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Fujiwara K, Kawai Y, Takada T, Shiroishi T, Saitou N, Suzuki H, Osada N. Insights into Mus musculus Population Structure across Eurasia Revealed by Whole-Genome Analysis. Genome Biol Evol 2022; 14:evac068. [PMID: 35524942 PMCID: PMC9122283 DOI: 10.1093/gbe/evac068] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2022] [Indexed: 11/13/2022] Open
Abstract
For more than 100 years, house mice (Mus musculus) have been used as a key animal model in biomedical research. House mice are genetically diverse, yet their genetic background at the global level has not been fully understood. Previous studies have suggested that they originated in South Asia and diverged into three major subspecies, almost simultaneously, approximately 110,000-500,000 years ago; however, they have spread across the world with the migration of modern humans in prehistoric and historic times (∼10,000 years ago to the present day) and have undergone secondary contact, which has complicated the genetic landscape of wild house mice. In this study, we sequenced the whole-genome sequences of 98 wild house mice collected from Eurasia, particularly East Asia, Southeast Asia, and South Asia. Although wild house mice were found to consist of three major genetic groups corresponding to the three major subspecies, individuals representing admixtures between subspecies were more prevalent in East Asia than has been previously recognized. Furthermore, several samples exhibited an incongruent pattern of genealogies between mitochondrial and autosomal genomes. Using samples that likely retained the original genetic components of subspecies with the least admixture, we estimated the pattern and timing of divergence among the subspecies. The estimated divergence time of the three subspecies was 187,000-226,000 years ago. These results will help us to understand the genetic diversity of wild mice on a global scale, and the findings will be particularly useful in future biomedical and evolutionary studies involving laboratory mice established from such wild mice.
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Affiliation(s)
- Kazumichi Fujiwara
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Japan
- Global Station for Big Data and Cybersecurity, GI-CoRE, Hokkaido University, Sapporo, Japan
| | - Yosuke Kawai
- Genome Medical Science Project (Toyama), National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Toyoyuki Takada
- Integrated BioResource Information Division, RIKEN BioResource Research Center, Tsukuba, Japan
| | | | | | - Hitoshi Suzuki
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan
| | - Naoki Osada
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Japan
- Global Station for Big Data and Cybersecurity, GI-CoRE, Hokkaido University, Sapporo, Japan
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2
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Alleva B, Brick K, Pratto F, Huang M, Camerini-Otero RD. Cataloging Human PRDM9 Allelic Variation Using Long-Read Sequencing Reveals PRDM9 Population Specificity and Two Distinct Groupings of Related Alleles. Front Cell Dev Biol 2021; 9:675286. [PMID: 34805134 PMCID: PMC8600002 DOI: 10.3389/fcell.2021.675286] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 10/11/2021] [Indexed: 11/29/2022] Open
Abstract
The PRDM9 protein determines sites of meiotic recombination in humans by directing meiotic DNA double-strand breaks to specific loci. Targeting specificity is encoded by a long array of C2H2 zinc fingers that bind to DNA. This zinc finger array is hypervariable, and the resulting alleles each have a potentially different DNA binding preference. The assessment of PRDM9 diversity is important for understanding the complexity of human population genetics, inheritance linkage patterns, and predisposition to genetic disease. Due to the repetitive nature of the PRDM9 zinc finger array, the large-scale sequencing of human PRDM9 is challenging. We, therefore, developed a long-read sequencing strategy to infer the diploid PRDM9 zinc finger array genotype in a high-throughput manner. From an unbiased study of PRDM9 allelic diversity in 720 individuals from seven human populations, we detected 69 PRDM9 alleles. Several alleles differ in frequency among human populations, and 32 alleles had not been identified by previous studies, which were heavily biased to European populations. PRDM9 alleles are distinguished by their DNA binding site preferences and fall into two major categories related to the most common PRDM9-A and PRDM9-C alleles. We also found that it is likely that inter-conversion between allele types is rare. By mapping meiotic double-strand breaks (DSBs) in the testis, we found that small variations in PRDM9 can substantially alter the meiotic recombination landscape, demonstrating that minor PRDM9 variants may play an under-appreciated role in shaping patterns of human recombination. In summary, our data greatly expands knowledge of PRDM9 diversity in humans.
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Affiliation(s)
- Benjamin Alleva
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Kevin Brick
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Florencia Pratto
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Mini Huang
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Rafael Daniel Camerini-Otero
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
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3
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Oh KP, Shiels AB, Shiels L, Blondel DV, Campbell KJ, Saah JR, Lloyd AL, Thomas PQ, Gould F, Abdo Z, Godwin JR, Piaggio AJ. Population genomics of invasive rodents on islands: Genetic consequences of colonization and prospects for localized synthetic gene drive. Evol Appl 2021; 14:1421-1435. [PMID: 34025776 PMCID: PMC8127709 DOI: 10.1111/eva.13210] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 12/22/2022] Open
Abstract
Introduced rodent populations pose significant threats worldwide, with particularly severe impacts on islands. Advancements in genome editing have motivated interest in synthetic gene drives that could potentially provide efficient and localized suppression of invasive rodent populations. Application of such technologies will require rigorous population genomic surveys to evaluate population connectivity, taxonomic identification, and to inform design of gene drive localization mechanisms. One proposed approach leverages the predicted shifts in genetic variation that accompany island colonization, wherein founder effects, genetic drift, and island-specific selection are expected to result in locally fixed alleles (LFA) that are variable in neighboring nontarget populations. Engineering of guide RNAs that target LFA may thus yield gene drives that spread within invasive island populations, but would have limited impacts on nontarget populations in the event of an escape. Here we used pooled whole-genome sequencing of invasive mouse (Mus musculus) populations on four islands along with paired putative source populations to test genetic predictions of island colonization and characterize locally fixed Cas9 genomic targets. Patterns of variation across the genome reflected marked reductions in allelic diversity in island populations and moderate to high degrees of differentiation from nearby source populations despite relatively recent colonization. Locally fixed Cas9 sites in female fertility genes were observed in all island populations, including a small number with multiplexing potential. In practice, rigorous sampling of presumptive LFA will be essential to fully assess risk of resistance alleles. These results should serve to guide development of improved, spatially limited gene drive design in future applications.
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Affiliation(s)
- Kevin P. Oh
- National Wildlife Research CenterUSDA APHIS Wildlife ServicesFort CollinsColoradoUSA
- Department of Microbiology, Immunology and PathologyColorado State UniversityFort CollinsColoradoUSA
| | - Aaron B. Shiels
- National Wildlife Research CenterUSDA APHIS Wildlife ServicesFort CollinsColoradoUSA
| | - Laura Shiels
- National Wildlife Research CenterUSDA APHIS Wildlife ServicesFort CollinsColoradoUSA
| | - Dimitri V. Blondel
- Department of Biological SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Karl J. Campbell
- Island ConservationPuerto AyoraEcuador
- School of Agriculture and Food SciencesThe University of QueenslandGattonQueenslandAustralia
| | - J. Royden Saah
- Island ConservationPuerto AyoraEcuador
- Genetic Engineering and Society CenterNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Alun L. Lloyd
- Genetic Engineering and Society CenterNorth Carolina State UniversityRaleighNorth CarolinaUSA
- Biomathematics Graduate Program and Department of MathematicsNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Paul Q. Thomas
- The Robinson Research Institute and School of MedicineThe University of AdelaideAdelaideSouth AustraliaAustralia
| | - Fred Gould
- Genetic Engineering and Society CenterNorth Carolina State UniversityRaleighNorth CarolinaUSA
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Zaid Abdo
- Department of Microbiology, Immunology and PathologyColorado State UniversityFort CollinsColoradoUSA
| | - John R. Godwin
- Department of Biological SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA
- Genetic Engineering and Society CenterNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Antoinette J. Piaggio
- National Wildlife Research CenterUSDA APHIS Wildlife ServicesFort CollinsColoradoUSA
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Li Y, Fujiwara K, Osada N, Kawai Y, Takada T, Kryukov AP, Abe K, Yonekawa H, Shiroishi T, Moriwaki K, Saitou N, Suzuki H. House mouse Mus musculus dispersal in East Eurasia inferred from 98 newly determined complete mitochondrial genome sequences. Heredity (Edinb) 2021; 126:132-147. [PMID: 32934361 PMCID: PMC7852662 DOI: 10.1038/s41437-020-00364-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/28/2020] [Accepted: 08/28/2020] [Indexed: 11/09/2022] Open
Abstract
The Eurasian house mouse Mus musculus is useful for tracing prehistorical human movement related to the spread of farming. We determined whole mitochondrial DNA (mtDNA) sequences (ca. 16,000 bp) of 98 wild-derived individuals of two subspecies, M. m. musculus (MUS) and M. m. castaneus (CAS). We revealed directional dispersals reaching as far as the Japanese Archipelago from their homelands. Our phylogenetic analysis indicated that the eastward movement of MUS was characterised by five step-wise regional extension events: (1) broad spatial expansion into eastern Europe and the western part of western China, (2) dispersal to the eastern part of western China, (3) dispersal to northern China, (4) dispersal to the Korean Peninsula and (5) colonisation and expansion in the Japanese Archipelago. These events were estimated to have occurred during the last 2000-18,000 years. The dispersal of CAS was characterised by three events: initial divergences (ca. 7000-9000 years ago) of haplogroups in northernmost China and the eastern coast of India, followed by two population expansion events that likely originated from the Yangtze River basin to broad areas of South and Southeast Asia, including Sri Lanka, Bangladesh and Indonesia (ca. 4000-6000 years ago) and to Yunnan, southern China and the Japanese Archipelago (ca. 2000-3500). This study provides a solid framework for the spatiotemporal movement of the human-associated organisms in Holocene Eastern Eurasia using whole mtDNA sequences, reliable evolutionary rates and accurate branching patterns. The information obtained here contributes to the analysis of a variety of animals and plants associated with prehistoric human migration.
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Affiliation(s)
- Yue Li
- Graduate School of Environmental Science, Hokkaido University, North 10, West 5, Kita-ku, Sapporo, 060-0810, Japan
| | - Kazumichi Fujiwara
- Graduate School of Information Science and Technology, Hokkaido University, North 14, West 9, Kita-ku, Sapporo, 060-0814, Japan
- Global Station for Big Data and Cybersecurity, GI-CoRE, Hokkaido University, North 14, West 9, Kita-ku, Sapporo, 060-0814, Japan
| | - Naoki Osada
- Graduate School of Information Science and Technology, Hokkaido University, North 14, West 9, Kita-ku, Sapporo, 060-0814, Japan
- Global Station for Big Data and Cybersecurity, GI-CoRE, Hokkaido University, North 14, West 9, Kita-ku, Sapporo, 060-0814, Japan
| | - Yosuke Kawai
- Genome Medical Science Project (Toyama), National Center for Global Health and Medicine, 1-21-1, Toyama, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Toyoyuki Takada
- Integrated Bioresource Information Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, 305-0074, Japan
| | - Alexey P Kryukov
- Far Eastern Branch of the Russian Academy of Sciences, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Vladivostok, 690022, Russia
| | - Kuniya Abe
- Technology and Development Team for Mammalian Genome Dynamics, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, 305-0074, Japan
| | - Hiromichi Yonekawa
- Laboratory for Transgenic Technology, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kami-kitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | | | - Kazuo Moriwaki
- RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, 305-0074, Japan
- National Institute of Genetics, 1111 Yata, Mishima, 411-8540, Japan
| | - Naruya Saitou
- Population Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, 411-8540, Japan
- School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara-cho, 903-0215, Japan
| | - Hitoshi Suzuki
- Graduate School of Environmental Science, Hokkaido University, North 10, West 5, Kita-ku, Sapporo, 060-0810, Japan.
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Kuwayama T, Nunome M, Kinoshita G, Abe K, Suzuki H. Heterogeneous genetic make-up of Japanese house mice (Mus musculus) created by multiple independent introductions and spatio-temporally diverse hybridization processes. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx076] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Vallier M, Abou Chakra M, Hindersin L, Linnenbrink M, Traulsen A, Baines JF. Evaluating the maintenance of disease-associated variation at the blood group-related gene B4galnt2 in house mice. BMC Evol Biol 2017; 17:187. [PMID: 28806915 PMCID: PMC5557512 DOI: 10.1186/s12862-017-1035-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 08/04/2017] [Indexed: 11/16/2022] Open
Abstract
Background B4galnt2 is a blood group-related glycosyltransferase that displays cis-regulatory variation for its tissue-specific expression patterns in house mice. The wild type allele, found e.g. in the C57BL/6 J strain, directs intestinal expression of B4galnt2, which is the pattern observed among vertebrates, including humans. An alternative allele class found in the RIIIS/J strain and other mice instead drives expression in blood vessels, which leads to a phenotype similar to type 1 von Willebrand disease (VWD), a common human bleeding disorder. We previously showed that alternative B4galnt2 alleles are subject to long-term balancing selection in mice and that variation in B4galnt2 expression influences host-microbe interactions in the intestine. This suggests that the costs of prolonged bleeding in RIIIS/J allele-bearing mice might be outweighed by benefits associated with resistance against gastrointestinal pathogens. However, the conditions under which such trade-offs could lead to the long-term maintenance of disease-associated variation at B4galnt2 are unclear. Results To explore the persistence of B4galnt2 alleles in wild populations of house mice, we combined B4galnt2 haplotype frequency data together with a mathematical model based on an evolutionary game framework with a modified Wright-Fisher process. In particular, given the potential for a heterozygote advantage as a possible explanation for balancing selection, we focused on heterozygous mice, which express B4galnt2 in both blood vessels and the gastrointestinal tract. We show that B4galnt2 displays an interesting spatial allelic distribution in Western Europe, likely due to the recent action of natural selection. Moreover, we found that the genotype frequencies observed in nature can be produced by pathogen-driven selection when both heterozygotes and RIIIS/J homozygotes are protected against infection and the fitness cost of bleeding is roughly half that of infection. Conclusion By comparing the results of our models to the patterns of polymorphism at B4galnt2 in natural populations, we are able to recognize the long-term maintenance of the RIIIS/J allele through host-pathogen interactions as a viable hypothesis. Further, our models identify that a putative dominant-, yet unknown protective function of the RIIIS/J allele appears to be more likely than a protective loss of intestinal B4galnt2 expression in RIIIS/J homozygotes. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-1035-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marie Vallier
- Max Planck Institute for Evolutionary Biology, Evolutionary Genomics, Plön, Germany.,Institute for Experimental Medicine, Section of Evolutionary Medicine, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Maria Abou Chakra
- Max Planck Institute for Evolutionary Biology, Evolutionary Theory, Plön, Germany.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Laura Hindersin
- Max Planck Institute for Evolutionary Biology, Evolutionary Theory, Plön, Germany
| | - Miriam Linnenbrink
- Max Planck Institute for Evolutionary Biology, Evolutionary Genomics, Plön, Germany
| | - Arne Traulsen
- Max Planck Institute for Evolutionary Biology, Evolutionary Theory, Plön, Germany
| | - John F Baines
- Max Planck Institute for Evolutionary Biology, Evolutionary Genomics, Plön, Germany. .,Institute for Experimental Medicine, Section of Evolutionary Medicine, Christian-Albrechts-University of Kiel, Kiel, Germany.
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Geographical distribution of Toxoplasma gondii genotypes in Asia: A link with neighboring continents. INFECTION GENETICS AND EVOLUTION 2017; 53:227-238. [PMID: 28583867 DOI: 10.1016/j.meegid.2017.06.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 06/01/2017] [Accepted: 06/02/2017] [Indexed: 11/21/2022]
Abstract
Defining the pattern of genetic diversity of Toxoplasma gondii is important to understand its worldwide distribution. During the last decades, a large number of studies have been published on Toxoplasma genotypes circulating in Europe, in North and South America. Two continents are still largely unexplored, Africa and, to a less extent, Asia. In this last continent, an increasing number of publications reported genotypes circulating in diverse provinces of China, but very few data are available for other Asian countries. After a systematic database search, 47 papers related to T. gondii genotypes in Asia were analyzed. Genetic characterization of DNA was performed by microsatellite markers, or more usually by a multiplex PCR using 11 PCR-RFLP markers, allowing data comparison to draw a first global picture of the population structure of this parasite throughout Asia. Overall, 390 isolates or DNA extracts were completely typed by PCR-RFLP and/or microsatellite marker methods, revealing 36 different PCR-RFLP or equivalent microsatellite genotypes: 15 genotypes identified by a ToxoDB number and 21 atypical or unique genotypes. The most common genotype found in Asia is the genotype ToxoDB#9 (Chinese 1). The clonal types I, II and II variant, and III were also commonly found in Asia. The geographical distribution of these genotypes across Asia may reflect either a continuum with Europe for the western part of Asia (presence of Type II), or the circulation of strains through animal migration or human activities between Africa and the Southwestern part of Asia (Africa 1 genotype in Turkey or ToxoDB#20 both I Sri-Lanka and in Ethiopia or Egypt). Although there are some indications of a genetic population structure in Southeast Asian countries different from the rest of Asia, more studies in this tropical part of Asia will be necessary for a region which represent as well as Africa one of the missing links of the T. gondii genetic diversity.
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Harr B, Karakoc E, Neme R, Teschke M, Pfeifle C, Pezer Ž, Babiker H, Linnenbrink M, Montero I, Scavetta R, Abai MR, Molins MP, Schlegel M, Ulrich RG, Altmüller J, Franitza M, Büntge A, Künzel S, Tautz D. Genomic resources for wild populations of the house mouse, Mus musculus and its close relative Mus spretus. Sci Data 2016; 3:160075. [PMID: 27622383 PMCID: PMC5020872 DOI: 10.1038/sdata.2016.75] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 07/29/2016] [Indexed: 12/20/2022] Open
Abstract
Wild populations of the house mouse (Mus musculus) represent the raw genetic material for the classical inbred strains in biomedical research and are a major model system for evolutionary biology. We provide whole genome sequencing data of individuals representing natural populations of M. m. domesticus (24 individuals from 3 populations), M. m. helgolandicus (3 individuals), M. m. musculus (22 individuals from 3 populations) and M. spretus (8 individuals from one population). We use a single pipeline to map and call variants for these individuals and also include 10 additional individuals of M. m. castaneus for which genomic data are publically available. In addition, RNAseq data were obtained from 10 tissues of up to eight adult individuals from each of the three M. m. domesticus populations for which genomic data were collected. Data and analyses are presented via tracks viewable in the UCSC or IGV genome browsers. We also provide information on available outbred stocks and instructions on how to keep them in the laboratory.
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Affiliation(s)
- Bettina Harr
- Max-Planck Institute for Evolutionary Biology, August-Thienemanstrasse 2, 24306 Plön, Germany
| | - Emre Karakoc
- Max-Planck Institute for Evolutionary Biology, August-Thienemanstrasse 2, 24306 Plön, Germany
| | - Rafik Neme
- Max-Planck Institute for Evolutionary Biology, August-Thienemanstrasse 2, 24306 Plön, Germany
| | - Meike Teschke
- Max-Planck Institute for Evolutionary Biology, August-Thienemanstrasse 2, 24306 Plön, Germany
| | - Christine Pfeifle
- Max-Planck Institute for Evolutionary Biology, August-Thienemanstrasse 2, 24306 Plön, Germany
| | - Željka Pezer
- Max-Planck Institute for Evolutionary Biology, August-Thienemanstrasse 2, 24306 Plön, Germany
| | - Hiba Babiker
- Max-Planck Institute for Evolutionary Biology, August-Thienemanstrasse 2, 24306 Plön, Germany
| | - Miriam Linnenbrink
- Max-Planck Institute for Evolutionary Biology, August-Thienemanstrasse 2, 24306 Plön, Germany
| | - Inka Montero
- Max-Planck Institute for Evolutionary Biology, August-Thienemanstrasse 2, 24306 Plön, Germany
| | - Rick Scavetta
- Max-Planck Institute for Evolutionary Biology, August-Thienemanstrasse 2, 24306 Plön, Germany
| | - Mohammad Reza Abai
- Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, Tehran 1417613151, Iran
| | - Marta Puente Molins
- Laboratorio de Anatomía Animal, Departamento de Biología Animal, Facultad de Ciencias, Universidad de Vigo, 36200 Vigo, Spain
| | - Mathias Schlegel
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute for Novel and Emerging Infectious Diseases, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Rainer G Ulrich
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute for Novel and Emerging Infectious Diseases, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), University of Cologne, Weyertal 115b, 50931 Cologne, Germany.,Institute of Human Genetics, Universitätsklinik Köln, Kerpener Str. 34, 50931 Köln, Germany
| | - Marek Franitza
- Cologne Center for Genomics (CCG), University of Cologne, Weyertal 115b, 50931 Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Anna Büntge
- Max-Planck Institute for Evolutionary Biology, August-Thienemanstrasse 2, 24306 Plön, Germany
| | - Sven Künzel
- Max-Planck Institute for Evolutionary Biology, August-Thienemanstrasse 2, 24306 Plön, Germany
| | - Diethard Tautz
- Max-Planck Institute for Evolutionary Biology, August-Thienemanstrasse 2, 24306 Plön, Germany
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Morgan AP, Holt JM, McMullan RC, Bell TA, Clayshulte AMF, Didion JP, Yadgary L, Thybert D, Odom DT, Flicek P, McMillan L, de Villena FPM. The Evolutionary Fates of a Large Segmental Duplication in Mouse. Genetics 2016; 204:267-85. [PMID: 27371833 PMCID: PMC5012392 DOI: 10.1534/genetics.116.191007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/27/2016] [Indexed: 01/21/2023] Open
Abstract
Gene duplication and loss are major sources of genetic polymorphism in populations, and are important forces shaping the evolution of genome content and organization. We have reconstructed the origin and history of a 127-kbp segmental duplication, R2d, in the house mouse (Mus musculus). R2d contains a single protein-coding gene, Cwc22 De novo assembly of both the ancestral (R2d1) and the derived (R2d2) copies reveals that they have been subject to nonallelic gene conversion events spanning tens of kilobases. R2d2 is also a hotspot for structural variation: its diploid copy number ranges from zero in the mouse reference genome to >80 in wild mice sampled from around the globe. Hemizygosity for high copy-number alleles of R2d2 is associated in cis with meiotic drive; suppression of meiotic crossovers; and copy-number instability, with a mutation rate in excess of 1 per 100 transmissions in some laboratory populations. Our results provide a striking example of allelic diversity generated by duplication and demonstrate the value of de novo assembly in a phylogenetic context for understanding the mutational processes affecting duplicate genes.
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Affiliation(s)
- Andrew P Morgan
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - J Matthew Holt
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Rachel C McMullan
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Timothy A Bell
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Amelia M-F Clayshulte
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - John P Didion
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Liran Yadgary
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - David Thybert
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Cambridge, CB10 1SD, United Kingdom
| | - Duncan T Odom
- Cancer Research United Kingdom Cambridge Institute, University of Cambridge, CB2 0RE, United Kingdom Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, United Kingdom
| | - Paul Flicek
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Cambridge, CB10 1SD, United Kingdom Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, United Kingdom
| | - Leonard McMillan
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
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10
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Abstract
The general development of immune response in the short and long term is a product of the antigenic environment in which a species resides. Colonization of a novel antigenic environment by a species would be expected to alter the immune system. Animals that successfully adapt their immune responses will successfully colonize new locations. However, founder events associated with colonization by limited numbers of individuals from a source population will constrain adaptability. How these contradicting forces shape immunity in widely distributed species is unknown. The western house mouse (Mus musculus domesticus) spread globally from the Indo-Pakistani cradle, often in association with human migration and settlement. In the present study, we tested the hypothesis that wild-derived outbred laboratory populations of house mice from their original range (Iran) and historically recent European invasive populations (from France and Germany) present differences in immune functional diversity corresponding to recent historical founder events in Europe and movement to novel antigenic environments. We found that (1) European mice had lower total white blood cell (WBC) counts but higher immunoglobulin E concentrations than their Iranian counterparts, and (2) there were no significant differences in the measured immunological parameters among European populations. The results indicate that founder events in European mice and selection pressure exerted by the composition of local parasitic helminth communities underlie the observed patterns.
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Affiliation(s)
- Jundong Tian
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315, Berlin, Germany
- Department of Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany
| | - Heribert Hofer
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315, Berlin, Germany
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315, Berlin, Germany
| | - Gábor Á Czirják
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315, Berlin, Germany.
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11
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Phifer-Rixey M, Nachman MW. Insights into mammalian biology from the wild house mouse Mus musculus. eLife 2015; 4. [PMID: 25875302 PMCID: PMC4397906 DOI: 10.7554/elife.05959] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/26/2015] [Indexed: 12/22/2022] Open
Abstract
The house mouse, Mus musculus, was established in the early 1900s as one of the first genetic model organisms owing to its short generation time, comparatively large litters, ease of husbandry, and visible phenotypic variants. For these reasons and because they are mammals, house mice are well suited to serve as models for human phenotypes and disease. House mice in the wild consist of at least three distinct subspecies and harbor extensive genetic and phenotypic variation both within and between these subspecies. Wild mice have been used to study a wide range of biological processes, including immunity, cancer, male sterility, adaptive evolution, and non-Mendelian inheritance. Despite the extensive variation that exists among wild mice, classical laboratory strains are derived from a limited set of founders and thus contain only a small subset of this variation. Continued efforts to study wild house mice and to create new inbred strains from wild populations have the potential to strengthen house mice as a model system. DOI:http://dx.doi.org/10.7554/eLife.05959.001
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Affiliation(s)
- Megan Phifer-Rixey
- Department of Integrative Biology, University of California, Berkeley, Berkeley, United States and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, United States
| | - Michael W Nachman
- Department of Integrative Biology, University of California, Berkeley, Berkeley, United States and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, United States
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12
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Kodama S, Nunome M, Moriwaki K, Suzuki H. Ancient onset of geographical divergence, interpopulation genetic exchange, and natural selection on theMc1rcoat-colour gene in the house mouse (Mus musculus). Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12471] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sayaka Kodama
- Laboratory of Ecology and Genetics; Graduate School of Environmental Earth Science; Hokkaido University; Kita-ku Sapporo 060-0810 Japan
| | - Mitsuo Nunome
- Laboratory of Animal Genetics; Department of Applied Molecular Biosciences; Graduate School of Bioagricultural Sciences; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8601 Japan
| | - Kazuo Moriwaki
- RIKEN; Bioresource Center; Tsukuba Ibaraki 305-0074 Japan
| | - Hitoshi Suzuki
- Laboratory of Ecology and Genetics; Graduate School of Environmental Earth Science; Hokkaido University; Kita-ku Sapporo 060-0810 Japan
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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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Abstract
One approach to understanding the genetic basis of speciation is to scan the genomes of recently diverged taxa to identify highly differentiated regions. The house mouse, Mus musculus, provides a useful system for the study of speciation. Three subspecies (M. m. castaneus, M. m. domesticus, and M. m. musculus) diverged ∼350 KYA, are distributed parapatrically, show varying degrees of reproductive isolation in laboratory crosses, and hybridize in nature. We sequenced the testes transcriptomes of multiple wild-derived inbred lines from each subspecies to identify highly differentiated regions of the genome, to identify genes showing high expression divergence, and to compare patterns of differentiation among subspecies that have different demographic histories and exhibit different levels of reproductive isolation. Using a sliding-window approach, we found many genomic regions with high levels of sequence differentiation in each of the pairwise comparisons among subspecies. In all comparisons, the X chromosome was more highly differentiated than the autosomes. Sequence differentiation and expression divergence were greater in the M. m. domesticus-M. m. musculus comparison than in either pairwise comparison with M. m. castaneus, which is consistent with laboratory crosses that show the greatest reproductive isolation between M. m. domesticus and M. m. musculus. Coalescent simulations suggest that differences in estimates of effective population size can account for many of the observed patterns. However, there was an excess of highly differentiated regions relative to simulated distributions under a wide range of demographic scenarios. Overlap of some highly differentiated regions with previous results from QTL mapping and hybrid zone studies points to promising candidate regions for reproductive isolation.
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Buard J, Rivals E, Dunoyer de Segonzac D, Garres C, Caminade P, de Massy B, Boursot P. Diversity of Prdm9 zinc finger array in wild mice unravels new facets of the evolutionary turnover of this coding minisatellite. PLoS One 2014; 9:e85021. [PMID: 24454780 PMCID: PMC3890296 DOI: 10.1371/journal.pone.0085021] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Accepted: 11/20/2013] [Indexed: 12/23/2022] Open
Abstract
In humans and mice, meiotic recombination events cluster into narrow hotspots whose genomic positions are defined by the PRDM9 protein via its DNA binding domain constituted of an array of zinc fingers (ZnFs). High polymorphism and rapid divergence of the Prdm9 gene ZnF domain appear to involve positive selection at DNA-recognition amino-acid positions, but the nature of the underlying evolutionary pressures remains a puzzle. Here we explore the variability of the Prdm9 ZnF array in wild mice, and uncovered a high allelic diversity of both ZnF copy number and identity with the caracterization of 113 alleles. We analyze features of the diversity of ZnF identity which is mostly due to non-synonymous changes at codons -1, 3 and 6 of each ZnF, corresponding to amino-acids involved in DNA binding. Using methods adapted to the minisatellite structure of the ZnF array, we infer a phylogenetic tree of these alleles. We find the sister species Mus spicilegus and M. macedonicus as well as the three house mouse (Mus musculus) subspecies to be polyphyletic. However some sublineages have expanded independently in Mus musculus musculus and M. m. domesticus, the latter further showing phylogeographic substructure. Compared to random genomic regions and non-coding minisatellites, none of these patterns appears exceptional. In silico prediction of DNA binding sites for each allele, overlap of their alignments to the genome and relative coverage of the different families of interspersed repeated elements suggest a large diversity between PRDM9 variants with a potential for highly divergent distributions of recombination events in the genome with little correlation to evolutionary distance. By compiling PRDM9 ZnF protein sequences in Primates, Muridae and Equids, we find different diversity patterns among the three amino-acids most critical for the DNA-recognition function, suggesting different diversification timescales.
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Affiliation(s)
- Jérôme Buard
- Institute of Human Genetics, UPR 1142, Centre National de la Recherche Scientifique, Montpellier, France
| | - Eric Rivals
- Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier, UMR 5506, Université Montpellier 2, Centre National de la Recherche Scientifique, Montpellier, France
- Institut de Biologie Computationnelle, Montpellier, France
| | - Denis Dunoyer de Segonzac
- Institute of Human Genetics, UPR 1142, Centre National de la Recherche Scientifique, Montpellier, France
- Institut des Sciences de l'Evolution Montpellier, Université Montpellier 2, Centre National de la Recherche Scientifique, Institut de Recherche pour le Développement, Montpellier, France
| | - Charlotte Garres
- Institute of Human Genetics, UPR 1142, Centre National de la Recherche Scientifique, Montpellier, France
- Institut des Sciences de l'Evolution Montpellier, Université Montpellier 2, Centre National de la Recherche Scientifique, Institut de Recherche pour le Développement, Montpellier, France
| | - Pierre Caminade
- Institut des Sciences de l'Evolution Montpellier, Université Montpellier 2, Centre National de la Recherche Scientifique, Institut de Recherche pour le Développement, Montpellier, France
| | - Bernard de Massy
- Institute of Human Genetics, UPR 1142, Centre National de la Recherche Scientifique, Montpellier, France
| | - Pierre Boursot
- Institut des Sciences de l'Evolution Montpellier, Université Montpellier 2, Centre National de la Recherche Scientifique, Institut de Recherche pour le Développement, Montpellier, France
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Potter KM, Hipkins VD, Mahalovich MF, Means RE. Mitochondrial DNA haplotype distribution patterns in Pinus ponderosa (Pinaceae): range-wide evolutionary history and implications for conservation. AMERICAN JOURNAL OF BOTANY 2013; 100:1562-1579. [PMID: 23876453 DOI: 10.3732/ajb.1300039] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
PREMISE OF THE STUDY Ponderosa pine (Pinus ponderosa Douglas ex P. Lawson & C. Lawson) exhibits complicated patterns of morphological and genetic variation across its range in western North America. This study aims to clarify P. ponderosa evolutionary history and phylogeography using a highly polymorphic mitochondrial DNA marker, with results offering insights into how geographical and climatological processes drove the modern evolutionary structure of tree species in the region. METHODS We amplified the mtDNA nad1 second intron minisatellite region for 3,100 trees representing 104 populations, and sequenced all length variants. We estimated population-level haplotypic diversity and determined diversity partitioning among varieties, races and populations. After aligning sequences of minisatellite repeat motifs, we evaluated evolutionary relationships among haplotypes. KEY RESULTS The geographical structuring of the 10 haplotypes corresponded with division between Pacific and Rocky Mountain varieties. Pacific haplotypes clustered with high bootstrap support, and appear to have descended from Rocky Mountain haplotypes. A greater proportion of diversity was partitioned between Rocky Mountain races than between Pacific races. Areas of highest haplotypic diversity were the southern Sierra Nevada mountain range in California, northwestern California, and southern Nevada. CONCLUSIONS Pinus ponderosa haplotype distribution patterns suggest a complex phylogeographic history not revealed by other genetic and morphological data, or by the sparse paleoecological record. The results appear consistent with long-term divergence between the Pacific and Rocky Mountain varieties, along with more recent divergences not well-associated with race. Pleistocene refugia may have existed in areas of high haplotypic diversity, as well as the Great Basin, Southwestern United States/northern Mexico, and the High Plains.
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Affiliation(s)
- Kevin M Potter
- Department of Forestry and Environmental Resources, North Carolina State University, Research Triangle Park, North Carolina 27709, USA.
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17
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Staubach F, Lorenc A, Messer PW, Tang K, Petrov DA, Tautz D. Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (Mus musculus). PLoS Genet 2012; 8:e1002891. [PMID: 22956910 PMCID: PMC3431316 DOI: 10.1371/journal.pgen.1002891] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Accepted: 06/11/2012] [Indexed: 11/19/2022] Open
Abstract
General parameters of selection, such as the frequency and strength of positive selection in natural populations or the role of introgression, are still insufficiently understood. The house mouse (Mus musculus) is a particularly well-suited model system to approach such questions, since it has a defined history of splits into subspecies and populations and since extensive genome information is available. We have used high-density single-nucleotide polymorphism (SNP) typing arrays to assess genomic patterns of positive selection and introgression of alleles in two natural populations of each of the subspecies M. m. domesticus and M. m. musculus. Applying different statistical procedures, we find a large number of regions subject to apparent selective sweeps, indicating frequent positive selection on rare alleles or novel mutations. Genes in the regions include well-studied imprinted loci (e.g. Plagl1/Zac1), homologues of human genes involved in adaptations (e.g. alpha-amylase genes) or in genetic diseases (e.g. Huntingtin and Parkin). Haplotype matching between the two subspecies reveals a large number of haplotypes that show patterns of introgression from specific populations of the respective other subspecies, with at least 10% of the genome being affected by partial or full introgression. Using neutral simulations for comparison, we find that the size and the fraction of introgressed haplotypes are not compatible with a pure migration or incomplete lineage sorting model. Hence, it appears that introgressed haplotypes can rise in frequency due to positive selection and thus can contribute to the adaptive genomic landscape of natural populations. Our data support the notion that natural genomes are subject to complex adaptive processes, including the introgression of haplotypes from other differentiated populations or species at a larger scale than previously assumed for animals. This implies that some of the admixture found in inbred strains of mice may also have a natural origin.
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Affiliation(s)
- Fabian Staubach
- Max Planck Institute for Evolutionary Biology, Plön, Germany
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18
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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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19
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SIAHSARVIE ROOHOLLAH, AUFFRAY JEANCHRISTOPHE, DARVISH JAMSHID, RAJABI-MAHAM HASSAN, YU HONTSEN, AGRET SYLVIE, BONHOMME FRANÇOIS, CLAUDE JULIEN. Patterns of morphological evolution in the mandible of the house mouse Mus musculus (Rodentia: Muridae). Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2011.01821.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Britton-Davidian J, Cazaux B, Catalan J. Chromosomal dynamics of nucleolar organizer regions (NORs) in the house mouse: micro-evolutionary insights. Heredity (Edinb) 2011; 108:68-74. [PMID: 22086078 DOI: 10.1038/hdy.2011.105] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Variation in the number and chromosomal location of nucleolar organizer regions (NORs) was studied in the house mouse, Mus musculus (2n=40). From an origin in Western Asia, this species colonized the Middle East, Europe and Asia. This expansion was accompanied by diversification into five subspecies. NOR diversity was revealed by fluorescence in situ hybridization using 18S and 28S probes on specimens spanning Asia to Western Europe. The results showed that the house mouse genome possessed a large number of NOR-bearing autosomes and a surprisingly high rate of polymorphism for the presence/absence of rRNA genes on all these chromosomes. All NOR sites were adjacent to the centromere except for two that were telomeric. Subspecific differentiation established from the NOR frequency data was concordant with the overall pattern of radiation proposed from molecular studies, but highlighted several discrepancies that need to be further addressed. NOR diversity in M. musculus consisted of a large number of polymorphic NORs that were common to at least two subspecies, and a smaller number of NORs that were unique to one subspecies. The most parsimonious scenario argues in favor of a subspecific differentiation by lineage sorting of ancestral NOR polymorphisms; only the unique NORs would have appeared by inter-chromosomal transposition, except for the two telomeric ones that may have originated by hybridization with another species. Such a scenario provides an alternative view from the one prevailing in most systematic and phylogenetic analyses that NORs have a high transposition rate due to concerted evolution of rRNA genes.
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Affiliation(s)
- J Britton-Davidian
- Institut des Sciences de l'Evolution, Université Montpellier 2, Montpellier cedex, France.
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Duvaux L, Belkhir K, Boulesteix M, Boursot P. Isolation and gene flow: inferring the speciation history of European house mice. Mol Ecol 2011; 20:5248-64. [PMID: 22066696 DOI: 10.1111/j.1365-294x.2011.05343.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Inferring the history of isolation and gene flow during species differentiation can inform us on the processes underlying their formation. Following their recent expansion in Europe, two subspecies of the house mouse (Mus musculus domesticus and Mus musculus musculus) have formed a hybrid zone maintained by hybrid incompatibilities and possibly behavioural reinforcement, offering a good model of incipient speciation. We reconstruct the history of their divergence using an approximate Bayesian computation framework and sequence variation at 57 autosomal loci. We find support for a long isolation period preceding the advent of gene flow around 200,000 generations ago, much before the formation of the European hybrid zone a few thousand years ago. The duration of the allopatric episode appears long enough (74% of divergence time) to explain the accumulation of many post-zygotic incompatibilities expressed in the present hybrid zone. The ancient contact inferred could have played a role in mating behaviour divergence and laid the ground for further reinforcement. We suggest that both subspecies originally colonized the Middle East from the northern Indian subcontinent, domesticus settling on the shores of the Persian Gulf and musculus on those of the Caspian Sea. Range expansions during interglacials would have induced secondary contacts, presumably in Iran, where they must have also interacted with Mus musculus castaneus. Future studies should incorporate this possibility, and we point to Iran and its surroundings as a hot spot for house mouse diversity and speciation studies.
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Affiliation(s)
- Ludovic Duvaux
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l'Evolution, CC063, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France.
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Yalcin B, Nicod J, Bhomra A, Davidson S, Cleak J, Farinelli L, Østerås M, Whitley A, Yuan W, Gan X, Goodson M, Klenerman P, Satpathy A, Mathis D, Benoist C, Adams DJ, Mott R, Flint J. Commercially available outbred mice for genome-wide association studies. PLoS Genet 2010; 6:e1001085. [PMID: 20838427 PMCID: PMC2932682 DOI: 10.1371/journal.pgen.1001085] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 07/23/2010] [Indexed: 12/02/2022] Open
Abstract
Genome-wide association studies using commercially available outbred mice can detect genes involved in phenotypes of biomedical interest. Useful populations need high-frequency alleles to ensure high power to detect quantitative trait loci (QTLs), low linkage disequilibrium between markers to obtain accurate mapping resolution, and an absence of population structure to prevent false positive associations. We surveyed 66 colonies for inbreeding, genetic diversity, and linkage disequilibrium, and we demonstrate that some have haplotype blocks of less than 100 Kb, enabling gene-level mapping resolution. The same alleles contribute to variation in different colonies, so that when mapping progress stalls in one, another can be used in its stead. Colonies are genetically diverse: 45% of the total genetic variation is attributable to differences between colonies. However, quantitative differences in allele frequencies, rather than the existence of private alleles, are responsible for these population differences. The colonies derive from a limited pool of ancestral haplotypes resembling those found in inbred strains: over 95% of sequence variants segregating in outbred populations are found in inbred strains. Consequently it is possible to impute the sequence of any mouse from a dense SNP map combined with inbred strain sequence data, which opens up the possibility of cataloguing and testing all variants for association, a situation that has so far eluded studies in completely outbred populations. We demonstrate the colonies' potential by identifying a deletion in the promoter of H2-Ea as the molecular change that strongly contributes to setting the ratio of CD4+ and CD8+ lymphocytes.
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Affiliation(s)
- Binnaz Yalcin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Jérôme Nicod
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Amarjit Bhomra
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Stuart Davidson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - James Cleak
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | | | - Adam Whitley
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Wei Yuan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Xiangchao Gan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Martin Goodson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ansu Satpathy
- Section on Immunology and Immunogenetics, Joslin Diabetes Center and Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Diane Mathis
- Section on Immunology and Immunogenetics, Joslin Diabetes Center and Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Christophe Benoist
- Section on Immunology and Immunogenetics, Joslin Diabetes Center and Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - David J. Adams
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Richard Mott
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Jonathan Flint
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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Abouelhoda M, El-Kalioby M, Giegerich R. WAMI: a web server for the analysis of minisatellite maps. BMC Evol Biol 2010; 10:167. [PMID: 20525398 PMCID: PMC2897807 DOI: 10.1186/1471-2148-10-167] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2009] [Accepted: 06/06/2010] [Indexed: 11/10/2022] Open
Abstract
Background Minisatellites are genomic loci composed of tandem arrays of short repetitive DNA segments. A minisatellite map is a sequence of symbols that represents the tandem repeat array such that the set of symbols is in one-to-one correspondence with the set of distinct repeats. Due to variations in repeat type and organization as well as copy number, the minisatellite maps have been widely used in forensic and population studies. In either domain, researchers need to compare the set of maps to each other, to build phylogenetic trees, to spot structural variations, and to study duplication dynamics. Efficient algorithms for these tasks are required to carry them out reliably and in reasonable time. Results In this paper we present WAMI, a web-server for the analysis of minisatellite maps. It performs the above mentioned computational tasks using efficient algorithms that take the model of map evolution into account. The WAMI interface is easy to use and the results of each analysis task are visualized. Conclusions To the best of our knowledge, WAMI is the first server providing all these computational facilities to the minisatellite community. The WAMI web-interface and the source code of the underlying programs are available at http://www.nubios.nileu.edu.eg/tools/wami.
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25
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Nunome M, Ishimori C, Aplin KP, Tsuchiya K, Yonekawa H, Moriwaki K, Suzuki H. Detection of recombinant haplotypes in wild mice (Mus musculus) provides new insights into the origin of Japanese mice. Mol Ecol 2010; 19:2474-89. [PMID: 20465587 DOI: 10.1111/j.1365-294x.2010.04651.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Japanese house mice (Mus musculus molossinus) are thought to be a hybrid lineage derived from two prehistoric immigrants, the subspecies M. m. musculus of northern Eurasia and M. m. castaneus of South Asia. Mice of the western European subspecies M. m. domesticus have been detected in Japanese ports and airports only. We examined haplotype structuring of a 200 kb stretch on chromosome 8 for 59 mice from throughout Eurasia, determining short segments (approximately 370-600 bp) of eight nuclear genes (Fanca, Spire2, Tcf25, Mc1r, Tubb3, Def8, Afg3l1 and Dbndd1) which are intermittently arranged in this order. Where possible we identified the subspecies origin for individual gene alleles and then designated haplotypes for concatenated alleles. We recovered 11 haplotypes among 19 Japanese mice examined, identified either as 'intact' haplotypes derived from the subspecies musculus (57.9%), domesticus (7.9%), and castaneus (2.6%), or as 'recombinant' haplotypes (31.6%). We also detected recombinant haplotypes unique to Sakhalin. The complex nature of the recombinant haplotypes suggests ancient introduction of all three subspecies components into the peripheral part of Eurasia or complicated genomic admixture before the movement from source areas. 'Intact'domesticus and castaneus haplotypes in other Japanese wild mice imply ongoing stowaway introductions. The method has general utility for assessing the history of genetic admixture and for disclosing ongoing genetic contamination.
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Affiliation(s)
- Mitsuo Nunome
- Laboratory of Ecology and Genetics, Graduate School of Environmental Earth Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
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Mayer C, Leese F, Tollrian R. Genome-wide analysis of tandem repeats in Daphnia pulex--a comparative approach. BMC Genomics 2010; 11:277. [PMID: 20433735 PMCID: PMC3152781 DOI: 10.1186/1471-2164-11-277] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Accepted: 04/30/2010] [Indexed: 11/10/2022] Open
Abstract
Background DNA tandem repeats (TRs) are not just popular molecular markers, but are also important genomic elements from an evolutionary and functional perspective. For various genomes, the densities of short TR types were shown to differ strongly among different taxa and genomic regions. In this study we analysed the TR characteristics in the genomes of Daphnia pulex and 11 other eukaryotic species. Characteristics of TRs in different genomic regions and among different strands are compared in details for D. pulex and the two model insects Apis mellifera and Drosophila melanogaster. Results Profound differences in TR characteristics were found among all 12 genomes compared in this study. In D. pulex, the genomic density of TRs was low compared to the arthropod species D. melanogaster and A. mellifera. For these three species, very few common features in repeat type usage, density distribution, and length characteristics were observed in the genomes and in different genomic regions. In introns and coding regions an unexpectedly high strandedness was observed for several repeat motifs. In D. pulex, the density of TRs was highest in introns, a rare feature in animals. In coding regions, the density of TRs with unit sizes 7-50 bp were more than three times as high as for 1-6 bp repeats. Conclusions TRs in the genome of D. pulex show several notable features, which distinguish it from the other genomes. Altogether, the highly non-random distribution of TRs among genomes, genomic regions and even among different DNA-stands raises many questions concerning their functional and evolutionary importance. The high density of TRs with a unit size longer than 6 bp found in non-coding and coding regions underpins the importance to include longer TR units in comparative analyses.
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Affiliation(s)
- Christoph Mayer
- Department of Animal Ecology, Evolution and Biodiversity, Ruhr University Bochum, Bochum, Germany.
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Halligan DL, Oliver F, Eyre-Walker A, Harr B, Keightley PD. Evidence for pervasive adaptive protein evolution in wild mice. PLoS Genet 2010; 6:e1000825. [PMID: 20107605 PMCID: PMC2809770 DOI: 10.1371/journal.pgen.1000825] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Accepted: 12/21/2009] [Indexed: 11/18/2022] Open
Abstract
The relative contributions of neutral and adaptive substitutions to molecular evolution has been one of the most controversial issues in evolutionary biology for more than 40 years. The analysis of within-species nucleotide polymorphism and between-species divergence data supports a widespread role for adaptive protein evolution in certain taxa. For example, estimates of the proportion of adaptive amino acid substitutions (alpha) are 50% or more in enteric bacteria and Drosophila. In contrast, recent estimates of alpha for hominids have been at most 13%. Here, we estimate alpha for protein sequences of murid rodents based on nucleotide polymorphism data from multiple genes in a population of the house mouse subspecies Mus musculus castaneus, which inhabits the ancestral range of the Mus species complex and nucleotide divergence between M. m. castaneus and M. famulus or the rat. We estimate that 57% of amino acid substitutions in murids have been driven by positive selection. Hominids, therefore, are exceptional in having low apparent levels of adaptive protein evolution. The high frequency of adaptive amino acid substitutions in wild mice is consistent with their large effective population size, leading to effective natural selection at the molecular level. Effective natural selection also manifests itself as a paucity of effectively neutral nonsynonymous mutations in M. m. castaneus compared to humans.
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Affiliation(s)
- Daniel L. Halligan
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Fiona Oliver
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Adam Eyre-Walker
- Centre for the Study of Evolution and School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Bettina Harr
- Max-Planck-Institute for Evolutionary Biology, Plön, Germany
| | - Peter D. Keightley
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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Adaptive evolution of interferon-gamma in Glire lineage and evidence for a recent selective sweep in Mus. m. domesticus. Genes Immun 2009; 10:297-308. [PMID: 19387460 DOI: 10.1038/gene.2009.22] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Interferon-gamma plays a key role in the immune response against intracellular pathogens. Its gene is located inside a cluster of cytokines from the interleukin-10 family. A comparison of the coding sequences in the mammalian Glire lineage indicates a possible action of positive Darwinian selection promoting rapid amino-acid changes in the branch leading to murine rodents represented by Mus and Rattus. Looking at genomic diversity of this gene inside the genus Mus, we could propose that a recent selective sweep has affected M. m. domesticus, this subspecies harbouring predominantly a single Ifng haplotype that differs from that of the other subspecies by a unique amino-acid difference in a key position of the molecule. The sweep seems to have affected a region of at most 50 kb as recombinants could be found at flanking conserved non-coding sequences. Functional differences were clearly apparent in cis-regulation of Ifng transcription between the domesticus and the musculus-type haplotypes. As the presence of the musculus haplotype in a predominantly domesticus background seems to promote susceptibility to chronic infection by Theiler's virus, these findings open interesting avenues for documenting immune system gene co-evolution.
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Johnsen JM, Teschke M, Pavlidis P, McGee BM, Tautz D, Ginsburg D, Baines JF. Selection on cis-regulatory variation at B4galnt2 and its influence on von Willebrand factor in house mice. Mol Biol Evol 2008; 26:567-78. [PMID: 19088380 PMCID: PMC2727395 DOI: 10.1093/molbev/msn284] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The RIIIS/J inbred mouse strain is a model for type 1 von Willebrand disease (VWD), a common human bleeding disorder. Low von Willebrand factor (VWF) levels in RIIIS/J are due to a regulatory mutation, Mvwf1, which directs a tissue-specific switch in expression of a glycosyltransferase, B4GALNT2, from intestine to blood vessel. We recently found that Mvwf1 lies on a founder allele common among laboratory mouse strains. To investigate the evolutionary forces operating at B4galnt2, we conducted a survey of DNA sequence polymorphism and microsatellite variation spanning the B4galnt2 gene region in natural Mus musculus domesticus populations. Two divergent haplotypes segregate in these natural populations, one of which corresponds to the RIIIS/J sequence. Different local populations display dramatic differences in the frequency of these haplotypes, and reduced microsatellite variability near B4galnt2 within the RIIIS/J haplotype is consistent with the recent action of natural selection. The level and pattern of DNA sequence polymorphism in the 5′ flanking region of the gene significantly deviates from the neutral expectation and suggests that variation in B4galnt2 expression may be under balancing selection and/or arose from a recently introgressed allele that subsequently increased in frequency due to natural selection. However, coalescent simulations indicate that the heterogeneity in divergence between haplotypes is greater than expected under an introgression model. Analysis of a population where the RIIIS/J haplotype is in high frequency reveals an association between this haplotype, the B4galnt2 tissue-specific switch, and a significant decrease in plasma VWF levels. Given these observations, we propose that low VWF levels may represent a fitness cost that is offset by a yet unknown benefit of the B4galnt2 tissue-specific switch. Similar mechanisms may account for the variability in VWF levels and high prevalence of VWD in other mammals, including humans.
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Affiliation(s)
- Jill M Johnsen
- Department of Internal Medicine, University of Michigan, USA
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Ferguson W, Dvora S, Gallo J, Orth A, Boissinot S. Long-term balancing selection at the west nile virus resistance gene, Oas1b, maintains transspecific polymorphisms in the house mouse. Mol Biol Evol 2008; 25:1609-18. [PMID: 18460447 DOI: 10.1093/molbev/msn106] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Oligoadenylate synthetases (OASs) are interferon-inducible enzymes that participate in the first line of defense against a wide range of viral infection. Recent studies have determined that Oas1b, a member of the OAS gene family in the house mouse (Mus musculus), provides specific protection against flavivirus infection (e.g., West Nile virus, dengue fever virus, and yellow fever virus). We characterized the nucleotide sequence variation in coding and noncoding regions of the Oas1b gene for a large number of wild-derived strains of M. musculus and related species. Our sequence analyses determined that this gene is one of the most polymorphic genes ever described in any mammal. The level of variation in noncoding regions of Oas1b is an order of magnitude higher than the level reported for other regions of the mouse genome and is significantly different from the level of intraspecific variation expected under neutrality. Furthermore, a phylogenetic analysis of intronic sequences demonstrated that Oas1b alleles are ancient and that their divergence predates several speciation events, resulting in transspecific polymorphisms. The amino acid sequence of Oas1b is also extremely variable, with 1 out of 7 amino acid positions being polymorphic within M. musculus. Oas1b alleles are comparatively more divergent at synonymous positions than most autosomal genes and the ratio of nonsynonymous to synonymous substitution is remarkably high, suggesting that positive selection has been acting on Oas1b. The ancestry of Oas1b polymorphisms and the high level of amino acid polymorphisms strongly suggest that the allelic variation at Oas1b has been maintained in mouse populations by long-term balancing selection.
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Affiliation(s)
- William Ferguson
- Department of Biology, Queens College, The City University of New York, USA
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RAJABI-MAHAM HASSAN, ORTH ANNIE, BONHOMME FRANÇOIS. Phylogeography and postglacial expansion of Mus musculus domesticus inferred from mitochondrial DNA coalescent, from Iran to Europe. Mol Ecol 2007; 17:627-41. [DOI: 10.1111/j.1365-294x.2007.03601.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Yang H, Bell TA, Churchill GA, Pardo-Manuel de Villena F. On the subspecific origin of the laboratory mouse. Nat Genet 2007; 39:1100-7. [PMID: 17660819 DOI: 10.1038/ng2087] [Citation(s) in RCA: 243] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2007] [Accepted: 05/31/2007] [Indexed: 01/20/2023]
Abstract
The genome of the laboratory mouse is thought to be a mosaic of regions with distinct subspecific origins. We have developed a high-resolution map of the origin of the laboratory mouse by generating 25,400 phylogenetic trees at 100-kb intervals spanning the genome. On average, 92% of the genome is of Mus musculus domesticus origin, and the distribution of diversity is markedly nonrandom among the chromosomes. There are large regions of extremely low diversity, which represent blind spots for studies of natural variation and complex traits, and hot spots of diversity. In contrast with the mosaic model, we found that most of the genome has intermediate levels of variation of intrasubspecific origin. Finally, mouse strains derived from the wild that are supposed to represent different mouse subspecies show substantial intersubspecific introgression, which has strong implications for evolutionary studies that assume these are pure representatives of a given subspecies.
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Affiliation(s)
- Hyuna Yang
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
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