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Citation for Study 13356

Citation title: "Sampling strategies for species trees: The effects on phylogenetic inference of the number of genes, number of individuals, and whether loci are mitochondrial, sex-linked, or autosomal".

Study name: "Sampling strategies for species trees: The effects on phylogenetic inference of the number of genes, number of individuals, and whether loci are mitochondrial, sex-linked, or autosomal".

This study is part of submission 13356 (Status: Published).

Citation

Corl A., & Ellegren H. 2013. Sampling strategies for species trees: The effects on phylogenetic inference of the number of genes, number of individuals, and whether loci are mitochondrial, sex-linked, or autosomal. Molecular Phylogenetics and Evolution, 67: 358-366.

Authors

• Corl A. (submitter) 5103268813
• Ellegren H.

Abstract

Systematists can now use multi-locus data to construct species trees that take into account the stochastic nature of gene tree divergence among populations. There is a need to evaluate the new methods for species tree reconstruction in order to determine what kinds of loci to use and the most effective sampling schemes in terms of numbers of genes and numbers of individuals per species. Here we study sampling strategies with an empirical data set for six shorebird species in which we sequenced 1 mitochondrial, 12 autosomal, and 12 Z-linked loci for >8 individuals/species. We found that sampling greater numbers of genes resulted in substantial improvements to the resolution of the species tree, but sampling greater numbers of individuals had minor effects. We found that Z-linked loci significantly outperformed autosomal loci at all levels of sampling, which likely resulted from the lower effective population size of the Z-linked loci. Therefore, sex-linked loci are likely to be a powerful tool for multi-locus phylogenetic studies. We found that adding a mitochondrial gene to a set of Z-linked or autosomal loci substantially improved the resolution of the tree. Overall, our results help evaluate how best to maximize phylogenetic resolution while minimizing the costs of sequencing and computation when performing species tree analyses.

Keywords

*BEAST, effective population size, sex chromosomes, mtDNA, Z chromosome, Charadriiformes, shorebirds, phylogeny, gene tree, species tree

External links

• Other URL: http://dx.doi.org/10.1016/j.ympev.2013.02.002

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S13356
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref21325,
  	 author = {Ammon  Corl and Hans  Ellegren},
  	 title = {Sampling strategies for species trees: The effects on phylogenetic inference of the number of genes, number of individuals, and whether loci are mitochondrial, sex-linked, or autosomal},
  	 year = {2013},
  	 keywords = {*BEAST, effective population size, sex chromosomes, mtDNA, Z chromosome, Charadriiformes, shorebirds, phylogeny, gene tree, species tree},
  	 doi = {},
  	 url = {http://dx.doi.org/10.1016/j.ympev.2013.02.002},
  	 pmid = {},
  	 journal = {Molecular Phylogenetics and Evolution},
  	 volume = {67},
  	 number = {},
  	 pages = {358--366},
  	 abstract = {Systematists can now use multi-locus data to construct species trees that take into account the stochastic nature of gene tree divergence among populations.  There is a need to evaluate the new methods for species tree reconstruction in order to determine what kinds of loci to use and the most effective sampling schemes in terms of numbers of genes and numbers of individuals per species.  Here we study sampling strategies with an empirical data set for six shorebird species in which we sequenced 1 mitochondrial, 12 autosomal, and 12 Z-linked loci for >8 individuals/species.  We found that sampling greater numbers of genes resulted in substantial improvements to the resolution of the species tree, but sampling greater numbers of individuals had minor effects.  We found that Z-linked loci significantly outperformed autosomal loci at all levels of sampling, which likely resulted from the lower effective population size of the Z-linked loci.  Therefore, sex-linked loci are likely to be a powerful tool for multi-locus phylogenetic studies.  We found that adding a mitochondrial gene to a set of Z-linked or autosomal loci substantially improved the resolution of the tree.  Overall, our results help evaluate how best to maximize phylogenetic resolution while minimizing the costs of sequencing and computation when performing species tree analyses.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 21325
  AU  - Corl,Ammon 
  AU  - Ellegren,Hans 
  T1  - Sampling strategies for species trees: The effects on phylogenetic inference of the number of genes, number of individuals, and whether loci are mitochondrial, sex-linked, or autosomal
  PY  - 2013
  KW  - *BEAST
  KW  - effective population size
  KW  - sex chromosomes
  KW  - mtDNA
  KW  - Z chromosome
  KW  - Charadriiformes
  KW  - shorebirds
  KW  - phylogeny
  KW  - gene tree
  KW  - species tree
  UR  - http://dx.doi.org/10.1016/j.ympev.2013.02.002
  N2  - Systematists can now use multi-locus data to construct species trees that take into account the stochastic nature of gene tree divergence among populations.  There is a need to evaluate the new methods for species tree reconstruction in order to determine what kinds of loci to use and the most effective sampling schemes in terms of numbers of genes and numbers of individuals per species.  Here we study sampling strategies with an empirical data set for six shorebird species in which we sequenced 1 mitochondrial, 12 autosomal, and 12 Z-linked loci for >8 individuals/species.  We found that sampling greater numbers of genes resulted in substantial improvements to the resolution of the species tree, but sampling greater numbers of individuals had minor effects.  We found that Z-linked loci significantly outperformed autosomal loci at all levels of sampling, which likely resulted from the lower effective population size of the Z-linked loci.  Therefore, sex-linked loci are likely to be a powerful tool for multi-locus phylogenetic studies.  We found that adding a mitochondrial gene to a set of Z-linked or autosomal loci substantially improved the resolution of the tree.  Overall, our results help evaluate how best to maximize phylogenetic resolution while minimizing the costs of sequencing and computation when performing species tree analyses.
  L3  - 
  JF  - Molecular Phylogenetics and Evolution
  VL  - 67
  IS  - 
  SP  - 358
  EP  - 366
  ER  -