coalescence

A coalescent-based estimator of genetic drift, and acoustic divergence in the Pteronotus parnellii species complex

Determining the processes responsible for phenotypic variation is one of the central tasks of evolutionary biology. While the importance of acoustic traits for foraging and communication in echolocating mammals suggests adaptation, the seldom-tested …

Sex-biased dispersal produces high error rates in mitochondrial distance-based and tree-based species delimitation

Species delimitation using mitochondrial sequences aims to identify species as morphological expertise and biodiversity both decline. Species delimitation in animals relies completely or in part on 2 criteria: genetic distance and reciprocal …

Accounting for molecular stochasticity in systematic revisions: Species limits and phylogeny of Paroaria

Different frameworks have been proposed for using molecular data in systematic revisions, but there is ongoing debate on their applicability, merits and shortcomings. In this paper we examine the fit between morphological and molecular data in the systematic revision of Paroaria, a group of conspicuous song- birds endemic to South America. We delimited species based on examination of 600 specimens, and developed distance-gap, and distance- and character-based coalescent simulations to test species limits with molecular data. The morphological and molecular data collected were then analyzed using parsi- mony, maximum likelihood, and Bayesian phylogenetics. The simulations were better at evaluating the new species limits than using genetic distances. Species diversity within Paroaria had been underesti- mated by 60%, and the revised genus comprises eight species. Phylogenetic analyses consistently recov- ered a congruent topology for the most recently derived species in the genus, but the most basal divergences were not resolved with these data. The systematic and phylogenetic hypotheses developed here are relevant to both setting conservation priorities and understanding the biogeography of South America.