Phylogenomic species delimitation in microendemic frogs of the Brazilian Atlantic Forest

Marcio R Pie,Marcos R Bornschein,Luiz F Ribeiro,Brant C Faircloth,John E Mccormack

doi:10.1016/j.ympev.2019.106627

Abstract

The advent of next-generation sequencing allows researchers to use large-scale datasets for species delimitation analyses, yet one can envision an inflection point where the added accuracy of including more loci does not offset the increased computational burden. One alternative to including all loci could be to prioritize the analysis of loci for which there is an expectation of high informativeness. Here, we explore the issue of species delimitation and locus selection with montane species from two anuran genera that have been isolated in sky islands across the southern Brazilian Atlantic Forest: Melanophryniscus (Bufonidae) and Brachycephalus (Brachycephalidae). To delimit species, we obtained genetic data using target enrichment of ultraconserved elements from 32 populations (13 for Melanophryniscus and 19 for Brachycephalus), and we were able to create datasets that included over 800 loci with no missing data. We ranked loci according to their number of parsimony-informative sites, and we performed species delimitation analyses using BPP with the most informative 10, 20, 40, 80, 160, 320, and 640 loci. We identified three types of phylogenetic node: nodes with either consistently high or low support regardless of the number of loci or their informativeness and nodes that were initially poorly supported where support became stronger as we included more data. When viewed across all sensitivity analyses, our results suggest that the current species richness in both genera is likely underestimated. In addition, our results show the effects of different sampling strategies on species delimitation using phylogenomic datasets.

Highlights

Accurate species delimitation forms the basis of much of biodiversity research (Sites and Marshall 2004; Adams et al 2014)
Montane species in these genera have been isolated in sky islands across the southern Brazilian Atlantic Forest, which led to the formation of a number of microendemic species
The first is the development of species delimitation methods (e.g. Yang 2002; Rannala and Yang 2003; Knowles and Carstens 2007; Yang and Rannala 2010; Ence and Carstens 2011; see Rannala 2015 for a recent review) that are based on the multispecies coalescent (MSC) model (Takahata et al 1995; Rannala and Yang 2003)

Summary

Introduction

Accurate species delimitation forms the basis of much of biodiversity research (Sites and Marshall 2004; Adams et al 2014). Some recent speciation events might need a large number of loci to be properly detected, suggesting that researchers should use the largest number of loci possible Central to this question is how page: 5 varying the number and their informativeness affects performance of species delimitation methods. Melanophryniscus of the southern Brazilian Atlantic Forests are characterized by montane endemic species with restricted and isolated distributions in cloud forests, campos de altitude, and grasslands (Langone et al 2008; Steinbach-Padilha 2008; Bornschein et al 2015) These include five of the 29 currently described Melanophryniscus species (Frost 2017): M. alipioi, M. biancae, M. milanoi, M. vilavelhensis, and M. xanthostomus. In addition to investigating species limits in Brachycephalus and Melanophryniscus, we explored the importance of locus variation (informativeness) and locus number on the ideal species delimitation schemes

Objectives

Methods

Results

Conclusion