1
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Thompson KA, Brandvain Y, Coughlan JM, Delmore KE, Justen H, Linnen CR, Ortiz-Barrientos D, Rushworth CA, Schneemann H, Schumer M, Stelkens R. The Ecology of Hybrid Incompatibilities. Cold Spring Harb Perspect Biol 2024; 16:a041440. [PMID: 38151331 PMCID: PMC11368197 DOI: 10.1101/cshperspect.a041440] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Ecologically mediated selection against hybrids, caused by hybrid phenotypes fitting poorly into available niches, is typically viewed as distinct from selection caused by epistatic Dobzhansky-Muller hybrid incompatibilities. Here, we show how selection against transgressive phenotypes in hybrids manifests as incompatibility. After outlining our logic, we summarize current approaches for studying ecology-based selection on hybrids. We then quantitatively review QTL-mapping studies and find traits differing between parent taxa are typically polygenic. Next, we describe how verbal models of selection on hybrids translate to phenotypic and genetic fitness landscapes, highlighting emerging approaches for detecting polygenic incompatibilities. Finally, in a synthesis of published data, we report that trait transgression-and thus possibly extrinsic hybrid incompatibility in hybrids-escalates with the phenotypic divergence between parents. We discuss conceptual implications and conclude that studying the ecological basis of hybrid incompatibility will facilitate new discoveries about mechanisms of speciation.
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Affiliation(s)
- Ken A Thompson
- Department of Biology, Stanford University, Stanford, California 94305, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
| | - Yaniv Brandvain
- Department of Plant and Microbial Biology, University of Minnesota - Twin Cities, St Paul, Minnesota 55108, USA
| | - Jenn M Coughlan
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
| | - Kira E 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
| | - Catherine R Linnen
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences, The University of Queensland, Centre of Excellence for Plant Success in Nature and Agriculture, St Lucia, Queensland 4072, Australia
| | - Catherine A Rushworth
- Department of Biology and Ecology Center, Utah State University, Logan, Utah 84322, USA
| | - Hilde Schneemann
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Molly Schumer
- Department of Biology, Stanford University, Stanford, California 94305, USA
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., Calnali 43240, Mexico
- Hanna H. Gray Fellow, Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Rike Stelkens
- Division of Population Genetics, Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
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2
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Le Rouzic A, Roumet M, Widmer A, Clo J. Detecting directional epistasis and dominance from cross-line analyses in alpine populations of Arabidopsis thaliana. J Evol Biol 2024; 37:839-847. [PMID: 38712591 DOI: 10.1093/jeb/voae056] [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: 04/20/2023] [Revised: 04/08/2024] [Accepted: 05/02/2024] [Indexed: 05/08/2024]
Abstract
The contribution of non-additive genetic effects to the genetic architecture of fitness and to the evolutionary potential of populations has been a topic of theoretical and empirical interest for a long time. Yet, the empirical study of these effects in natural populations remains scarce, perhaps because measuring dominance and epistasis relies heavily on experimental line crosses. In this study, we explored the contribution of dominance and epistasis in natural alpine populations of Arabidopsis thaliana for 2 fitness traits, the dry biomass and the estimated number of siliques, measured in a greenhouse. We found that, on average, crosses between inbred lines of A. thaliana led to mid-parent heterosis for dry biomass but outbreeding depression for an estimated number of siliques. While heterosis for dry biomass was due to dominance, we found that outbreeding depression for an estimated number of siliques could be attributed to the breakdown of beneficial epistatic interactions. We simulated and discussed the implication of these results for the adaptive potential of the studied populations, as well as the use of line-cross analyses to detect non-additive genetic effects.
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Affiliation(s)
- Arnaud Le Rouzic
- Université Paris-Saclay, CNRS, IRD, UMR Evolution, Génomes, Comportement et Ecologie, Gif-Sur-Yvette, France
| | - Marie Roumet
- CTU Bern, University of Bern, Bern, Switzerland
- Institute of Integrative Biology, ETH Zurich, Zürich, Switzerland
| | - Alex Widmer
- Institute of Integrative Biology, ETH Zurich, Zürich, Switzerland
| | - Josselin Clo
- CNRS, University of Lille, UMR 8198-Evo-Eco-Paleo, Lille, France
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3
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Schneemann H, De Sanctis B, Welch JJ. Fisher's Geometric Model as a Tool to Study Speciation. Cold Spring Harb Perspect Biol 2024; 16:a041442. [PMID: 38253415 PMCID: PMC11216183 DOI: 10.1101/cshperspect.a041442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Interactions between alleles and across environments play an important role in the fitness of hybrids and are at the heart of the speciation process. Fitness landscapes capture these interactions and can be used to model hybrid fitness, helping us to interpret empirical observations and clarify verbal models. Here, we review recent progress in understanding hybridization outcomes through Fisher's geometric model, an intuitive and analytically tractable fitness landscape that captures many fitness patterns observed across taxa. We use case studies to show how the model parameters can be estimated from different types of data and discuss how these estimates can be used to make inferences about the divergence history and genetic architecture. We also highlight some areas where the model's predictions differ from alternative incompatibility-based models, such as the snowball effect and outlier patterns in genome scans.
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Affiliation(s)
- Hilde Schneemann
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Bianca De Sanctis
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
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4
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Yukilevich R, Aoki F, Egan S, Zhang L. Coevolutionary Interactions between Sexual and Habitat Isolation during Reinforcement. Cold Spring Harb Perspect Biol 2024; 16:a041431. [PMID: 38316551 PMCID: PMC11065176 DOI: 10.1101/cshperspect.a041431] [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: 02/07/2024]
Abstract
Speciation often involves the evolution of multiple genetic-based barriers to gene flow (i.e., "coupling"). However, barriers may exhibit a diversity of evolutionary interactions during speciation. These dynamics are important in reinforcement, where selection may favor different prezygotic isolating barriers to avoid maladaptive hybridization. Here we study the interaction between evolution of sexual and habitat isolation. We first review the empirical literature where both barriers were explicitly considered, and then develop a population genetic model of reinforcement. Most studies of both sexual and habitat isolation were found in phytophagous insect systems. In 76% of these studies, both barriers coevolved; the remaining cases either showed only habitat isolation (21%) or only sexual isolation (3%). Our two-allele genetic mechanism model of each barrier also found that these often coevolved, but habitat isolation was generally more effective during reinforcement. Depending on the fitness of hybrids (e.g., Dobzhansky-Muller incompatibilities) and initial migration rate, these barriers could either facilitate, curtail, or have no effect on each other. This indicates that basic parameters will alter the underlying evolutionary dynamics, and thus the nature of "speciation coupling" will be highly variable in natural systems. Finally, we studied initially asymmetrical migration rates and found that populations with higher initial emigration evolved stronger habitat isolation, while populations that initially received more immigrants exhibited stronger sexual isolation. These results are in line with observations in some empirical studies, but more data is needed to test their generality.
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Affiliation(s)
- Roman Yukilevich
- Department of Biology, Union College, Integrated Science and Engineering Complex, Schenectady, New York 12308, USA
| | - Fumio Aoki
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USA
| | - Scott Egan
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
| | - Linyi Zhang
- Department of Biological Sciences, George Washington University, Washington, D.C. 20052, USA
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5
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Yukilevich R, Aoki F. Evolution of choosiness dictates whether search costs of mate choice enhance speciation by sexual selection. J Evol Biol 2022; 35:1045-1059. [PMID: 35830473 DOI: 10.1111/jeb.14036] [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: 11/02/2021] [Accepted: 05/25/2022] [Indexed: 11/29/2022]
Abstract
The role of sexual selection in speciation is implicated in both empirical case studies and larger comparative works. However, sexual selection faces two major problems in driving speciation. First, because females with novel preferences search for their initially rare males, search costs are expected to curtail initial sexual divergence. Second, if these populations come back into sympatry, sexual divergence may be erased due to hybridization. A major goal is to understand which conditions increase the likelihood of overcoming these problems. Here we generated a diploid population genetic model of how female search costs and evolution of female 'choosiness' (i.e. preference strength) interact to drive speciation in allopatry and secondary contact. We studied the model using numerical simulations in the context of two different male traits, ecologically 'arbitrary' versus 'magic' traits. First, in allopatry, without female search costs only minor and fluctuating sexual isolation evolved. In contrast, with female search costs, sexual isolation was highly curtailed with arbitrary male traits but was greatly facilitated with magic traits. However, because search costs selected for reduced choosiness, sexual isolation with magic traits was eventually eroded, the rate determined by the genetic architecture of choosiness. These factors also played a key role in secondary contact; with evolvable choosiness and female search costs, pure sexual selection models collapsed upon secondary contact. However, when we added selection against hybrids (i.e. reinforcement) to this model, we found that speciation could be maintained under a wide range of conditions with arbitrary male traits, but not with magic male traits. This surprisingly suggests that arbitrary male traits are in some cases more likely to aid speciation than magic male traits. We discuss these findings and relate them to empirical literature on female choosiness within species and in hybrids.
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Affiliation(s)
- Roman Yukilevich
- Department of Biology, Union College, Schenectady, New York, USA
| | - Fumio Aoki
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
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6
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Fezza TJ, Siderhurst MS, Jang EB, Stacy EA, Price DK. Phenotypic disruption of cuticular hydrocarbon production in hybrids between sympatric species of Hawaiian picture-wing Drosophila. Sci Rep 2022; 12:4865. [PMID: 35318342 PMCID: PMC8941103 DOI: 10.1038/s41598-022-08635-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 03/10/2022] [Indexed: 12/12/2022] Open
Abstract
Interspecies hybrids can express phenotypic traits far outside the range of parental species. The atypical traits of hybrids provide insight into differences in the factors that regulate the expression of these traits in the parental species. In some cases, the unusual phenotypic traits of hybrids can lead to phenotypic dysfunction with hybrids experiencing reduced survival or reproduction. Cuticular hydrocarbons (CHCs) in insects are important phenotypic traits that serve several functions, including desiccation resistance and pheromones for mating. We used gas chromatography mass spectrometry to investigate the differences in CHC production between two closely related sympatric Hawaiian picture-wing Drosophila species, Drosophila heteroneura and D. silvestris, and their F1 and backcross hybrid offspring. CHC profiles differed between males of the two species, with substantial sexual dimorphism in D. silvestris but limited sexual dimorphism in D. heteroneura. Surprisingly, F1 hybrids did not produce three CHCs, and the abundances of several other CHCs occurred outside the ranges present in the two parental species. Backcross hybrids produced all CHCs with greater variation than observed in F1 or parental species. Overall, these results suggest that the production of CHCs was disrupted in F1 and backcross hybrids, which may have important consequences for their survival or reproduction.
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Affiliation(s)
- Thomas J Fezza
- Tropical Conservation Biology and Environmental Sciences, University of Hawaii at Hilo, 200 West Kawili St., Hilo, HI, 96720, USA
| | - Matthew S Siderhurst
- Department of Chemistry, Eastern Mennonite University, 1200 Park Rd, Harrisonburg, VA, 22802, USA
| | - Eric B Jang
- Tropical Crop and Commodity Protection Research, D.K.I, U.S. Pacific Basin Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, 64 Nowelo Street, Hilo, HI, 96720, USA
| | - Elizabeth A Stacy
- Tropical Conservation Biology and Environmental Sciences, University of Hawaii at Hilo, 200 West Kawili St., Hilo, HI, 96720, USA.,School of Life Sciences, University of Nevada, Las Vegas, USA
| | - Donald K Price
- Tropical Conservation Biology and Environmental Sciences, University of Hawaii at Hilo, 200 West Kawili St., Hilo, HI, 96720, USA. .,School of Life Sciences, University of Nevada, Las Vegas, USA.
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7
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Clo J, Ronfort J, Gay L. Fitness consequences of hybridization in a predominantly selfing species: insights into the role of dominance and epistatic incompatibilities. Heredity (Edinb) 2021; 127:393-400. [PMID: 34365470 PMCID: PMC8478955 DOI: 10.1038/s41437-021-00465-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
Studying the consequences of hybridization on plant performance is insightful to understand the adaptive potential of populations, notably at local scales. Due to reduced effective recombination, predominantly selfing species are organized in highly homozygous multi-locus-genotypes (or lines) that accumulate genetic differentiation both among- and within-populations. This high level of homozygosity facilitates the dissection of the genetic basis of hybrid performance in highly selfing species, which gives insights into the mechanisms of reproductive isolation between lines. Here, we explored the fitness consequences of hybridization events between natural inbred lines of the predominantly selfing species Medicago truncatula, at both within- and among-populations scales. We found that hybridization has opposite effects pending on studied fitness proxies, with dry mass showing heterosis, and seed production showing outbreeding depression. Although we found significant patterns of heterosis and outbreeding depression, they did not differ significantly for within- compared to among-population crosses. Family-based analyses allowed us to determine that hybrid differentiation was mostly due to dominance and epistasis. Dominance and/or dominant epistatic interactions increased dry mass, while decreasing seed production, and recessive epistatic interactions mostly had a positive effect on both fitness proxies. Our results illustrate how genetic incompatibilities can accumulate at a very local scale among multi-locus-genotypes, and how non-additive genetic effects contribute to heterosis and outbreeding depression.
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Affiliation(s)
- Josselin Clo
- grid.463758.b0000 0004 0445 8705AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France ,grid.4491.80000 0004 1937 116XDepartment of Botany, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Joëlle Ronfort
- grid.463758.b0000 0004 0445 8705AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Laurène Gay
- grid.463758.b0000 0004 0445 8705AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
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8
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Simon A, Bierne N, Welch JJ. Coadapted genomes and selection on hybrids: Fisher's geometric model explains a variety of empirical patterns. Evol Lett 2018; 2:472-498. [PMID: 30283696 PMCID: PMC6145440 DOI: 10.1002/evl3.66] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/02/2018] [Accepted: 06/06/2018] [Indexed: 12/27/2022] Open
Abstract
Natural selection plays a variety of roles in hybridization, speciation, and admixture. Most research has focused on two extreme cases: crosses between closely related inbred lines, where hybrids are fitter than their parents, or crosses between effectively isolated species, where hybrids suffer severe breakdown. But many natural populations must fall into intermediate regimes, with multiple types of gene interaction, and these are more difficult to study. Here, we develop a simple fitness landscape model, and show that it naturally interpolates between previous modeling approaches, which were designed for the extreme cases, and invoke either mildly deleterious recessives, or discrete hybrid incompatibilities. Our model yields several new predictions, which we test with genomic data from Mytilus mussels, and published data from plants (Zea, Populus, and Senecio) and animals (Mus, Teleogryllus, and Drosophila). The predictions are generally supported, and the model explains a number of surprising empirical patterns. Our approach enables novel and complementary uses of genome-wide datasets, which do not depend on identifying outlier loci, or "speciation genes" with anomalous effects. Given its simplicity and flexibility, and its predictive successes with a wide range of data, the approach should be readily extendable to other outstanding questions in the study of hybridization.
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Affiliation(s)
- Alexis Simon
- Institut des Sciences de l'Évolution UMR5554, Université de MontpellierCNRS‐IRD‐EPHE‐UMFrance
- Department of GeneticsUniversity of CambridgeDowning St. CambridgeCB23EHUnited Kingdom
| | - Nicolas Bierne
- Institut des Sciences de l'Évolution UMR5554, Université de MontpellierCNRS‐IRD‐EPHE‐UMFrance
- Department of GeneticsUniversity of CambridgeDowning St. CambridgeCB23EHUnited Kingdom
| | - John J. Welch
- Department of GeneticsUniversity of CambridgeDowning St. CambridgeCB23EHUnited Kingdom
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9
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Bermond G, Cavigliasso F, Mallez S, Spencer J, Guillemaud T. No clear effect of admixture between two European invading outbreaks of Diabrotica virgifera virgifera in natura. PLoS One 2014; 9:e106139. [PMID: 25170837 PMCID: PMC4149517 DOI: 10.1371/journal.pone.0106139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 08/01/2014] [Indexed: 11/18/2022] Open
Abstract
In this study, we challenged the hypothesis that admixture may have had a positive impact in the context of the European invasion of the western corn rootworm (WCR), Diabrotica virgifera virgifera, LeConte. This beetle was introduced in Europe from the USA several times since the 1980's. The multiple introductions of this major pest of cultivated corn led to the formation of two major outbreaks in North Western (NW) Italy and in Central and South Eastern (CSE) Europe that eventually merged into a secondary contact zone where insects from both outbreaks interbreed. We collected about 600 insects from this contact zone and genotyped them using 13 microsatellite markers. Three types of information were obtained from the collected individuals: (i) their survival under starvation; (ii) their admixed status, determined through a Bayesian method of genetic clustering and (iii) their mating probability, studied via the detection, isolation and genotyping of sperm in female spermathecae. Twenty six % and 12% of the individuals were assigned to the NW Italy or the CSE Europe parental types, respectively, and 23% and 39% to the F1 and backcross hybrid types, respectively. Globally, our results do not reveal any significant impact of the admixed status on the mating probability and on the choice of mating partners. However the admixed status had a sex- and sampling site-dependent effect on survival in adults under starvation. In addition sex had an effect on survival, with mortality hazard about 3 times larger in males than in females. The consequences of these findings for the evolution of the admixture zone of northern Italy are discussed.
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Affiliation(s)
- Gérald Bermond
- UMR 1355 Institut Sophia Agrobiotech, INRA, Sophia Antipolis, France
- UMR Institut Sophia Agrobiotech, Université de Nice-Sophia Antipolis, Sophia Antipolis, France
- UMR 7254 Institut Sophia Agrobiotech, CNRS, Sophia Antipolis, France
- * E-mail:
| | - Fanny Cavigliasso
- UMR 1355 Institut Sophia Agrobiotech, INRA, Sophia Antipolis, France
- UMR Institut Sophia Agrobiotech, Université de Nice-Sophia Antipolis, Sophia Antipolis, France
- UMR 7254 Institut Sophia Agrobiotech, CNRS, Sophia Antipolis, France
| | - Sophie Mallez
- UMR 1355 Institut Sophia Agrobiotech, INRA, Sophia Antipolis, France
- UMR Institut Sophia Agrobiotech, Université de Nice-Sophia Antipolis, Sophia Antipolis, France
- UMR 7254 Institut Sophia Agrobiotech, CNRS, Sophia Antipolis, France
| | - Joseph Spencer
- Illinois Natural History Survey, University of Illinois, Champaign, Illinois, United States of America
| | - Thomas Guillemaud
- UMR 1355 Institut Sophia Agrobiotech, INRA, Sophia Antipolis, France
- UMR Institut Sophia Agrobiotech, Université de Nice-Sophia Antipolis, Sophia Antipolis, France
- UMR 7254 Institut Sophia Agrobiotech, CNRS, Sophia Antipolis, France
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10
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Matute DR, Gavin-Smyth J, Liu G. Variable post-zygotic isolation in Drosophila melanogaster/D. simulans
hybrids. J Evol Biol 2014; 27:1691-705. [DOI: 10.1111/jeb.12422] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 04/13/2014] [Accepted: 04/28/2014] [Indexed: 11/29/2022]
Affiliation(s)
- D. R. Matute
- Department of Human Genetics; The University of Chicago; Chicago IL USA
- The Chicago Fellows Program; The University of Chicago; Chicago IL USA
| | - J. Gavin-Smyth
- The Chicago Fellows Program; The University of Chicago; Chicago IL USA
- Department of Ecology and Evolution; The University of Chicago; Chicago IL USA
| | - G. Liu
- Department of Human Genetics; The University of Chicago; Chicago IL USA
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11
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Corbett-Detig RB, Zhou J, Clark AG, Hartl DL, Ayroles JF. Genetic incompatibilities are widespread within species. Nature 2013; 504:135-7. [PMID: 24196712 PMCID: PMC4844467 DOI: 10.1038/nature12678] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 09/17/2013] [Indexed: 11/23/2022]
Abstract
The importance of epistasis — non-additive interactions between alleles — in shaping population fitness has long been a controversial topic, hampered in part by lack of empirical evidence1,2,3,4. Traditionally, epistasis is inferred based on non-independence of genotypic values between loci for a given trait. However epistasis for fitness should also have a genomic footprint5,6,7. To capture this signal, we have developed a simple approach that relies on detecting genotype ratio distortion (GRD) as a signal for epistasis, and we confirm experimentally that instances of GRD represent loci with epistatic fitness effects. In applying this method to a large panel of Drosophila melanogaster recombinant inbred lines8, 9, we conservatively estimate that any two haploid genomes in this study are expected to harbor 1.15 pairs of incompatible alleles. This observation has important implications for speciation genetics, as it indicates that the raw material to drive reproductive isolation is segregating contemporaneously within species and does not necessarily require, as proposed by the Dobzhansky–Muller model, the emergence of incompatible mutations independently derived and fixed in allopatry. The relevance of our result extends beyond speciation, as it demonstrates that epistasis is widespread but that it may often go undetected due to lack of statistical power or lack of genome-wide scope of the experiments.
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Affiliation(s)
- Russell B Corbett-Detig
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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12
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Demuth JP, Flanagan RJ, Delph LF. Genetic architecture of isolation between two species of Silene with sex chromosomes and Haldane's rule. Evolution 2013; 68:332-42. [PMID: 24117135 DOI: 10.1111/evo.12269] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 08/23/2013] [Indexed: 12/26/2022]
Abstract
Examination of the genetic architecture of hybrid breakdown can provide insight into the genetic mechanisms of commonly observed isolating phenomena such as Haldane's rule. We used line-cross analysis to dissect the genetic architecture of divergence between two plant species that exhibit Haldane's rule for male sterility and rarity, Silene latifolia and Silene diclinis. We made 15 types of crosses, including reciprocal F1, F2, backcrosses, and later-generation crosses, grew the seeds to flowering, and measured the number of viable ovules, proportion of viable pollen, and sex ratio. Typically, Haldane's rule for male rarity in XY animal hybrids is explained by interactions involving recessive X-linked alleles that are deleterious when hemizygous (dominance theory), whereas sterility is explained by rapid evolution of spermatogenesis genes (faster-male evolution). In contrast, we found that the genetic mechanisms underlying Haldane's rule between the two Silene species did not follow these conventions. Dominance theory was sufficient to explain male sterility, but male rarity likely involved faster-male evolution. We also found an effect of the neo-sex chromosomes of S. diclinis on the extreme rarity of some hybrid males. Our findings suggest that the genetic architecture of Haldane's rule in dioecious plants may differ from those commonly found in animals.
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Affiliation(s)
- Jeffery P Demuth
- Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, Texas, 76019
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13
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Fitzpatrick BM. Alternative forms for genomic clines. Ecol Evol 2013; 3:1951-66. [PMID: 23919142 PMCID: PMC3728937 DOI: 10.1002/ece3.609] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 04/22/2013] [Accepted: 04/24/2013] [Indexed: 11/30/2022] Open
Abstract
Understanding factors regulating hybrid fitness and gene exchange is a major research challenge for evolutionary biology. Genomic cline analysis has been used to evaluate alternative patterns of introgression, but only two models have been used widely and the approach has generally lacked a hypothesis testing framework for distinguishing effects of selection and drift. I propose two alternative cline models, implement multivariate outlier detection to identify markers associated with hybrid fitness, and simulate hybrid zone dynamics to evaluate the signatures of different modes of selection. Analysis of simulated data shows that previous approaches are prone to false positives (multinomial regression) or relatively insensitive to outlier loci affected by selection (Barton's concordance). The new, theory-based logit-logistic cline model is generally best at detecting loci affecting hybrid fitness. Although some generalizations can be made about different modes of selection, there is no one-to-one correspondence between pattern and process. These new methods will enhance our ability to extract important information about the genetics of reproductive isolation and hybrid fitness. However, much remains to be done to relate statistical patterns to particular evolutionary processes. The methods described here are implemented in a freely available package “HIest” for the R statistical software (CRAN; http://cran.r-project.org/).
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Affiliation(s)
- Benjamin M Fitzpatrick
- Department of Ecology and Evolutionary Biology, University of Tennessee Knoxville, Tennessee, 37996
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14
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Dittrich-Reed DR, Fitzpatrick BM. Transgressive Hybrids as Hopeful Monsters. Evol Biol 2012; 40:310-315. [PMID: 23687396 PMCID: PMC3655218 DOI: 10.1007/s11692-012-9209-0] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 11/06/2012] [Indexed: 01/27/2023]
Abstract
The origin of novelty is a critical subject for evolutionary biologists. Early geneticists speculated about the sudden appearance of new species via special macromutations, epitomized by Goldschmidt’s infamous “hopeful monster”. Although these ideas were easily dismissed by the insights of the Modern Synthesis, a lingering fascination with the possibility of sudden, dramatic change has persisted. Recent work on hybridization and gene exchange suggests an underappreciated mechanism for the sudden appearance of evolutionary novelty that is entirely consistent with the principles of modern population genetics. Genetic recombination in hybrids can produce transgressive phenotypes, “monstrous” phenotypes beyond the range of parental populations. Transgressive phenotypes can be products of epistatic interactions or additive effects of multiple recombined loci. We compare several epistatic and additive models of transgressive segregation in hybrids and find that they are special cases of a general, classic quantitative genetic model. The Dobzhansky-Muller model predicts “hopeless” monsters, sterile and inviable transgressive phenotypes. The Bateson model predicts “hopeful” monsters with fitness greater than either parental population. The complementation model predicts both. Transgressive segregation after hybridization can rapidly produce novel phenotypes by recombining multiple loci simultaneously. Admixed populations will also produce many similar recombinant phenotypes at the same time, increasing the probability that recombinant “hopeful monsters” will establish true-breeding evolutionary lineages. Recombination is not the only (or even most common) process generating evolutionary novelty, but might be the most credible mechanism for sudden appearance of new forms.
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Fitzpatrick BM. Estimating ancestry and heterozygosity of hybrids using molecular markers. BMC Evol Biol 2012; 12:131. [PMID: 22849298 PMCID: PMC3572440 DOI: 10.1186/1471-2148-12-131] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 07/13/2012] [Indexed: 12/03/2022] Open
Abstract
Background Hybridization, genetic mixture of distinct populations, gives rise to myriad recombinant genotypes. Characterizing the genomic composition of hybrids is critical for studies of hybrid zone dynamics, inheritance of traits, and consequences of hybridization for evolution and conservation. Hybrid genomes are often summarized either by an estimate of the proportion of alleles coming from each ancestral population or classification into discrete categories like F1, F2, backcross, or merely “hybrid” vs. “pure”. In most cases, it is not realistic to classify individuals into the restricted set of classes produced in the first two generations of admixture. However, the continuous ancestry index misses an important dimension of the genotype. Joint consideration of ancestry together with interclass heterozygosity (proportion of loci with alleles from both ancestral populations) captures all of the information in the discrete classification without the unrealistic assumption that only two generations of admixture have transpired. Methods I describe a maximum likelihood method for joint estimation of ancestry and interclass heterozygosity. I present two worked examples illustrating the value of the approach for describing variation among hybrid populations and evaluating the validity of the assumption underlying discrete classification. Results Naively classifying natural hybrids into the standard six line cross categories can be misleading, and false classification can be a serious problem for datasets with few molecular markers. My analysis underscores previous work showing that many (50 or more) ancestry informative markers are needed to avoid erroneous classification. Conclusion Although classification of hybrids might often be misleading, valuable inferences can be obtained by focusing directly on distributions of ancestry and heterozygosity. Estimating and visualizing the joint distribution of ancestry and interclass heterozygosity is an effective way to compare the genetic structure of hybrid populations and these estimates can be used in classic quantitative genetic methods for assessing additive, dominant, and epistatic genetic effects on hybrid phenotypes and fitness. The methods are implemented in a freely available package “HIest” for the R statistical software (
http://cran.r-project.org/web/packages/HIest/index.html).
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Affiliation(s)
- Benjamin M Fitzpatrick
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA.
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A stochastic model for the development of Bateson-Dobzhansky-Muller incompatibilities that incorporates protein interaction networks. Math Biosci 2012; 238:49-53. [PMID: 22465838 DOI: 10.1016/j.mbs.2012.03.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 03/12/2012] [Accepted: 03/14/2012] [Indexed: 12/16/2022]
Abstract
Speciation is characterized by the development of reproductive isolating barriers between diverging groups. Intrinsic post-zygotic barriers of the type envisioned by Bateson, Dobzhansky, and Muller are deleterious epistatic interactions among loci that reduce hybrid fitness, leading to reproductive isolation. The first formal population genetic model of the development of these barriers was published by Orr in 1995, and here we develop a more general model of this process by incorporating finite protein-protein interaction networks, which reduce the probability of deleterious interactions in vivo. Our model shows that the development of deleterious interactions is limited by the density of the protein-protein interaction network. We have confirmed our analytical predictions of the number of possible interactions given the number of allele substitutions by using simulations on the Saccharomyces cerevisiae protein-protein interaction network. These results allow us to define the rate at which deleterious interactions are expected to form, and hence the speciation rate, for any protein-protein interaction network.
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Johnson JR, Fitzpatrick BM, Shaffer HB. Retention of low-fitness genotypes over six decades of admixture between native and introduced tiger salamanders. BMC Evol Biol 2010; 10:147. [PMID: 20482794 PMCID: PMC2889957 DOI: 10.1186/1471-2148-10-147] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Accepted: 05/18/2010] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Introductions of non-native tiger salamanders into the range of California tiger salamanders have provided a rare opportunity to study the early stages of secondary contact and hybridization. We produced first- and second-generation hybrid salamanders in the lab and measured viability among these early-generation hybrid crosses to determine the strength of the initial barrier to gene exchange. We also created contemporary-generation hybrids in the lab and evaluated the extent to which selection has affected fitness over approximately 20 generations of admixture. Additionally, we examined the inheritance of quantitative phenotypic variation to better understand how evolution has progressed since secondary contact. RESULTS We found significant variation in the fitness of hybrids, with non-native backcrosses experiencing the highest survival and F2 hybrids the lowest. Contemporary-generation hybrids had similar survival to that of F2 families, contrary to our expectation that 20 generations of selection in the wild would eliminate unfit genotypes and increase survival. Hybrid survival clearly exhibited effects of epistasis, whereas size and growth showed mostly additive genetic variance, and time to metamorphosis showed substantial dominance. CONCLUSIONS Based on first- and second- generation cross types, our results suggest that the initial barrier to gene flow between these two species was relatively weak, and subsequent evolution has been generally slow. The persistence of low-viability recombinant hybrid genotypes in some contemporary populations illustrates that while hybridization can provide a potent source of genetic variation upon which natural selection can act, the sorting of fit from unfit gene combinations might be inefficient in highly admixed populations. Spatio-temporal fluctuation in selection or complex genetics has perhaps stalled adaptive evolution in this system despite selection for admixed genotypes within generations.
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Affiliation(s)
- Jarrett R Johnson
- Department of Evolution and Ecology & Center for Population Biology, University of California, Davis, CA 95616, USA
| | - Benjamin M Fitzpatrick
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - H Bradley Shaffer
- Department of Evolution and Ecology & Center for Population Biology, University of California, Davis, CA 95616, USA
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Elnaccash TW, Tonsor SJ. Something old and something new: wedding recombinant inbred lines with traditional line cross analysis increases power to describe gene interactions. PLoS One 2010; 5:e10200. [PMID: 20419131 PMCID: PMC2855707 DOI: 10.1371/journal.pone.0010200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Accepted: 02/18/2010] [Indexed: 11/19/2022] Open
Abstract
In this paper we present a novel approach to quantifying genetic architecture that combines recombinant inbred lines (RIL) with line cross analysis (LCA). LCA is a method of quantifying directional genetic effects (i.e. summed effects of all loci) that differentiate two parental lines. Directional genetic effects are thought to be critical components of genetic architecture for the long term response to selection and as a cause of inbreeding depression. LCA typically begins with two inbred parental lines that are crossed to produce several generations such as F1, F2, and backcrosses to each parent. When a RIL population (founded from the same P1 and P2 as was used to found the line cross population) is added to the LCA, the sampling variance of several nonadditive genetic effect estimates is greatly reduced. Specifically, estimates of directional dominance, additive x additive, and dominance x dominance epistatic effects are reduced by 92%, 94%, and 56% respectively. The RIL population can be simultaneously used for QTL identification, thus uncovering the effects of specific loci or genomic regions as elements of genetic architecture. LCA and QTL mapping with RIL provide two qualitatively different measures of genetic architecture with the potential to overcome weaknesses of each approach alone. This approach provides cross-validation of the estimates of additive and additive x additive effects, much smaller confidence intervals on dominance, additive x additive and dominance x dominance estimates, qualitatively different measures of genetic architecture, and the potential when used together to balance the weaknesses of LCA or RIL QTL analyses when used alone.
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Affiliation(s)
- Tarek W Elnaccash
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America.
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Chang AS, Noor MAF. Epistasis modifies the dominance of loci causing hybrid male sterility in the Drosophila pseudoobscura species group. Evolution 2009; 64:253-60. [PMID: 19686263 DOI: 10.1111/j.1558-5646.2009.00823.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Speciation, the evolution of reproductive isolation between populations, serves as the driving force for generating biodiversity. Postzygotic barriers to gene flow, such as F(1) hybrid sterility and inviability, play important roles in the establishment and maintenance of biological species. F(1) hybrid incompatibilities in taxa that obey Haldane's rule, the observation that the heterogametic sex suffers greater hybrid fitness problems than the homogametic sex, are thought to often result from interactions between recessive-acting X-linked loci and dominant-acting autosomal loci. Because they play such prominent roles in producing hybrid incompatibilities, we examine the dominance and nature of epistasis between alleles derived from Drosophila persimilis that confer hybrid male sterility in the genetic background of its sister species, D. pseudoobscura bogotana. We show that epistasis elevates the apparent dominance of individually recessive-acting QTL such that they can contribute to F(1) hybrid sterility. These results have important implications for assumptions underlying theoretical models of hybrid incompatibilities and may offer a possible explanation for why, to date, identification of dominant-acting autosomal "speciation genes" has been challenging.
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Affiliation(s)
- Audrey S Chang
- Department of Biology, Duke University, Durham, North Carolina 27708, USA.
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Fitzpatrick BM, Johnson JR, Kump DK, Shaffer HB, Smith JJ, Voss SR. Rapid fixation of non-native alleles revealed by genome-wide SNP analysis of hybrid tiger salamanders. BMC Evol Biol 2009; 9:176. [PMID: 19630983 PMCID: PMC2724412 DOI: 10.1186/1471-2148-9-176] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Accepted: 07/24/2009] [Indexed: 01/10/2023] Open
Abstract
Background Hybrid zones represent valuable opportunities to observe evolution in systems that are unusually dynamic and where the potential for the origin of novelty and rapid adaptation co-occur with the potential for dysfunction. Recently initiated hybrid zones are particularly exciting evolutionary experiments because ongoing natural selection on novel genetic combinations can be studied in ecological time. Moreover, when hybrid zones involve native and introduced species, complex genetic patterns present important challenges for conservation policy. To assess variation of admixture dynamics, we scored a large panel of markers in five wild hybrid populations formed when Barred Tiger Salamanders were introduced into the range of California Tiger Salamanders. Results At three of 64 markers, introduced alleles have largely displaced native alleles within the hybrid populations. Another marker (GNAT1) showed consistent heterozygote deficits in the wild, and this marker was associated with embryonic mortality in laboratory F2's. Other deviations from equilibrium expectations were idiosyncratic among breeding ponds, consistent with highly stochastic demographic effects. Conclusion While most markers retain native and introduced alleles in expected proportions, strong selection appears to be eliminating native alleles at a smaller set of loci. Such rapid fixation of alleles is detectable only in recently formed hybrid zones, though it might be representative of dynamics that frequently occur in nature. These results underscore the variable and mosaic nature of hybrid genomes and illustrate the potency of recombination and selection in promoting variable, and often unpredictable genetic outcomes. Introgression of a few, strongly selected introduced alleles should not necessarily affect the conservation status of California Tiger Salamanders, but suggests that genetically pure populations of this endangered species will be difficult to maintain.
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