1
|
Cutter AD. Beyond Haldane's rule: Sex-biased hybrid dysfunction for all modes of sex determination. eLife 2024; 13:e96652. [PMID: 39158559 PMCID: PMC11333046 DOI: 10.7554/elife.96652] [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: 02/07/2024] [Accepted: 08/06/2024] [Indexed: 08/20/2024] Open
Abstract
Haldane's rule occupies a special place in biology as one of the few 'rules' of speciation, with empirical support from hundreds of species. And yet, its classic purview is restricted taxonomically to the subset of organisms with heteromorphic sex chromosomes. I propose explicit acknowledgement of generalized hypotheses about Haldane's rule that frame sex bias in hybrid dysfunction broadly and irrespective of the sexual system. The consensus view of classic Haldane's rule holds that sex-biased hybrid dysfunction across taxa is a composite phenomenon that requires explanations from multiple causes. Testing of the multiple alternative hypotheses for Haldane's rule is, in many cases, applicable to taxa with homomorphic sex chromosomes, environmental sex determination, haplodiploidy, and hermaphroditism. Integration of a variety of biological phenomena about hybrids across diverse sexual systems, beyond classic Haldane's rule, will help to derive a more general understanding of the contributing forces and mechanisms that lead to predictable sex biases in evolutionary divergence and speciation.
Collapse
Affiliation(s)
- Asher D Cutter
- Department of Ecology & Evolutionary Biology, University of TorontoTorontoCanada
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Szabo N, Cutter AD. Experimental evolution of hybrid populations to identify Dobzhansky-Muller incompatibility loci. Ecol Evol 2024; 14:e10972. [PMID: 38333096 PMCID: PMC10851027 DOI: 10.1002/ece3.10972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/04/2023] [Accepted: 12/10/2023] [Indexed: 02/10/2024] Open
Abstract
Epistatic interactions between loci that reduce fitness in interspecies hybrids, Dobzhansky-Muller incompatibilities (DMIs), contribute genetically to the inviability and infertility within hybrid populations. It remains a challenge, however, to identify the loci that contribute to DMIs as causes of reproductive isolation between species. Here, we assess through forward simulation the power of evolve-and-resequence (E&R) experimental evolution of hybrid populations to map DMI loci. We document conditions under which such a mapping strategy may be most feasible and demonstrate how mapping power is sensitive to biologically relevant parameters such as one-way versus two-way incompatibility type, selection strength, recombination rate, and dominance interactions. We also assess the influence of parameters under direct control of an experimenter, including duration of experimental evolution and number of replicate populations. We conclude that an E&R strategy for mapping DMI loci, and other cases of epistasis, can be a viable option under some circumstances for study systems with short generation times like Caenorhabditis nematodes.
Collapse
Affiliation(s)
- Nicole Szabo
- Department of Ecology & Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
| | - Asher D. Cutter
- Department of Ecology & Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
Reifová R, Ament-Velásquez SL, Bourgeois Y, Coughlan J, Kulmuni J, Lipinska AP, Okude G, Stevison L, Yoshida K, Kitano J. Mechanisms of Intrinsic Postzygotic Isolation: From Traditional Genic and Chromosomal Views to Genomic and Epigenetic Perspectives. Cold Spring Harb Perspect Biol 2023; 15:a041607. [PMID: 37696577 PMCID: PMC10547394 DOI: 10.1101/cshperspect.a041607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
Intrinsic postzygotic isolation typically appears as reduced viability or fertility of interspecific hybrids caused by genetic incompatibilities between diverged parental genomes. Dobzhansky-Muller interactions among individual genes, and chromosomal rearrangements causing problems with chromosome synapsis and recombination in meiosis, have both long been considered as major mechanisms behind intrinsic postzygotic isolation. Recent research has, however, suggested that the genetic basis of intrinsic postzygotic isolation can be more complex and involves, for example, overall divergence of the DNA sequence or epigenetic changes. Here, we review the mechanisms of intrinsic postzygotic isolation from genic, chromosomal, genomic, and epigenetic perspectives across diverse taxa. We provide empirical evidence for these mechanisms, discuss their importance in the speciation process, and highlight questions that remain unanswered.
Collapse
Affiliation(s)
- Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, 128 00 Prague, Czech Republic
| | | | - Yann Bourgeois
- DIADE, University of Montpellier, CIRAD, IRD, 34090 Montpellier, France
| | - Jenn Coughlan
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
| | - Jonna Kulmuni
- Institute for Biodiversity and Ecosystem Dynamics, Department of Evolutionary and Population Biology, University of Amsterdam, 1012 Amsterdam, The Netherlands
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, 00100 Helsinki, Finland
| | - Agnieszka P Lipinska
- Department of Algal Development and Evolution, Max Planck Institute for Biology, 72076 Tuebingen, Germany
- CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Genta Okude
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Laurie Stevison
- Department of Biological Sciences, Auburn University, Auburn, Alabama 36849, USA
| | - Kohta Yoshida
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Jun Kitano
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| |
Collapse
|
6
|
Horta-Lacueva QJB, Jónsson ZO, Thorholludottir DAV, Hallgrímsson B, Kapralova KH. Rapid and biased evolution of canalization during adaptive divergence revealed by dominance in gene expression variability during Arctic charr early development. Commun Biol 2023; 6:897. [PMID: 37652977 PMCID: PMC10471602 DOI: 10.1038/s42003-023-05264-5] [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: 05/27/2022] [Accepted: 08/21/2023] [Indexed: 09/02/2023] Open
Abstract
Adaptive evolution may be influenced by canalization, the buffering of developmental processes from environmental and genetic perturbations, but how this occurs is poorly understood. Here, we explore how gene expression variability evolves in diverging and hybridizing populations, by focusing on the Arctic charr (Salvelinus alpinus) of Thingvallavatn, a classic case of divergence between feeding habitats. We report distinct profiles of gene expression variance for both coding RNAs and microRNAs between the offspring of two contrasting morphs (benthic/limnetic) and their hybrids reared in common conditions and sampled at two key points of cranial development. Gene expression variance in the hybrids is substantially affected by maternal effects, and many genes show biased expression variance toward the limnetic morph. This suggests that canalization, as inferred by gene expression variance, can rapidly diverge in sympatry through multiple gene pathways, which are associated with dominance patterns possibly biasing evolutionary trajectories and mitigating the effects of hybridization on adaptive evolution.
Collapse
Affiliation(s)
- Quentin Jean-Baptiste Horta-Lacueva
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland.
- Department of Biology, Lund University, Lund, Sweden.
| | | | - Dagny A V Thorholludottir
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- University of Veterinary Medicine Vienna, Institute of Population Genetics, Vienna, Austria
| | - Benedikt Hallgrímsson
- Department of Cell Biology and Anatomy, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Kalina Hristova Kapralova
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland.
- The Institute for Experimental Pathology at Keldur, University of Iceland, Reykjavík, Iceland.
| |
Collapse
|
7
|
Alario A, Trevino M, Justen H, Woodman CJ, Roth TC, Delmore KE. Learning and memory in hybrid migratory songbirds: cognition as a reproductive isolating barrier across seasons. Sci Rep 2023; 13:10866. [PMID: 37407574 DOI: 10.1038/s41598-023-37379-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/21/2023] [Indexed: 07/07/2023] Open
Abstract
Hybrid zones can be used to identify traits that maintain reproductive isolation and contribute to speciation. Cognitive traits may serve as post-mating reproductive isolating barriers, reducing the fitness of hybrids if, for example, misexpression occurs in hybrids and disrupts important neurological mechanisms. We tested this hypothesis in a hybrid zone between two subspecies of Swainson's thrushes (Catharus ustulatus) using two cognitive tests-an associative learning spatial test and neophobia test. We included comparisons across the sexes and seasons (spring migration and winter), testing if hybrid females performed worse than males (as per Haldane's rule) and if birds (regardless of ancestry or sex) performed better during migration, when they are building navigational maps and encountering new environments. We documented reduced cognitive abilities in hybrids, but this result was limited to males and winter. Hybrid females did not perform worse than males in either season. Although season was a significant predictor of performance, contrary to our prediction, all birds learned faster during the winter. The hypothesis that cognitive traits could serve as post-mating isolating barriers is relatively new; this is one of the first tests in a natural hybrid zone and non-food-caching species. We also provide one of the first comparisons of cognitive abilities between seasons. Future neurostructural and neurophysiological work should be used to examine mechanisms underlying our behavioral observations.
Collapse
Affiliation(s)
- Ashley Alario
- Texas A&M University, 3528 TAMU, College Station, TX, 77843, USA
| | - Marlene Trevino
- Texas A&M University, 3528 TAMU, College Station, TX, 77843, USA
| | - Hannah Justen
- Texas A&M University, 3528 TAMU, College Station, TX, 77843, USA
| | | | - Timothy C Roth
- Department of Psychology, Franklin and Marshall College, Lancaster, PA, 17603, USA
| | - Kira E Delmore
- Texas A&M University, 3528 TAMU, College Station, TX, 77843, USA.
| |
Collapse
|
8
|
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.
Collapse
Affiliation(s)
- Asher D Cutter
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Poikela N, Laetsch DR, Kankare M, Hoikkala A, Lohse K. Experimental introgression in Drosophila: Asymmetric postzygotic isolation associated with chromosomal inversions and an incompatibility locus on the X chromosome. Mol Ecol 2023; 32:854-866. [PMID: 36461113 PMCID: PMC10107139 DOI: 10.1111/mec.16803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/16/2022] [Accepted: 11/23/2022] [Indexed: 12/04/2022]
Abstract
Interspecific gene flow (introgression) is an important source of new genetic variation, but selection against it can reinforce reproductive barriers between interbreeding species. We used an experimental approach to trace the role of chromosomal inversions and incompatibility genes in preventing introgression between two partly sympatric Drosophila virilis group species, D. flavomontana and D. montana. We backcrossed F1 hybrid females from a cross between D. flavomontana female and D. montana male with the males of the parental species for two generations and sequenced pools of parental strains and their reciprocal second generation backcross (BC2 mon and BC2 fla) females. Contrasting the observed amount of introgression (mean hybrid index, HI) in BC2 female pools along the genome to simulations under different scenarios allowed us to identify chromosomal regions of restricted and increased introgression. We found no deviation from the HI expected under a neutral null model for any chromosome for the BC2 mon pool, suggesting no evidence for genetic incompatibilities in backcrosses towards D. montana. In contrast, the BC2 fla pool showed high variation in the observed HI between different chromosomes, and massive reduction of introgression on the X chromosome (large X-effect). This observation is compatible with reduced recombination combined with at least one dominant incompatibility locus residing within the X inversion(s). Overall, our study suggests that genetic incompatibilities arising within chromosomal inversions can play an important role in speciation.
Collapse
Affiliation(s)
- Noora Poikela
- Department of Biological and Environmental Science, University of Jyväskylä, Jyvaskyla, Finland
| | - Dominik R Laetsch
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Maaria Kankare
- Department of Biological and Environmental Science, University of Jyväskylä, Jyvaskyla, Finland
| | - Anneli Hoikkala
- Department of Biological and Environmental Science, University of Jyväskylä, Jyvaskyla, Finland
| | - Konrad Lohse
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
11
|
Olasege BS, Porto-Neto LR, Tahir MS, Gouveia GC, Cánovas A, Hayes BJ, Fortes MRS. Correlation scan: identifying genomic regions that affect genetic correlations applied to fertility traits. BMC Genomics 2022; 23:684. [PMID: 36195838 PMCID: PMC9533527 DOI: 10.1186/s12864-022-08898-7] [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: 01/07/2022] [Accepted: 09/19/2022] [Indexed: 11/10/2022] Open
Abstract
Although the genetic correlations between complex traits have been estimated for more than a century, only recently we have started to map and understand the precise localization of the genomic region(s) that underpin these correlations. Reproductive traits are often genetically correlated. Yet, we don't fully understand the complexities, synergism, or trade-offs between male and female fertility. In this study, we used reproductive traits in two cattle populations (Brahman; BB, Tropical Composite; TC) to develop a novel framework termed correlation scan (CS). This framework was used to identify local regions associated with the genetic correlations between male and female fertility traits. Animals were genotyped with bovine high-density single nucleotide polymorphisms (SNPs) chip assay. The data used consisted of ~1000 individual records measured through frequent ovarian scanning for age at first corpus luteum (AGECL) and a laboratory assay for serum levels of insulin growth hormone (IGF1 measured in bulls, IGF1b, or cows, IGF1c). The methodology developed herein used correlations of 500-SNP effects in a 100-SNPs sliding window in each chromosome to identify local genomic regions that either drive or antagonize the genetic correlations between traits. We used Fisher's Z-statistics through a permutation method to confirm which regions of the genome harboured significant correlations. About 30% of the total genomic regions were identified as driving and antagonizing genetic correlations between male and female fertility traits in the two populations. These regions confirmed the polygenic nature of the traits being studied and pointed to genes of interest. For BB, the most important chromosome in terms of local regions is often located on bovine chromosome (BTA) 14. However, the important regions are spread across few different BTA's in TC. Quantitative trait loci (QTLs) and functional enrichment analysis revealed many significant windows co-localized with known QTLs related to milk production and fertility traits, especially puberty. In general, the enriched reproductive QTLs driving the genetic correlations between male and female fertility are the same for both cattle populations, while the antagonizing regions were population specific. Moreover, most of the antagonizing regions were mapped to chromosome X. These results suggest regions of chromosome X for further investigation into the trade-offs between male and female fertility. We compared the CS with two other recently proposed methods that map local genomic correlations. Some genomic regions were significant across methods. Yet, many significant regions identified with the CS were overlooked by other methods.
Collapse
Affiliation(s)
- Babatunde S Olasege
- The University of Queensland, School of Chemistry and Molecular Biosciences, Saint Lucia Campus, Brisbane, QLD, 4072, Australia.,CSIRO Agriculture and Food, Saint Lucia, QLD, 4067, Australia
| | | | - Muhammad S Tahir
- The University of Queensland, School of Chemistry and Molecular Biosciences, Saint Lucia Campus, Brisbane, QLD, 4072, Australia.,CSIRO Agriculture and Food, Saint Lucia, QLD, 4067, Australia
| | - Gabriela C Gouveia
- Animal Science Department, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Angela Cánovas
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada
| | - Ben J Hayes
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation (QAAFI), Saint Lucia Campus, Brisbane, QLD, 4072, Australia
| | - Marina R S Fortes
- The University of Queensland, School of Chemistry and Molecular Biosciences, Saint Lucia Campus, Brisbane, QLD, 4072, Australia. .,The University of Queensland, Queensland Alliance for Agriculture and Food Innovation (QAAFI), Saint Lucia Campus, Brisbane, QLD, 4072, Australia.
| |
Collapse
|
12
|
Dagilis AJ, Peede D, Coughlan JM, Jofre GI, D'Agostino ERR, Mavengere H, Tate AD, Matute DR. A need for standardized reporting of introgression: Insights from studies across eukaryotes. Evol Lett 2022; 6:344-357. [PMID: 36254258 PMCID: PMC9554761 DOI: 10.1002/evl3.294] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/04/2022] [Accepted: 06/12/2022] [Indexed: 01/04/2023] Open
Abstract
With the rise of affordable next-generation sequencing technology, introgression-or the exchange of genetic materials between taxa-has become widely perceived to be a ubiquitous phenomenon in nature. Although this claim is supported by several keystone studies, no thorough assessment of the frequency of introgression across eukaryotes in nature has been performed to date. In this manuscript, we aim to address this knowledge gap by examining patterns of introgression across eukaryotes. We collated a single statistic, Patterson's D, which can be used as a test for introgression across 123 studies to further assess how taxonomic group, divergence time, and sequencing technology influence reports of introgression. Overall, introgression has mostly been measured in plants and vertebrates, with less attention given to the rest of the Eukaryotes. We find that the most frequently used metrics to detect introgression are difficult to compare across studies and even more so across biological systems due to differences in study effort, reporting standards, and methodology. Nonetheless, our analyses reveal several intriguing patterns, including the observation that differences in sequencing technologies may bias values of Patterson's D and that introgression may differ throughout the course of the speciation process. Together, these results suggest the need for a unified approach to quantifying introgression in natural communities and highlight important areas of future research that can be better assessed once this unified approach is met.
Collapse
Affiliation(s)
| | - David Peede
- Biology DepartmentUniversity of North CarolinaChapel HillNCUSA
- Department of Ecology, Evolution, and Organismal BiologyBrown UniversityProvidenceRIUSA
- Center for Computational Molecular BiologyBrown UniversityProvidenceRIUSA
| | - Jenn M. Coughlan
- Biology DepartmentUniversity of North CarolinaChapel HillNCUSA
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
| | - Gaston I. Jofre
- Biology DepartmentUniversity of North CarolinaChapel HillNCUSA
| | - Emmanuel R. R. D'Agostino
- Biology DepartmentUniversity of North CarolinaChapel HillNCUSA
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNJUSA
| | - Heidi Mavengere
- Biology DepartmentUniversity of North CarolinaChapel HillNCUSA
| | | | | |
Collapse
|
13
|
Oomen RA, Hutchings JA. Genomic reaction norms inform predictions of plastic and adaptive responses to climate change. J Anim Ecol 2022; 91:1073-1087. [PMID: 35445402 PMCID: PMC9325537 DOI: 10.1111/1365-2656.13707] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 04/05/2022] [Indexed: 12/11/2022]
Abstract
Genomic reaction norms represent the range of gene expression phenotypes (usually mRNA transcript levels) expressed by a genotype along an environmental gradient. Reaction norms derived from common‐garden experiments are powerful approaches for disentangling plastic and adaptive responses to environmental change in natural populations. By treating gene expression as a phenotype in itself, genomic reaction norms represent invaluable tools for exploring causal mechanisms underlying organismal responses to climate change across multiple levels of biodiversity. Our goal is to provide the context, framework and motivation for applying genomic reaction norms to study the responses of natural populations to climate change. Here, we describe the utility of integrating genomics with common‐garden‐gradient experiments under a reaction norm analytical framework to answer fundamental questions about phenotypic plasticity, local adaptation, their interaction (i.e. genetic variation in plasticity) and future adaptive potential. An experimental and analytical framework for constructing and analysing genomic reaction norms is presented within the context of polygenic climate change responses of structured populations with gene flow. Intended for a broad eco‐evo readership, we first briefly review adaptation with gene flow and the importance of understanding the genomic basis and spatial scale of adaptation for conservation and management of structured populations under anthropogenic change. Then, within a high‐dimensional reaction norm framework, we illustrate how to distinguish plastic, differentially expressed (difference in reaction norm intercepts) and differentially plastic (difference in reaction norm slopes) genes, highlighting the areas of opportunity for applying these concepts. We conclude by discussing how genomic reaction norms can be incorporated into a holistic framework to understand the eco‐evolutionary dynamics of climate change responses from molecules to ecosystems. We aim to inspire researchers to integrate gene expression measurements into common‐garden experimental designs to investigate the genomics of climate change responses as sequencing costs become increasingly accessible.
Collapse
Affiliation(s)
- Rebekah A Oomen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.,Centre for Coastal Research (CCR), University of Agder, Kristiansand, Norway
| | - Jeffrey A Hutchings
- Centre for Coastal Research (CCR), University of Agder, Kristiansand, Norway.,Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Institute of Marine Research, Flødevigen Marine Research Station, His, Norway
| |
Collapse
|
14
|
Imbalanced segregation of recombinant haplotypes in hybrid populations reveals inter- and intrachromosomal Dobzhansky-Muller incompatibilities. PLoS Genet 2022; 18:e1010120. [PMID: 35344560 PMCID: PMC8989332 DOI: 10.1371/journal.pgen.1010120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 04/07/2022] [Accepted: 02/25/2022] [Indexed: 11/19/2022] Open
Abstract
Dobzhansky-Muller incompatibilities (DMIs) are a major component of reproductive isolation between species. DMIs imply negative epistasis and are exposed when two diverged populations hybridize. Mapping the locations of DMIs has largely relied on classical genetic mapping. Approaches to date are hampered by low power and the challenge of identifying DMI loci on the same chromosome, because strong initial linkage of parental haplotypes weakens statistical tests. Here, we propose new statistics to infer negative epistasis from haplotype frequencies in hybrid populations. When two divergent populations hybridize, the variance in heterozygosity at two loci decreases faster with time at DMI loci than at random pairs of loci. When two populations hybridize at near-even admixture proportions, the deviation of the observed variance from its expectation becomes negative for the DMI pair. This negative deviation enables us to detect intermediate to strong negative epistasis both within and between chromosomes. In practice, the detection window in hybrid populations depends on the demographic scenario, the recombination rate, and the strength of epistasis. When the initial proportion of the two parental populations is uneven, only strong DMIs can be detected with our method unless migration prevents parental haplotypes from being lost. We use the new statistics to infer candidate DMIs from three hybrid populations of swordtail fish. We identify numerous new DMI candidates, some of which are inferred to interact with several loci within and between chromosomes. Moreover, we discuss our results in the context of an expected enrichment in intrachromosomal over interchromosomal DMIs.
Collapse
|
15
|
Moran BM, Payne C, Langdon Q, Powell DL, Brandvain Y, Schumer M. The genomic consequences of hybridization. eLife 2021; 10:e69016. [PMID: 34346866 PMCID: PMC8337078 DOI: 10.7554/elife.69016] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/09/2021] [Indexed: 12/29/2022] Open
Abstract
In the past decade, advances in genome sequencing have allowed researchers to uncover the history of hybridization in diverse groups of species, including our own. Although the field has made impressive progress in documenting the extent of natural hybridization, both historical and recent, there are still many unanswered questions about its genetic and evolutionary consequences. Recent work has suggested that the outcomes of hybridization in the genome may be in part predictable, but many open questions about the nature of selection on hybrids and the biological variables that shape such selection have hampered progress in this area. We synthesize what is known about the mechanisms that drive changes in ancestry in the genome after hybridization, highlight major unresolved questions, and discuss their implications for the predictability of genome evolution after hybridization.
Collapse
Affiliation(s)
- Benjamin M Moran
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
| | - Cheyenne Payne
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
| | - Quinn Langdon
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Daniel L Powell
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
| | - Yaniv Brandvain
- Department of Ecology, Evolution & Behavior and Plant and Microbial Biology, University of MinnesotaMinneapolisUnited States
| | - Molly Schumer
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
- Hanna H. Gray Fellow, Howard Hughes Medical InstituteStanfordUnited States
| |
Collapse
|
16
|
Pfennig KS. Biased Hybridization and Its Impact on Adaptive Introgression. Trends Ecol Evol 2021; 36:488-497. [PMID: 33752896 DOI: 10.1016/j.tree.2021.02.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 02/20/2021] [Accepted: 02/22/2021] [Indexed: 02/07/2023]
Abstract
Gene exchange between species can influence ecological and evolutionary processes ranging from population rescue to adaptive radiation. Genomic tools have provided new insights into the prevalence and nature of gene exchange between species. However, much remains unknown of how ecological, behavioral, and evolutionary factors determine what genetic variation moves between species in the first place. In particular, more research is needed that evaluates whether such factors bias gene flow from one species to another, and whether any such biases affect how genetic variation from another species is ultimately retained in the genome of a given species. Addressing this issue is crucial in a changing world where hybridization and introgression might determine which species succeed and which become extinct.
Collapse
Affiliation(s)
- Karin S Pfennig
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA.
| |
Collapse
|
17
|
Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190528. [PMID: 32654637 PMCID: PMC7423269 DOI: 10.1098/rstb.2019.0528] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2020] [Indexed: 12/12/2022] Open
Abstract
Speciation, that is, the evolution of reproductive barriers eventually leading to complete isolation, is a crucial process generating biodiversity. Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. We argue that the evolution of strong RI is likely to involve different processes, or new interactions among processes, compared with the evolution of the first reproductive barriers. Transition to strong RI may be brought about by changing external conditions, for example, following secondary contact. However, the increasing levels of RI themselves create opportunities for new barriers to evolve and, and interaction or coupling among barriers. These changing processes may depend on genomic architecture and leave detectable signals in the genome. We outline outstanding questions and suggest more theoretical and empirical work, considering both patterns and processes associated with strong RI, is needed to understand how speciation is completed. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
Collapse
Affiliation(s)
- Jonna Kulmuni
- Organismal and Evolutionary Biology, University of Helsinki, Finland
| | - Roger K. Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
- Department of Marine Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Kay Lucek
- Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Vincent Savolainen
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
| | | |
Collapse
|
18
|
|