DOI: 10.5061/dryad.v033k
title: Data from: Multi-locus sequence data illuminate demographic drivers of Pleistocene speciation in semi-arid southern Australian birds (Cinclosoma spp.)

description: Background: During 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. Results: A 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. Conclusions: Our
 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.
description: Cinclosoma
 CoordinatesGeneland Infile:
 Coordinates file has 2 columns for spatial coordinates (long, lat), with
 no missing data, comma delimitedCinclosoma
 _CodominantGeneland Infile: Diploid
 genotype file for has 22 columns (11 nulear loci), sequencing data
 converted to allelic data, missing data= NA, comma
 delimited.Cinclosoma_IM_inIMa2 infile: 2 populations (Cinclosoma castanotum and Cinclosoma clarum), 11 nuclear and 1 mtDNA locus.Cinclosoma_noST_SB_inIMa2 infile with putative C. clarum fordianum removed: 2 populations (Cinclosoma castanotum and Cinclosoma clarum), 11 nuclear and 1 mtDNA locus.castanotum_EBSPEBSP xml infile for Cinclosoma castanotum run in Beast v1.7.5. EBSP run uses mtDNA rate and one nuclear loci. This was chosen based on locus closest to average of all loci. All loci (except one) are within the bounds of the Ellegren (2013) Annual Review of Ecology and Systematics. The one outside is only a tiny fraction lower.clarum_noST_SB_EBSPEBSP xml infile for Cinclosoma clarum (putative Cinclosoma clarum fordianum removed) run in Beast v1.7.5. EBSP run uses mtDNA rate and one nuclear loci. This was chosen based on locus closest to average of all loci. All loci (except one) are within the bounds of the Ellegren (2013) Annual Review of Ecology and Systematics. The one outside is only a tiny fraction lower.