CiteULike

Delicious

Connotea

Citation for Study 2014

Citation title: "Comparison of species tree methods for reconstructing the phylogeny of bearded manakins (Aves: Pipridae: Manacus) from multilocus sequence data.".

This study was previously identified under the legacy study ID S2006 (Status: Published).

Citation

Brumfield R., Liu L., Lum D., & Edwards S. 2008. Comparison of species tree methods for reconstructing the phylogeny of bearded manakins (Aves: Pipridae: Manacus) from multilocus sequence data. Systematic Biology, 57(5): 719-731.

Authors

• Brumfield R.
• Liu L.
• Lum D.
• Edwards S.

Abstract

While the power of multi-locus data in estimating species trees is apparent, it is also clear that the analytical methodologies for doing so are still maturing. For example, of the methods currently available for estimating species trees from multiocus data, the Bayesian method introduced by Liu and Pearl (2007; BEST) is the only one that provides nodal support values. Using gene sequences from five nuclear loci, we explored two analytical methods (deep coalescence and BEST) to reconstruct the species tree of the five primary Manacus OTUs: M. aurantiacus, M. candei, M. vitellinus, populations of M. manacus from west of the Andes (M. manacus (w)), and populations of M. manacus from east of the Andes (M. manacus (e)). Both BEST and deep coalescence supported a sister relationship between M. vitellinus and M. manacus (w).A lower probability tree from the BEST analysis and one of the most parsimonious deep coalescence trees also supported a sister relationship between M. candei and M. aurantiacus. Because hybrid zones connect the distributions of most Manacus species, we examined the potential influence of post-divergence gene flow on the sister relationship of parapatrically distributed M. vitellinus and M. manacus (w). An isolation-with-migration (IM) analysis found relatively high levels of gene flow between M. vitellinus and M. manacus (w). Whether the gene flow is obscuring a true sister relationship between M. manacus (w) and M. manacus (e) remained unclear, pointing to the need for more detailed models accommodating multispecies, multilocus DNA sequence data.

External links

• DOI: 10.1080/10635150802422290

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S2014
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref14848,
  	 author = {Robb T.  Brumfield and Leo X.  Liu and D. E.  Lum and Scott V.  Edwards},
  	 title = {Comparison of species tree methods for reconstructing the phylogeny of bearded manakins (Aves: Pipridae: Manacus) from multilocus sequence data.},
  	 year = {2008},
  	 keywords = {},
  	 doi = {10.1080/10635150802422290},
  	 url = {},
  	 pmid = {},
  	 journal = {Systematic Biology},
  	 volume = {57},
  	 number = {5},
  	 pages = {719--731},
  	 abstract = {While the power of multi-locus data in estimating species trees is apparent, it is also clear that the analytical methodologies for doing so are still maturing. For example, of the methods currently available for estimating species trees from multiocus data, the Bayesian method introduced by Liu and Pearl (2007; BEST) is the only one that provides nodal support values. Using gene sequences from five nuclear loci, we explored two analytical methods (deep coalescence and BEST) to reconstruct the species tree of the five primary Manacus OTUs: M. aurantiacus, M. candei, M. vitellinus, populations of M. manacus from west of the Andes (M. manacus (w)), and populations of M. manacus from east of the Andes (M. manacus (e)). Both BEST and deep coalescence supported a sister relationship between M. vitellinus and M. manacus (w).A lower probability tree from the BEST analysis and one of the most parsimonious deep coalescence trees also supported a sister relationship between M. candei and M. aurantiacus. Because hybrid zones connect the distributions of most Manacus species, we examined the potential influence of post-divergence gene flow on the sister relationship of parapatrically distributed M. vitellinus and M. manacus (w). An isolation-with-migration (IM) analysis found relatively high levels of gene flow between M. vitellinus and M. manacus (w). Whether the gene flow is obscuring a true sister relationship between M. manacus (w) and M. manacus (e) remained unclear, pointing to the need for more detailed models accommodating multispecies, multilocus DNA sequence data.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 14848
  AU  - Brumfield,Robb T. 
  AU  - Liu,Leo X. 
  AU  - Lum,D. E. 
  AU  - Edwards,Scott V. 
  T1  - Comparison of species tree methods for reconstructing the phylogeny of bearded manakins (Aves: Pipridae: Manacus) from multilocus sequence data.
  PY  - 2008
  KW  - 
  UR  - http://dx.doi.org/10.1080/10635150802422290
  N2  - While the power of multi-locus data in estimating species trees is apparent, it is also clear that the analytical methodologies for doing so are still maturing. For example, of the methods currently available for estimating species trees from multiocus data, the Bayesian method introduced by Liu and Pearl (2007; BEST) is the only one that provides nodal support values. Using gene sequences from five nuclear loci, we explored two analytical methods (deep coalescence and BEST) to reconstruct the species tree of the five primary Manacus OTUs: M. aurantiacus, M. candei, M. vitellinus, populations of M. manacus from west of the Andes (M. manacus (w)), and populations of M. manacus from east of the Andes (M. manacus (e)). Both BEST and deep coalescence supported a sister relationship between M. vitellinus and M. manacus (w).A lower probability tree from the BEST analysis and one of the most parsimonious deep coalescence trees also supported a sister relationship between M. candei and M. aurantiacus. Because hybrid zones connect the distributions of most Manacus species, we examined the potential influence of post-divergence gene flow on the sister relationship of parapatrically distributed M. vitellinus and M. manacus (w). An isolation-with-migration (IM) analysis found relatively high levels of gene flow between M. vitellinus and M. manacus (w). Whether the gene flow is obscuring a true sister relationship between M. manacus (w) and M. manacus (e) remained unclear, pointing to the need for more detailed models accommodating multispecies, multilocus DNA sequence data.
  L3  - 10.1080/10635150802422290
  JF  - Systematic Biology
  VL  - 57
  IS  - 5
  SP  - 719
  EP  - 731
  ER  -