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Kai H, Takada N, Thomson V, Suzuki H. Region-Specific Genetic Diversity of Black Rats ( Rattus rattus Complex) in Southeast and East Asia Shaped by Rapid Population Expansion Events. Zoolog Sci 2024; 41:290-301. [PMID: 38809868 DOI: 10.2108/zs230065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 12/27/2023] [Indexed: 05/31/2024]
Abstract
Among the six mitochondrial DNA lineages of the black rat (Rattus rattus Complex; RrC), lineages II and IV are widespread in Southeast and East Asia. This study explored their demographic history using 17 new sequences from the Miyako Islands in the Ryukyu archipelago, together with 178 publicly available cytochrome b sequences. We defined six and two haplotype groups showing rapid population expansion signals in Lineages II and IV, respectively. The six haplotype groups of Lineage II were represented by haplotypes from 1) Myanmar/Bangladesh/Northeast India, 2) Laos, 3) Thailand, 4) Indonesia/Philippines, 5) Vietnam/southern China, and 6) the Ryukyu archipelago. These expansion times were estimated using time-dependent evolutionary rates to be 115,300 years ago (ya), 128,500 ya, 9600 ya, 10,600 ya, 7200 ya, and 1400 ya, respectively, although all had large confidence intervals. The two groups of Lineage IV were recovered from the mainland and islands of Southeast Asia with predicted expansion times of 197,000 ya and 5800 ya, respectively. These results suggest that climatic fluctuations during the last 200,000 years of the Quaternary, affected the population dynamics in subtropical areas at different times. Furthermore, the results of the younger rapid expansion events of RrC suggest the possibility of agricultural advancement and dispersal of Neolithic farmers to different areas within the mainland and islands of Southeast Asia during the Holocene. A subset of rats from the Miyako Islands were found to have the same lineage IV haplotypes as those in Southeast Asia, suggesting a recent introduction of these new lineages.
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Affiliation(s)
- Hajime Kai
- Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Nobuhiro Takada
- Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
| | - Vicki Thomson
- Centre for Conservation Ecology and Genomics, University of Canberra, Bruce, ACT 2617, Australia
| | - Hitoshi Suzuki
- Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan,
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Elkin J, Martin A, Courtier-Orgogozo V, Santos ME. Analysis of the genetic loci of pigment pattern evolution in vertebrates. Biol Rev Camb Philos Soc 2023; 98:1250-1277. [PMID: 37017088 DOI: 10.1111/brv.12952] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 04/06/2023]
Abstract
Vertebrate pigmentation patterns are amongst the best characterised model systems for studying the genetic basis of adaptive evolution. The wealth of available data on the genetic basis for pigmentation evolution allows for analysis of trends and quantitative testing of evolutionary hypotheses. We employed Gephebase, a database of genetic variants associated with natural and domesticated trait variation, to examine trends in how cis-regulatory and coding mutations contribute to vertebrate pigmentation phenotypes, as well as factors that favour one mutation type over the other. We found that studies with lower ascertainment bias identified higher proportions of cis-regulatory mutations, and that cis-regulatory mutations were more common amongst animals harbouring a higher number of pigment cell classes. We classified pigmentation traits firstly according to their physiological basis and secondly according to whether they affect colour or pattern, and identified that carotenoid-based pigmentation and variation in pattern boundaries are preferentially associated with cis-regulatory change. We also classified genes according to their developmental, cellular, and molecular functions. We found a greater proportion of cis-regulatory mutations in genes implicated in upstream developmental processes compared to those involved in downstream cellular functions, and that ligands were associated with a higher proportion of cis-regulatory mutations than their respective receptors. Based on these trends, we discuss future directions for research in vertebrate pigmentation evolution.
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Affiliation(s)
- Joel Elkin
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, 800 22nd St. NW, Suite 6000, Washington, DC, 20052, USA
| | | | - M Emília Santos
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
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3
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Takeishi T, Fujiwara K, Osada N, Mita A, Takada T, Shiroishi T, Suzuki H. Phylogeographic study using nuclear genome sequences of <i>Asip</i> to infer the origins of ventral fur color variation in the house mouse <i>Mus musculus</i>. Genes Genet Syst 2021; 96:271-284. [DOI: 10.1266/ggs.21-00075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Toki Takeishi
- Laboratory of Ecology and Genetics Graduate School of Environmental Science, Hokkaido University
| | - Kazumichi Fujiwara
- Graduate School of Information Science and Technology, Hokkaido University
| | - Naoki Osada
- Graduate School of Information Science and Technology, Hokkaido University
| | | | - Toyoyuki Takada
- Integrated Bioresource Information Division, RIKEN BioResource Research Center
| | | | - Hitoshi Suzuki
- Laboratory of Ecology and Genetics Graduate School of Environmental Science, Hokkaido University
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4
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Tsunoi T, Noju K, Eto T, Suzuki H. A 1-bp deletion in Mc1r in a Norway rat (Rattus norvegicus) from Sado Island, Japan gives rise to a yellowish color variant: an insight into mammalian MC1R variants. Genes Genet Syst 2021; 96:89-97. [PMID: 33994400 DOI: 10.1266/ggs.20-00049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The melanocortin-1 receptor gene (MC1R) controls production of the pigments eumelanin and pheomelanin. Changes in MC1R lead to variation in coat color in mammals, which can range from entirely black (melanism) to yellowish. In this study, we report a case of a wild-caught Norway rat (Rattus norvegicus) from Sado Island, Japan with a yellowish coat color. Upon sequencing the whole coding region of the Mc1r gene (954 bp), we found a 1-bp deletion at site 337 (c.337del), indicative of a frameshift mutation, which was characterized as a severe loss-of-function or null mutation. A spectrophotometer was used to measure coat color, revealing that the rat had a distinctly lighter coat, based on lightness score, than mice with homozygous similar loss-of-function mutations. This implies that loss-of-function mutations can yield different phenotypes in murine rodents. The loss-of-function-mutant rat exhibited a contrasting coat pattern consisting of darker and lighter colors along its dorsal and ventral sides, respectively. Similar patterns have been observed in homozygous MC1R-deficient mutants in other mammals, implying that the countershading pattern can still be expressed despite the absence of MC1R in the melanocyte.
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Affiliation(s)
- Takeru Tsunoi
- Graduate School of Environmental Science, Hokkaido University
| | - Koki Noju
- Graduate School of Science, Hokkaido University
| | - Takeshi Eto
- Faculty of Agriculture, University of the Ryukyus
| | - Hitoshi Suzuki
- Graduate School of Environmental Science, Hokkaido University
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5
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Dinets V, Asada K. Noble savages: human-independent Rattus rats in Japan. J NAT HIST 2021. [DOI: 10.1080/00222933.2020.1845409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Vladimir Dinets
- Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
- Psychology Department, University of Tennessee, Knoxville, TN, USA
| | - Keishu Asada
- Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
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Suzuki H, Kinoshita G, Tsunoi T, Noju K, Araki K. Mouse Hair Significantly Lightened Through Replacement of the Cysteine Residue in the N-Terminal Domain of Mc1r Using the CRISPR/Cas9 System. J Hered 2020; 111:640-645. [PMID: 33252683 DOI: 10.1093/jhered/esaa054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/27/2020] [Indexed: 11/13/2022] Open
Abstract
A loss-of-function mutation in the melanocortin 1 receptor gene (MC1R), which switches off the eumelanin production, causes yellowish coat color variants in mammals. In a wild population of sables (Martes zibellina) in Hokkaido, Japan, the mutation responsible for a bright yellow coat color variant was inferred to be a cysteine replacement at codon 35 of the N-terminal extracellular domain of the Mc1r receptor. In the present study, we validated these findings by applying genome editing on Mc1r in mouse strains C3H/HeJ and C57BL/6N, altering the codon for cysteine (Cys33Phe). The resulting single amino acid substitution (Cys33Phe) and unintentionally generated frameshift mutations yielded a color variant exhibiting substantially brighter body color, indicating that the Cys35 replacement produced sufficient MC1R loss of function to confirm that this mutation is responsible for producing the Hokkaido sable yellow color variant. Notably, the yellowish mutant mouse phenotype exhibited brown coloration in subapical hair on the dorsal side in both the C3H/HeJ and C57BL/6N strains, despite the inability of the latter to produce the agouti signaling protein (Asip). This darker hair and body coloration was not apparent in the Hokkaido sable variant, implying the presence of an additional genetic system shaping yellowish hair variability.
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Affiliation(s)
- Hitoshi Suzuki
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan
| | - Gohta Kinoshita
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Takeru Tsunoi
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan
| | - Koki Noju
- Graduate School of Science, Hokkaido University, Sapporo, Japan
| | - Kimi Araki
- and Division of Developmental Genetics, Institute of Resource Development and Analysis, Kumamoto University, Honjo, Kumamoto, Japan
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Species and genetic diversity of Bandicota (Murinae, Rodentia) from Myanmar based on mitochondrial and nuclear gene sequences. MAMMAL RES 2020. [DOI: 10.1007/s13364-020-00491-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Russell JC, Robins JH, Fewster RM. Phylogeography of Invasive Rats in New Zealand. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00048] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Sakuma Y, Matsunami M, Takada T, Suzuki H. Multiple Conserved Elements Structuring Inverted Repeats in the Mammalian Coat Color-Related Gene Asip. Zoolog Sci 2019; 36:23-30. [PMID: 31116535 DOI: 10.2108/zs180081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 09/17/2018] [Indexed: 11/17/2022]
Abstract
In the agouti signaling gene protein (Asip) of the house mouse (Mus musculus), inverted repeat (IR) arrays are known to exist in a non-coding region adjacent to the ventral-specific promoter region and the accompanying two exons (exons 1A and 1A'), which are around 100 kb upstream from the amino acid coding regions of exons 2, 3, and 4. To determine the gene structure of mammalian Asip and to elucidate trends in its evolution, non-coding sequences of six rodent (mouse, rat, Chinese hamster, squirrel, guinea pig, and naked mole rat) and three non-rodent (rabbit, human, and cow) species were retrieved from databases and compared. Our homology search analyses revealed the presence of three to five highly conserved non-coding elements (CNE). These CNEs were found to form IRs in rodents and lagomorphs. Combinations of IRs were further shown to build symmetric, long IR arrays. Intra- and inter-specific comparisons of the sequences of three universal CNEs showed homogeneity between CNE pairs within species. This implies that certain evolutionary constraints maintained the IR structure in the rodent and rabbit species.
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Affiliation(s)
- Yuki Sakuma
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
| | - Masatoshi Matsunami
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan, .,Graduate School of Medicine, University of the Ryukyus, Nishihara-cho 903-0215, Japan,
| | - Toyoyuki Takada
- Mammalian Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Hitoshi Suzuki
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
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10
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Phylogeography of the black rat Rattus rattus in India and the implications for its dispersal history in Eurasia. Biol Invasions 2018. [DOI: 10.1007/s10530-018-1830-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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Sasamori S, Wiewel AS, Thomson VA, Kobayashi M, Nakata K, Suzuki H. Potential Causative Mutation for Melanism in Rats Identified in the Agouti Signaling Protein Gene (Asip) of the Rattus rattus Species Complex on Okinawa Island, Japan. Zoolog Sci 2017; 34:513-522. [PMID: 29219041 DOI: 10.2108/zs170027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The occurrence of black fur, or melanism, in many mammalian species is known to be linked to DNA sequence variation in the agouti signaling protein (Asip) gene, which is a major determinant of eumelanin and pheomelanin pigments in coat color. We investigated 38 agouti (i.e., banded wildtype) and four melanistic Rattus rattus species complex (RrC) lineage II specimens from Okinawa Island, Ryukyu Islands, Japan, for genetic variation in three exons and associated flanking regions in the Asip gene. On Okinawa, a predicted loss-of-function mutation caused by a cysteine to serine amino acid change at p.124C>S (c.370T>A) in the highly conserved functional domain of Asip was found in melanistic rats, but was absent in agouti specimens, suggesting that the p.124C>S mutation is responsible for the observed melanism. Phylogeographic analysis found that Asip sequences from Okinawan RrC lineage II, including both agouti and melanistic specimens, differed from: 1) both agouti and melanistic RrC lineage I from Otaru, Hokkaido, Japan, and 2) agouti RrC lineages I and II from South Australia. This suggests the possibility of in-situ mutation of the Asip gene, either within the RrC lineage II population on Okinawa or in an unsampled RrC lineage II population with biogeographic links to Okinawa, although incomplete lineage sorting could not be ruled out.
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Affiliation(s)
- Shoichi Sasamori
- 1 Division of Bioscience, Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Andrew S Wiewel
- 2 School of Biological Sciences, University of Adelaide, North Terrace, Adelaide SA 5005, Australia
| | - Vicki A Thomson
- 2 School of Biological Sciences, University of Adelaide, North Terrace, Adelaide SA 5005, Australia
| | - Motoko Kobayashi
- 1 Division of Bioscience, Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Katsushi Nakata
- 3 Yambaru Wildlife Conservation Center, Ministry of the Environment, Kunigami-son, Okinawa 905-1413, Japan
| | - Hitoshi Suzuki
- 1 Division of Bioscience, Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
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12
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Sakuma Y, Ranorosoa MC, Kinoshita G, Shimoji H, Tsuchiya K, Ohdachi SD, Arai S, Tanaka C, Ramino H, Suzuki H. Variation in the Coat-Color-Controlling Genes,Mc1randAsip, in the House MouseMus musculusfrom Madagascar. MAMMAL STUDY 2016. [DOI: 10.3106/041.041.0303] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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13
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Chingangbam DS, Laishram JM, Suzuki H. Molecular phylogenetic characterization of common murine rodents from Manipur, Northeast India. Genes Genet Syst 2016; 90:21-30. [PMID: 26119663 DOI: 10.1266/ggs.90.21] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The Indian subcontinent and Southeast Asia are hotspots of murine biodiversity, but no species from the Arakan Mountain system that demarcates the border between the two areas has been subjected to molecular phylogenetic analyses. We examined the mitochondrial cytochrome b gene sequences in six murine species (the Rattus rattus species complex, R. norvegicus, R. nitidus, Berylmys manipulus, Niviventer sp. and Mus musculus) from Manipur, which is located at the western foot of the mountain range. The sequences of B. manipulus and Niviventer sp. examined here were distinct from available congeneric sequences in the databases, with sequence divergences of 10-15%. Substantial degrees of intrapopulation divergence were detected in R. nitidus and the R. rattus species complex from Manipur, implying ancient habitation of the species in this region, while the recent introduction by modern and prehistoric human activities was suggested for R. norvegicus and M. musculus, respectively. In the nuclear gene Mc1r, also analyzed here, the R. rattus species complex from Manipur was shown to possess allelic sequences related to those from the Indian subcontinent in addition to those from East Asia. These results not only fill gaps in the phylogenetic knowledge of each taxon examined but also provide valuable insight to better understand the biogeographic importance of the Arakan Mountain system in generating the species and genetic diversity of murine rodents.
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Nunome M, Kinoshita G, Tomozawa M, Torii H, Matsuki R, Yamada F, Matsuda Y, Suzuki H. Lack of association between winter coat colour and genetic population structure in the Japanese hare,Lepus brachyurus(Lagomorpha: Leporidae). Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12245] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mitsuo Nunome
- Laboratory of Animal Genetics; Department of Applied Molecular Biosciences; Graduate School of Bioagricultural Sciences; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8601 Japan
| | - Gohta Kinoshita
- Laboratory of Ecology and Genetics; Faculty of Environmental Earth Science; Hokkaido University; Kita-ku Sapporo 060-0810 Japan
| | | | - Harumi Torii
- Center for Natural Environment Education; Nara University of Education; Takabatake-cho Nara 630-8528 Japan
| | - Rikyu Matsuki
- Environmental Science Research Laboratory; Central Research Institute of Electric Power Industry; 1646 Abiko Chiba 270-1194 Japan
| | - Fumio Yamada
- Forestry and Forest Products Research Institute; PO Box 16 Tsukuba Norin Ibaraki 305-8687 Japan
| | - Yoichi Matsuda
- Laboratory of Animal Genetics; Department of Applied Molecular Biosciences; Graduate School of Bioagricultural Sciences; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8601 Japan
| | - Hitoshi Suzuki
- Laboratory of Ecology and Genetics; Faculty of Environmental Earth Science; Hokkaido University; Kita-ku Sapporo 060-0810 Japan
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Yasuda SP, Gamage CD, Koizumi N, Nishio S, Isozumi R, Shimizu K, Koma T, Amada T, Suzuki H, Yoshimatsu K, Arikawa J. Distinct genetic characteristics of Sri Lankan Rattus and Bandicota (Murinae, Rodentia) inferred from mitochondrial and nuclear markers. Genes Genet Syst 2014; 89:71-80. [DOI: 10.1266/ggs.89.71] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Shumpei P. Yasuda
- Department of Microbiology, Hokkaido University Graduate School of Medicine
| | - Chandika D. Gamage
- Department of Microbiology, Hokkaido University Graduate School of Medicine
| | - Nobuo Koizumi
- Department of Bacteriology, National Institute of Infectious Diseases
| | - Sanae Nishio
- Department of Microbiology, Hokkaido University Graduate School of Medicine
| | - Rie Isozumi
- Department of Microbiology, Hokkaido University Graduate School of Medicine
| | - Kenta Shimizu
- Department of Microbiology, Hokkaido University Graduate School of Medicine
| | - Takaaki Koma
- Department of Microbiology, Hokkaido University Graduate School of Medicine
| | - Takako Amada
- Department of Microbiology, Hokkaido University Graduate School of Medicine
| | - Hitoshi Suzuki
- Laboratory of Ecology and Genetics, Graduate School of Environmental Earth Science, Hokkaido University
| | - Kumiko Yoshimatsu
- Department of Microbiology, Hokkaido University Graduate School of Medicine
| | - Jiro Arikawa
- Department of Microbiology, Hokkaido University Graduate School of Medicine
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Suzuki H. Evolutionary and phylogeographic views on Mc1r and Asip variation in mammals. Genes Genet Syst 2013; 88:155-64. [DOI: 10.1266/ggs.88.155] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Hitoshi Suzuki
- Laboratory of Ecology and Genetics, Graduate School of Environmental Earth Science, Hokkaido University
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Kambe Y, Nakata K, Yasuda SP, Suzuki H. Genetic characterization of Okinawan black rats showing coat color polymorphisms of white spotting and melanism. Genes Genet Syst 2012; 87:29-38. [PMID: 22531792 DOI: 10.1266/ggs.87.29] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We examined pelage color variation in wild populations of black rats (the Rattus rattus species complex) in the Yambaru forest area, northern Okinawa Island, Ryukyu Archipelago, Japan. Our field study revealed that 8.7% (38/438) and 0.2% (4/2500) of rats exhibited two types of coat color: white spotting and melanism, respectively. Using 34 representative animals, the phylogeography of the population was inferred using a nuclear gene marker, i.e., sequences (954 bp) of the melanocortin-1 receptor (Mc1r) gene responsible for the melanistic form in black rats. Four sequences from Okinawa were characterized as R. tanezumi, the Asian strain of black rat. Notably, neither of the phenotypic characters of white spotting or melanism was associated with the Mc1r haplotypes. Analysis of mitochondrial cytochrome b (Cytb) sequences (1140 bp) revealed that four haplotypes recovered from Okinawa clustered with the clade of R. tanezumi and differed by one or more bases from haplotypes at other localities in Japan and Asian countries. Thus, both variants may have arisen in the native rat population of Okinawa without interaction with the lineage of R. rattus, which exhibits a worldwide distribution and displays such coat color variants. The Yambaru population of black rats has thus experienced its own evolutionary history in allopatry for a substantial period of time (e.g., 10,000 years), which has preserved valuable genetic polymorphisms and will be useful for assessing the ecological consequences of genetic variation in natural populations.
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Affiliation(s)
- Yoshikazu Kambe
- Division of Bioscience, Graduate School of Environmental Earth Science, Hokkaido University, Sapporo, Japan
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18
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Aplin KP, Suzuki H, Chinen AA, Chesser RT, Ten Have J, Donnellan SC, Austin J, Frost A, Gonzalez JP, Herbreteau V, Catzeflis F, Soubrier J, Fang YP, Robins J, Matisoo-Smith E, Bastos ADS, Maryanto I, Sinaga MH, Denys C, Van Den Bussche RA, Conroy C, Rowe K, Cooper A. Multiple geographic origins of commensalism and complex dispersal history of Black Rats. PLoS One 2011; 6:e26357. [PMID: 22073158 PMCID: PMC3206810 DOI: 10.1371/journal.pone.0026357] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Accepted: 09/25/2011] [Indexed: 01/22/2023] Open
Abstract
The Black Rat (Rattus rattus) spread out of Asia to become one of the world's worst agricultural and urban pests, and a reservoir or vector of numerous zoonotic diseases, including the devastating plague. Despite the global scale and inestimable cost of their impacts on both human livelihoods and natural ecosystems, little is known of the global genetic diversity of Black Rats, the timing and directions of their historical dispersals, and the risks associated with contemporary movements. We surveyed mitochondrial DNA of Black Rats collected across their global range as a first step towards obtaining an historical genetic perspective on this socioeconomically important group of rodents. We found a strong phylogeographic pattern with well-differentiated lineages of Black Rats native to South Asia, the Himalayan region, southern Indochina, and northern Indochina to East Asia, and a diversification that probably commenced in the early Middle Pleistocene. We also identified two other currently recognised species of Rattus as potential derivatives of a paraphyletic R. rattus. Three of the four phylogenetic lineage units within R. rattus show clear genetic signatures of major population expansion in prehistoric times, and the distribution of particular haplogroups mirrors archaeologically and historically documented patterns of human dispersal and trade. Commensalism clearly arose multiple times in R. rattus and in widely separated geographic regions, and this may account for apparent regionalism in their associated pathogens. Our findings represent an important step towards deeper understanding the complex and influential relationship that has developed between Black Rats and humans, and invite a thorough re-examination of host-pathogen associations among Black Rats.
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Affiliation(s)
- Ken P Aplin
- Australian National Wildlife Collection, CSIRO Ecosystem Sciences, Canberra, Australia.
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