Coalescent-based species delimitation in an integrative taxonomy

Assessing species boundaries and the phylogenetic position of the rare Szechwan ratsnake, Euprepiophis perlaceus (Serpentes: Colubridae), using coalescent-based methods

“…Delimiting species and clarifying the phylogenetic relationship among taxa are crucial objectives in systematics, both of which are important for enumerating and understanding the origins of biodiversity and implementing conservation management strategies (Myers et al, 2013;Fujita et al, 2012;O'Meara, 2010;Sites and Marshall, 2004;Wilson, 2003). For taxon delimitation, a species concept and the criteria to define the species boundaries are necessary.…”

“…molecular, morphological, ecological, and behavioral) for taxonomy is expected to reduce subjectivity in delimiting taxa (Dayrat, 2005;Leaché et al, 2009;Padial et al, 2010;Schlick-Steiner et al, 2010;Yeates et al, 2011). However, in situations where cryptic species with indistinct morphological and ecological properties are present, integrative methods will not yield a clear result since different types of data may yield discordant conclusions (Fujita et al, 2012;Wiens and Penkrot, 2002). Coalescent models, which describe the evolutionary processes of populations by tracing alleles back to their most recent common ancestor in a mathematical and probabilistic framework (Kingman, 2000;Wakeley, 2008) have been recommended for species delimitation and species tree inference (Fujita et al, 2012;O'Meara, 2010).…”

“…However, in situations where cryptic species with indistinct morphological and ecological properties are present, integrative methods will not yield a clear result since different types of data may yield discordant conclusions (Fujita et al, 2012;Wiens and Penkrot, 2002). Coalescent models, which describe the evolutionary processes of populations by tracing alleles back to their most recent common ancestor in a mathematical and probabilistic framework (Kingman, 2000;Wakeley, 2008) have been recommended for species delimitation and species tree inference (Fujita et al, 2012;O'Meara, 2010). Gene trees of different loci should sort randomly when assuming a panmictic population without selection, migration or linkage.…”

“…Similarly, coalescent model based methods use multi-locus markers to estimate important parameters for inferring a species tree given lineage sorting (e.g. population size h and divergence time s, Fujita et al, 2012).…”

Phylogenetic Pattern, Evolutionary Processes and Species Delimitation in the Genus Echinococcus

“…For example, if we consider the genotypes of E. canadensis, there are four different species trees that are compatible with the mtDNA phylogeny and these species trees contain different numbers of population demographic parameters (Figure 3). Bayesian or 24 maximum likelihood approaches can be used to evaluate the fit of parameter estimates from gene trees to those expected from different species trees (Fujita et al, 2012).…”