May 24, 2015

RAD sequencing enables unprecedented phylogenetic resolution and objective species delimitation in recalcitrant divergent taxa

BioRxiv : the Preprint Server for Biology
Santiago Herrera, Timothy M Shank

Abstract

Species delimitation is problematic in many taxa due to the difficulty of evaluating predictions from species delimitation hypotheses, which chiefly relay on subjective interpretations of morphological observations and/or DNA sequence data. This problem is exacerbated in recalcitrant taxa for which genetic resources are scarce and inadequate to resolve questions regarding evolutionary relationships and uniqueness. In this case study we demonstrate the empirical utility of restriction site associated DNA sequencing (RAD-seq) by unambiguously resolving phylogenetic relationships among recalcitrant octocoral taxa with divergences greater than 80 million years. We objectively infer robust species boundaries in the genus Paragorgia , which contains some of the most important ecosystem engineers in the deep-sea, by testing alternative taxonomy-guided or unguided species delimitation hypotheses using the Bayes factors delimitation method (BFD*) with genome-wide single nucleotide polymorphism data. We present conclusive evidence rejecting the current morphological species delimitation model for the genus Paragorgia and indicating the presence of cryptic species boundaries associated with environmental variables. We argue that the suita...Continue Reading

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Mentioned in this Paper

CFC1 gene
Genome
Restriction Site
Paragorgia
Human DNA Sequencing
Morphological
Radiology Studies
Objective (Goal)
Site
Sequencing

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