1
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Dumont BL, Gatti DM, Ballinger MA, Lin D, Phifer-Rixey M, Sheehan MJ, Suzuki TA, Wooldridge LK, Frempong HO, Lawal RA, Churchill GA, Lutz C, Rosenthal N, White JK, Nachman MW. Into the Wild: A novel wild-derived inbred strain resource expands the genomic and phenotypic diversity of laboratory mouse models. PLoS Genet 2024; 20:e1011228. [PMID: 38598567 PMCID: PMC11034653 DOI: 10.1371/journal.pgen.1011228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/22/2024] [Accepted: 03/18/2024] [Indexed: 04/12/2024] Open
Abstract
The laboratory mouse has served as the premier animal model system for both basic and preclinical investigations for over a century. However, laboratory mice capture only a subset of the genetic variation found in wild mouse populations, ultimately limiting the potential of classical inbred strains to uncover phenotype-associated variants and pathways. Wild mouse populations are reservoirs of genetic diversity that could facilitate the discovery of new functional and disease-associated alleles, but the scarcity of commercially available, well-characterized wild mouse strains limits their broader adoption in biomedical research. To overcome this barrier, we have recently developed, sequenced, and phenotyped a set of 11 inbred strains derived from wild-caught Mus musculus domesticus. Each of these "Nachman strains" immortalizes a unique wild haplotype sampled from one of five environmentally distinct locations across North and South America. Whole genome sequence analysis reveals that each strain carries between 4.73-6.54 million single nucleotide differences relative to the GRCm39 mouse reference, with 42.5% of variants in the Nachman strain genomes absent from current classical inbred mouse strain panels. We phenotyped the Nachman strains on a customized pipeline to assess the scope of disease-relevant neurobehavioral, biochemical, physiological, metabolic, and morphological trait variation. The Nachman strains exhibit significant inter-strain variation in >90% of 1119 surveyed traits and expand the range of phenotypic diversity captured in classical inbred strain panels. These novel wild-derived inbred mouse strain resources are set to empower new discoveries in both basic and preclinical research.
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Affiliation(s)
- Beth L. Dumont
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, Maine, United States of America
| | - Daniel M. Gatti
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Mallory A. Ballinger
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
| | - Dana Lin
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Megan Phifer-Rixey
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Michael J. Sheehan
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, United States of America
| | - Taichi A. Suzuki
- College of Health Solutions and Biodesign Center for Health Through Microbiomes, Arizona State University, Tempe, Arizona, United States of America
| | - Lydia K. Wooldridge
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Hilda Opoku Frempong
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
- Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, Maine, United States of America
| | - Raman Akinyanju Lawal
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Gary A. Churchill
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, Maine, United States of America
| | - Cathleen Lutz
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Nadia Rosenthal
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, Maine, United States of America
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Jacqueline K. White
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Michael W. Nachman
- Department of Integrative Biology, Museum of Vertebrate Zoology, and Center for Computational Biology, University of California, Berkeley, Berkeley, California, United States of America
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2
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AbuAlia KFN, Damm E, Ullrich KK, Mukaj A, Parvanov E, Forejt J, Odenthal-Hesse L. Natural variation in the zinc-finger-encoding exon of Prdm9 affects hybrid sterility phenotypes in mice. Genetics 2024; 226:iyae004. [PMID: 38217871 PMCID: PMC10917509 DOI: 10.1093/genetics/iyae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/15/2024] Open
Abstract
PRDM9-mediated reproductive isolation was first described in the progeny of Mus musculus musculus (MUS) PWD/Ph and Mus musculus domesticus (DOM) C57BL/6J inbred strains. These male F1 hybrids fail to complete chromosome synapsis and arrest meiosis at prophase I, due to incompatibilities between the Prdm9 gene and hybrid sterility locus Hstx2. We identified 14 alleles of Prdm9 in exon 12, encoding the DNA-binding domain of the PRDM9 protein in outcrossed wild mouse populations from Europe, Asia, and the Middle East, 8 of which are novel. The same allele was found in all mice bearing introgressed t-haplotypes encompassing Prdm9. We asked whether 7 novel Prdm9 alleles in MUS populations and the t-haplotype allele in 1 MUS and 3 DOM populations induce Prdm9-mediated reproductive isolation. The results show that only combinations of the dom2 allele of DOM origin and the MUS msc1 allele ensure complete infertility of intersubspecific hybrids in outcrossed wild populations and inbred mouse strains examined so far. The results further indicate that MUS mice may share the erasure of PRDM9msc1 binding motifs in populations with different Prdm9 alleles, which implies that erased PRDM9 binding motifs may be uncoupled from their corresponding Prdm9 alleles at the population level. Our data corroborate the model of Prdm9-mediated hybrid sterility beyond inbred strains of mice and suggest that sterility alleles of Prdm9 may be rare.
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Affiliation(s)
- Khawla F N AbuAlia
- Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, Plön D-24306, Germany
| | - Elena Damm
- Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, Plön D-24306, Germany
| | - Kristian K Ullrich
- Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, Plön D-24306, Germany
| | - Amisa Mukaj
- Laboratory of Mouse Molecular Genetics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
| | - Emil Parvanov
- Laboratory of Mouse Molecular Genetics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
- Department of Translational Stem Cell Biology, Research Institute of the Medical University of Varna, 9002 Varna, Bulgaria
- Ludwig Boltzmann Institute for Digital Health and Patient Safety, Medical University of Vienna, 1090 Vienna, Austria
| | - Jiri Forejt
- Laboratory of Mouse Molecular Genetics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
| | - Linda Odenthal-Hesse
- Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, Plön D-24306, Germany
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3
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Szabo N, Cutter AD. Experimental evolution of hybrid populations to identify Dobzhansky-Muller incompatibility loci. Ecol Evol 2024; 14:e10972. [PMID: 38333096 PMCID: PMC10851027 DOI: 10.1002/ece3.10972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/04/2023] [Accepted: 12/10/2023] [Indexed: 02/10/2024] Open
Abstract
Epistatic interactions between loci that reduce fitness in interspecies hybrids, Dobzhansky-Muller incompatibilities (DMIs), contribute genetically to the inviability and infertility within hybrid populations. It remains a challenge, however, to identify the loci that contribute to DMIs as causes of reproductive isolation between species. Here, we assess through forward simulation the power of evolve-and-resequence (E&R) experimental evolution of hybrid populations to map DMI loci. We document conditions under which such a mapping strategy may be most feasible and demonstrate how mapping power is sensitive to biologically relevant parameters such as one-way versus two-way incompatibility type, selection strength, recombination rate, and dominance interactions. We also assess the influence of parameters under direct control of an experimenter, including duration of experimental evolution and number of replicate populations. We conclude that an E&R strategy for mapping DMI loci, and other cases of epistasis, can be a viable option under some circumstances for study systems with short generation times like Caenorhabditis nematodes.
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Affiliation(s)
- Nicole Szabo
- Department of Ecology & Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
| | - Asher D. Cutter
- Department of Ecology & Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
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4
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Jensen A, Swift F, de Vries D, Beck RMD, Kuderna LFK, Knauf S, Chuma IS, Keyyu JD, Kitchener AC, Farh K, Rogers J, Marques-Bonet T, Detwiler KM, Roos C, Guschanski K. Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation. Mol Biol Evol 2023; 40:msad247. [PMID: 37987553 PMCID: PMC10691879 DOI: 10.1093/molbev/msad247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/17/2023] [Accepted: 11/09/2023] [Indexed: 11/22/2023] Open
Abstract
Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the world's largest primate radiations, we show that rampant gene flow characterizes their evolutionary history and identify ancient hybridization across deeply divergent lineages that differ in ecology, morphology, and karyotypes. Some hybridization events resulted in mitochondrial introgression between distant lineages, likely facilitated by cointrogression of coadapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. In line with reports from other systems that hybridization might facilitate diversification, we find that some of the most species-rich guenon clades are of admixed origin. This study provides important insights into the prevalence, role, and outcomes of ancestral hybridization in a large mammalian radiation.
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Affiliation(s)
- Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala SE-75236, Sweden
| | - Frances Swift
- School of Biological Sciences, Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Lukas F K Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald – Insel Riems 17493, Germany
| | | | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Arusha, Tanzania
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh EH1 1JF, UK
- School of Geosciences, University of Edinburgh, Edinburgh EH8 9XP, UK
| | - Kyle Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona 08003, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, Barcelona 08010, Spain
| | - Kate M Detwiler
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, USA
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen 37077, Germany
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala SE-75236, Sweden
- School of Biological Sciences, Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
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5
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Abstract
The raison d'être of meiosis is shuffling of genetic information via Mendelian segregation and, within individual chromosomes, by DNA crossing-over. These outcomes are enabled by a complex cellular program in which interactions between homologous chromosomes play a central role. We first provide a background regarding the basic principles of this program. We then summarize the current understanding of the DNA events of recombination and of three processes that involve whole chromosomes: homolog pairing, crossover interference, and chiasma maturation. All of these processes are implemented by direct physical interaction of recombination complexes with underlying chromosome structures. Finally, we present convergent lines of evidence that the meiotic program may have evolved by coupling of this interaction to late-stage mitotic chromosome morphogenesis.
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Affiliation(s)
- Denise Zickler
- Institute for Integrative Biology of the Cell (I2BC), Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA;
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6
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Hunnicutt KE, Callahan C, Keeble S, Moore EC, Good JM, Larson EL. Different complex regulatory phenotypes underlie hybrid male sterility in divergent rodent crosses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564782. [PMID: 37961317 PMCID: PMC10634954 DOI: 10.1101/2023.10.30.564782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Hybrid incompatibilities are a critical component of species barriers and may arise due to negative interactions between divergent regulatory elements in parental species. We used a comparative approach to identify common themes in the regulatory phenotypes associated with hybrid male sterility in two divergent rodent crosses, dwarf hamsters and house mice. We investigated three potential characteristic regulatory phenotypes in hybrids including the propensity towards over or underexpression relative to parental species, the influence of developmental stage on the extent of misexpression, and the role of the sex chromosomes on misexpression phenotypes. In contrast to near pervasive overexpression in hybrid house mice, we found that misexpression in hybrid dwarf hamsters was dependent on developmental stage. In both house mouse and dwarf hamster hybrids, however, misexpression increased with the progression of spermatogenesis, although to varying extents and with potentially different consequences. In both systems, we detected sex-chromosome specific overexpression in stages of spermatogenesis where inactivated X chromosome expression was expected, but the hybrid overexpression phenotypes were fundamentally different. Importantly, misexpression phenotypes support the presence of multiple histological blocks to spermatogenesis in dwarf hamster hybrids, including a potential role of meiotic stalling early in spermatogenesis. Collectively, we demonstrate that while there are some similarities in hybrid regulatory phenotypes of house mice and dwarf hamsters, there are also clear differences that point towards unique mechanisms underlying hybrid male sterility in each system. Our results highlight the potential of comparative approaches in helping to understand the importance of disrupted gene regulation in speciation.
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Affiliation(s)
| | - Colin Callahan
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812
| | - Sara Keeble
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812
| | - Emily C. Moore
- University of Denver, Department of Biological Sciences, Denver, CO, 80208
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812
| | - Jeffrey M. Good
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812
| | - Erica L. Larson
- University of Denver, Department of Biological Sciences, Denver, CO, 80208
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7
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Baker Z, Przeworski M, Sella G. Down the Penrose stairs, or how selection for fewer recombination hotspots maintains their existence. eLife 2023; 12:e83769. [PMID: 37830496 DOI: 10.7554/elife.83769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/12/2023] [Indexed: 10/14/2023] Open
Abstract
In many species, meiotic recombination events tend to occur in narrow intervals of the genome, known as hotspots. In humans and mice, double strand break (DSB) hotspot locations are determined by the DNA-binding specificity of the zinc finger array of the PRDM9 protein, which is rapidly evolving at residues in contact with DNA. Previous models explained this rapid evolution in terms of the need to restore PRDM9 binding sites lost to gene conversion over time, under the assumption that more PRDM9 binding always leads to more DSBs. This assumption, however, does not align with current evidence. Recent experimental work indicates that PRDM9 binding on both homologs facilitates DSB repair, and that the absence of sufficient symmetric binding disrupts meiosis. We therefore consider an alternative hypothesis: that rapid PRDM9 evolution is driven by the need to restore symmetric binding because of its role in coupling DSB formation and efficient repair. To this end, we model the evolution of PRDM9 from first principles: from its binding dynamics to the population genetic processes that govern the evolution of the zinc finger array and its binding sites. We show that the loss of a small number of strong binding sites leads to the use of a greater number of weaker ones, resulting in a sharp reduction in symmetric binding and favoring new PRDM9 alleles that restore the use of a smaller set of strong binding sites. This decrease, in turn, drives rapid PRDM9 evolutionary turnover. Our results therefore suggest that the advantage of new PRDM9 alleles is in limiting the number of binding sites used effectively, rather than in increasing net PRDM9 binding. By extension, our model suggests that the evolutionary advantage of hotspots may have been to increase the efficiency of DSB repair and/or homolog pairing.
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Affiliation(s)
- Zachary Baker
- Department of Systems Biology, Columbia University, New York, United States
- Department of Biological Sciences, Columbia University, New York, United States
| | - Molly Przeworski
- Department of Systems Biology, Columbia University, New York, United States
- Department of Biological Sciences, Columbia University, New York, United States
- Program for Mathematical Genomics, Columbia University, New York, United States
| | - Guy Sella
- Department of Biological Sciences, Columbia University, New York, United States
- Program for Mathematical Genomics, Columbia University, New York, United States
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8
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Reifová R, Ament-Velásquez SL, Bourgeois Y, Coughlan J, Kulmuni J, Lipinska AP, Okude G, Stevison L, Yoshida K, Kitano J. Mechanisms of Intrinsic Postzygotic Isolation: From Traditional Genic and Chromosomal Views to Genomic and Epigenetic Perspectives. Cold Spring Harb Perspect Biol 2023; 15:a041607. [PMID: 37696577 PMCID: PMC10547394 DOI: 10.1101/cshperspect.a041607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
Intrinsic postzygotic isolation typically appears as reduced viability or fertility of interspecific hybrids caused by genetic incompatibilities between diverged parental genomes. Dobzhansky-Muller interactions among individual genes, and chromosomal rearrangements causing problems with chromosome synapsis and recombination in meiosis, have both long been considered as major mechanisms behind intrinsic postzygotic isolation. Recent research has, however, suggested that the genetic basis of intrinsic postzygotic isolation can be more complex and involves, for example, overall divergence of the DNA sequence or epigenetic changes. Here, we review the mechanisms of intrinsic postzygotic isolation from genic, chromosomal, genomic, and epigenetic perspectives across diverse taxa. We provide empirical evidence for these mechanisms, discuss their importance in the speciation process, and highlight questions that remain unanswered.
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Affiliation(s)
- Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, 128 00 Prague, Czech Republic
| | | | - Yann Bourgeois
- DIADE, University of Montpellier, CIRAD, IRD, 34090 Montpellier, France
| | - Jenn Coughlan
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
| | - Jonna Kulmuni
- Institute for Biodiversity and Ecosystem Dynamics, Department of Evolutionary and Population Biology, University of Amsterdam, 1012 Amsterdam, The Netherlands
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, 00100 Helsinki, Finland
| | - Agnieszka P Lipinska
- Department of Algal Development and Evolution, Max Planck Institute for Biology, 72076 Tuebingen, Germany
- CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Genta Okude
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Laurie Stevison
- Department of Biological Sciences, Auburn University, Auburn, Alabama 36849, USA
| | - Kohta Yoshida
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Jun Kitano
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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9
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Dumont BL, Gatti D, Ballinger MA, Lin D, Phifer-Rixey M, Sheehan MJ, Suzuki TA, Wooldridge LK, Frempong HO, Churchill G, Lutz C, Rosenthal N, White JK, Nachman MW. Into the Wild: A novel wild-derived inbred strain resource expands the genomic and phenotypic diversity of laboratory mouse models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.21.558738. [PMID: 37790321 PMCID: PMC10542534 DOI: 10.1101/2023.09.21.558738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The laboratory mouse has served as the premier animal model system for both basic and preclinical investigations for a century. However, laboratory mice capture a narrow subset of the genetic variation found in wild mouse populations. This consideration inherently restricts the scope of potential discovery in laboratory models and narrows the pool of potentially identified phenotype-associated variants and pathways. Wild mouse populations are reservoirs of predicted functional and disease-associated alleles, but the sparsity of commercially available, well-characterized wild mouse strains limits their broader adoption in biomedical research. To overcome this barrier, we have recently imported, sequenced, and phenotyped a set of 11 wild-derived inbred strains developed from wild-caught Mus musculus domesticus. Each of these "Nachman strains" immortalizes a unique wild haplotype sampled from five environmentally diverse locations across North and South America: Saratoga Springs, New York, USA; Gainesville, Florida, USA; Manaus, Brazil; Tucson, Arizona, USA; and Edmonton, Alberta, Canada. Whole genome sequence analysis reveals that each strain carries between 4.73-6.54 million single nucleotide differences relative to the mouse reference assembly, with 42.5% of variants in the Nachman strain genomes absent from classical inbred mouse strains. We phenotyped the Nachman strains on a customized pipeline to assess the scope of disease-relevant neurobehavioral, biochemical, physiological, metabolic, and morphological trait variation. The Nachman strains exhibit significant inter-strain variation in >90% of 1119 surveyed traits and expand the range of phenotypic diversity captured in classical inbred strain panels alone. Taken together, our work introduces a novel wild-derived inbred mouse strain resource that will enable new discoveries in basic and preclinical research. These strains are currently available through The Jackson Laboratory Repository under laboratory code NachJ.
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Affiliation(s)
- Beth L Dumont
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
- Tufts University, Graduate School of Biomedical Sciences, 136 Harrison Ave, Boston, MA, 02111, USA
- The University of Maine, Graduate School of Biomedical Science and Engineering, 5775 Stodder Hall, Room 46, Orono, ME, 04469, USA
| | - Daniel Gatti
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Mallory A Ballinger
- Department of Integrative Biology, Center for Computational Biology, and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Dana Lin
- Department of Integrative Biology, Center for Computational Biology, and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Michael J Sheehan
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Taichi A Suzuki
- College of Health Solutions and Biodesign Center for Health Through Microbiomes, Arizona State University, Tempe, AZ, USA 85281
| | | | - Hilda Opoku Frempong
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
- The University of Maine, Graduate School of Biomedical Science and Engineering, 5775 Stodder Hall, Room 46, Orono, ME, 04469, USA
| | - Gary Churchill
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
- Tufts University, Graduate School of Biomedical Sciences, 136 Harrison Ave, Boston, MA, 02111, USA
- The University of Maine, Graduate School of Biomedical Science and Engineering, 5775 Stodder Hall, Room 46, Orono, ME, 04469, USA
| | - Cathleen Lutz
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Nadia Rosenthal
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
- Tufts University, Graduate School of Biomedical Sciences, 136 Harrison Ave, Boston, MA, 02111, USA
- The University of Maine, Graduate School of Biomedical Science and Engineering, 5775 Stodder Hall, Room 46, Orono, ME, 04469, USA
| | | | - Michael W Nachman
- Department of Integrative Biology, Center for Computational Biology, and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
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10
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Kitano J, Yoshida K. Do sex-linked male meiotic drivers contribute to intrinsic hybrid incompatibilities? Recent empirical studies from flies and rodents. Curr Opin Genet Dev 2023; 81:102068. [PMID: 37354886 DOI: 10.1016/j.gde.2023.102068] [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: 03/04/2023] [Revised: 05/29/2023] [Accepted: 05/29/2023] [Indexed: 06/26/2023]
Abstract
Intrinsic hybrid incompatibility is one of the important isolating barriers between species. In organisms with sex chromosomes, intrinsic hybrid incompatibility often follows two rules: Haldane's rule and large-X effects. One explanation for these two rules is that sex chromosomes are hotspots for meiotic drivers that can cause intrinsic hybrid incompatibility between geographically isolated populations. Although this hypothesis seems plausible and several empirical data are consistent with it, we are still unsure whether such mechanisms occur in nature, particularly with respect to speciation with gene flow. Here, we review empirical studies that have investigated the roles of meiotic drive in sex-chromosome evolution and speciation and propose future studies necessary for testing this hypothesis.
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Affiliation(s)
- Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima 1111, Shizuoka 411-8540, Japan.
| | - Kohta Yoshida
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima 1111, Shizuoka 411-8540, Japan; Department for Integrative Evolutionary Biology, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany. https://twitter.com/PristionXY
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11
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Garretson A, Dumont BL, Handel MA. Reproductive genomics of the mouse: implications for human fertility and infertility. Development 2023; 150:dev201313. [PMID: 36779988 PMCID: PMC10836652 DOI: 10.1242/dev.201313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
Genetic analyses of mammalian gametogenesis and fertility have the potential to inform about two important and interrelated clinical areas: infertility and contraception. Here, we address the genetics and genomics underlying gamete formation, productivity and function in the context of reproductive success in mammalian systems, primarily mouse and human. Although much is known about the specific genes and proteins required for meiotic processes and sperm function, we know relatively little about other gametic determinants of overall fertility, such as regulation of gamete numbers, duration of gamete production, and gamete selection and function in fertilization. As fertility is not a binary trait, attention is now appropriately focused on the oligogenic, quantitative aspects of reproduction. Multiparent mouse populations, created by complex crossing strategies, exhibit genetic diversity similar to human populations and will be valuable resources for genetic discovery, helping to overcome current limitations to our knowledge of mammalian reproductive genetics. Finally, we discuss how what we know about the genomics of reproduction can ultimately be brought to the clinic, informing our concepts of human fertility and infertility, and improving assisted reproductive technologies.
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Affiliation(s)
- Alexis Garretson
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Tufts University, Graduate School of Biomedical Sciences, 136 Harrison Ave, Boston, MA 02111, USA
| | - Beth L. Dumont
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Tufts University, Graduate School of Biomedical Sciences, 136 Harrison Ave, Boston, MA 02111, USA
| | - Mary Ann Handel
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Tufts University, Graduate School of Biomedical Sciences, 136 Harrison Ave, Boston, MA 02111, USA
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12
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Chou JY, Hsu PC, Leu JY. Enforcement of Postzygotic Species Boundaries in the Fungal Kingdom. Microbiol Mol Biol Rev 2022; 86:e0009822. [PMID: 36098649 PMCID: PMC9769731 DOI: 10.1128/mmbr.00098-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Understanding the molecular basis of speciation is a primary goal in evolutionary biology. The formation of the postzygotic reproductive isolation that causes hybrid dysfunction, thereby reducing gene flow between diverging populations, is crucial for speciation. Using various advanced approaches, including chromosome replacement, hybrid introgression and transcriptomics, population genomics, and experimental evolution, scientists have revealed multiple mechanisms involved in postzygotic barriers in the fungal kingdom. These results illuminate both unique and general features of fungal speciation. Our review summarizes experiments on fungi exploring how Dobzhansky-Muller incompatibility, killer meiotic drive, chromosome rearrangements, and antirecombination contribute to postzygotic reproductive isolation. We also discuss possible evolutionary forces underlying different reproductive isolation mechanisms and the potential roles of the evolutionary arms race under the Red Queen hypothesis and epigenetic divergence in speciation.
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Affiliation(s)
- Jui-Yu Chou
- Department of Biology, National Changhua University of Education, Changhua, Taiwan
| | - Po-Chen Hsu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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13
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Wooldridge LK, Dumont BL. Rapid Evolution of the Fine-scale Recombination Landscape in Wild House Mouse (Mus musculus) Populations. Mol Biol Evol 2022; 40:6889355. [PMID: 36508360 PMCID: PMC9825251 DOI: 10.1093/molbev/msac267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 11/23/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
Meiotic recombination is an important evolutionary force and an essential meiotic process. In many species, recombination events concentrate into hotspots defined by the site-specific binding of PRMD9. Rapid evolution of Prdm9's zinc finger DNA-binding array leads to remarkably abrupt shifts in the genomic distribution of hotspots between species, but the question of how Prdm9 allelic variation shapes the landscape of recombination between populations remains less well understood. Wild house mice (Mus musculus) harbor exceptional Prdm9 diversity, with >150 alleles identified to date, and pose a particularly powerful system for addressing this open question. We employed a coalescent-based approach to construct broad- and fine-scale sex-averaged recombination maps from contemporary patterns of linkage disequilibrium in nine geographically isolated wild house mouse populations, including multiple populations from each of three subspecies. Comparing maps between wild mouse populations and subspecies reveals several themes. First, we report weak fine- and broad-scale recombination map conservation across subspecies and populations, with genetic divergence offering no clear prediction for recombination map divergence. Second, most hotspots are unique to one population, an outcome consistent with minimal sharing of Prdm9 alleles between surveyed populations. Finally, by contrasting aggregate hotspot activity on the X versus autosomes, we uncover evidence for population-specific differences in the degree and direction of sex dimorphism for recombination. Overall, our findings illuminate the variability of both the broad- and fine-scale recombination landscape in M. musculus and underscore the functional impact of Prdm9 allelic variation in wild mouse populations.
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14
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Kopania EEK, Watson EM, Rathje CC, Skinner BM, Ellis PJI, Larson EL, Good JM. The contribution of sex chromosome conflict to disrupted spermatogenesis in hybrid house mice. Genetics 2022; 222:iyac151. [PMID: 36194004 PMCID: PMC9713461 DOI: 10.1093/genetics/iyac151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/27/2022] [Indexed: 12/13/2022] Open
Abstract
Incompatibilities on the sex chromosomes are important in the evolution of hybrid male sterility, but the evolutionary forces underlying this phenomenon are unclear. House mice (Mus musculus) lineages have provided powerful models for understanding the genetic basis of hybrid male sterility. X chromosome-autosome interactions cause strong incompatibilities in M. musculus F1 hybrids, but variation in sterility phenotypes suggests a more complex genetic basis. In addition, XY chromosome conflict has resulted in rapid expansions of ampliconic genes with dosage-dependent expression that is essential to spermatogenesis. Here, we evaluated the contribution of XY lineage mismatch to male fertility and stage-specific gene expression in hybrid mice. We performed backcrosses between two house mouse subspecies to generate reciprocal Y-introgression strains and used these strains to test the effects of XY mismatch in hybrids. Our transcriptome analyses of sorted spermatid cells revealed widespread overexpression of the X chromosome in sterile F1 hybrids independent of Y chromosome subspecies origin. Thus, postmeiotic overexpression of the X chromosome in sterile F1 mouse hybrids is likely a downstream consequence of disrupted meiotic X-inactivation rather than XY gene copy number imbalance. Y chromosome introgression did result in subfertility phenotypes and disrupted expression of several autosomal genes in mice with an otherwise nonhybrid genomic background, suggesting that Y-linked incompatibilities contribute to reproductive barriers, but likely not as a direct consequence of XY conflict. Collectively, these findings suggest that rapid sex chromosome gene family evolution driven by genomic conflict has not resulted in strong male reproductive barriers between these subspecies of house mice.
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Affiliation(s)
- Emily E K Kopania
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Eleanor M Watson
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - Claudia C Rathje
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | | | - Peter J I Ellis
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Erica L Larson
- Department of Biological Sciences, University of Denver, Denver, CO 80208, USA
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
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15
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Valiskova B, Gregorova S, Lustyk D, Šimeček P, Jansa P, Forejt J. Genic and Chromosomal Components of Prdm9-Driven Hybrid Male Sterility in Mice (Mus musculus). Genetics 2022; 222:6655690. [PMID: 35924978 PMCID: PMC9434306 DOI: 10.1093/genetics/iyac116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 07/27/2022] [Indexed: 11/14/2022] Open
Abstract
Hybrid sterility contributes to speciation by preventing gene flow between related taxa. Prdm9, the first and only hybrid male sterility (HMS) gene known in vertebrates, predetermines the sites of recombination between homologous chromosomes and their synapsis in early meiotic prophase. The asymmetric binding of PRDM9 to heterosubspecific homologs of Mus m. musculus x Mus m. domesticus F1 hybrids and increase of PRDM9-independent DNA double-strand break (DSB) hotspots results in difficult to repair DSBs, incomplete synapsis of homologous chromosomes and meiotic arrest at the first meiotic prophase. Here we show that Prdm9 behaves as a major HMS gene in mice outside the Mus m. musculus x Mus m. domesticus F1 hybrids, in the genomes composed of Mus m. castaneus and Mus m. musculus chromosomes segregating on the Mus m. domesticus background. The Prdm9cst/dom2 (castaneus/domesticus) allelic combination secures meiotic synapsis, testes weight and sperm count within physiological limits, while the Prdm9msc1/dom2 (musculus/domesticus) males show a range of fertility impairment. Out of five quantitative trait loci contributing to the Prdm9msc1/dom2-related infertility, four control either meiotic synapsis or fertility phenotypes and one controls both, synapsis and fertility. Whole-genome genotyping of individual chromosomes showed preferential involvement of nonrecombinant musculus chromosomes in asynapsis in accordance with the chromosomal character of HMS. Moreover, we show that the overall asynapsis rate can be estimated solely from the genotype of individual males by scoring the effect of nonrecombinant musculus chromosomes. Prdm9-controlled HMS represents an example of genetic architecture of HMS consisting of genic and chromosomal components.
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Affiliation(s)
- Barbora Valiskova
- Laboratory of Mouse Molecular Genetics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec 252 50, Czech Republic
| | - Sona Gregorova
- Laboratory of Mouse Molecular Genetics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec 252 50, Czech Republic
| | - Diana Lustyk
- Laboratory of Mouse Molecular Genetics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec 252 50, Czech Republic
| | - Petr Šimeček
- Central Laboratory of Bioinformatics, CEITEC—Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
| | - Petr Jansa
- Laboratory of Mouse Molecular Genetics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec 252 50, Czech Republic
| | - Jiří Forejt
- Corresponding author: Laboratory of Mouse Molecular Genetics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Průmyslová 595, Vestec 25250, Czech Republic.
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16
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Gasic S, Mihola O, Trachtulec Z. Prdm9 deficiency of rat oocytes causes synapsis among non-homologous chromosomes and aneuploidy. Mamm Genome 2022; 33:590-605. [PMID: 35596034 DOI: 10.1007/s00335-022-09954-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/28/2022] [Indexed: 10/18/2022]
Abstract
Aneuploidy (abnormal chromosome number) accompanies reduced ovarian function in humans and mice, but the reasons behind this concomitance remain underexplored. Some variants in the human gene encoding histone-3-lysine-4,36-trimethyltransferase PRDM9 are associated with aneuploidy, and other variants with ovarian function reduced by premature ovarian failure (POF), but no link between POF and aneuploidy has been revealed. SHR/OlaIpcv rat females lacking PRDM9 manifest POF-a reduced follicle number, litter size, and reproductive age. Here, we explored this model to test how POF relates to oocyte euploidy. The mutant rat females displayed increased oocyte aneuploidy and embryonic death of their offspring compared to controls. Because rat PRDM9 positions meiotic DNA breaks, we investigated the repair of these breaks. Fertile control rodents carry pachytene oocytes with synapsed homologous chromosomes and repaired breaks, while sterile Prdm9-deficient mice carry pachytene-like oocytes with many persisting breaks and asynapsed chromosomes. However, most PRDM9-lacking rat oocytes displayed a few persisting breaks and non-homologous synapsis (NHS). HORMAD2 protein serves as a barrier to sister-chromatid repair and a signal for the synapsis and DNA repair checkpoints. NHS but not asynapsis was associated with HORMAD2 levels similar to the levels on rat pachytene chromosomes with homologous synapsis. NHS was accompanied by crossing-over decreased below the minimum that is essential for euploidy. We argue that the increased mutant rat aneuploidy is due to NHS, which allows some oocytes to pass meiotic checkpoints without one crossing-over per chromosomal pair, leading to segregation errors, and thereby NHS links POF to aneuploidy.
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Affiliation(s)
- Srdjan Gasic
- Laboratory of Germ Cell Development, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ondrej Mihola
- Laboratory of Germ Cell Development, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Zdenek Trachtulec
- Laboratory of Germ Cell Development, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.
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17
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Larson EL, Kopania EEK, Hunnicutt KE, Vanderpool D, Keeble S, Good JM. Stage-specific disruption of X chromosome expression during spermatogenesis in sterile house mouse hybrids. G3 (BETHESDA, MD.) 2022; 12:jkab407. [PMID: 34864964 PMCID: PMC9210296 DOI: 10.1093/g3journal/jkab407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/16/2021] [Indexed: 01/09/2023]
Abstract
Hybrid sterility is a complex phenotype that can result from the breakdown of spermatogenesis at multiple developmental stages. Here, we disentangle two proposed hybrid male sterility mechanisms in the house mice, Mus musculus domesticus and M. m. musculus, by comparing patterns of gene expression in sterile F1 hybrids from a reciprocal cross. We found that hybrid males from both cross directions showed disrupted X chromosome expression during prophase of meiosis I consistent with a loss of meiotic sex chromosome inactivation (MSCI) and Prdm9-associated sterility, but that the degree of disruption was greater in mice with an M. m. musculus X chromosome consistent with previous studies. During postmeiotic development, gene expression on the X chromosome was only disrupted in one cross direction, suggesting that misexpression at this later stage was genotype-specific and not a simple downstream consequence of MSCI disruption which was observed in both reciprocal crosses. Instead, disrupted postmeiotic expression may depend on the magnitude of earlier disrupted MSCI, or the disruption of particular X-linked genes or gene networks. Alternatively, only hybrids with a potential deficit of Sly copies, a Y-linked ampliconic gene family, showed overexpression in postmeiotic cells, consistent with a previously proposed model of antagonistic coevolution between the X- and Y-linked ampliconic genes contributing to disrupted expression late in spermatogenesis. The relative contributions of these two regulatory mechanisms and their impact on sterility phenotypes await further study. Our results further support the hypothesis that X-linked hybrid sterility in house mice has a variable genetic basis, and that genotype-specific disruption of gene regulation contributes to overexpression of the X chromosome at different stages of development. Overall, these findings underscore the critical role of epigenetic regulation of the X chromosome during spermatogenesis and suggest that these processes are prone to disruption in hybrids.
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Affiliation(s)
- Erica L Larson
- Department of Biological Sciences, University of Denver, Denver, CO 80208, USA
| | - Emily E K Kopania
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Kelsie E Hunnicutt
- Department of Biological Sciences, University of Denver, Denver, CO 80208, USA
| | - Dan Vanderpool
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Sara Keeble
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
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