Mitogenomic phylogenetic analyses of the Delphinidae with an emphasis on the Globicephalinae.

Julia T Vilstrup,M Thomas P Gilbert,Danielle Kreb,Kelly M Robertson,Eske Willerslev,Andrew D Foote,Michael Krützen,Ludovic Orlando,Guido J Parra,Simon Yw Ho,Philippe Verborgh,Phillip A Morin,Renaud De Stephanis

doi:10.1186/1471-2148-11-65

Abstract

BackgroundPrevious DNA-based phylogenetic studies of the Delphinidae family suggest it has undergone rapid diversification, as characterised by unresolved and poorly supported taxonomic relationships (polytomies) for some of the species within this group. Using an increased amount of sequence data we test between alternative hypotheses of soft polytomies caused by rapid speciation, slow evolutionary rate and/or insufficient sequence data, and hard polytomies caused by simultaneous speciation within this family. Combining the mitogenome sequences of five new and 12 previously published species within the Delphinidae, we used Bayesian and maximum-likelihood methods to estimate the phylogeny from partitioned and unpartitioned mitogenome sequences. Further ad hoc tests were then conducted to estimate the support for alternative topologies.ResultsWe found high support for all the relationships within our reconstructed phylogenies, and topologies were consistent between the Bayesian and maximum-likelihood trees inferred from partitioned and unpartitioned data. Resolved relationships included the placement of the killer whale (Orcinus orca) as sister taxon to the rest of the Globicephalinae subfamily, placement of the Risso's dolphin (Grampus griseus) within the Globicephalinae subfamily, removal of the white-beaked dolphin (Lagenorhynchus albirostris) from the Delphininae subfamily and the placement of the rough-toothed dolphin (Steno bredanensis) as sister taxon to the rest of the Delphininae subfamily rather than within the Globicephalinae subfamily. The additional testing of alternative topologies allowed us to reject all other putative relationships, with the exception that we were unable to reject the hypothesis that the relationship between L. albirostris and the Globicephalinae and Delphininae subfamilies was polytomic.ConclusionDespite their rapid diversification, the increased sequence data yielded by mitogenomes enables the resolution of a strongly supported, bifurcating phylogeny, and a chronology of the divergences within the Delphinidae family. This highlights the benefits and potential application of large mitogenome datasets to resolve long-standing phylogenetic uncertainties.

Highlights

Previous DNA-based phylogenetic studies of the Delphinidae family suggest it has undergone rapid diversification, as characterised by unresolved and poorly supported taxonomic relationships for some of the species within this group
Sequencing In total 18 mitogenome sequences were generated for this study, including multiple representatives per species
Phylogenetic analyses Phylogenetic estimates were consistent across Bayesian and maximum-likelihood methods used in this study, including partitioned and unpartitioned analyses on the full data set, and a subset consisting of a single representative per species

Summary

Introduction

Previous DNA-based phylogenetic studies of the Delphinidae family suggest it has undergone rapid diversification, as characterised by unresolved and poorly supported taxonomic relationships (polytomies) for some of the species within this group. The mitochondrial genome is typically non-recombining, has a relatively high substitution rate, and has a smaller effective population size than the nuclear genome [1]. These properties can increase the probability of congruence between the mitochondrial gene tree and the species tree, helping to resolve relationships between recently. Unlikely [11], a ‘hard’ molecular polytomy could be the result of a true simultaneous speciation event into multiple daughter species [9,12,13,14] Such events could occur when multiple populations of an ancestral species become simultaneously isolated during periods of rapid environmental change [12]. Simultaneous adaptive radiation into multiple species could occur in sympatry due to intra-specific competition and assortative mating if species occupy a narrow niche width [15]

Methods

Results

Conclusion