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Citation for Study 11925

Citation title: "Accuracy and precision of species trees: effects of locus, individual, and base pair sampling on inference of species trees in lizards of the Liolaemus darwinii group (Squamata, Liolaemidae)".

Study name: "Accuracy and precision of species trees: effects of locus, individual, and base pair sampling on inference of species trees in lizards of the Liolaemus darwinii group (Squamata, Liolaemidae)".

This study is part of submission 11925 (Status: Published).

Citation

Camargo A., Avila L.J., Morando M., & Sites J.W. 2012. Accuracy and precision of species trees: effects of locus, individual, and base pair sampling on inference of species trees in lizards of the Liolaemus darwinii group (Squamata, Liolaemidae). Systematic Biology, 61(2): 272-288.

Authors

• Camargo A. (submitter) (++ 598) 96 850 999
• Avila L.J.
• Morando M.
• Sites J.W.

Abstract

Molecular phylogenetics has entered a new era in which species trees are estimated from a collection of gene trees using methods that accommodate their heterogeneity and discordance with the species tree. Empirical evaluation of species trees is necessary to assess the performance (i.e., accuracy and precision) of these methods with real data, which consists of gene genealogies likely shaped by different historical and demographic processes. We analyzed 20 loci for 16 species of the South American lizards of the Liolaemus darwinii species group and reconstructed a species tree with *BEAST, then compared the performance of this method under different sampling strategies of loci, individuals, and sequence lengths. We found an increase in the accuracy and precision of species trees with the number of loci, but for any number of loci, accuracy substantially decreased only when using only one individual per species or 25% of the full sequence length (∼ 147 bp). In addition, locus "informativeness" was an important factor in the accuracy/precision of species trees when using a few loci, but it became increasingly irrelevant with additional loci. Our empirical results combined with the previous simulation studies suggest that there is an optimal range of sampling effort of loci, individuals, and sequence lengths for a given speciation history and information content of the data. Future studies should be directed toward further assessment of other factors that can impact performance of species trees, including gene flow, locus "informativeness," tree shape, missing data, and errors in species delimitation.

Keywords

Accuracy, coalescent, Liolaemus, phylogeny, precision, sampling, South America, species trees

External links

• DOI: 10.1093/sysbio/syr105
• PMID: 220763
• Other URL: http://academic.oup.com/sysbio/article-lookup/doi/10.1093/sysbio/syr105

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S11925
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref20047,
  	 author = {Arley  Camargo and Luciano Javier Avila and Mariana  Morando and Jack W. Sites},
  	 title = {Accuracy and precision of species trees: effects of locus, individual, and base pair sampling on inference of species trees in lizards of the Liolaemus darwinii group (Squamata, Liolaemidae)},
  	 year = {2012},
  	 keywords = {Accuracy, coalescent, Liolaemus, phylogeny, precision, sampling, South America, species trees},
  	 doi = {10.1093/sysbio/syr105},
  	 url = {http://academic.oup.com/sysbio/article-lookup/doi/10.1093/sysbio/syr105},
  	 pmid = {220763},
  	 journal = {Systematic Biology},
  	 volume = {61},
  	 number = {2},
  	 pages = {272--288},
  	 abstract = {Molecular phylogenetics has entered a new era in which species trees are estimated from a collection of gene trees using methods that accommodate their heterogeneity and discordance with the species tree. Empirical evaluation of species trees is necessary to assess the performance (i.e., accuracy and precision) of these methods with real data, which consists of gene genealogies likely shaped by different historical and demographic processes. We analyzed 20 loci for 16 species of the South American lizards of the Liolaemus darwinii species group and reconstructed a species tree with *BEAST, then compared the performance of this method under different sampling strategies of loci, individuals, and sequence lengths. We found an increase in the accuracy and precision of species trees with the number of loci, but for any number of loci, accuracy substantially decreased only when using only one individual per species or 25% of the full sequence length (∼ 147 bp). In addition, locus "informativeness" was an important factor in the accuracy/precision of species trees when using a few loci, but it became increasingly irrelevant with additional loci. Our empirical results combined with the previous simulation studies suggest that there is an optimal range of sampling effort of loci, individuals, and sequence lengths for a given speciation history and information content of the data. Future studies should be directed toward further assessment of other factors that can impact performance of species trees, including gene flow, locus "informativeness," tree shape, missing data, and errors in species delimitation.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 20047
  AU  - Camargo,Arley 
  AU  - Avila,Luciano Javier
  AU  - Morando,Mariana 
  AU  - Sites,Jack W.
  T1  - Accuracy and precision of species trees: effects of locus, individual, and base pair sampling on inference of species trees in lizards of the Liolaemus darwinii group (Squamata, Liolaemidae)
  PY  - 2012
  KW  - Accuracy
  KW  - coalescent
  KW  - Liolaemus
  KW  - phylogeny
  KW  - precision
  KW  - sampling
  KW  - South America
  KW  - species trees
  UR  - http://academic.oup.com/sysbio/article-lookup/doi/10.1093/sysbio/syr105
  N2  - Molecular phylogenetics has entered a new era in which species trees are estimated from a collection of gene trees using methods that accommodate their heterogeneity and discordance with the species tree. Empirical evaluation of species trees is necessary to assess the performance (i.e., accuracy and precision) of these methods with real data, which consists of gene genealogies likely shaped by different historical and demographic processes. We analyzed 20 loci for 16 species of the South American lizards of the Liolaemus darwinii species group and reconstructed a species tree with *BEAST, then compared the performance of this method under different sampling strategies of loci, individuals, and sequence lengths. We found an increase in the accuracy and precision of species trees with the number of loci, but for any number of loci, accuracy substantially decreased only when using only one individual per species or 25% of the full sequence length (∼ 147 bp). In addition, locus "informativeness" was an important factor in the accuracy/precision of species trees when using a few loci, but it became increasingly irrelevant with additional loci. Our empirical results combined with the previous simulation studies suggest that there is an optimal range of sampling effort of loci, individuals, and sequence lengths for a given speciation history and information content of the data. Future studies should be directed toward further assessment of other factors that can impact performance of species trees, including gene flow, locus "informativeness," tree shape, missing data, and errors in species delimitation.
  L3  - 10.1093/sysbio/syr105
  JF  - Systematic Biology
  VL  - 61
  IS  - 2
  SP  - 272
  EP  - 288
  ER  -