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dc.contributor.author Fujisawa, Tomochika
dc.contributor.author Barraclough, Timothy G.
dc.date.accessioned 2013-06-17T17:19:45Z
dc.date.available 2013-06-17T17:19:45Z
dc.date.issued 2013-05-16
dc.identifier doi:10.5061/dryad.0hv88
dc.identifier.citation Fujisawa T, Barraclough TG (2013) Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent approach: a revised method and evaluation on simulated data sets. Systematic Biology 62(5): 707-724.
dc.identifier.uri http://hdl.handle.net/10255/dryad.45586
dc.description DNA barcoding-type studies assemble single-locus data from large samples of individuals and species, and have provided new kinds of data for evolutionary surveys of diversity. An important goal of many such studies is to delimit evolutionarily significant species units, especially in biodiversity surveys from environmental DNA samples. The Generalized Mixed Yule Coalescent (GMYC) method is a likelihood method for delimiting species by fitting within- and between-species branching models to reconstructed gene trees. Although the method has been widely used, it has not previously been described in detail or evaluated fully against simulations of alternative scenarios of true patterns of population variation and divergence between species. Here, we present important reformulations to the GMYC method as originally specified, and demonstrate its robustness to a range of departures from its simplifying assumptions. The main factor affecting the accuracy of delimitation is the mean population size of species relative to divergence times between them. Other departures from the model assumptions, such as varying population sizes among species, alternative scenarios for speciation and extinction, and population growth or subdivision within species, have relatively smaller effects. Our simulations demonstrate that support measures derived from the likelihood function provide a robust indication of when the model performs well and when it leads to inaccurate delimitations. Finally, the so-called single-threshold version of the method outperforms the multiple-threshold version of the method on simulated data: we argue that this might represent a fundamental limit due to the nature of evidence used to delimit species in this approach. Together with other studies comparing its performance relative to other methods, our findings support the robustness of GMYC as a tool for delimiting species when only single-locus information is available.
dc.relation.haspart doi:10.5061/dryad.0hv88/1
dc.relation.haspart doi:10.5061/dryad.0hv88/2
dc.relation.haspart doi:10.5061/dryad.0hv88/3
dc.relation.haspart doi:10.5061/dryad.0hv88/4
dc.relation.isreferencedby doi:10.1093/sysbio/syt033
dc.relation.isreferencedby PMID:23681854
dc.subject species
dc.subject speciation
dc.subject neutral
dc.subject genealogical
dc.subject DNA
dc.subject clusters
dc.subject coalescent
dc.title Data from: Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent approach: a revised method and evaluation on simulated data sets
dc.type Article *
dc.contributor.correspondingAuthor Barraclough, Timothy G.
prism.publicationName Systematic Biology

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Title Fujisawa.SupplementaryTable&Figures
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Description Supplementary table and figures for Fujisawa and Barraclough 2013
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Title Fujisawa.Rcode
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Description Zipped file containing the R code for simulations and analyses reported in Fujisawa and Barraclough 2013
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Title tigerbeetle_trees
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Description Tiger beetle trees from Pons et al. 2006 and 2011 used as examples in Fujisawa and Barraclough 2013
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Title Fujisawa.SimulationAtoH.outputs
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Description Simulated trees used in Fujisawa and Barraclough 2013
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