1
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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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2
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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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3
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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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4
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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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5
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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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6
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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] [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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7
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Palma-Vera SE, Reyer H, Langhammer M, Reinsch N, Derezanin L, Fickel J, Qanbari S, Weitzel JM, Franzenburg S, Hemmrich-Stanisak G, Schoen J. Genomic characterization of the world's longest selection experiment in mouse reveals the complexity of polygenic traits. BMC Biol 2022; 20:52. [PMID: 35189878 PMCID: PMC8862358 DOI: 10.1186/s12915-022-01248-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 02/07/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Long-term selection experiments are a powerful tool to understand the genetic background of complex traits. The longest of such experiments has been conducted in the Research Institute for Farm Animal Biology (FBN), generating extreme mouse lines with increased fertility, body mass, protein mass and endurance. For >140 generations, these lines have been maintained alongside an unselected control line, representing a valuable resource for understanding the genetic basis of polygenic traits. However, their history and genomes have not been reported in a comprehensive manner yet. Therefore, the aim of this study is to provide a summary of the breeding history and phenotypic traits of these lines along with their genomic characteristics. We further attempt to decipher the effects of the observed line-specific patterns of genetic variation on each of the selected traits. RESULTS Over the course of >140 generations, selection on the control line has given rise to two extremely fertile lines (>20 pups per litter each), two giant growth lines (one lean, one obese) and one long-distance running line. Whole genome sequencing analysis on 25 animals per line revealed line-specific patterns of genetic variation among lines, as well as high levels of homozygosity within lines. This high degree of distinctiveness results from the combined effects of long-term continuous selection, genetic drift, population bottleneck and isolation. Detection of line-specific patterns of genetic differentiation and structural variation revealed multiple candidate genes behind the improvement of the selected traits. CONCLUSIONS The genomes of the Dummerstorf trait-selected mouse lines display distinct patterns of genomic variation harbouring multiple trait-relevant genes. Low levels of within-line genetic diversity indicate that many of the beneficial alleles have arrived to fixation alongside with neutral alleles. This study represents the first step in deciphering the influence of selection and neutral evolutionary forces on the genomes of these extreme mouse lines and depicts the genetic complexity underlying polygenic traits.
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Affiliation(s)
- Sergio E Palma-Vera
- Institute of Reproductive Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.
| | - Henry Reyer
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Martina Langhammer
- Institute of Genetics and Biometry, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Norbert Reinsch
- Institute of Genetics and Biometry, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Lorena Derezanin
- Institute of Reproductive Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
- Department of Evolutionary Genetics, Research Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | - Joerns Fickel
- Department of Evolutionary Genetics, Research Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
- University of Potsdam, Institute for Biochemistry and Biology, Potsdam, Germany
| | - Saber Qanbari
- Institute of Genetics and Biometry, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Joachim M Weitzel
- Institute of Reproductive Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | | | | | - Jennifer Schoen
- Institute of Reproductive Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
- Department of Reproduction Biology, Research Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
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8
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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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9
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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] [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)
| | - Jeffrey M. Good
- University of Montana, Division of Biological Sciences, Missoula, MO, 59812
| | - Erica L. Larson
- University of Denver, Department of Biological Sciences, Denver, CO, 80208
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10
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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: 17] [Impact Index Per Article: 5.7] [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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11
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Nomura S, Fujisawa T, Sota T. Role of sex-concordant gene expression in the coevolution of exaggerated male and female genitalia in a beetle group. Mol Biol Evol 2021; 38:3593-3605. [PMID: 33905498 PMCID: PMC8382896 DOI: 10.1093/molbev/msab122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Some sexual traits, including genitalia, have undergone coevolutionary diversification
toward exaggerated states in both sexes among closely related species, but the underlying
genetic mechanisms that allow correlated character evolution between the sexes are poorly
understood. Here, we studied interspecific differences in gene expression timing profiles
involved in the correlated evolution of corresponding male and female genital parts in
three species of ground beetle in Carabus (Ohomopterus).
The male and female genital parts maintain morphological matching, whereas large
interspecific variation in genital part size has occurred in the genital coevolution
between the sexes toward exaggeration. We analyzed differences in gene expression involved
in the interspecific differences in genital morphology using whole transcriptome data from
genital tissues during genital morphogenesis. We found that the gene expression variance
attributed to sex was negligible for the majority of differentially expressed genes, thus
exhibiting sex-concordant expression, although large variances were attributed to stage
and species differences. For each sex, we obtained co-expression gene networks and hub
genes from differentially expressed genes between species that might be involved in
interspecific differences in genital morphology. These gene networks were common to both
sexes, and both sex-discordant and sex-concordant gene expression were likely involved in
species-specific genital morphology. In particular, the gene expression related to
exaggerated genital size showed no significant intersexual differences, implying that the
genital sizes in both sexes are controlled by the same gene network with sex-concordant
expression patterns, thereby facilitating the coevolution of exaggerated genitalia between
the sexes while maintaining intersexual matching.
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Affiliation(s)
- Shota Nomura
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, Japan
| | - Tomochika Fujisawa
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, Japan.,The Center for Data Science Education and Research, Shiga University, Hikone, Shiga, 522-8522, Japan
| | - Teiji Sota
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, Japan
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12
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Brekke TD, Moore EC, Campbell-Staton SC, Callahan CM, Cheviron ZA, Good JM. X chromosome-dependent disruption of placental regulatory networks in hybrid dwarf hamsters. Genetics 2021; 218:6168998. [PMID: 33710276 DOI: 10.1093/genetics/iyab043] [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: 10/23/2020] [Accepted: 02/16/2021] [Indexed: 11/14/2022] Open
Abstract
Embryonic development in mammals is highly sensitive to changes in gene expression within the placenta. The placenta is also highly enriched for genes showing parent-of-origin or imprinted expression, which is predicted to evolve rapidly in response to parental conflict. However, little is known about the evolution of placental gene expression, or if divergence of placental gene expression plays an important role in mammalian speciation. We used crosses between two species of dwarf hamsters (Phodopus sungorus and Phodopus campbelli) to examine the genetic and regulatory underpinnings of severe placental overgrowth in their hybrids. Using quantitative genetic mapping and mitochondrial substitution lines, we show that overgrowth of hybrid placentas was primarily caused by genetic differences on the maternally inherited P. sungorus X chromosome. Mitochondrial interactions did not contribute to abnormal hybrid placental development, and there was only weak correspondence between placental disruption and embryonic growth. Genome-wide analyses of placental transcriptomes from the parental species and first- and second-generation hybrids revealed a central group of co-expressed X-linked and autosomal genes that were highly enriched for maternally biased expression. Expression of this gene network was strongly correlated with placental size and showed widespread misexpression dependent on epistatic interactions with X-linked hybrid incompatibilities. Collectively, our results indicate that the X chromosome is likely to play a prominent role in the evolution of placental gene expression and the accumulation of hybrid developmental barriers between mammalian species.
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Affiliation(s)
- Thomas D Brekke
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA.,School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - Emily C Moore
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
| | - Shane C Campbell-Staton
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA.,Department of Ecology and Evolutionary Biology; Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Colin M Callahan
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
| | - Zachary A Cheviron
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
| | - Jeffrey M Good
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
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13
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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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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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