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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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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3
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Stankowski S, Chase MA, McIntosh H, Streisfeld MA. Integrating top-down and bottom-up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. Mol Ecol 2023; 32:2041-2054. [PMID: 36651268 DOI: 10.1111/mec.16849] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/04/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023]
Abstract
Understanding the phenotypic and genetic architecture of reproductive isolation is a long-standing goal of speciation research. In several systems, large-effect loci contributing to barrier phenotypes have been characterized, but such causal connections are rarely known for more complex genetic architectures. In this study, we combine "top-down" and "bottom-up" approaches with demographic modelling toward an integrated understanding of speciation across a monkeyflower hybrid zone. Previous work suggests that pollinator visitation acts as a primary barrier to gene flow between two divergent red- and yellow-flowered ecotypes of Mimulus aurantiacus. Several candidate isolating traits and anonymous single nucleotide polymorphism loci under divergent selection have been identified, but their genomic positions remain unknown. Here, we report findings from demographic analyses that indicate this hybrid zone formed by secondary contact, but that subsequent gene flow was restricted by widespread barrier loci across the genome. Using a novel, geographic cline-based genome scan, we demonstrate that candidate barrier loci are broadly distributed across the genome, rather than mapping to one or a few "islands of speciation." Quantitative trait locus (QTL) mapping reveals that most floral traits are highly polygenic, with little evidence that QTL colocalize, indicating that most traits are genetically independent. Finally, we find little evidence that QTL and candidate barrier loci overlap, suggesting that some loci contribute to other forms of reproductive isolation. Our findings highlight the challenges of understanding the genetic architecture of reproductive isolation and reveal that barriers to gene flow other than pollinator isolation may play an important role in this system.
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Affiliation(s)
- Sean Stankowski
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Madeline A Chase
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Hanna McIntosh
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
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4
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Díaz‐Ruiz F, Vaquerizas PH, Márquez AL, Delibes‐Mateos M, Piorno V, Castro F, Ramírez E, Farfán MÁ, Olivero J, Real R, Villafuerte R. Unravelling the historical biogeography of the European rabbit subspecies in the Iberian Peninsula. Mamm Rev 2022. [DOI: 10.1111/mam.12306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Francisco Díaz‐Ruiz
- Biogeography, Diversity and Conservation Research Team, Dpto. Biología Animal, Facultad de Ciencias Universidad de Málaga Campus de Teatinos 29071 Málaga Spain
| | - Patricia H. Vaquerizas
- Instituto de Estudios Sociales Avanzados (IESA‐CSIC) Campo Santo de los Mártires 7 14004 Córdoba Spain
| | - Ana Luz Márquez
- Biogeography, Diversity and Conservation Research Team, Dpto. Biología Animal, Facultad de Ciencias Universidad de Málaga Campus de Teatinos 29071 Málaga Spain
| | - Miguel Delibes‐Mateos
- Instituto de Estudios Sociales Avanzados (IESA‐CSIC) Campo Santo de los Mártires 7 14004 Córdoba Spain
| | - Vicente Piorno
- Parque Nacional de las Islas Atlánticas de Galicia. Consellería de Medio Ambiente Territorio e Vivenda. Xunta de Galicia Rúa Oliva 3 36202 Vigo Pontevedra Spain
| | - Francisca Castro
- Departamento de Didácticas Específicas, Avda. San Alberto Magno, Universidad de Córdoba, “Sociedad, Ecología y Gestión del Medio Ambiente, UCO‐IESA” Unidad Asociada al CSIC 14004 Córdoba Spain
| | - Esther Ramírez
- Instituto de Investigación en Recursos Cinegéticos (IREC) CSIC‐UCLM‐JCCM Ronda de Toledo n° 12 13071 Ciudad Real Spain
| | - Miguel Ángel Farfán
- Biogeography, Diversity and Conservation Research Team, Dpto. Biología Animal, Facultad de Ciencias Universidad de Málaga Campus de Teatinos 29071 Málaga Spain
| | - Jesús Olivero
- Biogeography, Diversity and Conservation Research Team, Dpto. Biología Animal, Facultad de Ciencias Universidad de Málaga Campus de Teatinos 29071 Málaga Spain
- Instituto IBYDA Centro de Experimentación Grice‐Hutchinson Loma de San Julián 2, Barriada de San Julián 29004 Málaga Spain
| | - Raimundo Real
- Biogeography, Diversity and Conservation Research Team, Dpto. Biología Animal, Facultad de Ciencias Universidad de Málaga Campus de Teatinos 29071 Málaga Spain
- Instituto IBYDA Centro de Experimentación Grice‐Hutchinson Loma de San Julián 2, Barriada de San Julián 29004 Málaga Spain
| | - Rafael Villafuerte
- Instituto de Estudios Sociales Avanzados (IESA‐CSIC) Campo Santo de los Mártires 7 14004 Córdoba Spain
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5
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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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6
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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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7
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Fraïsse C, Sachdeva H. The rates of introgression and barriers to genetic exchange between hybridizing species: sex chromosomes vs autosomes. Genetics 2021; 217:6042694. [PMID: 33724409 DOI: 10.1093/genetics/iyaa025] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/23/2020] [Indexed: 12/14/2022] Open
Abstract
Interspecific crossing experiments have shown that sex chromosomes play a major role in reproductive isolation between many pairs of species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has rarely been evaluated quantitatively compared to Autosomes. This genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of an XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow for the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different sex-averaged effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression on the X (or Z) compared to autosomes. This effect can be enhanced by certain types of sex-biased forces, but it remains overall small (except when alleles causing incompatibilities are recessive). We discuss these predictions in the light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems.
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Affiliation(s)
- Christelle Fraïsse
- Institute of Science and Technology Austria, Klosterneuburg 3400, Austria.,CNRS, Univ. Lille, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Himani Sachdeva
- Institute of Science and Technology Austria, Klosterneuburg 3400, Austria.,Mathematics and BioSciences Group, Faculty of Mathematics, University of Vienna, A-1090 Vienna, Austria
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8
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Clinal genomic analysis reveals strong reproductive isolation across a steep habitat transition in stickleback fish. Nat Commun 2021; 12:4850. [PMID: 34381033 PMCID: PMC8358029 DOI: 10.1038/s41467-021-25039-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 07/20/2021] [Indexed: 11/29/2022] Open
Abstract
How ecological divergence causes strong reproductive isolation between populations in close geographic contact remains poorly understood at the genomic level. We here study this question in a stickleback fish population pair adapted to contiguous, ecologically different lake and stream habitats. Clinal whole-genome sequence data reveal numerous genome regions (nearly) fixed for alternative alleles over a distance of just a few hundred meters. This strong polygenic adaptive divergence must constitute a genome-wide barrier to gene flow because a steep cline in allele frequencies is observed across the entire genome, and because the cline center closely matches the habitat transition. Simulations confirm that such strong divergence can be maintained by polygenic selection despite high dispersal and small per-locus selection coefficients. Finally, comparing samples from near the habitat transition before and after an unusual ecological perturbation demonstrates the fragility of the balance between gene flow and selection. Overall, our study highlights the efficacy of divergent selection in maintaining reproductive isolation without physical isolation, and the analytical power of studying speciation at a fine eco-geographic and genomic scale. How ecological divergence causes reproductive isolation between populations in close contact remains poorly understood at the genomic level. This study presents a clinal investigation based on whole-genome sequencing to characterize reproductive isolation between threespine stickleback adapted to contiguous but ecologically different lake and stream habitats.
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9
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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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10
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Velo-Antón G, Lourenço A, Galán P, Nicieza A, Tarroso P. Landscape resistance constrains hybridization across contact zones in a reproductively and morphologically polymorphic salamander. Sci Rep 2021; 11:9259. [PMID: 33927228 PMCID: PMC8085075 DOI: 10.1038/s41598-021-88349-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/07/2021] [Indexed: 02/02/2023] Open
Abstract
Explicitly accounting for phenotypic differentiation together with environmental heterogeneity is crucial to understand the evolutionary dynamics in hybrid zones. Species showing intra-specific variation in phenotypic traits that meet across environmentally heterogeneous regions constitute excellent natural settings to study the role of phenotypic differentiation and environmental factors in shaping the spatial extent and patterns of admixture in hybrid zones. We studied three environmentally distinct contact zones where morphologically and reproductively divergent subspecies of Salamandra salamandra co-occur: the pueriparous S. s. bernardezi that is mostly parapatric to its three larviparous subspecies neighbours. We used a landscape genetics framework to: (i) characterise the spatial location and extent of each contact zone; (ii) assess patterns of introgression and hybridization between subspecies pairs; and (iii) examine the role of environmental heterogeneity in the evolutionary dynamics of hybrid zones. We found high levels of introgression between parity modes, and between distinct phenotypes, thus demonstrating the evolution to pueriparity alone or morphological differentiation do not lead to reproductive isolation between these highly divergent S. salamandra morphotypes. However, we detected substantial variation in patterns of hybridization across contact zones, being lower in the contact zone located on a topographically complex area. We highlight the importance of accounting for spatial environmental heterogeneity when studying evolutionary dynamics of hybrid zones.
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Affiliation(s)
- Guillermo Velo-Antón
- grid.5808.50000 0001 1503 7226CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão. R. Padre Armando Quintas, 4485-661 Vairão, Portugal ,grid.6312.60000 0001 2097 6738Universidade de Vigo, Grupo de Ecoloxía Animal, Departamento de Ecoloxía e Bioloxía Animal, Torre Cacti (Lab 97), 36310 Vigo, Spain
| | - André Lourenço
- grid.5808.50000 0001 1503 7226CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão. R. Padre Armando Quintas, 4485-661 Vairão, Portugal ,grid.5808.50000 0001 1503 7226Departamento de Biologia da Faculdade de Ciências, Universidade do Porto. Rua Campo Alegre, 4169-007 Porto, Portugal
| | - Pedro Galán
- grid.8073.c0000 0001 2176 8535Grupo de Investigación en Bioloxía Evolutiva (GIBE), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, Campus da Zapateira, s/n, 15071 A Coruña, Spain
| | - Alfredo Nicieza
- grid.10863.3c0000 0001 2164 6351Departamento de Biologıa de Organismos y Sistemas, Universidad de Oviedo, Oviedo, Spain ,grid.10863.3c0000 0001 2164 6351Unidad Mixta de Investigacion en Biodiversidad (UMIB), CSIC-Universidad de Oviedo-Principado de Asturias, Mieres, Spain
| | - Pedro Tarroso
- grid.5808.50000 0001 1503 7226CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão. R. Padre Armando Quintas, 4485-661 Vairão, Portugal
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11
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Keeping an eye on the use of eye-lens weight as a universal indicator of age for European wild rabbits. Sci Rep 2021; 11:8711. [PMID: 33888785 PMCID: PMC8062486 DOI: 10.1038/s41598-021-88087-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/08/2021] [Indexed: 11/09/2022] Open
Abstract
Accurate methods for age determination are critical to the knowledge of wildlife populations' age structure and, therefore, to their successful management. The reliability of age estimation may have profound economic and ecological consequences on the management of the European wild rabbits, Oryctolagus cuniculus, in its native and introduced range, where it is a keystone species and a major pest, respectively. As in other mammal species, European rabbits' age is often estimated using the Gompertz relationship between age and lens' weight. The growth rate formula has been developed based on data collected from European rabbits introduced in Australia, where a single subspecies (O. cuniculus cuniculus, Occ) is present. However, this curve has never been validated in the species native range, the Iberian Peninsula, where two subspecies (Occ, and O. c. algirus, Oca) coexist naturally. In this study, we tested the relationship between age and lens' weight using 173 Occ and 112 Oca wild rabbits that were surveyed in two experimental facilities in Spain. Our findings show that, in the native range, the published growth curve formula fits well Occ but not Oca data. Therefore, we recommend using the formula reported in this study to estimate the age of Oca (Lens dry weight = 240 × 10(-64.9/(Age+32))). This study supports Oca rabbits' distinctiveness revealed by previous studies, which suggests that management interventions should be applied to protect this subspecies whose distribution range is very narrow and whose populations seem to be declining. More broadly, our findings point to the importance of testing the suitability of growth curves defined for other species with different genetic forms as occurs in the European wild rabbit case.
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12
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Funosas G, Triadó-Margarit X, Castro F, Villafuerte R, Delibes-Mateos M, Rouco C, Casamayor EO. Individual fate and gut microbiome composition in the European wild rabbit (Oryctolagus cuniculus). Sci Rep 2021; 11:766. [PMID: 33436896 PMCID: PMC7804928 DOI: 10.1038/s41598-020-80782-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/30/2020] [Indexed: 01/12/2023] Open
Abstract
Studies connecting microbiome composition and functional performance in wildlife have received little attention and understanding their connections with wildlife physical condition are sorely needed. We studied the variation in gut microbiota (hard fecal pellets) between allopatric subspecies of the European wild rabbit in wild populations and in captured individuals studied under captivity. We evaluated the influence of environmental and host-specific factors. The microbiome of wild rabbit populations reduced its heterogeneity under controlled conditions. None of the host-specific factors tested correlated with the microbiota composition. We only observed significant intra-group dispersion for the age factor. The most diverse microbiomes were rich in Ruminococcaceae potentially holding an enriched functional profile with dominance of cellulases and xylanases, and suggesting higher efficiency in the digestion of fiber-rich food. Conversely, low diversity gut microbiomes showed dominance of Enterobacteriaceae potentially rich in amylases. We preliminary noticed geographical variations in field populations with higher dominance of Ruminococcaceae in south-western than in north-eastern Spain. Spatial differences appeared not to be subspecies driven, since they were lost in captivity, but environmentally driven, although differences in social structure and behavior may also play a role that deserve further investigations. A marginally significant relationship between the Ruminococcaceae/Enterobacteriaceae ratio and potential life expectancy was observed in captive rabbits. We hypothesize that the gut microbiome may determine the efficiency of feeding resource exploitation, and can also be a potential proxy for life expectancy, with potential applications for the management of declining wild herbivorous populations. Such hypotheses remain to be explored in the future.
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Affiliation(s)
- Gerard Funosas
- Microbial Community Ecology, Centre for Advanced Studies of Blanes-Spanish Council for Research CEAB-CSIC, Accés Cala St Francesc, 14, 17300, Blanes, Spain
| | - Xavier Triadó-Margarit
- Microbial Community Ecology, Centre for Advanced Studies of Blanes-Spanish Council for Research CEAB-CSIC, Accés Cala St Francesc, 14, 17300, Blanes, Spain
| | - Francisca Castro
- Departamento de Didácticas Específicas, Universidad de Córdoba, Sociedad, Ecología y Gestión del Medio Ambiente, UCO-IESA, Unidad Asociada al CSIC, 14004, Córdoba, Spain
| | - Rafael Villafuerte
- Institute of Advanced Social Studies-Spanish Council for Research (IESA-CSIC), 14004, Córdoba, Spain
| | - Miguel Delibes-Mateos
- Institute of Advanced Social Studies-Spanish Council for Research (IESA-CSIC), 14004, Córdoba, Spain
| | - Carlos Rouco
- Ecology Area, Faculty of Science, University of Cordoba, Sociedad, Ecología y Gestión del Medio Ambiente, UCO-IESA, Unidad Asociada al CSIC, 14071, Córdoba, Spain
| | - Emilio O Casamayor
- Microbial Community Ecology, Centre for Advanced Studies of Blanes-Spanish Council for Research CEAB-CSIC, Accés Cala St Francesc, 14, 17300, Blanes, Spain.
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13
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Stewart KA, Taylor SA. Leveraging eDNA to expand the study of hybrid zones. Mol Ecol 2020; 29:2768-2776. [PMID: 32557920 PMCID: PMC7496085 DOI: 10.1111/mec.15514] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 04/18/2020] [Accepted: 06/05/2020] [Indexed: 02/06/2023]
Abstract
Hybrid zones are important windows into ecological and evolutionary processes. Our understanding of the significance and prevalence of hybridization in nature has expanded with the generation and analysis of genome‐spanning data sets. That said, most hybridization research still has restricted temporal and spatial resolution, which limits our ability to draw broad conclusions about evolutionary and conservation related outcomes. Here, we argue that rapidly advancing environmental DNA (eDNA) methodology could be adopted for studies of hybrid zones to increase temporal sampling (contemporary and historical), refine and geographically expand sampling density, and collect data for taxa that are difficult to directly sample. Genomic data in the environment offer the potential for near real‐time biological tracking of hybrid zones, and eDNA provides broad, but as yet untapped, potential to address eco‐evolutionary questions.
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Affiliation(s)
- Kathryn A Stewart
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Scott A Taylor
- Department Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
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14
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Campbell P, Arévalo L, Martin H, Chen C, Sun S, Rowe AH, Webster MS, Searle JB, Pasch B. Vocal divergence is concordant with genomic evidence for strong reproductive isolation in grasshopper mice ( Onychomys). Ecol Evol 2019; 9:12886-12896. [PMID: 31788222 PMCID: PMC6875671 DOI: 10.1002/ece3.5770] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 12/13/2022] Open
Abstract
Behavioral barriers to gene flow often evolve faster than intrinsic incompatibilities and can eliminate the opportunity for hybridization between interfertile species. While acoustic signal divergence is a common driver of premating isolation in birds and insects, its contribution to speciation in mammals is less studied. Here we characterize the incidence of, and potential barriers to, hybridization among three closely related species of grasshopper mice (genus Onychomys). All three species use long-distance acoustic signals to attract and localize mates; Onychomys arenicola and Onychomys torridus are acoustically similar and morphologically cryptic whereas Onychomys leucogaster is larger and acoustically distinct. We used genotyping-by-sequencing (GBS) to test for evidence of introgression in 227 mice from allopatric and sympatric localities in the western United States and northern Mexico. We conducted laboratory mating trials for all species pairs to assess reproductive compatibility, and recorded vocalizations from O. arenicola and O. torridus in sympatry and allopatry to test for evidence of acoustic character displacement. Hybridization was rare in nature and, contrary to prior evidence for O. torridus/O. arenicola hybrids, only involved O. leucogaster and O. arenicola. In contrast, laboratory crosses between O. torridus and O. arenicola produced litters whereas O. leucogaster and O. arenicola crosses did not. Call fundamental frequency in O. torridus and O. arenicola was indistinguishable in allopatry but significantly differentiated in sympatry, a pattern consistent with reproductive character displacement. These results suggest that assortative mating based on a long-distance signal is an important isolating mechanism between O. torridus and O. arenicola and highlight the importance of behavioral barriers in determining the permeability of species boundaries.
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Affiliation(s)
- Polly Campbell
- Department of Integrative BiologyOklahoma State UniversityStillwaterOKUSA
- Department of Evolution, Ecology, and Organismal BiologyUniversity of California, RiversideRiversideCAUSA
| | - Lena Arévalo
- Department of Integrative BiologyOklahoma State UniversityStillwaterOKUSA
- Department of Developmental PathologyUniversity of BonnBonnGermany
| | - Heather Martin
- Department of Integrative BiologyOklahoma State UniversityStillwaterOKUSA
| | - Charles Chen
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOKUSA
| | - Shuzhen Sun
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOKUSA
- Department of Forest and Conservation SciencesForest Science CentreThe University of British ColumbiaVancouverBCCanada
| | - Ashlee H. Rowe
- Department of BiologyThe University of OklahomaNormanOKUSA
| | - Michael S. Webster
- Macaulay LibraryCornell Lab of OrnithologyCornell UniversityIthacaNYUSA
- Department of Neurobiology and BehaviorCornell UniversityIthacaNYUSA
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNYUSA
| | - Bret Pasch
- Department of Biological SciencesNorthern Arizona UniversityFlagstaffAZUSA
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15
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Larsen PA, Matocq MD. Emerging genomic applications in mammalian ecology, evolution, and conservation. J Mammal 2019. [DOI: 10.1093/jmammal/gyy184] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Peter A Larsen
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA
| | - Marjorie D Matocq
- Department of Natural Resources and Environmental Science; Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, USA
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16
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Baiz MD, Tucker PK, Cortés-Ortiz L. Multiple forms of selection shape reproductive isolation in a primate hybrid zone. Mol Ecol 2019; 28:1056-1069. [PMID: 30582763 PMCID: PMC6888905 DOI: 10.1111/mec.14966] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 10/22/2018] [Indexed: 01/02/2023]
Abstract
Speciation occurs when populations diverge and become reproductively isolated from each other. Natural selection is commonly accepted to play a large role in this process, and it has been widely assumed that reproductive isolation often results as a by-product of divergence driven by adaptation in allopatry. When such populations come into secondary contact, reinforcement can act to strengthen reproductive isolation, but the frequency and importance of this process are still unknown. Here, we explored genomic signatures of selection in allopatry and sympatry for loci associated with reproductive isolation using a natural primate hybrid zone. By analysing reduced-representation sequencing data, we quantified admixture and population structure across a howler monkey hybrid zone and examined the relationship between locus-specific differentiation and introgression. We detected extensive admixture that was mostly limited to the narrow contact zone. Loci with reduced introgression into the heterospecific genomic background (the pattern expected for loci associated with reproductive isolation due to selection against hybrids) were significantly more differentiated between allopatric parental populations than loci with neutral and increased introgression, supporting the hypothesis that reproductive isolation is a by-product of divergence in allopatry. Further, loci with reduced introgression showed greater differentiation in sympatry than in allopatry, suggesting a role for reinforcement. Thus, our results reflect multiple forms of selection that have shaped reproductive isolation in this system. We conclude that reproductive isolation may have initially been driven by divergence in allopatry, but later reinforced by divergent selection in sympatry.
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Affiliation(s)
- Marcella D Baiz
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - Priscilla K Tucker
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - Liliana Cortés-Ortiz
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
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17
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Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Mol Ecol 2019; 28:1375-1393. [PMID: 30537056 PMCID: PMC6518922 DOI: 10.1111/mec.14972] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 10/07/2018] [Accepted: 10/08/2018] [Indexed: 12/22/2022]
Abstract
Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients.
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Affiliation(s)
- Rui Faria
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Pragya Chaube
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Hernán E Morales
- Department of Marine Sciences, Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
| | - Tomas Larsson
- Department of Marine Sciences, Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, Florida
| | - Emily M Lemmon
- Department of Biological Science, Florida State University, Tallahassee, Florida
| | - Marina Rafajlović
- Department of Marine Sciences, Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
| | - Marina Panova
- Department of Marine Sciences at Tjärnö, Centre for Marine Evolutionary Biology, University of Gothenburg, Strömstad, Sweden
| | - Mark Ravinet
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Kerstin Johannesson
- Department of Marine Sciences at Tjärnö, Centre for Marine Evolutionary Biology, University of Gothenburg, Strömstad, Sweden
| | - Anja M Westram
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,IST Austria, Klosterneuburg, Austria
| | - Roger K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Department of Marine Sciences at Tjärnö, Centre for Marine Evolutionary Biology, University of Gothenburg, Strömstad, Sweden
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18
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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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19
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Hamilton JA, Miller JM. From transects to transcripts: Teasing apart the architecture of reproductive isolation. Mol Ecol 2019; 27:1339-1341. [PMID: 29663588 DOI: 10.1111/mec.14516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 01/19/2018] [Indexed: 11/29/2022]
Abstract
Understanding the processes underlying speciation has long been a challenge to evolutionary biologists. This spurs from difficulties teasing apart the various mechanisms that contribute to the evolution of barriers to reproduction. The study by Rafati et al. () in this issue of Molecular Ecology combines spatially explicit whole-genome resequencing with evaluation of differential gene expression across individuals with mixed ancestry to associate the genomic architecture of reproductive barriers with expression of reproductive incompatibilities. In a natural hybrid zone between rabbit subspecies, Oryctolagus cuniculus cuniculus and O. c. algirus (Figure ), Rafati et al. () use landscape-level patterns of allele frequency variation to identify potential candidate regions of the genome associated with reproductive isolation. These candidate regions are used to test predictions associated with the genomic architecture of reproductive barriers, including the role of structural rearrangements, enrichment of functional categories associated with incompatibilities, and the contribution of protein-coding versus regulatory changes. A lack of structural rearrangements and limited protein-coding changes in candidate regions point towards the importance of regulatory variation as major contributors to genetic incompatibilities, while functional enrichments indicate overrepresentation of genes associated with male infertility. To quantify phenotypic expression of proposed incompatibilities, the authors assess gene expression of experimental crosses. Extensive misregulation of gene expression within the testes of backcross hybrids relative to F1 and parental individuals provides an important link between genotype and phenotype, validating hypotheses developed from assessment of genomic architectures. Together, this work shows how pairing natural hybrid zones with experimental crosses can be used to link observations in nature to mechanistic underpinnings that may be tested experimentally.
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Affiliation(s)
- Jill A Hamilton
- Department of Biological Sciences, North Dakota State University, Fargo, ND, USA
| | - Joshua M Miller
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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20
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Hurley LL, Rowe M, Griffith SC. Differential sperm-egg interactions in experimental pairings between two subspecies and their hybrids in a passerine bird. Ecol Evol 2018; 8:11725-11732. [PMID: 30598770 PMCID: PMC6303703 DOI: 10.1002/ece3.4624] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 09/03/2018] [Indexed: 12/11/2022] Open
Abstract
Speciation research has largely overlooked reproductive barriers acting between copulation and the formation of the zygote (i.e., postmating, prezygotic [PMPZ] barriers), especially in internally fertilizing vertebrates. Nonetheless, it is becoming clear that PMPZ reproductive barriers can play a role in the formation and maintenance of species boundaries. We investigated sperm-egg interactions in the recently diverged subspecies pairs of the long-tailed finch, Poephila acuticauda acuticauda and P. a. hecki, to explore potential PMPZ barriers. Specifically, we compared the number of sperm reaching the perivitelline layer (PVL) of the ova, and hence the site of fertilization, in both intra- and inter-subspecies pairings and pairings of F1 hybrid adults with one parental subspecies. Although we found no difference in PVL sperm number among intra- and inter-subspecific pairs, a significantly lower number of sperm reached the site of fertilization in a backcross pairing. As low numbers of PVL sperm appear to be associated with low fertilization success in birds, our findings offer insight into the potential role of postcopulatory processes in limiting gene flow between the subspecies and may help explain the relatively narrow hybrid zone that exists in the wild in this species. Though further work is needed to gain a comprehensive understanding of the morphological, physiological, and molecular mechanisms underlying our results, our study supports the role of PMPZ reproductive barriers in avian speciation, even in recently diverged taxa, that may not yet be fully genetically incompatible.
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Affiliation(s)
- Laura L. Hurley
- Department of Biological SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Melissah Rowe
- Natural History Museum, University of OsloOsloNorway
- Centre for Ecological and Evolutionary Synthesis, Department of BiosciencesUniversity of OsloOsloNorway
| | - Simon C. Griffith
- Department of Biological SciencesMacquarie UniversitySydneyNew South WalesAustralia
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21
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Whole-genome comparison of endogenous retrovirus segregation across wild and domestic host species populations. Proc Natl Acad Sci U S A 2018; 115:11012-11017. [PMID: 30297425 PMCID: PMC6205466 DOI: 10.1073/pnas.1815056115] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Although recent advances in sequencing and computational analyses have facilitated use of endogenous retroviruses (ERVs) for deciphering coevolution among retroviruses and their hosts, sampling effects from different host populations present major challenges. Here we utilize available whole-genome data from wild and domesticated European rabbit (Oryctolagus cuniculus sp.) populations, sequenced as DNA pools by paired-end Illumina technology, for identifying segregating reference as well as nonreference ERV loci, to reveal their variation along the host phylogeny and domestication history. To produce new viruses, retroviruses must insert a proviral DNA copy into the host nuclear DNA. Occasional proviral insertions into the host germline have been passed down through generations as inherited ERVs during millions of years. These ERVs represent retroviruses that were active at the time of infection and thus present a remarkable record of historical virus-host associations. To examine segregating ERVs in host populations, we apply a reference library search strategy for anchoring ERV-associated short-sequence read pairs from pooled whole-genome sequences to reference genome assembly positions. We show that most ERVs segregate along host phylogeny but also uncover radiation of some ERVs, identified as segregating loci among wild and domestic rabbits. The study targets pertinent issues regarding genome sampling when examining virus-host evolution from the genomic ERV record and offers improved scope regarding common strategies for single-nucleotide variant analyses in host population comparative genomics.
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22
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Campbell CR, Poelstra JW, Yoder AD. What is Speciation Genomics? The roles of ecology, gene flow, and genomic architecture in the formation of species. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly063] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | - J W Poelstra
- Department of Biology, Duke University, Durham, NC, USA
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC, USA
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