151
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Avril A, Zahnd S, Djordjevic J, Chapuisat M. No mate preference associated with the supergene controlling social organization in Alpine silver ants. J Evol Biol 2019; 32:742-748. [PMID: 31016785 DOI: 10.1111/jeb.13479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 03/22/2019] [Accepted: 04/16/2019] [Indexed: 01/30/2023]
Abstract
Disassortative mating is a powerful mechanism stabilizing polymorphisms at sex chromosomes and other supergenes. The Alpine silver ant, Formica selysi, has two forms of social organization-single-queen and multiple-queen colonies-determined by alternate haplotypes at a large supergene. Here, we explore whether mate preference contributes to the maintenance of the genetic polymorphism at the social supergene. With mate choice experiments, we found that females and males mated randomly with respect to social form. Moreover, queens were able to produce offspring irrespective of whether they had mated with a male from the same or the alternative social form. Yet, females originating from single-queen colonies were more fertile, suggesting that they may be more successful at independent colony founding. We conclude that the pattern of asymmetric assortative mating documented from mature F. selysi colonies in the field is not caused by mate preferences or major genetic incompatibilities between social forms. More generally, we found no evidence that disassortative mate preference contributes to the maintenance of polymorphism at this supergene controlling ant social organization.
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Affiliation(s)
- Amaury Avril
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Sacha Zahnd
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | - Michel Chapuisat
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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152
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Benowitz KM, Coleman JM, Matzkin LM. Assessing the Architecture of Drosophila mojavensis Locomotor Evolution with Bulk Segregant Analysis. G3 (BETHESDA, MD.) 2019; 9:1767-1775. [PMID: 30926724 PMCID: PMC6505136 DOI: 10.1534/g3.119.400036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 03/22/2019] [Indexed: 11/24/2022]
Abstract
Behavior is frequently predicted to be especially important for evolution in novel environments. If these predictions are accurate, there might be particular patterns of genetic architecture associated with recently diverged behaviors. Specifically, it has been predicted that behaviors linked to population divergence should be underpinned by a few genes of relatively large effect, compared to architectures of intrapopulation behavioral variation, which is considered to be highly polygenic. More mapping studies of behavioral variation between recently diverged populations are needed to continue assessing the generality of these predictions. Here, we used a bulk segregant mapping approach to dissect the genetic architecture of a locomotor trait that has evolved between two populations of the cactophilic fly Drosophila mojavensis We created an F8 mapping population of 1,500 individuals from advanced intercross lines and sequenced the 10% of individuals with the highest and lowest levels of locomotor activity. Using three alternative statistical approaches, we found strong evidence for two relatively large-effect QTL that is localized in a region homologous to a region of densely packed behavior loci in Drosophila melanogaster, suggesting that clustering of behavior genes may display relatively deep evolutionary conservation. Broadly, our data are most consistent with a polygenic architecture, though with several loci explaining a high proportion of variation in comparison to similar behavioral traits. We further note the presence of several antagonistic QTL linked to locomotion and discuss these results in light of theories regarding behavioral evolution and the effect size and direction of QTL for diverging traits in general.
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Affiliation(s)
- Kyle M Benowitz
- Department of Entomology, University of Arizona, Tucson, AZ 85721
| | - Joshua M Coleman
- Department of Entomology, University of Arizona, Tucson, AZ 85721
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville AL 35899
| | - Luciano M Matzkin
- Department of Entomology, University of Arizona, Tucson, AZ 85721
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721
- BIO5 Institute, University of Arizona, Tucson, AZ 85721
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153
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Kim KW, Jackson BC, Zhang H, Toews DPL, Taylor SA, Greig EI, Lovette IJ, Liu MM, Davison A, Griffith SC, Zeng K, Burke T. Genetics and evidence for balancing selection of a sex-linked colour polymorphism in a songbird. Nat Commun 2019; 10:1852. [PMID: 31015412 PMCID: PMC6478913 DOI: 10.1038/s41467-019-09806-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 03/22/2019] [Indexed: 11/09/2022] Open
Abstract
Colour polymorphisms play a key role in sexual selection and speciation, yet the mechanisms that generate and maintain them are not fully understood. Here, we use genomic and transcriptomic tools to identify the precise genetic architecture and evolutionary history of a sex-linked colour polymorphism in the Gouldian finch Erythrura gouldiae that is also accompanied by remarkable differences in behaviour and physiology. We find that differences in colour are associated with an ~72-kbp region of the Z chromosome in a putative regulatory region for follistatin, an antagonist of the TGF-β superfamily genes. The region is highly differentiated between morphs, unlike the rest of the genome, yet we find no evidence that an inversion is involved in maintaining the distinct haplotypes. Coalescent simulations confirm that there is elevated nucleotide diversity and an excess of intermediate frequency alleles at this locus. We conclude that this pleiotropic colour polymorphism is most probably maintained by balancing selection.
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Affiliation(s)
- Kang-Wook Kim
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK.
| | - Benjamin C Jackson
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Hanyuan Zhang
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - David P L Toews
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, 159 Sapsucker Woods Road, Ithaca, NY, 14850, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, NY, 14853, USA
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Scott A Taylor
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, 159 Sapsucker Woods Road, Ithaca, NY, 14850, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, NY, 14853, USA
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Emma I Greig
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, 159 Sapsucker Woods Road, Ithaca, NY, 14850, USA
| | - Irby J Lovette
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, 159 Sapsucker Woods Road, Ithaca, NY, 14850, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, NY, 14853, USA
| | - Mengning M Liu
- School of Biology, University of Nottingham, University Park, NG7 2RD, Nottingham, UK
| | - Angus Davison
- School of Biology, University of Nottingham, University Park, NG7 2RD, Nottingham, UK
| | - Simon C Griffith
- Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Kai Zeng
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK.
| | - Terry Burke
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK.
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154
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Choudhury RR, Rogivue A, Gugerli F, Parisod C. Impact of polymorphic transposable elements on linkage disequilibrium along chromosomes. Mol Ecol 2019; 28:1550-1562. [DOI: 10.1111/mec.15014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 12/26/2018] [Indexed: 01/03/2023]
Affiliation(s)
| | - Aude Rogivue
- WSL Swiss Federal Research Institute Birmensdorf Switzerland
| | - Felix Gugerli
- WSL Swiss Federal Research Institute Birmensdorf Switzerland
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155
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Flagel LE, Blackman BK, Fishman L, Monnahan PJ, Sweigart A, Kelly JK. GOOGA: A platform to synthesize mapping experiments and identify genomic structural diversity. PLoS Comput Biol 2019; 15:e1006949. [PMID: 30986215 PMCID: PMC6483263 DOI: 10.1371/journal.pcbi.1006949] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 04/25/2019] [Accepted: 03/15/2019] [Indexed: 11/18/2022] Open
Abstract
Understanding genomic structural variation such as inversions and translocations is a key challenge in evolutionary genetics. We develop a novel statistical approach to comparative genetic mapping to detect large-scale structural mutations from low-level sequencing data. The procedure, called Genome Order Optimization by Genetic Algorithm (GOOGA), couples a Hidden Markov Model with a Genetic Algorithm to analyze data from genetic mapping populations. We demonstrate the method using both simulated data (calibrated from experiments on Drosophila melanogaster) and real data from five distinct crosses within the flowering plant genus Mimulus. Application of GOOGA to the Mimulus data corrects numerous errors (misplaced sequences) in the M. guttatus reference genome and confirms or detects eight large inversions polymorphic within the species complex. Finally, we show how this method can be applied in genomic scans to improve the accuracy and resolution of Quantitative Trait Locus (QTL) mapping.
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Affiliation(s)
- Lex E. Flagel
- Bayer Crop Science, Chesterfield, MO, United States of America
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, United States of America
- * E-mail: (LEF); (JKK)
| | - Benjamin K. Blackman
- Department of Plant and Microbial Biology, University of California—Berkeley, Berkeley, CA, United States of America
| | - Lila Fishman
- Division of Biological Sciences, University of Montana, Missoula, MT, United States of America
| | - Patrick J. Monnahan
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, United States of America
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, United States of America
| | - Andrea Sweigart
- Department of Genetics, University of Georgia, Athens, GA, United States of America
| | - John K. Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, United States of America
- * E-mail: (LEF); (JKK)
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156
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Andrade P, Pinho C, Pérez I de Lanuza G, Afonso S, Brejcha J, Rubin CJ, Wallerman O, Pereira P, Sabatino SJ, Bellati A, Pellitteri-Rosa D, Bosakova Z, Bunikis I, Carretero MA, Feiner N, Marsik P, Paupério F, Salvi D, Soler L, While GM, Uller T, Font E, Andersson L, Carneiro M. Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard. Proc Natl Acad Sci U S A 2019; 116:5633-5642. [PMID: 30819892 DOI: 10.1101/481895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023] Open
Abstract
Reptiles use pterin and carotenoid pigments to produce yellow, orange, and red colors. These conspicuous colors serve a diversity of signaling functions, but their molecular basis remains unresolved. Here, we show that the genomes of sympatric color morphs of the European common wall lizard (Podarcis muralis), which differ in orange and yellow pigmentation and in their ecology and behavior, are virtually undifferentiated. Genetic differences are restricted to two small regulatory regions near genes associated with pterin [sepiapterin reductase (SPR)] and carotenoid [beta-carotene oxygenase 2 (BCO2)] metabolism, demonstrating that a core gene in the housekeeping pathway of pterin biosynthesis has been coopted for bright coloration in reptiles and indicating that these loci exert pleiotropic effects on other aspects of physiology. Pigmentation differences are explained by extremely divergent alleles, and haplotype analysis revealed abundant transspecific allele sharing with other lacertids exhibiting color polymorphisms. The evolution of these conspicuous color ornaments is the result of ancient genetic variation and cross-species hybridization.
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Affiliation(s)
- Pedro Andrade
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Catarina Pinho
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Guillem Pérez I de Lanuza
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Sandra Afonso
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Jindřich Brejcha
- Department of Philosophy and History of Science, Faculty of Science, Charles University, 128 00 Prague 2, Czech Republic
- Department of Zoology, National Museum, 193 00 Prague, Czech Republic
- Ethology Laboratory, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, 469 80 Paterna, Spain
| | - Carl-Johan Rubin
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 752 36 Uppsala, Sweden
| | - Ola Wallerman
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 752 36 Uppsala, Sweden
| | - Paulo Pereira
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Stephen J Sabatino
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Adriana Bellati
- Department of Earth and Environmental Sciences, University of Pavia, 27100 Pavia, Italy
| | | | - Zuzana Bosakova
- Department of Analytical Chemistry, Faculty of Science, Charles University, 128 43 Prague 2, Czech Republic
| | - Ignas Bunikis
- Science for Life Laboratory Uppsala, Department of Immunology, Genetics and Pathology, Uppsala University, 752 36 Uppsala, Sweden
| | - Miguel A Carretero
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
| | | | - Petr Marsik
- Department of Food Science, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 21 Prague 6, Czech Republic
| | - Francisco Paupério
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Daniele Salvi
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
- Department of Health, Life and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Lucile Soler
- Science for Life Laboratory, National Bioinformatics Infrastructure Sweden (NBIS), 751 23 Uppsala, Sweden
| | - Geoffrey M While
- School of Biological Sciences, University of Tasmania, Hobart, TAS 7005 Tasmania, Australia
- Department of Zoology, University of Oxford, OX1 3PS Oxford, United Kingdom
| | - Tobias Uller
- Department of Biology, Lund University, 223 62 Lund, Sweden
| | - Enrique Font
- Ethology Laboratory, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, 469 80 Paterna, Spain
| | - Leif Andersson
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 752 36 Uppsala, Sweden;
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843
| | - Miguel Carneiro
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal;
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
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157
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Lowry DB, Popovic D, Brennan DJ, Holeski LM. Mechanisms of a locally adaptive shift in allocation among growth, reproduction, and herbivore resistance in
Mimulus guttatus
*. Evolution 2019; 73:1168-1181. [DOI: 10.1111/evo.13699] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 01/21/2019] [Accepted: 01/31/2019] [Indexed: 12/24/2022]
Affiliation(s)
- David B. Lowry
- Department of Plant BiologyMichigan State University East Lansing Michigan 48824
- Program in Ecology, Evolutionary Biology, and BehaviorMichigan State University East Lansing Michigan 48824
- Plant Resilience Institute,Michigan State University East Lansing Michigan 48824
| | - Damian Popovic
- Department of Plant BiologyMichigan State University East Lansing Michigan 48824
- Program in Ecology, Evolutionary Biology, and BehaviorMichigan State University East Lansing Michigan 48824
| | - Darlene J. Brennan
- Department of Plant BiologyMichigan State University East Lansing Michigan 48824
| | - Liza M. Holeski
- Department of Biological SciencesNorthern Arizona University Flagstaff Arizona 86011
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158
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Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard. Proc Natl Acad Sci U S A 2019; 116:5633-5642. [PMID: 30819892 PMCID: PMC6431182 DOI: 10.1073/pnas.1820320116] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Reptiles show an amazing color diversity based on variation in melanins, carotenoids, and pterins. This study reveals genes controlling differences between three color morphs (white, orange, and yellow) in the common wall lizard. Orange pigmentation, due to high levels of orange/red pterins in skin, is caused by genetic changes in the sepiapterin reductase gene. Yellow skin, showing high levels of yellow carotenoids, is controlled by the beta-carotene oxygenase 2 locus. Thus, the color polymorphism in the common wall lizard is associated with changes in two small regions of the genome containing genes with crucial roles in pterin and carotenoid metabolism. These genes are likely to have pleiotropic effects on behavior and other traits associated with the different color morphs. Reptiles use pterin and carotenoid pigments to produce yellow, orange, and red colors. These conspicuous colors serve a diversity of signaling functions, but their molecular basis remains unresolved. Here, we show that the genomes of sympatric color morphs of the European common wall lizard (Podarcis muralis), which differ in orange and yellow pigmentation and in their ecology and behavior, are virtually undifferentiated. Genetic differences are restricted to two small regulatory regions near genes associated with pterin [sepiapterin reductase (SPR)] and carotenoid [beta-carotene oxygenase 2 (BCO2)] metabolism, demonstrating that a core gene in the housekeeping pathway of pterin biosynthesis has been coopted for bright coloration in reptiles and indicating that these loci exert pleiotropic effects on other aspects of physiology. Pigmentation differences are explained by extremely divergent alleles, and haplotype analysis revealed abundant transspecific allele sharing with other lacertids exhibiting color polymorphisms. The evolution of these conspicuous color ornaments is the result of ancient genetic variation and cross-species hybridization.
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159
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Lopes PC, Lindholm AK. A selfish genetic element linked to increased lifespan impacts metabolism in female house mice. J Exp Biol 2019; 223:jeb.212704. [DOI: 10.1242/jeb.212704] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/28/2019] [Indexed: 01/30/2023]
Abstract
Gene drive systems can lead to the evolution of traits that further enhance the transmission of the driving element. In gene drive, one allele is transmitted to offspring at a higher frequency than the homologous allele. This has a range of consequences, which generally include a reduction in fitness of the carrier of the driving allele, making such systems “selfish”. The t haplotype is one such driver, found in house mice. It is linked to a reduction in litter size in matings among heterozygous animals, but also to increased lifespan in wild females that carry it. Here, we tested whether carrying the t haplotype was associated with altered resting metabolic rate (RMR). We show that females carrying the t haplotype decrease RMR as they increase in size, compared to wildtype females or males of either genotype. Our study elucidates a plausible mechanism by which a selfish genetic element increases lifespan.
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Affiliation(s)
- Patricia C. Lopes
- Schmid College of Science and Technology, Chapman University, Orange, CA, USA
| | - Anna K. Lindholm
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
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160
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Ross KG, Shoemaker D. Unexpected patterns of segregation distortion at a selfish supergene in the fire ant Solenopsis invicta. BMC Genet 2018; 19:101. [PMID: 30404617 PMCID: PMC6223060 DOI: 10.1186/s12863-018-0685-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 10/12/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The Sb supergene in the fire ant Solenopsis invicta determines the form of colony social organization, with colonies whose inhabitants bear the element containing multiple reproductive queens and colonies lacking it containing only a single queen. Several features of this supergene - including suppressed recombination, presence of deleterious mutations, association with a large centromere, and "green-beard" behavior - suggest that it may be a selfish genetic element that engages in transmission ratio distortion (TRD), defined as significant departures in progeny allele frequencies from Mendelian inheritance ratios. We tested this possibility by surveying segregation ratios in embryo progenies of 101 queens of the "polygyne" social form (3512 embryos) using three supergene-linked markers and twelve markers outside the supergene. RESULTS Significant departures from Mendelian ratios were observed at the supergene loci in 3-5 times more progenies than expected in the absence of TRD and than found, on average, among non-supergene loci. Also, supergene loci displayed the greatest mean deviations from Mendelian ratios among all study loci, although these typically were modest. A surprising feature of the observed inter-progeny variation in TRD was that significant deviations involved not only excesses of supergene alleles but also similarly frequent excesses of the alternate alleles on the homologous chromosome. As expected given the common occurrence of such "drive reversal" in this system, alleles associated with the supergene gain no consistent transmission advantage over their alternate alleles at the population level. Finally, we observed low levels of recombination and incomplete gametic disequilibrium across the supergene, including between adjacent markers within a single inversion. CONCLUSIONS Our data confirm the prediction that the Sb supergene is a selfish genetic element capable of biasing its own transmission during reproduction, yet counterselection for suppressor loci evidently has produced an evolutionary stalemate in TRD between the variant homologous haplotypes on the "social chromosome". Evidence implicates prezygotic segregation distortion as responsible for the TRD we document, with "true" meiotic drive the most likely mechanism. Low levels of recombination and incomplete gametic disequilibrium across the supergene suggest that selection does not preserve a single uniform supergene haplotype responsible for inducing polygyny.
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Affiliation(s)
- Kenneth G. Ross
- Department of Entomology, University of Georgia, Athens, GA USA
| | - DeWayne Shoemaker
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN USA
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161
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Behavior-dependent cis regulation reveals genes and pathways associated with bower building in cichlid fishes. Proc Natl Acad Sci U S A 2018; 115:E11081-E11090. [PMID: 30397142 PMCID: PMC6255178 DOI: 10.1073/pnas.1810140115] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Many behaviors are associated with heritable genetic variation [Kendler and Greenspan (2006) Am J Psychiatry 163:1683-1694]. Genetic mapping has revealed genomic regions or, in a few cases, specific genes explaining part of this variation [Bendesky and Bargmann (2011) Nat Rev Gen 12:809-820]. However, the genetic basis of behavioral evolution remains unclear. Here we investigate the evolution of an innate extended phenotype, bower building, among cichlid fishes of Lake Malawi. Males build bowers of two types, pits or castles, to attract females for mating. We performed comparative genome-wide analyses of 20 bower-building species and found that these phenotypes have evolved multiple times with thousands of genetic variants strongly associated with this behavior, suggesting a polygenic architecture. Remarkably, F1 hybrids of a pit-digging and a castle-building species perform sequential construction of first a pit and then a castle bower. Analysis of brain gene expression in these hybrids showed that genes near behavior-associated variants display behavior-dependent allele-specific expression with preferential expression of the pit-digging species allele during pit digging and of the castle-building species allele during castle building. These genes are highly enriched for functions related to neurodevelopment and neural plasticity. Our results suggest that natural behaviors are associated with complex genetic architectures that alter behavior via cis-regulatory differences whose effects on gene expression are specific to the behavior itself.
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162
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Kapun M, Flatt T. The adaptive significance of chromosomal inversion polymorphisms inDrosophila melanogaster. Mol Ecol 2018; 28:1263-1282. [DOI: 10.1111/mec.14871] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/01/2018] [Accepted: 09/10/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Martin Kapun
- Department of BiologyUniversity of Fribourg Fribourg Switzerland
| | - Thomas Flatt
- Department of BiologyUniversity of Fribourg Fribourg Switzerland
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163
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Inversion frequencies and phenotypic effects are modulated by the environment: insights from a reciprocal transplant study in Coelopa frigida. Evol Ecol 2018. [DOI: 10.1007/s10682-018-9960-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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164
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Lotterhos KE, Yeaman S, Degner J, Aitken S, Hodgins KA. Modularity of genes involved in local adaptation to climate despite physical linkage. Genome Biol 2018; 19:157. [PMID: 30290843 PMCID: PMC6173883 DOI: 10.1186/s13059-018-1545-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 09/18/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Linkage among genes experiencing different selection pressures can make natural selection less efficient. Theory predicts that when local adaptation is driven by complex and non-covarying stresses, increased linkage is favored for alleles with similar pleiotropic effects, with increased recombination favored among alleles with contrasting pleiotropic effects. Here, we introduce a framework to test these predictions with a co-association network analysis, which clusters loci based on differing associations. We use this framework to study the genetic architecture of local adaptation to climate in lodgepole pine, Pinus contorta, based on associations with environments. RESULTS We identify many clusters of candidate genes and SNPs associated with distinct environments, including aspects of aridity and freezing, and discover low recombination rates among some candidate genes in different clusters. Only a few genes contain SNPs with effects on more than one distinct aspect of climate. There is limited correspondence between co-association networks and gene regulatory networks. We further show how associations with environmental principal components can lead to misinterpretation. Finally, simulations illustrate both benefits and caveats of co-association networks. CONCLUSIONS Our results support the prediction that different selection pressures favor the evolution of distinct groups of genes, each associating with a different aspect of climate. But our results went against the prediction that loci experiencing different sources of selection would have high recombination among them. These results give new insight into evolutionary debates about the extent of modularity, pleiotropy, and linkage in the evolution of genetic architectures.
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Affiliation(s)
- Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern Marine Science Center, 430 Nahant Rd, Nahant, MA, 01908, USA.
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N1N4, Canada
| | - Jon Degner
- Department of Forest and Conservation Sciences, Faculty of Forestry, Vancouver, BC, V6T 1Z4, Canada
| | - Sally Aitken
- Department of Forest and Conservation Sciences, Faculty of Forestry, Vancouver, BC, V6T 1Z4, Canada
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Wellington Rd, Clayton, Melbourne, VIC, 3800, Australia
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165
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Affenzeller S, Cerveau N, Jackson DJ. Identification and validation of reference genes for qPCR in the terrestrial gastropod Cepaea nemoralis. PLoS One 2018; 13:e0201396. [PMID: 30157182 PMCID: PMC6114279 DOI: 10.1371/journal.pone.0201396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 07/13/2018] [Indexed: 12/12/2022] Open
Abstract
Identifying and understanding mechanisms that generate phenotypic diversity is a fundamental goal of evolutionary biology. With a diversity of pigmented shell morphotypes governed by Mendelian patterns of inheritance, the common grove snail Cepaea nemoralis (Linnaeus, 1758) has been a model for evolutionary biologists and population geneticists for decades. However, the genetic mechanisms by which C. nemoralis generates this pigmented shell diversity remain unknown. An important first step in investigating this pigmentation pattern is to establish a set of validated reference genes for differential gene expression assays. Here we have evaluated eleven candidate genes for reverse transcription quantitative polymerase chain reaction (qPCR) in C. nemoralis. Five of these were housekeeping genes traditionally employed as qPCR reference genes in other species, while six alternative genes were selected de novo from C. nemoralis transcriptome data based on the stability of their expression levels. We tested all eleven candidates for expression stability in four sub-adult tissues of C. nemoralis: pigmented mantle, unpigmented mantle, head and foot. We find that two commonly employed housekeeping genes (alpha tubulin, glyceraldehyde 3-phosphate dehydrogenase) are unsuitable for use as qPCR reference genes in C. nemoralis. The traditional housekeeping gene UBIquitin on the other hand performed very well. Additionally, an RNA-directed DNA polymerase (RNAP), a Potassium Channel Protein (KCHP) and a Prenylated Rab acceptor protein 1 (PRAP), identified de novo from transcriptomic data, were the most stably expressed genes in different tissue combinations. We also tested expression stability over two seasons and found that, although other genes are more stable within a single season, beta actin (BACT) and elongation factor 1 alpha (EF1α) were the most reliable reference genes across seasons.
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Affiliation(s)
- Susanne Affenzeller
- Department of Geobiology, Georg-August University of Göttingen, Göttingen, Germany
| | - Nicolas Cerveau
- Department of Geobiology, Georg-August University of Göttingen, Göttingen, Germany
| | - Daniel John Jackson
- Department of Geobiology, Georg-August University of Göttingen, Göttingen, Germany
- * E-mail:
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166
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Abstract
The keystone species concept is used in ecology to describe individual species with disproportionately large effects on their communities. We extend this idea to the level of genes with disproportionately large effects on ecological processes. Such 'keystone genes' (KGs) would underlie traits involved in species interactions or causing critical biotic and/or abiotic changes that influence emergent community and ecosystem properties. We propose a general framework for how KGs could be identified, while keeping KGs under the umbrella of 'ecologically important genes' (EIGs) that also include categories such as 'foundation genes', 'ecosystem engineering genes', and more. Although likely rare, KGs and other EIGs could dominate certain ecological processes; thus, their discovery and study are relevant for understanding eco-evolutionary dynamics.
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167
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Avril A, Purcell J, Brelsford A, Chapuisat M. Asymmetric assortative mating and queen polyandry are linked to a supergene controlling ant social organization. Mol Ecol 2018; 28:1428-1438. [PMID: 30003603 DOI: 10.1111/mec.14793] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/02/2018] [Accepted: 07/06/2018] [Indexed: 01/04/2023]
Abstract
Nonrecombining genomic variants underlie spectacular social polymorphisms, from bird mating systems to ant social organization. Because these "social supergenes" affect multiple phenotypic traits linked to survival and reproduction, explaining their persistence remains a substantial challenge. Here, we investigate how large nonrecombining genomic variants relate to colony social organization, mating system and dispersal in the Alpine silver ant, Formica selysi. The species has colonies headed by a single queen (monogynous) and colonies headed by multiple queens (polygynous). We confirmed that a supergene with alternate haplotypes-Sm and Sp-underlies this polymorphism in social structure: Females from mature monogynous colonies had the Sm/Sm genotype, while those from polygynous colonies were Sm/Sp and Sp/Sp. Queens heading monogynous colonies were exclusively mated with Sm males. In contrast, queens heading polygynous colonies were mated with Sp males and Sm males. Sm males, which are only produced by monogynous colonies, accounted for 22.9% of the matings with queens from mature polygynous colonies. This asymmetry between social forms in the degree of assortative mating generates unidirectional male-mediated gene flow from the monogynous to the polygynous social form. Biased gene flow was confirmed by a significantly higher number of private alleles in the polygynous social form. Moreover, heterozygous queens were three times as likely as homozygous queens to be multiply mated. This study reveals that the supergene variants jointly affect social organization and multiple components of the mating system that alter the transmission of the variants and thus influence the dynamics of the system.
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Affiliation(s)
- Amaury Avril
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Jessica Purcell
- Department of Entomology, University of California Riverside, Riverside, California
| | - Alan Brelsford
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, California
| | - Michel Chapuisat
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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168
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The Genetics of a Behavioral Speciation Phenotype in an Island System. Genes (Basel) 2018; 9:genes9070346. [PMID: 29996514 PMCID: PMC6070818 DOI: 10.3390/genes9070346] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/03/2018] [Accepted: 07/03/2018] [Indexed: 12/30/2022] Open
Abstract
Mating behavior divergence can make significant contributions to reproductive isolation and speciation in various biogeographic contexts. However, whether the genetic architecture underlying mating behavior divergence is related to the biogeographic history and the tempo and mode of speciation remains poorly understood. Here, we use quantitative trait locus (QTL) mapping to infer the number, distribution, and effect size of mating song rhythm variations in the crickets Laupala eukolea and Laupala cerasina, which occur on different islands (Maui and Hawaii). We then compare these results with a similar study of an independently evolving species pair that diverged within the same island. Finally, we annotate the L. cerasina transcriptome and test whether the QTL fall in functionally enriched genomic regions. We document a polygenic architecture behind the song rhythm divergence in the inter-island species pair that is remarkably similar to that previously found for an intra-island species pair in the same genus. Importantly, the QTL regions were significantly enriched for potential homologs of the genes involved in pathways that may be modulating the cricket song rhythm. These clusters of loci could constrain the spatial genomic distribution of the genetic variation underlying the cricket song variation and harbor several candidate genes that merit further study.
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169
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Olsen KM, Small LL. Micro- and macroevolutionary adaptation through repeated loss of a complete metabolic pathway. THE NEW PHYTOLOGIST 2018; 219:757-766. [PMID: 29708583 DOI: 10.1111/nph.15184] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/27/2018] [Indexed: 05/27/2023]
Abstract
There is growing evidence for the convergent evolution of physically linked gene clusters encoding chemical defense pathways. Metabolic clusters are proposed to evolve because they ensure co-inheritance of all required genes where the defense is favored, and prevent inheritance of toxic partial pathways where it is not. This hypothesis rests on the assumption that clusters evolve in species where selection favors intraspecific polymorphism for the defense; however, they have not been examined in polymorphic species. We examined metabolic cluster evolution in relation to an adaptive polymorphism for cyanogenic glucoside (CNglc) production in clover. Using 163 accessions, we performed CNglc assays, BAC sequencing, Southern hybridizations and molecular evolutionary analyses. We find that the CNglc pathway forms a 138-kb cluster in white clover, and that the adaptive polymorphism occurs through presence/absence of the complete cluster. Component genes are orthologous to those in the distantly related legume Lotus japonicus. These findings provide empirical support for the co-inheritance hypothesis, and they indicate that adaptive CNglc variation in white clover evolves through recurrent deletions of the entire pathway. They further indicate that the shared ancestor of many important legume crops was likely cyanogenic and that this defense was lost repeatedly over the last 50 Myr.
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Affiliation(s)
- Kenneth M Olsen
- Biology Department, Washington University, Campus Box 1137, St Louis, MO, 63130-4899, USA
| | - Linda L Small
- Biology Department, Washington University, Campus Box 1137, St Louis, MO, 63130-4899, USA
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170
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Durmaz E, Benson C, Kapun M, Schmidt P, Flatt T. An inversion supergene in Drosophila underpins latitudinal clines in survival traits. J Evol Biol 2018; 31:1354-1364. [PMID: 29904977 DOI: 10.1111/jeb.13310] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 04/09/2018] [Accepted: 06/04/2018] [Indexed: 01/18/2023]
Abstract
Chromosomal inversions often contribute to local adaptation across latitudinal clines, but the underlying selective mechanisms remain poorly understood. We and others have previously shown that a clinal inversion polymorphism in Drosophila melanogaster, In(3R)Payne, underpins body size clines along the North American and Australian east coasts. Here, we ask whether this polymorphism also contributes to clinal variation in other fitness-related traits, namely survival traits (lifespan, survival upon starvation and survival upon cold shock). We generated homokaryon lines, either carrying the inverted or standard chromosomal arrangement, isolated from populations approximating the endpoints of the North American cline (Florida, Maine) and phenotyped the flies at two growth temperatures (18 °C, 25 °C). Across both temperatures, high-latitude flies from Maine lived longer and were more stress resistant than low-latitude flies from Florida, as previously observed. Interestingly, we find that this latitudinal pattern is partly explained by the clinal distribution of the In(3R)P polymorphism, which is at ~ 50% frequency in Florida but absent in Maine: inverted karyotypes tended to be shorter-lived and less stress resistant than uninverted karyotypes. We also detected an interaction between karyotype and temperature on survival traits. As In(3R)P influences body size and multiple survival traits, it can be viewed as a 'supergene', a cluster of tightly linked loci affecting multiple complex phenotypes. We conjecture that the inversion cline is maintained by fitness trade-offs and balancing selection across geography; elucidating the mechanisms whereby this inversion affects alternative, locally adapted phenotypes across the cline is an important task for future work.
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Affiliation(s)
- Esra Durmaz
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Clare Benson
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,School of Biological Sciences, University of Manchester, Manchester, UK
| | - Martin Kapun
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Paul Schmidt
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas Flatt
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Department of Biology, University of Fribourg, Fribourg, Switzerland
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171
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San-Jose LM, Roulin A. Toward Understanding the Repeated Occurrence of Associations between Melanin-Based Coloration and Multiple Phenotypes. Am Nat 2018; 192:111-130. [PMID: 30016163 DOI: 10.1086/698010] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Melanin is the most widespread pigment in organisms. Melanin-based coloration has been repeatedly observed to be associated with the same traits and in the same direction in different vertebrate and insect species. However, whether any factors that are common to different taxa account for the repeated evolution of melanin-phenotype associations remains unclear. We propose to approach this question from the perspective of convergent and parallel evolution to clarify to what extent different species have evolved the same associations owing to a shared genetic basis and being subjected to similar selective pressures. Our current understanding of the genetic basis of melanin-phenotype associations allows for both convergent and parallel evolution, but this understanding is still limited. Further research is needed to clarify the generality and interdependencies of the different proposed mechanisms (supergenes, pleiotropy based on hormones, or neural crest cells). The general ecological scenarios whereby melanin-based coloration is under selection-protection from ultraviolet radiation, thermoregulation in cold environments, or as a signal of social status-offer a good opportunity to study how melanin-phenotype associations evolve. Reviewing these scenarios shows that some traits associated with melanin-based coloration might be selected together with coloration by also favoring adaptation but that other associated traits might impede adaptation, which may be indicative of genetic constraints. We therefore encourage further research on the relative roles that selection and genetic constraints play in shaping multiple melanin-phenotype associations. Placed into a phylogenetic context, this will help clarify to what extent these associations result from convergent or parallel evolutionary processes and why melanin-phenotype associations are so common across the tree of life.
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172
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Eco-Evolutionary Genomics of Chromosomal Inversions. Trends Ecol Evol 2018; 33:427-440. [DOI: 10.1016/j.tree.2018.04.002] [Citation(s) in RCA: 274] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 01/17/2023]
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173
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Supergene Evolution Triggered by the Introgression of a Chromosomal Inversion. Curr Biol 2018; 28:1839-1845.e3. [DOI: 10.1016/j.cub.2018.04.072] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 03/29/2018] [Accepted: 04/18/2018] [Indexed: 12/30/2022]
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174
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Huang YC, Dang VD, Chang NC, Wang J. Multiple large inversions and breakpoint rewiring of gene expression in the evolution of the fire ant social supergene. Proc Biol Sci 2018; 285:20180221. [PMID: 29769360 PMCID: PMC5966598 DOI: 10.1098/rspb.2018.0221] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/16/2018] [Indexed: 12/16/2022] Open
Abstract
Supergenes consist of co-adapted loci that segregate together and are associated with adaptive traits. In the fire ant Solenopsis invicta, two 'social' supergene variants regulate differences in colony queen number and other traits. Suppressed recombination in this system is maintained, in part, by a greater than 9 Mb inversion, but the supergene is larger. Has the supergene in S. invicta undergone multiple large inversions? The initial gene content of the inverted allele of a supergene would be the same as that of the wild-type allele. So, how did the inversion increase in frequency? To address these questions, we cloned one extreme breakpoint in the fire ant supergene. In doing so, we found a second large (greater than 800 Kb) rearrangement. Furthermore, we determined the temporal order of the two big inversions based on the translocation pattern of a third small fragment. Because the S. invicta supergene lacks evolutionary strata, our finding of multiple inversions may support an introgression model of the supergene. Finally, we showed that one of the inversions swapped the promoter of a breakpoint-adjacent gene, which might have conferred a selective advantage relative to the non-inverted allele. Our findings provide a rare example of gene alterations arising directly from an inversion event.
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Affiliation(s)
- Yu-Ching Huang
- Biodiversity Research Center, Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Viet Dai Dang
- Biodiversity Research Center, Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, Republic of China
- Biodiversity Taiwan International Graduate Program, Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, Republic of China
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan, Republic of China
- Department of Zoology, Southern Institute of Ecology, Hochiminh, Vietnam
| | - Ni-Chen Chang
- Biodiversity Research Center, Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, Republic of China
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - John Wang
- Biodiversity Research Center, Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, Republic of China
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175
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Piggott CVH, Verspoor E, Greer R, Hooker O, Newton J, Adams CE. Phenotypic and resource use partitioning amongst sympatric, lacustrine brown trout, Salmo trutta. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly032] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Camilla V H Piggott
- Scottish Centre for Ecology & the Natural Environment, IBAHCM, University of Glasgow, Rowardennan, Glasgow, UK
| | - Eric Verspoor
- The Rivers and Lochs Institute, University of the Highlands and Islands, Inverness, UK
| | | | - Oliver Hooker
- Scottish Centre for Ecology & the Natural Environment, IBAHCM, University of Glasgow, Rowardennan, Glasgow, UK
- PR Statistics, Hope Park Crescent, Edinburgh, UK
| | - Jason Newton
- NERC Life Sciences Mass Spectrometry Facility, SUERC, East Kilbride, UK
| | - Colin E Adams
- Scottish Centre for Ecology & the Natural Environment, IBAHCM, University of Glasgow, Rowardennan, Glasgow, UK
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176
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Iijima T, Kajitani R, Komata S, Lin CP, Sota T, Itoh T, Fujiwara H. Parallel evolution of Batesian mimicry supergene in two Papilio butterflies, P. polytes and P. memnon. SCIENCE ADVANCES 2018; 4:eaao5416. [PMID: 29675466 PMCID: PMC5906075 DOI: 10.1126/sciadv.aao5416] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 03/06/2018] [Indexed: 05/06/2023]
Abstract
Batesian mimicry protects animals from predators when mimics resemble distasteful models. The female-limited Batesian mimicry in Papilio butterflies is controlled by a supergene locus switching mimetic and nonmimetic forms. In Papilio polytes, recent studies revealed that a highly diversified region (HDR) containing doublesex (dsx-HDR) constitutes the supergene with dimorphic alleles and is likely maintained by a chromosomal inversion. In the closely related Papilio memnon, which exhibits a similar mimicry polymorphism, we performed whole-genome sequence analyses in 11 butterflies, which revealed a nearly identical dsx-HDR containing three genes (dsx, Nach-like, and UXT) with dimorphic sequences strictly associated with the mimetic/nonmimetic phenotypes. In addition, expression of these genes, except that of Nach-like in female hind wings, showed differences correlated with phenotype. The dimorphic dsx-HDR in P. memnon is maintained without a chromosomal inversion, suggesting that a separate mechanism causes and maintains allelic divergence in these genes. More abundant accumulation of transposable elements and repetitive sequences in the dsx-HDR than in other genomic regions may contribute to the suppression of chromosomal recombination. Gene trees for Dsx, Nach-like, and UXT indicated that mimetic alleles evolved independently in the two Papilio species. These results suggest that the genomic region involving the above three genes has repeatedly diverged so that two allelic sequences of this region function as developmental switches for mimicry polymorphism in the two Papilio species. The supergene structures revealed here suggest that independent evolutionary processes with different genetic mechanisms have led to parallel evolution of similar female-limited polymorphisms underlying Batesian mimicry in Papilio butterflies.
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Affiliation(s)
- Takuro Iijima
- Department of Integrated Biosciences, University of Tokyo, Kashiwa, Japan
| | - Rei Kajitani
- Department of Biological Information, Tokyo Institute of Technology, Meguro-ku, Japan
| | - Shinya Komata
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Chung-Ping Lin
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Teiji Sota
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Takehiko Itoh
- Department of Biological Information, Tokyo Institute of Technology, Meguro-ku, Japan
| | - Haruhiko Fujiwara
- Department of Integrated Biosciences, University of Tokyo, Kashiwa, Japan
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177
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Genetic Dissection of a Supergene Implicates Tfap2a in Craniofacial Evolution of Threespine Sticklebacks. Genetics 2018; 209:591-605. [PMID: 29593029 DOI: 10.1534/genetics.118.300760] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 03/26/2018] [Indexed: 02/07/2023] Open
Abstract
In nature, multiple adaptive phenotypes often coevolve and can be controlled by tightly linked genetic loci known as supergenes. Dissecting the genetic basis of these linked phenotypes is a major challenge in evolutionary genetics. Multiple freshwater populations of threespine stickleback fish (Gasterosteus aculeatus) have convergently evolved two constructive craniofacial traits, longer branchial bones and increased pharyngeal tooth number, likely as adaptations to dietary differences between marine and freshwater environments. Prior QTL mapping showed that both traits are partially controlled by overlapping genomic regions on chromosome 21 and that a regulatory change in Bmp6 likely underlies the tooth number QTL. Here, we mapped the branchial bone length QTL to a 155 kb, eight-gene interval tightly linked to, but excluding the coding regions of Bmp6 and containing the candidate gene Tfap2a Further recombinant mapping revealed this bone length QTL is separable into at least two loci. During embryonic and larval development, Tfap2a was expressed in the branchial bone primordia, where allele specific expression assays revealed the freshwater allele of Tfap2a was expressed at lower levels relative to the marine allele in hybrid fish. Induced loss-of-function mutations in Tfap2a revealed an essential role in stickleback craniofacial development and show that bone length is sensitive to Tfap2a dosage in heterozygotes. Combined, these results suggest that closely linked but genetically separable changes in Bmp6 and Tfap2a contribute to a supergene underlying evolved skeletal gain in multiple freshwater stickleback populations.
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178
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Hedrick PW, Tuttle EM, Gonser RA. Negative-Assortative Mating in the White-Throated Sparrow. J Hered 2018; 109:223-231. [PMID: 29040605 PMCID: PMC6307691 DOI: 10.1093/jhered/esx086] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 09/29/2017] [Indexed: 11/12/2022] Open
Abstract
Nonrandom mating based on phenotype has been observed in a number of organisms, but a very high proportion of these examples are of assortative mating. The strongest example of negative-assortative mating is for white-striped versus tan-striped crown in the white-throated sparrow, where about 98% of the observed pairings (mated pairs or social pairs) are between mates with different phenotypes and the correlation between mating types is -0.964. Although nonrandom mating has been explored theoretically for decades, these models have generally not focused on specific well-documented examples. Here we have developed a model to investigate the dynamics and equilibrium of this iconic example. The observed pattern of mating appears to be the result of 96% negative-assortative mating and a 17% advantage of W (white) male × T (tan) female matings compared to the reciprocal T male × W female matings. The equilibrium heterozygosity given these values is 0.500, very close to the 0.501 observed in our large sample of pairings, and this heterozygosity has been maintained for the 29 years from 1988 to 2016. In addition, the equilibrium frequency of 2m inversion determining the white-striped phenotype has been maintained at a frequency very close to its equilibrium frequency of 0.25. Overall, this model demonstrates how evolutionary genetic models can be used to understand negative-assortative mating.
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Affiliation(s)
| | - Elaina M Tuttle
- The Department of Biology and Center for Genomic Advocacy, Indiana State University, Terre Haute, IN
| | - Rusty A Gonser
- The Department of Biology and Center for Genomic Advocacy, Indiana State University, Terre Haute, IN
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179
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Van Den Berg HA. Darwin endures, despite disparagement. Sci Prog 2018; 101:32-51. [PMID: 29422119 PMCID: PMC10365159 DOI: 10.3184/003685018x15166188312386] [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] [Indexed: 11/17/2022]
Abstract
Evolution lies at the heart of the life sciences, and Charles Darwin is a towering historical figure within evolutionary science. One testimony to his lasting influence is that declaring Darwin to have been wrong all along remains a provocative way to command attention. The present paper discusses various strands of 'Darwin was wrong' partisans and their divergent views and motives: some are looking to Darwin to justify or condemn the political ideologies that they support or reject; others are concerned with the corrupting influence that the bleak cosmic outlook of evolution is deemed to exert on the moral or religious rectitude of impressionable minds, or regard Darwinism as a direct assault on religion; philosophers question the very coherence of the entire enterprise; and certain biologists aspire to go down in history as even greater than Darwin. It is sobering to reflect that this diverse group is united only by their poor grasp of Darwin's theory of natural selection.
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180
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Rapid regulatory evolution of a nonrecombining autosome linked to divergent behavioral phenotypes. Proc Natl Acad Sci U S A 2018; 115:2794-2799. [PMID: 29483264 PMCID: PMC5856536 DOI: 10.1073/pnas.1717721115] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In the white-throated sparrow (Zonotrichia albicollis), the second chromosome bears a striking resemblance to sex chromosomes. First, within each breeding pair of birds, one bird is homozygous for the standard arrangement of the chromosome (ZAL2/ZAL2) and its mate is heterozygous for a different version (ZAL2/ZAL2m). Second, recombination is profoundly suppressed between the two versions, leading to genetic differentiation between them. Third, the ZAL2m version is linked with phenotypic traits, such as bright plumage, high aggression, and low parental behavior, which are usually associated with males. These similarities to sex chromosomes suggest that the evolutionary mechanisms that shape sex chromosomes, in particular genetic degeneration of the heterogametic version due to the suppression of recombination, are likely important in this system as well. Here, we investigated patterns of protein sequence evolution and gene expression evolution between the ZAL2 and ZAL2m chromosomes by whole-genome sequencing and transcriptome analyses. Patterns of protein evolution exhibited only weak signals of genetic degeneration, and few genes harbored signatures of positive selection. We found substantial evidence of transcriptome evolution, such as significant expression divergence between ZAL2 and ZAL2m alleles and signatures of dosage compensation for highly expressed genes. These results suggest that, early in the evolution of heteromorphic chromosomes, gene expression divergence and dosage compensation can prevail before large-scale genetic degeneration. Our results show further that suppression of recombination between heteromorphic chromosomes can lead to the evolution of alternative (sex-like) behavioral phenotypes before substantial genetic degeneration.
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181
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Kappel C, Huu CN, Lenhard M. A short story gets longer: recent insights into the molecular basis of heterostyly. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5719-5730. [PMID: 29099983 DOI: 10.1093/jxb/erx387] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 10/09/2017] [Indexed: 06/07/2023]
Abstract
Heterostyly is a fascinating adaptation to promote outbreeding and a classical paradigm of botany. In the most common type of heterostyly, plants either form flowers with long styles and short stamens, or short styles and long stamens. This reciprocal organ positioning reduces pollen wastage and promotes cross-pollination, thus increasing male fitness. In addition, in many heterostylous species selfing and the generation of unfit progeny due to inbreeding depression is limited by a self-incompatibility system, thus promoting female fitness. The two floral forms are genetically determined by the S locus as a complex supergene, namely a chromosomal region containing several individual genes that control the different traits, such as style or stamen length, and are held together by very tight linkage due to suppressed recombination. Recent molecular-genetic studies in several systems, including Turnera, Fagopyrum, Linum, and Primula have begun to identify and characterize the causal heterostyly genes residing at the S locus. An emerging theme from several families is that the dominant S haplotype represents a hemizygous region not present on the recessive s haplotype. This provides an explanation for the suppressed recombination and suggests a scenario for the chromosomal evolution of the S locus. In this review, we discuss the results from recent molecular-genetic analyses in light of the classical models on the genetics and evolution of heterostyly.
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Affiliation(s)
- Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, Germany
| | - Cuong Nguyen Huu
- Institute for Biochemistry and Biology, University of Potsdam, Germany
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182
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Mullon C, Keller L, Lehmann L. Social polymorphism is favoured by the co-evolution of dispersal with social behaviour. Nat Ecol Evol 2017; 2:132-140. [PMID: 29203923 DOI: 10.1038/s41559-017-0397-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 10/27/2017] [Indexed: 11/09/2022]
Abstract
Dispersal determines gene flow among groups in a population and so plays a major role in many ecological and evolutionary processes. As gene flow shapes kin structure, dispersal is important to the evolution of social behaviours that influence reproduction within groups. Conversely, dispersal depends on kin structure and social behaviour. Dispersal and social behaviour therefore co-evolve, but the nature and consequences of this interplay are not well understood. Here, we show that it readily leads to the emergence of two social morphs: a sessile, benevolent morph expressed by individuals who tend to increase the reproduction of others within their group relative to their own; and a dispersive, self-serving morph expressed by individuals who tend to increase their own reproduction. This social polymorphism arises due to a positive linkage between the loci responsible for dispersal and social behaviour, leading to benevolent individuals preferentially interacting with relatives and self-serving individuals with non-relatives. We find that this linkage is favoured under a large spectrum of conditions, suggesting that associations between dispersal and other social traits should be common in nature. In line with this prediction, dispersers across a wide range of organisms have been reported to differ in their social tendencies from non-dispersers.
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Affiliation(s)
- Charles Mullon
- Department of Ecology and Evolution, University of Lausanne, 1004, Lausanne, Switzerland.
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, 1004, Lausanne, Switzerland.
| | - Laurent Lehmann
- Department of Ecology and Evolution, University of Lausanne, 1004, Lausanne, Switzerland
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183
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Peichel CL, Marques DA. The genetic and molecular architecture of phenotypic diversity in sticklebacks. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2015.0486. [PMID: 27994127 DOI: 10.1098/rstb.2015.0486] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2016] [Indexed: 11/12/2022] Open
Abstract
A major goal of evolutionary biology is to identify the genotypes and phenotypes that underlie adaptation to divergent environments. Stickleback fish, including the threespine stickleback (Gasterosteus aculeatus) and the ninespine stickleback (Pungitius pungitius), have been at the forefront of research to uncover the genetic and molecular architecture that underlies phenotypic diversity and adaptation. A wealth of quantitative trait locus (QTL) mapping studies in sticklebacks have provided insight into long-standing questions about the distribution of effect sizes during adaptation as well as the role of genetic linkage in facilitating adaptation. These QTL mapping studies have also provided a basis for the identification of the genes that underlie phenotypic diversity. These data have revealed that mutations in regulatory elements play an important role in the evolution of phenotypic diversity in sticklebacks. Genetic and molecular studies in sticklebacks have also led to new insights on the genetic basis of repeated evolution and suggest that the same loci are involved about half of the time when the same phenotypes evolve independently. When the same locus is involved, selection on standing variation and repeated mutation of the same genes have both contributed to the evolution of similar phenotypes in independent populations.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Catherine L Peichel
- Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - David A Marques
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Department of Fish Ecology and Evolution, Eawag, Swiss Federal Institute for Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
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184
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Complex History and Differentiation Patterns of the t-Haplotype, a Mouse Meiotic Driver. Genetics 2017; 208:365-375. [PMID: 29138255 PMCID: PMC5753869 DOI: 10.1534/genetics.117.300513] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 11/07/2017] [Indexed: 11/18/2022] Open
Abstract
The t-haplotype, a mouse meiotic driver found on chromosome 17, has been a model for autosomal segregation distortion for close to a century, but several questions remain regarding its biology and evolutionary history. A recently published set of population genomics resources for wild mice includes several individuals heterozygous for the t-haplotype, which we use to characterize this selfish element at the genomic and transcriptomic level. Our results show that large sections of the t-haplotype have been replaced by standard homologous sequences, possibly due to occasional events of recombination, and that this complicates the inference of its history. As expected for a long genomic segment of very low recombination, the t-haplotype carries an excess of fixed nonsynonymous mutations compared to the standard chromosome. This excess is stronger for regions that have not undergone recent recombination, suggesting that occasional gene flow between the t and the standard chromosome may provide a mechanism to regenerate coding sequences that have accumulated deleterious mutations. Finally, we find that t-complex genes with altered expression largely overlap with deleted or amplified regions, and that carrying a t-haplotype alters the testis expression of genes outside of the t-complex, providing new leads into the pathways involved in the biology of this segregation distorter.
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185
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Zhang W, Westerman E, Nitzany E, Palmer S, Kronforst MR. Tracing the origin and evolution of supergene mimicry in butterflies. Nat Commun 2017; 8:1269. [PMID: 29116078 PMCID: PMC5677128 DOI: 10.1038/s41467-017-01370-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 09/12/2017] [Indexed: 12/30/2022] Open
Abstract
Supergene mimicry is a striking phenomenon but we know little about the evolution of this trait in any species. Here, by studying genomes of butterflies from a recent radiation in which supergene mimicry has been isolated to the gene doublesex, we show that sexually dimorphic mimicry and female-limited polymorphism are evolutionarily related as a result of ancient balancing selection combined with independent origins of similar morphs in different lineages and secondary loss of polymorphism in other lineages. Evolutionary loss of polymorphism appears to have resulted from an interaction between natural selection and genetic drift. Furthermore, molecular evolution of the supergene is dominated not by adaptive protein evolution or balancing selection, but by extensive hitchhiking of linked variants on the mimetic dsx haplotype that occurred at the origin of mimicry. Our results suggest that chance events have played important and possibly opposing roles throughout the history of this classic example of adaptation.
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Affiliation(s)
- Wei Zhang
- Department of Ecology & Evolution, University of Chicago, Chicago, IL, 60637, USA
| | - Erica Westerman
- Department of Ecology & Evolution, University of Chicago, Chicago, IL, 60637, USA
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Eyal Nitzany
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, 60637, USA
| | - Stephanie Palmer
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, 60637, USA
| | - Marcus R Kronforst
- Department of Ecology & Evolution, University of Chicago, Chicago, IL, 60637, USA.
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186
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Sun Y, Svedberg J, Hiltunen M, Corcoran P, Johannesson H. Large-scale suppression of recombination predates genomic rearrangements in Neurospora tetrasperma. Nat Commun 2017; 8:1140. [PMID: 29074958 PMCID: PMC5658415 DOI: 10.1038/s41467-017-01317-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 09/08/2017] [Indexed: 12/21/2022] Open
Abstract
A common feature of eukaryote genomes is large chromosomal regions where recombination is absent or strongly reduced, but the factors that cause this reduction are not well understood. Genomic rearrangements have often been implicated, but they may also be a consequence of recombination suppression rather than a cause. In this study, we generate eight high-quality genomic data sets of the filamentous ascomycete Neurospora tetrasperma, a fungus that lacks recombination over most of its largest chromosome. The genomes surprisingly reveal collinearity of the non-recombining regions and although large inversions are enriched in these regions, we conclude these inversions to be derived and not the cause of the suppression. To our knowledge, this is the first time that non-recombining, genic regions as large as 86% of a full chromosome (or 8 Mbp), are shown to be collinear. These findings are of significant interest for our understanding of the evolution of sex chromosomes and other supergene complexes.
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Affiliation(s)
- Yu Sun
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jesper Svedberg
- Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Markus Hiltunen
- Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Pádraic Corcoran
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Hanna Johannesson
- Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden.
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187
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Chromosome Synapsis and Recombination in Male Hybrids between Two Chromosome Races of the Common Shrew (Sorex araneus L., Soricidae, Eulipotyphla). Genes (Basel) 2017; 8:genes8100282. [PMID: 29053571 PMCID: PMC5664132 DOI: 10.3390/genes8100282] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/08/2017] [Accepted: 10/17/2017] [Indexed: 11/17/2022] Open
Abstract
Hybrid zones between chromosome races of the common shrew (Sorex araneus) provide exceptional models to study the potential role of chromosome rearrangements in the initial steps of speciation. The Novosibirsk and Tomsk races differ by a series of Robertsonian fusions with monobrachial homology. They form a narrow hybrid zone and generate hybrids with both simple (chain of three chromosomes) and complex (chain of eight or nine) synaptic configurations. Using immunolocalisation of the meiotic proteins, we examined chromosome pairing and recombination in males from the hybrid zone. Homozygotes and simple heterozygotes for Robertsonian fusions showed a low frequency of synaptic aberrations (<10%). The carriers of complex synaptic configurations showed multiple pairing abnormalities, which might lead to reduced fertility. The recombination frequency in the proximal regions of most chromosomes of all karyotypes was much lower than in the other regions. The strong suppression of recombination in the pericentromeric regions and co-segregation of race specific chromosomes involved in the long chains would be expected to lead to linkage disequilibrium between genes located there. Genic differentiation, together with the high frequency of pairing aberrations in male carriers of the long chains, might contribute to maintenance of the narrow hybrid zone.
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188
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Jacobs A, Womack R, Chen M, Gharbi K, Elmer KR. Significant Synteny and Colocalization of Ecologically Relevant Quantitative Trait Loci Within and Across Species of Salmonid Fishes. Genetics 2017; 207:741-754. [PMID: 28760747 PMCID: PMC5629336 DOI: 10.1534/genetics.117.300093] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 07/21/2017] [Indexed: 11/18/2022] Open
Abstract
The organization of functional regions within genomes has important implications for evolutionary potential. Considerable research effort has gone toward identifying the genomic basis of phenotypic traits of interest through quantitative trait loci (QTL) analyses. Less research has assessed the arrangement of QTL in the genome within and across species. To investigate the distribution, extent of colocalization, and the synteny of QTL for ecologically relevant traits, we used a comparative genomic mapping approach within and across a range of salmonid species. We compiled 943 QTL from all available species [lake whitefish (Coregonus clupeaformis), coho salmon (Oncorhynchus kisutch), rainbow trout (O. mykiss), Chinook salmon (O. tshawytscha), Atlantic salmon (Salmo salar), and Arctic charr (Salvelinus alpinus)]. We developed a novel analytical framework for mapping and testing the distribution of these QTL. We found no correlation between QTL density and gene density at the chromosome level but did at the fine-scale. Two chromosomes were significantly enriched for QTL. We found multiple synteny blocks for morphological, life history, and physiological traits across species, but only morphology and physiology had significantly more than expected. Two or three pairs of traits were significantly colocalized in three species (lake whitefish, coho salmon, and rainbow trout). Colocalization and fine-scale synteny suggest genetic linkage between traits within species and a conserved genetic basis across species. However, this pattern was weak overall, with colocalization and synteny being relatively rare. These findings advance our understanding of the role of genomic organization in the renowned ecological and phenotypic variability of salmonid fishes.
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Affiliation(s)
- Arne Jacobs
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, UK
| | - Robyn Womack
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, UK
| | - Mel Chen
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, UK
- School of Mathematics and Statistics, College of Science and Engineering, University of Glasgow, G12 8QQ, UK
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, EH9 3FL, UK
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, UK
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189
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Kerkvliet J, de Boer T, Schilthuizen M, Kraaijeveld K. Candidate genes for shell colour polymorphism in Cepaea nemoralis. PeerJ 2017; 5:e3715. [PMID: 28948095 PMCID: PMC5607911 DOI: 10.7717/peerj.3715] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/29/2017] [Indexed: 12/15/2022] Open
Abstract
The characteristic ground colour and banding patterns on shells of the land snail Cepaea nemoralis form a classic study system for genetics and adaptation as it varies widely between individuals. We use RNAseq analysis to identify candidate genes underlying this polymorphism. We sequenced cDNA from the foot and the mantle (the shell-producing tissue) of four individuals of two phenotypes and produced a de novo transcriptome of 147,397 contigs. Differential expression analysis identified a set of 1,961 transcripts that were upregulated in mantle tissue. Sequence variant analysis resulted in a set of 2,592 transcripts with single nucleotide polymorphisms (SNPs) that differed consistently between the phenotypes. Inspection of the overlap between the differential expression analysis and SNP analysis yielded a set of 197 candidate transcripts, of which 38 were annotated. Four of these transcripts are thought to be involved in production of the shell’s nacreous layer. Comparison with morph-associated Restriction-site Associated DNA (RAD)-tags from a published study yielded eight transcripts that were annotated as metallothionein, a protein that is thought to inhibit the production of melanin in melanocytes. These results thus provide an excellent starting point for the elucidation of the genetic regulation of the Cepaea nemoralis shell colour polymorphism.
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Affiliation(s)
- Jesse Kerkvliet
- Bio-informatics, University of Applied Sciences Leiden, Leiden, The Netherlands
| | - Tjalf de Boer
- MicroLife Solutions, Amsterdam, The Netherlands.,Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | - Ken Kraaijeveld
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Leiden Genome Technology Center, Leiden University Medical Center, Leiden, The Netherlands
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190
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Pracana R, Levantis I, Martínez‐Ruiz C, Stolle E, Priyam A, Wurm Y. Fire ant social chromosomes: Differences in number, sequence and expression of odorant binding proteins. Evol Lett 2017; 1:199-210. [PMID: 30283649 PMCID: PMC6121795 DOI: 10.1002/evl3.22] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 07/17/2017] [Accepted: 07/27/2017] [Indexed: 12/14/2022] Open
Abstract
Variation in social behavior is common yet our knowledge of the mechanisms underpinning its evolution is limited. The fire ant Solenopsis invicta provides a textbook example of a Mendelian element controlling social organization: alternate alleles of a genetic element first identified as encoding an odorant binding protein (OBP) named Gp-9 determine whether a colony accepts one or multiple queens. The potential roles of such a protein in perceiving olfactory cues and evidence of positive selection on its amino acid sequence made it an appealing candidate gene. However, we recently showed that recombination is suppressed between Gp-9 and hundreds of other genes as part of a >19 Mb supergene-like region carried by a pair of social chromosomes. This finding raises the need to reassess the potential role of Gp-9. We identify 23 OBPs in the fire ant genome assembly, including nine located in the region of suppressed recombination with Gp-9. For six of these, the alleles carried by the two variants of the supergene-like region differ in protein-coding sequence and thus likely in function, with Gp-9 showing the strongest evidence of positive selection. We identify an additional OBP specific to the Sb variant of the region. Finally, we find that 14 OBPs are differentially expressed between single- and multiple-queen colonies. These results are consistent with multiple OBPs playing a role in determining social structure.
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Affiliation(s)
- Rodrigo Pracana
- School of Biological and Chemical SciencesQueen Mary University of LondonE1 4NSLondonUnited Kingdom
| | - Ilya Levantis
- School of Biological and Chemical SciencesQueen Mary University of LondonE1 4NSLondonUnited Kingdom
| | - Carlos Martínez‐Ruiz
- School of Biological and Chemical SciencesQueen Mary University of LondonE1 4NSLondonUnited Kingdom
| | - Eckart Stolle
- School of Biological and Chemical SciencesQueen Mary University of LondonE1 4NSLondonUnited Kingdom
| | - Anurag Priyam
- School of Biological and Chemical SciencesQueen Mary University of LondonE1 4NSLondonUnited Kingdom
| | - Yannick Wurm
- School of Biological and Chemical SciencesQueen Mary University of LondonE1 4NSLondonUnited Kingdom
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191
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Holmes IA, Grundler MR, Davis Rabosky AR. Predator Perspective Drives Geographic Variation in Frequency-Dependent Polymorphism. Am Nat 2017; 190:E78-E93. [PMID: 28937812 DOI: 10.1086/693159] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Color polymorphism in natural populations can manifest as a striking patchwork of phenotypes in space, with neighboring populations characterized by dramatic differences in morph composition. These geographic mosaics can be challenging to explain in the absence of localized selection because they are unlikely to result from simple isolation-by-distance or clinal variation in selective regimes. To identify processes that can lead to the formation of geographic mosaics, we developed a simulation-based model to explore the influence of predator perspective, selection, migration, and genetic linkage of color loci on allele frequencies in polymorphic populations over space and time. Using simulated populations inspired by the biology of Heliconius longwing butterflies, Cepaea land snails, Oophaga poison frogs, and Sonora ground snakes, we found that the relative sizes of predator and prey home ranges can produce large differences in morph composition between neighboring populations under both positive and negative frequency-dependent selection. We also demonstrated the importance of the interaction of predator perspective with the type of frequency dependence and localized directional selection across migration and selection intensities. Our results show that regional-scale predation can promote the formation of phenotypic mosaics in prey species, without the need to invoke spatial variation in selective regimes. We suggest that predator behavior can play an important and underappreciated role in the formation and maintenance of geographic mosaics in polymorphic species.
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192
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Abstract
The study of insect social behavior has offered tremendous insight into the molecular mechanisms mediating behavioral and phenotypic plasticity. Genomic applications to the study of eusocial insect species, in particular, have led to several hypotheses for the processes underlying the molecular evolution of behavior. Advances in understanding the genetic control of social organization have also been made, suggesting an important role for supergenes in the evolution of divergent behavioral phenotypes. Intensive study of social phenotypes across species has revealed that behavior and caste are controlled by an interaction between genetic and environmentally mediated effects and, further, that gene expression and regulation mediate plastic responses to environmental signals. However, several key methodological flaws that are hindering progress in the study of insect social behavior remain. After reviewing the current state of knowledge, we outline ongoing challenges in experimental design that remain to be overcome in order to advance the field.
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Affiliation(s)
- Chelsea A Weitekamp
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland; ,
| | - Romain Libbrecht
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, 55128 Mainz, Germany;
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland; ,
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193
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Barth JMI, Berg PR, Jonsson PR, Bonanomi S, Corell H, Hemmer-Hansen J, Jakobsen KS, Johannesson K, Jorde PE, Knutsen H, Moksnes PO, Star B, Stenseth NC, Svedäng H, Jentoft S, André C. Genome architecture enables local adaptation of Atlantic cod despite high connectivity. Mol Ecol 2017. [DOI: 10.1111/mec.14207] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Julia M. I. Barth
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis (CEES); University of Oslo; Oslo Norway
| | - Paul R. Berg
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis (CEES); University of Oslo; Oslo Norway
- Faculty of Medicine; Centre for Molecular Medicine Norway (NCMM); University of Oslo; Oslo Norway
| | - Per R. Jonsson
- Department of Marine Sciences - Tjärnö; University of Gothenburg; Strömstad Sweden
| | - Sara Bonanomi
- Section for Marine Living Resources; National Institute of Aquatic Resources; Technical University of Denmark; Silkeborg Denmark
- National Research Council (CNR); Fisheries Section; Institute of Marine Sciences (ISMAR); Ancona Italy
| | - Hanna Corell
- Department of Marine Sciences - Tjärnö; University of Gothenburg; Strömstad Sweden
| | - Jakob Hemmer-Hansen
- Section for Marine Living Resources; National Institute of Aquatic Resources; Technical University of Denmark; Silkeborg Denmark
| | - Kjetill S. Jakobsen
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis (CEES); University of Oslo; Oslo Norway
| | - Kerstin Johannesson
- Department of Marine Sciences - Tjärnö; University of Gothenburg; Strömstad Sweden
| | - Per Erik Jorde
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis (CEES); University of Oslo; Oslo Norway
| | - Halvor Knutsen
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis (CEES); University of Oslo; Oslo Norway
- Institute of Marine Research; Flødevigen; His Norway
- Department of Natural Sciences; Centre for Coastal Research; University of Agder; Kristiansand Norway
| | - Per-Olav Moksnes
- Department of Marine Sciences; University of Gothenburg; Gothenburg Sweden
| | - Bastiaan Star
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis (CEES); University of Oslo; Oslo Norway
| | - Nils Chr. Stenseth
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis (CEES); University of Oslo; Oslo Norway
- Department of Natural Sciences; Centre for Coastal Research; University of Agder; Kristiansand Norway
| | - Henrik Svedäng
- Swedish Institute for the Marine Environment (SIME); Gothenburg Sweden
| | - Sissel Jentoft
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis (CEES); University of Oslo; Oslo Norway
- Department of Natural Sciences; Centre for Coastal Research; University of Agder; Kristiansand Norway
| | - Carl André
- Department of Marine Sciences - Tjärnö; University of Gothenburg; Strömstad Sweden
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194
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Pracana R, Priyam A, Levantis I, Nichols RA, Wurm Y. The fire ant social chromosome supergene variant Sb shows low diversity but high divergence from SB. Mol Ecol 2017; 26:2864-2879. [PMID: 28220980 PMCID: PMC5485014 DOI: 10.1111/mec.14054] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 01/22/2017] [Accepted: 02/06/2017] [Indexed: 02/01/2023]
Abstract
Variation in social behaviour is common, yet little is known about the genetic architectures underpinning its evolution. A rare exception is in the fire ant Solenopsis invicta: Alternative variants of a supergene region determine whether a colony will have exactly one or up to dozens of queens. The two variants of this region are carried by a pair of 'social chromosomes', SB and Sb, which resemble a pair of sex chromosomes. Recombination is suppressed between the two chromosomes in the supergene region. While the X-like SB can recombine with itself in SB/SB queens, recombination is effectively absent in the Y-like Sb because Sb/Sb queens die before reproducing. Here, we analyse whole-genome sequences of eight haploid SB males and eight haploid Sb males. We find extensive SB-Sb differentiation throughout the >19-Mb-long supergene region. We find no evidence of 'evolutionary strata' with different levels of divergence comparable to those reported in several sex chromosomes. A high proportion of substitutions between the SB and Sb haplotypes are nonsynonymous, suggesting inefficacy of purifying selection in Sb sequences, similar to that for Y-linked sequences in XY systems. Finally, we show that the Sb haplotype of the supergene region has 635-fold less nucleotide diversity than the rest of the genome. We discuss how this reduction could be due to a recent selective sweep affecting Sb specifically or associated with a population bottleneck during the invasion of North America by the sampled population.
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Affiliation(s)
- Rodrigo Pracana
- School of Biological and Chemical SciencesQueen Mary University of LondonMile End RoadLondonE1 4NSUK
| | - Anurag Priyam
- School of Biological and Chemical SciencesQueen Mary University of LondonMile End RoadLondonE1 4NSUK
| | - Ilya Levantis
- School of Biological and Chemical SciencesQueen Mary University of LondonMile End RoadLondonE1 4NSUK
| | - Richard A. Nichols
- School of Biological and Chemical SciencesQueen Mary University of LondonMile End RoadLondonE1 4NSUK
| | - Yannick Wurm
- School of Biological and Chemical SciencesQueen Mary University of LondonMile End RoadLondonE1 4NSUK
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195
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Roda F, Walter GM, Nipper R, Ortiz‐Barrientos D. Genomic clustering of adaptive loci during parallel evolution of an Australian wildflower. Mol Ecol 2017; 26:3687-3699. [DOI: 10.1111/mec.14150] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 03/07/2017] [Accepted: 04/03/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Federico Roda
- School of Biological Sciences The University of Queensland St. Lucia QLD Australia
- Harvard University Boston MA USA
| | - Greg M. Walter
- School of Biological Sciences The University of Queensland St. Lucia QLD Australia
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Bay RA, Rose N, Barrett R, Bernatchez L, Ghalambor CK, Lasky JR, Brem RB, Palumbi SR, Ralph P. Predicting Responses to Contemporary Environmental Change Using Evolutionary Response Architectures. Am Nat 2017; 189:463-473. [DOI: 10.1086/691233] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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197
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Barney BT, Munkholm C, Walt DR, Palumbi SR. Highly localized divergence within supergenes in Atlantic cod (Gadus morhua) within the Gulf of Maine. BMC Genomics 2017; 18:271. [PMID: 28359300 PMCID: PMC5374575 DOI: 10.1186/s12864-017-3660-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 03/25/2017] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Atlantic cod (Gadus morhua), is known to vary genetically across the North Atlantic, Greenland, and Newfoundland. This genetic variation occurs both spatially and temporally through decades of heavy fishing, and is concentrated in three linkage disequilibrium blocks, previously defined by pedigreed linkage mapping analysis. Variation within these genomic regions is correlated with both seawater temperature and behavioral ecotype. The full extent and nature of these linkage groups is important information for interpreting cod genetic structure as a tool for future fisheries management. RESULTS We conducted whole genome sequencing for 31 individual cod from three sub-populations in the Gulf of Maine. Across the genome, we found 3,390,654 intermediate to high frequency Single Nucleotide Polymorphisms (SNPs). We show that pairwise linkage analysis among these SNPs is a powerful tool to detect linkage disequilibrium clusters by recovering the three previously detected linkage groups and identifying the 1031 genes contained therein. Across these genes, we found significant population differentiation among spawning groups in the Gulf of Maine and between Georges Bank and Gulf of Maine. Coordinated divergence among these genes and their differentiation at both short and long spatial scales suggests that they are acting as linked supergenes in local adaptation of cod populations. CONCLUSIONS Differentiation between SNPs in linkage disequilibrium blocks is the major signal of genetic differentiation between all groups tested within the Gulf of Maine. Our data provide a map of genes contained in these blocks, allowing an enhanced search for neutral genetic structure for demographic inference and fisheries modeling. Patterns of selection and the history of populations may be possible to identify in cod using this description of linkage disequilibrium blocks and future data sets to robustly separate neutral and selected genetic markers.
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Affiliation(s)
- Bryan T. Barney
- Department of Biology, Hopkins Marine Station, Stanford University, 120 Ocean View Boulevard, Pacific Grove, CA 92950 USA
| | - Christiane Munkholm
- Gloucester Marine Genomics Institute, 55 Blackburn Center, Gloucester, MA 01930 USA
| | - David R. Walt
- Gloucester Marine Genomics Institute, 55 Blackburn Center, Gloucester, MA 01930 USA
| | - Stephen R. Palumbi
- Department of Biology, Hopkins Marine Station, Stanford University, 120 Ocean View Boulevard, Pacific Grove, CA 92950 USA
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198
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Reijnen BT, van der Meij SET. Coat of many colours-DNA reveals polymorphism of mantle patterns and colouration in Caribbean Cyphoma Röding, 1798 (Gastropoda, Ovulidae). PeerJ 2017; 5:e3018. [PMID: 28265504 PMCID: PMC5337085 DOI: 10.7717/peerj.3018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 01/23/2017] [Indexed: 11/20/2022] Open
Abstract
The iconic gastropod genus Cyphoma is commonly observed in the Caribbean, where it lives in association with various octocorallian hosts. Each species in the genus Cyphoma has a unique, characteristic mantle pattern and colouration, which separates the valid taxa. Because of its abundance and recognisability Cyphoma gibbosum has been used as a model organism in several studies concerning allelochemicals, reef degradation, and physical defence mechanisms. Molecular analyses based on four molecular markers (COI, 16S, H3 and 28S) for three Cyphoma species (C. gibbosum, C. mcgintyi, C. signatum) and an unidentified black morph, collected from three localities in the Caribbean, show that they represent morphological varieties of a single, genetically homogeneous species. This outcome is in agreement with previous anatomical studies. As a result C. mcgintyi and C. signatum are synonymised with C. gibbosum, which is a key result for future work using C. gibbosum as a model organism. The striking morphological differences in mantle pattern and colouration are hypothesised to be the result of one of three possible scenarios: rapid divergence, supergenes (including balanced polymorphism), or incipient speciation.
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Affiliation(s)
| | - Sancia E T van der Meij
- Naturalis Biodiversity Center, Leiden, The Netherlands; Oxford University Museum of Natural History, University of Oxford, Oxford, United Kingdom; Linacre College, Oxford, United Kingdom
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199
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Llaurens V, Whibley A, Joron M. Genetic architecture and balancing selection: the life and death of differentiated variants. Mol Ecol 2017; 26:2430-2448. [PMID: 28173627 DOI: 10.1111/mec.14051] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 12/15/2016] [Accepted: 12/19/2016] [Indexed: 01/02/2023]
Abstract
Balancing selection describes any form of natural selection, which results in the persistence of multiple variants of a trait at intermediate frequencies within populations. By offering up a snapshot of multiple co-occurring functional variants and their interactions, systems under balancing selection can reveal the evolutionary mechanisms favouring the emergence and persistence of adaptive variation in natural populations. We here focus on the mechanisms by which several functional variants for a given trait can arise, a process typically requiring multiple epistatic mutations. We highlight how balancing selection can favour specific features in the genetic architecture and review the evolutionary and molecular mechanisms shaping this architecture. First, balancing selection affects the number of loci underlying differentiated traits and their respective effects. Control by one or few loci favours the persistence of differentiated functional variants by limiting intergenic recombination, or its impact, and may sometimes lead to the evolution of supergenes. Chromosomal rearrangements, particularly inversions, preventing adaptive combinations from being dissociated are increasingly being noted as features of such systems. Similarly, due to the frequency of heterozygotes maintained by balancing selection, dominance may be a key property of adaptive variants. High heterozygosity and limited recombination also influence associated genetic load, as linked recessive deleterious mutations may be sheltered. The capture of deleterious elements in a locus under balancing selection may reinforce polymorphism by further promoting heterozygotes. Finally, according to recent genomewide scans, balanced polymorphism might be more pervasive than generally thought. We stress the need for both functional and ecological studies to characterize the evolutionary mechanisms operating in these systems.
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Affiliation(s)
- Violaine Llaurens
- Institut de Systématique Evolution et Biodiversité (UMR 7205 CNRS, MNHN, UPMC, EPHE), Muséum National d'Histoire Naturelle - CP50, 45 rue Buffon, 75005, Paris, France
| | - Annabel Whibley
- Cell and Developmental Biology, John Innes Centre, Norwich, Norfolk, NR4 7UH, UK
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive (UMR 5175 CNRS, Université de Montpellier, Université Paul Valéry Montpellier, EPHE), 1919 route de Mende, 34293, Montpellier, France
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200
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Sunnucks P, Morales HE, Lamb AM, Pavlova A, Greening C. Integrative Approaches for Studying Mitochondrial and Nuclear Genome Co-evolution in Oxidative Phosphorylation. Front Genet 2017; 8:25. [PMID: 28316610 PMCID: PMC5334354 DOI: 10.3389/fgene.2017.00025] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/17/2017] [Indexed: 01/24/2023] Open
Abstract
In animals, interactions among gene products of mitochondrial and nuclear genomes (mitonuclear interactions) are of profound fitness, evolutionary, and ecological significance. Most fundamentally, the oxidative phosphorylation (OXPHOS) complexes responsible for cellular bioenergetics are formed by the direct interactions of 13 mitochondrial-encoded and ∼80 nuclear-encoded protein subunits in most animals. It is expected that organisms will develop genomic architecture that facilitates co-adaptation of these mitonuclear interactions and enhances biochemical efficiency of OXPHOS complexes. In this perspective, we present principles and approaches to understanding the co-evolution of these interactions, with a novel focus on how genomic architecture might facilitate it. We advocate that recent interdisciplinary advances assist in the consolidation of links between genotype and phenotype. For example, advances in genomics allow us to unravel signatures of selection in mitochondrial and nuclear OXPHOS genes at population-relevant scales, while newly published complete atomic-resolution structures of the OXPHOS machinery enable more robust predictions of how these genes interact epistatically and co-evolutionarily. We use three case studies to show how integrative approaches have improved the understanding of mitonuclear interactions in OXPHOS, namely those driving high-altitude adaptation in bar-headed geese, allopatric population divergence in Tigriopus californicus copepods, and the genome architecture of nuclear genes coding for mitochondrial functions in the eastern yellow robin.
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Affiliation(s)
- Paul Sunnucks
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
| | - Hernán E. Morales
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
- Department of Marine Sciences, University of GothenburgGothenburg, Sweden
| | - Annika M. Lamb
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
| | - Alexandra Pavlova
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
| | - Chris Greening
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
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