Delimiting Species Using Single-Locus Data and the Generalized Mixed Yule Coalescent Approach: A Revised Method and Evaluation on Simulated Data Sets

Abstract

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. [Clusters; coalescent; DNA; genealogical; neutral; speciation; species.]

Fifteen species in one: deciphering the Brachionus plicatilis species complex (Rotifera, Monogononta) through DNA taxonomy

“…The generalised mixed Yule coalescent (GMYC) model was applied to search for evidence of independently evolving entities akin to species, optimising the threshold between within-species coalescent processes and between-species Yule processes on the branching patterns (Fujisawa & Barraclough, 2013). GMYC models were run on (i) the BEAST trees for the three alignments (COI, ITS, and CO1 ?…”

High diversity in Keratella cochlearis (Rotifera, Monogononta): morphological and genetic evidence

“…We inferred mtDNA groups within K. cochlearis with the generalised mixed Yule coalescent (GMYC) approach (Fujisawa & Barraclough, 2013), the Poisson tree process model (PTP; Zhang et al, 2013), and the automatic barcode gap discovery (ABGD; Puillandre et al, 2012) and compared the results. For all methods, the outgroup was excluded prior to the analyses.…”

Difference without distinction? Gaps in cyanobacterial systematics; when more is just too much

“…Also, species described under ICNP are much less frequent than under ICN. PTP outperforms other automatic delimitation algorithms such as GMYC (Fujisawa & Barraclough 2013;Pons et al 2006), because it does not require an often error-prone ultrametric tree and it has significantly faster performance on large datasets (Zhang et al 2013).…”