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Yan X, Terai Y, Widayati KA, Itoigawa A, Purba LHPS, Fahri F, Suryobroto B, Imai H. Functional divergence of the pigmentation gene melanocortin-1 receptor (MC1R) in six endemic Macaca species on Sulawesi Island. Sci Rep 2022; 12:7593. [PMID: 35534524 PMCID: PMC9085793 DOI: 10.1038/s41598-022-11681-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 04/28/2022] [Indexed: 11/20/2022] Open
Abstract
Coat color is often highly variable within and between animal taxa. Among hundreds of pigmentation-related genes, melanocortin-1 receptor (MC1R) plays key roles in regulating the synthesis of the dark eumelanin and the red–yellow pheomelanin. The six species of macaques that inhabit Sulawesi Island diverged rapidly from their common ancestor, M. nemestrina. Unlike most macaques, Sulawesi macaques commonly have a dark coat color, with divergence in shade and color pattern. To clarify the genetic and evolutionary basis for coat color in Sulawesi macaques, we investigated the MC1R sequences and functional properties, including basal cAMP production and α-MSH-induced activity in vitro. We found fixed non-synonymous substitutions in MC1R in each species. Furthermore, we found that six species-specific variants corresponded with variation in agonist-induced and basal activity of MC1R. Inconsistent with the dark coat color, four substitutions independently caused decreases in the basal activity of MC1R in M. hecki, M. nigra, M. tonkeana, and M. ochreata. Selective analysis suggested MC1R of M. nigra and M. nigrescens underwent purifying selection. Overall, our results suggest that fixed differences in MC1R resulted in different functional characteristics and might contribute to divergence in color among the six Sulawesi macaque species.
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Affiliation(s)
- Xiaochan Yan
- Molecular Biology Section, Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Japan
| | - Yohey Terai
- Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies, Hayama, Japan
| | | | - Akihiro Itoigawa
- Molecular Biology Section, Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Japan
| | | | - Fahri Fahri
- Department of Biology, Tadulako University, Palu, Indonesia
| | | | - Hiroo Imai
- Molecular Biology Section, Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Japan.
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Munds RA, Titus CL, Moreira LAA, Eggert LS, Blomquist GE. Examining the molecular basis of coat color in a nocturnal primate family (Lorisidae). Ecol Evol 2021; 11:4442-4459. [PMID: 33976821 PMCID: PMC8093732 DOI: 10.1002/ece3.7338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 02/03/2023] Open
Abstract
Organisms use color for camouflage, sexual signaling, or as a warning sign of danger. Primates are one of the most vibrantly colored Orders of mammals. However, the genetics underlying their coat color are poorly known, limiting our ability to study molecular aspects of its evolution. The role of the melanocortin 1 receptor (MC1R) in color evolution has been implicated in studies on rocket pocket mice (Chaetodipus intermediusi), toucans (Ramphastidae), and many domesticated animals. From these studies, we know that changes in MC1R result in a yellow/red or a brown/black morphology. Here, we investigate the evolution of MC1R in Lorisidae, a monophyletic nocturnal primate family, with some genera displaying high contrast variation in color patterns and other genera being monochromatic. Even more unique, the Lorisidae family has the only venomous primate: the slow loris (Nycticebus). Research has suggested that the contrasting coat patterns of slow lorises are aposematic signals for their venom. If so, we predict the MC1R in slow lorises will be under positive selection. In our study, we found that Lorisidae MC1R is under purifying selection (ω = 0.0912). In Lorisidae MC1R, there were a total of 75 variable nucleotides, 18 of which were nonsynonymous. Six of these nonsynonymous substitutions were found on the Perodicticus branch, which our reconstructions found to be the only member of Lorisidae that has predominantly lighter coat color; no substitutions were associated with Nycticebus. Our findings generate new insight into the genetics of pelage color and evolution among a unique group of nocturnal mammals and suggest putative underpinnings of monochromatic color evolution in the Perodicticus lineage.
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Affiliation(s)
- Rachel A. Munds
- Department of Anthropology & ArchaeologyUniversity of CalgaryCalgaryABCanada
- Nocturnal Primate Research GroupOxford Brookes UniversityOxfordUK
| | - Chelsea L. Titus
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
| | - Lais A. A. Moreira
- Department of Anthropology & ArchaeologyUniversity of CalgaryCalgaryABCanada
| | - Lori S. Eggert
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
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Matsudaira K, Hamada Y, Bunlungsup S, Ishida T, San AM, Malaivijitnond S. Whole Mitochondrial Genomic and Y-Chromosomal Phylogenies of Burmese Long-Tailed Macaque (Macaca fascicularis aurea) Suggest Ancient Hybridization between fascicularis and sinica Species Groups. J Hered 2019; 109:360-371. [PMID: 29186474 DOI: 10.1093/jhered/esx108] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 11/17/2017] [Indexed: 01/09/2023] Open
Abstract
Macaca fascicularis aurea (Burmese long-tailed macaque) is 1 of the 10 subspecies of Macaca fascicularis. Despite having few morphological differences from other subspecies, a recent phylogeographic study showed that M. f. aurea is clearly distinct genetically from Macaca fascicularis fascicularis (common long-tailed macaque) and suggests that M. f. aurea experienced a disparate evolutionary pathway versus other subspecies. To construct a detailed evolutionary history of M. f. aurea and its relationships with other macaque species, we performed phylogenetic analyses and divergence time estimation of whole mitochondrial genomes (2 M. f. aurea, 8 M. f. fascicularis, and 16 animals of 12 macaque species) and 2871 bp of the Y chromosome (1 M. f. aurea, 2 M. f. fascicularis, and 5 animals of 5 macaque species) and haplotype network analysis of 758 bp of the Y chromosome (1 M. f. aurea, 2 M. f. fascicularis, and 21 animals of 19 macaque species). Whereas the Y chromosome of M. f. aurea clustered with those of the fascicularis species group in the phylogenetic and haplotype network analyses, its mtDNA clustered within the clade of the sinica species group. Based on this phylogenetic incongruence and the estimated divergence times, we propose that proto-M. f. aurea underwent hybridization with a population of the sinica species group between 2.5 and 0.95 MYA after divergence from the common ancestor of M. fascicularis. Hybridization and introgression might have been central in the evolution of M. f. aurea, similar to what occurred in the evolution of other macaque species and subspecies.
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Affiliation(s)
- Kazunari Matsudaira
- Department of Biology, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand.,National Primate Research Center of Thailand, Chulalongkorn University, Saraburi, Thailand
| | - Yuzuru Hamada
- Evolutionary Morphology Section, Department of Evolution and Phylogeny, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Srichan Bunlungsup
- Department of Biology, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
| | - Takafumi Ishida
- Unit of Human Biology and Genetics, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Aye Mi San
- Department of Zoology, University of Yangon, Kamayut, Yangon, Myanmar
| | - Suchinda Malaivijitnond
- Department of Biology, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand.,National Primate Research Center of Thailand, Chulalongkorn University, Saraburi, Thailand
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Bradley BJ, Gerald MS, Widdig A, Mundy NI. Coat Color Variation and Pigmentation Gene Expression in Rhesus Macaques (Macaca mulatta). J MAMM EVOL 2012. [DOI: 10.1007/s10914-012-9212-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Ge D, Lissovsky AA, Xia L, Cheng C, Smith AT, Yang Q. Reevaluation of several taxa of Chinese lagomorphs (Mammalia: Lagomorpha) described on the basis of pelage phenotype variation. Mamm Biol 2012. [DOI: 10.1016/j.mambio.2011.09.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Corso J, Gonçalves GL, de Freitas TRO. Sequence variation in the melanocortin-1 receptor (MC1R) pigmentation gene and its role in the cryptic coloration of two South American sand lizards. Genet Mol Biol 2012; 35:81-7. [PMID: 22481878 PMCID: PMC3313520 DOI: 10.1590/s1415-47572012005000015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 12/02/2011] [Indexed: 11/21/2022] Open
Abstract
In reptiles, dorsal body darkness often varies with substrate color or temperature environment, and is generally presumed to be an adaptation for crypsis or thermoregulation. However, the genetic basis of pigmentation is poorly known in this group. In this study we analyzed the coding region of the melanocortin-1-receptor (MC1R) gene, and therefore its role underlying the dorsal color variation in two sympatric species of sand lizards (Liolaemus) that inhabit the southeastern coast of South America: L. occipitalis and L. arambarensis. The first is light-colored and occupies aeolic pale sand dunes, while the second is brownish and lives in a darker sandy habitat. We sequenced 630 base pairs of MC1R in both species. In total, 12 nucleotide polymorphisms were observed, and four amino acid replacement sites, but none of them could be associated with a color pattern. Comparative analysis indicated that these taxa are monomorphic for amino acid sites that were previously identified as functionally important in other reptiles. Thus, our results indicate that MC1R is not involved in the pigmentation pattern observed in Liolaemus lizards. Therefore, structural differences in other genes, such as ASIP, or variation in regulatory regions of MC1R may be responsible for this variation. Alternatively, the phenotypic differences observed might be a consequence of non-genetic factors, such as thermoregulatory mechanisms.
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Affiliation(s)
- Josmael Corso
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
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Bradley BJ, Lawler RR. Linking genotypes, phenotypes, and fitness in wild primate populations. Evol Anthropol 2011; 20:104-19. [DOI: 10.1002/evan.20306] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Nakayama K, Shotake T, Takeneka O, Ishida T. Variations in the Coding Region of the Agouti Signaling Protein Gene Do Not Explain Agouti/Non-agouti Phenotypes in Macaques. J MAMM EVOL 2010. [DOI: 10.1007/s10914-010-9137-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Shimada T, Sato JJ, Aplin KP, Suzuki H. Comparative analysis of evolutionary modes in Mc1r coat color gene in wild mice and mustelids. Genes Genet Syst 2009; 84:225-31. [PMID: 19745571 DOI: 10.1266/ggs.84.225] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Sequences from ten species of Mus (Rodentia, Muridae) of the melanocortin-1 receptor (Mc1r) gene (945 bp), which plays a key role in coat color determination, were compared with an existing Mc1r dataset (ca. 498 bp) from 12 species of Mustela and Martes (Carnivora, Mustelidae). The dN/dS ratio (omega) was estimated at 0.19 for Mus and 0.35 for the mustelids, using a likelihood-based one-ratio model with empirical codon frequencies. Running the model with equal codon frequencies gave a dramatic increase in omega for the mustelids (1.02) but not for Mus (0.31), indicating stronger codon usage bias in Mc1r among mustelids. When omega was estimated with the free-ratio model, significantly accelerated rates of amino acid replacement (nearly 1 in omega) were seen in several regions of the Mus phylogeny, such as in the ancestral subgeneric lineages, possibly associated with ecological niche shifting. Our results suggest that both functional constraints on coat color variation and selective constraints on codon usage bias have participated in structuring Mc1r gene sequences. Furthermore, they suggest that these contrasting influences have acted differentially in Mus and the mustelid lineages, and also differentially during the course of evolution within the genus Mus.
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Affiliation(s)
- Tomofumi Shimada
- Division of Bioscience, Graduate School of Environmental Earth Science, Hokkaido University, Kita-ku, Sapporo, Japan
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