Summary of estimates made using internal and external calibrations for the three data sets presented in this study

a<p>Range of 22 divergence time estimates</p

Bayesian age estimates for nodes labelled in Figure 3

<p>Bayesian age estimates for nodes labelled in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001615#pone-0001615-g003" target="_blank">Figure 3</a></p

Phylogenetic tree illustrating the impact of using extraspecific and intraspecific calibration points.

<p>The tree shows the locations of nucleotide changes (small vertical bars). The nucleotide changes within the study species represent segregating sites, some of which will be fixed in the long term, but most of which will be removed by drift or selection. The changes between the study species and outgroup species represent substitutions. If an estimate of the evolutionary rate is calibrated using an external calibration point, such as the split between the study and outgroup species, then the intraspecific rate will be underestimated. This will lead to an overestimation of times to divergence, including the age of the most recent common ancestor of the study species.</p

Divergence time estimates for conspecific phylogroups from 22 bird species

a<p>All taxa are members of Order Passeriformes, with the exception of Picidae (Order Piciformes).</p>b<p>Gamma-corrected distance estimated by Weir and Schluter <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001615#pone.0001615-Weir2" target="_blank">[42]</a>.</p>c<p>Divergence times older than 250 kyr are italicised.</p

Bayesian skyline plots showing the recent demographic history of bowhead whales, estimated using phylogenetic analysis of three alignments of the mitochondrial control region: (a) combined alignment of 68 modern haplotypes and 99 radiocarbon-dated, ancient DNA sequences; (b) modern sequences only; and (c) ancient sequences only.

<p>All three plots are drawn to the vertical and horizontal scales.</p

AppendixS4_QIIME_script

Scripts used for analyses in QIIME

AppendixS2_Aligned_sequences

Alignment of representative sequences generated for this study

AppendixS3_R_script

Scripts used for analyses in R

TableS3_Sites

Table with geographic coordinates of data collection locations

Table 1_withMOTU

Taxonomic assignment of MOTUs through the BOLD online identification engine using two different methods: the neighbour-joining hierarchical tree-based ‘strict’ (S) and the sequence similarity ‘best match’ (BM) approach (Ross et al. 2008). Only sequences with >98% similarity were considered as a possible match: >98% for a “genus” match and >99% for a “species” match. For the BM approach, only matches with sampling sites in Australia were considered; * indicates sampling sites in south-western WA while ** indicates sampling sites in WA but outside of the south-west. Species highlighted in grey are thought to use hearing based defences against the echolocation calls of bats. This table is a modified version of Table 1 and includes each associated MOTU