Bayesian species delimitation using multilocus sequence data

By Ziheng Yang, Bruce Rannala. Proceedings of the National Academy of Sciences of the United States of America, 2010

1,320 citations recorded by the source corpus.

Subfields: Ecological Modeling, Ecology, Genetics

View Paper: https://www.semanticscholar.org/paper/2f9b0bd593acfa816b56919a7b2f3e4c142cadf6

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Citations in the corpus

Molecular phylogenetics: principles and practice (2012, background): “Such data can also be used to delimit species (that is, to determine whether a population consists of one or two species, for example) 121,122 .”
The art and science of species delimitation (2015, neutral): “Although (Yang and Rannala, 2010.) have previously associated the model underlying Bayesian species delimitation methods with the Biological Species Concept, reproductive isolation is a sufficient condition for identification of species under the model but not a necessary one (the delimited species…”
Species taxonomy of birds: Which null hypothesis? (2014, background): “Alternatively, advantageous mtDNA of one species may sweep through and replace that of the other species as a positive source of climatic adaptation (Zink and Barrowclough 2008, McKay and Zink 2010, Rheindt and Edwards 2011).”
Species delimitation and relationships: The dance of the seven veils (2015, methodology): “Several software packages are now available that use the multispecies coalescent framework (MSC; Appendix 1) formulized by Yang & Rannala (2010).”
Species Delimitation in Herpetology (2019, methodology): “Hence, multispecies coalescent theory (MSC) often is applied to the species delimitation problem (Leaché and Fujita, 2010; Yang and Rannala, 2010; Zhang et al., 2011; Leaché et al., 2014; Yang, 2015).”
Species Delimitation using Genome-Wide SNP Data (2013, background): “Bayes factor species delimitation has a number of advantages over other Bayesian species delimitation approaches Yang and Rannala (2010).”
The BPP program for species tree estimation and species delimitation (2015, methodology): “We assign a gamma prior G(2, 1000) for all parameters, and 0 ~ G(2, 2000) for the age of the root, while the other divergence time parameters are assigned the uniform Dirichlet prior (Yang and Rannala, 2010: equation 2).”
How to fail at species delimitation (2013, methodology): “Existing models range from nonparametric (e.g. Wiens & Penkrot 2002) to highly parameterized models (e.g. Yang & Rannala 2010).”
DNA-based species delimitation in algae (2014, methodology): “…are difficult to distinguish based on phenotypic features, and have been applied in various eukaryotic groups including animals (Carstens & Dewey, 2010; Leaché & Fujita, 2010; Yang & Rannala, 2010; Camargo et al., 2012), fungi (Leavitt et al., 2011) and land plants (Barrett & Freudenstein, 2011).”
A general species delimitation method with applications to phylogenetic placements (2013, methodology): “In analogy to BP&P (Yang and Rannala, 2010) and GMYC (Pons et al.”
Reproductive isolation and the causes of speciation rate variation in nature (2016, methodology): “Coalescent-based species delimitation using population genetic data (Pons et al., 2006; Yang & Rannala, 2010) represents a trend towards greater practical application of BSClike species concepts to taxonomy (Fujita et al., 2012), although the use of these models is still restricted to a small…”
Unguided Species Delimitation Using DNA Sequence Data from Multiple Loci (2014, methodology): “A general approach to investigating the evolutionary and genetic structure of a group of related organisms using multilocus genetic sequence data can be envisioned as follows: 1) Assign individuals to populations whose members currently interbreed, 2) determine whether the populations are geneticall”
Species Delimitation: A Decade After the Renaissance (2013, neutral): “have the potential of incorporating previous information about species limits derived from non-molecular data into prior distributions of genetic-based analyses [67].”
Goodbye morphology? A paradigm shift in the delimitation of species in lichenized fungi (2011, background): “Thickened branches are proportional to the level of posterior probability support, and speciation probabilities at all nodes (see [Yang and Rannala 2010] were greater than 0.95.”
Delimiting Species Using Single-Locus Data and the Generalized Mixed Yule Coalescent Approach: A Revised Method and Evaluation on Simulated Data Sets (2013, methodology): “A key challenge for multilocus approaches is to find efficient algorithms for searching alternative delimitations (Yang and Rannala 2010).”
The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence times (2015, neutral): “1) using the program MCCOAL (Rannala and Yang, 2003; Yang and Rannala, 2010).”