1
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Kapun M, Mitchell ED, Kawecki TJ, Schmidt P, Flatt T. An Ancestral Balanced Inversion Polymorphism Confers Global Adaptation. Mol Biol Evol 2023; 40:msad118. [PMID: 37220650 PMCID: PMC10234209 DOI: 10.1093/molbev/msad118] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/17/2023] [Accepted: 05/19/2023] [Indexed: 05/25/2023] Open
Abstract
Since the pioneering work of Dobzhansky in the 1930s and 1940s, many chromosomal inversions have been identified, but how they contribute to adaptation remains poorly understood. In Drosophila melanogaster, the widespread inversion polymorphism In(3R)Payne underpins latitudinal clines in fitness traits on multiple continents. Here, we use single-individual whole-genome sequencing, transcriptomics, and published sequencing data to study the population genomics of this inversion on four continents: in its ancestral African range and in derived populations in Europe, North America, and Australia. Our results confirm that this inversion originated in sub-Saharan Africa and subsequently became cosmopolitan; we observe marked monophyletic divergence of inverted and noninverted karyotypes, with some substructure among inverted chromosomes between continents. Despite divergent evolution of this inversion since its out-of-Africa migration, derived non-African populations exhibit similar patterns of long-range linkage disequilibrium between the inversion breakpoints and major peaks of divergence in its center, consistent with balancing selection and suggesting that the inversion harbors alleles that are maintained by selection on several continents. Using RNA-sequencing, we identify overlap between inversion-linked single-nucleotide polymorphisms and loci that are differentially expressed between inverted and noninverted chromosomes. Expression levels are higher for inverted chromosomes at low temperature, suggesting loss of buffering or compensatory plasticity and consistent with higher inversion frequency in warm climates. Our results suggest that this ancestrally tropical balanced polymorphism spread around the world and became latitudinally assorted along similar but independent climatic gradients, always being frequent in subtropical/tropical areas but rare or absent in temperate climates.
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Affiliation(s)
- Martin Kapun
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Division of Cell and Developmental Biology, Medical University of Vienna, Vienna, Austria
- Natural History Museum Vienna, Zentrale Forschungslaboratorien, Vienna, Austria
| | - Esra Durmaz Mitchell
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Tadeusz J Kawecki
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Paul Schmidt
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, 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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2
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Koch EL, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evol Lett 2021; 5:196-213. [PMID: 34136269 PMCID: PMC8190449 DOI: 10.1002/evl3.227] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 02/06/2021] [Accepted: 03/29/2021] [Indexed: 01/11/2023] Open
Abstract
Chromosomal inversions have long been recognized for their role in local adaptation. By suppressing recombination in heterozygous individuals, they can maintain coadapted gene complexes and protect them from homogenizing effects of gene flow. However, to fully understand their importance for local adaptation we need to know their influence on phenotypes under divergent selection. For this, the marine snail Littorina saxatilis provides an ideal study system. Divergent ecotypes adapted to wave action and crab predation occur in close proximity on intertidal shores with gene flow between them. Here, we used F2 individuals obtained from crosses between the ecotypes to test for associations between genomic regions and traits distinguishing the Crab‐/Wave‐adapted ecotypes including size, shape, shell thickness, and behavior. We show that most of these traits are influenced by two previously detected inversion regions that are divergent between ecotypes. We thus gain a better understanding of one important underlying mechanism responsible for the rapid and repeated formation of ecotypes: divergent selection acting on inversions. We also found that some inversions contributed to more than one trait suggesting that they may contain several loci involved in adaptation, consistent with the hypothesis that suppression of recombination within inversions facilitates differentiation in the presence of gene flow.
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Affiliation(s)
- Eva L Koch
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom
| | - Hernán E Morales
- Evolutionary Genetics Section Globe Institute University of Copenhagen Copenhagen Denmark.,Department of Marine Sciences University of Gothenburg Strömstad 45296 Sweden
| | - Jenny Larsson
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom
| | - Anja M Westram
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom.,IST Austria Klosterneuburg Austria
| | - Rui Faria
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom.,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal
| | - Alan R Lemmon
- Department of Scientific Computing Florida State University Tallahassee Florida FL 32306-4120
| | - E Moriarty Lemmon
- Department of Biological Science Florida State University Tallahassee Florida FL 32306-4295
| | - Kerstin Johannesson
- Department of Marine Sciences University of Gothenburg Strömstad 45296 Sweden
| | - Roger K Butlin
- Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom.,Department of Marine Sciences University of Gothenburg Strömstad 45296 Sweden
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3
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Abstract
Drosophila melanogaster, a small dipteran of African origin, represents one of the best-studied model organisms. Early work in this system has uniquely shed light on the basic principles of genetics and resulted in a versatile collection of genetic tools that allow to uncover mechanistic links between genotype and phenotype. Moreover, given its worldwide distribution in diverse habitats and its moderate genome-size, Drosophila has proven very powerful for population genetics inference and was one of the first eukaryotes whose genome was fully sequenced. In this book chapter, we provide a brief historical overview of research in Drosophila and then focus on recent advances during the genomic era. After describing different types and sources of genomic data, we discuss mechanisms of neutral evolution including the demographic history of Drosophila and the effects of recombination and biased gene conversion. Then, we review recent advances in detecting genome-wide signals of selection, such as soft and hard selective sweeps. We further provide a brief introduction to background selection, selection of noncoding DNA and codon usage and focus on the role of structural variants, such as transposable elements and chromosomal inversions, during the adaptive process. Finally, we discuss how genomic data helps to dissect neutral and adaptive evolutionary mechanisms that shape genetic and phenotypic variation in natural populations along environmental gradients. In summary, this book chapter serves as a starting point to Drosophila population genomics and provides an introduction to the system and an overview to data sources, important population genetic concepts and recent advances in the field.
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4
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Crow T, Ta J, Nojoomi S, Aguilar-Rangel MR, Torres Rodríguez JV, Gates D, Rellán-Álvarez R, Sawers R, Runcie D. Gene regulatory effects of a large chromosomal inversion in highland maize. PLoS Genet 2020; 16:e1009213. [PMID: 33270639 PMCID: PMC7752097 DOI: 10.1371/journal.pgen.1009213] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 12/21/2020] [Accepted: 10/19/2020] [Indexed: 12/25/2022] Open
Abstract
Chromosomal inversions play an important role in local adaptation. Inversions can capture multiple locally adaptive functional variants in a linked block by repressing recombination. However, this recombination suppression makes it difficult to identify the genetic mechanisms underlying an inversion's role in adaptation. In this study, we used large-scale transcriptomic data to dissect the functional importance of a 13 Mb inversion locus (Inv4m) found almost exclusively in highland populations of maize (Zea mays ssp. mays). Inv4m was introgressed into highland maize from the wild relative Zea mays ssp. mexicana, also present in the highlands of Mexico, and is thought to be important for the adaptation of these populations to cultivation in highland environments. However, the specific genetic variants and traits that underlie this adaptation are not known. We created two families segregating for the standard and inverted haplotypes of Inv4m in a common genetic background and measured gene expression effects associated with the inversion across 9 tissues in two experimental conditions. With these data, we quantified both the global transcriptomic effects of the highland Inv4m haplotype, and the local cis-regulatory variation present within the locus. We found diverse physiological effects of Inv4m across the 9 tissues, including a strong effect on the expression of genes involved in photosynthesis and chloroplast physiology. Although we could not confidently identify the causal alleles within Inv4m, this research accelerates progress towards understanding this inversion and will guide future research on these important genomic features.
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Affiliation(s)
- Taylor Crow
- Department of Plant Sciences/University of California, Davis, California, United States of America
| | - James Ta
- Department of Plant Sciences/University of California, Davis, California, United States of America
| | - Saghi Nojoomi
- Department of Plant Sciences/University of California, Davis, California, United States of America
| | - M. Rocío Aguilar-Rangel
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados (CINVESTAV- IPN), Irapuato CP 36821, Guanajuato, Mexico
- Corteva Agriscience, Agriculture Division of DowDuPont, Tlajomulco, Jalisco, Mexico
| | - Jorge Vladimir Torres Rodríguez
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados (CINVESTAV- IPN), Irapuato CP 36821, Guanajuato, Mexico
| | - Daniel Gates
- Department of Evolution and Ecology/University of California, Davis, California, United States of America
| | - Rubén Rellán-Álvarez
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados (CINVESTAV- IPN), Irapuato CP 36821, Guanajuato, Mexico
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Ruairidh Sawers
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados (CINVESTAV- IPN), Irapuato CP 36821, Guanajuato, Mexico
- Department of Plant Science, Pennsylvania State University, State College, Pennsylvania, United States of America
| | - Daniel Runcie
- Department of Plant Sciences/University of California, Davis, California, United States of America
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Tuo Y, Chu W, Zhang J, Cheng J, Chen L, Bao L, Xiao T. Analysis of Natural Selection of Immune Genes in Spinibarbus caldwelli by Transcriptome Sequencing. Front Genet 2020; 11:714. [PMID: 32793279 PMCID: PMC7393255 DOI: 10.3389/fgene.2020.00714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 06/11/2020] [Indexed: 12/03/2022] Open
Abstract
Spinibarbus caldwelli is an omnivorous cyprinid fish that is distributed widely in China. To investigate the adaptive evolution of S. caldwelli, the muscle transcriptome was sequenced by Illumina HiSeq 4000 platform. A total of 80,447,367 reads were generated by next-generation sequencing. Also, 211,386 unigenes were obtained by de novo assembly. Additionally, we calculated that the divergence time between S. caldwelli and Sinocyclocheilus grahami is 23.14 million years ago (Mya). And both of them diverged from Ctenopharyngodon idellus 46.95 Mya. Furthermore, 38 positive genes were identified by calculating Ka/Ks ratios from 9225 orthologs. Among them, several immune-related genes were identified as positively selected, such as POLR3B, PIK3C3, TOPORS, FASTKD3, CYPLP1A1, and UACA. Our results throw light on the nature of the natural selection of S. caldwelli and contribute to future immunological and transcriptome studies.
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Affiliation(s)
- Yun Tuo
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha, China.,College of Life Science and Resources Environment, Yichun University, Yichun, China
| | - Wuying Chu
- Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Jianshe Zhang
- Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Jia Cheng
- Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Lin Chen
- Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Lingsheng Bao
- Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Tiaoyi Xiao
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha, China
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6
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Ríos N, Casanova A, Hermida M, Pardo BG, Martínez P, Bouza C, García G. Population Genomics in Rhamdia quelen (Heptapteridae, Siluriformes) Reveals Deep Divergence and Adaptation in the Neotropical Region. Genes (Basel) 2020; 11:genes11010109. [PMID: 31963477 PMCID: PMC7017130 DOI: 10.3390/genes11010109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/10/2020] [Accepted: 01/14/2020] [Indexed: 12/16/2022] Open
Abstract
Rhamdia quelen, a Neotropical fish with hybridization between highly divergent mitochondrial DNA (mtDNA) lineages, represents an interesting evolutionary model. Previous studies suggested that there might be demographic differences between coastal lagoons and riverine environments, as well as divergent populations that could be reproductively isolated. Here, we investigated the genetic diversity pattern of this taxon in the Southern Neotropical Basin system that includes the La Plata Basin, Patos-Merin lagoon basin and the coastal lagoons draining to the SW Atlantic Ocean, through a population genomics approach using 2b-RAD-sequencing-derived single nucleotide polymorphisms (SNPs). The genomic scan identified selection footprints associated with divergence and suggested local adaptation environmental drivers. Two major genomic clusters latitudinally distributed in the Northern and Southern basins were identified, along with consistent signatures of divergent selection between them. Population structure based on the whole set of loci and on the presumptive neutral vs. adaptive loci showed deep genomic divergence between the two major clusters. Annotation of the most consistent SNPs under divergent selection revealed some interesting candidate genes for further functional studies. Moreover, signals of adaptation to a coastal lagoon environment mediated by purifying selection were found. These new insights provide a better understanding of the complex evolutionary history of R. quelen in the southernmost basin of the Neotropical region.
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Affiliation(s)
- Néstor Ríos
- Sección Genética Evolutiva, Facultad de Ciencias, UdelaR, Iguá 4225, Montevideo 11400, Uruguay;
- Correspondence: ; Tel.: +598-25258618 (ext. 140)
| | - Adrián Casanova
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus de Lugo, Universidade de Santiago de Compostela, Avenida Carballo Calero s/n, E-27002 Lugo, Spain; (A.C.); (M.H.); (B.G.P.); (P.M.); (C.B.)
| | - Miguel Hermida
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus de Lugo, Universidade de Santiago de Compostela, Avenida Carballo Calero s/n, E-27002 Lugo, Spain; (A.C.); (M.H.); (B.G.P.); (P.M.); (C.B.)
| | - Belén G. Pardo
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus de Lugo, Universidade de Santiago de Compostela, Avenida Carballo Calero s/n, E-27002 Lugo, Spain; (A.C.); (M.H.); (B.G.P.); (P.M.); (C.B.)
- Instituto de Acuicultura, Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela, Spain
| | - Paulino Martínez
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus de Lugo, Universidade de Santiago de Compostela, Avenida Carballo Calero s/n, E-27002 Lugo, Spain; (A.C.); (M.H.); (B.G.P.); (P.M.); (C.B.)
- Instituto de Acuicultura, Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela, Spain
| | - Carmen Bouza
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus de Lugo, Universidade de Santiago de Compostela, Avenida Carballo Calero s/n, E-27002 Lugo, Spain; (A.C.); (M.H.); (B.G.P.); (P.M.); (C.B.)
- Instituto de Acuicultura, Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela, Spain
| | - Graciela García
- Sección Genética Evolutiva, Facultad de Ciencias, UdelaR, Iguá 4225, Montevideo 11400, Uruguay;
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7
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Abstract
In this perspective, we evaluate the explanatory power of the neutral theory of molecular evolution, 50 years after its introduction by Kimura. We argue that the neutral theory was supported by unreliable theoretical and empirical evidence from the beginning, and that in light of modern, genome-scale data, we can firmly reject its universality. The ubiquity of adaptive variation both within and between species means that a more comprehensive theory of molecular evolution must be sought.
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Affiliation(s)
- Andrew D Kern
- Department of Genetics, Rutgers University, Piscataway, NJ
| | - Matthew W Hahn
- Department of Biology and Department of Computer Science, Indiana University Bloomington, IN
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8
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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: 6.9] [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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9
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Gould BA, Chen Y, Lowry DB. Gene regulatory divergence between locally adapted ecotypes in their native habitats. Mol Ecol 2018; 27:4174-4188. [PMID: 30168223 DOI: 10.1111/mec.14852] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 08/15/2018] [Accepted: 08/19/2018] [Indexed: 01/04/2023]
Abstract
Local adaptation is a key driver of ecological specialization and the formation of new species. Despite its importance, the evolution of gene regulatory divergence among locally adapted populations is poorly understood, especially how that divergence manifests in nature. Here, we evaluate gene expression divergence and allele-specific gene expression responses for locally adapted coastal perennial and inland annual accessions of the yellow monkeyflower, Mimulus guttatus, in a field reciprocal transplant experiment. Overall, 6765 (73%) of surveyed genes were differentially expressed between coastal and inland habitats, while 7213 (77%) were differentially expressed between the coastal perennial and inland annual accessions. Cis-regulatory variation was pervasive, affecting 79% (5532) of differentially expressed genes. We detected trans effects for 52% (3611) of differentially expressed genes. Expression plasticity of alleles across habitats (G × E interactions) appears to be relatively common (affecting 18% of transcripts) and could minimize fitness trade-offs at loci that contribute to local adaptation. We also found evidence that at least one chromosomal inversion may act as supergene by holding together haplotypes of differentially expressed genes, but this pattern depends on habitat context. Our results highlight multiple key patterns regarding the relationship between gene expression and the evolution of locally adapted populations.
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Affiliation(s)
- Billie A Gould
- Department of Plant Biology, Michigan State University, East Lansing, Michigan.,Myriad Women's Health, South San Francisco, California
| | - Yani Chen
- Department of Plant Biology, Michigan State University, East Lansing, Michigan
| | - David B Lowry
- Department of Plant Biology, Michigan State University, East Lansing, Michigan.,Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, Michigan.,Plant Resilience Institute, Michigan State University, East Lansing, Michigan
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10
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Cheng C, Tan JC, Hahn MW, Besansky NJ. Systems genetic analysis of inversion polymorphisms in the malaria mosquito Anopheles gambiae. Proc Natl Acad Sci U S A 2018; 115:E7005-E7014. [PMID: 29987007 PMCID: PMC6064990 DOI: 10.1073/pnas.1806760115] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Inversion polymorphisms in the African malaria vector Anopheles gambiae segregate along climatic gradients of aridity. Despite indirect evidence of their adaptive significance, little is known of the phenotypic targets of selection or the underlying genetic mechanisms. Here we adopt a systems genetics approach to explore the interaction of two inversions on opposite arms of chromosome 2 with gender, climatic conditions, and one another. We measure organismal traits and transcriptional profiles in 8-d-old adults of both sexes and four alternative homokaryotypic classes reared under two alternative climatic regimes. We show that karyotype strongly influences both organismal traits and transcriptional profiles but that the strength and direction of the effects depend upon complex interactions with gender and environmental conditions and between inversions on independent arms. Our data support the suppressed recombination model for the role of inversions in local adaptation, and-supported by transcriptional and physiological measurements following perturbation with the drug rapamycin-suggest that one mechanism underlying their adaptive role may be the maintenance of energy homeostasis.
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Affiliation(s)
- Changde Cheng
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - John C Tan
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN 47405
- Department of Computer Science, Indiana University, Bloomington, IN 47405
| | - Nora J Besansky
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556;
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
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11
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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: 3.6] [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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12
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The Effect of Common Inversion Polymorphisms In(2L)t and In(3R)Mo on Patterns of Transcriptional Variation in Drosophila melanogaster. G3-GENES GENOMES GENETICS 2017; 7:3659-3668. [PMID: 28916647 PMCID: PMC5677173 DOI: 10.1534/g3.117.1133] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Chromosomal inversions are a ubiquitous feature of genetic variation. Theoretical models describe several mechanisms by which inversions can drive adaptation and be maintained as polymorphisms. While inversions have been shown previously to be under selection, or contain genetic variation under selection, the specific phenotypic consequences of inversions leading to their maintenance remain unclear. Here we use genomic sequence and expression data from the Drosophila Genetic Reference Panel (DGRP) to explore the effects of two cosmopolitan inversions, In(2L)t and In(3R)Mo, on patterns of transcriptional variation. We demonstrate that each inversion has a significant effect on transcript abundance for hundreds of genes across the genome. Inversion-affected loci (IAL) appear both within inversions as well as on unlinked chromosomes. Importantly, IAL do not appear to be influenced by the previously reported genome-wide expression correlation structure. We found that five genes involved with sterol uptake, four of which are Niemann-Pick Type 2 orthologs, are upregulated in flies with In(3R)Mo but do not have SNPs in linkage disequilibrium (LD) with the inversion. We speculate that this upregulation is driven by genetic variation in mod(mdg4) that is in LD with In(3R)Mo. We find that there is little evidence for a regional or position effect of inversions on gene expression at the chromosomal level, but do find evidence for the distal breakpoint of In(3R)Mo interrupting one gene and possibly disassociating the two flanking genes from regulatory elements.
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13
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Lee CR, Wang B, Mojica JP, Mandáková T, Prasad KVSK, Goicoechea JL, Perera N, Hellsten U, Hundley HN, Johnson J, Grimwood J, Barry K, Fairclough S, Jenkins JW, Yu Y, Kudrna D, Zhang J, Talag J, Golser W, Ghattas K, Schranz ME, Wing R, Lysak MA, Schmutz J, Rokhsar DS, Mitchell-Olds T. Young inversion with multiple linked QTLs under selection in a hybrid zone. Nat Ecol Evol 2017; 1:119. [PMID: 28812690 PMCID: PMC5607633 DOI: 10.1038/s41559-017-0119] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 02/16/2017] [Indexed: 12/23/2022]
Abstract
Fixed chromosomal inversions can reduce gene flow and promote speciation in two ways: by suppressing recombination and by carrying locally favoured alleles at multiple loci. However, it is unknown whether favoured mutations slowly accumulate on older inversions or if young inversions spread because they capture pre-existing adaptive quantitative trait loci (QTLs). By genetic mapping, chromosome painting and genome sequencing, we have identified a major inversion controlling ecologically important traits in Boechera stricta. The inversion arose since the last glaciation and subsequently reached local high frequency in a hybrid speciation zone. Furthermore, the inversion shows signs of positive directional selection. To test whether the inversion could have captured existing, linked QTLs, we crossed standard, collinear haplotypes from the hybrid zone and found multiple linked phenology QTLs within the inversion region. These findings provide the first direct evidence that linked, locally adapted QTLs may be captured by young inversions during incipient speciation.
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Affiliation(s)
- Cheng-Ruei Lee
- Department of Biology, Duke University, Box 90338, Durham, North Carolina 27708, USA
- Institute of Ecology and Evolutionary Biology and Institute of Plant Biology, National Taiwan University, Taipei 10617, Taiwan ROC
| | - Baosheng Wang
- Department of Biology, Duke University, Box 90338, Durham, North Carolina 27708, USA
- Department of Plant Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Julius P Mojica
- Department of Biology, Duke University, Box 90338, Durham, North Carolina 27708, USA
| | - Terezie Mandáková
- Plant Cytogenomics Group, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno CZ-62500, Czech Republic
| | | | - Jose Luis Goicoechea
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Nadeesha Perera
- Department of Biology, Duke University, Box 90338, Durham, North Carolina 27708, USA
| | - Uffe Hellsten
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Hope N Hundley
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Jenifer Johnson
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Stephen Fairclough
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Jerry W Jenkins
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Yeisoo Yu
- Phyzen Genomics Institute, Phyzen Inc., Seoul 151-836, South Korea
| | - Dave Kudrna
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Jianwei Zhang
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Jayson Talag
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Wolfgang Golser
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Kathryn Ghattas
- Department of Biology, Duke University, Box 90338, Durham, North Carolina 27708, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University and Research Center, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Rod Wing
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Martin A Lysak
- Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Daniel S Rokhsar
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Thomas Mitchell-Olds
- Department of Biology, Duke University, Box 90338, Durham, North Carolina 27708, USA
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14
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Ayala D, Acevedo P, Pombi M, Dia I, Boccolini D, Costantini C, Simard F, Fontenille D. Chromosome inversions and ecological plasticity in the main African malaria mosquitoes. Evolution 2017; 71:686-701. [PMID: 28071788 DOI: 10.1111/evo.13176] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/22/2016] [Indexed: 01/30/2023]
Abstract
Chromosome inversions have fascinated the scientific community, mainly because of their role in the rapid adaption of different taxa to changing environments. However, the ecological traits linked to chromosome inversions have been poorly studied. Here, we investigated the roles played by 23 chromosome inversions in the adaptation of the four major African malaria mosquitoes to local environments in Africa. We studied their distribution patterns by using spatially explicit modeling and characterized the ecogeographical determinants of each inversion range. We then performed hierarchical clustering and constrained ordination analyses to assess the spatial and ecological similarities among inversions. Our results show that most inversions are environmentally structured, suggesting that they are actively involved in processes of local adaptation. Some inversions exhibited similar geographical patterns and ecological requirements among the four mosquito species, providing evidence for parallel evolution. Conversely, common inversion polymorphisms between sibling species displayed divergent ecological patterns, suggesting that they might have a different adaptive role in each species. These results are in agreement with the finding that chromosomal inversions play a role in Anopheles ecotypic adaptation. This study establishes a strong ecological basis for future genome-based analyses to elucidate the genetic mechanisms of local adaptation in these four mosquitoes.
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Affiliation(s)
- Diego Ayala
- UMR 224 MIVEGEC/ESV, IRD, Montpellier, 34394, France.,CIRMF, BP 769, Franceville, Gabon
| | - Pelayo Acevedo
- SaBio, Instituto de Investigación en Recursos Cinegéticos (IREC), CSIC-UCLM-JCCM, Ciudad Real, 13005, Spain
| | - Marco Pombi
- Sezione di Parassitologia, Dipartimento di Scienze di Sanità Pubblica, Università di Roma "La Sapienza,", Rome, 00185, Italy
| | - Ibrahima Dia
- Medical Entomology Unit, Institut Pasteur de Dakar, BP 220, Dakar, Senegal
| | - Daniela Boccolini
- Department MIPI, Unit Vector-Borne Diseases and International Health, Istituto Superiore di Sanità, Rome, 00161, Italy
| | | | | | - Didier Fontenille
- UMR 224 MIVEGEC/ESV, IRD, Montpellier, 34394, France.,Current Address: Institut Pasteur du Cambodge, BP 983, Phnom Penh, Cambodia
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15
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Puerma E, Orengo DJ, Aguadé M. The origin of chromosomal inversions as a source of segmental duplications in the Sophophora subgenus of Drosophila. Sci Rep 2016; 6:30715. [PMID: 27470196 PMCID: PMC4965816 DOI: 10.1038/srep30715] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 07/05/2016] [Indexed: 01/06/2023] Open
Abstract
Chromosomal inversions can contribute to the adaptation of organisms to their environment by capturing particular advantageous allelic combinations of a set of genes included in the inverted fragment and also by advantageous functional changes due to the inversion process itself that might affect not only the expression of flanking genes but also their dose and structure. Of the two mechanisms originating inversions —ectopic recombination, and staggered double-strand breaks and subsequent repair— only the latter confers the inversion the potential to have dosage effects and/or to generate advantageous chimeric genes. In Drosophila subobscura, there is ample evidence for the adaptive character of its chromosomal polymorphism, with an important contribution of some warm-climate arrangements such as E1+2+9+12. Here, we have characterized the breakpoints of inversion E12 and established that it originated through the staggered-break mechanism like four of the five inversions of D. subobscura previously studied. This mechanism that also predominates in the D. melanogaster lineage might be prevalent in the Sophophora subgenus and contribute to the adaptive character of the polymorphic and fixed inversions of its species. Finally, we have shown that the D. subobscura inversion breakpoint regions have generally been disrupted by additional structural changes occurred at different time scales.
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Affiliation(s)
- Eva Puerma
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Dorcas J Orengo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Montserrat Aguadé
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
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16
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Kapun M, Fabian DK, Goudet J, Flatt T. Genomic Evidence for Adaptive Inversion Clines in Drosophila melanogaster. Mol Biol Evol 2016; 33:1317-36. [PMID: 26796550 DOI: 10.1093/molbev/msw016] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Clines in chromosomal inversion polymorphisms-presumably driven by climatic gradients-are common but there is surprisingly little evidence for selection acting on them. Here we address this long-standing issue in Drosophila melanogaster by using diagnostic single nucleotide polymorphism (SNP) markers to estimate inversion frequencies from 28 whole-genome Pool-seq samples collected from 10 populations along the North American east coast. Inversions In(3L)P, In(3R)Mo, and In(3R)Payne showed clear latitudinal clines, and for In(2L)t, In(2R)NS, and In(3R)Payne the steepness of the clinal slopes changed between summer and fall. Consistent with an effect of seasonality on inversion frequencies, we detected small but stable seasonal fluctuations of In(2R)NS and In(3R)Payne in a temperate Pennsylvanian population over 4 years. In support of spatially varying selection, we observed that the cline in In(3R)Payne has remained stable for >40 years and that the frequencies of In(2L)t and In(3R)Payne are strongly correlated with climatic factors that vary latitudinally, independent of population structure. To test whether these patterns are adaptive, we compared the amount of genetic differentiation of inversions versus neutral SNPs and found that the clines in In(2L)t and In(3R)Payne are maintained nonneutrally and independent of admixture. We also identified numerous clinal inversion-associated SNPs, many of which exhibit parallel differentiation along the Australian cline and reside in genes known to affect fitness-related traits. Together, our results provide strong evidence that inversion clines are maintained by spatially-and perhaps also temporally-varying selection. We interpret our data in light of current hypotheses about how inversions are established and maintained.
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Affiliation(s)
- Martin Kapun
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Daniel K Fabian
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Thomas Flatt
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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17
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Berg PR, Jentoft S, Star B, Ring KH, Knutsen H, Lien S, Jakobsen KS, André C. Adaptation to Low Salinity Promotes Genomic Divergence in Atlantic Cod (Gadus morhua L.). Genome Biol Evol 2015; 7:1644-63. [PMID: 25994933 PMCID: PMC4494048 DOI: 10.1093/gbe/evv093] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
How genomic selection enables species to adapt to divergent environments is a fundamental question in ecology and evolution. We investigated the genomic signatures of local adaptation in Atlantic cod (Gadus morhua L.) along a natural salinity gradient, ranging from 35‰ in the North Sea to 7‰ within the Baltic Sea. By utilizing a 12 K SNPchip, we simultaneously assessed neutral and adaptive genetic divergence across the Atlantic cod genome. Combining outlier analyses with a landscape genomic approach, we identified a set of directionally selected loci that are strongly correlated with habitat differences in salinity, oxygen, and temperature. Our results show that discrete regions within the Atlantic cod genome are subject to directional selection and associated with adaptation to the local environmental conditions in the Baltic- and the North Sea, indicating divergence hitchhiking and the presence of genomic islands of divergence. We report a suite of outlier single nucleotide polymorphisms within or closely located to genes associated with osmoregulation, as well as genes known to play important roles in the hydration and development of oocytes. These genes are likely to have key functions within a general osmoregulatory framework and are important for the survival of eggs and larvae, contributing to the buildup of reproductive isolation between the low-salinity adapted Baltic cod and the adjacent cod populations. Hence, our data suggest that adaptive responses to the environmental conditions in the Baltic Sea may contribute to a strong and effective reproductive barrier, and that Baltic cod can be viewed as an example of ongoing speciation.
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Affiliation(s)
- Paul R Berg
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Norway
| | - Kristoffer H Ring
- Centre for Development and the Environment (SUM), University of Oslo, Norway
| | - Halvor Knutsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Norway Institute of Marine Research (IMR), Flødevigen, His, Norway University of Agder, Kristiansand, Norway
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Norway
| | - Carl André
- Department of Biology and Environmental Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
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18
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Tyukmaeva VI, Veltsos P, Slate J, Gregson E, Kauranen H, Kankare M, Ritchie MG, Butlin RK, Hoikkala A. Localization of quantitative trait loci for diapause and other photoperiodically regulated life history traits important in adaptation to seasonally varying environments. Mol Ecol 2015; 24:2809-19. [PMID: 25877951 DOI: 10.1111/mec.13202] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 04/02/2015] [Accepted: 04/08/2015] [Indexed: 12/31/2022]
Abstract
Seasonally changing environments at high latitudes present great challenges for the reproduction and survival of insects, and photoperiodic cues play an important role in helping them to synchronize their life cycle with prevalent and forthcoming conditions. We have mapped quantitative trait loci (QTL) responsible for the photoperiodic regulation of four life history traits, female reproductive diapause, cold tolerance, egg-to-eclosion development time and juvenile body weight in Drosophila montana strains from different latitudes in Canada and Finland. The F2 progeny of the cross was reared under a single photoperiod (LD cycle 16:8), which the flies from the Canadian population interpret as early summer and the flies from the Finnish population as late summer. The analysis revealed a unique QTL for diapause induction on the X chromosome and several QTL for this and the other measured traits on the 4th chromosome. Flies' cold tolerance, egg-to-eclosion development time and juvenile body weight had several QTL also on the 2nd, 3rd and 5th chromosome, some of the peaks overlapping with each other. These results suggest that while the downstream output of females' photoperiodic diapause response is partly under a different genetic control from that of the other traits in the given day length, all traits also share some QTL, possibly involving genes with pleiotropic effects and/or multiple tightly linked genes. Nonoverlapping QTL detected for some of the traits also suggest that the traits are potentially capable of independent evolution, even though this may be restricted by epistatic interactions and/or correlations and trade-offs between the traits.
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Affiliation(s)
- Venera I Tyukmaeva
- Department of Biological and Environmental Science, University of Jyväskylä, Survontie 9, PO Box 35, Jyväskylä, 40014, Finland.,School of Biology, Dyers Brae, University of St Andrews, Greenside Place, St Andrews, Fife, KY16 9TH, UK
| | - Paris Veltsos
- School of Biology, Dyers Brae, University of St Andrews, Greenside Place, St Andrews, Fife, KY16 9TH, UK
| | - Jon Slate
- Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Emma Gregson
- Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.,School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Hannele Kauranen
- Department of Biological and Environmental Science, University of Jyväskylä, Survontie 9, PO Box 35, Jyväskylä, 40014, Finland
| | - Maaria Kankare
- Department of Biological and Environmental Science, University of Jyväskylä, Survontie 9, PO Box 35, Jyväskylä, 40014, Finland
| | - Michael G Ritchie
- School of Biology, Dyers Brae, University of St Andrews, Greenside Place, St Andrews, Fife, KY16 9TH, UK
| | - Roger K Butlin
- Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.,Sven Lovén Centre for Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, SE 452 96, Sweden
| | - Anneli Hoikkala
- Department of Biological and Environmental Science, University of Jyväskylä, Survontie 9, PO Box 35, Jyväskylä, 40014, Finland
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19
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Oneal E, Lowry DB, Wright KM, Zhu Z, Willis JH. Divergent population structure and climate associations of a chromosomal inversion polymorphism across the Mimulus guttatus species complex. Mol Ecol 2014; 23:2844-60. [PMID: 24796267 DOI: 10.1111/mec.12778] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/14/2014] [Accepted: 04/26/2014] [Indexed: 12/12/2022]
Abstract
Chromosomal rearrangement polymorphisms are common and increasingly found to be associated with adaptive ecological divergence and speciation. Rearrangements, such as inversions, reduce recombination in heterozygous individuals and thus can protect favourable allelic combinations at linked loci, facilitating their spread in the presence of gene flow. Recently, we identified a chromosomal inversion polymorphism that contributes to ecological adaptation and reproductive isolation between annual and perennial ecotypes of the yellow monkeyflower, Mimulus guttatus. Here we evaluate the population genetic structure of this inverted region in comparison with the collinear regions of the genome across the M. guttatus species complex. We tested whether annual and perennial M. guttatus exhibit different patterns of divergence for loci in the inverted and noninverted regions of the genome. We then evaluated whether there are contrasting climate associations with these genomic regions through redundancy analysis. We found that the inversion exhibits broadly different patterns of divergence among annual and perennial M. guttatus and is associated with environmental variation across population accessions. This study is the first widespread population genetic survey of the diversity of the M. guttatus species complex. Our findings contribute to a greater understanding of morphological, ecological, and genetic evolutionary divergence across this highly diverse group of closely related ecotypes and species. Finally, understanding species relationships among M. guttatus sp. has hitherto been stymied by accumulated evidence of substantial gene flow among populations as well as designated species. Nevertheless, our results shed light on these relationships and provide insight into adaptation in life history traits within the complex.
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Affiliation(s)
- Elen Oneal
- Department of Biology, Duke University, PO Box 90338, Durham, NC 27708, USA
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20
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Ayala D, Ullastres A, González J. Adaptation through chromosomal inversions in Anopheles. Front Genet 2014; 5:129. [PMID: 24904633 PMCID: PMC4033225 DOI: 10.3389/fgene.2014.00129] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 04/22/2014] [Indexed: 12/29/2022] Open
Abstract
Chromosomal inversions have been repeatedly involved in local adaptation in a large number of animals and plants. The ecological and behavioral plasticity of Anopheles species-human malaria vectors-is mirrored by high amounts of polymorphic inversions. The adaptive significance of chromosomal inversions has been consistently attested by strong and significant correlations between their frequencies and a number of phenotypic traits. Here, we provide an extensive literature review of the different adaptive traits associated with chromosomal inversions in the genus Anopheles. Traits having important consequences for the success of present and future vector control measures, such as insecticide resistance and behavioral changes, are discussed.
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Affiliation(s)
- Diego Ayala
- UMR 224 MIVEGEC/BEES, IRD Montpellier, France ; Unité d'Entomologie Médicale, Centre International de Recherches Médicales de Franceville Franceville, Gabon
| | - Anna Ullastres
- Comparative and Computational Genomics, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra) Barcelona, Spain
| | - Josefa González
- Comparative and Computational Genomics, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra) Barcelona, Spain
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21
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Pearse DE, Miller MR, Abadía-Cardoso A, Garza JC. Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout. Proc Biol Sci 2014; 281:20140012. [PMID: 24671976 DOI: 10.1098/rspb.2014.0012] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Rapid adaptation to novel environments may drive changes in genomic regions through natural selection. Such changes may be population-specific or, alternatively, may involve parallel evolution of the same genomic region in multiple populations, if that region contains genes or co-adapted gene complexes affecting the selected trait(s). Both quantitative and population genetic approaches have identified associations between specific genomic regions and the anadromous (steelhead) and resident (rainbow trout) life-history strategies of Oncorhynchus mykiss. Here, we use genotype data from 95 single nucleotide polymorphisms and show that the distribution of variation in a large region of one chromosome, Omy5, is strongly associated with life-history differentiation in multiple above-barrier populations of rainbow trout and their anadromous steelhead ancestors. The associated loci are in strong linkage disequilibrium, suggesting the presence of a chromosomal inversion or other rearrangement limiting recombination. These results provide the first evidence of a common genomic basis for life-history variation in O. mykiss in a geographically diverse set of populations and extend our knowledge of the heritable basis of rapid adaptation of complex traits in novel habitats.
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Affiliation(s)
- Devon E Pearse
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, , 110 Shaffer Road, Santa Cruz, CA 95060, USA, Institute of Marine Sciences, University of California, , Santa Cruz, CA 95060, USA, Institute of Molecular Biology, University of Oregon, , Eugene, OR 97403, USA, Department of Animal Science, University of California, , One Shields Avenue, Davis, CA 95616, USA
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22
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Abstract
Drosophila melanogaster, an ancestrally African species, has recently spread throughout the world, associated with human activity. The species has served as the focus of many studies investigating local adaptation relating to latitudinal variation in non-African populations, especially those from the United States and Australia. These studies have documented the existence of shared, genetically determined phenotypic clines for several life history and morphological traits. However, there are no studies designed to formally address the degree of shared latitudinal differentiation at the genomic level. Here we present our comparative analysis of such differentiation. Not surprisingly, we find evidence of substantial, shared selection responses on the two continents, probably resulting from selection on standing ancestral variation. The polymorphic inversion In(3R)P has an important effect on this pattern, but considerable parallelism is also observed across the genome in regions not associated with inversion polymorphism. Interestingly, parallel latitudinal differentiation is observed even for variants that are not particularly strongly differentiated, which suggests that very large numbers of polymorphisms are targets of spatially varying selection in this species.
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23
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Lee YW, Gould BA, Stinchcombe JR. Identifying the genes underlying quantitative traits: a rationale for the QTN programme. AOB PLANTS 2014; 6:plu004. [PMID: 24790125 PMCID: PMC4038433 DOI: 10.1093/aobpla/plu004] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Accepted: 01/01/2014] [Indexed: 05/19/2023]
Abstract
The goal of identifying the genes or even nucleotides underlying quantitative and adaptive traits has been characterized as the 'QTN programme' and has recently come under severe criticism. Part of the reason for this criticism is that much of the QTN programme has asserted that finding the genes and nucleotides for adaptive and quantitative traits is a fundamental goal, without explaining why it is such a hallowed goal. Here we outline motivations for the QTN programme that offer general insight, regardless of whether QTNs are of large or small effect, and that aid our understanding of the mechanistic dynamics of adaptive evolution. We focus on five areas: (i) vertical integration of insight across different levels of biological organization, (ii) genetic parallelism and the role of pleiotropy in shaping evolutionary dynamics, (iii) understanding the forces maintaining genetic variation in populations, (iv) distinguishing between adaptation from standing variation and new mutation, and (v) the role of genomic architecture in facilitating adaptation. We argue that rather than abandoning the QTN programme, we should refocus our efforts on topics where molecular data will be the most effective for testing hypotheses about phenotypic evolution.
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Affiliation(s)
- Young Wha Lee
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, CanadaM5S 3B2
| | - Billie A. Gould
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, CanadaM5S 3B2
| | - John R. Stinchcombe
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, CanadaM5S 3B2
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, CanadaM5S 3B2
- Corresponding author's e-mail address:
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24
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A sequential coalescent algorithm for chromosomal inversions. Heredity (Edinb) 2013; 111:200-9. [PMID: 23632894 DOI: 10.1038/hdy.2013.38] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 02/04/2013] [Accepted: 03/25/2013] [Indexed: 01/06/2023] Open
Abstract
Chromosomal inversions are common in natural populations and are believed to be involved in many important evolutionary phenomena, including speciation, the evolution of sex chromosomes and local adaptation. While recent advances in sequencing and genotyping methods are leading to rapidly increasing amounts of genome-wide sequence data that reveal interesting patterns of genetic variation within inverted regions, efficient simulation methods to study these patterns are largely missing. In this work, we extend the sequential Markovian coalescent, an approximation to the coalescent with recombination, to include the effects of polymorphic inversions on patterns of recombination. Results show that our algorithm is fast, memory-efficient and accurate, making it feasible to simulate large inversions in large populations for the first time. The SMC algorithm enables studies of patterns of genetic variation (for example, linkage disequilibria) and tests of hypotheses (using simulation-based approaches) that were previously intractable.
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