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

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

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

Summaries of effects of SNPs in <i>ADRBs</i> and <i>PPARG</i>.

<p>A) ADRBs with energy expense-type allele found only in humans stimulate the digestion of accumulated fat in adipocytes at a higher level. A lot of generated free fatty acids (FFA) stimulate both transcription of the uncoupling protein (<i>UCP1</i>) gene and the activity of UCP1 proteins, which generate heat in mitochondria. GL: glycerol. B) PPARG activates differentiation from precursor cells into small-sized adipocytes, which secrete insulin-sensitive factors. PPARG with <i>Ala12</i> found only in humans causes reduction of transcriptional activity of PPARG and leads to protection from high-fat-diet-induced hypertrophy of adipocytes, which secrete insulin-resistant factors <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043461#pone.0043461-Kadowaki2" target="_blank">[30]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043461#pone.0043461-Hara1" target="_blank">[34]</a>.</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

All NHP had <i>Arg64</i> allele in <i>ADRB3</i>.

<p>A) Restriction map of <i>ADRB3</i> digested with <i>Mva</i>I for humans and NHP. B) RFLP patterns of PCR product of <i>ADRB3</i> digested with <i>Mva</i>I for humans and NHP. Lane 1: PCR products of a human; not digested (112 bp). Lane 2: fragments of the human <i>Trp64/Trp64</i> (61, 34 and 17 bp which was undetectable at this concentration.) Lane3: fragments of human <i>Arg64/Trp64</i> (95, 61, 34 and 17 bp). Lane 4 to lane 12: fragments from <i>P. troglodytes</i>, <i>G. gorilla</i>, <i>P. pygmaeus</i>, <i>H. agilis</i>, <i>M. mulatta</i>, <i>M. fuscata</i>, <i>M. fascicularis</i>, <i>M. nemestrina</i>, and <i>M. radiata</i>, respectively (95 bp instead of 61 and 34 bp).</p

Nucleotide sequences in <i>PPARG</i> of primates.

<p>The determined sequences of <i>G. gorilla</i> (AB669114), <i>P. pygmaeus</i> (AB669115), and <i>M. fuscata</i> (AB669116) together with the Ensembl database of human (ENSG00000132170), <i>P. troglodytes</i> (ENSPTRG00000014632) and <i>M. mulatta</i> (ENSMMUG00000007191). Underline shows the restriction site (GCGC) with <i>HhaI</i>. The restriction site region of <i>M. fascicularis</i> (AY048695) from the GenBank database was the same as in other macaques. One nucleotide of primer F was changed to create the restriction site of <i>HhaI </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043461#pone.0043461-Hara1" target="_blank">[34]</a>.</p

All hominoids had <i>Gly16</i> allele in <i>ADRB2</i>.

<p>A) Restriction map of <i>ADRB2</i> for the 16^th amino acid digested with <i>BsrD</i>I (GCAATGNN). This restriction map was predicted from the nucleotide sequences of hominoids (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043461#pone-0043461-g001" target="_blank">Fig. 1</a>). B) RFLP patterns of PCR products of <i>ADRB2</i> for the 16^th amino acid digested with <i>BsrD</i>I in hominoids. Lane 1: PCR product of a human; not digested (200 bp). Lane 2: Fragments of human <i>Arg16/Gly16</i> (130,108 and 56 bp (22 and 14 bp fragments were undetectable)). Lane 3 to lane 6: Fragments from <i>P. troglodytes</i>, <i>G. gorilla</i>, <i>P. pygmaeus</i>, and <i>H. agilis</i>, respectively (108 and 22 bp instead of 130 bp).</p