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Fujiwara K, Kubo S, Endo T, Takada T, Shiroishi T, Suzuki H, Osada N. Inference of selective forces on house mouse genomes during secondary contact in East Asia. Genome Res 2024; 34:366-375. [PMID: 38508692 PMCID: PMC11067880 DOI: 10.1101/gr.278828.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/15/2024] [Indexed: 03/22/2024]
Abstract
The house mouse (Mus musculus), which is commensal to humans, has spread globally via human activities, leading to secondary contact between genetically divergent subspecies. This pattern of genetic admixture can provide insights into the selective forces at play in this well-studied model organism. Our analysis of 163 house mouse genomes, with a particular focus on East Asia, revealed substantial admixture between the subspecies castaneus and musculus, particularly in Japan and southern China. We revealed, despite the different level of autosomal admixture among regions, that all Y Chromosomes in the East Asian samples belonged to the musculus-type haplogroup, potentially explained by genomic conflict under sex-ratio distortion owing to varying copy numbers of ampliconic genes on sex chromosomes, Slx and Sly Our computer simulations, designed to replicate the observed scenario, show that the preferential fixation of musculus-type Y Chromosomes can be achieved with a slight increase in the male-to-female birth ratio. We also investigated the influence of selection on the posthybridization of the subspecies castaneus and musculus in Japan. Even though the genetic background of most Japanese samples closely resembles the subspecies musculus, certain genomic regions overrepresented the castaneus-like genetic components, particularly in immune-related genes. Furthermore, a large genomic block (∼2 Mbp) containing a vomeronasal/olfactory receptor gene cluster predominantly harbored castaneus-type haplotypes in the Japanese samples, highlighting the crucial role of olfaction-based recognition in shaping hybrid genomes.
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Affiliation(s)
- Kazumichi Fujiwara
- Mouse Genomics Resource Laboratory, National Institute of Genetics, Mishima 411-8540, Japan
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo 060-0814, Japan
| | - Shunpei Kubo
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo 060-0814, Japan
| | - Toshinori Endo
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo 060-0814, Japan
| | - Toyoyuki Takada
- Integrated BioResource Information Division, RIKEN BioResource Research Center, Tsukuba 305-0074, Japan
| | | | - Hitoshi Suzuki
- Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Naoki Osada
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo 060-0814, Japan;
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2
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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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3
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Morgan AP, Hughes JJ, Didion JP, Jolley WJ, Campbell KJ, Threadgill DW, Bonhomme F, Searle JB, de Villena FPM. Population structure and inbreeding in wild house mice (Mus musculus) at different geographic scales. Heredity (Edinb) 2022; 129:183-194. [PMID: 35764696 PMCID: PMC9411160 DOI: 10.1038/s41437-022-00551-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 11/08/2022] Open
Abstract
House mice (Mus musculus) have spread globally as a result of their commensal relationship with humans. In the form of laboratory strains, both inbred and outbred, they are also among the most widely used model organisms in biomedical research. Although the general outlines of house mouse dispersal and population structure are well known, details have been obscured by either limited sample size or small numbers of markers. Here we examine ancestry, population structure, and inbreeding using SNP microarray genotypes in a cohort of 814 wild mice spanning five continents and all major subspecies of Mus, with a focus on M. m. domesticus. We find that the major axis of genetic variation in M. m. domesticus is a south-to-north gradient within Europe and the Mediterranean. The dominant ancestry component in North America, Australia, New Zealand, and various small offshore islands are of northern European origin. Next we show that inbreeding is surprisingly pervasive and highly variable, even between nearby populations. By inspecting the length distribution of homozygous segments in individual genomes, we find that inbreeding in commensal populations is mostly due to consanguinity. Our results offer new insight into the natural history of an important model organism for medicine and evolutionary biology.
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Affiliation(s)
- Andrew P Morgan
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
- Department of Medicine, Duke University Hospital, Durham, NC, USA.
| | - Jonathan J Hughes
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - John P Didion
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Independent Scientist, San Diego, CA, USA
| | | | | | - David W Threadgill
- Institute for Genome Sciences and Society, Texas A&M University, College Station, TX, USA
| | - Francois Bonhomme
- Institut des Sciences de l'Évolution Montpellier, Université de Montpellier, Montpellier, France
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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4
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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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5
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Genomic Analysis Reveals Subdivision of Black Rats (Rattus rattus) in India, Origin of the Worldwide Species Spread. Genes (Basel) 2022; 13:genes13020267. [PMID: 35205312 PMCID: PMC8871742 DOI: 10.3390/genes13020267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 12/04/2022] Open
Abstract
In contrast to the detailed and globally extensive studies on the spread of the commensal black rat, Rattus rattus, there has been relatively little work on the phylogeography of the species within India, from where this spread originated. Taking a genomic approach, we typed 27 R. rattus samples from Peninsular India using the genotyping-by-sequencing (GBS) method. Filtering and alignment of the FASTQ files yielded 1499 genome-wide SNPs. Phylogenomic tree reconstruction revealed a distinct subdivision in the R. rattus population, manifested as two clusters corresponding to the east and west coasts of India. We also identified signals of admixture between these two subpopulations, separated by an Fst of 0.20. This striking genomic difference between the east and west coast populations mirrors what has previously been described with mitochondrial DNA sequencing. It is notable that the west coast population of R. rattus has been spread globally, reflecting the origins of commensalism of the species in Western India and the subsequent transport by humans worldwide.
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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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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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8
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Mus musculus populations in Western Australia lack VKORC1 mutations conferring resistance to first generation anticoagulant rodenticides: Implications for conservation and biosecurity. PLoS One 2020; 15:e0236234. [PMID: 32970676 PMCID: PMC7513997 DOI: 10.1371/journal.pone.0236234] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/18/2020] [Indexed: 11/28/2022] Open
Abstract
Background Humans routinely attempt to manage pest rodent populations with anticoagulant rodenticides (ARs). We require information on resistance to ARs within rodent populations to have effective eradication programs that minimise exposure in non-target species. Mutations to the VKORC1 gene have been shown to confer resistance in rodents with high proportions of resistance in mice found in all European populations tested. We screened mutations in Mus musculus within Western Australia, by sampling populations from the capital city (Perth) and a remote island (Browse Island). These are the first Australian mouse populations screened for resistance using this method. Additionally, the mitochondrial D-loop of house mice was sequenced to explore population genetic structure, identify the origin of Western Australian mice, and to elucidate whether resistance was linked to certain haplotypes. Results No resistance-related VKORC1 mutations were detected in either house mouse population. A genetic introgression in the intronic sequence of the VKORC1 gene of Browse Island house mouse was detected which is thought to have originated through hybridisation with the Algerian mouse (Mus spretus). Analysis of the mitochondrial D-loop reported two haplotypes in the house mouse population of Perth, and two haplotypes in the population of Browse Island. Conclusions Both house mouse populations exhibited no genetic resistance to ARs, in spite of free use of ARs in Western Australia. Therefore weaker anticoagulant rodenticides can be employed in pest control and eradication attempts, which will result in reduced negative impacts on non-target species. Biosecurity measures must be in place to avoid introduction of resistant house mice, and new house mouse subspecies to Western Australia.
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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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10
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Puckett EE, Magnussen E, Khlyap LA, Strand TM, Lundkvist Å, Munshi-South J. Genomic analyses reveal three independent introductions of the invasive brown rat (Rattus norvegicus) to the Faroe Islands. Heredity (Edinb) 2019; 124:15-27. [PMID: 31399718 DOI: 10.1038/s41437-019-0255-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 07/10/2019] [Accepted: 07/20/2019] [Indexed: 11/09/2022] Open
Abstract
Population genomics offers innovative approaches to test hypotheses related to the source and timing of introduction of invasive species. These approaches are particularly appropriate to study colonization of island ecosystems. The brown rat is a cold-hardy global invasive that has reached most of the world's island ecosystems, including even highly isolated archipelagoes such as the Faroe Islands in the North Atlantic Ocean. Historic records tell of rats rafting to the southern island of Suðuroy in 1768 following a shipwreck off the coast of Scotland, then expanding across the archipelago. We investigated the demographic history of brown rats in the Faroes using 50,174 SNPs. We inferred three independent introductions of rats, including to Suðuroy, the islands of Borðoy and Viðoy, and onto Streymoy from which they expanded to Eysturoy and Vágar. All Faroese populations showed signs of strong bottlenecks and declining effective population size. We inferred that these founder events removed low frequency alleles, the exact data needed to estimate recent demographic histories. Therefore, we were unable to accurately estimate the timing of each invasion. The difficulties with demographic inference may be applicable to other invasive species, particularly those with extreme and recent bottlenecks. We identified three invasions of brown rats to the Faroe Islands that resulted in highly differentiated populations that will be useful for future studies of life history variation and genomic adaptation.
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Affiliation(s)
- Emily E Puckett
- Department of Biological Sciences, University of Memphis, Memphis, TN, USA. .,Louis Calder Center- Biological Field Station, Fordham University, Armonk, NY, USA.
| | - Eyðfinn Magnussen
- Faculty of Science and Technology, University of the Faroe Islands, Tórshavn, Faroe Islands
| | - Liudmila A Khlyap
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Tanja M Strand
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden.,National Veterinary Institute (SVA), Department of Microbiology, Uppsala, Sweden
| | - Åke Lundkvist
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Jason Munshi-South
- Louis Calder Center- Biological Field Station, Fordham University, Armonk, NY, USA
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Quina AS, Durão AF, Muñoz-Muñoz F, Ventura J, da Luz Mathias M. Population effects of heavy metal pollution in wild Algerian mice (Mus spretus). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 171:414-424. [PMID: 30639867 DOI: 10.1016/j.ecoenv.2018.12.062] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 12/13/2018] [Accepted: 12/21/2018] [Indexed: 06/09/2023]
Abstract
Heavy metal mining is one of the largest sources of environmental pollution. The analysis of different types of biomarkers in sentinel species living in contaminated areas provides a measure of the degree of the ecological impact of pollution and is thus a valuable tool for human and environmental risk assessments. In previous studies we found that specimens from two populations of the Algerian mice (Mus spretus) living in two abandoned heavy metal mines (Aljustrel and Preguiça, Portugal) had higher body burdens of heavy metals, which led to alterations in enzymatic activities and in haematological, histological and genotoxic parameters, than mice from a nearby reference population. We have now analysed individuals from the same sites at the biometric and genetic levels to get a broader portrayal of the impact of heavy metal pollution on biodiversity, from molecules to populations. Size and shape variations of the mouse mandible were searched by implementing the geometric morphometric method. Population genetic differentiation and diversity parameters (φST estimates; nucleotide and haplotype diversities) were studied using the mitochondrial cytochrome b gene (Cytb) and the control region (CR). The morphometric analyses revealed that animals from the three sites differed significantly in the shape of the mandible, but mandibular shape varied in a more resembling way within individuals of both mine sites, which is highly suggestive for an effect of environmental quality on normal development pathways in Algerian mice. Also, antisymmetry in mandible size and shape was detected in all populations, making these traits not reliable indicators of developmental instability. Overall little genetic differentiation was found among the three populations, although pairwise φST comparisons revealed that the Aljustrel and the Preguiça populations were each differentiated from the other two populations in Cytb and in CR, respectively. Genetic diversity parameters revealed higher genetic diversity for Cytb in the population from Aljustrel, while in the population from Preguiça diversity of the two markers changed in opposite directions, higher genetic diversity in CR and lower in Cytb, compared to the reference population. Demographic changes and increased mutation rates may explain these findings. We show that developmental patterns and genetic composition of wild populations of a small mammal can be affected by chronic heavy metal exposure within a relatively short time. Anthropogenic stress may thus influence the evolutionary path of natural populations, with largely unpredictable ecological costs.
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Affiliation(s)
- Ana Sofia Quina
- Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa (FCUL), Lisboa, Portugal; Centro de Estudos do Ambiente e do Mar - Lisboa (CESAM; FCUL), Lisboa, Portugal.
| | - Ana Filipa Durão
- Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa (FCUL), Lisboa, Portugal
| | - Francesc Muñoz-Muñoz
- Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Campus de Bellaterra, Cerdanyola del Vallès, Spain
| | - Jacint Ventura
- Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Campus de Bellaterra, Cerdanyola del Vallès, Spain
| | - Maria da Luz Mathias
- Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa (FCUL), Lisboa, Portugal; Centro de Estudos do Ambiente e do Mar - Lisboa (CESAM; FCUL), Lisboa, Portugal
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12
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Zeng L, Ming C, Li Y, Su LY, Su YH, Otecko NO, Dalecky A, Donnellan S, Aplin K, Liu XH, Song Y, Zhang ZB, Esmailizadeh A, Sohrabi SS, Nanaei HA, Liu HQ, Wang MS, Ag Atteynine S, Rocamora G, Brescia F, Morand S, Irwin DM, Peng MS, Yao YG, Li HP, Wu DD, Zhang YP. Out of Southern East Asia of the Brown Rat Revealed by Large-Scale Genome Sequencing. Mol Biol Evol 2019; 35:149-158. [PMID: 29087519 DOI: 10.1093/molbev/msx276] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The geographic origin and migration of the brown rat (Rattus norvegicus) remain subjects of considerable debate. In this study, we sequenced whole genomes of 110 wild brown rats with a diverse world-wide representation. We reveal that brown rats migrated out of southern East Asia, rather than northern Asia as formerly suggested, into the Middle East and then to Europe and Africa, thousands of years ago. Comparison of genomes from different geographical populations reveals that many genes involved in the immune system experienced positive selection in the wild brown rat.
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Affiliation(s)
- Lin Zeng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Chen Ming
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yan Li
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Yunnan University, Kunming, China
| | - Ling-Yan Su
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, China
| | - Yan-Hua Su
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Newton O Otecko
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Ambroise Dalecky
- Institut de Recherche pour le Développement (Ird), CBGP (UMR INRA/IRD/Cirad/Montpellier SupAgro), Montferrier sur Lez cedex, France.,Institut de Recherche pour le Développement (Ird), LPED (UMR AMU/IRD), Marseille, France
| | - Stephen Donnellan
- University of Adelaide and the South Australian Museum, Adelaide, Australia
| | - Ken Aplin
- Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington, DC
| | - Xiao-Hui Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ying Song
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhi-Bin Zhang
- State Key Laboratory of Integrated Management on Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Saeed S Sohrabi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | | | - He-Qun Liu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Solimane Ag Atteynine
- Institut de Recherche pour le Développement (Ird), IMBE (UMR AMU/CNRS/IRD/UAPV), Bamako, Mali.,Faculté des Sciences et Techniques (FST), Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Gérard Rocamora
- Island Biodiversity & Conservation Center, University of Seychelles, Mahé, Seychelles
| | - Fabrice Brescia
- Diversité Biologique et Fonctionnelle des Ecosystèmes, Institut Agronomique néo-Calédonien, Port Laguerre, Paita, New Caledonia
| | - Serge Morand
- CNRS-CIRAD, Centre d'Infectiologie Christophe Mérieux du Laos, Vientiane, Lao PDR
| | - David M Irwin
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Ming-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Yong-Gang Yao
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, China
| | - Hai-Peng Li
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Yunnan University, Kunming, China
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13
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Souquet L, Chevret P, Ganem G, Auffray JC, Ledevin R, Agret S, Hautier L, Renaud S. Back to the wild: does feralization affect the mandible of non-commensal house mice (Mus musculus domesticus)? Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/bly218] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Louise Souquet
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université Claude Bernard Lyon, CNRS, Villeurbanne cedex, France
| | - Pascale Chevret
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université Claude Bernard Lyon, CNRS, Villeurbanne cedex, France
| | - Guila Ganem
- Institut des Sciences de l’Evolution, Université de Montpellier, UMR 5554 CNRS, IRD, EPHE, Place Eugène Bataillon, Montpellier cedex, France
| | - Jean-Christophe Auffray
- Institut des Sciences de l’Evolution, Université de Montpellier, UMR 5554 CNRS, IRD, EPHE, Place Eugène Bataillon, Montpellier cedex, France
| | - Ronan Ledevin
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université Claude Bernard Lyon, CNRS, Villeurbanne cedex, France
| | - Sylvie Agret
- Institut des Sciences de l’Evolution, Université de Montpellier, UMR 5554 CNRS, IRD, EPHE, Place Eugène Bataillon, Montpellier cedex, France
| | - Lionel Hautier
- Institut des Sciences de l’Evolution, Université de Montpellier, UMR 5554 CNRS, IRD, EPHE, Place Eugène Bataillon, Montpellier cedex, France
| | - Sabrina Renaud
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université Claude Bernard Lyon, CNRS, Villeurbanne cedex, France
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14
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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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15
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Ravinet M, Elgvin TO, Trier C, Aliabadian M, Gavrilov A, Sætre GP. Signatures of human-commensalism in the house sparrow genome. Proc Biol Sci 2018; 285:rspb.2018.1246. [PMID: 30089626 DOI: 10.1098/rspb.2018.1246] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 07/11/2018] [Indexed: 02/07/2023] Open
Abstract
House sparrows (Passer domesticus) are a hugely successful anthrodependent species; occurring on nearly every continent. Yet, despite their ubiquity and familiarity to humans, surprisingly little is known about their origins. We sought to investigate the evolutionary history of the house sparrow and identify the processes involved in its transition to a human-commensal niche. We used a whole genome resequencing dataset of 120 individuals from three Eurasian species, including three populations of Bactrianus sparrows, a non-commensal, divergent house sparrow lineage occurring in the Near East. Coalescent modelling supports a split between house and Bactrianus sparrow 11 Kya and an expansion in the house sparrow at 6 Kya, consistent with the spread of agriculture following the Neolithic revolution. Commensal house sparrows therefore likely moved into Europe with the spread of agriculture following this period. Using the Bactrianus sparrow as a proxy for a pre-commensal, ancestral house population, we performed a comparative genome scan to identify genes potentially involved with adaptation to an anthropogenic niche. We identified potential signatures of recent, positive selection in the genome of the commensal house sparrow that are absent in Bactrianus populations. The strongest selected region encompasses two major candidate genes; COL11A-which regulates craniofacial and skull development and AMY2A, part of the amylase gene family which has previously been linked to adaptation to high-starch diets in humans and dogs. Our work examines human-commensalism in an evolutionary framework, identifies genomic regions likely involved in rapid adaptation to this new niche and ties the evolution of this species to the development of modern human civilization.
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Affiliation(s)
- Mark Ravinet
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Tore Oldeide Elgvin
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway.,Natural History Museum, University of Oslo, Oslo, Norway
| | - Cassandra Trier
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | | | - Andrey Gavrilov
- Institute of Zoology, Ministry of Education and Science of the Republic of Kazakhstan, Astana, Kazakhstan
| | - Glenn-Peter Sætre
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
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16
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Renaud S, Ledevin R, Souquet L, Gomes Rodrigues H, Ginot S, Agret S, Claude J, Herrel A, Hautier L. Evolving Teeth Within a Stable Masticatory Apparatus in Orkney Mice. Evol Biol 2018. [DOI: 10.1007/s11692-018-9459-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Potapov GS, Kondakov AV, Kolosova YS, Tomilova AA, Filippov BY, Gofarov MY, Bolotov IN. Widespread continental mtDNA lineages prevail in the bumblebee fauna of Iceland. Zookeys 2018:141-153. [PMID: 30057467 PMCID: PMC6056568 DOI: 10.3897/zookeys.774.26466] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/13/2018] [Indexed: 11/12/2022] Open
Abstract
Origins of the fauna in Iceland is controversial, although the majority of modern research supports the postglacial colonization of this island by terrestrial invertebrates rather than their long-term survival in glacial refugia. In this study, we use three bumblebee species as a model to test the hypothesis regarding possible cryptic refugia in Iceland and to evaluate a putative origin of recently introduced taxa. Bombusjonellus is thought to be a possible native Icelandic lineage, whereas B.lucorum and B.hortorum were evidently introduced in the second half of the 20th century. These phylogeographic analyses reveal that the Icelandic Bombusjonellus shares two COI lineages, one of which also occurs in populations on the British Isles and in mainland Europe, but a second lineage (BJ-02) has not been recorded anywhere. These results indicate that this species may have colonized Iceland two times and that the lineage BJ-02 may reflect a more ancient Late Pleistocene or Early Holocene founder event (e.g., from the British Isles). The Icelandic populations of both Bombuslucorum and B.hortorum share the COI lineages that were recorded as widespread throughout Eurasia, from the European countries across Russia to China and Japan. The findings presented here highlight that the bumblebee fauna of Iceland comprises mainly widespread ubiquitous lineages that arrived via natural or human-mediated dispersal events from the British Isles or the mainland.
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Affiliation(s)
- Grigory S Potapov
- Northern (Arctic) Federal University, Arkhangelsk 163002, Russian Federation.,Federal Center for Integrated Arctic Research of the Russian Academy of Sciences, Arkhangelsk 163000, Russian Federation
| | - Alexander V Kondakov
- Northern (Arctic) Federal University, Arkhangelsk 163002, Russian Federation.,Federal Center for Integrated Arctic Research of the Russian Academy of Sciences, Arkhangelsk 163000, Russian Federation
| | - Yulia S Kolosova
- Northern (Arctic) Federal University, Arkhangelsk 163002, Russian Federation.,Federal Center for Integrated Arctic Research of the Russian Academy of Sciences, Arkhangelsk 163000, Russian Federation
| | - Alena A Tomilova
- Federal Center for Integrated Arctic Research of the Russian Academy of Sciences, Arkhangelsk 163000, Russian Federation
| | - Boris Yu Filippov
- Northern (Arctic) Federal University, Arkhangelsk 163002, Russian Federation
| | - Mikhail Yu Gofarov
- Northern (Arctic) Federal University, Arkhangelsk 163002, Russian Federation.,Federal Center for Integrated Arctic Research of the Russian Academy of Sciences, Arkhangelsk 163000, Russian Federation
| | - Ivan N Bolotov
- Northern (Arctic) Federal University, Arkhangelsk 163002, Russian Federation.,Federal Center for Integrated Arctic Research of the Russian Academy of Sciences, Arkhangelsk 163000, Russian Federation
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18
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Puckett EE, Park J, Combs M, Blum MJ, Bryant JE, Caccone A, Costa F, Deinum EE, Esther A, Himsworth CG, Keightley PD, Ko A, Lundkvist Å, McElhinney LM, Morand S, Robins J, Russell J, Strand TM, Suarez O, Yon L, Munshi-South J. Global population divergence and admixture of the brown rat (Rattus norvegicus). Proc Biol Sci 2017; 283:rspb.2016.1762. [PMID: 27798305 DOI: 10.1098/rspb.2016.1762] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 09/26/2016] [Indexed: 11/12/2022] Open
Abstract
Native to China and Mongolia, the brown rat (Rattus norvegicus) now enjoys a worldwide distribution. While black rats and the house mouse tracked the regional development of human agricultural settlements, brown rats did not appear in Europe until the 1500s, suggesting their range expansion was a response to relatively recent increases in global trade. We inferred the global phylogeography of brown rats using 32 k SNPs, and detected 13 evolutionary clusters within five expansion routes. One cluster arose following a southward expansion into Southeast Asia. Three additional clusters arose from two independent eastward expansions: one expansion from Russia to the Aleutian Archipelago, and a second to western North America. Westward expansion resulted in the colonization of Europe from which subsequent rapid colonization of Africa, the Americas and Australasia occurred, and multiple evolutionary clusters were detected. An astonishing degree of fine-grained clustering between and within sampling sites underscored the extent to which urban heterogeneity shaped genetic structure of commensal rodents. Surprisingly, few individuals were recent migrants, suggesting that recruitment into established populations is limited. Understanding the global population structure of R. norvegicus offers novel perspectives on the forces driving the spread of zoonotic disease, and aids in development of rat eradication programmes.
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Affiliation(s)
- Emily E Puckett
- Louis Calder Center, Biological Field Station, Fordham University, Armonk, NY 10504, USA
| | - Jane Park
- Louis Calder Center, Biological Field Station, Fordham University, Armonk, NY 10504, USA
| | - Matthew Combs
- Louis Calder Center, Biological Field Station, Fordham University, Armonk, NY 10504, USA
| | - Michael J Blum
- Xavier Center for Bioenvironmental Research, Tulane University, New Orleans, LA 70112, USA
| | | | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, PO Box 208106, New Haven, CT 06520-8106, USA
| | - Federico Costa
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Brazil
| | - Eva E Deinum
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK.,Mathematical and Statistical Methods Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Alexandra Esther
- Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Horticulture and Forests, Vertebrate Research, Julius Kühn Institute, Münster, Germany
| | - Chelsea G Himsworth
- Animal Health Centre, British Columbia Ministry of Agriculture, 1767 Angus Campbell Road, Abbotsford, British Columbia, Canada V3G 2M3
| | - Peter D Keightley
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Albert Ko
- Laboratory of Epidemiology and Public Health, Yale University, New Haven, CT, USA
| | - Åke Lundkvist
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Lorraine M McElhinney
- Wildlife Zoonoses and Vector Borne Disease Research Group, Animal and Plant Health Agency (APHA), Woodham Lane, New Haw Surrey, UK
| | - Serge Morand
- CNRS-CIRAD, Centre d'Infectiologie Christophe Mérieux du Laos, Vientiane, Lao PDR
| | - Judith Robins
- Department of Anthropology, University of Auckland, Private Bag 92019, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - James Russell
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand.,Department of Statistics, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Tanja M Strand
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Olga Suarez
- Laboratorio de Ecologia de Roedores Urbanos, IEGEBA-CONICET, EGE-Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires Pabellon II, Ciudad Universitaria (C1428EHA), Buenos Aires, Argentina
| | - Lisa Yon
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Jason Munshi-South
- Louis Calder Center, Biological Field Station, Fordham University, Armonk, NY 10504, USA
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19
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Abstract
Homo sapiens phylogeography begins with the species' origin nearly 200 kya in Africa. First signs of the species outside Africa (in Arabia) are from 125 kya. Earliest dates elsewhere are now 100 kya in China, 45 kya in Australia and southern Europe (maybe even 60 kya in Australia), 32 kya in northeast Siberia, and maybe 20 kya in the Americas. Humans reached arctic regions and oceanic islands last-arctic North America about 5 kya, mid- and eastern Pacific islands about 2-1 kya, and New Zealand about 700 y ago. Initial routes along coasts seem the most likely given abundant and easily harvested shellfish there as indicated by huge ancient oyster shell middens on all continents. Nevertheless, the effect of geographic barriers-mountains and oceans-is clear. The phylogeographic pattern of diasporas from several single origins-northeast Africa to Eurasia, southeast Eurasia to Australia, and northeast Siberia to the Americas-allows the equivalent of a repeat experiment on the relation between geography and phylogenetic and cultural diversity. On all continents, cultural diversity is high in productive low latitudes, presumably because such regions can support populations of sustainable size in a small area, therefore allowing a high density of cultures. Of course, other factors operate. South America has an unusually low density of cultures in its tropical latitudes. A likely factor is the phylogeographic movement of peoples from the Old World bringing novel and hence, lethal diseases to the New World, a foretaste, perhaps, of present day global transport of tropical diseases.
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20
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Genetic structure and invasion history of the house mouse (Mus musculus domesticus) in Senegal, West Africa: a legacy of colonial and contemporary times. Heredity (Edinb) 2017; 119:64-75. [PMID: 28353686 DOI: 10.1038/hdy.2017.18] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 02/24/2017] [Accepted: 02/25/2017] [Indexed: 02/07/2023] Open
Abstract
Knowledge of the genetic make-up and demographic history of invasive populations is critical to understand invasion mechanisms. Commensal rodents are ideal models to study whether complex invasion histories are typical of introductions involving human activities. The house mouse Mus musculus domesticus is a major invasive synanthropic rodent originating from South-West Asia. It has been largely studied in Europe and on several remote islands, but the genetic structure and invasion history of this taxon have been little investigated in several continental areas, including West Africa. In this study, we focussed on invasive populations of M. m. domesticus in Senegal. In this focal area for European settlers, the distribution area and invasion spread of the house mouse is documented by decades of data on commensal rodent communities. Genetic variation at one mitochondrial locus and 16 nuclear microsatellite markers was analysed from individuals sampled in 36 sites distributed across the country. A combination of phylogeographic and population genetics methods showed that there was a single introduction event on the northern coast of Senegal, from an exogenous (probably West European) source, followed by a secondary introduction from northern Senegal into a coastal site further south. The geographic locations of these introduction sites were consistent with the colonial history of Senegal. Overall, the marked microsatellite genetic structure observed in Senegal, even between sites located close together, revealed a complex interplay of different demographic processes occurring during house mouse spatial expansion, including sequential founder effects and stratified dispersal due to human transport along major roads.
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21
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Ledevin R, Chevret P, Ganem G, Britton-Davidian J, Hardouin EA, Chapuis JL, Pisanu B, da Luz Mathias M, Schlager S, Auffray JC, Renaud S. Phylogeny and adaptation shape the teeth of insular mice. Proc Biol Sci 2017; 283:rspb.2015.2820. [PMID: 26842576 DOI: 10.1098/rspb.2015.2820] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
By accompanying human travels since prehistorical times, the house mouse dispersed widely throughout the world, and colonized many islands. The origin of the travellers determined the phylogenetic source of the insular mice, which encountered diverse ecological and environmental conditions on the various islands. Insular mice are thus an exceptional model to disentangle the relative role of phylogeny, ecology and climate in evolution. Molar shape is known to vary according to phylogeny and to respond to adaptation. Using for the first time a three-dimensional geometric morphometric approach, compared with a classical two-dimensional quantification, the relative effects of size variation, phylogeny, climate and ecology were investigated on molar shape diversity across a variety of islands. Phylogeny emerged as the factor of prime importance in shaping the molar. Changes in competition level, mostly driven by the presence or absence of the wood mouse on the different islands, appeared as the second most important effect. Climate and size differences accounted for slight shape variation. This evidences a balanced role of random differentiation related to history of colonization, and of adaptation possibly related to resource exploitation.
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Affiliation(s)
- Ronan Ledevin
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, CNRS, Université Lyon 1, Campus de la Doua, Villeurbanne 69622, France
| | - Pascale Chevret
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, CNRS, Université Lyon 1, Campus de la Doua, Villeurbanne 69622, France
| | - Guila Ganem
- Institut des Sciences de l'Evolution de Montpellier, UMR 5554, Université Montpellier, CNRS, IRD, EPHE, Montpellier 34095, France
| | - Janice Britton-Davidian
- Institut des Sciences de l'Evolution de Montpellier, UMR 5554, Université Montpellier, CNRS, IRD, EPHE, Montpellier 34095, France
| | - Emilie A Hardouin
- Faculty of Sciences and Technology, Bournemouth University, Christchurch House, Talbot Campus, Poole, Dorset BH12 5BB, UK
| | - Jean-Louis Chapuis
- Centre d'Ecologie et des Sciences de la Conservation, UMR 7204, Muséum National d'Histoire, Naturelle, 61 rue Buffon, Paris 75005, France
| | - Benoit Pisanu
- Centre d'Ecologie et des Sciences de la Conservation, UMR 7204, Muséum National d'Histoire, Naturelle, 61 rue Buffon, Paris 75005, France
| | - Maria da Luz Mathias
- Centro de Estudos do Ambiente e Mar and Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal
| | - Stefan Schlager
- Anthropologie, Medizinische Fakultät der Albert Ludwigs, Universität Freiburg, Freiburg 79104, Germany
| | - Jean-Christophe Auffray
- Institut des Sciences de l'Evolution de Montpellier, UMR 5554, Université Montpellier, CNRS, IRD, EPHE, Montpellier 34095, France
| | - Sabrina Renaud
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, CNRS, Université Lyon 1, Campus de la Doua, Villeurbanne 69622, France
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22
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Evolutionary history and species delimitations: a case study of the hazel dormouse, Muscardinus avellanarius. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0892-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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23
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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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24
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How genetics, history and geography limit potential explanations of invasions by house mice Mus musculus in New Zealand. Biol Invasions 2016. [DOI: 10.1007/s10530-016-1099-0] [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]
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25
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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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26
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Gargan LM, Cornette R, Yearsley JM, Montgomery WI, Paupério J, Alves PC, Butler F, Pascal M, Tresset A, Herrel A, Lusby J, Tosh DG, Searle JB, McDevitt AD. Molecular and morphological insights into the origin of the invasive greater white-toothed shrew (Crocidura russula) in Ireland. Biol Invasions 2016. [DOI: 10.1007/s10530-016-1056-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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27
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Global divergence of the human follicle mite Demodex folliculorum: Persistent associations between host ancestry and mite lineages. Proc Natl Acad Sci U S A 2015; 112:15958-63. [PMID: 26668374 DOI: 10.1073/pnas.1512609112] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Microscopic mites of the genus Demodex live within the hair follicles of mammals and are ubiquitous symbionts of humans, but little molecular work has been done to understand their genetic diversity or transmission. Here we sampled mite DNA from 70 human hosts of diverse geographic ancestries and analyzed 241 sequences from the mitochondrial genome of the species Demodex folliculorum. Phylogenetic analyses recovered multiple deep lineages including a globally distributed lineage common among hosts of European ancestry and three lineages that primarily include hosts of Asian, African, and Latin American ancestry. To a great extent, the ancestral geography of hosts predicted the lineages of mites found on them; 27% of the total molecular variance segregated according to the regional ancestries of hosts. We found that D. folliculorum populations are stable on an individual over the course of years and that some Asian and African American hosts maintain specific mite lineages over the course of years or generations outside their geographic region of birth or ancestry. D. folliculorum haplotypes were much more likely to be shared within families and between spouses than between unrelated individuals, indicating that transmission requires close contact. Dating analyses indicated that D. folliculorum origins may predate modern humans. Overall, D. folliculorum evolution reflects ancient human population divergences, is consistent with an out-of-Africa dispersal hypothesis, and presents an excellent model system for further understanding the history of human movement.
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28
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Haniza MZH, Adams S, Jones EP, MacNicoll A, Mallon EB, Smith RH, Lambert MS. Large-scale structure of brown rat (Rattus norvegicus) populations in England: effects on rodenticide resistance. PeerJ 2015; 3:e1458. [PMID: 26664802 PMCID: PMC4675108 DOI: 10.7717/peerj.1458] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 11/10/2015] [Indexed: 11/20/2022] Open
Abstract
The brown rat (Rattus norvegicus) is a relatively recent (<300 years) addition to the British fauna, but by association with negative impacts on public health, animal health and agriculture, it is regarded as one of the most important vertebrate pest species. Anticoagulant rodenticides were introduced for brown rat control in the 1950s and are widely used for rat control in the UK, but long-standing resistance has been linked to control failures in some regions. One thus far ignored aspect of resistance biology is the population structure of the brown rat. This paper investigates the role population structure has on the development of anticoagulant resistance. Using mitochondrial and microsatellite DNA, we examined 186 individuals (from 15 counties in England and one location in Wales near the Wales–England border) to investigate the population structure of rural brown rat populations. We also examined individual rats for variations of the VKORC1 gene previously associated with resistance to anticoagulant rodenticides. We show that the populations were structured to some degree, but that this was only apparent in the microsatellite data and not the mtDNA data. We discuss various reasons why this is the case. We show that the population as a whole appears not to be at equilibrium. The relative lack of diversity in the mtDNA sequences examined can be explained by founder effects and a subsequent spatial expansion of a species introduced to the UK relatively recently. We found there was a geographical distribution of resistance mutations, and relatively low rate of gene flow between populations, which has implications for the development and management of anticoagulant resistance.
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Affiliation(s)
- Mohd Z H Haniza
- Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris , Tanjung Malim Perak , Malaysia
| | - Sally Adams
- School of Life Sciences, University of Warwick , Coventry , United Kingdom
| | | | | | - Eamonn B Mallon
- Department of Genetics, University of Leicester , Leicester , United Kingdom
| | - Robert H Smith
- School of Applied Sciences, University of Huddersfield , Huddersfield , United Kingdom
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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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Renaud S, Dufour AB, Hardouin EA, Ledevin R, Auffray JC. Once upon Multivariate Analyses: When They Tell Several Stories about Biological Evolution. PLoS One 2015; 10:e0132801. [PMID: 26192946 PMCID: PMC4507858 DOI: 10.1371/journal.pone.0132801] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 06/19/2015] [Indexed: 01/09/2023] Open
Abstract
Geometric morphometrics aims to characterize of the geometry of complex traits. It is therefore by essence multivariate. The most popular methods to investigate patterns of differentiation in this context are (1) the Principal Component Analysis (PCA), which is an eigenvalue decomposition of the total variance-covariance matrix among all specimens; (2) the Canonical Variate Analysis (CVA, a.k.a. linear discriminant analysis (LDA) for more than two groups), which aims at separating the groups by maximizing the between-group to within-group variance ratio; (3) the between-group PCA (bgPCA) which investigates patterns of between-group variation, without standardizing by the within-group variance. Standardizing within-group variance, as performed in the CVA, distorts the relationships among groups, an effect that is particularly strong if the variance is similarly oriented in a comparable way in all groups. Such shared direction of main morphological variance may occur and have a biological meaning, for instance corresponding to the most frequent standing genetic variation in a population. Here we undertake a case study of the evolution of house mouse molar shape across various islands, based on the real dataset and simulations. We investigated how patterns of main variance influence the depiction of among-group differentiation according to the interpretation of the PCA, bgPCA and CVA. Without arguing about a method performing ‘better’ than another, it rather emerges that working on the total or between-group variance (PCA and bgPCA) will tend to put the focus on the role of direction of main variance as line of least resistance to evolution. Standardizing by the within-group variance (CVA), by dampening the expression of this line of least resistance, has the potential to reveal other relevant patterns of differentiation that may otherwise be blurred.
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Affiliation(s)
- Sabrina Renaud
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, CNRS, University Lyon 1, 69622 Villeurbanne, France
- * E-mail:
| | - Anne-Béatrice Dufour
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, CNRS, University Lyon 1, 69622 Villeurbanne, France
| | - Emilie A. Hardouin
- Max Planck Institute of Evolutionary Biology, August-Thienemann-Str. 2, Plön, Germany
- Faculty of Science and Technology, Bournemouth University, Christchurch House, Talbot Campus, Poole, Dorset, United Kingdom
| | - Ronan Ledevin
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, CNRS, University Lyon 1, 69622 Villeurbanne, France
| | - Jean-Christophe Auffray
- Institut des Sciences de l’Evolution de Montpellier, UMR 5554, CNRS, University Montpellier 2, Montpellier, France
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31
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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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32
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Frantz AC, McDevitt AD, Pope LC, Kochan J, Davison J, Clements CF, Elmeros M, Molina-Vacas G, Ruiz-Gonzalez A, Balestrieri A, Van Den Berge K, Breyne P, Do Linh San E, Ågren EO, Suchentrunk F, Schley L, Kowalczyk R, Kostka BI, Ćirović D, Šprem N, Colyn M, Ghirardi M, Racheva V, Braun C, Oliveira R, Lanszki J, Stubbe A, Stubbe M, Stier N, Burke T. Revisiting the phylogeography and demography of European badgers (Meles meles) based on broad sampling, multiple markers and simulations. Heredity (Edinb) 2014; 113:443-53. [PMID: 24781805 PMCID: PMC4220720 DOI: 10.1038/hdy.2014.45] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 02/04/2014] [Accepted: 02/14/2014] [Indexed: 11/09/2022] Open
Abstract
Although the phylogeography of European mammals has been extensively investigated since the 1990s, many studies were limited in terms of sampling distribution, the number of molecular markers used and the analytical techniques employed, frequently leading to incomplete postglacial recolonisation scenarios. The broad-scale genetic structure of the European badger (Meles meles) is of interest as it may result from historic restriction to glacial refugia and/or recent anthropogenic impact. However, previous studies were based mostly on samples from western Europe, making it difficult to draw robust conclusions about the location of refugia, patterns of postglacial expansion and recent demography. In the present study, continent-wide sampling and analyses with multiple markers provided evidence for two glacial refugia (Iberia and southeast Europe) that contributed to the genetic variation observed in badgers in Europe today. Approximate Bayesian computation provided support for a colonisation of Scandinavia from both Iberian and southeastern refugia. In the whole of Europe, we observed a decline in genetic diversity with increasing latitude, suggesting that the reduced diversity in the peripheral populations resulted from a postglacial expansion processes. Although MSVAR v.1.3 also provided evidence for recent genetic bottlenecks in some of these peripheral populations, the simulations performed to estimate the method's power to correctly infer the past demography of our empirical populations suggested that the timing and severity of bottlenecks could not be established with certainty. We urge caution against trying to relate demographic declines inferred using MSVAR with particular historic or climatological events.
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Affiliation(s)
- A C Frantz
- NERC Biomolecular Analysis Facility,
Department of Animal and Plant Sciences, University of Sheffield,
Sheffield, UK
- Musée National d'Histoire
Naturelle, Luxembourg, Luxembourg
| | - A D McDevitt
- School of Biology and Environmental
Science, University College Dublin, Dublin,
Ireland
| | - L C Pope
- School of Biological Science, University
of Queensland, St Lucia, Queensland,
Australia
| | - J Kochan
- Department of Genetics and Animal
Breeding, Wrocław University of Environmental and Life Sciences,
Wrocław, Poland
| | - J Davison
- Institute of Ecology and Earth Sciences,
University of Tartu, Tartu, Estonia
| | - C F Clements
- NERC Biomolecular Analysis Facility,
Department of Animal and Plant Sciences, University of Sheffield,
Sheffield, UK
| | - M Elmeros
- Department of Bioscience, Aarhus
University, Rønde, Denmark
| | - G Molina-Vacas
- Animal Biology Department, University of
Barcelona, Barcelona, Spain
| | - A Ruiz-Gonzalez
- Department of Zoology, Biogeography and
Population Dynamics Research Group, University of the Basque Country,
UPV/EHU, Vitoria-Gasteiz, Spain
| | - A Balestrieri
- Department of Biosciences, University
of Milan, Milan, Italy
| | - K Van Den Berge
- Research Institute for Nature and
Forest, Geraardsbergen, Belgium
| | - P Breyne
- Research Institute for Nature and
Forest, Geraardsbergen, Belgium
| | - E Do Linh San
- Department of Zoology and Entomology,
University of Fort Hare, Alice, South Africa
| | - E O Ågren
- National Veterinary Institute,
Department of Pathology and Wildlife Diseases, Uppsala,
Sweden
| | - F Suchentrunk
- Research Institute of Wildlife Ecology,
University of Veterinary Medicine Vienna, Vienna,
Austria
| | - L Schley
- Administration de la nature et des
forêts, Luxembourg, Luxembourg
| | - R Kowalczyk
- Mammal Research Institute,
Bialowieza, Poland
| | - B I Kostka
- Queen's University Belfast,
Northern Ireland, UK
| | - D Ćirović
- Faculty of Biology, University of
Belgrade, Belgrade, Serbia
| | - N Šprem
- Department of Fisheries, Beekeeping,
Game Management and Special Zoology, University of Zagreb,
Zagreb, Croatia
| | - M Colyn
- CNRS, UMR 6553, ECOBIO,
Université de Rennes 1, Rennes, France
| | - M Ghirardi
- Università degli Studi di
Torino, Torino, Italy
| | - V Racheva
- Balkani Wildlife Society,
Sofia, Bulgaria
| | - C Braun
- 9 chemin du Kilbs,
Bischoffsheim, France
| | - R Oliveira
- Departamento de Zoologia e
Antropologia, Faculdade de Ciências da Universidade do Porto,
Porto, Portugal
| | - J Lanszki
- Department of Nature Conservation,
University of Kaposvár, Kaposvár,
Hungary
| | - A Stubbe
- Domplatz 4,
Halle/Saale, Germany
| | - M Stubbe
- Domplatz 4,
Halle/Saale, Germany
| | - N Stier
- Institute of Forest Botany and Forest
Zoology, Dresden University of Technology, Tharandt,
Germany
| | - T Burke
- NERC Biomolecular Analysis Facility,
Department of Animal and Plant Sciences, University of Sheffield,
Sheffield, UK
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33
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McCormick H, Cursons R, Wilkins RJ, King CM. Location of a contact zone between Mus musculus domesticus and M. m. domesticus with M. m. castaneus mtDNA in southern New Zealand. Mamm Biol 2014. [DOI: 10.1016/j.mambio.2014.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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34
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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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35
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Song Y, Lan Z, Kohn MH. Mitochondrial DNA phylogeography of the Norway rat. PLoS One 2014; 9:e88425. [PMID: 24586325 PMCID: PMC3938417 DOI: 10.1371/journal.pone.0088425] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 01/08/2014] [Indexed: 11/18/2022] Open
Abstract
Central Eastern Asia, foremost the area bordering northern China and Mongolia, has been thought to be the geographic region where Norway rats (Rattus norvegicus) have originated. However recent fossil analyses pointed to their origin in southern China. Moreover, whereas analyses of fossils dated the species' origin as ∼1.2–1.6 million years ago (Mya), molecular analyses yielded ∼0.5–2.9 Mya. Here, to study the geographic origin of the Norway rat and its spread across the globe we analyzed new and all published mitochondrial DNA cytochrome-b (cyt-b; N = 156) and D-loop (N = 212) sequences representing wild rats from four continents and select inbred strains. Our results are consistent with an origin of the Norway rat in southern China ∼1.3 Mya, subsequent prehistoric differentiation and spread in China and Asia from an initially weakly structured ancestral population, followed by further spread and differentiation across the globe during historic times. The recent spreading occurred mostly from derived European populations rather than from archaic Asian populations. We trace laboratory strains to wild lineages from Europe and North America and these represent a subset of the diversity of the rat; leaving Asian lineages largely untapped as a resource for biomedical models. By studying rats from Europe we made the observation that mtDNA diversity cannot be interpreted without consideration of pest control and, possibly, the evolution of rodenticide resistance. However, demographic models explored by forward-time simulations cannot fully explain the low mtDNA diversity of European rats and lack of haplotype sharing with their source from Asia. Comprehensive nuclear marker analyses of a larger sample of Norway rats representing the world are needed to better resolve the evolutionary history of wild rats and of laboratory rats, as well as to better understand the evolution of anticoagulant resistance.
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Affiliation(s)
- Ying Song
- Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas, United States of America,
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Weed and Rodent Biology and Management, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhenjiang Lan
- Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas, United States of America,
| | - Michael H. Kohn
- Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas, United States of America,
- * E-mail:
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36
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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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37
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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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38
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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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39
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Multiple origins of the western European house mouse in the Aeolian Archipelago: clues from mtDNA and chromosomes. Biol Invasions 2012. [DOI: 10.1007/s10530-012-0322-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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40
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Rajabi-Maham H, Orth A, Siahsarvie R, Boursot P, Darvish J, Bonhomme F. The south-eastern house mouse Mus musculus castaneus (Rodentia: Muridae) is a polytypic subspecies. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01957.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Hassan Rajabi-Maham
- Department of Animal Biology; Faculty of Biological Sciences; Shahid Beheshti University; G.C., velenjak; Tehran; 19839-63113; Iran
| | - Annie Orth
- Institut des Sciences de l'Evolution; ISEM; CNRS UMR 5554, CC 063, Université Montpellier 2, Place E. Bataillon; 34095; Montpellier; France
| | | | - Pierre Boursot
- Institut des Sciences de l'Evolution; ISEM; CNRS UMR 5554, CC 063, Université Montpellier 2, Place E. Bataillon; 34095; Montpellier; France
| | - Jamshid Darvish
- Rodentology Research Department; Ferdowsi University of Mashhad; Mashhad; 91775-1436; Iran
| | - François Bonhomme
- Institut des Sciences de l'Evolution; ISEM; CNRS UMR 5554, CC 063, Université Montpellier 2, Place E. Bataillon; 34095; Montpellier; France
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Jones EP, Skirnisson K, McGovern TH, Gilbert MTP, Willerslev E, Searle JB. Fellow travellers: a concordance of colonization patterns between mice and men in the North Atlantic region. BMC Evol Biol 2012; 12:35. [PMID: 22429664 PMCID: PMC3315747 DOI: 10.1186/1471-2148-12-35] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 03/19/2012] [Indexed: 11/15/2022] Open
Abstract
Background House mice (Mus musculus) are commensals of humans and therefore their phylogeography can reflect human colonization and settlement patterns. Previous studies have linked the distribution of house mouse mitochondrial (mt) DNA clades to areas formerly occupied by the Norwegian Vikings in Norway and the British Isles. Norwegian Viking activity also extended further westwards in the North Atlantic with the settlement of Iceland, short-lived colonies in Greenland and a fleeting colony in Newfoundland in 1000 AD. Here we investigate whether house mouse mtDNA sequences reflect human history in these other regions as well. Results House mice samples from Iceland, whether from archaeological Viking Age material or from modern-day specimens, had an identical mtDNA haplotype to the clade previously linked with Norwegian Vikings. From mtDNA and microsatellite data, the modern-day Icelandic mice also share the low genetic diversity shown by their human hosts on Iceland. Viking Age mice from Greenland had an mtDNA haplotype deriving from the Icelandic haplotype, but the modern-day Greenlandic mice belong to an entirely different mtDNA clade. We found no genetic association between modern Newfoundland mice and the Icelandic/ancient Greenlandic mice (no ancient Newfoundland mice were available). The modern day Icelandic and Newfoundland mice belong to the subspecies M. m. domesticus, the Greenlandic mice to M. m. musculus. Conclusions In the North Atlantic region, human settlement history over a thousand years is reflected remarkably by the mtDNA phylogeny of house mice. In Iceland, the mtDNA data show the arrival and continuity of the house mouse population to the present day, while in Greenland the data suggest the arrival, subsequent extinction and recolonization of house mice - in both places mirroring the history of the European human host populations. If house mice arrived in Newfoundland with the Viking settlers at all, then, like the humans, their presence was also fleeting and left no genetic trace. The continuity of mtDNA haplotype in Iceland over 1000 years illustrates that mtDNA can retain the signature of the ancestral house mouse founders. We also show that, in terms of genetic variability, house mouse populations may also track their host human populations.
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Affiliation(s)
- E P Jones
- Department of Biology, University of York, PO Box 373, York YO10 5YW, UK.
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Gabriel SI, Stevens MI, Mathias MDL, Searle JB. Of mice and 'convicts': origin of the Australian house mouse, Mus musculus. PLoS One 2011; 6:e28622. [PMID: 22174847 PMCID: PMC3236204 DOI: 10.1371/journal.pone.0028622] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 11/11/2011] [Indexed: 11/18/2022] Open
Abstract
The house mouse, Mus musculus, is one of the most ubiquitous invasive species worldwide and in Australia is particularly common and widespread, but where it originally came from is still unknown. Here we investigated this origin through a phylogeographic analysis of mitochondrial DNA sequences (D-loop) comparing mouse populations from Australia with those from the likely regional source area in Western Europe. Our results agree with human historical associations, showing a strong link between Australia and the British Isles. This outcome is of intrinsic and applied interest and helps to validate the colonization history of mice as a proxy for human settlement history.
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Affiliation(s)
- Sofia I. Gabriel
- Department of Biology, University of York, York, United Kingdom
- CESAM–Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Mark I. Stevens
- South Australian Museum, and School of Earth and Environmental Sciences, University of Adelaide, Adelaide, Australia
| | - Maria da Luz Mathias
- CESAM–Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Jeremy B. Searle
- Department of Biology, University of York, York, United Kingdom
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, New York, United States of America
- * E-mail:
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LOXDALE HUGHD, LUSHAI GUGS, HARVEY JEFFREYA. The evolutionary improbability of ‘generalism’ in nature, with special reference to insects. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01627.x] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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JONES ELEANORP, JENSEN JENSKJELD, MAGNUSSEN EYĐFINN, GREGERSEN NOOMI, HANSEN HEIDIS, SEARLE JEREMYB. A molecular characterization of the charismatic Faroe house mouse. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2010.01597.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Jones EP, Van Der Kooij J, Solheim R, Searle JB. Norwegian house mice (Mus musculus musculus/domesticus): distributions, routes of colonization and patterns of hybridization. Mol Ecol 2010; 19:5252-64. [PMID: 21044192 DOI: 10.1111/j.1365-294x.2010.04874.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigated the distributions and routes of colonization of two commensal subspecies of house mouse in Norway: Mus musculus domesticus and M. m. musculus. Five nuclear markers (Abpa, D11 cenB2, Btk, SMCY and Zfy2) and a morphological feature (tail length) were used to differentiate the two subspecies and assess their distributions, and mitochondrial (mt) D-loop sequences helped to elucidate their colonization history. M. m. domesticus is the more widespread of the two subspecies, occupying the western and southern coast of Norway, while M. m. musculus is found along Norway's southeastern coast and east from there to Sweden. Two sections of the hybrid zone between the two subspecies were localized in Norway. However, hybrid forms also occur well away from that hybrid zone, the most prevalent of which are mice with a M. m. musculus-type Y chromosome and an otherwise M. m. domesticus genome. MtDNA D-loop sequences of the mice revealed a complex phylogeography within M. m. domesticus, reflecting passive human transport to Norway, probably during the Viking period. M. m. musculus may have colonized earlier. If so, that leaves open the possibility that M. m. domesticus replaced M. m. musculus from much of Norway, with the widely distributed hybrids a relict of this process. Overall, the effects of hybridization are evident in house mice throughout Norway.
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Affiliation(s)
- Eleanor P Jones
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK.
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Bloomquist EW, Lemey P, Suchard MA. Three roads diverged? Routes to phylogeographic inference. Trends Ecol Evol 2010; 25:626-32. [PMID: 20863591 PMCID: PMC2956787 DOI: 10.1016/j.tree.2010.08.010] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Revised: 08/25/2010] [Accepted: 08/26/2010] [Indexed: 11/29/2022]
Abstract
Phylogeographic methods facilitate inference of the geographical history of genetic lineages. Recent examples explore human migration and the origins of viral pandemics. There is longstanding disagreement over the use and validity of certain phylogeographic inference methodologies. In this paper, we highlight three distinct frameworks for phylogeographic inference to give a taste of this disagreement. Each of the three approaches presents a different viewpoint on phylogeography, most fundamentally on how we view the relationship between the inferred history of a sample and the history of the population the sample is embedded in. Satisfactory resolution of this relationship between history of the tree and history of the population remains a challenge for all but the most trivial models of phylogeographic processes. Intriguingly, we believe that some recent methods that entirely avoid inference about the history of the population will eventually help to reach a resolution.
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Affiliation(s)
- Erik W. Bloomquist
- Mathematical Biosciences Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, K.U. Leuven, Leuven 3000, Belgium
| | - Marc A. Suchard
- Department of Biostatistics, UCLA School of Public Health, Los Angeles, CA 90095, USA
- Departments of Biomathematics and Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA, Phone: (310) 825-7442, Fax: (310) 825-8685,
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Gabriel SI, Jóhannesdóttir F, Jones EP, Searle JB. Colonization, mouse-style. BMC Biol 2010; 8:131. [PMID: 20977781 PMCID: PMC2964602 DOI: 10.1186/1741-7007-8-131] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 10/21/2010] [Indexed: 11/16/2022] Open
Abstract
Several recent papers, including one in BMC Evolutionary Biology, examine the colonization history of house mice. As well as background for the analysis of mouse adaptation, such studies offer a perspective on the history of movements of the humans that accidentally transported the mice. See research article: http://www.biomedcentral.com/1471-2148/10/325
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Affiliation(s)
- Sofia I Gabriel
- CESAM - Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisbon, Portugal
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Bonhomme F, Orth A, Cucchi T, Rajabi-Maham H, Catalan J, Boursot P, Auffray JC, Britton-Davidian J. Genetic differentiation of the house mouse around the Mediterranean basin: matrilineal footprints of early and late colonization. Proc Biol Sci 2010; 278:1034-43. [PMID: 20880891 DOI: 10.1098/rspb.2010.1228] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The molecular signatures of the recent expansion of the western house mouse, Mus musculus domesticus, around the Mediterranean basin are investigated through the study of mitochondrial D-loop polymorphism on a 1313 individual dataset. When reducing the complexity of the matrilineal network to a series of haplogroups (HGs), our main results indicate that: (i) several HGs are recognized which seem to have almost simultaneously diverged from each other, confirming a recent expansion for the whole subspecies; (ii) some HGs are geographically delimited while others are widespread, indicative of multiple introductions or secondary exchanges; (iii) mice from the western and the eastern coasts of Africa harbour largely different sets of HGs; and (iv) HGs from the two shores of the Mediterranean are more similar in the west than in the east. This pattern is in keeping with the two-step westward expansion proposed by zooarchaeological data, an early one coincident with the Neolithic progression and limited to the eastern Mediterranean and a later one, particularly evident in the western Mediterranean, related to the generalization of maritime trade during the first millennium BC and onwards. The dispersal of mice along with humans, which continues until today, has for instance left complex footprints on the long ago colonized Cyprus or more simple ones on the much more recently populated Canary Islands.
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Affiliation(s)
- François Bonhomme
- Institut des Sciences de l'Evolution, Université Montpellier 2, CNRS UMR5554, Montpellier, France.
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Gündüz I, Pollock CL, Giménez MD, Förster DW, White TA, Sans-Fuentes MA, Hauffe HC, Ventura J, López-Fuster MJ, Searle JB. Staggered chromosomal hybrid zones in the house mouse: relevance to reticulate evolution and speciation. Genes (Basel) 2010; 1:193-209. [PMID: 24710041 PMCID: PMC3954089 DOI: 10.3390/genes1020193] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Revised: 07/05/2010] [Accepted: 07/08/2010] [Indexed: 01/14/2023] Open
Abstract
In the house mouse there are numerous chromosomal races distinguished by different combinations of metacentric chromosomes. These may come into contact with each other and with the ancestral all-acrocentric race, and form hybrid zones. The chromosomal clines that make up these hybrid zones may be coincident or separated from each other (staggered). Such staggered hybrid zones are interesting because they may include populations of individuals homozygous for a mix of features of the hybridising races. We review the characteristics of four staggered hybrid zones in the house mouse and discuss whether they are examples of primary or secondary contact and whether they represent reticulate evolution or not. However, the most important aspect of staggered hybrid zones is that the homozygous populations within the zones have the potential to expand their distributions and become new races (a process termed 'zonal raciation'). In this way they can add to the total 'stock' of chromosomal races in the species concerned. Speciation is an infrequent phenomenon that may involve an unusual set of circumstances. Each one of the products of zonal raciation has the potential to become a new species and by having more races increases the chance of a speciation event.
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Affiliation(s)
- Islam Gündüz
- Department of Biology, University of York, PO Box 373, York YO10 5YW, UK.
| | | | - Mabel D Giménez
- Department of Biology, University of York, PO Box 373, York YO10 5YW, UK.
| | - Daniel W Förster
- Department of Biology, University of York, PO Box 373, York YO10 5YW, UK.
| | - Thomas A White
- School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, UK.
| | - Maria A Sans-Fuentes
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
| | - Heidi C Hauffe
- Department of Biology, University of York, PO Box 373, York YO10 5YW, UK.
| | - Jacint Ventura
- Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia, Facultat de Biociènces, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - María José López-Fuster
- Departament de Biologia Animal, Facultat de Biologia, Universitat de Barcelona, Avda. Diagonal 645, 08028 Barcelona, Spain.
| | - Jeremy B Searle
- Department of Biology, University of York, PO Box 373, York YO10 5YW, UK.
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Ruffino L, Vidal E. Early colonization of Mediterranean islands by Rattus rattus: a review of zooarcheological data. Biol Invasions 2010. [DOI: 10.1007/s10530-009-9681-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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