Estimates of the proportion of the sampled genomic regions for which the most closely related haplotype comes from each study population, for chimpanzees and humans.

<p>Parentheses show the empirical central 95% region of the distribution of values for the 100 re-samples of the human data.</p

Map of the geographic distribution of four populations of common chimpanzee.

<p><i>After </i><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002504#pgen.1002504-Gonder2" target="_blank">[<i>3</i>]</a><i>, Figure 6b</i>. Colours show the ranges of each population (yellow - <i>P. t. troglodytes</i>, red - <i>P. t. ellioti</i>, blue - <i>P. t. verus</i>, green - <i>P. t. schweinfurthii</i>) with major rivers indicated. The Sanaga River in Cameroon has been proposed to form the boundary between the ranges of <i>P. t. ellioti</i> and <i>P. t. troglodytes</i>.</p

Pairwise F_ST values for human samples.

<p>Parentheses show the empirical central 95% region of the distribution of values for the 100 re-samples of the human data.</p

Structure estimates of ancestry in three populations.

<p>For each sampled individual the figure shows the estimated proportion of ancestry from Structure's three putative ancestral populations, with <i>P. t. troglodytes</i> in yellow, <i>P. t. ellioti</i> in red and <i>P. t. verus</i> in blue. Structure reveals the same pattern of group memberships as PCA, and additionally suggests that <i>P. t. troglodytes</i> and <i>P. t. ellioti</i> individuals may share more DNA from the other group than either shares with <i>P. t. verus</i> (blue). The two known hybrid individuals (C024, C025, with ancestry estimated at close to 50% in each of <i>P. t. troglodytes</i> and <i>P. t. verus</i>) and two <i>P. t. ellioti</i> chimpanzees with <i>P. t. troglodytes</i>-like mtDNA (C127, C541) are labelled.</p

Nucleotide alignment for exon 3 of the X-linked opsin gene (Indriidae)

Nucleotide alignment of consensus sequences for exon 3 of the X-linked opsin gene (Plain Text file in FASTA format generated in Geneious). Sequences represent 10 species of Indriidae

Nucleotide alignment for exon 5 of the X-linked opsin gene (Indriidae)

Nucleotide alignment of consensus sequences for exon 5 of the X-linked opsin gene (Plain Text file in FASTA format generated in Geneious). Sequences represent 10 species of Indriidae

Supplementary Materials: Novel opsin gene variation in large-bodied, diurnal lemurs

Details on sample collection and opsin genotypin