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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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Konuma J, Fujisawa T, Nishiyama T, Kasahara M, Shibata TF, Nozawa M, Shigenobu S, Toyoda A, Hasebe M, Sota T. Odd-Paired is Involved in Morphological Divergence of Snail-Feeding Beetles. Mol Biol Evol 2024; 41:msae110. [PMID: 38857185 PMCID: PMC11214159 DOI: 10.1093/molbev/msae110] [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: 12/12/2023] [Revised: 04/15/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024] Open
Abstract
Body shape and size diversity and their evolutionary rates correlate with species richness at the macroevolutionary scale. However, the molecular genetic mechanisms underlying the morphological diversification across related species are poorly understood. In beetles, which account for one-fourth of the known species, adaptation to different trophic niches through morphological diversification appears to have contributed to species radiation. Here, we explored the key genes for the morphological divergence of the slender to stout body shape related to divergent feeding methods on large to small snails within the genus Carabus. We show that the zinc-finger transcription factor encoded by odd-paired (opa) controls morphological variation in the snail-feeding ground beetle Carabus blaptoides. Specifically, opa was identified as the gene underlying the slender to stout morphological difference between subspecies through genetic mapping and functional analysis via gene knockdown. Further analyses revealed that changes in opa cis-regulatory sequences likely contributed to the differences in body shape and size between C. blaptoides subspecies. Among opa cis-regulatory sequences, single nucleotide polymorphisms on the transcription factor binding sites may be associated with the morphological differences between C. blaptoides subspecies. opa was highly conserved in a wide range of taxa, especially in beetles. Therefore, opa may play an important role in adaptive morphological divergence in beetles.
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Affiliation(s)
- Junji Konuma
- Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, Japan
| | - Tomochika Fujisawa
- Center for Data Science Education and Research, Shiga University, Hikone, Shiga, Japan
| | - Tomoaki Nishiyama
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Ishikawa, Japan
| | - Masahiro Kasahara
- Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Chiba, Japan
| | | | - Masafumi Nozawa
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
- Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | | | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Mitsuyasu Hasebe
- National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, The Graduate School for Advanced Studies (SOKENDAI), Okazaki, Aichi, Japan
| | - Teiji Sota
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, Japan
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3
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Zhang S, Kubota K. Local ecological divergence of two closely related stag beetles based on genetic, morphological, and environmental analyses. Ecol Evol 2022; 12:e8837. [PMID: 35449584 PMCID: PMC9013855 DOI: 10.1002/ece3.8837] [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: 10/30/2021] [Revised: 03/19/2022] [Accepted: 03/29/2022] [Indexed: 11/10/2022] Open
Abstract
The process of phenotypic adaptation to the environments is widely recognized. However, comprehensive studies integrating phylogenetic, phenotypic, and ecological approaches to assess this process are scarce. Our study aims to assess whether local adaptation may explain intraspecific differentiation by quantifying multidimensional differences among populations in closely related lucanid species, Platycerus delicatulus and Platycerus kawadai, which are endemic saproxylic beetles in Japan. First, we determined intraspecific analysis units based on nuclear and mitochondrial gene analyses of Platycerus delicatulus and Platycerus kawadai under sympatric and allopatric conditions. Then, we compared differences in morphology and environmental niche between populations (analysis units) within species. We examined the relationship between morphology and environmental niche via geographic distance. P. kawadai was subdivided into the “No introgression” and “Introgression” populations based on mitochondrial COI gene – nuclear ITS region discordance. P. delicatulus was subdivided into “Allopatric” and “Sympatric” populations. Body length differed significantly among the populations of each species. For P. delicatulus, character displacement was suggested. For P. kawadai, the morphological difference was likely caused by geographic distance or genetic divergence rather than environmental differences. The finding showed that the observed mitochondrial–nuclear discordance is likely due to historical mitochondrial introgression following a range of expansion. Our results show that morphological variation among populations of P. delicatulus and P. kawadai reflects an ecological adaptation process based on interspecific interactions, geographic distance, or genetic divergence. Our results will deepen understanding of ecological specialization processes across the distribution and adaptation of species in natural systems.
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Affiliation(s)
- Sheng‐Nan Zhang
- Department of Forest Science Graduate School of Agricultural and Life Sciences The University of Tokyo Tokyo Japan
| | - Kôhei Kubota
- Department of Forest Science Graduate School of Agricultural and Life Sciences The University of Tokyo Tokyo Japan
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Thompson KA, Urquhart-Cronish M, Whitney KD, Rieseberg LH, Schluter D. Patterns, Predictors, and Consequences of Dominance in Hybrids. Am Nat 2021; 197:E72-E88. [PMID: 33625966 DOI: 10.1086/712603] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractCompared to those of their parents, are the traits of first-generation (F1) hybrids typically intermediate, biased toward one parent, or mismatched for alternative parental phenotypes? To address this empirical gap, we compiled data from 233 crosses in which traits were measured in a common environment for two parent taxa and their F1 hybrids. We find that individual traits in F1s are halfway between the parental midpoint and one parental value. Considering pairs of traits together, a hybrid's bivariate phenotype tends to resemble one parent (parent bias) about 50% more than the other, while also exhibiting a similar magnitude of mismatch due to different traits having dominance in conflicting directions. Using data from an experimental field planting of recombinant hybrid sunflowers, we illustrate that parent bias improves fitness, whereas mismatch reduces fitness. Our study has three major conclusions. First, hybrids are not phenotypically intermediate but rather exhibit substantial mismatch. Second, dominance is likely determined by the idiosyncratic evolutionary trajectories of individual traits and populations. Finally, selection against hybrids likely results from selection against both intermediate and mismatched phenotypes.
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Akiyama K, Jang TW, Park YH, Shinohara T, Konuma J, Liang H, Kubota K, Sota T, Ishikawa R, Kim JL, Kim JK, Takami Y. Phylogeographical analysis of character displacement in feeding phenotypes of snail-feeding Acoptolabrus ground beetles. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Ecological character displacement predicts that interspecific resource competition results in greater trait divergence between species in sympatry than in allopatry. However, other processes, such as ecological sorting, result in the same pattern of trait variation. In this study, we characterize character displacement in eight species of snail-feeding Acoptolabrus ground beetles in the Far East. Acoptolabrus exhibit divergent feeding phenotypes, including species with a slender forebody that is able to intrude into large shells and species with stout heads and mandibles for crushing small shells. The pattern of character displacement in feeding phenotypes was confirmed by multivariate analysis of body dimensions. Molecular phylogenetic analysis, divergence time estimation and biogeographical analysis revealed that sympatry and phenotypic divergence occurred repeatedly during the Pleistocene and almost simultaneously within each geographical area. Comparative analysis revealed that the evolution of feeding phenotypes best fitted a selective model with three adaptive optima, corresponding to the three cases of sympatry with a congener. Repeated coincidences of sympatry and adaptive differentiation in feeding phenotypes suggested causal relationships, although the precise order of events was difficult to discriminate. This study provides insight into the spatiotemporal dynamics of interspecific interactions and adaptive phenotypic diversification.
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Affiliation(s)
- Kazutoshi Akiyama
- Graduate School of Human Development and Environment, Kobe University, Nada, Kobe, Japan
| | - Tae Woong Jang
- College of Forest and Environmental Sciences, Kangwon National University, Chuncheon, Korea
| | - Yong Hwan Park
- Graduate School of Human Development and Environment, Kobe University, Nada, Kobe, Japan
- College of Forest and Environmental Sciences, Kangwon National University, Chuncheon, Korea
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Korea
| | - Tadashi Shinohara
- Graduate School of Human Development and Environment, Kobe University, Nada, Kobe, Japan
| | - Junji Konuma
- Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, Japan
| | - Hongbin Liang
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Kohei Kubota
- Department of Forest Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Teiji Sota
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, Japan
| | | | - Jung Lark Kim
- Department of Health Management, Uiduk University, Gyeongju, Korea
| | - Jong Kuk Kim
- College of Forest and Environmental Sciences, Kangwon National University, Chuncheon, Korea
| | - Yasuoki Takami
- Graduate School of Human Development and Environment, Kobe University, Nada, Kobe, Japan
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Ma WJ, Carpentier F, Giraud T, Hood ME. Differential Gene Expression between Fungal Mating Types Is Associated with Sequence Degeneration. Genome Biol Evol 2020; 12:243-258. [PMID: 32058544 PMCID: PMC7150583 DOI: 10.1093/gbe/evaa028] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2020] [Indexed: 12/13/2022] Open
Abstract
Degenerative mutations in non-recombining regions, such as in sex chromosomes, may lead to differential expression between alleles if mutations occur stochastically in one or the other allele. Reduced allelic expression due to degeneration has indeed been suggested to occur in various sex-chromosome systems. However, whether an association occurs between specific signatures of degeneration and differential expression between alleles has not been extensively tested, and sexual antagonism can also cause differential expression on sex chromosomes. The anther-smut fungus Microbotryum lychnidis-dioicae is ideal for testing associations between specific degenerative signatures and differential expression because 1) there are multiple evolutionary strata on the mating-type chromosomes, reflecting successive recombination suppression linked to mating-type loci; 2) separate haploid cultures of opposite mating types help identify differential expression between alleles; and 3) there is no sexual antagonism as a confounding factor accounting for differential expression. We found that differentially expressed genes were enriched in the four oldest evolutionary strata compared with other genomic compartments, and that, within compartments, several signatures of sequence degeneration were greater for differentially expressed than non-differentially expressed genes. Two particular degenerative signatures were significantly associated with lower expression levels within differentially expressed allele pairs: upstream insertion of transposable elements and mutations truncating the protein length. Other degenerative mutations associated with differential expression included nonsynonymous substitutions and altered intron or GC content. The association between differential expression and allele degeneration is relevant for a broad range of taxa where mating compatibility or sex is determined by genes located in large regions where recombination is suppressed.
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Affiliation(s)
- Wen-Juan Ma
- Department of Biology, Amherst College, Amherst, MA
| | - Fantin Carpentier
- Ecologie Systematique et Evolution, Université Paris-Saclay, CNRS, AgroParisTech, Orsay, France
| | - Tatiana Giraud
- Ecologie Systematique et Evolution, Université Paris-Saclay, CNRS, AgroParisTech, Orsay, France
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Komurai R, Fujisawa T, Okuzaki Y, Sota T. Genomic regions and genes related to inter-population differences in body size in the ground beetle Carabus japonicus. Sci Rep 2017; 7:7773. [PMID: 28798311 PMCID: PMC5552851 DOI: 10.1038/s41598-017-08362-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 07/11/2017] [Indexed: 11/14/2022] Open
Abstract
Body size is a key trait in diversification among animal species, and revealing the gene regions responsible for body size diversification among populations or related species is important in evolutionary biology. We explored the genomic regions associated with body size differences in Carabus japonicus ground beetle populations by quantitative trait locus (QTL) mapping of F2 hybrids from differently sized parents from two populations using restriction site-associated DNA sequencing and de novo assembly of the beetle whole genome. The assembled genome had a total length of 191 Mb with a scaffold N50 of 0.73 Mb; 14,929 protein-coding genes were predicted. Three QTLs on different linkage groups had major effects on the overall size, which is composed chiefly of elytral length. In addition, we found QTLs on autosomal and X chromosomal linkage groups that affected head length and width, thoracic width, and elytral width. We determined the gene loci potentially related to control of body size in scaffolds of the genome sequence, which contained the QTL regions. The genetic basis of body size variation based on a small number of major loci would promote differentiation in body size in response to selection pressures related to variations in environmental conditions and inter-specific interactions.
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Affiliation(s)
- Ryohei Komurai
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, Japan
| | - Tomochika Fujisawa
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, Japan
| | - Yutaka Okuzaki
- Field Science Center for Northern Biosphere, Hokkaido University, Tomakomai, 053-0035, Japan
| | - Teiji Sota
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, Japan.
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Sasakawa K. Utility of geometric morphometrics for inferring feeding habit from mouthpart morphology in insects: tests with larval Carabidae (Insecta: Coleoptera). Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12727] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kôji Sasakawa
- Laboratory of Zoology; Department of Science Education; Faculty of Education; Chiba University; 1-33 Yayoi-cho, Inage-ku Chiba 263-8522 Japan
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9
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Konuma J, Yamamoto S, Sota T. Morphological integration and pleiotropy in the adaptive body shape of the snail-feeding carabid beetleDamaster blaptoides. Mol Ecol 2014; 23:5843-54. [DOI: 10.1111/mec.12976] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 10/16/2014] [Accepted: 10/20/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Junji Konuma
- Department of Zoology; Graduate School of Science; Kyoto University; Kitashirakawa-Oiwake Sakyo Kyoto 606-8502 Japan
- Department of Biology; Faculty of Science; Toho University; 2-2-1 Miyama Funabashi Chiba 274-8510 Japan
| | - Satoshi Yamamoto
- Department of Zoology; Graduate School of Science; Kyoto University; Kitashirakawa-Oiwake Sakyo Kyoto 606-8502 Japan
- Faculty of Human Development; Graduate School of Human Development and Environment; Kobe University; Nada Kobe 657-8501 Japan
| | - Teiji Sota
- Department of Zoology; Graduate School of Science; Kyoto University; Kitashirakawa-Oiwake Sakyo Kyoto 606-8502 Japan
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Konuma J, Sota T, Chiba S. A maladaptive intermediate form: a strong trade-off revealed by hybrids between two forms of a snail-feeding beetle. Ecology 2014; 94:2638-44. [PMID: 24400515 DOI: 10.1890/12-2041.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Although trade-off curves between fitness components are essential in theoretical studies of ecological specialization, few empirical studies have actually determined these curves experimentally. Using the snail-feeding carabid beetle Damaster blaptoides, which is endemic to the Japanese archipelago, we estimated the trade-off curve for feeding success with alternative foraging behaviors that are linked to varying morphology. First, we crossed a stout-bodied and a slender-bodied subspecies and produced their F1 and backcross hybrids, which exhibited intermediate body shapes. Then we compared the snail-feeding success of these beetles. Stout beetles could eat small snails by crushing shells, whereas slender beetles could eat large snails by inserting their heads into shells. Although hybrids with intermediate body shapes attempted to employ both strategies, they frequently failed at both. The relationship between feeding success rate and beetle body shape was represented by an inward bending curve, which implies a strong trade-off that can cause disruptive selection, leading to ecological specialization. We suggest that the intermediately shaped beetles were maladapted for snail-feeding and that disruptive selection may have played an important role in the morphological divergence of these beetles.
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Affiliation(s)
- Junji Konuma
- Department of Zoology, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake, Sakyo, Kyoto 6068502, Japan.
| | - Teiji Sota
- Department of Zoology, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake, Sakyo, Kyoto 6068502, Japan
| | - Satoshi Chiba
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Aobayama, Sendai 980 8578, Japan
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