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Preckler-Quisquater S, Quinn CB, Sacks BN. Maintenance of a narrow hybrid zone between native and introduced red foxes (Vulpes vulpes) despite conspecificity and high dispersal capabilities. Mol Ecol 2024; 33:e17418. [PMID: 38847182 DOI: 10.1111/mec.17418] [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: 01/30/2024] [Revised: 05/04/2024] [Accepted: 05/13/2024] [Indexed: 06/27/2024]
Abstract
Human-facilitated introductions of nonnative populations can lead to secondary contact between allopatric lineages, resulting in lineage homogenisation or the formation of stable hybrid zones maintained by reproductive barriers. We investigated patterns of gene flow between the native Sacramento Valley red fox (Vulpes vulpes patwin) and introduced conspecifics of captive-bred origin in California's Central Valley. Considering their recent divergence (20-70 kya), we hypothesised that any observed barriers to gene flow were primarily driven by pre-zygotic (e.g. behavioural differences) rather than post-zygotic (e.g. reduced hybrid fitness) barriers. We also explored whether nonnative genes could confer higher fitness in the human-dominated landscape resulting in selective introgression into the native population. Genetic analysis of red foxes (n = 682) at both mitochondrial (cytochrome b + D-loop) and nuclear (19,051 SNPs) loci revealed narrower cline widths than expected under a simulated model of unrestricted gene flow, consistent with the existence of reproductive barriers. We identified several loci with reduced introgression that were previously linked to behavioural divergence in captive-bred and domestic canids, supporting pre-zygotic, yet possibly hereditary, barriers as a mechanism driving the narrowness and stability of the hybrid zone. Several loci with elevated gene flow from the nonnative into the native population were linked to genes associated with domestication and adaptation to human-dominated landscapes. This study contributes to our understanding of hybridisation dynamics in vertebrates, particularly in the context of species introductions and landscape changes, underscoring the importance of considering how multiple mechanisms may be maintaining lineages at the species and subspecies level.
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Affiliation(s)
- Sophie Preckler-Quisquater
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Cate B Quinn
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
- USDA Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Missoula, Montana, USA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
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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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Runemark A, Moore EC, Larson EL. Hybridization and gene expression: Beyond differentially expressed genes. Mol Ecol 2024:e17303. [PMID: 38411307 DOI: 10.1111/mec.17303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/06/2024] [Accepted: 02/15/2024] [Indexed: 02/28/2024]
Abstract
Gene expression has a key role in reproductive isolation, and studies of hybrid gene expression have identified mechanisms causing hybrid sterility. Here, we review the evidence for altered gene expression following hybridization and outline the mechanisms shown to contribute to altered gene expression in hybrids. Transgressive gene expression, transcending that of both parental species, is pervasive in early generation sterile hybrids, but also frequently observed in viable, fertile hybrids. We highlight studies showing that hybridization can result in transgressive gene expression, also in established hybrid lineages or species. Such extreme patterns of gene expression in stabilized hybrid taxa suggest that altered hybrid gene expression may result in hybridization-derived evolutionary novelty. We also conclude that while patterns of misexpression in hybrids are well documented, the understanding of the mechanisms causing misexpression is lagging. We argue that jointly assessing differences in cell composition and cell-specific changes in gene expression in hybrids, in addition to assessing changes in chromatin and methylation, will significantly advance our understanding of the basis of altered gene expression. Moreover, uncovering to what extent evolution of gene expression results in altered expression for individual genes, or entire networks of genes, will advance our understanding of how selection moulds gene expression. Finally, we argue that jointly studying the dual roles of altered hybrid gene expression, serving both as a mechanism for reproductive isolation and as a substrate for hybrid ecological adaptation, will lead to significant advances in our understanding of the evolution of gene expression.
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Affiliation(s)
- Anna Runemark
- Department of Biology, Lund University, Lund, Sweden
| | - Emily C Moore
- Department of Biological Sciences, University of Denver, Denver, Colorado, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Erica L Larson
- Department of Biological Sciences, University of Denver, Denver, Colorado, USA
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4
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Delmore K, Justen H, Kay KM, Kitano J, Moyle LC, Stelkens R, Streisfeld MA, Yamasaki YY, Ross J. Genomic Approaches Are Improving Taxonomic Representation in Genetic Studies of Speciation. Cold Spring Harb Perspect Biol 2024; 16:a041438. [PMID: 37848243 PMCID: PMC10835617 DOI: 10.1101/cshperspect.a041438] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
Until recently, our understanding of the genetics of speciation was limited to a narrow group of model species with a specific set of characteristics that made genetic analysis feasible. Rapidly advancing genomic technologies are eliminating many of the distinctions between laboratory and natural systems. In light of these genomic developments, we review the history of speciation genetics, advances that have been gleaned from model and non-model organisms, the current state of the field, and prospects for broadening the diversity of taxa included in future studies. Responses to a survey of speciation scientists across the world reveal the ongoing division between the types of questions that are addressed in model and non-model organisms. To bridge this gap, we suggest integrating genetic studies from model systems that can be reared in the laboratory or greenhouse with genomic studies in related non-models where extensive ecological knowledge exists.
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Affiliation(s)
- Kira Delmore
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Hannah Justen
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Kathleen M Kay
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, California 95060, USA
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Leonie C Moyle
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Rike Stelkens
- Division of Population Genetics, Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| | - Matthew A Streisfeld
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, USA
| | - Yo Y Yamasaki
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Joseph Ross
- Department of Biology, California State University, Fresno, California 93740, USA
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5
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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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Louder MIM, Justen H, Kimmitt AA, Lawley KS, Turner LM, Dickman JD, Delmore KE. Gene regulation and speciation in a migratory divide between songbirds. Nat Commun 2024; 15:98. [PMID: 38167733 PMCID: PMC10761872 DOI: 10.1038/s41467-023-44352-2] [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: 04/16/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Behavioral variation abounds in nature. This variation is important for adaptation and speciation, but its molecular basis remains elusive. Here, we use a hybrid zone between two subspecies of songbirds that differ in migration - an ecologically important and taxonomically widespread behavior---to gain insight into this topic. We measure gene expression in five brain regions. Differential expression between migratory states was dominated by circadian genes in all brain regions. The remaining patterns were largely brain-region specific. For example, expression differences between the subspecies that interact with migratory state likely help maintain reproductive isolation in this system and were documented in only three brain regions. Contrary to existing work on regulatory mechanisms underlying species-specific traits, two lines of evidence suggest that trans- (vs. cis) regulatory changes underlie these patterns - no evidence for allele-specific expression in hybrids and minimal associations between genomic differentiation and expression differences. Additional work with hybrids shows expression levels were often distinct (transgressive) from parental forms. Behavioral contrasts and functional enrichment analyses allowed us to connect these patterns to mitonuclear incompatibilities and compensatory responses to stress that could exacerbate selection on hybrids and contribute to speciation.
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Affiliation(s)
| | - Hannah Justen
- Biology Department, Texas A&M University, College Station, TX, USA
| | | | - Koedi S Lawley
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Leslie M Turner
- Milner Centre for Evolution, Department of Biology & Biochemistry, University of Bath, Bath, UK
| | - J David Dickman
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Kira E Delmore
- Biology Department, Texas A&M University, College Station, TX, USA.
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7
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Čížková D, Schmiedová L, Kváč M, Sak B, Macholán M, Piálek J, Kreisinger J. The effect of host admixture on wild house mouse gut microbiota is weak when accounting for spatial autocorrelation. Mol Ecol 2024; 33:e17192. [PMID: 37933543 DOI: 10.1111/mec.17192] [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: 04/19/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 11/08/2023]
Abstract
The question of how interactions between the gut microbiome and vertebrate hosts contribute to host adaptation and speciation is one of the major problems in current evolutionary research. Using bacteriome and mycobiome metabarcoding, we examined how these two components of the gut microbiota vary with the degree of host admixture in secondary contact between two house mouse subspecies (Mus musculus musculus and M. m. domesticus). We used a large data set collected at two replicates of the hybrid zone and model-based statistical analyses to ensure the robustness of our results. Assuming that the microbiota of wild hosts suffers from spatial autocorrelation, we directly compared the results of statistical models that were spatially naive with those that accounted for spatial autocorrelation. We showed that neglecting spatial autocorrelation can strongly affect the results and lead to misleading conclusions. The spatial analyses showed little difference between subspecies, both in microbiome composition and in individual bacterial lineages. Similarly, the degree of admixture had minimal effects on the gut bacteriome and mycobiome and was caused by changes in a few microbial lineages that correspond to the common symbionts of free-living house mice. In contrast to previous studies, these data do not support the hypothesis that the microbiota plays an important role in host reproductive isolation in this particular model system.
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Affiliation(s)
- Dagmar Čížková
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
| | - Lucie Schmiedová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Kváč
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Agriculture and Technology, South Bohemia University, České Budějovice, Czech Republic
| | - Bohumil Sak
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Miloš Macholán
- Laboratory of Mammalian Evolutionary Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
| | - Jaroslav Piálek
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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8
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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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9
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Lobo D, López-Bao JV, Godinho R. The population bottleneck of the Iberian wolf impacted genetic diversity but not admixture with domestic dogs: A temporal genomic approach. Mol Ecol 2023; 32:5986-5999. [PMID: 37855673 DOI: 10.1111/mec.17171] [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: 03/30/2023] [Revised: 09/25/2023] [Accepted: 10/06/2023] [Indexed: 10/20/2023]
Abstract
After decades of intense persecution, the Iberian wolf subspecies faced a severe bottleneck in the 1970s that considerably reduced its range and population size, nearly leading to its extinction in central and southern Iberian Peninsula. Such population decline could have impacted the genetic diversity of Iberian wolves through different processes, namely genetic drift and dynamics of hybridization with domestic dogs. By contrasting the genomes of 68 contemporary with 54 historical samples spanning the periods before and immediately after the 1970s bottleneck, we found evidence of its impact on genetic diversity and dynamics of wolf-dog hybridization. Our genome-wide assessment revealed that wolves and dogs form two well-differentiated genetic groups in Iberia and that hybridization rates did not increase during the bottleneck. However, an increased number of hybrid individuals was found over time during the population re-expansion, particularly at the edge of the wolf range. We estimated a low percentage of dog ancestry (~1.4%) in historical samples, suggesting that dog introgression was not a key driver for wolf extinction in central and southern Iberia. Our findings also unveil a significant decline in genetic diversity in contemporary samples, with the highest proportion of homozygous segments in the genome being recently inherited. Overall, our study provides unprecedented insight into the impact of a sharp decline on the Iberian wolf genome and refines our understanding of the ecological and evolutionary drivers of wolf-dog hybridization in the wild.
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Affiliation(s)
- Diana Lobo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - José Vicente López-Bao
- Biodiversity Research Institute (CSIC - Oviedo University - Principality of Asturias) Oviedo University, Mieres, Spain
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Johannesburg, South Africa
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10
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Li J, Lee CR. The role of gene presence-absence variations on genetic incompatibility in Asian rice. THE NEW PHYTOLOGIST 2023; 239:778-791. [PMID: 37194454 PMCID: PMC7615310 DOI: 10.1111/nph.18969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/18/2023] [Indexed: 05/18/2023]
Abstract
Genetic incompatibilities are widespread between species. However, it remains unclear whether they all originated after population divergence as suggested by the Bateson-Dobzhansky-Muller model, and if not, what is their prevalence and distribution within populations. The gene presence-absence variations (PAVs) provide an opportunity for investigating gene-gene incompatibility. Here, we searched for the repulsion of coexistence between gene PAVs to identify the negative interaction of gene functions separately in two Oryza sativa subspecies. Many PAVs are involved in subspecies-specific negative epistasis and segregate at low-to-intermediate frequencies in focal subspecies but at low or high frequencies in the other subspecies. Incompatible PAVs are enriched in two functional groups, defense response and protein phosphorylation, which are associated with plant immunity and consistent with autoimmunity being a known mechanism of hybrid incompatibility in plants. Genes in the two enriched functional groups are older and seldom directly interact with each other. Instead, they interact with other younger gene PAVs with diverse functions. Our results illustrate the landscape of genetic incompatibility at gene PAVs in rice, where many incompatible pairs have already segregated as polymorphisms within subspecies, and many are novel negative interactions between older defense-related genes and younger genes with diverse functions.
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Affiliation(s)
- Juan Li
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 106319, Taiwan
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
- Swiss Institute for Bioinformatics, 1015 Lausanne, Switzerland
| | - Cheng-Ruei Lee
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 106319, Taiwan
- Institute of Plant Biology, National Taiwan University, Taipei 106319, Taiwan
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11
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Cutter AD. Speciation and development. Evol Dev 2023; 25:289-327. [PMID: 37545126 DOI: 10.1111/ede.12454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/13/2023] [Accepted: 07/20/2023] [Indexed: 08/08/2023]
Abstract
Understanding general principles about the origin of species remains one of the foundational challenges in evolutionary biology. The genomic divergence between groups of individuals can spawn hybrid inviability and hybrid sterility, which presents a tantalizing developmental problem. Divergent developmental programs may yield either conserved or divergent phenotypes relative to ancestral traits, both of which can be responsible for reproductive isolation during the speciation process. The genetic mechanisms of developmental evolution involve cis- and trans-acting gene regulatory change, protein-protein interactions, genetic network structures, dosage, and epigenetic regulation, all of which also have roots in population genetic and molecular evolutionary processes. Toward the goal of demystifying Darwin's "mystery of mysteries," this review integrates microevolutionary concepts of genetic change with principles of organismal development, establishing explicit links between population genetic process and developmental mechanisms in the production of macroevolutionary pattern. This integration aims to establish a more unified view of speciation that binds process and mechanism.
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Affiliation(s)
- Asher D Cutter
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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12
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Lollar MJ, Biewer-Heisler TJ, Danen CE, Pool JE. Hybrid breakdown in male reproduction between recently diverged Drosophila melanogaster populations has a complex and variable genetic architecture. Evolution 2023; 77:1550-1563. [PMID: 37071601 PMCID: PMC10309968 DOI: 10.1093/evolut/qpad060] [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: 10/25/2022] [Revised: 03/15/2023] [Accepted: 04/14/2023] [Indexed: 04/19/2023]
Abstract
Secondary contact between formerly isolated populations may result in hybrid breakdown, in which untested allelic combinations in hybrids are maladaptive and limit genetic exchange. Studying early-stage reproductive isolation may yield key insights into the genetic architectures and evolutionary forces underlying the first steps toward speciation. Here, we leverage the recent worldwide expansion of Drosophila melanogaster to test for hybrid breakdown between populations that diverged within the last 13,000 years. We found clear evidence for hybrid breakdown in male reproduction, but not female reproduction or viability, supporting the prediction that hybrid breakdown affects the heterogametic sex first. The frequency of non-reproducing F2 males varied among different crosses involving the same southern African and European populations, as did the qualitative effect of cross direction, implying a genetically variable basis of hybrid breakdown and a role for uniparentally inherited factors. The levels of breakdown observed in F2 males were not recapitulated in backcrossed individuals, consistent with the existence of incompatibilities with at least three partners. Thus, some of the very first steps toward reproductive isolation could involve incompatibilities with complex and variable genetic architectures. Collectively, our findings emphasize this system's potential for future studies on the genetic and organismal basis of early-stage reproductive isolation.
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Affiliation(s)
- Matthew J Lollar
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, United States
| | | | - Clarice E Danen
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - John E Pool
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, United States
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13
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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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14
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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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15
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Doms S, Fokt H, Rühlemann MC, Chung CJ, Kuenstner A, Ibrahim SM, Franke A, Turner LM, Baines JF. Key features of the genetic architecture and evolution of host-microbe interactions revealed by high-resolution genetic mapping of the mucosa-associated gut microbiome in hybrid mice. eLife 2022; 11:75419. [PMID: 35866635 PMCID: PMC9307277 DOI: 10.7554/elife.75419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 06/14/2022] [Indexed: 12/13/2022] Open
Abstract
Determining the forces that shape diversity in host-associated bacterial communities is critical to understanding the evolution and maintenance of metaorganisms. To gain deeper understanding of the role of host genetics in shaping gut microbial traits, we employed a powerful genetic mapping approach using inbred lines derived from the hybrid zone of two incipient house mouse species. Furthermore, we uniquely performed our analysis on microbial traits measured at the gut mucosal interface, which is in more direct contact with host cells and the immune system. Several mucosa-associated bacterial taxa have high heritability estimates, and interestingly, 16S rRNA transcript-based heritability estimates are positively correlated with cospeciation rate estimates. Genome-wide association mapping identifies 428 loci influencing 120 taxa, with narrow genomic intervals pinpointing promising candidate genes and pathways. Importantly, we identified an enrichment of candidate genes associated with several human diseases, including inflammatory bowel disease, and functional categories including innate immunity and G-protein-coupled receptors. These results highlight key features of the genetic architecture of mammalian host-microbe interactions and how they diverge as new species form. The digestive system, particularly the large intestine, hosts many types of bacteria which together form the gut microbiome. The exact makeup of different bacterial species is specific to an individual, but microbiomes are often more similar between related individuals, and more generally, across related species. Whether this is because individuals share similar environments or similar genetic backgrounds remains unclear. These two factors can be disentangled by breeding different animal lineages – which have different genetic backgrounds while belonging to the same species – and then raising the progeny in the same environment. To investigate this question, Doms et al. studied the genes and microbiomes of mice resulting from breeding strains from multiple locations in a natural hybrid zone between different subspecies. The experiments showed that 428 genetic regions affected the makeup of the microbiome, many of which were known to be associated with human diseases. Further analysis revealed 79 genes that were particularly interesting, as they were involved in recognition and communication with bacteria. These results show how the influence of the host genome on microbiome composition becomes more specialized as animals evolve. Overall, the work by Doms et al. helps to pinpoint the genes that impact the microbiome; this knowledge could be helpful to examine how these interactions contribute to the emergence of conditions such as diabetes or inflammatory bowel disease, which are linked to perturbations in gut bacteria.
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Affiliation(s)
- Shauni Doms
- Max Planck Institute for Evolutionary Biology, Plön, Germany.,Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Hanna Fokt
- Max Planck Institute for Evolutionary Biology, Plön, Germany.,Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Malte Christoph Rühlemann
- Institute for Clinical Molecular Biology (IKMB), Kiel University, Kiel, Germany.,Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Cecilia J Chung
- Max Planck Institute for Evolutionary Biology, Plön, Germany.,Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Axel Kuenstner
- Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Saleh M Ibrahim
- Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany.,Sharjah Institute of Medical Research, Sharjah, United Arab Emirates
| | - Andre Franke
- Institute for Clinical Molecular Biology (IKMB), Kiel University, Kiel, Germany
| | - Leslie M Turner
- Milner Centre for Evolution, Department of Biology & Biochemistry, University of Bath, Bath, United Kingdom
| | - John F Baines
- Max Planck Institute for Evolutionary Biology, Plön, Germany.,Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
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16
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Roberts EK, Tardif S, Wright EA, Platt RN, Bradley RD, Hardy DM. Rapid divergence of a gamete recognition gene promoted macroevolution of Eutheria. Genome Biol 2022; 23:155. [PMID: 35821049 PMCID: PMC9275260 DOI: 10.1186/s13059-022-02721-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 06/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Speciation genes contribute disproportionately to species divergence, but few examples exist, especially in vertebrates. Here we test whether Zan, which encodes the sperm acrosomal protein zonadhesin that mediates species-specific adhesion to the egg's zona pellucida, is a speciation gene in placental mammals. RESULTS Genomic ontogeny reveals that Zan arose by repurposing of a stem vertebrate gene that was lost in multiple lineages but retained in Eutheria on acquiring a function in egg recognition. A 112-species Zan sequence phylogeny, representing 17 of 19 placental Orders, resolves all species into monophyletic groups corresponding to recognized Orders and Suborders, with <5% unsupported nodes. Three other rapidly evolving germ cell genes (Adam2, Zp2, and Prm1), a paralogous somatic cell gene (TectA), and a mitochondrial gene commonly used for phylogenetic analyses (Cytb) all yield trees with poorer resolution than the Zan tree and inferior topologies relative to a widely accepted mammalian supertree. Zan divergence by intense positive selection produces dramatic species differences in the protein's properties, with ordinal divergence rates generally reflecting species richness of placental Orders consistent with expectations for a speciation gene that acts across a wide range of taxa. Furthermore, Zan's combined phylogenetic utility and divergence exceeds those of all other genes known to have evolved in Eutheria by positive selection, including the only other mammalian speciation gene, Prdm9. CONCLUSIONS Species-specific egg recognition conferred by Zan's functional divergence served as a mode of prezygotic reproductive isolation that promoted the extraordinary adaptive radiation and success of Eutheria.
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Affiliation(s)
- Emma K. Roberts
- Department of Biological Sciences, Texas Tech University, Lubbock, TX USA
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX USA
| | - Steve Tardif
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX USA
- Reproductive Biology Division, JangoBio, Fitchburg, WI USA
| | - Emily A. Wright
- Department of Biological Sciences, Texas Tech University, Lubbock, TX USA
| | - Roy N. Platt
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX USA
| | - Robert D. Bradley
- Department of Biological Sciences, Texas Tech University, Lubbock, TX USA
- Natural Science Research Laboratory, Museum of Texas Tech University, Lubbock, TX USA
| | - Daniel M. Hardy
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX USA
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17
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Balard A, Heitlinger E. Shifting focus from resistance to disease tolerance: A review on hybrid house mice. Ecol Evol 2022; 12:e8889. [PMID: 35571751 PMCID: PMC9077717 DOI: 10.1002/ece3.8889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 04/11/2022] [Accepted: 04/14/2022] [Indexed: 11/10/2022] Open
Abstract
Parasites have been proposed to modulate the fitness of hybridizing hosts in part based on observations in the European house mouse hybrid zone (HMHZ), a tension zone in which hybrids show reduced fitness. We here review evidence (1) for parasite load differences in hybrid versus parental mice and (2) for health and fitness effects of parasites promoting or preventing introgression and hybridization. The question of relative resistance or susceptibility of hybrids to parasites in the HMHZ has long been controversial. Recent field studies found hybrids to be more resistant than mice from parental subspecies against infections with pinworms and protozoans (Eimeria spp.). We argue that the field studies underlying the contradictory impression of hybrid susceptibility have limitations in sample size, statistical analysis and scope, focusing only on macroparasites. We suggest that weighted evidence from field studies indicate hybrid resistance. Health is a fitness component through which resistance can modulate overall fitness. Resistance, however, should not be extrapolated directly to a fitness effect, as the relationship between resistance and health can be modulated by tolerance. In our own recent work, we found that the relationship between health and resistance (tolerance) differs between infections with the related species E. falciformis and E. ferrisi. Health and tolerance need to be assessed directly and the choice of parasite has made this difficult in previous experimental studies of house mice. We discuss how experimental Eimeria spp. infections in hybrid house mice can address resistance, health and tolerance in conjunction.
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Affiliation(s)
- Alice Balard
- Department of Molecular ParasitologyInstitute for BiologyHumboldt University Berlin (HU)BerlinGermany
- Research Group Ecology and Evolution of Molecular Parasite‐Host InteractionsLeibniz‐Institut for Zoo and Wildlife Research (IZW) im Forschungsverbund Berlin e.V.BerlinGermany
| | - Emanuel Heitlinger
- Department of Molecular ParasitologyInstitute for BiologyHumboldt University Berlin (HU)BerlinGermany
- Research Group Ecology and Evolution of Molecular Parasite‐Host InteractionsLeibniz‐Institut for Zoo and Wildlife Research (IZW) im Forschungsverbund Berlin e.V.BerlinGermany
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18
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Imbalanced segregation of recombinant haplotypes in hybrid populations reveals inter- and intrachromosomal Dobzhansky-Muller incompatibilities. PLoS Genet 2022; 18:e1010120. [PMID: 35344560 PMCID: PMC8989332 DOI: 10.1371/journal.pgen.1010120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 04/07/2022] [Accepted: 02/25/2022] [Indexed: 11/19/2022] Open
Abstract
Dobzhansky-Muller incompatibilities (DMIs) are a major component of reproductive isolation between species. DMIs imply negative epistasis and are exposed when two diverged populations hybridize. Mapping the locations of DMIs has largely relied on classical genetic mapping. Approaches to date are hampered by low power and the challenge of identifying DMI loci on the same chromosome, because strong initial linkage of parental haplotypes weakens statistical tests. Here, we propose new statistics to infer negative epistasis from haplotype frequencies in hybrid populations. When two divergent populations hybridize, the variance in heterozygosity at two loci decreases faster with time at DMI loci than at random pairs of loci. When two populations hybridize at near-even admixture proportions, the deviation of the observed variance from its expectation becomes negative for the DMI pair. This negative deviation enables us to detect intermediate to strong negative epistasis both within and between chromosomes. In practice, the detection window in hybrid populations depends on the demographic scenario, the recombination rate, and the strength of epistasis. When the initial proportion of the two parental populations is uneven, only strong DMIs can be detected with our method unless migration prevents parental haplotypes from being lost. We use the new statistics to infer candidate DMIs from three hybrid populations of swordtail fish. We identify numerous new DMI candidates, some of which are inferred to interact with several loci within and between chromosomes. Moreover, we discuss our results in the context of an expected enrichment in intrachromosomal over interchromosomal DMIs.
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19
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Hagberg L, Celemín E, Irisarri I, Hawlitschek O, Bella JL, Mott T, Pereira RJ. Extensive introgression at late stages of species formation: Insights from grasshopper hybrid zones. Mol Ecol 2022; 31:2384-2399. [PMID: 35191134 DOI: 10.1111/mec.16406] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/02/2022] [Accepted: 02/14/2022] [Indexed: 11/30/2022]
Abstract
The process of species formation is characterised by the accumulation of multiple reproductive barriers. The evolution of hybrid male sterility, or Haldane's rule, typically characterises later stages of species formation, when reproductive isolation is strongest. Yet, understanding how quickly reproductive barriers evolve and their consequences for maintaining genetic boundaries between emerging species remains a challenging task because it requires studying taxa that hybridise in nature. Here, we address these questions using the meadow grasshopper Pseudochorthippus parallelus, where populations that show multiple reproductive barriers, including hybrid male sterility, hybridise in two natural hybrid zones. Using mitochondrial data, we infer that such populations have diverged some 100,000 years ago, at the beginning of the last glacial cycle in Europe. Nuclear data shows that contractions at multiple glacial refugia, and post-glacial expansions have facilitated genetic differentiation between lineages that today interact in hybrid zones. We find extensive introgression throughout the sampled species range, irrespective of current strength of reproductive isolation. Populations exhibiting hybrid male sterility in two hybrid zones show repeatable patterns of genomic differentiation, consistent with shared genomic constraints affecting ancestral divergence or with the role of those regions in reproductive isolation. Together, our results suggest that reproductive barriers that characterise late stages of species formation can evolve relatively quickly, particularly when associated with strong demographic changes. Moreover, we show that such barriers persist in the face of extensive gene flow, allowing future studies to identify associated genomic regions.
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Affiliation(s)
- Linda Hagberg
- Division of Evolutionary Biology, Faculty of Biology II, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2, 82152, Planegg-Martinsried, Germany
| | - Enrique Celemín
- Division of Evolutionary Biology, Faculty of Biology II, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2, 82152, Planegg-Martinsried, Germany.,Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476, Potsdam, Germany
| | - Iker Irisarri
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077, Göttingen, Germany.,Campus Institute Data Science (CIDAS), Göttingen, Germany
| | - Oliver Hawlitschek
- Leibniz Institute for the Analysis of Biodiversity Change, Zoological Museum, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany.,Zoologische Staatssammlung (SNSB-ZSM), Münchhausenstr. 21, 81247, Munich, Germany
| | - José L Bella
- Departamento de Biología (Genética), Facultad de Ciencias, Universidad Autónoma de Madrid, 28049, Madrid, Spain.,Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Tamí Mott
- Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, 57072-900, Maceió, Alagoas, Brazil
| | - Ricardo J Pereira
- Division of Evolutionary Biology, Faculty of Biology II, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2, 82152, Planegg-Martinsried, Germany
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20
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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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21
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Hunnicutt KE, Good JM, Larson EL. Unraveling patterns of disrupted gene expression across a complex tissue. Evolution 2022; 76:275-291. [PMID: 34882778 PMCID: PMC9355168 DOI: 10.1111/evo.14420] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 11/11/2021] [Accepted: 11/26/2021] [Indexed: 02/03/2023]
Abstract
Whole tissue RNASeq is the standard approach for studying gene expression divergence in evolutionary biology and provides a snapshot of the comprehensive transcriptome for a given tissue. However, whole tissues consist of diverse cell types differing in expression profiles, and the cellular composition of these tissues can evolve across species. Here, we investigate the effects of different cellular composition on whole tissue expression profiles. We compared gene expression from whole testes and enriched spermatogenesis populations in two species of house mice, Mus musculus musculus and M. m. domesticus, and their sterile and fertile F1 hybrids, which differ in both cellular composition and regulatory dynamics. We found that cellular composition differences skewed expression profiles and differential gene expression in whole testes samples. Importantly, both approaches were able to detect large-scale patterns such as disrupted X chromosome expression, although whole testes sampling resulted in decreased power to detect differentially expressed genes. We encourage researchers to account for histology in RNASeq and consider methods that reduce sample complexity whenever feasible. Ultimately, we show that differences in cellular composition between tissues can modify expression profiles, potentially altering inferred gene ontological processes, insights into gene network evolution, and processes governing gene expression evolution.
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Affiliation(s)
- Kelsie E Hunnicutt
- Department of Biological Sciences, University of Denver, Denver, Colorado, 80208
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812
| | - Erica L Larson
- Department of Biological Sciences, University of Denver, Denver, Colorado, 80208
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22
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Go AC, Civetta A. Divergence of X-linked trans regulatory proteins and the misexpression of gene targets in sterile Drosophila pseudoobscura hybrids. BMC Genomics 2022; 23:30. [PMID: 34991488 PMCID: PMC8740060 DOI: 10.1186/s12864-021-08267-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/20/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The genetic basis of hybrid incompatibilities is characterized by pervasive cases of gene interactions. Sex chromosomes play a major role in speciation and X-linked hybrid male sterility (HMS) genes have been identified. Interestingly, some of these genes code for proteins with DNA binding domains, suggesting a capability to act as trans-regulatory elements and disturb the expression of a large number of gene targets. To understand how interactions between trans- and cis-regulatory elements contribute to speciation, we aimed to map putative X-linked trans-regulatory elements and to identify gene targets with disrupted gene expression in sterile hybrids between the subspecies Drosophila pseudoobscura pseudoobscura and D. p. bogotana. RESULTS We find six putative trans-regulatory proteins within previously mapped X chromosome HMS loci with sequence changes that differentiate the two subspecies. Among them, the previously characterized HMS gene Overdrive (Ovd) had the largest number of amino acid changes between subspecies, with some substitutions localized within the protein's DNA binding domain. Using an introgression approach, we detected transcriptional responses associated with a sterility/fertility Ovd allele swap. We found a network of 52 targets of Ovd and identified cis-regulatory effects among target genes with disrupted expression in sterile hybrids. However, a combined analysis of polymorphism and divergence in non-coding sequences immediately upstream of target genes found no evidence of changes in candidate regulatory proximal cis-elements. Finally, peptidases were over-represented among target genes. CONCLUSIONS We provide evidence of divergence between subspecies within the DNA binding domain of the HMS protein Ovd and identify trans effects on the expression of 52 gene targets. Our results identify a network of trans-cis interactions with possible effects on HMS. This network provides molecular evidence of gene × gene incompatibilities as contributors to hybrid dysfunction.
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Affiliation(s)
- Alwyn C Go
- Department of Biology, University of Winnipeg, 515 Portage Ave, Winnipeg, MB, R3B 2E9, Canada
| | - Alberto Civetta
- Department of Biology, University of Winnipeg, 515 Portage Ave, Winnipeg, MB, R3B 2E9, Canada.
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23
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Jazayeri O, Farahmand Araghi S, Aghajanzadeh TA, Mir Moammadrezaei F. Up-regulation of Arl4a gene expression by broccoli aqueous extract is associated with improved spermatogenesis in mouse testes. BIOMEDICA : REVISTA DEL INSTITUTO NACIONAL DE SALUD 2021; 41:706-720. [PMID: 34936255 PMCID: PMC8768486 DOI: 10.7705/biomedica.5962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 07/15/2021] [Indexed: 11/21/2022]
Abstract
INTRODUCTION Broccoli (Brassica oleracea) is well known for its properties as an anticancer, antioxidant, and scavenger of free radicals. However, its benefits in enhancing spermatogenesis have not been well established. OBJECTIVE To study broccoli aqueous extract effects on sperm factors and the expression of genes Catsper1, Catsper2, Arl4a, Sox5, and Sox9 in sperm factors in mice. MATERIAL AND METHODS Male mice were divided randomly into six groups: (1) Control; (2) cadmium (3 mg/kg of mouse body weight); (3) orally treated with 200 μl broccoli aqueous extract (1 g ml-1); (4) orally treated with 400 μl of broccoli aqueous extract; (5) orally treated with 200 broccoli aqueous extract plus cadmium, and (6) orally treated with 400 μl of broccoli aqueous extract plus cadmium. We analyzed the sperms factors and Catsper1, Catsper2, Arl4a, Sox5, and Sox9 gene expression. RESULTS An obvious improvement in sperm count and a slight enhancement in sperm motility were observed in mice treated with broccoli extract alone or with cadmium. Sperm viability was reduced by broccoli extract except for the 200 μl dose with cadmium, which significantly increased it. Interestingly, Arl4a gene expression increased in the 400 μl broccoli-treated group. Likewise, the Arl4a mRNA level in mice treated with cadmium and 200 μl of broccoli extract was higher than in the cadmium-treated mice. Furthermore, broccoli extract enhanced the mRNA level of Catsper2 and Sox5 genes in mice treated with 200 μl and 400 μl broccoli extract plus cadmium compared with the group treated solely with cadmium. CONCLUSION The higher sperm count in broccoli-treated mice opens the way for the development of pharmaceutical products for infertile men.
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Affiliation(s)
- Omid Jazayeri
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran.
| | - Setareh Farahmand Araghi
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran.
| | - Tahereh A Aghajanzadeh
- Department of Plant Sciences, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran.
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24
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Bredemeyer KR, Seabury CM, Stickney MJ, McCarrey JR, vonHoldt BM, Murphy WJ. Rapid Macrosatellite Evolution Promotes X-Linked Hybrid Male Sterility in a Feline Interspecies Cross. Mol Biol Evol 2021; 38:5588-5609. [PMID: 34519828 PMCID: PMC8662614 DOI: 10.1093/molbev/msab274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The sterility or inviability of hybrid offspring produced from an interspecific mating result from incompatibilities between parental genotypes that are thought to result from divergence of loci involved in epistatic interactions. However, attributes contributing to the rapid evolution of these regions also complicates their assembly, thus discovery of candidate hybrid sterility loci is difficult and has been restricted to a small number of model systems. Here we reported rapid interspecific divergence at the DXZ4 macrosatellite locus in an interspecific cross between two closely related mammalian species: the domestic cat (Felis silvestris catus) and the Jungle cat (Felis chaus). DXZ4 is an interesting candidate due to its structural complexity, copy number variability, and described role in the critical yet complex biological process of X-chromosome inactivation. However, the full structure of DXZ4 was absent or incomplete in nearly every available mammalian genome assembly given its repetitive complexity. We compared highly continuous genomes for three cat species, each containing a complete DXZ4 locus, and discovered that the felid DXZ4 locus differs substantially from the human ortholog, and that it varies in copy number between cat species. Additionally, we reported expression, methylation, and structural conformation profiles of DXZ4 and the X chromosome during stages of spermatogenesis that have been previously associated with hybrid male sterility. Collectively, these findings suggest a new role for DXZ4 in male meiosis and a mechanism for feline interspecific incompatibility through rapid satellite divergence.
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Affiliation(s)
- Kevin R Bredemeyer
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA
| | | | - Mark J Stickney
- Veterinary Medical Teaching Hospital, Texas A&M University, College Station, TX, USA
| | - John R McCarrey
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, USA
| | | | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA
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25
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Powell DL, Moran B, Kim B, Banerjee SM, Aguillon SM, Fascinetto-Zago P, Langdon Q, Schumer M. Two new hybrid populations expand the swordtail hybridization model system. Evolution 2021; 75:2524-2539. [PMID: 34460102 PMCID: PMC8659863 DOI: 10.1111/evo.14337] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/11/2021] [Accepted: 06/22/2021] [Indexed: 12/25/2022]
Abstract
Natural hybridization events provide unique windows into the barriers that keep species apart as well as the consequences of their breakdown. Here, we characterize hybrid populations formed between the northern swordtail fish Xiphophorus cortezi and Xiphophorus birchmanni from collection sites on two rivers. We use simulations and new genetic reference panels to develop sensitive and accurate local ancestry calling in this novel system. Strikingly, we find that hybrid populations on both rivers consist of two genetically distinct subpopulations: a cluster of pure X. birchmanni individuals and one of phenotypically intermediate hybrids that derive ∼85-90% of their genome from X. cortezi. Simulations suggest that initial hybridization occurred ∼150 generations ago at both sites, with little evidence for contemporary gene flow between subpopulations. This population structure is consistent with strong assortative mating between individuals of similar ancestry. The patterns of population structure uncovered here mirror those seen in hybridization between X. birchmanni and its sister species, Xiphophorus malinche, indicating an important role for assortative mating in the evolution of hybrid populations. Future comparisons will provide a window into the shared mechanisms driving the outcomes of hybridization not only among independent hybridization events between the same species but also across distinct species pairs.
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Affiliation(s)
- Daniel L. Powell
- Department of Biology, Stanford University,Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C.,Correspondence to: and
| | - Ben Moran
- Department of Biology, Stanford University,Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | | | - Shreya M. Banerjee
- Department of Biology, Stanford University,Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | - Stepfanie M. Aguillon
- Department of Biology, Stanford University,Department of Ecology and Evolutionary Biology, Cornell University
| | - Paola Fascinetto-Zago
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C.,Department of Biology, Texas A&M University
| | - Quinn Langdon
- Department of Biology, Stanford University,Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | - Molly Schumer
- Department of Biology, Stanford University,Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C.,Hanna H. Gray Fellow, Howard Hughes Medical Institutes,Correspondence to: and
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26
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Baiz MD, Tucker PK, Mueller JL, Cortés-Ortiz L. X-Linked Signature of Reproductive Isolation in Humans is Mirrored in a Howler Monkey Hybrid Zone. J Hered 2021; 111:419-428. [PMID: 32725191 PMCID: PMC7525826 DOI: 10.1093/jhered/esaa021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Indexed: 12/13/2022] Open
Abstract
Reproductive isolation is a fundamental step in speciation. While sex chromosomes have been linked to reproductive isolation in many model systems, including hominids, genetic studies of the contribution of sex chromosome loci to speciation for natural populations are relatively sparse. Natural hybrid zones can help identify genomic regions contributing to reproductive isolation, like hybrid incompatibility loci, since these regions exhibit reduced introgression between parental species. Here, we use a primate hybrid zone (Alouatta palliata × Alouatta pigra) to test for reduced introgression of X-linked SNPs compared to autosomal SNPs. To identify X-linked sequence in A. palliata, we used a sex-biased mapping approach with whole-genome re-sequencing data. We then used genomic cline analysis with reduced-representation sequence data for parental A. palliata and A. pigra individuals and hybrids (n = 88) to identify regions with non-neutral introgression. We identified ~26 Mb of non-repetitive, putatively X-linked genomic sequence in A. palliata, most of which mapped collinearly to the marmoset and human X chromosomes. We found that X-linked SNPs had reduced introgression and an excess of ancestry from A. palliata as compared to autosomal SNPs. One outlier region with reduced introgression overlaps a previously described "desert" of archaic hominin ancestry on the human X chromosome. These results are consistent with a large role for the X chromosome in speciation across animal taxa and further, suggest shared features in the genomic basis of the evolution of reproductive isolation in primates.
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Affiliation(s)
- Marcella D Baiz
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI.,Department of Biology, Pennsylvania State University, University Park, PA
| | - Priscilla K Tucker
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Jacob L Mueller
- Department of Human Genetics, University of Michigan, Ann Arbor, MI
| | - Liliana Cortés-Ortiz
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI
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27
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Moran BM, Payne C, Langdon Q, Powell DL, Brandvain Y, Schumer M. The genomic consequences of hybridization. eLife 2021; 10:e69016. [PMID: 34346866 PMCID: PMC8337078 DOI: 10.7554/elife.69016] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/09/2021] [Indexed: 12/29/2022] Open
Abstract
In the past decade, advances in genome sequencing have allowed researchers to uncover the history of hybridization in diverse groups of species, including our own. Although the field has made impressive progress in documenting the extent of natural hybridization, both historical and recent, there are still many unanswered questions about its genetic and evolutionary consequences. Recent work has suggested that the outcomes of hybridization in the genome may be in part predictable, but many open questions about the nature of selection on hybrids and the biological variables that shape such selection have hampered progress in this area. We synthesize what is known about the mechanisms that drive changes in ancestry in the genome after hybridization, highlight major unresolved questions, and discuss their implications for the predictability of genome evolution after hybridization.
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Affiliation(s)
- Benjamin M Moran
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
| | - Cheyenne Payne
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
| | - Quinn Langdon
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Daniel L Powell
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
| | - Yaniv Brandvain
- Department of Ecology, Evolution & Behavior and Plant and Microbial Biology, University of MinnesotaMinneapolisUnited States
| | - Molly Schumer
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
- Hanna H. Gray Fellow, Howard Hughes Medical InstituteStanfordUnited States
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28
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Forejt J, Jansa P, Parvanov E. Hybrid sterility genes in mice (Mus musculus): a peculiar case of PRDM9 incompatibility. Trends Genet 2021; 37:1095-1108. [PMID: 34238593 DOI: 10.1016/j.tig.2021.06.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/08/2021] [Accepted: 06/10/2021] [Indexed: 12/14/2022]
Abstract
Hybrid sterility is a critical step in the evolution of reproductive barriers between diverging taxa during the process of speciation. Recent studies of young subspecies of the house mouse revealed a multigenic nature and frequent polymorphism of hybrid sterility genes as well as the recurrent engagement of the meiosis-specific gene PR domain-containing 9 (Prdm9) and X-linked loci. Prdm9-controlled hybrid sterility is essentially chromosomal in nature, conditioned by the sequence divergence between subspecies. Depending on the Prdm9 interallelic interactions and the X-linked Hstx2 locus, the same homologs either regularly recombine and synapse, or show impaired DNA DSB repair, asynapsis, and early meiotic arrest. Thus, Prdm9-dependent hybrid sterility points to incompatibilities affecting meiotic recombination as a possible mechanism of reproductive isolation between (sub)species.
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Affiliation(s)
- Jiri Forejt
- Department of Mouse Molecular Genetics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec 252 50, Czech Republic.
| | - Petr Jansa
- Department of Mouse Molecular Genetics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec 252 50, Czech Republic
| | - Emil Parvanov
- Department of Mouse Molecular Genetics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec 252 50, Czech Republic
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29
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Pereira RJ, Lima TG, Pierce-Ward NT, Chao L, Burton RS. Recovery from hybrid breakdown reveals a complex genetic architecture of mitonuclear incompatibilities. Mol Ecol 2021; 30:6403-6416. [PMID: 34003535 DOI: 10.1111/mec.15985] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 03/29/2021] [Accepted: 05/11/2021] [Indexed: 01/03/2023]
Abstract
Reproductive isolation is often achieved when genes that are neutral or beneficial in their genomic background become functionally incompatible in a foreign genomic background, causing inviability, sterility or other forms of low fitness in hybrids. Recent studies suggest that mitonuclear interactions are among the initial incompatibilities to evolve at early stages of population divergence across taxa. Yet, the genomic architecture of mitonuclear incompatibilities has rarely been elucidated. We employ an experimental evolution approach starting with low-fitness F2 interpopulation hybrids of the copepod Tigriopus californicus, in which frequencies of compatible and incompatible nuclear alleles change in response to an alternative mitochondrial background. After about nine generations, we observe a generalized increase in population size and in survivorship, suggesting efficiency of selection against maladaptive phenotypes. Whole genome sequencing of evolved populations showed some consistent allele frequency changes across three replicates of each reciprocal cross, but markedly different patterns between mitochondrial backgrounds. In only a few regions (~6.5% of the genome), the same parental allele was overrepresented irrespective of the mitochondrial background. About 33% of the genome showed allele frequency changes consistent with divergent selection, with the location of these genomic regions strongly differing between mitochondrial backgrounds. In 87% and 89% of these genomic regions, the dominant nuclear allele matched the associated mitochondrial background, consistent with mitonuclear co-adaptation. These results suggest that mitonuclear incompatibilities have a complex polygenic architecture that differs between populations, potentially generating genome-wide barriers to gene flow between closely related taxa.
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Affiliation(s)
- Ricardo J Pereira
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Thiago G Lima
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - N Tessa Pierce-Ward
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Lin Chao
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ronald S Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
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30
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Mihola O, Landa V, Pratto F, Brick K, Kobets T, Kusari F, Gasic S, Smagulova F, Grey C, Flachs P, Gergelits V, Tresnak K, Silhavy J, Mlejnek P, Camerini-Otero RD, Pravenec M, Petukhova GV, Trachtulec Z. Rat PRDM9 shapes recombination landscapes, duration of meiosis, gametogenesis, and age of fertility. BMC Biol 2021; 19:86. [PMID: 33910563 PMCID: PMC8082845 DOI: 10.1186/s12915-021-01017-0] [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: 09/10/2020] [Accepted: 04/01/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Vertebrate meiotic recombination events are concentrated in regions (hotspots) that display open chromatin marks, such as trimethylation of lysines 4 and 36 of histone 3 (H3K4me3 and H3K36me3). Mouse and human PRDM9 proteins catalyze H3K4me3 and H3K36me3 and determine hotspot positions, whereas other vertebrates lacking PRDM9 recombine in regions with chromatin already opened for another function, such as gene promoters. While these other vertebrate species lacking PRDM9 remain fertile, inactivation of the mouse Prdm9 gene, which shifts the hotspots to the functional regions (including promoters), typically causes gross fertility reduction; and the reasons for these species differences are not clear. RESULTS We introduced Prdm9 deletions into the Rattus norvegicus genome and generated the first rat genome-wide maps of recombination-initiating double-strand break hotspots. Rat strains carrying the same wild-type Prdm9 allele shared 88% hotspots but strains with different Prdm9 alleles only 3%. After Prdm9 deletion, rat hotspots relocated to functional regions, about 40% to positions corresponding to Prdm9-independent mouse hotspots, including promoters. Despite the hotspot relocation and decreased fertility, Prdm9-deficient rats of the SHR/OlaIpcv strain produced healthy offspring. The percentage of normal pachytene spermatocytes in SHR-Prdm9 mutants was almost double than in the PWD male mouse oligospermic sterile mutants. We previously found a correlation between the crossover rate and sperm presence in mouse Prdm9 mutants. The crossover rate of SHR is more similar to sperm-carrying mutant mice, but it did not fully explain the fertility of the SHR mutants. Besides mild meiotic arrests at rat tubular stages IV (mid-pachytene) and XIV (metaphase), we also detected postmeiotic apoptosis of round spermatids. We found delayed meiosis and age-dependent fertility in both sexes of the SHR mutants. CONCLUSIONS We hypothesize that the relative increased fertility of rat versus mouse Prdm9 mutants could be ascribed to extended duration of meiotic prophase I. While rat PRDM9 shapes meiotic recombination landscapes, it is unnecessary for recombination. We suggest that PRDM9 has additional roles in spermatogenesis and speciation-spermatid development and reproductive age-that may help to explain male-specific hybrid sterility.
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Affiliation(s)
- Ondrej Mihola
- Laboratory of Germ Cell Development, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220, Prague, Czech Republic
| | - Vladimir Landa
- Laboratory of Genetics of Model Diseases, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Florencia Pratto
- National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kevin Brick
- National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tatyana Kobets
- Laboratory of Germ Cell Development, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220, Prague, Czech Republic
| | - Fitore Kusari
- Laboratory of Germ Cell Development, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220, Prague, Czech Republic
| | - Srdjan Gasic
- Laboratory of Germ Cell Development, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220, Prague, Czech Republic
| | - Fatima Smagulova
- Department of Biochemistry and Molecular Biology, Uniformed Services University of Health Sciences, Bethesda, MD, 20814, USA
- Present address: Inserm U1085 IRSET, 35042, Rennes, France
| | - Corinne Grey
- Institut de Génétique Humaine, CNRS UMR 9002, 34396, Montpellier, France
| | - Petr Flachs
- Laboratory of Germ Cell Development, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220, Prague, Czech Republic
- Present address: Division BIOCEV, Laboratory of Epigenetics of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220, Prague, Czech Republic
| | - Vaclav Gergelits
- Laboratory of Mouse Molecular Genetics, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220, Prague, Czech Republic
| | - Karel Tresnak
- Laboratory of Germ Cell Development, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220, Prague, Czech Republic
| | - Jan Silhavy
- Laboratory of Genetics of Model Diseases, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Mlejnek
- Laboratory of Genetics of Model Diseases, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - R Daniel Camerini-Otero
- National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Michal Pravenec
- Laboratory of Genetics of Model Diseases, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Galina V Petukhova
- Department of Biochemistry and Molecular Biology, Uniformed Services University of Health Sciences, Bethesda, MD, 20814, USA
| | - Zdenek Trachtulec
- Laboratory of Germ Cell Development, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220, Prague, Czech Republic.
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Xie HB, Wang LG, Fan CY, Zhang LC, Adeniyi CA, Yin X, Zeng ZB, Wang LX, Zhang YP. Genetic architecture underlying nascent speciation - The evolution of Eurasian pigs under domestication. Mol Biol Evol 2021; 38:3556-3566. [PMID: 33892509 PMCID: PMC8382894 DOI: 10.1093/molbev/msab117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Speciation is a process whereby the evolution of reproductive barriers leads to isolated species. Although many studies have addressed large-effect genetic footprints in the advanced stages of speciation, the genetics of reproductive isolation in nascent stage of speciation remains unclear. Here, we show that pig domestication offers an interesting model for studying the early stages of speciation in great details. Pig breeds have not evolved the large X-effect of hybrid incompatibility commonly observed between “good species.” Instead, deleterious epistatic interactions among multiple autosomal loci are common. These weak Dobzhansky–Muller incompatibilities confer partial hybrid inviability with sex biases in crosses between European and East Asian domestic pigs. The genomic incompatibility is enriched in pathways for angiogenesis, androgen receptor signaling and immunity, with an observation of many highly differentiated cis-regulatory variants. Our study suggests that partial hybrid inviability caused by pervasive but weak interactions among autosomal loci may be a hallmark of nascent speciation in mammals.
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Affiliation(s)
- Hai-Bing Xie
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Li-Gang Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chen-Yu Fan
- State Key Laboratory for Conservation and Utilization of Bio-resource, School of Life Science, Yunnan University, Kunming, China
| | - Long-Chao Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - C Adeola Adeniyi
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xue Yin
- State Key Laboratory for Conservation and Utilization of Bio-resource, School of Life Science, Yunnan University, Kunming, China
| | - Zhao-Bang Zeng
- Bioinformatics Research Center, Department of Horticultural Science, North Carolina State University, Raleigh, NC, USA
| | - Li-Xian Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,State Key Laboratory for Conservation and Utilization of Bio-resource, School of Life Science, Yunnan University, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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32
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Morgan K, Harr B, White MA, Payseur BA, Turner LM. Disrupted Gene Networks in Subfertile Hybrid House Mice. Mol Biol Evol 2021; 37:1547-1562. [PMID: 32076722 PMCID: PMC7253214 DOI: 10.1093/molbev/msaa002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The Dobzhansky–Muller (DM) model provides a widely accepted mechanism for the evolution of reproductive isolation: incompatible substitutions disrupt interactions between genes. To date, few candidate incompatibility genes have been identified, leaving the genes driving speciation mostly uncharacterized. The importance of interactions in the DM model suggests that gene coexpression networks provide a powerful framework to understand disrupted pathways associated with postzygotic isolation. Here, we perform weighted gene coexpression network analysis to infer gene interactions in hybrids of two recently diverged European house mouse subspecies, Mus mus domesticus and M. m. musculus, which commonly show hybrid male sterility or subfertility. We use genome-wide testis expression data from 467 hybrid mice from two mapping populations: F2s from a laboratory cross between wild-derived pure subspecies strains and offspring of natural hybrids captured in the Central Europe hybrid zone. This large data set enabled us to build a robust consensus network using hybrid males with fertile phenotypes. We identify several expression modules, or groups of coexpressed genes, that are disrupted in subfertile hybrids, including modules functionally enriched for spermatogenesis, cilium and sperm flagellum organization, chromosome organization, and DNA repair, and including genes expressed in spermatogonia, spermatocytes, and spermatids. Our network-based approach enabled us to hone in on specific hub genes likely to be influencing module-wide gene expression and hence potentially driving large-effect DM incompatibilities. A disproportionate number of hub genes lie within sterility loci identified previously in the hybrid zone mapping population and represent promising candidate barrier genes and targets for future functional analysis.
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Affiliation(s)
- Katy Morgan
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Bettina Harr
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | | | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin, Madison, WI
| | - Leslie M Turner
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
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Go AC, Civetta A. Hybrid Incompatibilities and Transgressive Gene Expression Between Two Closely Related Subspecies of Drosophila. Front Genet 2020; 11:599292. [PMID: 33362859 PMCID: PMC7758320 DOI: 10.3389/fgene.2020.599292] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/12/2020] [Indexed: 11/13/2022] Open
Abstract
Genome-wide assays of expression between species and their hybrids have identified genes that become either over- or underexpressed relative to the parental species (i.e., transgressive). Transgressive expression in hybrids is of interest because it highlights possible changes in gene regulation linked to hybrid dysfunction. Previous studies in Drosophila that used long-diverged species pairs with complete or nearly complete isolation (i.e., full sterility and partial inviability of hybrids) and high-levels of genome misregulation have found correlations between expression and coding sequence divergence. The work highlighted the possible effects of directional selection driving sequence divergence and transgressive expression. Whether the same is true for taxa at early stages of divergence that have only achieved partial isolation remains untested. Here, we reanalyze previously published genome expression data and available genome sequence reads from a pair of partially isolated subspecies of Drosophila to compare expression and sequence divergence. We find a significant correlation in rates of expression and sequence evolution, but no support for directional selection driving transgressive expression in hybrids. We find that most transgressive genes in hybrids show no differential expression between parental subspecies and used SNP data to explore the role of stabilizing selection through compensatory mutations. We also examine possible misregulation through cascade effects that could be driven by interacting gene networks or co-option of off-target cis-regulatory elements.
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Affiliation(s)
- Alwyn C Go
- Department of Biology, The University of Winnipeg, Winnipeg, MB, Canada
| | - Alberto Civetta
- Department of Biology, The University of Winnipeg, Winnipeg, MB, Canada
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Mukaj A, Piálek J, Fotopulosova V, Morgan AP, Odenthal-Hesse L, Parvanov ED, Forejt J. Prdm9 Intersubspecific Interactions in Hybrid Male Sterility of House Mouse. Mol Biol Evol 2020; 37:3423-3438. [PMID: 32642764 PMCID: PMC7743643 DOI: 10.1093/molbev/msaa167] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/11/2020] [Accepted: 07/01/2020] [Indexed: 12/12/2022] Open
Abstract
The classical definition posits hybrid sterility as a phenomenon when two parental taxa each of which is fertile produce a hybrid that is sterile. The first hybrid sterility gene in vertebrates, Prdm9, coding for a histone methyltransferase, was identified in crosses between two laboratory mouse strains derived from Mus mus musculus and M. m. domesticus subspecies. The unique function of PRDM9 protein in the initiation of meiotic recombination led to the discovery of the basic molecular mechanism of hybrid sterility in laboratory crosses. However, the role of this protein as a component of reproductive barrier outside the laboratory model remained unclear. Here, we show that the Prdm9 allelic incompatibilities represent the primary cause of reduced fertility in intersubspecific hybrids between M. m. musculus and M. m. domesticus including 16 musculus and domesticus wild-derived strains. Disruption of fertility phenotypes correlated with the rate of failure of synapsis between homologous chromosomes in meiosis I and with early meiotic arrest. All phenotypes were restored to normal when the domesticus Prdm9dom2 allele was substituted with the Prdm9dom2H humanized variant. To conclude, our data show for the first time the male infertility of wild-derived musculus and domesticus subspecies F1 hybrids controlled by Prdm9 as the major hybrid sterility gene. The impairment of fertility surrogates, testes weight and sperm count, correlated with increasing difficulties of meiotic synapsis of homologous chromosomes and with meiotic arrest, which we suppose reflect the increasing asymmetry of PRDM9-dependent DNA double-strand breaks.
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Affiliation(s)
- Amisa Mukaj
- Department of Mouse Molecular Genetics, Institute of Molecular Genetics of the Czech Academy of Science, Vestec, Czech Republic
| | - Jaroslav Piálek
- Research Facility Studenec, Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
| | - Vladana Fotopulosova
- Department of Mouse Molecular Genetics, Institute of Molecular Genetics of the Czech Academy of Science, Vestec, Czech Republic
| | | | - Linda Odenthal-Hesse
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Emil D Parvanov
- Department of Mouse Molecular Genetics, Institute of Molecular Genetics of the Czech Academy of Science, Vestec, Czech Republic
| | - Jiri Forejt
- Department of Mouse Molecular Genetics, Institute of Molecular Genetics of the Czech Academy of Science, Vestec, Czech Republic
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Ishishita S, Tatsumoto S, Kinoshita K, Nunome M, Suzuki T, Go Y, Matsuda Y. Transcriptome analysis revealed misregulated gene expression in blastoderms of interspecific chicken and Japanese quail F1 hybrids. PLoS One 2020; 15:e0240183. [PMID: 33044996 PMCID: PMC7549780 DOI: 10.1371/journal.pone.0240183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/22/2020] [Indexed: 11/29/2022] Open
Abstract
Hybrid incompatibility, such as sterility and inviability, prevents gene flow between closely-related populations as a reproductive isolation barrier. F1 hybrids between chickens and Japanese quail (hereafter, referred to as quail), exhibit a high frequency of developmental arrest at the preprimitive streak stage. To investigate the molecular basis of the developmental arrest at the preprimitive streak stage in chicken–quail F1 hybrid embryos, we investigated chromosomal abnormalities in the hybrid embryos using molecular cytogenetic analysis. In addition, we quantified gene expression in parental species and chicken- and quail-derived allele-specific expression in the hybrids at the early blastoderm and preprimitive streak stages by mRNA sequencing. Subsequently, we compared the directions of change in gene expression, including upregulation, downregulation, or no change, from the early blastoderm stage to the preprimitive streak stage between parental species and their hybrids. Chromosome analysis revealed that the cells of the hybrid embryos contained a fifty-fifty mixture of parental chromosomes, and numerical chromosomal abnormalities were hardly observed in the hybrid cells. Gene expression analysis revealed that a part of the genes that were upregulated from the early blastoderm stage to the preprimitive streak stage in both parental species exhibited no upregulation of both chicken- and quail-derived alleles in the hybrids. GO term enrichment analysis revealed that these misregulated genes are involved in various biological processes, including ribosome-mediated protein synthesis and cell proliferation. Furthermore, the misregulated genes included genes involved in early embryonic development, such as primitive streak formation and gastrulation. These results suggest that numerical chromosomal abnormalities due to a segregation failure does not cause the lethality of chicken–quail hybrid embryos, and that the downregulated expression of the genes that are involved in various biological processes, including translation and primitive streak formation, mainly causes the developmental arrest at the preprimitive streak stage in the hybrids.
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Affiliation(s)
- Satoshi Ishishita
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Shoji Tatsumoto
- Cognitive Genomics Research Group, Exploratory Research Center on Life and Living Systems (ExCELLs), National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Keiji Kinoshita
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Mitsuo Nunome
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Takayuki Suzuki
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
- Laboratory of Avian Bioscience, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Yasuhiro Go
- Cognitive Genomics Research Group, Exploratory Research Center on Life and Living Systems (ExCELLs), National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Yoichi Matsuda
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
- Laboratory of Avian Bioscience, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
- * E-mail:
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Widmayer SJ, Handel MA, Aylor DL. Age and Genetic Background Modify Hybrid Male Sterility in House Mice. Genetics 2020; 216:585-597. [PMID: 32817010 PMCID: PMC7536842 DOI: 10.1534/genetics.120.303474] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 08/11/2020] [Indexed: 12/15/2022] Open
Abstract
Hybrid male sterility (HMS) contributes to reproductive isolation commonly observed among house mouse (Mus musculus) subspecies, both in the wild and in laboratory crosses. Incompatibilities involving specific Prdm9 alleles and certain Chromosome (Chr) X genotypes are known determinants of fertility and HMS, and previous work in the field has demonstrated that genetic background modifies these two major loci. We constructed hybrids that have identical genotypes at Prdm9 and identical X chromosomes, but differ widely across the rest of the genome. In each case, we crossed female PWK/PhJ mice representative of the M. m. musculus subspecies to males from a classical inbred strain representative of M. m. domesticus: 129S1/SvImJ, A/J, C57BL/6J, or DBA/2J. We detected three distinct trajectories of fertility among the hybrids using breeding experiments. The PWK129S1 males were always infertile. PWKDBA2 males were fertile, despite their genotypes at the major HMS loci. We also observed age-dependent changes in fertility parameters across multiple genetic backgrounds. The PWKB6 and PWKAJ males were always infertile before 12 weeks and after 35 weeks. However, some PWKB6 and PWKAJ males were transiently fertile between 12 and 35 weeks. This observation could resolve previous contradictory reports about the fertility of PWKB6. Taken together, these results point to multiple segregating HMS modifier alleles, some of which have age-related modes of action. The ultimate identification of these alleles and their age-related mechanisms will advance understanding both of the genetic architecture of HMS and of how reproductive barriers are maintained between house mouse subspecies.
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Affiliation(s)
- Samuel J Widmayer
- Department of Biological Science, W.M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695
- Graduate Program in Genetics, North Carolina State University, Raleigh, North Carolina 27695
| | | | - David L Aylor
- Department of Biological Science, W.M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695
- Bioinformatics Research Center, Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina 27695
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina 27695
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Phifer-Rixey M, Harr B, Hey J. Further resolution of the house mouse (Mus musculus) phylogeny by integration over isolation-with-migration histories. BMC Evol Biol 2020; 20:120. [PMID: 32933487 PMCID: PMC7493149 DOI: 10.1186/s12862-020-01666-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/27/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The three main subspecies of house mice, Mus musculus castaneus, Mus musculus domesticus, and Mus musculus musculus, are estimated to have diverged ~ 350-500KYA. Resolution of the details of their evolutionary history is complicated by their relatively recent divergence, ongoing gene flow among the subspecies, and complex demographic histories. Previous studies have been limited to some extent by the number of loci surveyed and/or by the scope of the method used. Here, we apply a method (IMa3) that provides an estimate of a population phylogeny while allowing for complex histories of gene exchange. RESULTS Results strongly support a topology with M. m. domesticus as sister to M. m. castaneus and M. m. musculus. In addition, we find evidence of gene flow between all pairs of subspecies, but that gene flow is most restricted from M. m. musculus into M. m. domesticus. Estimates of other key parameters are dependent on assumptions regarding generation time and mutation rate in house mice. Nevertheless, our results support previous findings that the effective population size, Ne, of M. m. castaneus is larger than that of the other two subspecies, that the three subspecies began diverging ~ 130 - 420KYA, and that the time between divergence events was short. CONCLUSIONS Joint demographic and phylogenetic analyses of genomic data provide a clearer picture of the history of divergence in house mice.
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Affiliation(s)
| | - Bettina Harr
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, Plön, Germany
| | - Jody Hey
- Department of Biology, Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, USA
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Satokangas I, Martin SH, Helanterä H, Saramäki J, Kulmuni J. Multi-locus interactions and the build-up of reproductive isolation. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190543. [PMID: 32654649 PMCID: PMC7423273 DOI: 10.1098/rstb.2019.0543] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2020] [Indexed: 12/15/2022] Open
Abstract
All genes interact with other genes, and their additive effects and epistatic interactions affect an organism's phenotype and fitness. Recent theoretical and empirical work has advanced our understanding of the role of multi-locus interactions in speciation. However, relating different models to one another and to empirical observations is challenging. This review focuses on multi-locus interactions that lead to reproductive isolation (RI) through reduced hybrid fitness. We first review theoretical approaches and show how recent work incorporating a mechanistic understanding of multi-locus interactions recapitulates earlier models, but also makes novel predictions concerning the build-up of RI. These include high variance in the build-up rate of RI among taxa, the emergence of strong incompatibilities producing localized barriers to introgression, and an effect of population size on the build-up of RI. We then review recent experimental approaches to detect multi-locus interactions underlying RI using genomic data. We argue that future studies would benefit from overlapping methods like ancestry disequilibrium scans, genome scans of differentiation and analyses of hybrid gene expression. Finally, we highlight a need for further overlap between theoretical and empirical work, and approaches that predict what kind of patterns multi-locus interactions resulting in incompatibilities will leave in genome-wide polymorphism data. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
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Affiliation(s)
- I. Satokangas
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Viikinkaari 1, PO Box 65, 00014 Helsinki, Finland
| | - S. H. Martin
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh EH9 3FL, UK
| | - H. Helanterä
- Ecology and Genetics research unit, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - J. Saramäki
- Department of Computer Science, Aalto University, PO Box 11000, 00076 Aalto, Espoo, Finland
| | - J. Kulmuni
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Viikinkaari 1, PO Box 65, 00014 Helsinki, Finland
- Tvärminne Zoological Station, University of Helsinki, J. A. Palménin tie 260, 10900 Hanko, Finland
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Spatial and Temporal Dynamics of Contact Zones Between Chromosomal Races of House Mice, Mus musculus domesticus, on Madeira Island. Genes (Basel) 2020; 11:genes11070748. [PMID: 32640559 PMCID: PMC7397221 DOI: 10.3390/genes11070748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/30/2020] [Accepted: 07/01/2020] [Indexed: 01/29/2023] Open
Abstract
Analysis of contact zones between parapatric chromosomal races can help our understanding of chromosomal divergence and its influence on the speciation process. Monitoring the position and any movement of contact zones can allow particular insights. This study investigates the present (2012-2014) and past (1998-2002) distribution of two parapatric house mouse chromosomal races-PEDC (Estreito da Calheta) and PADC (Achadas da Cruz)-on Madeira Island, aiming to identify changes in the location and width of their contact. We also extended the 1998-2002 sampling area into the range of another chromosomal race-PLDB (Lugar de Baixo). Clinal analysis indicates no major geographic alterations in the distribution and chromosomal characteristics of the PEDC and PADC races but exhibited a significant shift in position of the Rb (7.15) fusion, resulting in the narrowing of the contact zone over a 10+ year period. We discuss how this long-lasting contact zone highlights the role of landscape on mouse movements, in turn influencing the chromosomal characteristics of populations. The expansion of the sampling area revealed new chromosomal features in the north and a new contact zone in the southern range involving the PEDC and PLDB races. We discuss how different interacting mechanisms (landscape resistance, behaviour, chromosomal incompatibilities, meiotic drive) may help to explain the pattern of chromosomal variation at these contacts between chromosomal races.
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Affiliation(s)
- Andrius J Dagilis
- Department of Biology, University of North Carolina, Chapel Hill, NC 27514, USA.
| | - Daniel R Matute
- Department of Biology, University of North Carolina, Chapel Hill, NC 27514, USA.
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Wagner DN, Curry RL, Chen N, Lovette IJ, Taylor SA. Genomic regions underlying metabolic and neuronal signaling pathways are temporally consistent in a moving avian hybrid zone. Evolution 2020; 74:1498-1513. [PMID: 32243568 DOI: 10.1111/evo.13970] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 03/25/2020] [Accepted: 03/26/2020] [Indexed: 12/15/2022]
Abstract
The study of hybrid zones can provide insight into the genetic basis of species differences that are relevant for the maintenance of reproductive isolation. Hybrid zones can also provide insight into climate change, species distributions, and evolution. The hybrid zone between black-capped chickadees (Poecile atricapillus) and Carolina chickadees (Poecile carolinensis) is shifting northward in response to increasing winter temperatures but is not increasing in width. This pattern indicates strong selection against chickadees with admixed genomes. Using high-resolution genomic data, we identified regions of the genomes that are outliers in both time points and do not introgress between the species; these regions may be involved in the maintenance of reproductive isolation. Genes involved in metabolic regulation processes were overrepresented in this dataset. Several gene ontology categories were also temporally consistent-including glutamate signaling, synaptic transmission, and catabolic processes-but the nucleotide variants leading to this pattern were not. Our results support recent findings that hybrids between black-capped and Carolina chickadees have higher basal metabolic rates than either parental species and suffer spatial memory and problem-solving deficits. Metabolic breakdown, as well as spatial memory and problem-solving, in hybrid chickadees may act as strong postzygotic isolation mechanisms in this moving hybrid zone.
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Affiliation(s)
- Dominique N Wagner
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, 80309
| | - Robert L Curry
- Department of Biology, Villanova University, Villanova, Pennsylvania, 19085
| | - Nancy Chen
- Department of Biology, University of Rochester, Rochester, New York, 14627
| | - Irby J Lovette
- Cornell Lab of Ornithology, Cornell University, Ithaca, New York, 14850
| | - Scott A Taylor
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, 80309
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Abstract
Mice (Mus musculus) and rats (Rattus norvegicus) have long served as model systems for biomedical research. However, they are also excellent models for studying the evolution of populations, subspecies, and species. Within the past million years, they have spread in various waves across large parts of the globe, with the most recent spread in the wake of human civilization. They have developed into commensal species, but have also been able to colonize extreme environments on islands free of human civilization. Given that ample genomic and genetic resources are available for these species, they have thus also become ideal mammalian systems for evolutionary studies on adaptation and speciation, particularly in the combination with the rapid developments in population genomics. The chapter provides an overview of the systems and their history, as well as of available resources.
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Affiliation(s)
- Kristian K Ullrich
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany.
| | - Diethard Tautz
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
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Johannesson K, Zagrodzka Z, Faria R, Marie Westram A, Butlin RK. Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? J Evol Biol 2019; 33:342-351. [PMID: 31724256 PMCID: PMC7079066 DOI: 10.1111/jeb.13570] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 11/07/2019] [Accepted: 11/12/2019] [Indexed: 11/25/2022]
Abstract
Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the "Crab" and "Wave" ecotypes of the snail Littorina saxatilis, divergent selection forms strong barriers to gene flow, while the role of post‐zygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Post‐zygotic barriers might include genetic incompatibilities (e.g. Dobzhansky–Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1,011 embryos (mean 130 ± 123), and abortion rates varied between 0% and 100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterized female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index, and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant post‐zygotic barriers contributing to ecotype divergence, and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females.
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Affiliation(s)
- Kerstin Johannesson
- Department of Marine Sciences at Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Zuzanna Zagrodzka
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Rui Faria
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | | | - Roger K Butlin
- Department of Marine Sciences at Tjärnö, University of Gothenburg, Strömstad, Sweden.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
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Go A, Alhazmi D, Civetta A. Altered expression of cell adhesion genes and hybrid male sterility between subspecies ofDrosophila pseudoobscura. Genome 2019; 62:657-663. [DOI: 10.1139/gen-2019-0066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Drosophila pseudoobscura pseudoobscura and Drosophila pseudoobscura bogotana are two closely related subspecies with incomplete reproductive isolation. A genome-wide comparison of expression in hybrids relative to parental subspecies has been previously used to identify genes with significant changes in expression uniquely associated with the sterile condition. The misexpression (i.e., gene expression beyond levels found in parentals) of such genes could be directly linked to the onset of sterility or could alternatively be caused by incompatibilities in a hybrid genome without a direct link to sterility. Cell adhesion was previously found to be one of the largest gene ontologies with changes in expression linked to sterility. Here we used gene expression assays in fertile backcross male progeny, along with introgression progeny in which we swap a major hybrid male sterility (HMS) allele, to generate fertile and sterile males genotypically similar to F1sterile hybrids. We identify a cell adhesion gene (GA10921) whose change in expression is directly linked to sterility and modulated by a previously characterized HMS protein. GA10921 adds to our rather limited knowledge of changes in gene expression associated with HMS, and to the identification of gene interacting partners linked to HMS.
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Affiliation(s)
- Alwyn Go
- Department of Biology, University of Winnipeg, Winnipeg, MB R3B 2E9, Canada
- Department of Biology, University of Winnipeg, Winnipeg, MB R3B 2E9, Canada
| | - Doaa Alhazmi
- Department of Biology, University of Winnipeg, Winnipeg, MB R3B 2E9, Canada
- Department of Biology, University of Winnipeg, Winnipeg, MB R3B 2E9, Canada
| | - Alberto Civetta
- Department of Biology, University of Winnipeg, Winnipeg, MB R3B 2E9, Canada
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Tusso S, Nieuwenhuis BPS, Sedlazeck FJ, Davey JW, Jeffares DC, Wolf JBW. Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast. Mol Biol Evol 2019; 36:1975-1989. [PMID: 31225876 PMCID: PMC6736153 DOI: 10.1093/molbev/msz126] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mutation and recombination are key evolutionary processes governing phenotypic variation and reproductive isolation. We here demonstrate that biodiversity within all globally known strains of Schizosaccharomyces pombe arose through admixture between two divergent ancestral lineages. Initial hybridization was inferred to have occurred ∼20-60 sexual outcrossing generations ago consistent with recent, human-induced migration at the onset of intensified transcontinental trade. Species-wide heritable phenotypic variation was explained near-exclusively by strain-specific arrangements of alternating ancestry components with evidence for transgressive segregation. Reproductive compatibility between strains was likewise predicted by the degree of shared ancestry. To assess the genetic determinants of ancestry block distribution across the genome, we characterized the type, frequency, and position of structural genomic variation using nanopore and single-molecule real-time sequencing. Despite being associated with double-strand break initiation points, over 800 segregating structural variants exerted overall little influence on the introgression landscape or on reproductive compatibility between strains. In contrast, we found strong ancestry disequilibrium consistent with negative epistatic selection shaping genomic ancestry combinations during the course of hybridization. This study provides a detailed, experimentally tractable example that genomes of natural populations are mosaics reflecting different evolutionary histories. Exploiting genome-wide heterogeneity in the history of ancestral recombination and lineage-specific mutations sheds new light on the population history of S. pombe and highlights the importance of hybridization as a creative force in generating biodiversity.
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Affiliation(s)
- Sergio Tusso
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
- Department of Evolutionary Biology, Science for Life Laboratories, Uppsala University, Uppsala, Sweden
| | - Bart P S Nieuwenhuis
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - John W Davey
- Bioscience Technology Facility, Department of Biology, University of York, York, United Kingdom
| | - Daniel C Jeffares
- Department of Biology, University of York, York, United Kingdom
- York Biomedical Research Institute (YBRI), University of York, York, United Kingdom
| | - Jochen B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
- Department of Evolutionary Biology, Science for Life Laboratories, Uppsala University, Uppsala, Sweden
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Bresadola L, Caseys C, Castiglione S, Buerkle CA, Wegmann D, Lexer C. Admixture mapping in interspecific Populus hybrids identifies classes of genomic architectures for phytochemical, morphological and growth traits. THE NEW PHYTOLOGIST 2019; 223:2076-2089. [PMID: 31104343 PMCID: PMC6771622 DOI: 10.1111/nph.15930] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 05/06/2019] [Indexed: 05/03/2023]
Abstract
The genomic architecture of functionally important traits is key to understanding the maintenance of reproductive barriers and trait differences when divergent populations or species hybridize. We conducted a genome-wide association study (GWAS) to study trait architecture in natural hybrids of two ecologically divergent Populus species. We genotyped 472 seedlings from a natural hybrid zone of Populus alba and Populus tremula for genome-wide markers from reduced representation sequencing, phenotyped the plants in common gardens for 46 phytochemical (phenylpropanoid), morphological and growth traits, and used a Bayesian polygenic model for mapping. We detected three classes of genomic architectures: traits with finite, detectable associations of genetic loci with phenotypic variation in addition to highly polygenic heritability; traits with indications for polygenic heritability only; and traits with no detectable heritability. For the first class, we identified genome regions with plausible candidate genes for phenylpropanoid biosynthesis or its regulation, including MYB transcription factors and glycosyl transferases. GWAS in natural, recombinant hybrids represent a promising step towards resolving the genomic architecture of phenotypic traits in long-lived species. This facilitates the fine-mapping and subsequent functional characterization of genes and networks causing differences in hybrid performance and fitness.
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Affiliation(s)
- Luisa Bresadola
- Department of BiologyUniversity of FribourgChemin du Musée 101700FribourgSwitzerland
| | - Céline Caseys
- Department of BiologyUniversity of FribourgChemin du Musée 101700FribourgSwitzerland
- Department of Plant SciencesUniversity of California DavisOne Shields AvenueDavisCA95616USA
| | - Stefano Castiglione
- Department of Chemistry and Biology ‘A. Zambelli’University of SalernoVia Giovanni Paolo II 13284084Fisciano, SalernoItaly
| | - C. Alex Buerkle
- Department of BotanyUniversity of Wyoming1000 E. University Ave.LaramieWY82071USA
| | - Daniel Wegmann
- Department of BiologyUniversity of FribourgChemin du Musée 101700FribourgSwitzerland
- Swiss Institute of Bioinformatics1700FribourgSwitzerland
| | - Christian Lexer
- Department of BiologyUniversity of FribourgChemin du Musée 101700FribourgSwitzerland
- Department of Botany and Biodiversity ResearchFaculty of Life SciencesUniversity of ViennaRennweg 12A‐1030ViennaAustria
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Lima CS, Magalhães RF, Marmontel M, Meirelles AC, Carvalho VL, Lavergne A, Thoisy BDE, Santos FR. A hybrid swarm of manatees along the Guianas coastline, a peculiar environment under the influence of the Amazon River plume. AN ACAD BRAS CIENC 2019; 91:e20190325. [PMID: 31460594 DOI: 10.1590/0001-3765201920190325] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/29/2019] [Indexed: 12/23/2022] Open
Abstract
The West Indian (Trichechus manatus) and Amazonian (T. inunguis) manatees have a sympatric occurrence at the mouth of the Amazon River. A result of this interspecific encounter is the occurrence of hybrids, which are frequently found along the coasts of Amapá state in Brazil, French Guiana and Guyana. Here we present new genetic evidence indicating the occurrence of a hybrid swarm along the Guianas Shield coastline, which is an interspecific hybrid zone that also separates T. manatus populations located east (Brazil) and west (Caribbean, Gulf of Mexico, Florida and Antilles). In addition, we suggest that this hybrid population occupies a peculiar mangrove-rich environment under strong influence of the Amazon River plume, which requires an independent management and should be considered a special conservation area.
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Affiliation(s)
- Camilla S Lima
- Laboratório de Biodiversidade e Evolução Molecular, Departamento de Genética, Ecologia e Evolução, ICB, Universidade Federal de Minas Gerais, Av. Antonio Carlos, 6627, 31270-010 Belo Horizonte, MG, Brazil
| | - Rafael F Magalhães
- Programa de Pós-Graduação em Zoologia, Departamento de Zoologia, ICB, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, 31270-901 Belo Horizonte, MG, Brazil
| | - Miriam Marmontel
- Instituto de Desenvolvimento Sustentável Mamirauá, Estrada do Bexiga, 2584, Fonte Boa, 69553-225 Tefé, AM, Brazil
| | - Ana Carolina Meirelles
- Associação de Pesquisa e Preservação de Ecossistemas Aquáticos/Aquasis, Av. José Alencar, 150, Sesc Iparana, 61627-010 Caucaia, CE, Brazil
| | - Vitor Luz Carvalho
- Associação de Pesquisa e Preservação de Ecossistemas Aquáticos/Aquasis, Av. José Alencar, 150, Sesc Iparana, 61627-010 Caucaia, CE, Brazil
| | - Anne Lavergne
- Institut Pasteur de Guyane, 23 Avenue Pasteur, BP 6010, Cayenne Cedex 97306, French Guiana, France
| | - Benoit DE Thoisy
- Institut Pasteur de Guyane, 23 Avenue Pasteur, BP 6010, Cayenne Cedex 97306, French Guiana, France.,Kwata NGO, 16 Avenue Pasteur, BP 60672 97335, Cayenne, French Guiana, France
| | - Fabrício R Santos
- Laboratório de Biodiversidade e Evolução Molecular, Departamento de Genética, Ecologia e Evolução, ICB, Universidade Federal de Minas Gerais, Av. Antonio Carlos, 6627, 31270-010 Belo Horizonte, MG, Brazil
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48
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Taylor SA, Larson EL. Insights from genomes into the evolutionary importance and prevalence of hybridization in nature. Nat Ecol Evol 2019; 3:170-177. [DOI: 10.1038/s41559-018-0777-y] [Citation(s) in RCA: 211] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 12/04/2018] [Indexed: 01/27/2023]
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49
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Cortés-Ortiz L, Baiz MD, Hermida-Lagunes J, García-Orduña F, Rangel-Negrín A, Kitchen DM, Bergman TJ, Dias PAD, Canales-Espinosa D. Reduced Introgression of Sex Chromosome Markers in the Mexican Howler Monkey ( Alouatta palliata × A. pigra) Hybrid Zone. INT J PRIMATOL 2019; 40:114-131. [PMID: 30880850 PMCID: PMC6394575 DOI: 10.1007/s10764-018-0056-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 06/07/2018] [Indexed: 01/12/2023]
Abstract
Interspecific hybridization allows the introgression or movement of alleles from one genome to another. While some genomic regions freely exchange alleles during hybridization, loci associated with reproductive isolation do not intermix. In many model organisms, the X chromosome displays limited introgression compared to autosomes owing to the presence of multiple loci associated with hybrid sterility or inviability (the "large X-effect"). Similarly, if hybrids are produced, the heterogametic sex is usually inviable or sterile, a pattern known as Haldane's rule. We analyzed the patterns of introgression of genetic markers located in the mitochondrial (control region) and nuclear (autosomal microsatellites and sex chromosome genes) genomes of two howler monkey species (Alouatta palliata and A. pigra) that form a natural hybrid zone in southern Mexico, to evaluate whether the large X-effect and Haldane's rule affect the outcomes of hybridization between these sister species. To identify the level of admixture of each individual in the hybrid zone (N = 254) we analyzed individuals sampled outside the hybrid zone (109 A. pigra and 39 A. palliata) to determine allele frequencies of parental species and estimated a hybrid index based on nuclear markers. We then performed a cline analysis using individuals in the hybrid zone to determine patterns of introgression for each locus. Our analyses show that although the hybrid zone is bimodal (with no known F1 s and few recent generation hybrids) and quite narrow, there has been extensive introgression in both directions, and there is a large array of admixed individuals in the hybrid zone. Mitochondrial and most autosomal markers showed bidirectional introgression, but some had biased introgression toward one species or the other. All markers on the sex chromosomes and a few autosomal markers showed highly restricted introgression. This pattern is consistent with the hypothesis that the sex chromosomes make a disproportionate contribution to reproductive isolation, and our results broaden the taxonomic representation of these patterns across animal taxa.
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Affiliation(s)
- Liliana Cortés-Ortiz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48103 USA
| | - Marcella D Baiz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48103 USA
| | | | | | | | - Dawn M Kitchen
- Department of Anthropology, The Ohio State University, Columbus, OH 43210 USA
| | - Thore J Bergman
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48103 USA.,Department of Psychology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Pedro A D Dias
- Instituto de Neuroetología, Universidad Veracruzana, Xalapa, Veracruz, Mexico
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50
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Schwahn DJ, Wang RJ, White MA, Payseur BA. Genetic Dissection of Hybrid Male Sterility Across Stages of Spermatogenesis. Genetics 2018; 210:1453-1465. [PMID: 30333190 PMCID: PMC6283182 DOI: 10.1534/genetics.118.301658] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/12/2018] [Indexed: 12/19/2022] Open
Abstract
Hybrid sterility is a common form of reproductive isolation between nascent species. Although hybrid sterility is routinely documented and genetically dissected in speciation studies, its developmental basis is rarely examined, especially in generations beyond the F1 generation. To identify phenotypic and genetic determinants of hybrid male sterility from a developmental perspective, we characterized testis histology in 312 F2 hybrids generated by intercrossing inbred strains of Mus musculus domesticus and M. m. musculus, two subspecies of house mice. Hybrids display a range of histologic abnormalities that indicate defective spermatogenesis. Among these abnormalities, we quantified decreased testis size, reductions in spermatocyte and spermatid number, increased apoptosis of meiosis I spermatocytes, and more multinucleated syncytia. Collectively, our phenotypic data point to defects in meiosis I as a primary barrier to reproduction. We identified seven quantitative trait loci (QTL) controlling five histologic traits. A region of chromosome 17 that contains Prdm9, a gene known to confer F1 hybrid male sterility, affects multinucleated syncytia and round spermatids, potentially extending the phenotypic outcomes of this incompatibility. The X chromosome also plays a key role, with loci affecting multinucleated syncytia, apoptosis of round spermatids, and round spermatid numbers. We detected an epistatic interaction between QTL on chromosomes 17 and X for multinucleated syncytia. Our results refine the developmental basis of a key reproductive barrier in a classic model system for speciation genetics.
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Affiliation(s)
- Denise J Schwahn
- Research Animal Resources Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Richard J Wang
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Michael A White
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
- Department of Genetics, University of Georgia, Athens, Georgia 30602
| | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
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