The art and science of species delimitation

By Bruce Rannala. 2015

125 citations recorded by the source corpus.

DNA-based approaches to systematics have changed dramatically during the last two decades with the rise of DNA barcoding methods and newer multi-locus methods for species delimitation. During the last half-decade, partly driven by the new sequencing technologies, the focus has shifted to multi-locus sequence data and the identification of species within the framework of the multi-species coalescent (MSC). In this paper, I discuss model-based Bayesian methods for species delimitation that have been developed in recent years using the MSC. Several approximate methods for species delimitation (and their limitations) are also discussed. Explicit species delimitation models have the advantage of clarifying more precisely what is being delimited and what assumptions we are making in doing so. Moreover, the methods can be very powerful when applied to large multi-locus datasets and thus take full advantage of data generated using today’s technologies.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ff210e2668fab1026b79f6a54d3e74e3b8d39a0b

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Citations in the corpus

Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent (2018, methodology): “Both include options for handling diploid sequences by analytically integrating out the different phase resolutions (Gronau et al. 2011), and for calculating the marginal likelihood (Bayes Factors) through thermodynamic integration and Gaussian quadrature (Lartillot and Philippe 2006; Rannala and Ya”
ASAP: assemble species by automatic partitioning (2020, methodology): “In this category, the most popular methods are SpedeSTEM (Ence & Carstens, 2011), BPP (Yang & Rannala, 2014) and BFD (Leaché et al., 2014), reviewed (with other methods) in several articles (Camargo & Sites, 2013; Carstens et al., 2013; Fujita et al., 2012; Leavitt et al., 2015; Rannala, 2015).”
Genetic Diversity and Conservation Units: Dealing With the Species-Population Continuum in the Age of Genomics (2018, background): “Such populations can readily be diagnosed as separate evolutionary lineages by applying statistical delimitation methods to multilocus data (Carstens et al., 2013; Rannala, 2015), but are they ephemeral populations or durable species (Sukumaran and Knowles, 2017)? It certainly is possible, within th”