Multi-locus sequence data illuminate demographic drivers of Pleistocene speciation in semi-arid southern Australian birds (Cinclosoma spp.).

Gaynor Dolman,Leo Joseph

doi:10.1186/s12862-016-0798-6

Abstract

BackgroundDuring the Pleistocene, shifts of species distributions and their isolation in disjunct refugia led to varied outcomes in how taxa diversified. Some species diverged, others did not. Here, we begin to address another facet of the role of the Pleistocene in generating today’s diversity. We ask which processes contributed to divergence in semi-arid southern Australian birds. We isolated 11 autosomal nuclear loci and one mitochondrial locus from a total of 29 specimens of the sister species pair, Chestnut Quail-thrush Cinclosoma castanotum and Copperback Quail-thrush C. clarum.ResultsA population clustering analysis confirmed the location of the current species boundary as a well-known biogeographical barrier in southern Australia, the Eyrean Barrier. Coalescent-based analyses placed the time of species divergence to the Middle Pleistocene. Gene flow between the species since divergence has been low. The analyses suggest the effective population size of the ancestor was 54 to 178 times smaller than populations since divergence. This contrasts with recent multi-locus studies in some other Australian birds (butcherbirds, ducks) where a lack of phenotypic divergence was accompanied by larger historical population sizes. Post-divergence population size histories of C. clarum and C. castanotum were inferred using the extended Bayesian skyline model. The population size of C. clarum increased substantially during the late Pleistocene and continued to increase through the Last Glacial Maximum and Holocene. The timing of this expansion across its vast range is broadly concordant with that documented in several other Australian birds. In contrast, effective population size of C. castanotum was much more constrained and may reflect its smaller range and more restricted habitat east of the Eyrean Barrier compared with that available to C. clarum to the west.ConclusionsOur results contribute to awareness of increased population sizes, following significant contractions, as having been important in shaping diversity in Australian arid and semi-arid zones. Further, we improve knowledge of the role of Pleistocene climatic shifts in areas of the planet that were not glaciated at that time but which still experienced that period’s cyclical climatic fluctuations.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0798-6) contains supplementary material, which is available to authorized users.

Highlights

During the Pleistocene, shifts of species distributions and their isolation in disjunct refugia led to varied outcomes in how taxa diversified
A largely unanswered central question is which processes drove these varying outcomes [2]? When speciation did occur, was it accompanied by increased genetic drift due to large reductions in population size when in contracted refugia, colonisation of newly suitable habitat, or divergent selection? If these processes acted in concert, how might their relative contributions be teased apart?
Population assignment is concordant with mitochondrial DNA (mtDNA) differentiation at the Eyrean Barrier and concordant with current species delimitation of C. clarum and C. castanotum [9]

Summary

Introduction

During the Pleistocene, shifts of species distributions and their isolation in disjunct refugia led to varied outcomes in how taxa diversified. Ranges expanded opening up potentially novel habitats and providing opportunity for secondary contact and gene flow [1]. The effect that these isolation events and shifts in distribution had on the diversification of species varies across taxa, some species having diverged and others remained cohesive [2]. When speciation did occur, was it accompanied by increased genetic drift due to large reductions in population size when in contracted refugia, colonisation of newly suitable habitat, or divergent selection? A largely unanswered central question is which processes drove these varying outcomes [2]? When speciation did occur, was it accompanied by increased genetic drift due to large reductions in population size when in contracted refugia, colonisation of newly suitable habitat, or divergent selection? If these processes acted in concert, how might their relative contributions be teased apart?

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