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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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Motokawa M, Makino T, Yato TO, Okabe S, Shiroma T, Toyama M, Ota H. First Record of Lineage IV of Rattus tanezumi (Rodentia: Muridae) from the southern Ryukyus, Japan. MAMMAL STUDY 2022. [DOI: 10.3106/ms2022-0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Masaharu Motokawa
- The Kyoto University Museum, Kyoto University, Kyoto 606-8501, Japan
| | - Tomohisa Makino
- Division of Biological Science, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Takashi O. Yato
- Division of Biological Science, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Shinya Okabe
- Division of Biological Science, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Tsunehiro Shiroma
- Cultural Properties Division, Okinawa Prefectural Board of Education, Naha, Okinawa 900-8571, Japan
| | - Masanao Toyama
- The Institute of Regional Study in Okinawa University, Naha, Okinawa 902-8521, Japan
| | - Hidetoshi Ota
- Institute of Natural and Environmental Sciences, University of Hyogo, and Museum of Nature and Human Activities, Sanda, Hyogo 669-1546, Japan
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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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Late Quaternary Environmental and Human Impacts on the Mitochondrial DNA Diversity of Four Commensal Rodents in Myanmar. J MAMM EVOL 2020. [DOI: 10.1007/s10914-020-09519-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AbstractWe addressed the spatiotemporal characteristics of four commensal rodent species occurring in Myanmar in comparison with other areas of the Indo-Malayan region. We examined sequence variations of the mitochondrial cytochrome b gene (Cytb) in the Pacific rat (Rattus exulans), roof rat (Rattus rattus complex, RrC), lesser bandicoot rat (Bandicota bengalensis), and house mouse (Mus musculus) using the recently developed time-dependent evolutionary rates of mtDNA. The Cytb sequences of RrC from Myanmar were shown to belong to RrC Lineage II, and their level of genetic diversity was relatively high compared to those of the other three species. RrC was found to have experienced bottleneck and rapid expansion events at least twice in the late Pleistocene period in Myanmar and a nearby region. Accordingly, paleoclimatic environmental fluctuations were shown to be an important factor affecting rodents in the subtropics of the Indo-Malayan region. Our results show that human activities during the last 10,000 years of the Holocene period affected the population dynamics of the rodent species examined, including introducing them to Myanmar from neighboring countries. Further study of these four commensal rodents in other geographic areas of the Indo-Malayan region would allow us to better understand the factors that drove their evolution and their ecological trends.
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Rode NO, Estoup A, Bourguet D, Courtier-Orgogozo V, Débarre F. Population management using gene drive: molecular design, models of spread dynamics and assessment of ecological risks. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01165-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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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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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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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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Mitochondrial phylogeography of the black rat supports a single invasion of the western Mediterranean basin. Biol Invasions 2015. [DOI: 10.1007/s10530-015-0842-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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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, Nunome M, Kinoshita G, Aplin KP, Vogel P, Kryukov AP, Jin ML, Han SH, Maryanto I, Tsuchiya K, Ikeda H, Shiroishi T, Yonekawa H, Moriwaki K. Evolutionary and dispersal history of Eurasian house mice Mus musculus clarified by more extensive geographic sampling of mitochondrial DNA. Heredity (Edinb) 2013; 111:375-90. [PMID: 23820581 DOI: 10.1038/hdy.2013.60] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2012] [Revised: 02/21/2013] [Accepted: 04/24/2013] [Indexed: 11/09/2022] Open
Abstract
We examined the sequence variation of mitochondrial DNA control region and cytochrome b gene of the house mouse (Mus musculus sensu lato) drawn from ca. 200 localities, with 286 new samples drawn primarily from previously unsampled portions of their Eurasian distribution and with the objective of further clarifying evolutionary episodes of this species before and after the onset of human-mediated long-distance dispersals. Phylogenetic analysis of the expanded data detected five equally distinct clades, with geographic ranges of northern Eurasia (musculus, MUS), India and Southeast Asia (castaneus, CAS), Nepal (unspecified, NEP), western Europe (domesticus, DOM) and Yemen (gentilulus). Our results confirm previous suggestions of Southwestern Asia as the likely place of origin of M. musculus and the region of Iran, Afghanistan, Pakistan, and northern India, specifically as the ancestral homeland of CAS. The divergence of the subspecies lineages and of internal sublineage differentiation within CAS were estimated to be 0.37-0.47 and 0.14-0.23 million years ago (mya), respectively, assuming a split of M. musculus and Mus spretus at 1.7 mya. Of the four CAS sublineages detected, only one extends to eastern parts of India, Southeast Asia, Indonesia, Philippines, South China, Northeast China, Primorye, Sakhalin and Japan, implying a dramatic range expansion of CAS out of its homeland during an evolutionary short time, perhaps associated with the spread of agricultural practices. Multiple and non-coincident eastward dispersal events of MUS sublineages to distant geographic areas, such as northern China, Russia and Korea, are inferred, with the possibility of several different routes.
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Affiliation(s)
- H Suzuki
- Laboratory of Ecology and Genetics, Graduate School of Environmental Earth Science, Hokkaido University, Sapporo, Japan
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12
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Conroy CJ, Rowe KC, Rowe KMC, Kamath PL, Aplin KP, Hui L, James DK, Moritz C, Patton JL. Cryptic genetic diversity in Rattus of the San Francisco Bay region, California. Biol Invasions 2012. [DOI: 10.1007/s10530-012-0323-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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13
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Contribution to the species composition and taxonomic status of some Rattus inhabiting Southern Vietnam and Sundaland. RUSSIAN JOURNAL OF THERIOLOGY 2012. [DOI: 10.15298/rusjtheriol.11.1.03] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Lack JB, Greene DU, Conroy CJ, Hamilton MJ, Braun JK, Mares MA, Van Den Bussche RA. Invasion facilitates hybridization with introgression in the Rattus rattus species complex. Mol Ecol 2012; 21:3545-61. [PMID: 22607228 DOI: 10.1111/j.1365-294x.2012.05620.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biological invasions result in novel species interactions, which can have significant evolutionary impacts on both native and invading taxa. One evolutionary concern with invasions is hybridization among lineages that were previously isolated, but make secondary contact in their invaded range(s). Black rats, consisting of several morphologically very similar but genetically distinct taxa that collectively have invaded six continents, are arguably the most successful mammalian invaders on the planet. We used mitochondrial cytochrome b sequences, two nuclear gene sequences (Atp5a1 and DHFR) and nine microsatellite loci to examine the distribution of three invasive black rat lineages (Rattus tanezumi, Rattus rattus I and R. rattus IV) in the United States and Asia and to determine the extent of hybridization among these taxa. Our analyses revealed two mitochondrial lineages that have spread to multiple continents, including a previously undiscovered population of R. tanezumi in the south-eastern United States, whereas the third lineage (R. rattus IV) appears to be confined to Southeast Asia. Analyses of nuclear DNA (both sequences and microsatellites) suggested significant hybridization is occurring among R. tanezumi and R. rattus I in the United States and also suggest hybridization between R. tanezumi and R. rattus IV in Asia, although further sampling of the latter species pair in Asia is required. Furthermore, microsatellite analyses suggest unidirectional introgression from both R. rattus I and R. rattus IV into R. tanezumi. Within the United States, introgression appears to be occurring to such a pronounced extent that we were unable to detect any nuclear genetic signal for R. tanezumi, and a similar pattern was detected in Asia.
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Affiliation(s)
- Justin B Lack
- Department of Zoology, 501 Life Sciences West, Oklahoma State University, Stillwater, OK 74078, USA.
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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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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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Kambe Y, Tanikawa T, Matsumoto Y, Tomozawa M, Aplin KP, Suzuki H. Origin of agouti-melanistic polymorphism in Wild Black Rats (Rattus rattus) inferred from Mc1r gene sequences. Zoolog Sci 2011; 28:560-7. [PMID: 21800996 DOI: 10.2108/zsj.28.560] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We examined nucleotide changes that underlie coat color variation in Black Rats (the Rattus rattus species complex), which show polymorphism in dorsal fur color, including either grayish brown (agouti) or black (melanistic) forms. We examined the full coding sequence of a gene known to produce melanism in other vertebrates-melanocortin-1-receptor gene Mc1r (954 bp) -using samples of both R. rattus (with 2n = 38) and its close relative Asian Black Rat (R. tanezumi; 2n = 42). We used 61 specimens from Japan with karyotype-known individuals and four samples from Pakistan. We found 11 allele sequences and constructed a network tree that shows two distinct clusters, with allelic segregation according to karyotype and by inference, representing the two species. We found that a nucleotide substitution from G to A at site 280, producing an amino acid change from glutamic acid to lysine, was associated with the dominant trait of the melanistic form of the coat color in R. rattus. Notably, the derived SNP 280A was found in a single allele, with the ancestral SNP 280G present in seven alleles. By contrast, all three alleles for R. tanezumi retain the ancestral SNP 280G. These results suggest a possible recent origin of melanism in R. rattus.
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Affiliation(s)
- Yoshikazu Kambe
- Division of Bioscience, Hokkaido University, Sapporo 060-0810, Japan
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CONROY CHRISJ, GUPTA ADITIM. Cranial morphology of the California vole (Microtus californicus, Cricetidae) in a contact zone. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01722.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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19
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Bastos AD, Nair D, Taylor PJ, Brettschneider H, Kirsten F, Mostert E, von Maltitz E, Lamb JM, van Hooft P, Belmain SR, Contrafatto G, Downs S, Chimimba CT. Genetic monitoring detects an overlooked cryptic species and reveals the diversity and distribution of three invasive Rattus congeners in South Africa. BMC Genet 2011; 12:26. [PMID: 21324204 PMCID: PMC3055845 DOI: 10.1186/1471-2156-12-26] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Accepted: 02/16/2011] [Indexed: 11/30/2022] Open
Abstract
Background South Africa's long and extensive trade activity has ensured ample opportunities for exotic species introduction. Whereas the rich biodiversity of endemic southern African fauna has been the focus of many studies, invasive vertebrates are generally overlooked despite potential impacts on biodiversity, health and agriculture. Genetic monitoring of commensal rodents in South Africa which uncovered the presence of Rattus tanezumi, a South-East Asian endemic not previously known to occur in Africa, provided the impetus for expanded studies on all invasive Rattus species present. Results To this end, intensified sampling at 28 South African localities and at one site in Swaziland, identified 149 Rattus specimens. Cytochrome b gene sequencing revealed the presence of two R. tanezumi, seven Rattus rattus and five Rattus norvegicus haplotypes in south Africa. Phylogenetic results were consistent with a single, recent R. tanezumi introduction and indicated that R. norvegicus and R. rattus probably became established following at least two and three independent introductions, respectively. Intra- and inter-specific diversity was highest in informal human settlements, with all three species occurring at a single metropolitan township site. Rattus norvegicus and R. rattus each occurred sympatrically with Rattus tanezumi at one and five sites, respectively. Karyotyping of selected R. rattus and R. tanezumi individuals identified diploid numbers consistent with those reported previously for these cryptic species. Ordination of bioclimatic variables and MaxEnt ecological niche modelling confirmed that the bioclimatic niche occupied by R. tanezumi in south Africa was distinct from that occupied in its naturalised range in south-east Asia suggesting that factors other than climate may influence the distribution of this species. Conclusions This study has highlighted the value of genetic typing for detecting cryptic invasive species, providing historical insights into introductions and for directing future sampling. The apparent ease with which a cryptic species can become established signals the need for broader implementation of genetic monitoring programmes. In addition to providing baseline data and potentially identifying high-risk introduction routes, the predictive power of ecological niche modelling is enhanced when species records are genetically verified.
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Affiliation(s)
- Armanda D Bastos
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Private Bag 20, Hatfield 0028, Pretoria, South Africa.
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Nunome M, Ishimori C, Aplin KP, Tsuchiya K, Yonekawa H, Moriwaki K, Suzuki H. Detection of recombinant haplotypes in wild mice (Mus musculus) provides new insights into the origin of Japanese mice. Mol Ecol 2010; 19:2474-89. [PMID: 20465587 DOI: 10.1111/j.1365-294x.2010.04651.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Japanese house mice (Mus musculus molossinus) are thought to be a hybrid lineage derived from two prehistoric immigrants, the subspecies M. m. musculus of northern Eurasia and M. m. castaneus of South Asia. Mice of the western European subspecies M. m. domesticus have been detected in Japanese ports and airports only. We examined haplotype structuring of a 200 kb stretch on chromosome 8 for 59 mice from throughout Eurasia, determining short segments (approximately 370-600 bp) of eight nuclear genes (Fanca, Spire2, Tcf25, Mc1r, Tubb3, Def8, Afg3l1 and Dbndd1) which are intermittently arranged in this order. Where possible we identified the subspecies origin for individual gene alleles and then designated haplotypes for concatenated alleles. We recovered 11 haplotypes among 19 Japanese mice examined, identified either as 'intact' haplotypes derived from the subspecies musculus (57.9%), domesticus (7.9%), and castaneus (2.6%), or as 'recombinant' haplotypes (31.6%). We also detected recombinant haplotypes unique to Sakhalin. The complex nature of the recombinant haplotypes suggests ancient introduction of all three subspecies components into the peripheral part of Eurasia or complicated genomic admixture before the movement from source areas. 'Intact'domesticus and castaneus haplotypes in other Japanese wild mice imply ongoing stowaway introductions. The method has general utility for assessing the history of genetic admixture and for disclosing ongoing genetic contamination.
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Affiliation(s)
- Mitsuo Nunome
- Laboratory of Ecology and Genetics, Graduate School of Environmental Earth Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
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Truong TT, Yoshimatsu K, Araki K, Lee BH, Nakamura I, Endo R, Shimizu K, Yasuda SP, Koma T, Taruishi M, Okumura M, Truong UN, Arikawa J. Molecular epidemiological and serological studies of hantavirus infection in northern Vietnam. J Vet Med Sci 2009; 71:1357-63. [PMID: 19887743 DOI: 10.1292/jvms.001357] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The distribution of anti-hantavirus antibodies in humans and rodents in northern Vietnam was examined. In total, 837 serum samples from healthy humans (617) and patients with fever (220), living in six different areas were screened for IgG antibodies against Hantaan or Seoul virus (SEOV) by ELISA, IFA, and Western blot analysis. Antibody-positive sera were identified in 7/617 (1.1%) healthy donors, 5/150 port workers in the port of Hai Phong, and 2/185 residents of Ha Nam Province. In comparison, positive sera were detected in 5/220 (2.3%) fever patients in the provinces of Ha Nam (1/58) and Thanh Hoa (4/146). Antibody-positive Rattus norvegicus were found in the provinces of Ha Nam (7/52) and Thanh Hoa (1/67), in Haibatrung District (7/43) in Hanoi, and in Hai Phong Port (21/62), while antibody-positive R. rattus (2/17) were found in Hai Phong Port. Part of the Gc region from the viral genome was amplified by RT-PCR using lung tissue samples from R. norvegicus in Haibatrung (2/7) and Hai Phong Port (7/9), but not from R. rattus (0/2). Viral sequences were located in the SEOV clade and formed a single lineage with Indonesian SEOV, suggesting that Vietnamese SEOV is part of a distinct lineage among Asian SEOVs.
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Tomozawa M, Suzuki H. A Trend of Central Versus Peripheral Structuring in Mitochondrial and Nuclear Gene Sequences of the Japanese Wood Mouse, Apodemus speciosus. Zoolog Sci 2008; 25:273-85. [DOI: 10.2108/zsj.25.273] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2007] [Accepted: 12/09/2007] [Indexed: 11/17/2022]
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Suzuki H, Filippucci MG, Chelomina GN, Sato JJ, Serizawa K, Nevo E. A Biogeographic View of Apodemus in Asia and Europe Inferred From Nuclear and Mitochondrial Gene Sequences. Biochem Genet 2008; 46:329-46. [DOI: 10.1007/s10528-008-9149-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2007] [Revised: 11/12/2007] [Accepted: 11/12/2007] [Indexed: 11/24/2022]
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