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Errbii M, Ernst UR, Lajmi A, Privman E, Gadau J, Schrader L. Evolutionary genomics of socially polymorphic populations of Pogonomyrmex californicus. BMC Biol 2024; 22:109. [PMID: 38735942 PMCID: PMC11089791 DOI: 10.1186/s12915-024-01907-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 04/30/2024] [Indexed: 05/14/2024] Open
Abstract
BACKGROUND Social insects vary considerably in their social organization both between and within species. In the California harvester ant, Pogonomyrmex californicus (Buckley 1867), colonies are commonly founded and headed by a single queen (haplometrosis, primary monogyny). However, in some populations in California (USA), unrelated queens cooperate not only during founding (pleometrosis) but also throughout the life of the colony (primary polygyny). The genetic architecture and evolutionary dynamics of this complex social niche polymorphism (haplometrosis vs pleometrosis) have remained unknown. RESULTS We provide a first analysis of its genomic basis and evolutionary history using population genomics comparing individuals from a haplometrotic population to those from a pleometrotic population. We discovered a recently evolved (< 200 k years), 8-Mb non-recombining region segregating with the observed social niche polymorphism. This region shares several characteristics with supergenes underlying social polymorphisms in other socially polymorphic ant species. However, we also find remarkable differences from previously described social supergenes. Particularly, four additional genomic regions not in linkage with the supergene show signatures of a selective sweep in the pleometrotic population. Within these regions, we find for example genes crucial for epigenetic regulation via histone modification (chameau) and DNA methylation (Dnmt1). CONCLUSIONS Altogether, our results suggest that social morph in this species is a polygenic trait involving a potential young supergene. Further studies targeting haplo- and pleometrotic individuals from a single population are however required to conclusively resolve whether these genetic differences underlie the alternative social phenotypes or have emerged through genetic drift.
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Affiliation(s)
- Mohammed Errbii
- Molecular Evolution and Sociobiology Group, Institute for Evolution and Biodiversity, University of Münster, Hüfferstr. 1, Münster, DE-48149, Germany
| | - Ulrich R Ernst
- Molecular Evolution and Sociobiology Group, Institute for Evolution and Biodiversity, University of Münster, Hüfferstr. 1, Münster, DE-48149, Germany
- Present Address: Apicultural State Institute, University of Hohenheim, Erna-Hruschka-Weg 6, Stuttgart, DE-70599, Germany
- Center for Biodiversity and Integrative Taxonomy (KomBioTa), University of Hohenheim, Stuttgart, DE-70599, Germany
| | - Aparna Lajmi
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
| | - Eyal Privman
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
| | - Jürgen Gadau
- Molecular Evolution and Sociobiology Group, Institute for Evolution and Biodiversity, University of Münster, Hüfferstr. 1, Münster, DE-48149, Germany.
| | - Lukas Schrader
- Molecular Evolution and Sociobiology Group, Institute for Evolution and Biodiversity, University of Münster, Hüfferstr. 1, Münster, DE-48149, Germany.
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2
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Chen J, Liu C, Li W, Zhang W, Wang Y, Clark AG, Lu J. From sub-Saharan Africa to China: Evolutionary history and adaptation of Drosophila melanogaster revealed by population genomics. SCIENCE ADVANCES 2024; 10:eadh3425. [PMID: 38630810 PMCID: PMC11023512 DOI: 10.1126/sciadv.adh3425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 03/13/2024] [Indexed: 04/19/2024]
Abstract
Drosophila melanogaster is a widely used model organism for studying environmental adaptation. However, the genetic diversity of populations in Asia is poorly understood, leaving a notable gap in our knowledge of the global evolution and adaptation of this species. We sequenced genomes of 292 D. melanogaster strains from various ecological settings in China and analyzed them along with previously published genome sequences. We have identified six global genetic ancestry groups, despite the presence of widespread genetic admixture. The strains from China represent a unique ancestry group, although detectable differentiation exists among populations within China. We deciphered the global migration and demography of D. melanogaster, and identified widespread signals of adaptation, including genetic changes in response to insecticides. We validated the effects of insecticide resistance variants using population cage trials and deep sequencing. This work highlights the importance of population genomics in understanding the genetic underpinnings of adaptation, an effort that is particularly relevant given the deterioration of ecosystems.
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Affiliation(s)
- Junhao Chen
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Chenlu Liu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Weixuan Li
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Wenxia Zhang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yirong Wang
- College of Biology, Hunan University, Changsha 410082, China
| | - Andrew G. Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
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3
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Fuentes‐Pardo AP, Stanley R, Bourne C, Singh R, Emond K, Pinkham L, McDermid JL, Andersson L, Ruzzante DE. Adaptation to seasonal reproduction and environment-associated factors drive temporal and spatial differentiation in northwest Atlantic herring despite gene flow. Evol Appl 2024; 17:e13675. [PMID: 38495946 PMCID: PMC10940790 DOI: 10.1111/eva.13675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024] Open
Abstract
Understanding how marine organisms adapt to local environments is crucial for predicting how populations will respond to global climate change. The genomic basis, environmental factors and evolutionary processes involved in local adaptation are however not well understood. Here we use Atlantic herring, an abundant, migratory and widely distributed marine fish with substantial genomic resources, as a model organism to evaluate local adaptation. We examined genomic variation and its correlation with environmental variables across a broad environmental gradient, for 15 spawning aggregations in Atlantic Canada and the United States. We then compared our results with available genomic data of northeast Atlantic populations. We confirmed that population structure lies in a fraction of the genome including likely adaptive genetic variants of functional importance. We discovered 10 highly differentiated genomic regions distributed across four chromosomes. Nine regions show strong association with seasonal reproduction. One region, corresponding to a known inversion on chromosome 12, underlies a latitudinal pattern discriminating populations north and south of a biogeographic transition zone on the Scotian Shelf. Genome-environment associations indicate that winter seawater temperature best correlates with the latitudinal pattern of this inversion. The variation at two so-called 'islands of divergence' related to seasonal reproduction appear to be private to the northwest Atlantic. Populations in the northwest and northeast Atlantic share variation at four of these divergent regions, simultaneously displaying significant diversity in haplotype composition at another four regions, which includes an undescribed structural variant approximately 7.7 Mb long on chromosome 8. Our results suggest that the timing and geographic location of spawning and early development may be under diverse selective pressures related to allelic fitness across environments. Our study highlights the role of genomic architecture, ancestral haplotypes and selection in maintaining adaptive divergence in species with large population sizes and presumably high gene flow.
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Affiliation(s)
- Angela P. Fuentes‐Pardo
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Ryan Stanley
- Fisheries and Oceans CanadaMaritimes RegionDartmouthNova ScotiaCanada
| | - Christina Bourne
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt John'sNewfoundland and LabradorCanada
| | - Rabindra Singh
- Fisheries and Oceans CanadaSt. Andrews Biological StationSt. AndrewsNew BrunswickCanada
| | - Kim Emond
- Fisheries and Oceans CanadaMaurice Lamontagne InstituteMont‐JoliQuebecCanada
| | - Lisa Pinkham
- Department of Marine ResourcesWest Boothbay HarborMaineUSA
| | - Jenni L. McDermid
- Fisheries and Oceans CanadaGulf Fisheries CentreMonctonNew BrunswickCanada
| | - Leif Andersson
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
- Department of Veterinary Integrative BiosciencesTexas A&M UniversityCollege StationTexasUSA
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4
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Nunez JCB, Lenhart BA, Bangerter A, Murray CS, Mazzeo GR, Yu Y, Nystrom TL, Tern C, Erickson PA, Bergland AO. A cosmopolitan inversion facilitates seasonal adaptation in overwintering Drosophila. Genetics 2024; 226:iyad207. [PMID: 38051996 PMCID: PMC10847723 DOI: 10.1093/genetics/iyad207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 11/28/2023] [Indexed: 12/07/2023] Open
Abstract
Fluctuations in the strength and direction of natural selection through time are a ubiquitous feature of life on Earth. One evolutionary outcome of such fluctuations is adaptive tracking, wherein populations rapidly adapt from standing genetic variation. In certain circumstances, adaptive tracking can lead to the long-term maintenance of functional polymorphism despite allele frequency change due to selection. Although adaptive tracking is likely a common process, we still have a limited understanding of aspects of its genetic architecture and its strength relative to other evolutionary forces such as drift. Drosophila melanogaster living in temperate regions evolve to track seasonal fluctuations and are an excellent system to tackle these gaps in knowledge. By sequencing orchard populations collected across multiple years, we characterized the genomic signal of seasonal demography and identified that the cosmopolitan inversion In(2L)t facilitates seasonal adaptive tracking and shows molecular footprints of selection. A meta-analysis of phenotypic studies shows that seasonal loci within In(2L)t are associated with behavior, life history, physiology, and morphological traits. We identify candidate loci and experimentally link them to phenotype. Our work contributes to our general understanding of fluctuating selection and highlights the evolutionary outcome and dynamics of contemporary selection on inversions.
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Affiliation(s)
- Joaquin C B Nunez
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
- Department of Biology, University of Vermont, 109 Carrigan Drive, Burlington, VT 05405, USA
| | - Benedict A Lenhart
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Alyssa Bangerter
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Connor S Murray
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Giovanni R Mazzeo
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Yang Yu
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Taylor L Nystrom
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Courtney Tern
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Priscilla A Erickson
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
- Department of Biology, University of Richmond, 138 UR Drive, Richmond, VA 23173, USA
| | - Alan O Bergland
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
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5
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Birchard K, Driver HG, Ademidun D, Bedolla-Guzmán Y, Birt T, Chown EE, Deane P, Harkness BAS, Morrin A, Masello JF, Taylor RS, Friesen VL. Circadian gene variation in relation to breeding season and latitude in allochronic populations of two pelagic seabird species complexes. Sci Rep 2023; 13:13692. [PMID: 37608061 PMCID: PMC10444859 DOI: 10.1038/s41598-023-40702-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 08/16/2023] [Indexed: 08/24/2023] Open
Abstract
Annual cues in the environment result in physiological changes that allow organisms to time reproduction during periods of optimal resource availability. Understanding how circadian rhythm genes sense these environmental cues and stimulate the appropriate physiological changes in response is important for determining the adaptability of species, especially in the advent of changing climate. A first step involves characterizing the environmental correlates of natural variation in these genes. Band-rumped and Leach's storm-petrels (Hydrobates spp.) are pelagic seabirds that breed across a wide range of latitudes. Importantly, some populations have undergone allochronic divergence, in which sympatric populations use the same breeding sites at different times of year. We investigated the relationship between variation in key functional regions of four genes that play an integral role in the cellular clock mechanism-Clock, Bmal1, Cry2 and Per2-with both breeding season and absolute latitude in these two species complexes. We discovered that allele frequencies in two genes, Clock and Bmal1, differed between seasonal populations in one archipelago, and also correlated with absolute latitude of breeding colonies. These results indicate that variation in these circadian rhythm genes may be involved in allochronic speciation, as well as adaptation to photoperiod at breeding locations.
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Affiliation(s)
- Katie Birchard
- Biology Department, Queen's University, Kingston, ON, K7L 3N6, Canada
- Apex Resource Management Solutions, Ottawa, ON, K2A 3K2, Canada
| | - Hannah G Driver
- Biology Department, Queen's University, Kingston, ON, K7L 3N6, Canada
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - Dami Ademidun
- Biology Department, Queen's University, Kingston, ON, K7L 3N6, Canada
| | | | - Tim Birt
- Biology Department, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Erin E Chown
- Biology Department, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Petra Deane
- Biology Department, Queen's University, Kingston, ON, K7L 3N6, Canada
- Mascoma LLC, Lallemand Inc., Lebanon, NH, 03766, USA
| | - Bronwyn A S Harkness
- Biology Department, Queen's University, Kingston, ON, K7L 3N6, Canada
- Environment and Climate Change Canada, Wildlife Research Division, Ottawa, ON, K1S 5B6, Canada
| | - Austin Morrin
- Biology Department, Queen's University, Kingston, ON, K7L 3N6, Canada
- Sims Animal Hospital, Kingston, ON, K7K 7E9, Canada
| | - Juan F Masello
- Department of Animal Behaviour, University of Bielefeld, 33615, Bielefeld, Germany
| | - Rebecca S Taylor
- Biology Department, Queen's University, Kingston, ON, K7L 3N6, Canada
- Environment and Climate Change Canada, Landscape Science and Technology Division, Ottawa, ON, K1S 5R1, Canada
| | - Vicki L Friesen
- Biology Department, Queen's University, Kingston, ON, K7L 3N6, Canada.
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6
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Fuentes‐Pardo AP, Farrell ED, Pettersson ME, Sprehn CG, Andersson L. The genomic basis and environmental correlates of local adaptation in the Atlantic horse mackerel ( Trachurus trachurus). Evol Appl 2023; 16:1201-1219. [PMID: 37360028 PMCID: PMC10286234 DOI: 10.1111/eva.13559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 04/21/2023] [Accepted: 05/07/2023] [Indexed: 06/28/2023] Open
Abstract
Understanding how populations adapt to their environment is increasingly important to prevent biodiversity loss due to overexploitation and climate change. Here we studied the population structure and genetic basis of local adaptation of Atlantic horse mackerel, a commercially and ecologically important marine fish that has one of the widest distributions in the eastern Atlantic. We analyzed whole-genome sequencing and environmental data of samples collected from the North Sea to North Africa and the western Mediterranean Sea. Our genomic approach indicated low population structure with a major split between the Mediterranean Sea and the Atlantic Ocean and between locations north and south of mid-Portugal. Populations from the North Sea are the most genetically distinct in the Atlantic. We discovered that most population structure patterns are driven by a few highly differentiated putatively adaptive loci. Seven loci discriminate the North Sea, two the Mediterranean Sea, and a large putative inversion (9.9 Mb) on chromosome 21 underlines the north-south divide and distinguishes North Africa. A genome-environment association analysis indicates that mean seawater temperature and temperature range, or factors correlated to them, are likely the main environmental drivers of local adaptation. Our genomic data broadly support the current stock divisions, but highlight areas of potential mixing, which require further investigation. Moreover, we demonstrate that as few as 17 highly informative SNPs can genetically discriminate the North Sea and North African samples from neighboring populations. Our study highlights the importance of both, life history and climate-related selective pressures in shaping population structure patterns in marine fish. It also supports that chromosomal rearrangements play a key role in local adaptation with gene flow. This study provides the basis for more accurate delineation of the horse mackerel stocks and paves the way for improving stock assessments.
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Affiliation(s)
| | - Edward D. Farrell
- EDF Scientific LimitedCorkIreland
- Killybegs Fishermen's OrganisationDonegalIreland
| | - Mats E. Pettersson
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - C. Grace Sprehn
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Leif Andersson
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
- Department of Veterinary Integrative BiosciencesTexas A&M UniversityCollege StationTexasUSA
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7
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [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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8
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Cridland JM, Contino CE, Begun DJ. Selection and geography shape male reproductive tract transcriptomes in Drosophila melanogaster. Genetics 2023; 224:iyad034. [PMID: 36869688 PMCID: PMC10474930 DOI: 10.1093/genetics/iyad034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 01/25/2023] [Accepted: 02/20/2023] [Indexed: 03/05/2023] Open
Abstract
Transcriptome analysis of several animal clades suggests that male reproductive tract gene expression evolves quickly. However, the factors influencing the abundance and distribution of within-species variation, the ultimate source of interspecific divergence, are poorly known. Drosophila melanogaster, an ancestrally African species that has recently spread throughout the world and colonized the Americas in the last roughly 100 years, exhibits phenotypic and genetic latitudinal clines on multiple continents, consistent with a role for spatially varying selection in shaping its biology. Nevertheless, geographic expression variation in the Americas is poorly described, as is its relationship to African expression variation. Here, we investigate these issues through the analysis of two male reproductive tissue transcriptomes [testis and accessory gland (AG)] in samples from Maine (USA), Panama, and Zambia. We find dramatic differences between these tissues in differential expression between Maine and Panama, with the accessory glands exhibiting abundant expression differentiation and the testis exhibiting very little. Latitudinal expression differentiation appears to be influenced by the selection of Panama expression phenotypes. While the testis shows little latitudinal expression differentiation, it exhibits much greater differentiation than the accessory gland in Zambia vs American population comparisons. Expression differentiation for both tissues is non-randomly distributed across the genome on a chromosome arm scale. Interspecific expression divergence between D. melanogaster and D. simulans is discordant with rates of differentiation between D. melanogaster populations. Strongly heterogeneous expression differentiation across tissues and timescales suggests a complex evolutionary process involving major temporal changes in the way selection influences expression evolution in these organs.
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Affiliation(s)
- Julie M Cridland
- Department of Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA
| | - Colin E Contino
- Department of Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA
| | - David J Begun
- Department of Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA
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9
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Love RR, Sikder JR, Vivero RJ, Matute DR, Schrider DR. Strong Positive Selection in Aedes aegypti and the Rapid Evolution of Insecticide Resistance. Mol Biol Evol 2023; 40:msad072. [PMID: 36971242 PMCID: PMC10118305 DOI: 10.1093/molbev/msad072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 02/13/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Aedes aegypti vectors the pathogens that cause dengue, yellow fever, Zika virus, and chikungunya and is a serious threat to public health in tropical regions. Decades of work has illuminated many aspects of Ae. aegypti's biology and global population structure and has identified insecticide resistance genes; however, the size and repetitive nature of the Ae. aegypti genome have limited our ability to detect positive selection in this mosquito. Combining new whole genome sequences from Colombia with publicly available data from Africa and the Americas, we identify multiple strong candidate selective sweeps in Ae. aegypti, many of which overlap genes linked to or implicated in insecticide resistance. We examine the voltage-gated sodium channel gene in three American cohorts and find evidence for successive selective sweeps in Colombia. The most recent sweep encompasses an intermediate-frequency haplotype containing four candidate insecticide resistance mutations that are in near-perfect linkage disequilibrium with one another in the Colombian sample. We hypothesize that this haplotype may continue to rapidly increase in frequency and perhaps spread geographically in the coming years. These results extend our knowledge of how insecticide resistance has evolved in this species and add to a growing body of evidence suggesting that Ae. aegypti has an extensive genomic capacity to rapidly adapt to insecticide-based vector control.
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Affiliation(s)
- R Rebecca Love
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NCUSA
| | - Josh R Sikder
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NCUSA
| | - Rafael J Vivero
- Programa de Estudio y Control de Enfermedades Tropicales, PECET, Universidad de Antioquia, Chapel Hill, NCColombia
| | - Daniel R Matute
- Department of Biology, College of Arts and Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Daniel R Schrider
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NCUSA
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10
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Kramer IM, Pfenninger M, Feldmeyer B, Dhimal M, Gautam I, Shreshta P, Baral S, Phuyal P, Hartke J, Magdeburg A, Groneberg DA, Ahrens B, Müller R, Waldvogel AM. Genomic profiling of climate adaptation in Aedes aegypti along an altitudinal gradient in Nepal indicates nongradual expansion of the disease vector. Mol Ecol 2023; 32:350-368. [PMID: 36305220 DOI: 10.1111/mec.16752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 10/21/2022] [Accepted: 10/25/2022] [Indexed: 01/11/2023]
Abstract
Driven by globalization, urbanization and climate change, the distribution range of invasive vector species has expanded to previously colder ecoregions. To reduce health-threatening impacts on humans, insect vectors are extensively studied. Population genomics can reveal the genomic basis of adaptation and help to identify emerging trends of vector expansion. By applying whole genome analyses and genotype-environment associations to populations of the main dengue vector Aedes aegypti, sampled along an altitudinal gradient in Nepal (200-1300 m), we identify putatively adaptive traits and describe the species' genomic footprint of climate adaptation to colder ecoregions. We found two differentiated clusters with significantly different allele frequencies in genes associated to climate adaptation between the highland population (1300 m) and all other lowland populations (≤800 m). We revealed nonsynonymous mutations in 13 of the candidate genes associated to either altitude, precipitation or cold tolerance and identified an isolation-by-environment differentiation pattern. Other than the expected gradual differentiation along the altitudinal gradient, our results reveal a distinct genomic differentiation of the highland population. Local high-altitude adaptation could be one explanation of the population's phenotypic cold tolerance. Carrying alleles relevant for survival under colder climate increases the likelihood of this highland population to a worldwide expansion into other colder ecoregions.
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Affiliation(s)
- Isabelle Marie Kramer
- Institute of Occupational, Social and Environmental Medicine, Goethe University, Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
| | - Barbara Feldmeyer
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | | | - Ishan Gautam
- Natural History Museum, Tribhuvan University, Kathmandu, Nepal
| | | | | | - Parbati Phuyal
- Institute of Occupational, Social and Environmental Medicine, Goethe University, Frankfurt am Main, Germany
| | - Juliane Hartke
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
| | - Axel Magdeburg
- Institute of Occupational, Social and Environmental Medicine, Goethe University, Frankfurt am Main, Germany
| | - David A Groneberg
- Institute of Occupational, Social and Environmental Medicine, Goethe University, Frankfurt am Main, Germany
| | - Bodo Ahrens
- Institute for Atmospheric and Environmental Sciences, Goethe University, Frankfurt am Main, Germany
| | - Ruth Müller
- Institute of Occupational, Social and Environmental Medicine, Goethe University, Frankfurt am Main, Germany.,Unit Entomology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Ann-Marie Waldvogel
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,Institute of Zoology, University of Cologne, Cologne, Germany
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11
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Burny C, Nolte V, Dolezal M, Schlötterer C. Genome-wide selection signatures reveal widespread synergistic effects of two different stressors in Drosophila melanogaster. Proc Biol Sci 2022; 289:20221857. [PMID: 36259211 PMCID: PMC9579754 DOI: 10.1098/rspb.2022.1857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Experimental evolution combined with whole-genome sequencing (evolve and resequence (E&R)) is a powerful approach to study the adaptive architecture of selected traits. Nevertheless, so far the focus has been on the selective response triggered by a single stressor. Building on the highly parallel selection response of founder populations with reduced variation, we evaluated how the presence of a second stressor affects the genomic selection response. After 20 generations of adaptation to laboratory conditions at either 18°C or 29°C, strong genome-wide selection signatures were observed. Only 38% of the selection signatures can be attributed to laboratory adaptation (no difference between temperature regimes). The remaining selection responses are either caused by temperature-specific effects, or reflect the joint effects of temperature and laboratory adaptation (same direction, but the magnitude differs between temperatures). The allele frequency changes resulting from the combined effects of temperature and laboratory adaptation were more extreme in the hot environment for 83% of the affected genomic regions-indicating widespread synergistic effects of the two stressors. We conclude that E&R with reduced genetic variation is a powerful approach to study genome-wide fitness consequences driven by the combined effects of multiple environmental factors.
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Affiliation(s)
- Claire Burny
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, Vienna 1210, Austria.,Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna 1210, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, Vienna 1210, Austria
| | - Marlies Dolezal
- Plattform Bioinformatik und Biostatistik, Vetmeduni Vienna, Vienna 1210, Austria
| | - Christian Schlötterer
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, Vienna 1210, Austria
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12
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Barnard-Kubow KB, Becker D, Murray CS, Porter R, Gutierrez G, Erickson P, Nunez JCB, Voss E, Suryamohan K, Ratan A, Beckerman A, Bergland AO. Genetic Variation in Reproductive Investment Across an Ephemerality Gradient in Daphnia pulex. Mol Biol Evol 2022; 39:msac121. [PMID: 35642301 PMCID: PMC9198359 DOI: 10.1093/molbev/msac121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Species across the tree of life can switch between asexual and sexual reproduction. In facultatively sexual species, the ability to switch between reproductive modes is often environmentally dependent and subject to local adaptation. However, the ecological and evolutionary factors that influence the maintenance and turnover of polymorphism associated with facultative sex remain unclear. We studied the ecological and evolutionary dynamics of reproductive investment in the facultatively sexual model species, Daphnia pulex. We found that patterns of clonal diversity, but not genetic diversity varied among ponds consistent with the predicted relationship between ephemerality and clonal structure. Reconstruction of a multi-year pedigree demonstrated the coexistence of clones that differ in their investment into male production. Mapping of quantitative variation in male production using lab-generated and field-collected individuals identified multiple putative quantitative trait loci (QTL) underlying this trait, and we identified a plausible candidate gene. The evolutionary history of these QTL suggests that they are relatively young, and male limitation in this system is a rapidly evolving trait. Our work highlights the dynamic nature of the genetic structure and composition of facultative sex across space and time and suggests that quantitative genetic variation in reproductive strategy can undergo rapid evolutionary turnover.
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Affiliation(s)
- Karen B Barnard-Kubow
- Department of Biology, University of Virginia, Charlottesville, VA, USA
- Department of Biology, James Madison University, Harrisonburg, VA, USA
| | - Dörthe Becker
- Department of Biology, University of Virginia, Charlottesville, VA, USA
- School of Biosciences, Ecology and Evolutionary Biology, University of Sheffield, Sheffield, UK
- Department of Biology, University of Marburg, Marburg, Germany
| | - Connor S Murray
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Robert Porter
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Grace Gutierrez
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | | | - Joaquin C B Nunez
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Erin Voss
- Department of Biology, University of Virginia, Charlottesville, VA, USA
- Department of Integrative Biology, UC Berkeley, Berkeley, CA, USA
| | | | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Andrew Beckerman
- School of Biosciences, Ecology and Evolutionary Biology, University of Sheffield, Sheffield, UK
| | - Alan O Bergland
- Department of Biology, University of Virginia, Charlottesville, VA, USA
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13
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Kapun M, Nunez JCB, Bogaerts-Márquez M, Murga-Moreno J, Paris M, Outten J, Coronado-Zamora M, Tern C, Rota-Stabelli O, Guerreiro MPG, Casillas S, Orengo DJ, Puerma E, Kankare M, Ometto L, Loeschcke V, Onder BS, Abbott JK, Schaeffer SW, Rajpurohit S, Behrman EL, Schou MF, Merritt TJS, Lazzaro BP, Glaser-Schmitt A, Argyridou E, Staubach F, Wang Y, Tauber E, Serga SV, Fabian DK, Dyer KA, Wheat CW, Parsch J, Grath S, Veselinovic MS, Stamenkovic-Radak M, Jelic M, Buendía-Ruíz AJ, Gómez-Julián MJ, Espinosa-Jimenez ML, Gallardo-Jiménez FD, Patenkovic A, Eric K, Tanaskovic M, Ullastres A, Guio L, Merenciano M, Guirao-Rico S, Horváth V, Obbard DJ, Pasyukova E, Alatortsev VE, Vieira CP, Vieira J, Torres JR, Kozeretska I, Maistrenko OM, Montchamp-Moreau C, Mukha DV, Machado HE, Lamb K, Paulo T, Yusuf L, Barbadilla A, Petrov D, Schmidt P, Gonzalez J, Flatt T, Bergland AO. Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource. Mol Biol Evol 2021; 38:5782-5805. [PMID: 34469576 PMCID: PMC8662648 DOI: 10.1093/molbev/msab259] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome data sets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate data sets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in >20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This data set, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental metadata. A web-based genome browser and web portal provide easy access to the SNP data set. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan data set. Our resource will enable population geneticists to analyze spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.
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Affiliation(s)
- Martin Kapun
- Department of Evolutionary Biology and Environmental Studies, University of
Zürich, Switzerland
- Department of Cell & Developmental Biology, Center of Anatomy and Cell
Biology, Medical University of Vienna, Vienna, Austria
| | - Joaquin C B Nunez
- Department of Biology, University of Virginia, Charlottesville,
VA, USA
| | | | - Jesús Murga-Moreno
- Department of Genetics and Microbiology, Universitat Autònoma de
Barcelona, Barcelona, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de
Barcelona, Barcelona, Spain
| | - Margot Paris
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Joseph Outten
- Department of Biology, University of Virginia, Charlottesville,
VA, USA
| | | | - Courtney Tern
- Department of Biology, University of Virginia, Charlottesville,
VA, USA
| | - Omar Rota-Stabelli
- Center Agriculture Food Environment, University of Trento, San Michele all'
Adige, Italy
| | | | - Sònia Casillas
- Department of Genetics and Microbiology, Universitat Autònoma de
Barcelona, Barcelona, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de
Barcelona, Barcelona, Spain
| | - Dorcas J Orengo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia,
Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de
Barcelona, Barcelona, Spain
| | - Eva Puerma
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia,
Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de
Barcelona, Barcelona, Spain
| | - Maaria Kankare
- Department of Biological and Environmental Science, University of
Jyväskylä, Jyväskylä, Finland
| | - Lino Ometto
- Department of Biology and Biotechnology, University of Pavia,
Pavia, Italy
| | | | - Banu S Onder
- Department of Biology, Hacettepe University, Ankara, Turkey
| | | | - Stephen W Schaeffer
- Department of Biology, The Pennsylvania State University,
University Park, PA, USA
| | - Subhash Rajpurohit
- Department of Biology, University of Pennsylvania, Philadelphia,
PA, USA
- Division of Biological and Life Sciences, School of Arts and Sciences,
Ahmedabad University, Ahmedabad, India
| | - Emily L Behrman
- Department of Biology, University of Pennsylvania, Philadelphia,
PA, USA
- Janelia Research Campus, Ashburn, VA, USA
| | - Mads F Schou
- Department of Biology, Aarhus University, Aarhus, Denmark
- Department of Biology, Lund University, Lund, Sweden
| | - Thomas J S Merritt
- Department of Chemistry & Biochemistry, Laurentian
University, Sudbury, ON, Canada
| | - Brian P Lazzaro
- Department of Entomology, Cornell University, Ithaca, NY,
USA
| | - Amanda Glaser-Schmitt
- Division of Evolutionary Biology, Faculty of Biology,
Ludwig-Maximilians-Universität, Munich, Germany
| | - Eliza Argyridou
- Division of Evolutionary Biology, Faculty of Biology,
Ludwig-Maximilians-Universität, Munich, Germany
| | - Fabian Staubach
- Department of Evolution and Ecology, University of Freiburg,
Freiburg, Germany
| | - Yun Wang
- Department of Evolution and Ecology, University of Freiburg,
Freiburg, Germany
| | - Eran Tauber
- Department of Evolutionary and Environmental Biology, Institute of Evolution,
University of Haifa, Haifa, Israel
| | - Svitlana V Serga
- Department of General and Medical Genetics, Taras Shevchenko National
University of Kyiv, Kyiv, Ukraine
- State Institution National Antarctic Scientific Center, Ministry of Education
and Science of Ukraine, Kyiv, Ukraine
| | - Daniel K Fabian
- Department of Genetics, University of Cambridge, Cambridge,
United Kingdom
| | - Kelly A Dyer
- Department of Genetics, University of Georgia, Athens, GA,
USA
| | | | - John Parsch
- Division of Evolutionary Biology, Faculty of Biology,
Ludwig-Maximilians-Universität, Munich, Germany
| | - Sonja Grath
- Division of Evolutionary Biology, Faculty of Biology,
Ludwig-Maximilians-Universität, Munich, Germany
| | | | | | - Mihailo Jelic
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | | | | | | | | | - Aleksandra Patenkovic
- Institute for Biological Research “Siniša Stanković”, National Institute of
Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Katarina Eric
- Institute for Biological Research “Siniša Stanković”, National Institute of
Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Marija Tanaskovic
- Institute for Biological Research “Siniša Stanković”, National Institute of
Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Anna Ullastres
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra,
Barcelona, Spain
| | - Lain Guio
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra,
Barcelona, Spain
| | - Miriam Merenciano
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra,
Barcelona, Spain
| | - Sara Guirao-Rico
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra,
Barcelona, Spain
| | - Vivien Horváth
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra,
Barcelona, Spain
| | - Darren J Obbard
- Institute of Evolutionary Biology, University of Edinburgh,
Edinburgh, United Kingdom
| | - Elena Pasyukova
- Institute of Molecular Genetics of the National Research Centre “Kurchatov
Institute”, Moscow, Russia
| | - Vladimir E Alatortsev
- Institute of Molecular Genetics of the National Research Centre “Kurchatov
Institute”, Moscow, Russia
| | - Cristina P Vieira
- Instituto de Biologia Molecular e Celular (IBMC), Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do
Porto, Porto, Portugal
| | - Jorge Vieira
- Instituto de Biologia Molecular e Celular (IBMC), Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do
Porto, Porto, Portugal
| | | | - Iryna Kozeretska
- Department of General and Medical Genetics, Taras Shevchenko National
University of Kyiv, Kyiv, Ukraine
- State Institution National Antarctic Scientific Center, Ministry of Education
and Science of Ukraine, Kyiv, Ukraine
| | - Oleksandr M Maistrenko
- Department of General and Medical Genetics, Taras Shevchenko National
University of Kyiv, Kyiv, Ukraine
- Structural and Computational Biology Unit, European Molecular Biology
Laboratory, Heidelberg, Germany
| | | | - Dmitry V Mukha
- Vavilov Institute of General Genetics, Russian Academy of
Sciences, Moscow, Russia
| | - Heather E Machado
- Department of Biology, Stanford University, Stanford, CA,
USA
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Keric Lamb
- Department of Biology, University of Virginia, Charlottesville,
VA, USA
| | - Tânia Paulo
- Departamento de Biologia Animal, Instituto Gulbenkian de Ciência,
Oeiras, Portugal
| | - Leeban Yusuf
- Center for Biological Diversity, University of St. Andrews, St
Andrews, United Kingdom
| | - Antonio Barbadilla
- Department of Genetics and Microbiology, Universitat Autònoma de
Barcelona, Barcelona, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de
Barcelona, Barcelona, Spain
| | - Dmitri Petrov
- Department of Biology, Stanford University, Stanford, CA,
USA
| | - Paul Schmidt
- Department of Biology, The Pennsylvania State University,
University Park, PA, USA
| | - Josefa Gonzalez
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra,
Barcelona, Spain
| | - Thomas Flatt
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Alan O Bergland
- Department of Biology, University of Virginia, Charlottesville,
VA, USA
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14
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Peng J, Svetec N, Zhao L. Intermolecular interactions drive protein adaptive and co-adaptive evolution at both species and population levels. Mol Biol Evol 2021; 39:6456312. [PMID: 34878126 PMCID: PMC8789070 DOI: 10.1093/molbev/msab350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Proteins are the building blocks for almost all the functions in cells. Understanding the molecular evolution of proteins and the forces that shape protein evolution is essential in understanding the basis of function and evolution. Previous studies have shown that adaptation frequently occurs at the protein surface, such as in genes involved in host–pathogen interactions. However, it remains unclear whether adaptive sites are distributed randomly or at regions associated with particular structural or functional characteristics across the genome, since many proteins lack structural or functional annotations. Here, we seek to tackle this question by combining large-scale bioinformatic prediction, structural analysis, phylogenetic inference, and population genomic analysis of Drosophila protein-coding genes. We found that protein sequence adaptation is more relevant to function-related rather than structure-related properties. Interestingly, intermolecular interactions contribute significantly to protein adaptation. We further showed that intermolecular interactions, such as physical interactions, may play a role in the coadaptation of fast-adaptive proteins. We found that strongly differentiated amino acids across geographic regions in protein-coding genes are mostly adaptive, which may contribute to the long-term adaptive evolution. This strongly indicates that a number of adaptive sites tend to be repeatedly mutated and selected throughout evolution in the past, present, and maybe future. Our results highlight the important roles of intermolecular interactions and coadaptation in the adaptive evolution of proteins both at the species and population levels.
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Affiliation(s)
- Junhui Peng
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA
| | - Nicolas Svetec
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA
| | - Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA
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15
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Kurogi Y, Mizuno Y, Imura E, Niwa R. Neuroendocrine Regulation of Reproductive Dormancy in the Fruit Fly Drosophila melanogaster: A Review of Juvenile Hormone-Dependent Regulation. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.715029] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Animals can adjust their physiology, helping them survive and reproduce under a wide range of environmental conditions. One of the strategies to endure unfavorable environmental conditions such as low temperature and limited food supplies is dormancy. In some insect species, this may manifest as reproductive dormancy, which causes their reproductive organs to be severely depleted under conditions unsuitable for reproduction. Reproductive dormancy in insects is induced by a reduction in juvenile hormones synthesized in the corpus allatum (pl. corpora allata; CA) in response to winter-specific environmental cues, such as low temperatures and short-day length. In recent years, significant progress has been made in the study of dormancy-inducing conditions dependent on CA control mechanisms in Drosophila melanogaster. This review summarizes dormancy control mechanisms in D. melanogaster and discusses the implications for future studies of insect dormancy, particularly focusing on juvenile hormone-dependent regulation.
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16
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Shahrestani P, King E, Ramezan R, Phillips M, Riddle M, Thornburg M, Greenspan Z, Estrella Y, Garcia K, Chowdhury P, Malarat G, Zhu M, Rottshaefer SM, Wraight S, Griggs M, Vandenberg J, Long AD, Clark AG, Lazzaro BP. The molecular architecture of Drosophila melanogaster defense against Beauveria bassiana explored through evolve and resequence and quantitative trait locus mapping. G3-GENES GENOMES GENETICS 2021; 11:6371870. [PMID: 34534291 PMCID: PMC8664422 DOI: 10.1093/g3journal/jkab324] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/17/2021] [Indexed: 12/02/2022]
Abstract
Little is known about the genetic architecture of antifungal immunity in natural populations. Using two population genetic approaches, quantitative trait locus (QTL) mapping and evolve and resequence (E&R), we explored D. melanogaster immune defense against infection with the fungus Beauveria bassiana. The immune defense was highly variable both in the recombinant inbred lines from the Drosophila Synthetic Population Resource used for our QTL mapping and in the synthetic outbred populations used in our E&R study. Survivorship of infection improved dramatically over just 10 generations in the E&R study, and continued to increase for an additional nine generations, revealing a trade-off with uninfected longevity. Populations selected for increased defense against B. bassiana evolved cross resistance to a second, distinct B. bassiana strain but not to bacterial pathogens. The QTL mapping study revealed that sexual dimorphism in defense depends on host genotype, and the E&R study indicated that sexual dimorphism also depends on the specific pathogen to which the host is exposed. Both the QTL mapping and E&R experiments generated lists of potentially causal candidate genes, although these lists were nonoverlapping.
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Affiliation(s)
- Parvin Shahrestani
- Department of Biological Science, California State University Fullerton, Fullerton CA, 92831, USA
| | - Elizabeth King
- Division of Biological Sciences, University of Missouri, Columbia MO, 65211, USA
| | - Reza Ramezan
- Department of Statistics and Actuarial Science, University of Waterloo, Waterloo ON, N2L 3G1, Canada
| | - Mark Phillips
- Department of Integrative Biology, Oregon State University, Corvallis OR, 97331, USA
| | - Melissa Riddle
- Department of Biological Science, California State University Fullerton, Fullerton CA, 92831, USA
| | - Marisa Thornburg
- Department of Biological Science, California State University Fullerton, Fullerton CA, 92831, USA
| | - Zachary Greenspan
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine CA, 92692, USA
| | | | - Kelly Garcia
- Department of Entomology, Cornell University, Ithaca NY, 14853, USA
| | - Pratik Chowdhury
- Department of Entomology, Cornell University, Ithaca NY, 14853, USA
| | - Glen Malarat
- Department of Entomology, Cornell University, Ithaca NY, 14853, USA
| | - Ming Zhu
- Department of Entomology, Cornell University, Ithaca NY, 14853, USA
| | | | - Stephen Wraight
- USDA ARS Emerging Pets and Pathogens Research Unit, Robert W. Holley Center for Agriculture & Health, Ithaca NY, 14853, USA
| | - Michael Griggs
- USDA ARS Emerging Pets and Pathogens Research Unit, Robert W. Holley Center for Agriculture & Health, Ithaca NY, 14853, USA
| | - John Vandenberg
- USDA ARS Emerging Pets and Pathogens Research Unit, Robert W. Holley Center for Agriculture & Health, Ithaca NY, 14853, USA
| | - Anthony D Long
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine CA, 92692, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca NY, 14853, USA
| | - Brian P Lazzaro
- Department of Entomology, Cornell University, Ithaca NY, 14853, USA
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17
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Voigt S, Kost L. Differences in temperature-sensitive expression of PcG-regulated genes among natural populations of Drosophila melanogaster. G3 (BETHESDA, MD.) 2021; 11:jkab237. [PMID: 34544136 PMCID: PMC8496320 DOI: 10.1093/g3journal/jkab237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/18/2021] [Indexed: 02/07/2023]
Abstract
Environmental temperature can affect chromatin-based gene regulation, in particular in ectotherms such as insects. Genes regulated by the Polycomb group (PcG) vary in their transcriptional output in response to changes in temperature. Expression of PcG-regulated genes typically increases with decreasing temperatures. Here, we examined variations in temperature-sensitive expression of PcG target genes in natural populations from different climates of Drosophila melanogaster, and differences thereof across different fly stages and tissues. Temperature-induced expression plasticity was found to be stage- and sex-specific with differences in the specificity between the examined PcG target genes. Some tissues and stages, however, showed a higher number of PcG target genes with temperature-sensitive expression than others. Overall, we found higher levels of temperature-induced expression plasticity in African tropical flies from the ancestral species range than in flies from temperate Europe. We also observed differences between temperate flies, however, with more reduction of expression plasticity in warm-temperate than in cold-temperate populations. Although in general, temperature-sensitive expression appeared to be detrimental in temperate climates, there were also cases in which plasticity was increased in temperate flies, as well as no changes in expression plasticity between flies from different climates.
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Affiliation(s)
- Susanne Voigt
- Applied Zoology, Faculty of Biology, Technische Universität Dresden, Dresden 01217, Germany
| | - Luise Kost
- Applied Zoology, Faculty of Biology, Technische Universität Dresden, Dresden 01217, Germany
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18
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Rodrigues MF, Vibranovski MD, Cogni R. Clinal and seasonal changes are correlated in Drosophila melanogaster natural populations. Evolution 2021; 75:2042-2054. [PMID: 34184262 DOI: 10.1111/evo.14300] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 06/08/2021] [Accepted: 06/14/2021] [Indexed: 12/22/2022]
Abstract
Spatial and seasonal variations in the environment are ubiquitous. Environmental heterogeneity can affect natural populations and lead to covariation between environment and allele frequencies. Drosophila melanogaster is known to harbor polymorphisms that change both with latitude and seasons. Identifying the role of selection in driving these changes is not trivial, because nonadaptive processes can cause similar patterns. Given the environment changes in similar ways across seasons and along the latitudinal gradient, one promising approach may be to look for parallelism between clinal and seasonal changes. Here, we test whether there is a genome-wide correlation between clinal and seasonal changes, and whether the pattern is consistent with selection. Allele frequency estimates were obtained from pooled samples from seven different locations along the east coast of the United States, and across seasons within Pennsylvania. We show that there is a genome-wide correlation between clinal and seasonal variations, which cannot be explained by linked selection alone. This pattern is stronger in genomic regions with higher functional content, consistent with natural selection. We derive a way to biologically interpret these correlations and show that around 3.7% of the common, autosomal variants could be under parallel seasonal and spatial selection. Our results highlight the contribution of natural selection in driving fluctuations in allele frequencies in natural fly populations and point to a shared genomic basis to climate adaptation that happens over space and time in D. melanogaster.
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Affiliation(s)
- Murillo F Rodrigues
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, 05508-090, Brazil.,Current Address: Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, 97403
| | - Maria D Vibranovski
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, 05508-090, Brazil
| | - Rodrigo Cogni
- Department of Ecology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, 05508-090, Brazil
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19
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Machado HE, Bergland AO, Taylor R, Tilk S, Behrman E, Dyer K, Fabian DK, Flatt T, González J, Karasov TL, Kim B, Kozeretska I, Lazzaro BP, Merritt TJS, Pool JE, O'Brien K, Rajpurohit S, Roy PR, Schaeffer SW, Serga S, Schmidt P, Petrov DA. Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation in Drosophila. eLife 2021; 10:e67577. [PMID: 34155971 PMCID: PMC8248982 DOI: 10.7554/elife.67577] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/21/2021] [Indexed: 11/16/2022] Open
Abstract
To advance our understanding of adaptation to temporally varying selection pressures, we identified signatures of seasonal adaptation occurring in parallel among Drosophila melanogaster populations. Specifically, we estimated allele frequencies genome-wide from flies sampled early and late in the growing season from 20 widely dispersed populations. We identified parallel seasonal allele frequency shifts across North America and Europe, demonstrating that seasonal adaptation is a general phenomenon of temperate fly populations. Seasonally fluctuating polymorphisms are enriched in large chromosomal inversions, and we find a broad concordance between seasonal and spatial allele frequency change. The direction of allele frequency change at seasonally variable polymorphisms can be predicted by weather conditions in the weeks prior to sampling, linking the environment and the genomic response to selection. Our results suggest that fluctuating selection is an important evolutionary force affecting patterns of genetic variation in Drosophila.
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Affiliation(s)
- Heather E Machado
- Department of Biology, Stanford UniversityStanfordUnited States
- Wellcome Sanger InstituteHinxtonUnited Kingdom
| | - Alan O Bergland
- Department of Biology, Stanford UniversityStanfordUnited States
- Department of Biology, University of VirginiaCharlottesvilleUnited States
| | - Ryan Taylor
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Susanne Tilk
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Emily Behrman
- Department of Biology, University of PennsylvaniaPhiladelphiaUnited States
| | - Kelly Dyer
- Department of Genetics, University of GeorgiaAthensUnited States
| | - Daniel K Fabian
- Institute of Population Genetics, Vetmeduni ViennaViennaAustria
- Centre for Pathogen Evolution, Department of Zoology, University of CambridgeCambridgeUnited Kingdom
| | - Thomas Flatt
- Institute of Population Genetics, Vetmeduni ViennaViennaAustria
- Department of Biology, University of FribourgFribourgSwitzerland
| | - Josefa González
- Institute of Evolutionary Biology, CSIC- Universitat Pompeu FabraBarcelonaSpain
| | - Talia L Karasov
- Department of Biology, University of UtahSalt Lake CityUnited States
| | - Bernard Kim
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Iryna Kozeretska
- Taras Shevchenko National University of KyivKyivUkraine
- National Antarctic Scientific Centre of Ukraine, Taras Shevchenko Blvd.KyivUkraine
| | - Brian P Lazzaro
- Department of Entomology, Cornell UniversityIthacaUnited States
| | - Thomas JS Merritt
- Department of Chemistry & Biochemistry, Laurentian UniversitySudburyCanada
| | - John E Pool
- Laboratory of Genetics, University of Wisconsin-MadisonMadisonUnited States
| | - Katherine O'Brien
- Department of Biology, University of PennsylvaniaPhiladelphiaUnited States
| | - Subhash Rajpurohit
- Department of Biology, University of PennsylvaniaPhiladelphiaUnited States
| | - Paula R Roy
- Department of Ecology and Evolutionary Biology, University of KansasLawrenceUnited States
| | - Stephen W Schaeffer
- Department of Biology, The Pennsylvania State UniversityUniversity ParkUnited States
| | - Svitlana Serga
- Taras Shevchenko National University of KyivKyivUkraine
- National Antarctic Scientific Centre of Ukraine, Taras Shevchenko Blvd.KyivUkraine
| | - Paul Schmidt
- Department of Biology, University of PennsylvaniaPhiladelphiaUnited States
| | - Dmitri A Petrov
- Department of Biology, Stanford UniversityStanfordUnited States
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20
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Wiberg RAW, Tyukmaeva V, Hoikkala A, Ritchie MG, Kankare M. Cold adaptation drives population genomic divergence in the ecological specialist, Drosophila montana. Mol Ecol 2021; 30:3783-3796. [PMID: 34047417 DOI: 10.1111/mec.16003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/10/2021] [Accepted: 05/20/2021] [Indexed: 12/18/2022]
Abstract
Detecting signatures of ecological adaptation in comparative genomics is challenging, but analysing population samples with characterised geographic distributions, such as clinal variation, can help identify genes showing covariation with important ecological variation. Here, we analysed patterns of geographic variation in the cold-adapted species Drosophila montana across phenotypes, genotypes and environmental conditions and tested for signatures of cold adaptation in population genomic divergence. We first derived the climatic variables associated with the geographic distribution of 24 populations across two continents to trace the scale of environmental variation experienced by the species, and measured variation in the cold tolerance of the flies of six populations from different geographic contexts. We then performed pooled whole genome sequencing of these six populations, and used Bayesian methods to identify SNPs where genetic differentiation is associated with both climatic variables and the population phenotypic measurements, while controlling for effects of demography and population structure. The top candidate SNPs were enriched on the X and fourth chromosomes, and they also lay near genes implicated in other studies of cold tolerance and population divergence in this species and its close relatives. We conclude that ecological adaptation has contributed to the divergence of D. montana populations throughout the genome and in particular on the X and fourth chromosomes, which also showed highest interpopulation FST . This study demonstrates that ecological selection can drive genomic divergence at different scales, from candidate genes to chromosome-wide effects.
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Affiliation(s)
- R A W Wiberg
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK
| | - V Tyukmaeva
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - A Hoikkala
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - M G Ritchie
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK
| | - M Kankare
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
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21
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Clark RD, Aardema ML, Andolfatto P, Barber PH, Hattori A, Hoey JA, Montes HR, Pinsky ML. Genomic signatures of spatially divergent selection at clownfish range margins. Proc Biol Sci 2021; 288:20210407. [PMID: 34102891 PMCID: PMC8187997 DOI: 10.1098/rspb.2021.0407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/11/2021] [Indexed: 01/25/2023] Open
Abstract
Understanding how evolutionary forces interact to drive patterns of selection and distribute genetic variation across a species' range is of great interest in ecology and evolution, especially in an era of global change. While theory predicts how and when populations at range margins are likely to undergo local adaptation, empirical evidence testing these models remains sparse. Here, we address this knowledge gap by investigating the relationship between selection, gene flow and genetic drift in the yellowtail clownfish, Amphiprion clarkii, from the core to the northern periphery of the species range. Analyses reveal low genetic diversity at the range edge, gene flow from the core to the edge and genomic signatures of local adaptation at 56 single nucleotide polymorphisms in 25 candidate genes, most of which are significantly correlated with minimum annual sea surface temperature. Several of these candidate genes play a role in functions that are upregulated during cold stress, including protein turnover, metabolism and translation. Our results illustrate how spatially divergent selection spanning the range core to the periphery can occur despite the potential for strong genetic drift at the range edge and moderate gene flow from the core populations.
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Affiliation(s)
- René D. Clark
- Department of Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901, USA
| | - Matthew L. Aardema
- Department of Biology, Montclair State University, 1 Normal Avenue, Montclair, NJ 07043, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, 200 Central Park West, New York, NY 10024-5102, USA
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, NY 10026, USA
| | - Paul H. Barber
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, CA 90095, USA
| | - Akihisa Hattori
- Faculty of Liberal Arts and Education, Shiga University, 2-5-1 Hiratsu, Otsu, Shiga 520-0862, Japan
| | - Jennifer A. Hoey
- Department of Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901, USA
- Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | | | - Malin L. Pinsky
- Department of Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901, USA
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22
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Betancourt NJ, Rajpurohit S, Durmaz E, Fabian DK, Kapun M, Flatt T, Schmidt P. Allelic polymorphism at foxo contributes to local adaptation in Drosophila melanogaster. Mol Ecol 2021; 30:2817-2830. [PMID: 33914989 PMCID: PMC8693798 DOI: 10.1111/mec.15939] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 04/13/2021] [Indexed: 01/09/2023]
Abstract
The insulin/insulin-like growth factor signalling pathway has been hypothesized as a major determinant of life-history profiles that vary adaptively in natural populations. In Drosophila melanogaster, multiple components of this pathway vary predictably with latitude; this includes foxo, a conserved gene that regulates insulin signalling and has pleiotropic effects on a variety of fitness-associated traits. We hypothesized that allelic variation at foxo contributes to genetic variance for size-related traits that vary adaptively with latitude. We first examined patterns of variation among natural populations along a latitudinal transect in the eastern United States and show that thorax length, wing area, wing loading, and starvation tolerance exhibit significant latitudinal clines for both males and females but that development time does not vary predictably with latitude. We then generated recombinant outbred populations and show that naturally occurring allelic variation at foxo, which exhibits stronger clinality than expected, is associated with the same traits that vary with latitude in the natural populations. Our results suggest that allelic variation at foxo contributes to adaptive patterns of life-history variation in natural populations of this genetic model.
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Affiliation(s)
| | - Subhash Rajpurohit
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
- Division of Biological and Life Sciences, Ahmedabad University, Ahmedabad, India
| | - Esra Durmaz
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Daniel K. Fabian
- Department of Genetics, University of Cambridge, Cambridge, UK
- European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Martin Kapun
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Thomas Flatt
- 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
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23
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Bourgeois YXC, Warren BH. An overview of current population genomics methods for the analysis of whole-genome resequencing data in eukaryotes. Mol Ecol 2021; 30:6036-6071. [PMID: 34009688 DOI: 10.1111/mec.15989] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/26/2021] [Accepted: 05/11/2021] [Indexed: 01/01/2023]
Abstract
Characterizing the population history of a species and identifying loci underlying local adaptation is crucial in functional ecology, evolutionary biology, conservation and agronomy. The constant improvement of high-throughput sequencing techniques has facilitated the production of whole genome data in a wide range of species. Population genomics now provides tools to better integrate selection into a historical framework, and take into account selection when reconstructing demographic history. However, this improvement has come with a profusion of analytical tools that can confuse and discourage users. Such confusion limits the amount of information effectively retrieved from complex genomic data sets, and impairs the diffusion of the most recent analytical tools into fields such as conservation biology. It may also lead to redundancy among methods. To address these isssues, we propose an overview of more than 100 state-of-the-art methods that can deal with whole genome data. We summarize the strategies they use to infer demographic history and selection, and discuss some of their limitations. A website listing these methods is available at www.methodspopgen.com.
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Affiliation(s)
| | - Ben H Warren
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, UA, CP 51, Paris, France
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24
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Huang Y, Lack JB, Hoppel GT, Pool JE. Parallel and Population-specific Gene Regulatory Evolution in Cold-Adapted Fly Populations. Genetics 2021; 218:6275754. [PMID: 33989401 PMCID: PMC8864734 DOI: 10.1093/genetics/iyab077] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 05/10/2021] [Indexed: 11/15/2022] Open
Abstract
Changes in gene regulation at multiple levels may comprise an important share of the molecular changes underlying adaptive evolution in nature. However, few studies have assayed within- and between-population variation in gene regulatory traits at a transcriptomic scale, and therefore inferences about the characteristics of adaptive regulatory changes have been elusive. Here, we assess quantitative trait differentiation in gene expression levels and alternative splicing (intron usage) between three closely related pairs of natural populations of Drosophila melanogaster from contrasting thermal environments that reflect three separate instances of cold tolerance evolution. The cold-adapted populations were known to show population genetic evidence for parallel evolution at the SNP level, and here we find evidence for parallel expression evolution between them, with stronger parallelism at larval and adult stages than for pupae. We also implement a flexible method to estimate cis- vs trans-encoded contributions to expression or splicing differences at the adult stage. The apparent contributions of cis- vs trans-regulation to adaptive evolution vary substantially among population pairs. While two of three population pairs show a greater enrichment of cis-regulatory differences among adaptation candidates, trans-regulatory differences are more likely to be implicated in parallel expression changes between population pairs. Genes with significant cis-effects are enriched for signals of elevated genetic differentiation between cold- and warm-adapted populations, suggesting that they are potential targets of local adaptation. These findings expand our knowledge of adaptive gene regulatory evolution and our ability to make inferences about this important and widespread process.
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Affiliation(s)
- Yuheng Huang
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.,Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Justin B Lack
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.,Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Grant T Hoppel
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - John E Pool
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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25
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Svedberg J, Shchur V, Reinman S, Nielsen R, Corbett-Detig R. Inferring Adaptive Introgression Using Hidden Markov Models. Mol Biol Evol 2021; 38:2152-2165. [PMID: 33502512 PMCID: PMC8097282 DOI: 10.1093/molbev/msab014] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Adaptive introgression-the flow of adaptive genetic variation between species or populations-has attracted significant interest in recent years and it has been implicated in a number of cases of adaptation, from pesticide resistance and immunity, to local adaptation. Despite this, methods for identification of adaptive introgression from population genomic data are lacking. Here, we present Ancestry_HMM-S, a hidden Markov model-based method for identifying genes undergoing adaptive introgression and quantifying the strength of selection acting on them. Through extensive validation, we show that this method performs well on moderately sized data sets for realistic population and selection parameters. We apply Ancestry_HMM-S to a data set of an admixed Drosophila melanogaster population from South Africa and we identify 17 loci which show signatures of adaptive introgression, four of which have previously been shown to confer resistance to insecticides. Ancestry_HMM-S provides a powerful method for inferring adaptive introgression in data sets that are typically collected when studying admixed populations. This method will enable powerful insights into the genetic consequences of admixture across diverse populations. Ancestry_HMM-S can be downloaded from https://github.com/jesvedberg/Ancestry_HMM-S/.
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Affiliation(s)
- Jesper Svedberg
- Department of Biomolecular Engineering, Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Vladimir Shchur
- National Research University Higher School of Economics, Moscow, Russian Federation
| | - Solomon Reinman
- Department of Biomolecular Engineering, Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Rasmus Nielsen
- National Research University Higher School of Economics, Moscow, Russian Federation
- Department of Integrative Biology and Department of Statistics, UC Berkeley, Berkeley, CA, USA
- Center for GeoGenetics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
- National Research University Higher School of Economics, Moscow, Russian Federation
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26
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Abstract
Plant pathogens can adapt to quantitative resistance, eroding its effectiveness. The aim of this work was to reveal the genomic basis of adaptation to such a resistance in populations of the fungus Pseudocercospora fijiensis, a major devastating pathogen of banana, by studying convergent adaptation on different cultivars. Samples from P. fijiensis populations showing a local adaptation pattern on new banana hybrids with quantitative resistance were compared, based on a genome scan approach, with samples from traditional and more susceptible cultivars in Cuba and the Dominican Republic. Whole-genome sequencing of pools of P. fijiensis isolates (pool-seq) sampled from three locations per country was conducted according to a paired population design. The findings of different combined analyses highly supported the existence of convergent adaptation on the study cultivars between locations within but not between countries. Five to six genomic regions involved in this adaptation were detected in each country. An annotation analysis and available biological data supported the hypothesis that some genes within the detected genomic regions may play a role in quantitative pathogenicity, including gene regulation. The results suggested that the genetic basis of fungal adaptation to quantitative plant resistance is at least oligogenic, while highlighting the existence of specific host-pathogen interactions for this kind of resistance.IMPORTANCE Understanding the genetic basis of pathogen adaptation to quantitative resistance in plants has a key role to play in establishing durable strategies for resistance deployment. In this context, a population genomic approach was developed for a major plant pathogen (the fungus Pseudocercospora fijiensis causing black leaf streak disease of banana) whereby samples from new resistant banana hybrids were compared with samples from more susceptible conventional cultivars in two countries. A total of 11 genomic regions for which there was strong evidence of selection by quantitative resistance were detected. An annotation analysis and available biological data supported the hypothesis that some of the genes within these regions may play a role in quantitative pathogenicity. These results suggested a polygenic basis of quantitative pathogenicity in this fungal pathogen and complex molecular plant-pathogen interactions in quantitative disease development involving several genes on both sides.
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27
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Bogaerts‐Márquez M, Guirao‐Rico S, Gautier M, González J. Temperature, rainfall and wind variables underlie environmental adaptation in natural populations of Drosophila melanogaster. Mol Ecol 2021; 30:938-954. [PMID: 33350518 PMCID: PMC7986194 DOI: 10.1111/mec.15783] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 02/06/2023]
Abstract
While several studies in a diverse set of species have shed light on the genes underlying adaptation, our knowledge on the selective pressures that explain the observed patterns lags behind. Drosophila melanogaster is a valuable organism to study environmental adaptation because this species originated in Southern Africa and has recently expanded worldwide, and also because it has a functionally well-annotated genome. In this study, we aimed to decipher which environmental variables are relevant for adaptation of D. melanogaster natural populations in Europe and North America. We analysed 36 whole-genome pool-seq samples of D. melanogaster natural populations collected in 20 European and 11 North American locations. We used the BayPass software to identify single nucleotide polymorphisms (SNPs) and transposable elements (TEs) showing signature of adaptive differentiation across populations, as well as significant associations with 59 environmental variables related to temperature, rainfall, evaporation, solar radiation, wind, daylight hours, and soil type. We found that in addition to temperature and rainfall, wind related variables are also relevant for D. melanogaster environmental adaptation. Interestingly, 23%-51% of the genes that showed significant associations with environmental variables were not found overly differentiated across populations. In addition to SNPs, we also identified 10 reference transposable element insertions associated with environmental variables. Our results showed that genome-environment association analysis can identify adaptive genetic variants that are undetected by population differentiation analysis while also allowing the identification of candidate environmental drivers of adaptation.
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Affiliation(s)
- María Bogaerts‐Márquez
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
- The European Drosophila Population Genomics Consortium (DrosEU)Université de MontpellierMontpellierFrance
| | - Sara Guirao‐Rico
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
- The European Drosophila Population Genomics Consortium (DrosEU)Université de MontpellierMontpellierFrance
| | - Mathieu Gautier
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgroUniversité de MontpellierMontpellierFrance
| | - Josefa González
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
- The European Drosophila Population Genomics Consortium (DrosEU)Université de MontpellierMontpellierFrance
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28
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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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29
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Sarikaya DP, Cridland J, Tarakji A, Sheehy H, Davis S, Kochummen A, Hatmaker R, Khan N, Chiu J, Begun DJ. Phenotypic coupling of sleep and starvation resistance evolves in D. melanogaster. BMC Evol Biol 2020; 20:126. [PMID: 32962630 PMCID: PMC7507639 DOI: 10.1186/s12862-020-01691-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/13/2020] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND One hypothesis for the function of sleep is that it serves as a mechanism to conserve energy. Recent studies have suggested that increased sleep can be an adaptive mechanism to improve survival under food deprivation in Drosophila melanogaster. To test the generality of this hypothesis, we compared sleep and its plastic response to starvation in a temperate and tropical population of Drosophila melanogaster. RESULTS We found that flies from the temperate population were more starvation resistant, and hypothesized that they would engage in behaviors that are considered to conserve energy, including increased sleep and reduced movement. Surprisingly, temperate flies slept less and moved more when they were awake compared to tropical flies, both under fed and starved conditions, therefore sleep did not correlate with population-level differences in starvation resistance. In contrast, total sleep and percent change in sleep when starved were strongly positively correlated with starvation resistance within the tropical population, but not within the temperate population. Thus, we observe unexpectedly complex relationships between starvation and sleep that vary both within and across populations. These observations falsify the simple hypothesis of a straightforward relationship between sleep and energy conservation. We also tested the hypothesis that starvation is correlated with metabolic phenotypes by investigating stored lipid and carbohydrate levels, and found that stored metabolites partially contributed towards variation starvation resistance. CONCLUSIONS Our findings demonstrate that the function of sleep under starvation can rapidly evolve on short timescales and raise new questions about the physiological correlates of sleep and the extent to which variation in sleep is shaped by natural selection.
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Affiliation(s)
- Didem P Sarikaya
- Department of Evolution and Ecology, University of California Davis, Davis, California, USA.
- Department of Molecular and Cellular Biology, University of California Davis, Davis, California, USA.
| | - Julie Cridland
- Department of Evolution and Ecology, University of California Davis, Davis, California, USA
| | - Adam Tarakji
- Department of Evolution and Ecology, University of California Davis, Davis, California, USA
| | - Hayley Sheehy
- Department of Evolution and Ecology, University of California Davis, Davis, California, USA
| | - Sophia Davis
- Department of Evolution and Ecology, University of California Davis, Davis, California, USA
| | - Ashley Kochummen
- Department of Evolution and Ecology, University of California Davis, Davis, California, USA
| | - Ryan Hatmaker
- Department of Evolution and Ecology, University of California Davis, Davis, California, USA
| | - Nossin Khan
- Department of Evolution and Ecology, University of California Davis, Davis, California, USA
| | - Joanna Chiu
- Department of Nematology and Entomology, University of California Davis, Davis, California, USA
| | - David J Begun
- Department of Evolution and Ecology, University of California Davis, Davis, California, USA
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30
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Kapun M, Barrón MG, Staubach F, Obbard DJ, Wiberg RAW, Vieira J, Goubert C, Rota-Stabelli O, Kankare M, Bogaerts-Márquez M, Haudry A, Waidele L, Kozeretska I, Pasyukova EG, Loeschcke V, Pascual M, Vieira CP, Serga S, Montchamp-Moreau C, Abbott J, Gibert P, Porcelli D, Posnien N, Sánchez-Gracia A, Grath S, Sucena É, Bergland AO, Guerreiro MPG, Onder BS, Argyridou E, Guio L, Schou MF, Deplancke B, Vieira C, Ritchie MG, Zwaan BJ, Tauber E, Orengo DJ, Puerma E, Aguadé M, Schmidt P, Parsch J, Betancourt AJ, Flatt T, González J. Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses. Mol Biol Evol 2020; 37:2661-2678. [PMID: 32413142 PMCID: PMC7475034 DOI: 10.1093/molbev/msaa120] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatiotemporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterize variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.
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Affiliation(s)
- Martin Kapun
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Department of Evolutionary Biology and Environmental Sciences, University of Zürich, Zürich, Switzerland
- Division of Cell and Developmental Biology, Medical University of Vienna, Vienna, Austria
| | - Maite G Barrón
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Fabian Staubach
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolutionary Biology and Ecology, University of Freiburg, Freiburg, Germany
| | - Darren J Obbard
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - R Axel W Wiberg
- The European Drosophila Population Genomics Consortium (DrosEU)
- Centre for Biological Diversity, School of Biology, University of St. Andrews, St Andrews, Scotland
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
| | - Jorge Vieira
- The European Drosophila Population Genomics Consortium (DrosEU)
- Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal
| | - Clément Goubert
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
| | - Omar Rota-Stabelli
- The European Drosophila Population Genomics Consortium (DrosEU)
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’ Adige, Italy
| | - Maaria Kankare
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - María Bogaerts-Márquez
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Annabelle Haudry
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
| | - Lena Waidele
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolutionary Biology and Ecology, University of Freiburg, Freiburg, Germany
| | - Iryna Kozeretska
- The European Drosophila Population Genomics Consortium (DrosEU)
- General and Medical Genetics Department, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
- State Institution National Antarctic Scientific Center of Ministry of Education and Science of Ukraine, Kyiv, Ukraine
| | - Elena G Pasyukova
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratory of Genome Variation, Institute of Molecular Genetics of RAS, Moscow, Russia
| | - Volker Loeschcke
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Bioscience—Genetics, Ecology and Evolution, Aarhus University, Aarhus C, Denmark
| | - Marta Pascual
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Cristina P Vieira
- The European Drosophila Population Genomics Consortium (DrosEU)
- Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal
| | - Svitlana Serga
- The European Drosophila Population Genomics Consortium (DrosEU)
- General and Medical Genetics Department, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Catherine Montchamp-Moreau
- The European Drosophila Population Genomics Consortium (DrosEU)
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France
| | - Jessica Abbott
- The European Drosophila Population Genomics Consortium (DrosEU)
- Section for Evolutionary Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Patricia Gibert
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
| | - Damiano Porcelli
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Animal and Plant Sciences, Sheffield, United Kingdom
| | - Nico Posnien
- The European Drosophila Population Genomics Consortium (DrosEU)
- Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Universität Göttingen, Göttingen, Germany
| | - Alejandro Sánchez-Gracia
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Sonja Grath
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Élio Sucena
- The European Drosophila Population Genomics Consortium (DrosEU)
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Alan O Bergland
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, University of Virginia, Charlottesville, VA
| | - Maria Pilar Garcia Guerreiro
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Banu Sebnem Onder
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, Faculty of Science, Hacettepe University, Ankara, Turkey
| | - Eliza Argyridou
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Lain Guio
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Mads Fristrup Schou
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Bioscience—Genetics, Ecology and Evolution, Aarhus University, Aarhus C, Denmark
- Section for Evolutionary Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Bart Deplancke
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Bio-engineering, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Cristina Vieira
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
| | - Michael G Ritchie
- The European Drosophila Population Genomics Consortium (DrosEU)
- Centre for Biological Diversity, School of Biology, University of St. Andrews, St Andrews, Scotland
| | - Bas J Zwaan
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratory of Genetics, Department of Plant Sciences, Wageningen University, Wageningen, Netherlands
| | - Eran Tauber
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Dorcas J Orengo
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Eva Puerma
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Montserrat Aguadé
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Paul Schmidt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, University of Pennsylvania, Philadelphia, PA
| | - John Parsch
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Andrea J Betancourt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolution, Ecology, and Behaviour, University of Liverpool, Liverpool, United Kingdom
| | - Thomas Flatt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Josefa González
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
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31
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Johri P, Charlesworth B, Jensen JD. Toward an Evolutionarily Appropriate Null Model: Jointly Inferring Demography and Purifying Selection. Genetics 2020; 215:173-192. [PMID: 32152045 PMCID: PMC7198275 DOI: 10.1534/genetics.119.303002] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/05/2020] [Indexed: 01/27/2023] Open
Abstract
The question of the relative evolutionary roles of adaptive and nonadaptive processes has been a central debate in population genetics for nearly a century. While advances have been made in the theoretical development of the underlying models, and statistical methods for estimating their parameters from large-scale genomic data, a framework for an appropriate null model remains elusive. A model incorporating evolutionary processes known to be in constant operation, genetic drift (as modulated by the demographic history of the population) and purifying selection, is lacking. Without such a null model, the role of adaptive processes in shaping within- and between-population variation may not be accurately assessed. Here, we investigate how population size changes and the strength of purifying selection affect patterns of variation at "neutral" sites near functional genomic components. We propose a novel statistical framework for jointly inferring the contribution of the relevant selective and demographic parameters. By means of extensive performance analyses, we quantify the utility of the approach, identify the most important statistics for parameter estimation, and compare the results with existing methods. Finally, we reanalyze genome-wide population-level data from a Zambian population of Drosophila melanogaster, and find that it has experienced a much slower rate of population growth than was inferred when the effects of purifying selection were neglected. Our approach represents an appropriate null model, against which the effects of positive selection can be assessed.
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Affiliation(s)
- Parul Johri
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287
| | - Brian Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, EH9 3FL, United Kingdom
| | - Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287
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32
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Walters AW, Hughes RC, Call TB, Walker CJ, Wilcox H, Petersen SC, Rudman SM, Newell PD, Douglas AE, Schmidt PS, Chaston JM. The microbiota influences the Drosophila melanogaster life history strategy. Mol Ecol 2020; 29:639-653. [PMID: 31863671 DOI: 10.1111/mec.15344] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 12/03/2019] [Accepted: 12/16/2019] [Indexed: 12/17/2022]
Abstract
Organisms are locally adapted when members of a population have a fitness advantage in one location relative to conspecifics in other geographies. For example, across latitudinal gradients, some organisms may trade off between traits that maximize fitness components in one, but not both, of somatic maintenance or reproductive output. Latitudinal gradients in life history strategies are traditionally attributed to environmental selection on an animal's genotype, without any consideration of the possible impact of associated microorganisms ("microbiota") on life history traits. Here, we show in Drosophila melanogaster, a key model for studying local adaptation and life history strategy, that excluding the microbiota from definitions of local adaptation is a major shortfall. First, we reveal that an isogenic fly line reared with different bacteria varies the investment in early reproduction versus somatic maintenance. Next, we show that in wild fruit flies, the abundance of these same bacteria was correlated with the latitude and life history strategy of the flies, suggesting geographic specificity of the microbiota composition. Variation in microbiota composition of locally adapted D. melanogaster could be attributed to both the wild environment and host genetic selection. Finally, by eliminating or manipulating the microbiota of fly lines collected across a latitudinal gradient, we reveal that host genotype contributes to latitude-specific life history traits independent of the microbiota and that variation in the microbiota can suppress or reverse the differences between locally adapted fly lines. Together, these findings establish the microbiota composition of a model animal as an essential consideration in local adaptation.
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Affiliation(s)
- Amber W Walters
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Rachel C Hughes
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Tanner B Call
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Carson J Walker
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Hailey Wilcox
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Samara C Petersen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Seth M Rudman
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Peter D Newell
- Department of Biological Sciences, SUNY Oswego, Oswego, NY, USA
| | - Angela E Douglas
- Department of Entomology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Paul S Schmidt
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - John M Chaston
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
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33
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Flatt T. Life-History Evolution and the Genetics of Fitness Components in Drosophila melanogaster. Genetics 2020; 214:3-48. [PMID: 31907300 PMCID: PMC6944413 DOI: 10.1534/genetics.119.300160] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/03/2019] [Indexed: 12/28/2022] Open
Abstract
Life-history traits or "fitness components"-such as age and size at maturity, fecundity and fertility, age-specific rates of survival, and life span-are the major phenotypic determinants of Darwinian fitness. Analyzing the evolution and genetics of these phenotypic targets of selection is central to our understanding of adaptation. Due to its simple and rapid life cycle, cosmopolitan distribution, ease of maintenance in the laboratory, well-understood evolutionary genetics, and its versatile genetic toolbox, the "vinegar fly" Drosophila melanogaster is one of the most powerful, experimentally tractable model systems for studying "life-history evolution." Here, I review what has been learned about the evolution and genetics of life-history variation in D. melanogaster by drawing on numerous sources spanning population and quantitative genetics, genomics, experimental evolution, evolutionary ecology, and physiology. This body of work has contributed greatly to our knowledge of several fundamental problems in evolutionary biology, including the amount and maintenance of genetic variation, the evolution of body size, clines and climate adaptation, the evolution of senescence, phenotypic plasticity, the nature of life-history trade-offs, and so forth. While major progress has been made, important facets of these and other questions remain open, and the D. melanogaster system will undoubtedly continue to deliver key insights into central issues of life-history evolution and the genetics of adaptation.
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Affiliation(s)
- Thomas Flatt
- Department of Biology, University of Fribourg, CH-1700, Switzerland
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34
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Accurate Allele Frequencies from Ultra-low Coverage Pool-Seq Samples in Evolve-and-Resequence Experiments. G3 (BETHESDA, MD.) 2019; 9:4159-4168. [PMID: 31636085 PMCID: PMC6893198 DOI: 10.1534/g3.119.400755] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Evolve-and-resequence (E+R) experiments leverage next-generation sequencing technology to track the allele frequency dynamics of populations as they evolve. While previous work has shown that adaptive alleles can be detected by comparing frequency trajectories from many replicate populations, this power comes at the expense of high-coverage (>100x) sequencing of many pooled samples, which can be cost-prohibitive. Here, we show that accurate estimates of allele frequencies can be achieved with very shallow sequencing depths (<5x) via inference of known founder haplotypes in small genomic windows. This technique can be used to efficiently estimate frequencies for any number of bi-allelic SNPs in populations of any model organism founded with sequenced homozygous strains. Using both experimentally-pooled and simulated samples of Drosophila melanogaster, we show that haplotype inference can improve allele frequency accuracy by orders of magnitude for up to 50 generations of recombination, and is robust to moderate levels of missing data, as well as different selection regimes. Finally, we show that a simple linear model generated from these simulations can predict the accuracy of haplotype-derived allele frequencies in other model organisms and experimental designs. To make these results broadly accessible for use in E+R experiments, we introduce HAF-pipe, an open-source software tool for calculating haplotype-derived allele frequencies from raw sequencing data. Ultimately, by reducing sequencing costs without sacrificing accuracy, our method facilitates E+R designs with higher replication and resolution, and thereby, increased power to detect adaptive alleles.
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Rudman SM, Greenblum S, Hughes RC, Rajpurohit S, Kiratli O, Lowder DB, Lemmon SG, Petrov DA, Chaston JM, Schmidt P. Microbiome composition shapes rapid genomic adaptation of Drosophila melanogaster. Proc Natl Acad Sci U S A 2019; 116:20025-20032. [PMID: 31527278 PMCID: PMC6778213 DOI: 10.1073/pnas.1907787116] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Population genomic data has revealed patterns of genetic variation associated with adaptation in many taxa. Yet understanding the adaptive process that drives such patterns is challenging; it requires disentangling the ecological agents of selection, determining the relevant timescales over which evolution occurs, and elucidating the genetic architecture of adaptation. Doing so for the adaptation of hosts to their microbiome is of particular interest with growing recognition of the importance and complexity of host-microbe interactions. Here, we track the pace and genomic architecture of adaptation to an experimental microbiome manipulation in replicate populations of Drosophila melanogaster in field mesocosms. Shifts in microbiome composition altered population dynamics and led to divergence between treatments in allele frequencies, with regions showing strong divergence found on all chromosomes. Moreover, at divergent loci previously associated with adaptation across natural populations, we found that the more common allele in fly populations experimentally enriched for a certain microbial group was also more common in natural populations with high relative abundance of that microbial group. These results suggest that microbiomes may be an agent of selection that shapes the pattern and process of adaptation and, more broadly, that variation in a single ecological factor within a complex environment can drive rapid, polygenic adaptation over short timescales.
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Affiliation(s)
- Seth M Rudman
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104;
| | | | - Rachel C Hughes
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602
| | - Subhash Rajpurohit
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Ozan Kiratli
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Dallin B Lowder
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602
| | - Skyler G Lemmon
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA 94305
| | - John M Chaston
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602
| | - Paul Schmidt
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
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36
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Durmaz E, Rajpurohit S, Betancourt N, Fabian DK, Kapun M, Schmidt P, Flatt T. A clinal polymorphism in the insulin signaling transcription factor foxo contributes to life-history adaptation in Drosophila. Evolution 2019; 73:1774-1792. [PMID: 31111462 PMCID: PMC6771989 DOI: 10.1111/evo.13759] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 05/04/2019] [Accepted: 05/06/2019] [Indexed: 12/11/2022]
Abstract
A fundamental aim of adaptation genomics is to identify polymorphisms that underpin variation in fitness traits. In Drosophila melanogaster, latitudinal life-history clines exist on multiple continents and make an excellent system for dissecting the genetics of adaptation. We have previously identified numerous clinal single-nucleotide polymorphism in insulin/insulin-like growth factor signaling (IIS), a pathway known from mutant studies to affect life history. However, the effects of natural variants in this pathway remain poorly understood. Here we investigate how two clinal alternative alleles at foxo, a transcriptional effector of IIS, affect fitness components (viability, size, starvation resistance, fat content). We assessed this polymorphism from the North American cline by reconstituting outbred populations, fixed for either the low- or high-latitude allele, from inbred DGRP lines. Because diet and temperature modulate IIS, we phenotyped alleles across two temperatures (18°C, 25°C) and two diets differing in sugar source and content. Consistent with clinal expectations, the high-latitude allele conferred larger body size and reduced wing loading. Alleles also differed in starvation resistance and expression of insulin-like receptor, a transcriptional target of FOXO. Allelic reaction norms were mostly parallel, with few GxE interactions. Together, our results suggest that variation in IIS makes a major contribution to clinal life-history adaptation.
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Affiliation(s)
- Esra Durmaz
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Department of BiologyUniversity of FribourgFribourgSwitzerland
| | - Subhash Rajpurohit
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPennsylvania19140
- Division of Biological and Life SciencesAhmedabad UniversityAhmedabadIndia
| | - Nicolas Betancourt
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPennsylvania19140
| | - Daniel K. Fabian
- European Molecular Biology LaboratoryEuropean Bioinformatics InstituteWellcome Genome Campus, HinxtonCambridgeUnited Kingdom
- Institut für PopulationsgenetikVetmeduni ViennaViennaAustria
- Vienna Graduate School of Population, GeneticsViennaAustria
| | - Martin Kapun
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Department of BiologyUniversity of FribourgFribourgSwitzerland
| | - Paul Schmidt
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPennsylvania19140
| | - Thomas Flatt
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Department of BiologyUniversity of FribourgFribourgSwitzerland
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37
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Hopper KR, Oppenheim SJ, Kuhn KL, Lanier K, Hoelmer KA, Heimpel GE, Meikle WG, O’Neil RJ, Voegtlin DG, Wu K, Woolley JB, Heraty JM. Counties not countries: Variation in host specificity among populations of an aphid parasitoid. Evol Appl 2019; 12:815-829. [PMID: 30976312 PMCID: PMC6439487 DOI: 10.1111/eva.12759] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/20/2018] [Accepted: 12/06/2018] [Indexed: 11/28/2022] Open
Abstract
Parasitic wasps are among the most species-rich groups on Earth. A major cause of this diversity may be local adaptation to host species. However, little is known about variation in host specificity among populations within parasitoid species. Not only is such knowledge important for understanding host-driven speciation, but because parasitoids often control pest insects and narrow host ranges are critical for the safety of biological control introductions, understanding variation in specificity and how it arises are crucial applications in evolutionary biology. Here, we report experiments on variation in host specificity among 16 populations of an aphid parasitoid, Aphelinus certus. We addressed several questions about local adaptation: Do parasitoid populations differ in host ranges or in levels of parasitism of aphid species within their host range? Are differences in parasitism among parasitoid populations related to geographical distance, suggesting clinal variation in abundances of aphid species? Or do nearby parasitoid populations differ in host use, as would be expected if differences in aphid abundances, and thus selection, were mosaic? Are differences in parasitism among parasitoid populations related to genetic distances among them? To answer these questions, we measured parasitism of a taxonomically diverse group of aphid species in laboratory experiments. Host range was the same for all the parasitoid populations, but levels of parasitism varied among aphid species, suggesting adaptation to locally abundant aphids. Differences in host specificity did not correlate with geographical distances among parasitoid populations, suggesting that local adaption is mosaic rather than clinal, with a spatial scale of less than 50 kilometers. We sequenced and assembled the genome of A. certus, made reduced-representation libraries for each population, analyzed for single nucleotide polymorphisms, and used these polymorphisms to estimate genetic differentiation among populations. Differences in host specificity correlated with genetic distances among the parasitoid populations.
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Affiliation(s)
- Keith R. Hopper
- Beneficial Insect Introductions Research UnitUSDA‐ARSNewarkDelaware
| | | | - Kristen L. Kuhn
- Beneficial Insect Introductions Research UnitUSDA‐ARSNewarkDelaware
| | - Kathryn Lanier
- Beneficial Insect Introductions Research UnitUSDA‐ARSNewarkDelaware
| | - Kim A. Hoelmer
- Beneficial Insect Introductions Research UnitUSDA‐ARSNewarkDelaware
| | | | - William G. Meikle
- European Biological Control LaboratoryUSDA‐ARSSt. Gely du Fesc CEDEXFrance
| | | | | | - Kongming Wu
- Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - James B. Woolley
- Department of EntomologyTexas A&M UniversityCollege StationTexas
| | - John M. Heraty
- Department of EntomologyUniversity of CaliforniaRiversideCalifornia
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38
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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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39
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Rech GE, Bogaerts-Márquez M, Barrón MG, Merenciano M, Villanueva-Cañas JL, Horváth V, Fiston-Lavier AS, Luyten I, Venkataram S, Quesneville H, Petrov DA, González J. Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila. PLoS Genet 2019; 15:e1007900. [PMID: 30753202 PMCID: PMC6372155 DOI: 10.1371/journal.pgen.1007900] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/16/2018] [Indexed: 11/30/2022] Open
Abstract
Most of the current knowledge on the genetic basis of adaptive evolution is based on the analysis of single nucleotide polymorphisms (SNPs). Despite increasing evidence for their causal role, the contribution of structural variants to adaptive evolution remains largely unexplored. In this work, we analyzed the population frequencies of 1,615 Transposable Element (TE) insertions annotated in the reference genome of Drosophila melanogaster, in 91 samples from 60 worldwide natural populations. We identified a set of 300 polymorphic TEs that are present at high population frequencies, and located in genomic regions with high recombination rate, where the efficiency of natural selection is high. The age and the length of these 300 TEs are consistent with relatively young and long insertions reaching high frequencies due to the action of positive selection. Besides, we identified a set of 21 fixed TEs also likely to be adaptive. Indeed, we, and others, found evidence of selection for 84 of these reference TE insertions. The analysis of the genes located nearby these 84 candidate adaptive insertions suggested that the functional response to selection is related with the GO categories of response to stimulus, behavior, and development. We further showed that a subset of the candidate adaptive TEs affects expression of nearby genes, and five of them have already been linked to an ecologically relevant phenotypic effect. Our results provide a more complete understanding of the genetic variation and the fitness-related traits relevant for adaptive evolution. Similar studies should help uncover the importance of TE-induced adaptive mutations in other species as well.
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Affiliation(s)
- Gabriel E. Rech
- Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - María Bogaerts-Márquez
- Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Maite G. Barrón
- Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Miriam Merenciano
- Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Vivien Horváth
- Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Anna-Sophie Fiston-Lavier
- Institut des Sciences de l'Evolution de Montpellier (UMR 5554, CNRS-UM-IRD-EPHE), Université de Montpellier, Place Eugène Bataillon, Montpellier, France
| | | | - Sandeep Venkataram
- Department of Biology, Stanford University, Stanford, CA, United States of America
| | | | - Dmitri A. Petrov
- Department of Biology, Stanford University, Stanford, CA, United States of America
| | - Josefa González
- Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
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40
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Guirao-Rico S, González J. Evolutionary insights from large scale resequencing datasets in Drosophila melanogaster. CURRENT OPINION IN INSECT SCIENCE 2019; 31:70-76. [PMID: 31109676 DOI: 10.1016/j.cois.2018.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/04/2018] [Accepted: 11/06/2018] [Indexed: 06/09/2023]
Abstract
Drosophila melanogaster has long been used as an evolutionary model system. Its small genome size, well-annotated genome, and ease of sampling, also makes it a choice species for genome resequencing studies. Hundreds of genomic samples from populations worldwide are available and are currently being used to tackle a wide range of evolutionary questions. In this review, we focused on three insights that have increased our understanding of the evolutionary history of this species, and that have implications for the study of evolutionary processes in other species as well. Because of technical limitations, most of the studies so far have focused on SNP variants. However, long-read sequencing techniques should allow us in the near future to include other type of genomic variants that also influence genome evolution.
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Affiliation(s)
- Sara Guirao-Rico
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Josefa González
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.
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41
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Behrman EL, Howick VM, Kapun M, Staubach F, Bergland AO, Petrov DA, Lazzaro BP, Schmidt PS. Rapid seasonal evolution in innate immunity of wild Drosophila melanogaster. Proc Biol Sci 2019; 285:rspb.2017.2599. [PMID: 29321302 DOI: 10.1098/rspb.2017.2599] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 12/05/2017] [Indexed: 12/12/2022] Open
Abstract
Understanding the rate of evolutionary change and the genetic architecture that facilitates rapid adaptation is a current challenge in evolutionary biology. Comparative studies show that genes with immune function are among the most rapidly evolving genes across a range of taxa. Here, we use immune defence in natural populations of Drosophila melanogaster to understand the rate of evolution in natural populations and the genetics underlying rapid change. We probed the immune system using the natural pathogens Enterococcus faecalis and Providencia rettgeri to measure post-infection survival and bacterial load of wild D. melanogaster populations collected across seasonal time along a latitudinal transect along eastern North America (Massachusetts, Pennsylvania and Virginia). There are pronounced and repeatable changes in the immune response over the approximately 10 generations between spring and autumn collections, with a significant but less distinct difference observed among geographical locations. Genes with known immune function are not enriched among alleles that cycle with seasonal time, but the immune function of a subset of seasonally cycling alleles in immune genes was tested using reconstructed outbred populations. We find that flies containing seasonal alleles in Thioester-containing protein 3 (Tep3) have different functional responses to infection and that epistatic interactions among seasonal Tep3 and Drosomycin-like 6 (Dro6) alleles underlie the immune phenotypes observed in natural populations. This rapid, cyclic response to seasonal environmental pressure broadens our understanding of the complex ecological and genetic interactions determining the evolution of immune defence in natural populations.
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Affiliation(s)
- Emily L Behrman
- Department of Biology, University of Pennsylvania, 433 S. University Ave., Philadelphia, PA 19104, USA
| | - Virginia M Howick
- Department of Entomology, Cornell University, 3125 Comstock Hall, Ithaca, NY 14853, USA
| | - Martin Kapun
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
| | - Fabian Staubach
- Department of Biology, Stanford University, 371 Serra St, Stanford, CA 94305-5020, USA.,Albert-Ludwigs University, Freiburg, Germany
| | - Alan O Bergland
- Department of Biology, Stanford University, 371 Serra St, Stanford, CA 94305-5020, USA.,Department of Biology, University of Virginia, 409 McCormic Rd, Charlottesville, VA 22904, USA
| | - Dmitri A Petrov
- Department of Biology, Stanford University, 371 Serra St, Stanford, CA 94305-5020, USA
| | - Brian P Lazzaro
- Department of Entomology, Cornell University, 3125 Comstock Hall, Ithaca, NY 14853, USA
| | - Paul S Schmidt
- Department of Biology, University of Pennsylvania, 433 S. University Ave., Philadelphia, PA 19104, USA
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42
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Adrion JR, Begun DJ, Hahn MW. Patterns of transposable element variation and clinality in
Drosophila. Mol Ecol 2019; 28:1523-1536. [DOI: 10.1111/mec.14961] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 11/14/2018] [Accepted: 11/15/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Jeffrey R. Adrion
- Department of Biology University of Oregon Eugene Oregon
- Department of Biology Indiana University Bloomington Indiana
| | - David J. Begun
- Department of Evolution and Ecology University of California Davis, Davis California
| | - Matthew W. Hahn
- Department of Biology Indiana University Bloomington Indiana
- Department of Computer Science Indiana University Bloomington Indiana
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43
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Functional Analysis of a Putative Target of Spatially Varying Selection in the Menin1 Gene of Drosophila melanogaster. G3-GENES GENOMES GENETICS 2019; 9:73-80. [PMID: 30404774 PMCID: PMC6325912 DOI: 10.1534/g3.118.200818] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
While significant effort has been devoted to investigating the potential influence of spatially varying selection on genomic variation, relatively little effort has been devoted to experimental analysis of putative variants or genes experiencing such selection. Previous population genetic work identified an amino acid polymorphism in the Mnn1 gene as one of the most strongly latitudinally differentiated SNPs in the genome of Drosophila melanogaster in the United States and Australia. Here we report the results of our transgenic analysis of this amino acid polymorphism. Genotypes carrying alternative Mnn1 alleles differed in multiple phenotypes in a direction generally consistent with phenotypic differences previously observed along latitudinal clines. These results support inferences from earlier population genomic work that this variant influences fitness, and support the idea that the alleles exhibiting clines may be likely to have pleiotropic effects that are correlated along the axes favored by natural selection.
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44
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Michalak P, Kang L, Schou MF, Garner HR, Loeschcke V. Genomic signatures of experimental adaptive radiation in Drosophila. Mol Ecol 2018; 28:600-614. [PMID: 30375065 DOI: 10.1111/mec.14917] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 10/03/2018] [Accepted: 10/17/2018] [Indexed: 12/12/2022]
Abstract
Abiotic environmental factors play a fundamental role in determining the distribution, abundance and adaptive diversification of species. Empowered by new technologies enabling rapid and increasingly accurate examination of genomic variation in populations, researchers may gain new insights into the genomic background of adaptive radiation and stress resistance. We investigated genomic variation across generations of large-scale experimental selection regimes originating from a single founder population of Drosophila melanogaster, diverging in response to ecologically relevant environmental stressors: heat shock, heat knock down, cold shock, desiccation and starvation. When compared to the founder population, and to parallel unselected controls, there were more than 100,000 single nucleotide polymorphisms (SNPs) displaying consistent allelic changes in response to selective pressures across generations. These SNPs were found in both coding and noncoding sequences, with the highest density in promoter regions, and involved a broad range of functionalities, including molecular chaperoning by heat-shock proteins. The SNP patterns were highly stressor-specific despite considerable variation among line replicates within each selection regime, as reflected by a principal component analysis, and co-occurred with selective sweep regions. Only ~15% of SNPs with putatively adaptive changes were shared by at least two selective regimes, while less than 1% of SNPs diverged in opposite directions. Divergent stressors driving evolution in the experimental system of adaptive radiation left distinct genomic signatures, most pronounced in starvation and heat-shock selection regimes.
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Affiliation(s)
- Pawel Michalak
- Edward Via College of Osteopathic Medicine, Blacksburg, Virginia.,One Health Research Center, Virginia-Maryland College of Veterinary Medicine, Blacksburg, Virginia.,Institute of Evolution, University of Haifa, Haifa, Israel
| | - Lin Kang
- Edward Via College of Osteopathic Medicine, Blacksburg, Virginia
| | - Mads F Schou
- Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Harold R Garner
- Edward Via College of Osteopathic Medicine, Blacksburg, Virginia.,The Gibbs Cancer Center and Research Institute, Spartanburg, SC, USA
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45
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Lasne C, Van Heerwaarden B, Sgrò CM, Connallon T. Quantifying the relative contributions of the X chromosome, autosomes, and mitochondrial genome to local adaptation. Evolution 2018; 73:262-277. [PMID: 30417348 DOI: 10.1111/evo.13647] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/29/2018] [Accepted: 11/01/2018] [Indexed: 12/20/2022]
Abstract
During local adaptation with gene flow, some regions of the genome are inherently more responsive to selection than others. Recent theory predicts that X-linked genes should disproportionately contribute to local adaptation relative to other genomic regions, yet this prediction remains to be tested. We carried out a multigeneration crossing scheme, using two cline-end populations of Drosophila melanogaster, to estimate the relative contributions of the X chromosome, autosomes, and mitochondrial genome to divergence in four traits involved in local adaptation (wing size, resistance to heat, desiccation, and starvation stresses). We found that the mitochondrial genome and autosomes contributed significantly to clinal divergence in three of the four traits. In contrast, the X made no significant contribution to divergence in these traits. Given the small size of the mitochondrial genome, our results indicate that it plays a surprisingly large role in clinal adaptation. In contrast, the X, which represents roughly 20% of the Drosophila genome, contributes negligibly-a pattern that conflicts with theoretical predictions. These patterns reinforce recent work implying a central role of mitochondria in climatic adaptation, and suggest that different genomic regions may play fundamentally different roles in processes of divergence with gene flow.
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Affiliation(s)
- Clementine Lasne
- School of Biological Sciences, Monash University, Clayton, Victoria, 3800, Australia
| | | | - Carla M Sgrò
- School of Biological Sciences, Monash University, Clayton, Victoria, 3800, Australia
| | - Tim Connallon
- School of Biological Sciences, Monash University, Clayton, Victoria, 3800, Australia
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46
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Structural Variants and Selective Sweep Foci Contribute to Insecticide Resistance in the Drosophila Genetic Reference Panel. G3-GENES GENOMES GENETICS 2018; 8:3489-3497. [PMID: 30190421 PMCID: PMC6222580 DOI: 10.1534/g3.118.200619] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Patterns of nucleotide polymorphism within populations of Drosophila melanogaster suggest that insecticides have been the selective agents driving the strongest recent bouts of positive selection. However, there is a need to explicitly link selective sweeps to the particular insecticide phenotypes that could plausibly account for the drastic selective responses that are observed in these non-target insects. Here, we screen the Drosophila Genetic Reference Panel with two common insecticides; malathion (an organophosphate) and permethrin (a pyrethroid). Genome-wide association studies map survival on malathion to two of the largest sweeps in the D. melanogaster genome; Ace and Cyp6g1. Malathion survivorship also correlates with lines which have high levels of Cyp12d1, Jheh1 and Jheh2 transcript abundance. Permethrin phenotypes map to the largest cluster of P450 genes in the Drosophila genome, however in contrast to a selective sweep driven by insecticide use, the derived allele seems to be associated with susceptibility. These results underscore previous findings that highlight the importance of structural variation to insecticide phenotypes: Cyp6g1 exhibits copy number variation and transposable element insertions, Cyp12d1 is tandemly duplicated, the Jheh loci are associated with a Bari1 transposable element insertion, and a Cyp6a17 deletion is associated with susceptibility.
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47
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Mateo L, Rech GE, González J. Genome-wide patterns of local adaptation in Western European Drosophila melanogaster natural populations. Sci Rep 2018; 8:16143. [PMID: 30385770 PMCID: PMC6212444 DOI: 10.1038/s41598-018-34267-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 10/12/2018] [Indexed: 12/21/2022] Open
Abstract
Signatures of spatially varying selection have been investigated both at the genomic and transcriptomic level in several organisms. In Drosophila melanogaster, the majority of these studies have analyzed North American and Australian populations, leading to the identification of several loci and traits under selection. However, several studies based mainly in North American populations showed evidence of admixture that likely contributed to the observed population differentiation patterns. Thus, disentangling demography from selection might be challenging when analyzing these populations. European populations could help identify loci under spatially varying selection provided that no recent admixture from African populations would have occurred. In this work, we individually sequence the genome of 42 European strains collected in populations from contrasting environments: Stockholm (Sweden) and Castellana Grotte (Southern Italy). We found low levels of population structure and no evidence of recent African admixture in these two populations. We thus look for patterns of spatially varying selection affecting individual genes and gene sets. Besides single nucleotide polymorphisms, we also investigated the role of transposable elements in local adaptation. We concluded that European populations are a good dataset to identify candidate loci under spatially varying selection. The analysis of the two populations sequenced in this work in the context of all the available D. melanogaster data allowed us to pinpoint genes and biological processes likely to be relevant for local adaptation. Identifying and analyzing populations with low levels of population structure and admixture should help to disentangle selective from non-selective forces underlying patterns of population differentiation in other species as well.
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Affiliation(s)
- Lidia Mateo
- Institute of Evolutionary Biology. CSIC-Universitat Pompeu Fabra. Passeig Maritim de la Barceloneta, 37-49. 08003, Barcelona, Spain
| | - Gabriel E Rech
- Institute of Evolutionary Biology. CSIC-Universitat Pompeu Fabra. Passeig Maritim de la Barceloneta, 37-49. 08003, Barcelona, Spain
| | - Josefa González
- Institute of Evolutionary Biology. CSIC-Universitat Pompeu Fabra. Passeig Maritim de la Barceloneta, 37-49. 08003, Barcelona, Spain.
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48
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Signor SA, New FN, Nuzhdin S. A Large Panel of Drosophila simulans Reveals an Abundance of Common Variants. Genome Biol Evol 2018; 10:189-206. [PMID: 29228179 PMCID: PMC5767965 DOI: 10.1093/gbe/evx262] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2017] [Indexed: 01/03/2023] Open
Abstract
The rapidly expanding availability of large NGS data sets provides an opportunity to investigate population genetics at an unprecedented scale. Drosophila simulans is the sister species of the model organism Drosophila melanogaster, and is often presumed to share similar demographic history. However, previous population genetic and ecological work suggests very different signatures of selection and demography. Here, we sequence a new panel of 170 inbred genotypes of a North American population of D. simulans, a valuable complement to the DGRP and other D. melanogaster panels. We find some unexpected signatures of demography, in the form of excess intermediate frequency polymorphisms. Simulations suggest that this is possibly due to a recent population contraction and selection. We examine the outliers in the D. simulans genome determined by a haplotype test to attempt to parse the contribution of demography and selection to the patterns observed in this population. Untangling the relative contribution of demography and selection to genomic patterns of variation is challenging, however, it is clear that although D. melanogaster was thought to share demographic history with D. simulans different forces are at work in shaping genomic variation in this population of D. simulans.
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Affiliation(s)
- Sarah A Signor
- Department of Molecular and Computational Biology, University of Southern California
| | - Felicia N New
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine
| | - Sergey Nuzhdin
- Department of Molecular and Computational Biology, University of Southern California
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49
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Lafuente E, Duneau D, Beldade P. Genetic basis of thermal plasticity variation in Drosophila melanogaster body size. PLoS Genet 2018; 14:e1007686. [PMID: 30256798 PMCID: PMC6175520 DOI: 10.1371/journal.pgen.1007686] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 10/08/2018] [Accepted: 09/10/2018] [Indexed: 11/18/2022] Open
Abstract
Body size is a quantitative trait that is closely associated to fitness and under the control of both genetic and environmental factors. While developmental plasticity for this and other traits is heritable and under selection, little is known about the genetic basis for variation in plasticity that can provide the raw material for its evolution. We quantified genetic variation for body size plasticity in Drosophila melanogaster by measuring thorax and abdomen length of females reared at two temperatures from a panel representing naturally segregating alleles, the Drosophila Genetic Reference Panel (DGRP). We found variation between genotypes for the levels and direction of thermal plasticity in size of both body parts. We then used a Genome-Wide Association Study (GWAS) approach to unravel the genetic basis of inter-genotype variation in body size plasticity, and used different approaches to validate selected QTLs and to explore potential pleiotropic effects. We found mostly “private QTLs”, with little overlap between the candidate loci underlying variation in plasticity for thorax versus abdomen size, for different properties of the plastic response, and for size versus size plasticity. We also found that the putative functions of plasticity QTLs were diverse and that alleles for higher plasticity were found at lower frequencies in the target population. Importantly, a number of our plasticity QTLs have been targets of selection in other populations. Our data sheds light onto the genetic basis of inter-genotype variation in size plasticity that is necessary for its evolution. Environmental conditions can influence development and lead to the production of phenotypes adjusted to the conditions adults will live in. This developmental plasticity, which can help organisms cope with environmental heterogeneity, is heritable and under selection. Its evolution will depend on available genetic variation. Using a panel of D. melanogaster flies representing naturally segregating alleles, we identified DNA sequence variants associated to variation in thermal plasticity for body size. We found that these variants correspond to a diverse set of functions and that their effects differ between body parts and properties of the thermal response. Our results shed new light onto the long discussed genes for plasticity.
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Affiliation(s)
- Elvira Lafuente
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- * E-mail: (EL); (PB)
| | - David Duneau
- UMR5174-CNRS, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, Toulouse, France
| | - Patrícia Beldade
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- UMR5174-CNRS, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, Toulouse, France
- * E-mail: (EL); (PB)
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50
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Yang Y, Edery I. Parallel clinal variation in the mid-day siesta of Drosophila melanogaster implicates continent-specific targets of natural selection. PLoS Genet 2018; 14:e1007612. [PMID: 30180162 PMCID: PMC6138418 DOI: 10.1371/journal.pgen.1007612] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 09/14/2018] [Accepted: 08/06/2018] [Indexed: 11/18/2022] Open
Abstract
Similar to many diurnal animals, Drosophila melanogaster exhibits a mid-day siesta that is more robust as ambient temperature rises, an adaptive response aimed at minimizing exposure to heat. Mid-day siesta levels are partly regulated by the thermosensitive splicing of a small intron (termed dmpi8) found in the 3’ untranslated region (UTR) of the circadian clock gene period (per). Using the well-studied D. melanogaster latitudinal cline along the eastern coast of Australia, we show that flies from temperate populations sleep less during the day compared to those from tropical regions. We identified combinations of four single nucleotide polymorphisms (SNPs) in the 3’ UTR of per that yield several different haplotypes. The two most abundant of these haplotypes exhibit a reciprocal tropical-temperate distribution in relative frequency. Intriguingly, transgenic flies with the major tropical isoform manifest increased daytime sleep and reduced dmpi8 splicing compared to those carrying the temperate variant. Our results strongly suggest that for a major portion of D. melanogaster in Australia, thermal adaptation of daily sleep behavior included spatially varying selection on ancestrally derived polymorphisms in the per 3’ UTR that differentially control dmpi8 splicing efficiency. Prior work showed that African flies from high altitudes manifest reduced mid-day siesta levels, indicative of parallel latitudinal and altitudinal adaptation across continents. However, geographical variation in per 3’ UTR haplotypes was not observed for African flies, providing a compelling case for inter-continental variation in factors targeted by natural selection in attaining a parallel adaptation. We propose that the ability to calibrate mid-day siesta levels to better match local temperature ranges is a key adaptation contributing to the successful colonization of D. melanogaster beyond its ancestral range in the lowlands of Sub-Saharan Africa. In warm climates many animals, including humans, exhibit a mid-day siesta, almost certainly a behavior meant to minimize the harm from prolonged exposure to the hot mid-day sun. But what about animals that adapted to cooler more temperate climates, might they have a less pronounced siesta? Indeed, we show that in the common fruit fly, Drosophila melanogaster, those from temperate regions in Australia exhibit less mid-day siesta compared to their tropical counterparts. Prior work showed that mid-day sleep levels are partially regulated by a ‘clock’ gene called period (per), which controls the timing of wake-sleep cycles in addition to other daily rhythms. We identified several DNA differences in the per gene that show geographical variation and contribute to the daytime sleep differences in flies from tropical and temperate regions via a mechanism that involves how well a temperature-sensitive intron in per is removed. A similar reduction in mid-day sleep was previously observed in African flies that adapted to the cooler temperatures found at high altitudes. Together, our findings provide a rare example where latitude and altitude lead to a similar behavioral adaptation to temperature. Moreover, the results suggest inter-continental differences in the evolutionary solutions used to attain the same thermal adaptation to cooler climates.
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Affiliation(s)
- Yong Yang
- Rutgers University, Center for Advanced Biotechnology and Medicine, New Jersey, United States of America
| | - Isaac Edery
- Rutgers University, Center for Advanced Biotechnology and Medicine, New Jersey, United States of America
- Department of Molecular Biology and Biochemistry, Rutgers University, Center for Advanced Biotechnology and Medicine, New Jersey, United States of America
- * E-mail:
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