scholarly journals Bayesian Species Delimitation Can Be Robust to Guide-Tree Inference Errors

2014 ◽  
Vol 63 (6) ◽  
pp. 993-1004 ◽  
Author(s):  
Chi Zhang ◽  
Bruce Rannala ◽  
Ziheng Yang
Keyword(s):  
Species Delimitation ◽  
Guide Tree ◽  
Tree Inference ◽  
Bayesian Species Delimitation

scholarly journals Species delimitation in the cyanolichen genus Rostania

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Alica Košuthová ◽  
Johannes Bergsten ◽  
Martin Westberg ◽  
Mats Wedin
Keyword(s):  
Species Delimitation ◽  
A Priori ◽  
The Other ◽  
Supporting Evidence ◽  
Coalescence Model ◽  
Guide Tree ◽  
Candidate Species ◽  
Substantial Correlation ◽  
Bayesian Species Delimitation ◽  
Β Tubulin

Abstract Background In this study, we investigate species limits in the cyanobacterial lichen genus Rostania (Collemataceae, Peltigerales, Lecanoromycetes). Four molecular markers (mtSSU rDNA, β-tubulin, MCM7, RPB2) were sequenced and analysed with two coalescent-based species delimitation methods: the Generalized Mixed Yule Coalescent model (GMYC) and a Bayesian species delimitation method (BPP) using a multispecies coalescence model (MSC), the latter with or without an a priori defined guide tree. Results Species delimitation analyses indicate the presence of eight strongly supported candidate species. Conclusive correlation between morphological/ecological characters and genetic delimitation could be found for six of these. Of the two additional candidate species, one is represented by a single sterile specimen and the other currently lacks morphological or ecological supporting evidence. Conclusions We conclude that Rostania includes a minimum of six species: R. ceranisca, R. multipunctata, R. occultata 1, R. occultata 2, R. occultata 3, and R. occultata 4,5,6. Three distinct Nostoc morphotypes occur in Rostania, and there is substantial correlation between these morphotypes and Rostania thallus morphology.

scholarly journals Uprooting phylogenetic uncertainty in coalescent species delimitation: A meta-analysis of empirical studies

2015 ◽  
Vol 61 (5) ◽  
pp. 866-873 ◽  
Author(s):  
Itzue W. Caviedes-Solis ◽  
Nassima M. Bouzid ◽  
Barbara L. Banbury ◽  
Adam D. Leaché
Keyword(s):  
Species Delimitation ◽  
Sequence Data ◽  
Meta Analysis ◽  
Empirical Studies ◽  
Species Tree ◽  
Species Trees ◽  
Posterior Probabilities ◽  
Guide Tree ◽  
Tree Topologies ◽  
Accurate Quantification

Abstract Phylogenetic and phylogeographic studies rely on the accurate quantification of biodiversity. In recent studies of taxonomically ambiguous groups, species boundaries are often determined based on multi-locus sequence data. Bayesian Phylogenetics and Phylogeography (BPP) is a coalescent-based method frequently used to delimit species; however, empirical studies suggest that the requirement of a user-specified guide tree biases the range of possible outcomes. We evaluate fifteen multi-locus datasets using the most recent iteration of BPP, which eliminates the need for a user-specified guide tree and reconstructs the species tree in synchrony with species delimitation (= unguided species delimitation). We found that the number of species recovered with guided versus unguided species delimitation was the same except for two cases, and that posterior probabilities were generally lower for the unguided analyses as a result of searching across species trees in addition to species delimitation models. The guide trees used in previous studies were often discordant with the species tree topologies estimated by BPP. We also compared species trees estimated using BPP and *BEAST and found that when the topologies are the same, BPP tends to give higher posterior probabilities.

scholarly journals Landscape genetics and species delimitation in the Andean palm rocket frog, Rheobates spp

2020 ◽  
Author(s):  
Gabrielle Genty ◽  
Carlos E. Guarnizo ◽  
Juan P. Ramírez ◽  
Lucas Barrientos ◽  
Andrew J. Crawford
Keyword(s):  
Genetic Divergence ◽  
Species Delimitation ◽  
Isolation By Distance ◽  
Genetic Distances ◽  
Nuclear Genes ◽  
Genetic Lineages ◽  
Local Environments ◽  
Isolation By Environment ◽  
Bayesian Species Delimitation ◽  
Landscape Genetic

AbstractThe complex topography of the species-rich northern Andes creates heterogeneous environmental landscapes that are hypothesized to have promoted population fragmentation and diversification by vicariance, gradients and/or the adaptation of species. Previous phylogenetic work on the Palm Rocket Frog (Anura: Aromobatidae: Rheobates spp.), endemic to mid-elevation forests of Colombia, suggested valleys were important in promoting divergence between lineages. In this study, we use a spatially, multi-locus population genetic approach of two mitochondrial and four nuclear genes from 25 samples representing the complete geographic range of the genus to delimit species and test for landscape effects on genetic divergence within Rheobates. We tested three landscape genetic models: isolation by distance, isolation by resistance, and isolation by environment. Bayesian species delimitation (BPP) and a Poisson Tree Process (PTP) model both recovered five highly divergent genetic lineages within Rheobates, rather than the three inferred in a previous study. We found that an isolation by environment provided the only variable significantly correlated with genetic distances for both mitochondrial and nuclear genes, suggesting that local adaptation may have a role driving the genetic divergence within this genus of frogs. Thus, genetic divergence in Rheobates may be driven by the local environments where these frogs live, even more so that by the environmental characteristics of the intervening regions among populations (i.e., geographic barriers).

Evaluating multilocus Bayesian species delimitation for discovery of cryptic mycorrhizal diversity

2017 ◽  
Vol 26 ◽  
pp. 74-84 ◽  
Author(s):  
Michael R. Whitehead ◽  
Renee A. Catullo ◽  
Monica Ruibal ◽  
Kingsley W. Dixon ◽  
Rod Peakall ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Bayesian Species Delimitation
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