Considering the Influence of Nonadaptive Evolution on Primate Color Vision

<div><p>Color vision in primates is variable across species, and it represents a rare trait in which the genetic mechanisms underlying phenotypic variation are fairly well-understood. Research on primate color vision has largely focused on adaptive explanations for observed variation, but it remains unclear why some species have trichromatic or polymorphic color vision while others are red-green color blind. Lemurs, in particular, are highly variable. While some species are polymorphic, many closely-related species are strictly dichromatic. We provide the first characterization of color vision in a wild population of red-bellied lemurs (<i>Eulemur rubriventer</i>, Ranomafana National Park, Madagascar) with a sample size (87 individuals; <i>N</i>_{X chromosomes} = 134) large enough to detect even rare variants (0.95 probability of detection at ≥ 3% frequency). By sequencing exon 5 of the X-linked opsin gene we identified opsin spectral sensitivity based on known diagnostic sites and found this population to be dichromatic and monomorphic for a long wavelength allele. Apparent fixation of this long allele is in contrast to previously published accounts of <i>Eulemur</i> species, which exhibit either polymorphic color vision or only the medium wavelength opsin. This unexpected result may represent loss of color vision variation, which could occur through selective processes and/or genetic drift (e.g., genetic bottleneck). To indirectly assess the latter scenario, we genotyped 55 adult red-bellied lemurs at seven variable microsatellite loci and used heterozygosity excess and <i>M</i>-ratio tests to assess if this population may have experienced a recent genetic bottleneck. Results of heterozygosity excess but not <i>M</i>-ratio tests suggest a bottleneck might have occurred in this red-bellied lemur population. Therefore, while selection may also play a role, the unique color vision observed in this population might have been influenced by a recent genetic bottleneck. These results emphasize the need to consider adaptive and nonadaptive mechanisms of color vision evolution in primates.</p></div

Study sites within and around RNP.

<p>Reprinted with modifications from [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0149664#pone.0149664.ref056" target="_blank">56</a>] under a CC BY license, with permission from Andrea Baden, original copyright 2011.</p

Results of <i>M</i>-ratio tests for the population of red-bellied lemurs in RNP.

<p><i>M</i> = observed average <i>M</i> calculated across all loci for the combined male-female, female-only, and male-only data sets. The percentage of <i>M</i> values falling below observed <i>M</i> are given for both <i>p</i>_<i>s</i> = 0.78 (proportion of multi-step mutations = 0.22) and <i>p</i>_<i>s</i> = 0.90 (proportion of multi-step mutations = 0.10).</p

Phylogenetic distribution of opsin variation based on the current study (*) and published data.

<p>Numbers represent current sample sizes (X chromosomes). Those denoted with “⁺” are from wild populations. All other samples are from captive individuals. References (from the top): <i>E</i>. <i>flavifrons</i> [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0149664#pone.0149664.ref037" target="_blank">37</a>], <i>E</i>. <i>fulvus</i> [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0149664#pone.0149664.ref043" target="_blank">43</a>], <i>E</i>. <i>collaris</i> [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0149664#pone.0149664.ref036" target="_blank">36</a>], <i>E</i>. <i>rubriventer</i> (this study), <i>E</i>. <i>mongoz</i> [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0149664#pone.0149664.ref011" target="_blank">11</a>]. Phylogeny from [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0149664#pone.0149664.ref078" target="_blank">78</a>]. <i>Eulemur</i> illustrations copyright 2015 Stephen D. Nash / Conservation International / IUCN SSC Primate Specialist Group and used in figure with permission from Stephen D. Nash.</p

Sample used in microsatellite analysis includes adult individuals that yielded confident genotypes at a minimum of 4 microsatellite loci.

<p>Sample used in microsatellite analysis includes adult individuals that yielded confident genotypes at a minimum of 4 microsatellite loci.</p

Variation at key <i>APOE</i> functional sites in <i>Homo</i> and <i>Pan</i>.

*<p>Gene nucleotide positions following notation of Fullerton et al. 2000 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047760#pone.0047760-Fullerton1" target="_blank">[27]</a>, and as given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047760#pone-0047760-g001" target="_blank">Figure 1</a>.</p>**<p>Based on two reads, one each from two fossil specimens: Vi33.25 and Vi33.26.</p

A schematic of the <i>APOE</i> gene.

<p>Structure and nucleotide position numbers follow Fullerton <i>et al</i>. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047760#pone.0047760-Fullerton1" target="_blank">[27]</a> and Ensembl (ENSG00000130203). The location of primers used in this study are given above (forward primers) and below (reverse primers) the labeled exons. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047760#pone.0047760.s002" target="_blank">Table S1</a> for primer and PCR-cycling information. An intronic SNP differentiating the two chimpanzee populations is highlighted in orange (position 2098*). SNP locations in red (3071 and 3073) represent putative <i>APOE</i> non-synonymous changes based on the chimpanzee genome assembly (Pan_troglodytes-2.1.4). Positions in blue (3205, 3937 and 4075) correspond to the amino acids (61, 112 and 158, respectively) that define the three human <i>APOE</i> alleles (E2, E3, E4). Position 4219^† (in green) represents the single, synonymous difference between the <i>P. t. verus</i> sequences generated in this study and that of Fullerton <i>et al.</i> (2000) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047760#pone.0047760-Fullerton1" target="_blank">[27]</a>. *corresponds to Ensembl coordinates 19∶45411002 for the human genome and 19∶50097633 for the chimpanzee genome. <b>^†</b>corresponds to Ensembl coordinates 19∶45412223 for the human genome.</p

Lineage-specific mutations mapped onto a schematic of the APOE protein (A) and primate phylogeny (B).

<p>Protein structure is modeled after Bu 2009 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047760#pone.0047760-Bu1" target="_blank">[65]</a>, and tree topology represents known evolutionary relationships based on genome-wide data <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047760#pone.0047760-Scally1" target="_blank">[46]</a>. Human mutations <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047760#pone.0047760-McLean1" target="_blank">[66]</a> at key residues 61, 112 and 158 are in red. Including residue 61, the human APOE protein has four fixed, <i>Homo</i>-specific, non-synonymous mutations, all of which seem to be shared with the Denisovan hominin (inferred from reads mapped to the human genome at <a href="http://www.genome.ucsc.edu" target="_blank">http://www.genome.ucsc.edu</a>). The chimpanzee APOE protein is monomorphic within and between subspecies, and is identical to the bonobo APOE protein. Mutation R15H (dotted arrow) is shared by gorillas, chimpanzees and bonobos likely as a result of incomplete lineage sorting rather than independent evolution <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047760#pone.0047760-Scally1" target="_blank">[46]</a>.</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