Imperial College London

ProfessorTimothyBarraclough

Faculty of Natural SciencesDepartment of Life Sciences (Silwood Park)

Professor of Evolutionary Biology
 
 
 
//

Contact

 

+44 (0)20 7594 2247t.barraclough Website

 
 
//

Location

 

N2.4Silwood ParkSilwood Park

//

Summary

 

Publications

Citation

BibTex format

@article{Tang:2014:10.1111/2041-210X.12246,
author = {Tang, CQ and Humphreys, AM and Fontaneto, D and Barraclough, TG},
doi = {10.1111/2041-210X.12246},
journal = {Methods in Ecology and Evolution},
pages = {1086--1094},
title = {Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data},
url = {http://dx.doi.org/10.1111/2041-210X.12246},
volume = {5},
year = {2014}
}

RIS format (EndNote, RefMan)

TY  - JOUR
AB - 1. Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The generalised mixed Yule coalescent (GMYC) and the Poisson tree process (PTP) are methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene trees as input, intended for use mostly with single-locus data such asDNAbarcodes. 2. Here, we assess how robust the GMYC and PTP are to different phylogenetic reconstruction and branch smoothingmethods.We reconstruct over 400 ultrametric trees using up to 30 different combinations of phylogenetic and smoothing methods and perform over 2000 separate species delimitation analyses across 16 empirical data sets. We then assess how variable diversity estimates are, in terms of richness and identity, with respect to species delimitation, phylogenetic and smoothing methods. 3. The PTP method generally generates diversity estimates that are more robust to different phylogenetic methods. The GMYC is more sensitive, but provides consistent estimates for BEAST trees. The lower consistency of GMYC estimates is likely a result of differences among gene trees introduced by the smoothing step. Unresolved nodes (real anomalies or methodological artefacts) affect both GMYC and PTP estimates, but have a greater effect on GMYC estimates. Branch smoothing is a difficult step and perhaps an underappreciated source of bias that may be widespread among studies of diversity and diversification. 4. Nevertheless, careful choice of phylogenetic method does produce equivalent PTP and GMYC diversity estimates. We recommend simultaneous use of the PTP model with any model-based gene tree (e.g. RAxML) and GMYCapproaches with BEAST trees for obtaining species hypotheses.
AU - Tang,CQ
AU - Humphreys,AM
AU - Fontaneto,D
AU - Barraclough,TG
DO - 10.1111/2041-210X.12246
EP - 1094
PY - 2014///
SN - 2041-210X
SP - 1086
TI - Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data
T2 - Methods in Ecology and Evolution
UR - http://dx.doi.org/10.1111/2041-210X.12246
UR - http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12246/abstract
UR - http://hdl.handle.net/10044/1/18180
VL - 5
ER -