@ARTICLE{TreeBASE2Ref22234,
author = {Jared Anthony Grummer and R. W. Bryson and Tod W Reeder},
title = {Species Delimitation Using Bayes Factors: Simulations and Application to the Sceloporus scalaris Species Group (Squamata: Phrynosomatidae)},
year = {2013},
keywords = {Incomplete lineage sorting, model choice, Bayesian, marginal likelihood estimation, Mexico, *BEAST, BP&P},
doi = {},
url = {http://},
pmid = {},
journal = {Systematic Biology},
volume = {},
number = {},
pages = {},
abstract = {Current molecular methods of species delimitation are limited by the types of species delimitation models and scenarios that can be tested. Bayes factors allow for more flexibility in testing non-nested species delimitation models and hypotheses of individual assignment to alternative lineages. Here, we examined the efficacy of Bayes factors in delimiting species through simulations and empirical data from the Sceloporus scalaris species group. Marginal likelihood scores of competing species delimitation models, from which Bayes factor values were compared, were estimated with four different methods: harmonic mean estimation, smoothed harmonic mean estimation, path-sampling/thermodynamic integration, and stepping-stone analysis. We also performed model selection using a posterior simulation-based analog of the Akaike information criterion through Markov chain Monte Carlo analysis (AICM). Bayes factor species delimitation results from the empirical data were then compared with results from the reversible-jump MCMC (rjMCMC) coalescent-based species delimitation method Bayesian Phylogenetics and Phylogeography (BP&P). Simulation results show that harmonic and smoothed harmonic mean estimators perform poorly compared to path sampling and stepping stone marginal likelihood estimators when identifying the true species delimitation model. Furthermore, Bayes factor species delimitation showed improved performance when species limits are tested by reassigning individuals between species, as opposed to either lumping or splitting lineages. In the empirical data, Bayes factor species delimitation through path sampling and stepping-stone analyses, as well as the rjMCMC method, each provide support for the recognition of all scalaris group taxa as independent evolutionary lineages. Bayes factor species delimitation and BP&P also support the recognition of three previously undescribed lineages. In both simulated and empirical datasets, harmonic and smoothed harmonic mean marginal likelihood estimators provided much higher marginal likelihood estimates than path sampling and stepping-stone estimators. The AICM displayed poor repeatability in both simulated and empirical datasets, and produced inconsistent model rankings across replicate runs with the empirical data. Our results suggest that species delimitation through the use of Bayes factors with marginal likelihood estimates via path-sampling or stepping-stone analyses provide a useful and complementary alternative to existing species delimitation methods.}
}
Taxa for Study 14522
Citation title:
"Species Delimitation Using Bayes Factors: Simulations and Application to the Sceloporus scalaris Species Group (Squamata: Phrynosomatidae)".
Study name:
"Species Delimitation Using Bayes Factors: Simulations and Application to the Sceloporus scalaris Species Group (Squamata: Phrynosomatidae)".
This study is part of submission 14522
(Status: Published).
Taxa
ID |
Taxon Label |
NCBI taxid |
uBIO namebankID |
1155957 |
Sceloporus aeneus aeneus |
|
204336
|
1156012 |
Sceloporus aeneus aeneus 02 |
|
204336
|
1156001 |
Sceloporus aeneus subniger |
|
204338
|
1155973 |
Sceloporus aeneus subniger 02 |
|
204338
|
1156021 |
Sceloporus aeneus subniger 03 |
|
204338
|
1155988 |
Sceloporus aeneus subniger 04 |
|
204338
|
1155999 |
Sceloporus aeneus subniger 05 |
|
204338
|
1156015 |
Sceloporus aeneus subniger 06 |
|
204338
|
1155996 |
Sceloporus aeneus subniger 07 |
|
204338
|
1155963 |
Sceloporus aeneus subniger 08 |
|
204338
|
1155969 |
Sceloporus aeneus subniger 09 |
|
204338
|
1155983 |
Sceloporus aeneus subniger 10 |
|
204338
|
1155977 |
Sceloporus aeneus subniger 11 |
|
204338
|
1155987 |
Sceloporus aeneus subniger 12 |
|
204338
|
1155970 |
Sceloporus aeneus subniger 13 |
|
204338
|
1155959 |
Sceloporus aeneus subniger 14 |
|
204338
|
1155994 |
Sceloporus aeneus subniger 15 |
|
204338
|
1156020 |
Sceloporus aeneus subniger 16 |
|
204338
|
1156016 |
Sceloporus aeneus subniger 17 |
|
204338
|
1155984 |
Sceloporus aeneus subniger 18 |
|
204338
|
1155997 |
Sceloporus bicanthalis |
57313
|
2544664
|
1155967 |
Sceloporus bicanthalis 02 |
57313
|
2544664
|
1155958 |
Sceloporus bicanthalis 03 |
57313
|
2544664
|
1156022 |
Sceloporus bicanthalis 04 |
57313
|
2544664
|
1156009 |
Sceloporus bicanthalis 05 |
57313
|
2544664
|
1155993 |
Sceloporus bicanthalis 06 |
57313
|
2544664
|
1155980 |
Sceloporus bicanthalis 07 |
57313
|
2544664
|
1155974 |
Sceloporus bicanthalis 08 |
57313
|
2544664
|
1155979 |
Sceloporus bicanthalis 09 |
57313
|
2544664
|
1156007 |
Sceloporus bicanthalis 10 |
57313
|
2544664
|
1156008 |
Sceloporus chaneyi |
57314
|
204347
|
1155966 |
Sceloporus chaneyi 02 |
57314
|
204347
|
1156002 |
Sceloporus chaneyi 03 |
57314
|
204347
|
1156000 |
Sceloporus chaneyi 04 |
57314
|
204347
|
1155976 |
Sceloporus clarkii |
235405
|
204349
|
1156014 |
Sceloporus graciosus |
43625
|
2544687
|
1155992 |
Sceloporus magister |
43627
|
2544714
|
1156024 |
Sceloporus samcolemani |
|
2544752
|
1155971 |
Sceloporus samcolemani 02 |
|
2544752
|
1155964 |
Sceloporus samcolemani 03 |
|
2544752
|
1155995 |
Sceloporus samcolemani 04 |
|
2544752
|
1156018 |
Sceloporus samcolemani 05 |
|
2544752
|
1155961 |
Sceloporus samcolemani 06 |
|
2544752
|
1156005 |
Sceloporus scalaris brownorum |
|
2549346
|
1156017 |
Sceloporus scalaris brownorum 02 |
|
2549346
|
1155965 |
Sceloporus scalaris brownorum 03 |
|
2549346
|
1155975 |
Sceloporus scalaris brownorum 04 |
|
2549346
|
1156010 |
Sceloporus scalaris brownorum 05 |
|
2549346
|
1155991 |
Sceloporus scalaris brownorum 06 |
|
2549346
|
1156006 |
Sceloporus scalaris brownorum 07 |
|
2549346
|
1155985 |
Sceloporus scalaris brownorum 08 |
|
2549346
|
1156003 |
Sceloporus scalaris scalaris |
|
2544754
|
1155982 |
Sceloporus scalaris scalaris 02 |
|
2544754
|
1156019 |
Sceloporus scalaris scalaris 03 |
|
2544754
|
1155962 |
Sceloporus scalaris scalaris 04 |
|
2544754
|
1156004 |
Sceloporus scalaris scalaris 05 |
|
2544754
|
1155986 |
Sceloporus scalaris scalaris 06 |
|
2544754
|
1156023 |
Sceloporus scalaris scalaris 07 |
|
2544754
|
1156013 |
Sceloporus scalaris scalaris 08 |
|
2544754
|
1156027 |
Sceloporus scalaris unicanthalis |
|
2544756
|
1156025 |
Sceloporus scalaris unicanthalis 02 |
|
2544756
|
1155981 |
Sceloporus slevini |
|
204495
|
1155960 |
Sceloporus slevini 02 |
|
204495
|
1155968 |
Sceloporus slevini 03 |
|
204495
|
1155978 |
Sceloporus slevini 04 |
|
204495
|
1155990 |
Sceloporus slevini 05 |
|
204495
|
1155998 |
Sceloporus slevini 06 |
|
204495
|
1156011 |
Sceloporus slevini 07 |
|
204495
|
1155989 |
Sceloporus slevini 08 |
|
204495
|
1156026 |
Sceloporus slevini 09 |
|
204495
|
1156028 |
Sceloporus slevini 10 |
|
204495
|
1155972 |
Sceloporus undulatus |
8520
|
2544779
|