here, to clarify the yet poorly resolved species phylogeny of hares and test hypotheses of mtDNA introgression we sequenced 14 nuclear DNA and two mtDNA fragments (8,196 bp and 1,113 bp respectively) in 50 specimens from 11 hare species from Eurasia, North America and Africa. By applying an Isolation-with-migration (IM) model to the nuclear data on subsets of species, we find evidence for very limited gene flow from L. timidus into most temperate European species, and not into the American boreal ones. Using a multi-locus coalescent based method we infer the species phylogeny, which we find highly incongruent with mtDNA phylogeny using parametric bootstrap. Simulations of mtDNA evolution under the speciation history inferred from nuclear genes did not support the hypothesis of mtDNA introgression from L. timidus into the American L. townsendii but did suggest introgression from L. timidus into four temperate European species. One such event likely resulted in the complete replacement of the aboriginal mtDNA of L. castroviejoi and of its sister species L. corsicanus. It is remarkable that mtDNA introgression in hares is frequent, extensive and always from the same donor arctic species. We discuss possible explanations for the phenomenon in relation to the dynamics of range expansions and species replacements during the climatic oscillations of the Pleistocene.

Keywords

Lepus, species-tree inference, discordant phylogenies, introgression, rapid radiation, coalescent simulations

External links

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S11662
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref19825,
  	 author = {Jose  Melo-Ferreira and Pierre  Boursot and Miguel  Carneiro and Pedro Jose Esteves and Liliana  Farelo and Paulo Celio Alves},
  	 title = {Recurrent Introgression of Mitochondrial DNA Among Hares (Lepus spp.) revealed by Species-tree Inference and Coalescent Simulations},
  	 year = {2011},
  	 keywords = {Lepus, species-tree inference, discordant phylogenies, introgression, rapid radiation, coalescent simulations},
  	 doi = {},
  	 url = {http://},
  	 pmid = {},
  	 journal = {Systematic Biology},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {Understanding recent speciation history requires merging phylogenetic and population genetics approaches, taking into account the persistence of ancestral polymorphism and possible introgression. The emergence of a clear phylogeny of hares (genus Lepus) has been hampered by poor genomic sampling and possible occurrence of mitochondrial DNA introgression from the arctic/boreal Lepus timidus into several European temperate and American boreal species. However, no formal test of introgression, taking also incomplete lineage sorting into account, has been done.  Here, to clarify the yet poorly resolved species phylogeny of hares and test hypotheses of mtDNA introgression we sequenced 14 nuclear DNA and two mtDNA fragments (8,196 bp and 1,113 bp respectively) in 50 specimens from 11 hare species from Eurasia, North America and Africa. By applying an Isolation-with-migration (IM) model to the nuclear data on subsets of species, we find evidence for very limited gene flow from L. timidus into most temperate European species, and not into the American boreal ones. Using a multi-locus coalescent based method we infer the species phylogeny, which we find highly incongruent with mtDNA phylogeny using parametric bootstrap. Simulations of mtDNA evolution under the speciation history inferred from nuclear genes did not support the hypothesis of mtDNA introgression from L. timidus into the American L. townsendii but did suggest introgression from L. timidus into four temperate European species. One such event likely resulted in the complete replacement of the aboriginal mtDNA of L. castroviejoi and of its sister species L. corsicanus. It is remarkable that mtDNA introgression in hares is frequent, extensive and always from the same donor arctic species. We discuss possible explanations for the phenomenon in relation to the dynamics of range expansions and species replacements during the climatic oscillations of the Pleistocene.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 19825
  AU  - Melo-Ferreira,Jose 
  AU  - Boursot,Pierre 
  AU  - Carneiro,Miguel 
  AU  - Esteves,Pedro Jose
  AU  - Farelo,Liliana 
  AU  - Alves,Paulo Celio
  T1  - Recurrent Introgression of Mitochondrial DNA Among Hares (Lepus spp.) revealed by Species-tree Inference and Coalescent Simulations
  PY  - 2011
  KW  - Lepus
  KW  - species-tree inference
  KW  - discordant phylogenies
  KW  - introgression
  KW  - rapid radiation
  KW  - coalescent simulations
  UR  - http://dx.doi.org/
  N2  - Understanding recent speciation history requires merging phylogenetic and population genetics approaches, taking into account the persistence of ancestral polymorphism and possible introgression. The emergence of a clear phylogeny of hares (genus Lepus) has been hampered by poor genomic sampling and possible occurrence of mitochondrial DNA introgression from the arctic/boreal Lepus timidus into several European temperate and American boreal species. However, no formal test of introgression, taking also incomplete lineage sorting into account, has been done.  Here, to clarify the yet poorly resolved species phylogeny of hares and test hypotheses of mtDNA introgression we sequenced 14 nuclear DNA and two mtDNA fragments (8,196 bp and 1,113 bp respectively) in 50 specimens from 11 hare species from Eurasia, North America and Africa. By applying an Isolation-with-migration (IM) model to the nuclear data on subsets of species, we find evidence for very limited gene flow from L. timidus into most temperate European species, and not into the American boreal ones. Using a multi-locus coalescent based method we infer the species phylogeny, which we find highly incongruent with mtDNA phylogeny using parametric bootstrap. Simulations of mtDNA evolution under the speciation history inferred from nuclear genes did not support the hypothesis of mtDNA introgression from L. timidus into the American L. townsendii but did suggest introgression from L. timidus into four temperate European species. One such event likely resulted in the complete replacement of the aboriginal mtDNA of L. castroviejoi and of its sister species L. corsicanus. It is remarkable that mtDNA introgression in hares is frequent, extensive and always from the same donor arctic species. We discuss possible explanations for the phenomenon in relation to the dynamics of range expansions and species replacements during the climatic oscillations of the Pleistocene.
  L3  - 
  JF  - Systematic Biology
  VL  - 
  IS  - 
  ER  -