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Renaud S, Amar L, Chevret P, Romestaing C, Quéré JP, Régis C, Lebrun R. Inner ear morphology in wild versus laboratory house mice. J Anat 2024; 244:722-738. [PMID: 38214368 PMCID: PMC11021637 DOI: 10.1111/joa.13998] [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: 07/31/2023] [Revised: 12/08/2023] [Accepted: 12/08/2023] [Indexed: 01/13/2024] Open
Abstract
The semicircular canals of the inner ear are involved in balance and velocity control. Being crucial to ensure efficient mobility, their morphology exhibits an evolutionary conservatism attributed to stabilizing selection. Release of selection in slow-moving animals has been argued to lead to morphological divergence and increased inter-individual variation. In its natural habitat, the house mouse Mus musculus moves in a tridimensional space where efficient balance is required. In contrast, laboratory mice in standard cages are severely restricted in their ability to move, which possibly reduces selection on the inner ear morphology. This effect was tested by comparing four groups of mice: several populations of wild mice trapped in commensal habitats in France; their second-generation laboratory offspring, to assess plastic effects related to breeding conditions; a standard laboratory strain (Swiss) that evolved for many generations in a regime of mobility reduction; and hybrids between wild offspring and Swiss mice. The morphology of the semicircular canals was quantified using a set of 3D landmarks and semi-landmarks analyzed using geometric morphometric protocols. Levels of inter-population, inter-individual (disparity) and intra-individual (asymmetry) variation were compared. All wild mice shared a similar inner ear morphology, in contrast to the important divergence of the Swiss strain. The release of selection in the laboratory strain obviously allowed for an important and rapid drift in the otherwise conserved structure. Shared traits between the inner ear of the lab strain and domestic pigs suggested a common response to mobility reduction in captivity. The lab-bred offspring of wild mice also differed from their wild relatives, suggesting plastic response related to maternal locomotory behavior, since inner ear morphology matures before birth in mammals. The signature observed in lab-bred wild mice and the lab strain was however not congruent, suggesting that plasticity did not participate to the divergence of the laboratory strain. However, contrary to the expectation, wild mice displayed slightly higher levels of inter-individual variation than laboratory mice, possibly due to the higher levels of genetic variance within and among wild populations compared to the lab strain. Differences in fluctuating asymmetry levels were detected, with the laboratory strain occasionally displaying higher asymmetry scores than its wild relatives. This suggests that there may indeed be a release of selection and/or a decrease in developmental stability in the laboratory strain.
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Affiliation(s)
- Sabrina Renaud
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR 5558, CNRS, Université Claude Bernard Lyon 1, Université de Lyon, Villeurbanne, France
| | - Léa Amar
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR 5558, CNRS, Université Claude Bernard Lyon 1, Université de Lyon, Villeurbanne, France
| | - Pascale Chevret
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR 5558, CNRS, Université Claude Bernard Lyon 1, Université de Lyon, Villeurbanne, France
| | - Caroline Romestaing
- Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), UMR 5023, CNRS, ENTPE, Université Claude Bernard Lyon 1, Université de Lyon, Villeurbanne, France
| | - Jean-Pierre Quéré
- Centre de Biologie et Gestion des Populations (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet, Montferrier-sur-Lez Cedex, France
| | - Corinne Régis
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR 5558, CNRS, Université Claude Bernard Lyon 1, Université de Lyon, Villeurbanne, France
| | - Renaud Lebrun
- Institut des Sciences de l'Évolution (ISE-M), UMR 5554, CNRS/UM/IRD/EPHE, Université de Montpellier, Montpellier, France
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Carromeu-Santos A, Mathias ML, Gabriel SI. Widespread distribution of rodenticide resistance-conferring mutations in the Vkorc1 gene among house mouse populations in Portuguese Macaronesian islands and Iberian Atlantic areas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:166290. [PMID: 37586516 DOI: 10.1016/j.scitotenv.2023.166290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 08/11/2023] [Accepted: 08/12/2023] [Indexed: 08/18/2023]
Abstract
Growing evidence of widespread resistance to anticoagulant rodenticides (ARs) in house mice pose significant challenges to pest control efforts. First-generation ARs were introduced in the early 1950s but resistance to these emerged later that decade. Second-generation rodenticides were then developed, with resistance being reported in the late 1970s. Research has linked resistance to ARs with mutations in the Vkorc1 gene, leading to the use of more toxic and environmentally harmful compounds. In this study, 243 tail tips of house mice from mainland Portugal and Southern Spain, the Azores and Madeira archipelagos were analysed for all 3 exons of the Vkorc1 gene. Mutations L128S, Y139C, along with the so-called spretus genotype Vkorc1spr are considered responsible for reduced susceptibility of house mice to ARs. All these sequence variants were broadly detected throughout the sampling regions. Vkorc1spr was the most often recorded among mainland populations, whereas Y139C was nearly ubiquitous among the insular populations. In contrast, L128S was only detected in mainland Portugal and four islands of the Azores archipelago. All first generation ARs such as warfarin and coumatetralyl are deemed ineffective against all Vkorc1 variants identified in this study. Second-generation bromadiolone and difenacoum should also be discarded to control populations carrying Vkorc1spr, Y139C or L128S mutations. Inadequate use of ARs in regions where resistant animals have been found in large proportions will result in the spreading of rodenticide resistance among rodent populations through the positive selection of non-susceptible individuals. Consequently, ineffectiveness of rodent control will increase and potentiate environmental contamination, hazarding non-target wildlife through secondary poisoning. We highlight the need for Vkorc1 screening as a crucial tool in rodent management, aiding in the selection of the most appropriate control/eradication method in order to prevent misuse of these toxic biocides and the spread of rodenticide resistance among house mouse populations.
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Affiliation(s)
- A Carromeu-Santos
- CESAM-Centro de Estudos do Ambiente e do Mar, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - M L Mathias
- CESAM-Centro de Estudos do Ambiente e do Mar, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - S I Gabriel
- CESAM-Centro de Estudos do Ambiente e do Mar, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; Departamento de Biologia da Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
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3
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Agwamba KD, Nachman MW. The demographic history of house mice (Mus musculus domesticus) in eastern North America. G3 (BETHESDA, MD.) 2023; 13:jkac332. [PMID: 36546306 PMCID: PMC9911051 DOI: 10.1093/g3journal/jkac332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 10/17/2022] [Accepted: 11/16/2022] [Indexed: 12/24/2022]
Abstract
The Western European house mouse (Mus musculus domesticus) is a widespread human commensal that has recently been introduced to North America. Its introduction to the Americas is thought to have resulted from the transatlantic movements of Europeans that began in the early 16th century. To study the details of this colonization history, we examine population structure, explore relevant demographic models, and infer the timing of divergence among house mouse populations in the eastern United States using published exome sequences from five North American populations and two European populations. For North American populations of house mice, levels of nucleotide variation were lower, and low-frequency alleles were less common than for European populations. These patterns provide evidence of a mild bottleneck associated with the movement of house mice into North America. Several analyses revealed that one North American population is genetically admixed, which indicates at least two source populations from Europe were independently introduced to eastern North America. Estimated divergence times between North American and German populations ranged between ∼1,000 and 7,000 years ago and overlapped with the estimated divergence time between populations from Germany and France. Demographic models comparing different North American populations revealed that these populations diverged from each other mostly within the last 500 years, consistent with the timing of the arrival of Western European settlers to North America. Together, these results support a recent introduction of Western European house mice to eastern North America, highlighting the effects of human migration and colonization on the spread of an invasive human commensal.
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Affiliation(s)
- Kennedy D Agwamba
- Center for Computational Biology, Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael W Nachman
- Center for Computational Biology, Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
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Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history. Nat Commun 2022; 13:2399. [PMID: 35504912 PMCID: PMC9064997 DOI: 10.1038/s41467-022-30009-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 03/18/2022] [Indexed: 11/29/2022] Open
Abstract
The distribution of the black rat (Rattus rattus) has been heavily influenced by its association with humans. The dispersal history of this non-native commensal rodent across Europe, however, remains poorly understood, and different introductions may have occurred during the Roman and medieval periods. Here, in order to reconstruct the population history of European black rats, we first generate a de novo genome assembly of the black rat. We then sequence 67 ancient and three modern black rat mitogenomes, and 36 ancient and three modern nuclear genomes from archaeological sites spanning the 1st-17th centuries CE in Europe and North Africa. Analyses of our newly reported sequences, together with published mitochondrial DNA sequences, confirm that black rats were introduced into the Mediterranean and Europe from Southwest Asia. Genomic analyses of the ancient rats reveal a population turnover in temperate Europe between the 6th and 10th centuries CE, coincident with an archaeologically attested decline in the black rat population. The near disappearance and re-emergence of black rats in Europe may have been the result of the breakdown of the Roman Empire, the First Plague Pandemic, and/or post-Roman climatic cooling. ‘Archaeogenetic analysis of black rat remains reveals that this species was introduced into temperate Europe twice, in the Roman and medieval periods. This population turnover was likely associated with multiple historical and environmental factors.’
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The introduction and diversity of commensal rodents in 19th century Australasia. Biol Invasions 2022. [DOI: 10.1007/s10530-021-02717-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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García-Rodríguez O, Hardouin EA, Hambleton E, Monteith J, Randall C, Richards MB, Edwards CJ, Stewart JR. Ancient mitochondrial DNA connects house mice in the British Isles to trade across Europe over three millennia. BMC Ecol Evol 2021; 21:9. [PMID: 33514313 PMCID: PMC7853306 DOI: 10.1186/s12862-021-01746-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/13/2021] [Indexed: 12/03/2022] Open
Abstract
Background The earliest records in Britain for the western European house mouse (Mus musculus domesticus) date from the Late Bronze Age. The arrival of this commensal species in Britain is thought to be related to human transport and trade with continental Europe. In order to study this arrival, we collected a total of 16 ancient mouse mandibulae from four early British archaeological sites, ranging from the Late Bronze Age to the Roman period. Results From these, we obtained ancient mitochondrial DNA (mtDNA) house mouse sequences from eight house mice from two of the sites dating from the Late Bronze to Middle Iron Age. We also obtained five ancient mtDNA wood mouse (Apodemus spp.) sequences from all four sites. The ancient house mouse sequences found in this study were from haplogroups E (N = 6) and D (N = 2). Modern British house mouse mtDNA sequences are primarily characterised by haplogroups E and F and, much less commonly, haplogroup D. Conclusions The presence of haplogroups D and E in our samples and the dating of the archaeological sites provide evidence of an early house mouse colonisation that may relate to Late Bronze Age/Iron Age trade and/or human expansion. Our results confirm the hypothesis, based on zooarchaeological evidence and modern mtDNA predictions, that house mice, with haplogroups D and E, were established in Britain by the Iron Age and, in the case of haplogroup E, possibly as early as the Late Bronze Age.
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Affiliation(s)
- Oxala García-Rodríguez
- Faculty of Science and Technology, Bournemouth University, Christchurch House, Talbot Campus, Poole, BH12 5BB, Dorset, UK.
| | - Emilie A Hardouin
- Faculty of Science and Technology, Bournemouth University, Christchurch House, Talbot Campus, Poole, BH12 5BB, Dorset, UK
| | - Ellen Hambleton
- Faculty of Science and Technology, Bournemouth University, Christchurch House, Talbot Campus, Poole, BH12 5BB, Dorset, UK
| | - Jonathan Monteith
- Faculty of Science and Technology, Bournemouth University, Christchurch House, Talbot Campus, Poole, BH12 5BB, Dorset, UK
| | - Clare Randall
- Faculty of Science and Technology, Bournemouth University, Christchurch House, Talbot Campus, Poole, BH12 5BB, Dorset, UK
| | - Martin B Richards
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Ceiridwen J Edwards
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - John R Stewart
- Faculty of Science and Technology, Bournemouth University, Christchurch House, Talbot Campus, Poole, BH12 5BB, Dorset, UK
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7
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Wilches R, Beluch WH, McConnell E, Tautz D, Chan YF. Independent evolution toward larger body size in the distinctive Faroe Island mice. G3-GENES GENOMES GENETICS 2021; 11:6062402. [PMID: 33561246 PMCID: PMC8022703 DOI: 10.1093/g3journal/jkaa051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/10/2020] [Indexed: 11/29/2022]
Abstract
Most phenotypic traits in nature involve the collective action of many genes. Traits that evolve repeatedly are particularly useful for understanding how selection may act on changing trait values. In mice, large body size has evolved repeatedly on islands and under artificial selection in the laboratory. Identifying the loci and genes involved in this process may shed light on the evolution of complex, polygenic traits. Here, we have mapped the genetic basis of body size variation by making a genetic cross between mice from the Faroe Islands, which are among the largest and most distinctive natural populations of mice in the world, and a laboratory mouse strain selected for small body size, SM/J. Using this F2 intercross of 841 animals, we have identified 111 loci controlling various aspects of body size, weight and growth hormone levels. By comparing against other studies, including the use of a joint meta-analysis, we found that the loci involved in the evolution of large size in the Faroese mice were largely independent from those of a different island population or other laboratory strains. We hypothesize that colonization bottleneck, historical hybridization, or the redundancy between multiple loci have resulted in the Faroese mice achieving an outwardly similar phenotype through a distinct evolutionary path.
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Affiliation(s)
- Ricardo Wilches
- Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany
| | - William H Beluch
- Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany
| | - Ellen McConnell
- Max Planck Institute for Evolutionary Biology, Department of Evolutionary Genetics, 24306 Plön, Germany
| | - Diethard Tautz
- Max Planck Institute for Evolutionary Biology, Department of Evolutionary Genetics, 24306 Plön, Germany
| | - Yingguang Frank Chan
- Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany
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Chevret P, Hautier L, Ganem G, Herman J, Agret S, Auffray JC, Renaud S. Genetic structure in Orkney island mice: isolation promotes morphological diversification. Heredity (Edinb) 2020; 126:266-278. [PMID: 32980864 DOI: 10.1038/s41437-020-00368-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/04/2020] [Accepted: 09/04/2020] [Indexed: 11/09/2022] Open
Abstract
Following human occupation, the house mouse has colonised numerous islands, exposing the species to a wide variety of environments. Such a colonisation process, involving successive founder events and bottlenecks, may either promote random evolution or facilitate adaptation, making the relative importance of adaptive and stochastic processes in insular evolution difficult to assess. Here, we jointly analyse genetic and morphometric variation in the house mice (Mus musculus domesticus) from the Orkney archipelago. Genetic analyses, based on mitochondrial DNA and microsatellites, revealed considerable genetic structure within the archipelago, suggestive of a high degree of isolation and long-lasting stability of the insular populations. Morphometric analyses, based on a quantification of the shape of the first upper molar, revealed considerable differentiation compared to Western European populations, and significant geographic structure in Orkney, largely congruent with the pattern of genetic divergence. Morphological diversification in Orkney followed a Brownian motion model of evolution, suggesting a primary role for random drift over adaptation to local environments. Substantial structuring of human populations in Orkney has recently been demonstrated, mirroring the situation found here in house mice. This synanthropic species may thus constitute a bioproxy of human structure and practices even at a very local scale.
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Affiliation(s)
- Pascale Chevret
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558 CNRS Université Lyon 1, Université de Lyon, Campus de la Doua, 69100, Villeurbanne, France.
| | - Lionel Hautier
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR 5554, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Guila Ganem
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR 5554, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Jeremy Herman
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh, EH1 1JF, UK
| | - Sylvie Agret
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR 5554, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Jean-Christophe Auffray
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR 5554, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Sabrina Renaud
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558 CNRS Université Lyon 1, Université de Lyon, Campus de la Doua, 69100, Villeurbanne, France
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Abstract
Mice (Mus musculus) and rats (Rattus norvegicus) have long served as model systems for biomedical research. However, they are also excellent models for studying the evolution of populations, subspecies, and species. Within the past million years, they have spread in various waves across large parts of the globe, with the most recent spread in the wake of human civilization. They have developed into commensal species, but have also been able to colonize extreme environments on islands free of human civilization. Given that ample genomic and genetic resources are available for these species, they have thus also become ideal mammalian systems for evolutionary studies on adaptation and speciation, particularly in the combination with the rapid developments in population genomics. The chapter provides an overview of the systems and their history, as well as of available resources.
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Affiliation(s)
- Kristian K Ullrich
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany.
| | - Diethard Tautz
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
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Myoshu H, Iwasa MA. Colonization and Differentiation Traits of the Japanese House Mouse, Mus musculus (Rodentia, Muridae), Inferred from Mitochondrial Haplotypes and External Body Characteristics. Zoolog Sci 2018; 35:222-232. [PMID: 29882501 DOI: 10.2108/zs170184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
To evaluate the colonization histories of the Japanese house mice (Mus musculus), phenotypic and genotypic admixtures of the subspecific traits were studied by evaluation of external body characteristics and mitochondrial gene elements. We analyzed mitochondrial Cytb gene and coat colorations and body dimensions as subspecific characteristics in mice from four areas of the Japanese Islands, the Sorachi, Ishikari and Iburi areas of Hokkaido, the Hidaka area of Hokkaido, and northeastern and central Honshu. Three occurrence patterns of the subspecific haplotypes of Cytb-the castaneus type only, the musculus type only, and the castaneus, musculus, and domesticus types together-were observed in the study areas. In central Honshu, the properties of haplotypes were in accord with the external characteristics as reported in previous findings. In contrast, complicated external characteristics were observed in the Hidaka area, where mice showed multiple haplotype properties. In addition, in northeastern Honshu, coat colorations were not in accord with haplotype properties and such discordance was also observed in most mice in the Sorachi, Ishikari and Iburi areas of Hokkaido. These complexities and discordances suggest that the genetic and phenotypic properties have been caused by different processes, not only through founder effects by migrations and subsequent subspecific hybridizations but also through differentiation in each study area.
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Affiliation(s)
- Hikari Myoshu
- Course in Natural Environment Studies, Graduate School of Bioresource Sciences, Nihon University, Kameino 1866, Fujisawa, Kanagawa 252-0880, Japan
| | - Masahiro A Iwasa
- Course in Natural Environment Studies, Graduate School of Bioresource Sciences, Nihon University, Kameino 1866, Fujisawa, Kanagawa 252-0880, Japan
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11
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Veale AJ, Russell JC, King CM. The genomic ancestry, landscape genetics and invasion history of introduced mice in New Zealand. ROYAL SOCIETY OPEN SCIENCE 2018; 5:170879. [PMID: 29410804 PMCID: PMC5792881 DOI: 10.1098/rsos.170879] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 12/15/2017] [Indexed: 06/07/2023]
Abstract
The house mouse (Mus musculus) provides a fascinating system for studying both the genomic basis of reproductive isolation, and the patterns of human-mediated dispersal. New Zealand has a complex history of mouse invasions, and the living descendants of these invaders have genetic ancestry from all three subspecies, although most are primarily descended from M. m. domesticus. We used the GigaMUGA genotyping array (approximately 135 000 loci) to describe the genomic ancestry of 161 mice, sampled from 34 locations from across New Zealand (and one Australian city-Sydney). Of these, two populations, one in the south of the South Island, and one on Chatham Island, showed complete mitochondrial lineage capture, featuring two different lineages of M. m. castaneus mitochondrial DNA but with only M. m. domesticus nuclear ancestry detectable. Mice in the northern and southern parts of the North Island had small traces (approx. 2-3%) of M. m. castaneus nuclear ancestry, and mice in the upper South Island had approximately 7-8% M. m. musculus nuclear ancestry including some Y-chromosomal ancestry-though no detectable M. m. musculus mitochondrial ancestry. This is the most thorough genomic study of introduced populations of house mice yet conducted, and will have relevance to studies of the isolation mechanisms separating subspecies of mice.
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Affiliation(s)
- Andrew J. Veale
- Department of Environmental and Animal Sciences, Unitec, 139 Carrington Road, Auckland 1025, New Zealand
| | - James C. Russell
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Carolyn M. King
- Environmental Research Institute, School of Science, University of Waikato, Private Bag 2105, Hamilton 3240, New Zealand
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12
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Andersen LW, Jacobsen M, Vedel-Smith C, Jensen TS. Mice as stowaways? Colonization history of Danish striped field mice. Biol Lett 2017; 13:rsbl.2017.0064. [PMID: 28679695 DOI: 10.1098/rsbl.2017.0064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 06/12/2017] [Indexed: 11/12/2022] Open
Abstract
Species from the steppe region of Eastern Europe likely colonized northwestern Europe in connection with agriculture after 6500 BP. The striped field mouse (Apodemus agrarius Pallas, 1783), is a steppe-derived species often found in human crops. It is common on the southern Danish islands of Lolland and Falster, which have been isolated from mainland Europe since approximately 10 300-8000 BP. Thus, this species could have been brought in with humans in connection with agriculture, or it could be an earlier natural invader. We sequenced 86 full mitochondrial genomes from the northwestern range of the striped field mouse, analysed phylogenetic relationships and estimated divergence time. The results supported human-induced colonization of Denmark in the Subatlantic or Subboreal period. A newly discovered population from Central Jutland in Denmark diverged from Falster approximately 100-670 years ago, again favouring human introduction. One individual from Sweden turned out to be a recent introduction from Central Jutland.
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Affiliation(s)
| | - Magnus Jacobsen
- Institute of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus, Denmark
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13
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Woods R, Marr MM, Brace S, Barnes I. The Small and the Dead: A Review of Ancient DNA Studies Analysing Micromammal Species. Genes (Basel) 2017; 8:E312. [PMID: 29117125 PMCID: PMC5704225 DOI: 10.3390/genes8110312] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/13/2017] [Accepted: 10/13/2017] [Indexed: 02/06/2023] Open
Abstract
The field of ancient DNA (aDNA) has recently been in a state of exponential growth, largely driven by the uptake of Next Generation Sequencing (NGS) techniques. Much of this work has focused on the mammalian megafauna and ancient humans, with comparatively less studies looking at micromammal fauna, despite the potential of these species in testing evolutionary, environmental and taxonomic theories. Several factors make micromammal fauna ideally suited for aDNA extraction and sequencing. Micromammal subfossil assemblages often include the large number of individuals appropriate for population level analyses, and, furthermore, the assemblages are frequently found in cave sites where the constant temperature and sheltered environment provide favourable conditions for DNA preservation. This review looks at studies that include the use of aDNA in molecular analysis of micromammal fauna, in order to examine the wide array of questions that can be answered in the study of small mammals using new palaeogenetic techniques. This study highlights the bias in current aDNA studies and assesses the future use of aDNA as a tool for the study of micromammal fauna.
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Affiliation(s)
- Roseina Woods
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Melissa M Marr
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
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14
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Herman JS, Jóhannesdóttir F, Jones EP, McDevitt AD, Michaux JR, White TA, Wójcik JM, Searle JB. Post-glacial colonization of Europe by the wood mouse,Apodemus sylvaticus: evidence of a northern refugium and dispersal with humans. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12882] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Jeremy S. Herman
- National Museums of Scotland; Chambers Street Edinburgh EH1 1JF UK
| | - Fríđa Jóhannesdóttir
- Department of Ecology and Evolutionary Biology; Cornell University; Corson Hall Ithaca NY 14853-2701 USA
| | | | - Allan D. McDevitt
- Ecosystems and Environment Research Centre; School of Environment and Life Sciences; University of Salford; Salford M5 4WT UK
- Mammal Research Institute; Polish Academy of Sciences; 17-230 Białowieża Poland
| | - Johan R. Michaux
- Unité de génétique de la conservation; Institut de Botanique; Université de Liège; 4000 Liège Belgique
| | - Thomas A. White
- Department of Ecology and Evolutionary Biology; Cornell University; Corson Hall Ithaca NY 14853-2701 USA
- Lancaster Environment Centre; Lancaster University; Lancaster LA1 4YQ UK
| | - Jan M. Wójcik
- Mammal Research Institute; Polish Academy of Sciences; 17-230 Białowieża Poland
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary Biology; Cornell University; Corson Hall Ithaca NY 14853-2701 USA
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15
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What can the geographic distribution of mtDNA haplotypes tell us about the invasion of New Zealand by house mice Mus musculus? Biol Invasions 2016. [DOI: 10.1007/s10530-016-1100-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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16
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Babiker H, Tautz D. Molecular and phenotypic distinction of the very recently evolved insular subspecies Mus musculus helgolandicus ZIMMERMANN, 1953. BMC Evol Biol 2015; 15:160. [PMID: 26268354 PMCID: PMC4535776 DOI: 10.1186/s12862-015-0439-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 07/29/2015] [Indexed: 11/10/2022] Open
Abstract
Background Populations and subspecies of the house mouse Mus musculus were able to invade new regions worldwide in the wake of human expansion. Here we investigate the origin and colonization history of the house mouse inhabiting the small island of Heligoland on the German Bight - Mus musculus helgolandicus. It was first described by Zimmermann in 1953, based on morphological descriptions which were considered to be a mosaic between the subspecies M. m. domesticus and M. m. musculus. Since mice on islands are excellent evolutionary model systems, we have focused here on a molecular characterization and an extended phenotype analysis. Results The molecular data show that the mice from Heligoland are derived from M. m. domesticus based on mitochondrial D-loop sequences as well as on four nuclear diagnostic markers, including one each from the sex-chromosomes. STRUCTURE analysis based on 21 microsatellite markers assigns Heligoland mice to a distinct population and D-loop network analysis suggests that they are derived from a single colonization event. In spite of mice from the mainland arriving by ships, they are apparently genetically refractory against further immigration. Mutation frequencies in complete mitochondrial genome sequences date the colonization age to approximately 400 years ago. Complete genome sequences from three animals revealed a genomic admixture with M. m. musculus genomic regions with at least 6.5 % of the genome affected. Geometric morphometric analysis of mandible shapes including skull samples from two time points during the last century suggest specific adaptations to a more carnivorous diet. Conclusions The molecular and morphological analyses confirm that M. m. helgolandicus consists of a distinct evolutionary lineage with specific adaptations. It shows a remarkable resilience against genetic mixture with mainland populations of M. m. domesticus despite major disturbances in the past century and a high ship traffic. The genomic admixture with M. m. musculus genetic material may have contributed to the genomic distinction of the Heligoland mice. In spite of its young age, M. m. helgolandicus may thus be considered as a true subspecies of Mus, whose evolution was triggered through fast divergence on a small island. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0439-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hiba Babiker
- Max Planck Institute for Evolutionary Biology, August-Thienemann Str. 2, 24306, Plön, Germany.
| | - Diethard Tautz
- Max Planck Institute for Evolutionary Biology, August-Thienemann Str. 2, 24306, Plön, Germany.
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17
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Conservation archaeogenomics: ancient DNA and biodiversity in the Anthropocene. Trends Ecol Evol 2015; 30:540-9. [PMID: 26169594 DOI: 10.1016/j.tree.2015.06.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 06/11/2015] [Accepted: 06/15/2015] [Indexed: 11/22/2022]
Abstract
There is growing consensus that we have entered the Anthropocene, a geologic epoch characterized by human domination of the ecosystems of the Earth. With the future uncertain, we are faced with understanding how global biodiversity will respond to anthropogenic perturbations. The archaeological record provides perspective on human-environment relations through time and across space. Ancient DNA (aDNA) analyses of plant and animal remains from archaeological sites are particularly useful for understanding past human-environment interactions, which can help guide conservation decisions during the environmental changes of the Anthropocene. Here, we define the emerging field of conservation archaeogenomics, which integrates archaeological and genomic data to generate baselines or benchmarks for scientists, managers, and policy-makers by evaluating climatic and human impacts on past, present, and future biodiversity.
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Dalecky A, Bâ K, Piry S, Lippens C, Diagne CA, Kane M, Sow A, Diallo M, Niang Y, Konečný A, Sarr N, Artige E, Charbonnel N, Granjon L, Duplantier JM, Brouat C. Range expansion of the invasive house mouse M
us musculus domesticus
in Senegal, West Africa: a synthesis of trapping data over three decades, 1983-2014. Mamm Rev 2015. [DOI: 10.1111/mam.12043] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Ambroise Dalecky
- Ird; LPED (UMR AMU/IRD); Marseille France
- Ird; CBGP (UMR INRA/IRD/Cirad/Montpellier SupAgro); Montferrier sur Lez cedex France
| | - Khalilou Bâ
- Ird; CBGP (UMR INRA/IRD/CIRAD/Montpellier SupAgro); Campus de Bel-Air BP1386 CP18524 Dakar Senegal
| | - Sylvain Piry
- Inra; CBGP (UMR INRA/IRD/Cirad/Montpellier SupAgro); Montferrier sur Lez cedex France
| | - Cédric Lippens
- Ird; CBGP (UMR INRA/IRD/Cirad/Montpellier SupAgro); Montferrier sur Lez cedex France
| | - Christophe A. Diagne
- Ird; CBGP (UMR INRA/IRD/CIRAD/Montpellier SupAgro); Campus de Bel-Air BP1386 CP18524 Dakar Senegal
- Department of Animal Biology; Cheick Anta Diop University; Dakar Senegal
| | - Mamadou Kane
- Ird; CBGP (UMR INRA/IRD/CIRAD/Montpellier SupAgro); Campus de Bel-Air BP1386 CP18524 Dakar Senegal
| | - Aliou Sow
- Ird; CBGP (UMR INRA/IRD/CIRAD/Montpellier SupAgro); Campus de Bel-Air BP1386 CP18524 Dakar Senegal
| | - Mamoudou Diallo
- Ird; CBGP (UMR INRA/IRD/CIRAD/Montpellier SupAgro); Campus de Bel-Air BP1386 CP18524 Dakar Senegal
| | - Youssoupha Niang
- Ird; CBGP (UMR INRA/IRD/CIRAD/Montpellier SupAgro); Campus de Bel-Air BP1386 CP18524 Dakar Senegal
| | - Adam Konečný
- Ird; CBGP (UMR INRA/IRD/Cirad/Montpellier SupAgro); Montferrier sur Lez cedex France
- Department of Botany and Zoology; Faculty of Science; Masaryk University; Brno Czech Republic
| | - Nathalie Sarr
- Ird; CBGP (UMR INRA/IRD/CIRAD/Montpellier SupAgro); Campus de Bel-Air BP1386 CP18524 Dakar Senegal
| | - Emmanuelle Artige
- Inra; CBGP (UMR INRA/IRD/Cirad/Montpellier SupAgro); Montferrier sur Lez cedex France
| | - Nathalie Charbonnel
- Inra; CBGP (UMR INRA/IRD/Cirad/Montpellier SupAgro); Montferrier sur Lez cedex France
| | - Laurent Granjon
- Ird; CBGP (UMR INRA/IRD/Cirad/Montpellier SupAgro); Montferrier sur Lez cedex France
| | - Jean-Marc Duplantier
- Ird; CBGP (UMR INRA/IRD/Cirad/Montpellier SupAgro); Montferrier sur Lez cedex France
| | - Carine Brouat
- Ird; CBGP (UMR INRA/IRD/Cirad/Montpellier SupAgro); Montferrier sur Lez cedex France
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19
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Commensalism facilitates gene flow in mountains: a comparison between two Rattus species. Heredity (Edinb) 2015; 115:253-61. [PMID: 25944468 DOI: 10.1038/hdy.2015.34] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Revised: 03/19/2015] [Accepted: 03/20/2015] [Indexed: 01/23/2023] Open
Abstract
Small mammal dispersal is strongly affected by geographical barriers. However, commensal small mammals may be passively transported over large distances and strong barriers by humans (often with agricultural products). This pattern should be especially apparent in topographically complex landscapes, such as mountain ranges, where valleys and/or peaks can limit dispersal of less vagile species. We predict that commensal species would have lower genetic differentiation and higher migration rates than related non-commensals in such landscapes. We contrasted population genetic differentiation in two sympatric Rattus species (R. satarae and R. rattus) in the Western Ghats mountains in southern India. We sampled rats from villages and adjacent forests in seven locations (20-640 km apart). Capture-based statistics confirmed that R. rattus is abundant in human settlements in this region, whereas R. satarae is non-commensal and found mostly in forests. Population structure analyses using ~970-bp mitochondrial control region and 17 microsatellite loci revealed higher differentiation for the non-commensal species (R. satarae F-statistics=0.420, 0.065, R. rattus F-statistics=0.195, 0.034; mitochondrial DNA, microsatellites, respectively). Genetic clustering analyses confirm that clusters in R. satarae are more distinct and less admixed than those in R. rattus. R. satarae shows higher slope for isolation-by-distance compared with R. rattus. Although mode of migration estimates do not strongly suggest higher rates in R. rattus than in R. satarae, they indicate that migration over long distances could still be higher in R. rattus. We suggest that association with humans could drive the observed pattern of differentiation in the commensal R. rattus, consequently impacting not only their dispersal abilities, but also their evolutionary trajectories.
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20
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Phifer-Rixey M, Nachman MW. Insights into mammalian biology from the wild house mouse Mus musculus. eLife 2015; 4. [PMID: 25875302 PMCID: PMC4397906 DOI: 10.7554/elife.05959] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/26/2015] [Indexed: 12/22/2022] Open
Abstract
The house mouse, Mus musculus, was established in the early 1900s as one of the first genetic model organisms owing to its short generation time, comparatively large litters, ease of husbandry, and visible phenotypic variants. For these reasons and because they are mammals, house mice are well suited to serve as models for human phenotypes and disease. House mice in the wild consist of at least three distinct subspecies and harbor extensive genetic and phenotypic variation both within and between these subspecies. Wild mice have been used to study a wide range of biological processes, including immunity, cancer, male sterility, adaptive evolution, and non-Mendelian inheritance. Despite the extensive variation that exists among wild mice, classical laboratory strains are derived from a limited set of founders and thus contain only a small subset of this variation. Continued efforts to study wild house mice and to create new inbred strains from wild populations have the potential to strengthen house mice as a model system. DOI:http://dx.doi.org/10.7554/eLife.05959.001
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Affiliation(s)
- Megan Phifer-Rixey
- Department of Integrative Biology, University of California, Berkeley, Berkeley, United States and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, United States
| | - Michael W Nachman
- Department of Integrative Biology, University of California, Berkeley, Berkeley, United States and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, United States
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21
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Jones EP, Searle JB. Differing Y chromosome versus mitochondrial DNA ancestry, phylogeography, and introgression in the house mouse. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12522] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Eleanor P. Jones
- Population Biology and Conservation Biology; Evolutionary Biology Centre; University of Uppsala; Uppsala Sweden
- Food and Environment Research Agency; Sand Hutton York YO41 1LZ UK
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary Biology; Cornell University; Ithaca NY 14853 USA
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22
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Gabriel SI, Mathias ML, Searle JB. Of mice and the 'Age of Discovery': the complex history of colonization of the Azorean archipelago by the house mouse (Mus musculus) as revealed by mitochondrial DNA variation. J Evol Biol 2014; 28:130-45. [PMID: 25394749 DOI: 10.1111/jeb.12550] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 11/02/2014] [Accepted: 11/10/2014] [Indexed: 11/30/2022]
Abstract
Humans have introduced many species onto remote oceanic islands. The house mouse (Mus musculus) is a human commensal and has consequently been transported to oceanic islands around the globe as an accidental stowaway. The history of these introductions can tell us not only about the mice themselves but also about the people that transported them. Following a phylogeographic approach, we used mitochondrial D-loop sequence variation (within an 849- to 864-bp fragment) to study house mouse colonization of the Azores. A total of 239 sequences were obtained from all nine islands, and interpretation was helped by previously published Iberian sequences and 66 newly generated Spanish sequences. A Bayesian analysis revealed presence in the Azores of most of the D-loop clades previously described in the domesticus subspecies of the house mouse, suggesting a complex colonization history of the archipelago as a whole from multiple geographical origins, but much less heterogeneity (often single colonization?) within islands. The expected historical link with mainland Portugal was reflected in the pattern of D-loop variation of some of the islands but not all. A more unexpected association with a distant North European source area was also detected in three islands, possibly reflecting human contact with the Azores prior to the 15th century discovery by Portuguese mariners. Widening the scope to colonization of the Macaronesian islands as a whole, human linkages between the Azores, Madeira, the Canaries, Portugal and Spain were revealed through the sharing of mouse sequences between these areas. From these and other data, we suggest mouse studies may help resolve historical uncertainties relating to the 'Age of Discovery'.
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Affiliation(s)
- S I Gabriel
- CESAM - Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal; Department of Biology, University of York, York, UK
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23
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Jing M, Yu HT, Bi X, Lai YC, Jiang W, Huang L. Phylogeography of Chinese house mice (Mus musculus musculus/castaneus): distribution, routes of colonization and geographic regions of hybridization. Mol Ecol 2014; 23:4387-405. [PMID: 25065953 DOI: 10.1111/mec.12873] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 07/22/2014] [Accepted: 07/23/2014] [Indexed: 11/27/2022]
Abstract
House mice (Mus musculus) are human commensals and have served as a primary model in biomedical, ecological and evolutionary research. Although there is detailed knowledge of the biogeography of house mice in Europe, little is known of the history of house mice in China, despite the fact that China encompasses an enormous portion of their range. In the present study, 535 house mice caught from 29 localities in China were studied by sequencing the mitochondrial D-loop and genotyping 10 nuclear microsatellite markers distributed on 10 chromosomes. Phylogenetic analyses revealed two evolutionary lineages corresponding to Mus musculus castaneus and Mus musculus musculus in the south and north, respectively, with the Yangtze River approximately representing the boundary. More detailed analyses combining published sequence data from mice sampled in neighbouring countries revealed the migration routes of the two subspecies into China: M. m. castaneus appeared to have migrated through a southern route (Yunnan and Guangxi), whereas M. m. musculus entered China from Kazakhstan through the north-west border (Xinjiang). Bayesian analysis of mitochondrial sequences indicated rapid population expansions in both subspecies, approximately 4650-9300 and 7150-14 300 years ago for M. m. castaneus and M. m. musculus, respectively. Interestingly, the migration routes of Chinese house mice coincide with the colonization routes of modern humans into China, and the expansion times of house mice are consistent with the development of agriculture in southern and northern China, respectively. Finally, our study confirmed the existence of a hybrid zone between M. m. castaneus and M. m. musculus in China. Further study of this hybrid zone will provide a useful counterpart to the well-studied hybrid zone between M. m. musculus and Mus musculus domesticus in central Europe.
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Affiliation(s)
- Meidong Jing
- College of Life Sciences, Ludong University, Yantai, Shandong, 264025, China
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24
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Rando JC, Pieper H, Alcover JA. Radiocarbon evidence for the presence of mice on Madeira Island (North Atlantic) one millennium ago. Proc Biol Sci 2014; 281:20133126. [PMID: 24523273 DOI: 10.1098/rspb.2013.3126] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Owing to the catastrophic extinction events that occurred following the Holocene arrival of alien species, extant oceanic island biotas are a mixture of recently incorporated alien fauna and remnants of the original fauna. Knowledge of the Late Quaternary pristine island faunas and a reliable chronology of the earliest presence of alien species on each archipelago are critical in understanding the magnitude and tempo of Quaternary island extinctions. Until now, two successive waves of human arrivals have been identified in the North Atlantic Macaronesian archipelagos (Azores, Madeira, Selvagens, Canary and Cape Verde Islands): 'aboriginal', which is limited to the Canary Islands around two millennia ago, and 'colonial', from the fourteenth century onwards. New surveys in Ponta de São Lourenço (Madeira Island) have allowed us to obtain and date ancient bones of mice. The date obtained (1033 ± 28 BP) documents the earliest evidence for the presence of mice on the island. This date extends the time frame in which the most significant ecological changes occurred on the island. It also suggests that humans could have reached Madeira before 1036 cal AD, around four centuries before Portugal officially took possession of the island.
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Affiliation(s)
- Juan Carlos Rando
- Departamento de Biología Animal (Zoología), Universidad de La Laguna Tenerife, , Canary Islands, Spain, Ulmenstrasse 21, Schwentinental 24223, Germany, Departament de Biodiversitat i Conservació, IMEDEA (CSIC-UIB), Cr Miquel Marquès 21, Esporles, Mallorca, Balearic Islands 07190, Spain, Department of Mammalogy, American Museum of Natural History, , New York, NY 10024-5192, USA
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25
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Gray MM, Wegmann D, Haasl RJ, White MA, Gabriel SI, Searle JB, Cuthbert RJ, Ryan PG, Payseur BA. Demographic history of a recent invasion of house mice on the isolated Island of Gough. Mol Ecol 2014; 23:1923-39. [PMID: 24617968 PMCID: PMC4086876 DOI: 10.1111/mec.12715] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 02/24/2014] [Accepted: 02/26/2014] [Indexed: 02/05/2023]
Abstract
Island populations provide natural laboratories for studying key contributors to evolutionary change, including natural selection, population size and the colonization of new environments. The demographic histories of island populations can be reconstructed from patterns of genetic diversity. House mice (Mus musculus) inhabit islands throughout the globe, making them an attractive system for studying island colonization from a genetic perspective. Gough Island, in the central South Atlantic Ocean, is one of the remotest islands in the world. House mice were introduced to Gough Island by sealers during the 19th century and display unusual phenotypes, including exceptionally large body size and carnivorous feeding behaviour. We describe genetic variation in Gough Island mice using mitochondrial sequences, nuclear sequences and microsatellites. Phylogenetic analysis of mitochondrial sequences suggested that Gough Island mice belong to Mus musculus domesticus, with the maternal lineage possibly originating in England or France. Cluster analyses of microsatellites revealed genetic membership for Gough Island mice in multiple coastal populations in Western Europe, suggesting admixed ancestry. Gough Island mice showed substantial reductions in mitochondrial and nuclear sequence variation and weak reductions in microsatellite diversity compared with Western European populations, consistent with a population bottleneck. Approximate Bayesian computation (ABC) estimated that mice recently colonized Gough Island (~100 years ago) and experienced a 98% reduction in population size followed by a rapid expansion. Our results indicate that the unusual phenotypes of Gough Island mice evolved rapidly, positioning these mice as useful models for understanding rapid phenotypic evolution.
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Affiliation(s)
- Melissa M. Gray
- Laboratory of Genetics, University of Wisconsin, Madison, WI 53706 USA
| | - Daniel Wegmann
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Ryan J. Haasl
- Laboratory of Genetics, University of Wisconsin, Madison, WI 53706 USA
| | - Michael A. White
- Laboratory of Genetics, University of Wisconsin, Madison, WI 53706 USA
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
| | - Sofia I. Gabriel
- Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, 1749–016 Lisbon, Portugal
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853-2701 USA
| | - Richard J. Cuthbert
- Royal Society for the Protection of Birds, The Lodge, Sandy, Bedfordshire, UK
| | - Peter G. Ryan
- Percy FitzPatrick Institute of African Ornithology, University of Cape Town, DST/NRF Centre of Excellence, Rondebosch 7701 South Africa
| | - Bret A. Payseur
- Laboratory of Genetics, University of Wisconsin, Madison, WI 53706 USA
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26
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Didion JP, de Villena FPM. Deconstructing Mus gemischus: advances in understanding ancestry, structure, and variation in the genome of the laboratory mouse. Mamm Genome 2013; 24:1-20. [PMID: 23223940 PMCID: PMC4034049 DOI: 10.1007/s00335-012-9441-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 11/05/2012] [Indexed: 01/26/2023]
Abstract
The laboratory mouse is an artificial construct with a complex relationship to its natural ancestors. In 2002, the mouse became the first mammalian model organism with a reference genome. Importantly, the mouse genome sequence was assembled from data on a single inbred laboratory strain, C57BL/6. Several large-scale genetic variant discovery efforts have been conducted, resulting in a catalog of tens of millions of SNPs and structural variants. High-density genotyping arrays covering a subset of those variants have been used to produce hundreds of millions of genotypes in laboratory stocks and a small number of wild mice. These landmark resources now enable us to determine relationships among laboratory mice, assign local ancestry at fine scale, resolve important controversies, and identify a new set of challenges-most importantly, the troubling scarcity of genetic data on the very natural populations from which the laboratory mouse was derived. Our aim with this review is to provide the reader with an historical context for the mouse as a model organism and to explain how practical decisions made in the past have influenced both the architecture of the laboratory mouse genome and the design and execution of current large-scale resources. We also provide examples on how the accomplishments of the past decade can be used by researchers to streamline the use of mice in their experiments and correctly interpret results. Finally, we propose future steps that will enable the mouse community to extend its successes in the decade to come.
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Affiliation(s)
- John P. Didion
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Center for Genome Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Center for Genome Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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27
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Gabriel SI, Mathias MDL, Searle JB. Genetic structure of house mouse (Mus musculusLinnaeus 1758) populations in the Atlantic archipelago of the Azores: colonization and dispersal. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Maria Da Luz Mathias
- Departamento de Biologia Animal; Faculdade de Ciências da Universidade de Lisboa; CESAM - Centre for Environmental and Marine Studies; 1749-016; Lisbon; Portugal
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28
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Cucchi T, Kovács ZE, Berthon R, Orth A, Bonhomme F, Evin A, Siahsarvie R, Darvish J, Bakhshaliyev V, Marro C. On the trail of Neolithic mice and men towards Transcaucasia: zooarchaeological clues from Nakhchivan (Azerbaijan). Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12004] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Zsófia Eszter Kovács
- Hungarian National Museum; National Heritage Protection Centre; Budapest; Hungary
| | | | - Annie Orth
- CNRS UMR5554; Institut des Sciences de l'Evolution; Université Montpellier 2; Montpellier; France
| | - François Bonhomme
- CNRS UMR5554; Institut des Sciences de l'Evolution; Université Montpellier 2; Montpellier; France
| | - Allowen Evin
- Archaeology Department; University of Aberdeen; Elphinstone Road, Aberdeen, AB24 3UF; Scotland; UK
| | | | | | - Veli Bakhshaliyev
- Department of Archaeology; National Academy of Science of Azerbaijan; Nakhchivan; Azerbaijan
| | - Catherine Marro
- UMR 5133, Archéorient, Environnements et Sociétés de l'Orient Ancien; Maison de l'Orient et de la Méditerranée; CNRS, Université Lyon 2; Lyon; France
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29
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Jones EP, Eager HM, Gabriel SI, Jóhannesdóttir F, Searle JB. Genetic tracking of mice and other bioproxies to infer human history. Trends Genet 2013; 29:298-308. [PMID: 23290437 DOI: 10.1016/j.tig.2012.11.011] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Revised: 11/13/2012] [Accepted: 11/29/2012] [Indexed: 10/27/2022]
Abstract
The long-distance movements made by humans through history are quickly erased by time but can be reconstructed by studying the genetic make-up of organisms that travelled with them. The phylogeography of the western house mouse (Mus musculus domesticus), whose current widespread distribution around the world has been caused directly by the movements of (primarily) European people, has proved particularly informative in a series of recent studies. The geographic distributions of genetic lineages in this commensal have been linked to the Iron Age movements within the Mediterranean region and Western Europe, the extensive maritime activities of the Vikings in the 9th to 11th centuries, and the colonisation of distant landmasses and islands by the Western European nations starting in the 15th century. We review here recent insights into human history based on phylogeographic studies of mice and other species that have travelled with humans, and discuss how emerging genomic methodologies will increase the precision of these inferences.
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Affiliation(s)
- Eleanor P Jones
- Mammal Research Institute, Polish Academy of Sciences, 17-230 Białowieża, Poland
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Comparing PreXMRV-2 gag sequence diversity in laboratory and wild mice using deep sequencing. Virus Res 2012; 169:30-7. [PMID: 22771940 DOI: 10.1016/j.virusres.2012.06.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 06/26/2012] [Accepted: 06/27/2012] [Indexed: 11/22/2022]
Abstract
It has recently been reported that the xenotropic murine leukemia virus-related virus (XMRV) derives from a laboratory recombinant. However, sequences with characteristics of the 5' half of XMRV (termed PreXMRV-2) have been identified in several laboratory mouse genomes and cell lines suggesting parts of the XMRV genome exist as naturally occurring retroviruses in mice. We compare here PreXMRV-2 gag sequence diversity in mice to that of reported XMRV-like sequences by testing a panel of wild mouse and common inbred laboratory mouse strain genomic DNAs and by using high throughput amplicon sequencing. Sequences with features typical of previously reported PreXMRV-2 sequences, among them a 24 nt deletion, were repeatedly identified in different wild mice and inbred mouse strains within a high background of non-XMRV-like sequences. However, Sanger sequencing of clones from amplicons failed to retrieve such sequences effectively. Phylogenetic analysis suggests that PreXMRV-2 gag sequences from mice, cell lines and patient samples belong to the same evolutionarily young clade and that such sequences are diverse and widespread within Mus musculus domesticus and laboratory mice derived from this species. No evidence of PreXMRV-2 like gag sequences could be obtained outside of the M. musculus lineage. The results suggest that accurate determination of presence, absence and relationships of specific murine retroviral strains benefit greatly from deep sequencing analysis.
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