A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals

Andrea M Quattrini,Catherine S Mcfadden,Keryea Soong,Ming-Shiou Jeng,Yehuda Benayahu,Tiana Wu

doi:10.1186/s12862-019-1427-y

Abstract

BackgroundOur ability to investigate processes shaping the evolutionary diversification of corals (Cnidaria: Anthozoa) is limited by a lack of understanding of species boundaries. Discerning species of corals has been challenging due to a multitude of factors, including homoplasious and plastic morphological characters and the use of molecular markers that are either not informative or have not completely sorted. Hybridization can also blur species boundaries by leading to incongruence between morphology and genetics. We used traditional DNA barcoding and restriction-site associated DNA sequencing combined with coalescence-based and allele-frequency methods to elucidate species boundaries and simultaneously examine the potential role of hybridization in a speciose genus of octocoral, Sinularia.ResultsSpecies delimitations using two widely used DNA barcode markers, mtMutS and 28S rDNA, were incongruent with one another and with the morphospecies identifications. When mtMutS and 28S were concatenated, a 0.3% genetic distance threshold delimited the majority of morphospecies. In contrast, 12 of the 15 examined morphospecies formed well-supported monophyletic clades in both concatenated RAxML phylogenies and SNAPP species trees of > 6000 RADSeq loci. DAPC and Structure analyses also supported morphospecies assignments, but indicated the potential for two additional cryptic species. Three morphologically distinct species pairs could not, however, be distinguished genetically. ABBA-BABA tests demonstrated significant admixture between some of those species, suggesting that hybridization may confound species delimitation in Sinularia.ConclusionsA genomic approach can help to guide species delimitation while simultaneously elucidating the processes generating coral diversity. Results support the hypothesis that hybridization is an important mechanism in the evolution of Anthozoa, including octocorals, and future research should examine the contribution of this mechanism in generating diversity across the coral tree of life.

Highlights

Our ability to investigate processes shaping the evolutionary diversification of corals (Cnidaria: Anthozoa) is limited by a lack of understanding of species boundaries
Species delimitation using Deoxyribonucleic acid (DNA) barcodes Neither the Mitochondrial mutS-like protein (mtMutS) (735 bp) nor the 28S Ribosomal deoxyribonucleic acid (rDNA) (764 bp) barcoding marker delimited all morphospecies of Sinularia (Table 1) when considered separately (Additional file 1: Figure S1, Additional file 4)
In several cases in which morphospecies could not be distinguished genetically but there was no evidence for admixture or hybridization, it will be necessary to validate whether or not the observed morphological differences are indicative of species boundaries or intraspecific variation

Summary

Introduction

Our ability to investigate processes shaping the evolutionary diversification of corals (Cnidaria: Anthozoa) is limited by a lack of understanding of species boundaries. Morphological traits have traditionally been used in classical taxonomy; use of characters that might not be diagnostic or are homoplasious can confound the interpretation of species boundaries Cryptic species, those that occur in sympatry, and species that have arisen via hybridization and introgression are often challenging to discriminate without genetic, ecological or behavioral data. The increased resolution of genomic data can potentially disentangle some of these issues, facilitating species delimitation while simultaneously furthering our understanding of processes that generate biodiversity [103]. Such an approach may provide a better evaluation of morphological traits and insights into their congruence with genetic data

Methods

Results

Conclusion