Median-joining networks for c<i>TAS2R</i>s.

<p>Circles represent haplotypes. Hap<i>n</i> indicates haplotype <i>n</i> (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043277#pone.0043277.s003" target="_blank">Table S1</a>). The letter (P) is added to pseudogenes. Color within the circle indicates each subspecies. Areas and numbers within color-coded parts of the circles indicate the numbers of sampled chromosomes. Numbers along branches indicate nucleotide positions of mutation between the haplotypes. Line styles of branches indicate mutation types of nucleotide changes.</p

The subspecies distribution of the number of haplotypes in the 28 c<i>TAS2R</i>s.

<p>(A, B) The distribution of all haplotypes in the 4 subspecies. (C, D) The distribution of high-frequency haplotypes in western and eastern chimpanzees. Subspecies of a Nigerian-Cameroonian chimpanzee was identified only maternally due to a lack of information about the antecedents in captivity. The number of non-functional haplotypes (segregating pseudogenes and whole-gene deletions) is indicated in parentheses. High-frequency haplotypes were observed in more than one sampled chromosome.</p

The histogram and cumulative frequency curve of <i>F</i>_ST in SNVs in the 28 c<i>TAS2R</i>s.

<p>This plot was composed from a total of 174 SNVs in western and eastern chimpanzees. Sampled chromosomes carrying whole-gene deletions were omitted from the calculation. Mutation types and amino acid positions of SNVs with higher <i>F</i>_ST are shown. Ancestral and derived amino acids were estimated from the haplotype networks. The protein locations are also shown based on Sugawara et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043277#pone.0043277-Sugawara1" target="_blank">[15]</a> (EC, extracellular region; TM, transmembrane region; IC, intracellular region).</p

A large-deletion variant involving the whole-gene deletions of c<i>TAS2R43</i>, c<i>TAS2R46</i>, c<i>TAS2R63P</i>, and c<i>TAS2R64</i>.

<p>(A) Genomic organization around the large-deletion region based on CGSC 2.1.3/panTro3. An electrophoresis image shows PCR products of each c<i>TAS2R</i> with subject ID numbers at the top. Only subject 156 did not produce amplicons of c<i>TAS2R43</i>, c<i>TAS2R46</i>, and c<i>TAS2R64</i>. In this subject, c<i>TAS2R63P</i>, <i>IntA</i>, and <i>IntB</i> were also not amplified, whereas <i>IntC</i> was amplified (data not shown). (B) Using intC_F and int31-63_R as a PCR primer pair, only subject 153 and 156 produced amplicons of the expected size of 4,760 bp based on CGSC 2.1.3/panTro3. Subjects 153 and 156 were thought to be a heterozygote and a homozygote for the large-deletion variant, respectively. The sequences around the breakpoints of the large-deletion variant had similar arrangements of retrotransposons (<i>AluJr</i>, <i>L1MEg</i>, and <i>L1ME3B</i>), which were annotated with RepeatMasker (<a href="http://www.repeatmasker.org" target="_blank">http://www.repeatmasker.org</a>).</p

Nucleotide diversity and divergence of c<i>TAS2R</i>s in western and eastern chimpanzees.

a<p>Data from Sugawara et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043277#pone.0043277-Sugawara1" target="_blank">[15]</a>.</p>b<p>Nucleotide diversity within the subspecies.</p>c<p>Synonymous diversity within the subspecies.</p>d<p>Non-synonymous diversity within the subspecies.</p>e<p>Tajima’s <i>D</i>. Two-sided Tajima’s <i>D</i> test were conducted using coalescent simulations under 10,000 replicates, assuming no recombination and a Poisson distribution of mutations along the lineages. *<i>P</i><0.05.</p>f<p>Nucleotide divergence beween western and eastern chimpanzees.</p

Analyses of natural selection of c<i>TAS2R</i>s in western and eastern chimpanzees.

a<p>Two-sided Fisher’s exact test.</p>b<p>Two-sided Wilcoxon rank sum test in comparison with data of non-coding loci from Fischer et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043277#pone.0043277-Fischer1" target="_blank">[22]</a>.</p>c<p>Data from Sugawara et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043277#pone.0043277-Sugawara1" target="_blank">[15]</a>.</p

Colobine mutants mimicking macaque

Functional data for colobine mutants mimicking macaqu

Colobine functional analysis

Functional data for colobine

MDH activity in strain AM1 grown on the methanol and succinate media with Ca²⁺ and/or La³⁺.

<p>Cells were grown aerobically in succinate (white bar) and methanol (gray bar) media with 30 µM La³⁺ and/or Ca²⁺ at 30°C. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050480#s2" target="_blank">Results</a> are shown as means with standard deviations (<i>n</i> = 3).</p

Phenotypic growth defects in strain Δ<i>mxaF</i> on methanol and succinate media.

<p>Growth on media containing Ca³⁺ (white circle), La³⁺ (gray circle), and Ca²⁺+La³⁺ (black circle). Graphs depict average data from three biological replicates.</p