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Gutiérrez-Guerrero YT, Phifer-Rixey M, Nachman MW. Across two continents: The genomic basis of environmental adaptation in house mice (Mus musculus domesticus) from the Americas. PLoS Genet 2024; 20:e1011036. [PMID: 38968323 PMCID: PMC11253941 DOI: 10.1371/journal.pgen.1011036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 07/17/2024] [Accepted: 06/10/2024] [Indexed: 07/07/2024] Open
Abstract
Replicated clines across environmental gradients can be strong evidence of adaptation. House mice (Mus musculus domesticus) were introduced to the Americas by European colonizers and are now widely distributed from Tierra del Fuego to Alaska. Multiple aspects of climate, such as temperature, vary predictably across latitude in the Americas. Past studies of North American populations across latitudinal gradients provided evidence of environmental adaptation in traits related to body size, metabolism, and behavior and identified candidate genes using selection scans. Here, we investigate genomic signals of environmental adaptation on a second continent, South America, and ask whether there is evidence of parallel adaptation across multiple latitudinal transects in the Americas. We first identified loci across the genome showing signatures of selection related to climatic variation in mice sampled across a latitudinal transect in South America, accounting for neutral population structure. Consistent with previous results, most candidate SNPs were in putatively regulatory regions. Genes that contained the most extreme outliers relate to traits such as body weight or size, metabolism, immunity, fat, eye function, and the cardiovascular system. We then compared these results with the results of analyses of published data from two transects in North America. While most candidate genes were unique to individual transects, we found significant overlap among candidate genes identified independently in the three transects. These genes are diverse, with functions relating to metabolism, immunity, cardiac function, and circadian rhythm, among others. We also found parallel shifts in allele frequency in candidate genes across latitudinal gradients. Finally, combining data from all three transects, we identified several genes associated with variation in body weight. Overall, our results provide strong evidence of shared responses to selection and identify genes that likely underlie recent environmental adaptation in house mice across North and South America.
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Affiliation(s)
- Yocelyn T. Gutiérrez-Guerrero
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
| | - Megan Phifer-Rixey
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Michael W. Nachman
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
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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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Padilla Perez DJ. Geographic and seasonal variation of the for gene reveal signatures of local adaptation in Drosophila melanogaster. J Evol Biol 2024; 37:201-211. [PMID: 38301664 DOI: 10.1093/jeb/voad018] [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: 07/03/2023] [Revised: 11/18/2023] [Accepted: 12/16/2023] [Indexed: 02/03/2024]
Abstract
In the early 1980s, the observation that Drosophila melanogaster larvae differed in their foraging behaviour laid the foundation for the work that would later lead to the discovery of the foraging gene (for) and its associated foraging phenotypes, rover and sitter. Since then, the molecular characterization of the for gene and our understanding of the mechanisms that maintain its phenotypic variants in the laboratory have progressed enormously. However, the significance and dynamics of such variation are yet to be investigated in nature. With the advent of next-generation sequencing, it is now possible to identify loci underlying the adaptation of populations in response to environmental variation. Here, I present the results of a genotype-environment association analysis that quantifies variation at the for gene among samples of D. melanogaster structured across space and time. These samples consist of published genomes of adult flies collected worldwide, and at least twice per site of collection (during spring and fall). Both an analysis of genetic differentiation based on Fst values and an analysis of population structure revealed an east-west gradient in allele frequency. This gradient may be the result of spatially varying selection driven by the seasonality of precipitation. These results support the hypothesis that different patterns of gene flow as expected under models of isolation by distance and potentially isolation by environment are driving genetic differentiation among populations. Overall, this study is essential for understanding the mechanisms underlying the evolution of foraging behaviour in D. melanogaster.
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Cheek RG, McLaughlin JF, Gamboa MP, Marshall CA, Johnson BM, Silver DB, Mauro AA, Ghalambor CK. A lack of genetic diversity and minimal adaptive evolutionary divergence in introduced Mysis shrimp after 50 years. Evol Appl 2024; 17:e13637. [PMID: 38283609 PMCID: PMC10818135 DOI: 10.1111/eva.13637] [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: 06/28/2023] [Revised: 11/17/2023] [Accepted: 12/07/2023] [Indexed: 01/30/2024] Open
Abstract
The successes of introduced populations in novel habitats often provide powerful examples of evolution and adaptation. In the 1950s, opossum shrimp (Mysis diluviana) individuals from Clearwater Lake in Minnesota, USA were transported and introduced to Twin Lakes in Colorado, USA by fisheries managers to supplement food sources for trout. Mysis were subsequently introduced from Twin Lakes into numerous lakes throughout Colorado. Because managers kept detailed records of the timing of the introductions, we had the opportunity to test for evolutionary divergence within a known time interval. Here, we used reduced representation genomic data to investigate patterns of genetic diversity, test for genetic divergence between populations, and for evidence of adaptive evolution within the introduced populations in Colorado. We found very low levels of genetic diversity across all populations, with evidence for some genetic divergence between the Minnesota source population and the introduced populations in Colorado. There was little differentiation among the Colorado populations, consistent with the known provenance of a single founding population, with the exception of the population from Gross Reservoir, Colorado. Demographic modeling suggests that at least one undocumented introduction from an unknown source population hybridized with the population in Gross Reservoir. Despite the overall low genetic diversity we observed, F ST outlier and environmental association analyses identified multiple loci exhibiting signatures of selection and adaptive variation related to elevation and lake depth. The success of introduced species is thought to be limited by genetic variation, but our results imply that populations with limited genetic variation can become established in a wide range of novel environments. From an applied perspective, the observed patterns of divergence between populations suggest that genetic analysis can be a useful forensic tool to determine likely sources of invasive species.
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Affiliation(s)
- Rebecca G. Cheek
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColoradoUSA
| | - Jessica F. McLaughlin
- Department of Environmental Science, Policy, and ManagementUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Maybellene P. Gamboa
- Department of Organismal Biology and EcologyColorado CollegeColorado SpringsColoradoUSA
| | - Craig A. Marshall
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
- Council on Science and TechnologyPrinceton UniversityPrincetonNew JerseyUSA
| | - Brett M. Johnson
- Department of Fish, Wildlife and Conservation BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Douglas B. Silver
- Department of Fish, Wildlife and Conservation BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Alexander A. Mauro
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColoradoUSA
- Department of Biology, Centre for Biodiversity Dynamics (CBD)Norwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Cameron K. Ghalambor
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColoradoUSA
- Department of Biology, Centre for Biodiversity Dynamics (CBD)Norwegian University of Science and Technology (NTNU)TrondheimNorway
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5
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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: 6] [Impact Index Per Article: 6.0] [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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6
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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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7
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McCulloch GA, Waters JM. Rapid adaptation in a fast-changing world: Emerging insights from insect genomics. GLOBAL CHANGE BIOLOGY 2023; 29:943-954. [PMID: 36333958 PMCID: PMC10100130 DOI: 10.1111/gcb.16512] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 10/07/2022] [Indexed: 05/31/2023]
Abstract
Many researchers have questioned the ability of biota to adapt to rapid anthropogenic environmental shifts. Here, we synthesize emerging genomic evidence for rapid insect evolution in response to human pressure. These new data reveal diverse genomic mechanisms (single locus, polygenic, structural shifts; introgression) underpinning rapid adaptive responses to a variety of anthropogenic selective pressures. While the effects of some human impacts (e.g. pollution; pesticides) have been previously documented, here we highlight startling new evidence for rapid evolutionary responses to additional anthropogenic processes such as deforestation. These recent findings indicate that diverse insect assemblages can indeed respond dynamically to major anthropogenic evolutionary challenges. Our synthesis also emphasizes the critical roles of genomic architecture, standing variation and gene flow in maintaining future adaptive potential. Broadly, it is clear that genomic approaches are essential for predicting, monitoring and responding to ongoing anthropogenic biodiversity shifts in a fast-changing world.
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8
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Chakraborty A, Walter GM, Monro K, Alves AN, Mirth CK, Sgrò CM. Within-population variation in body size plasticity in response to combined nutritional and thermal stress is partially independent from variation in development time. J Evol Biol 2023; 36:264-279. [PMID: 36208146 PMCID: PMC10092444 DOI: 10.1111/jeb.14099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 01/11/2023]
Abstract
Ongoing climate change has forced animals to face changing thermal and nutritional environments. Animals can adjust to such combinations of stressors via plasticity. Body size is a key trait influencing organismal fitness, and plasticity in this trait in response to nutritional and thermal conditions varies among genetically diverse, locally adapted populations. The standing genetic variation within a population can also influence the extent of body size plasticity. We generated near-isogenic lines from a newly collected population of Drosophila melanogaster at the mid-point of east coast Australia and assayed body size for all lines in combinations of thermal and nutritional stress. We found that isogenic lines showed distinct underlying patterns of body size plasticity in response to temperature and nutrition that were often different from the overall population response. We then tested whether plasticity in development time could explain, and therefore regulate, variation in body size to these combinations of environmental conditions. We selected five genotypes that showed the greatest variation in response to combined thermal and nutritional stress and assessed the correlation between response of developmental time and body size. While we found significant genetic variation in development time plasticity, it was a poor predictor of body size among genotypes. Our results therefore suggest that multiple developmental pathways could generate genetic variation in body size plasticity. Our study emphasizes the need to better understand genetic variation in plasticity within a population, which will help determine the potential for populations to adapt to ongoing environmental change.
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Affiliation(s)
| | - Greg M Walter
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Keyne Monro
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - André N Alves
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Christen K Mirth
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Carla M Sgrò
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
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9
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Green L, Coronado-Zamora M, Radío S, Rech GE, Salces-Ortiz J, González J. The genomic basis of copper tolerance in Drosophila is shaped by a complex interplay of regulatory and environmental factors. BMC Biol 2022; 20:275. [PMID: 36482348 PMCID: PMC9733279 DOI: 10.1186/s12915-022-01479-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 11/24/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Escalation in industrialization and anthropogenic activity have resulted in an increase of pollutants released into the environment. Of these pollutants, heavy metals such as copper are particularly concerning due to their bio-accumulative nature. Due to its highly heterogeneous distribution and its dual nature as an essential micronutrient and toxic element, the genetic basis of copper tolerance is likely shaped by a complex interplay of genetic and environmental factors. RESULTS In this study, we utilized the natural variation present in multiple populations of Drosophila melanogaster collected across Europe to screen for variation in copper tolerance. We found that latitude and the degree of urbanization at the collection sites, rather than any other combination of environmental factors, were linked to copper tolerance. While previously identified copper-related genes were not differentially expressed in tolerant vs. sensitive strains, genes involved in metabolism, reproduction, and protease induction contributed to the differential stress response. Additionally, the greatest transcriptomic and physiological responses to copper toxicity were seen in the midgut, where we found that preservation of gut acidity is strongly linked to greater tolerance. Finally, we identified transposable element insertions likely to play a role in copper stress response. CONCLUSIONS Overall, by combining genome-wide approaches with environmental association analysis, and functional analysis of candidate genes, our study provides a unique perspective on the genetic and environmental factors that shape copper tolerance in natural D. melanogaster populations and identifies new genes, transposable elements, and physiological traits involved in this complex phenotype.
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Affiliation(s)
- Llewellyn Green
- grid.5612.00000 0001 2172 2676Institute of Evolutionary Biology, CSIC, Universitat Pompeu Fabra, Barcelona, Spain
| | - Marta Coronado-Zamora
- grid.5612.00000 0001 2172 2676Institute of Evolutionary Biology, CSIC, Universitat Pompeu Fabra, Barcelona, Spain
| | - Santiago Radío
- grid.5612.00000 0001 2172 2676Institute of Evolutionary Biology, CSIC, Universitat Pompeu Fabra, Barcelona, Spain
| | - Gabriel E. Rech
- grid.5612.00000 0001 2172 2676Institute of Evolutionary Biology, CSIC, Universitat Pompeu Fabra, Barcelona, Spain
| | - Judit Salces-Ortiz
- grid.5612.00000 0001 2172 2676Institute of Evolutionary Biology, CSIC, Universitat Pompeu Fabra, Barcelona, Spain
| | - Josefa González
- grid.5612.00000 0001 2172 2676Institute of Evolutionary Biology, CSIC, Universitat Pompeu Fabra, Barcelona, Spain
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10
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Wang Z, Receveur JP, Pu J, Cong H, Richards C, Liang M, Chung H. Desiccation resistance differences in Drosophila species can be largely explained by variations in cuticular hydrocarbons. eLife 2022; 11:e80859. [PMID: 36473178 PMCID: PMC9757832 DOI: 10.7554/elife.80859] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
Maintaining water balance is a universal challenge for organisms living in terrestrial environments, especially for insects, which have essential roles in our ecosystem. Although the high surface area to volume ratio in insects makes them vulnerable to water loss, insects have evolved different levels of desiccation resistance to adapt to diverse environments. To withstand desiccation, insects use a lipid layer called cuticular hydrocarbons (CHCs) to reduce water evaporation from the body surface. It has long been hypothesized that the water-proofing capability of this CHC layer, which can confer different levels of desiccation resistance, depends on its chemical composition. However, it is unknown which CHC components are important contributors to desiccation resistance and how these components can determine differences in desiccation resistance. In this study, we used machine-learning algorithms, correlation analyses, and synthetic CHCs to investigate how different CHC components affect desiccation resistance in 50 Drosophila and related species. We showed that desiccation resistance differences across these species can be largely explained by variation in CHC composition. In particular, length variation in a subset of CHCs, the methyl-branched CHCs (mbCHCs), is a key determinant of desiccation resistance. There is also a significant correlation between the evolution of longer mbCHCs and higher desiccation resistance in these species. Given that CHCs are almost ubiquitous in insects, we suggest that evolutionary changes in insect CHC components can be a general mechanism for the evolution of desiccation resistance and adaptation to diverse and changing environments.
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Affiliation(s)
- Zinan Wang
- Department of Entomology, Michigan State UniversityEast LansingUnited States
- Ecology, Evolution, and Behavior Program, Michigan State UniversityEast LansingUnited States
| | - Joseph P Receveur
- Department of Entomology, Michigan State UniversityEast LansingUnited States
- Ecology, Evolution, and Behavior Program, Michigan State UniversityEast LansingUnited States
- Institute for Genome Sciences, University of MarylandBaltimoreUnited States
| | - Jian Pu
- Department of Entomology, Michigan State UniversityEast LansingUnited States
- College of Agriculture, Sichuan Agricultural UniversitySichuanChina
| | - Haosu Cong
- Department of Entomology, Michigan State UniversityEast LansingUnited States
| | - Cole Richards
- Department of Entomology, Michigan State UniversityEast LansingUnited States
| | - Muxuan Liang
- Department of Biostatistics, University of FloridaGainesvilleUnited States
| | - Henry Chung
- Department of Entomology, Michigan State UniversityEast LansingUnited States
- Ecology, Evolution, and Behavior Program, Michigan State UniversityEast LansingUnited States
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11
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Mayekar HV, Ramkumar DK, Garg D, Nair A, Khandelwal A, Joshi K, Rajpurohit S. Clinal variation as a tool to understand climate change. Front Physiol 2022; 13:880728. [PMID: 36304576 PMCID: PMC9593049 DOI: 10.3389/fphys.2022.880728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Clines are observable gradients that reflect continuous change in biological traits of species across geographical ranges. Clinal gradients could vary at geographic scales (latitude and altitude). Since clinal variations represent active genomic responses at the population level they (clines) provide an immense power to address questions related to climatic change. With the fast pace of climate change i.e. warming, populations are also likely to exhibit rapid responses; at both the phenotypic and genotypic levels. We seek to understand how clinal variation could be used to anticipate climatic responses using Drosophila, a pervasively used inter-disciplinary model system owing to its molecular repertoire. The genomic information coupled with the phenotypic variation greatly facilitates our understanding of the Drosophilidae response to climate change. We discuss traits associated with clinal variation at the phenotypic level as well as their underlying genetic regulators. Given prevailing climatic conditions and future projections for climate change, clines could emerge as monitoring tools to track the cross-talk between climatic variables and organisms.
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Affiliation(s)
| | | | | | | | | | | | - Subhash Rajpurohit
- Division of Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Ahmedabad, GJ, India
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12
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Carvalho C, Davis R, Connallon T, Gleadow RM, Moore JL, Uesugi A. Multivariate selection mediated by aridity predicts divergence of drought-resistant traits along natural aridity gradients of an invasive weed. THE NEW PHYTOLOGIST 2022; 234:1088-1100. [PMID: 35118675 PMCID: PMC9311224 DOI: 10.1111/nph.18018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
Geographical variation in the environment underpins selection for local adaptation and evolutionary divergence among populations. Because many environmental conditions vary across species' ranges, identifying the specific environmental variables underlying local adaptation is profoundly challenging. We tested whether natural selection mediated by aridity predicts clinal divergence among invasive populations of capeweed (Arctotheca calendula) that established and spread across southern Australia during the last two centuries. Using common garden experiments with two environmental treatments (wet and dry) that mimic aridity conditions across capeweed's invasive range, we estimated clinal divergence and effects of aridity on fitness and multivariate phenotypic selection in populations sampled along aridity gradients in Australia. We show that: (1) capeweed populations have relatively high fitness in aridity environments similar to their sampling locations; (2) the magnitude and direction of selection strongly differs between wet and dry treatments, with drought stress increasing the strength of selection; and (3) differences in directional selection between wet and dry treatments predict patterns of clinal divergence across the aridity gradient, particularly for traits affecting biomass, flowering phenology and putative antioxidant expression. Our results suggest that aridity-mediated selection contributes to trait diversification among invasive capeweed populations, possibly facilitating the expansion of capeweed across southern Australia.
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Affiliation(s)
- Carter Carvalho
- School of Biological SciencesMonash UniversityClaytonVic.3800Australia
| | - Rochelle Davis
- School of Biological SciencesMonash UniversityClaytonVic.3800Australia
| | - Tim Connallon
- School of Biological SciencesMonash UniversityClaytonVic.3800Australia
| | - Roslyn M. Gleadow
- School of Biological SciencesMonash UniversityClaytonVic.3800Australia
| | - Joslin L. Moore
- School of Biological SciencesMonash UniversityClaytonVic.3800Australia
| | - Akane Uesugi
- School of Biological SciencesMonash UniversityClaytonVic.3800Australia
- Biosciences and Food Technology DivisionSchool of ScienceRMIT UniversityBundooraVic.3083Australia
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13
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Gu X, Ross PA, Rodriguez-Andres J, Robinson KL, Yang Q, Lau MJ, Hoffmann AA. A wMel Wolbachia variant in Aedes aegypti from field-collected Drosophila melanogaster with increased phenotypic stability under heat stress. Environ Microbiol 2022; 24:2119-2135. [PMID: 35319146 PMCID: PMC9544352 DOI: 10.1111/1462-2920.15966] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/15/2022] [Accepted: 03/02/2022] [Indexed: 02/03/2023]
Abstract
Mosquito‐borne diseases remain a major cause of morbidity and mortality. Population replacement strategies involving the wMel strain of Wolbachia are being used widely to control mosquito‐borne diseases. However, these strategies may be influenced by temperature because wMel is vulnerable to heat. wMel infections in Drosophila melanogaster are genetically diverse, but few transinfections of wMel variants have been generated in Aedes aegypti. Here, we successfully transferred a wMel variant (termed wMelM) originating from a field‐collected D. melanogaster into Ae. aegypti. The new wMelM variant (clade I) is genetically distinct from the original wMel transinfection (clade III), and there are no genomic differences between wMelM in its original and transinfected host. We compared wMelM with wMel in its effects on host fitness, temperature tolerance, Wolbachia density, vector competence, cytoplasmic incompatibility and maternal transmission under heat stress in a controlled background. wMelM showed a higher heat tolerance than wMel, likely due to higher overall densities within the mosquito. Both wMel variants had minimal host fitness costs, complete cytoplasmic incompatibility and maternal transmission, and dengue virus blocking under laboratory conditions. Our results highlight phenotypic differences between Wolbachia variants and wMelM shows potential as an alternative strain in areas with strong seasonal temperature fluctuations.
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Affiliation(s)
- Xinyue Gu
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, Vic, Australia
| | - Perran A Ross
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, Vic, Australia
| | - Julio Rodriguez-Andres
- Peter Doherty Institute for Infection and Immunity and Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Vic, 3000, Australia
| | - Katie L Robinson
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, Vic, Australia
| | - Qiong Yang
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, Vic, Australia
| | - Meng-Jia Lau
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, Vic, Australia
| | - Ary A Hoffmann
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, Vic, Australia
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14
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Abstract
Selection in fruit flies leads to fast adaption to seasonal changes.
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Affiliation(s)
- Ary H Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Melbourne, Australia
| | - Thomas Flatt
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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15
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On the Trail of Spatial Patterns of Genetic Variation. Evol Biol 2021. [DOI: 10.1007/s11692-021-09552-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractThe accurate determination of the spatial trends on the variability of a species’ gene pool is essential to elucidate the underlying demographic-evolutionary events, thus helping to unravel the microevolutionary history of the population under study. Herein we present a new software called GenoCline, mainly addressed to detect genetic clines from allele, haplotype, and genome-wide data. This program package allows identifying the geographic orientation of clinal genetic variation through a system of iterative rotation of a virtual coordinate axis. Besides, GenoCline can perform complementary analyses to explore the potential origin of the genetic clines observed, including spatial autocorrelation, isolation by distance, centroid method, multidimensional scaling and Sammon projection. Among the advantages of this software is the ease in data entry and potential interconnection with other programs. Genetic and geographic data can be entered in spreadsheet table formatting (.xls), whereas genome-wide data can be imported in Eigensoft format. Genetic frequencies can also be exported in a format compatible with other programs dealing with population genetic and evolutionary biology analyses. All illustrations of results are saved in.svg format so that there will be high quality and easily editable vectorial graphs available for the researcher. Being implemented in Java, GenoCline is highly portable, thus working in different operating systems.
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16
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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: 6] [Impact Index Per Article: 2.0] [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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17
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Parkash R, Lambhod C, Pathak A. Developmental and adult acclimation impact cold and drought survival of invasive tropical Drosophila kikkawai. Biol Open 2021; 10:269022. [PMID: 34100898 PMCID: PMC8214421 DOI: 10.1242/bio.058527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 05/04/2021] [Indexed: 11/20/2022] Open
Abstract
Narrow distribution patterns of tropical Drosophila species are limited by lower resistance to cold or drought. In the invasive tropical Drosophila kikkawai, we tested whether developmental and adult acclimations at cooler temperatures could enhance its stress resistance level. Adult acclimation of winter collected body color morphs revealed a significant increase in the level of cold resistance. For light morph, its abundance during winter is not consistent with thermal-melanism hypothesis. However, higher cold acclimation capacity, as well as storage of energy metabolites could support its winter survival. In the wild-caught light and intermediate morphs, there is a lack of trade-off between cold and heat resistance but not in the case of dark morph. Developmental plasticity (15°C) resulted in the fivefold increase of cold survival at 0°C; and a twofold increase in desiccation resistance but a modest reduction (∼28–35%) in heat resistance as compared to morph strains reared at 25°C. Drought acclimation changes were significantly higher as compared with cold or heat pretreatment. We observed a trade-off between basal resistance and acclimation capacity for cold, heat, or drought resistance. For homeostatic energy balance, adult acclimation responses (cold versus drought; heat versus drought) caused compensatory plastic changes in the levels of proline or trehalose (shared patterns) but different patterns for total body lipids. In contrast, rapid cold or heat hardening-induced changes in energy metabolites were different as compared to acclimation. The ability of D. kikkawai to significantly increase stress tolerance through plasticity is likely to support its invasion potential. Summary: In body color morphs of tropical Drosophila kikkawai, plasticity induced a higher level of resistance to cold and drought as well as three energy metabolites, which are likely to support its invasive potential.
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Affiliation(s)
- Ravi Parkash
- Department of Genetics, Maharshi Dayanand University, Rohtak 124001, India
| | | | - Ankita Pathak
- Department of Genetics, Maharshi Dayanand University, Rohtak 124001, India
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18
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Yue L, Cao LJ, Chen JC, Gong YJ, Lin YH, Hoffmann AA, Wei SJ. Low levels of genetic differentiation with isolation by geography and environment in populations of Drosophila melanogaster from across China. Heredity (Edinb) 2021; 126:942-954. [PMID: 33686193 PMCID: PMC8178374 DOI: 10.1038/s41437-021-00419-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 01/31/2023] Open
Abstract
The fruit fly, Drosophila melanogaster, is a model species in evolutionary studies. However, population processes of this species in East Asia are poorly studied. Here we examined the population genetic structure of D. melanogaster across China. There were 14 mitochondrial haplotypes with 10 unique ones out of 23 known from around the globe. Pairwise FST values estimated from 15 novel microsatellites ranged from 0 to 0.11, with geographically isolated populations showing the highest level of genetic uniqueness. STRUCTURE analysis identified high levels of admixture at both the individual and population levels. Mantel tests indicated a strong association between genetic distance and geographical distance as well as environmental distance. Full redundancy analysis (RDA) showed that independent effects of environmental conditions and geography accounted for 62.10% and 31.58% of the total explained genetic variance, respectively. When geographic variables were constrained in a partial RDA analysis, the environmental variables bio2 (mean diurnal air temperature range), bio13 (precipitation of the wettest month), and bio15 (precipitation seasonality) were correlated with genetic distance. Our study suggests that demographic history, geographical isolation, and environmental factors have together shaped the population genetic structure of D. melanogaster after its introduction into China.
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Affiliation(s)
- Lei Yue
- grid.418260.90000 0004 0646 9053Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Li-Jun Cao
- grid.418260.90000 0004 0646 9053Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jin-Cui Chen
- grid.418260.90000 0004 0646 9053Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ya-Jun Gong
- grid.418260.90000 0004 0646 9053Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yan-Hao Lin
- grid.418260.90000 0004 0646 9053Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China ,International Department of Beijing No. 80 High School, Beijing, China
| | - Ary Anthony Hoffmann
- grid.1008.90000 0001 2179 088XBio21 Institute, School of BioSciences, The University of Melbourne, Victoria, Australia
| | - Shu-Jun Wei
- grid.418260.90000 0004 0646 9053Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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19
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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: 10] [Impact Index Per Article: 3.3] [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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20
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Bong LJ, Wang CY, Shiodera S, Haraguchi TF, Itoh M, Neoh KB. Effect of body lipid content is linked to nutritional adaptation in the acclimation responses of mesic-adapted Paederus to seasonal variations in desiccation stress. JOURNAL OF INSECT PHYSIOLOGY 2021; 131:104226. [PMID: 33736982 DOI: 10.1016/j.jinsphys.2021.104226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 03/11/2021] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
Desiccation stress causes mesic-adapted arthropods to lose their body water content. However, mesic-adapted Paederus beetles can survive over prolonged periods under dry field conditions, suggesting that these beetles adopt an array of water conservation mechanisms. We investigated the water balance mechanisms of field-collected Paederus adults over a 14-month sampling period. We also assessed their nutritional adaptations by performing a stable isotope analysis to examine their diet. The water loss rate (WLR) of the beetles was significantly associated with the rice crop cycle and saturation deficit. The cuticular permeability (CP) of adult beetles was maintained at < 30 µg cm-2h-1 mmHg-1; however, CP increased significantly with the WLR. This result indicates that CP might play a minor role in reducing excessive water loss in beetles. The beetles' body water content and percentage total body water content increased when the WLR was high. Trehalose, glucose, and glycogen did not appear to play a central role in enhancing the water reserves in the insects. The body lipid content ranged from 0.22 ± 0.06 to 0.87 ± 0.07 mg and was negatively associated with the WLR. This association indicates that the increase in internal metabolic water was mediated by lipid catabolism. Stable isotope analysis results revealed that the Paederus beetles shifted their diet to carbohydrate-rich plants when the saturation deficit increased and the associated WLR reached its peak; otherwise, they consumed a high amount of staple carbohydrate-poor herbivore prey. The accumulation of energy reserves in the form of lipids through seasonal dietary shifts may exert major effects on the survival and population success of mesic-adapted Paederus beetles.
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Affiliation(s)
- Lee-Jin Bong
- Department of Entomology, National Chung Hsing University, 145, Xingda Rd. South District, Taichung 402, Taiwan
| | - Chia-Yu Wang
- Department of Entomology, National Chung Hsing University, 145, Xingda Rd. South District, Taichung 402, Taiwan
| | - Satomi Shiodera
- Research Institute for Humanity and Nature, 457-4, Motoyama, Kamigamo, Kyoto 603-8047, Japan; Center for Southeast Asian Studies, Kyoto University, 46 Shimoadachi-cho, Yoshida Sakyo-ku, Kyoto 606-8501, Japan
| | - Takashi F Haraguchi
- Biodiversity Research Center, Research Institute of Environment, Agriculture and Fisheries, Osaka Prefecture, 10-4 Koyamotomachi, Neyagawa, Osaka 572-0088, Japan
| | - Masayuki Itoh
- School of Human Science and Environment, University of Hyogo, 1-1-12 Shin-zaike, Himeji, Hyogo, 670-0092, Japan
| | - Kok-Boon Neoh
- Department of Entomology, National Chung Hsing University, 145, Xingda Rd. South District, Taichung 402, Taiwan.
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21
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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: 10] [Impact Index Per Article: 3.3] [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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22
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Climate stress resistance in male Queensland fruit fly varies among populations of diverse geographic origins and changes during domestication. BMC Genet 2020; 21:135. [PMID: 33339509 PMCID: PMC7747409 DOI: 10.1186/s12863-020-00935-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background The highly polyphagous Queensland fruit fly (Bactrocera tryoni Froggatt) expanded its range substantially during the twentieth century and is now the most economically important insect pest of Australian horticulture, prompting intensive efforts to develop a Sterile Insect Technique (SIT) control program. Using a “common garden” approach, we have screened for natural genetic variation in key environmental fitness traits among populations from across the geographic range of this species and monitored changes in those traits induced during domestication. Results Significant variation was detected between the populations for heat, desiccation and starvation resistance and wing length (as a measure of body size). Desiccation resistance was correlated with both starvation resistance and wing length. Bioassay data for three resampled populations indicate that much of the variation in desiccation resistance reflects persistent, inherited differences among the populations. No latitudinal cline was detected for any of the traits and only weak correlations were found with climatic variables for heat resistance and wing length. All three stress resistance phenotypes and wing length changed significantly in certain populations with ongoing domestication but there was also a strong population by domestication interaction effect for each trait. Conclusions Ecotypic variation in heat, starvation and desiccation resistance was detected in Australian Qfly populations, and these stress resistances diminished rapidly during domestication. Our results indicate a need to select source populations for SIT strains which have relatively high climatic stress resistance and to minimise loss of that resistance during domestication.
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23
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Mallard F, Nolte V, Schlötterer C. The Evolution of Phenotypic Plasticity in Response to Temperature Stress. Genome Biol Evol 2020; 12:2429-2440. [PMID: 33022043 PMCID: PMC7846148 DOI: 10.1093/gbe/evaa206] [Citation(s) in RCA: 16] [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] [Accepted: 09/29/2020] [Indexed: 12/23/2022] Open
Abstract
Phenotypic plasticity is the ability of a single genotype to produce different phenotypes in response to environmental variation. The importance of phenotypic plasticity in natural populations and its contribution to phenotypic evolution during rapid environmental change is widely debated. Here, we show that thermal plasticity of gene expression in natural populations is a key component of its adaptation: evolution to novel thermal environments increases ancestral plasticity rather than mean genetic expression. We determined the evolution of plasticity in gene expression by conducting laboratory natural selection on a Drosophila simulans population in hot and cold environments. After more than 60 generations in the hot environment, 325 genes evolved a change in plasticity relative to the natural ancestral population. Plasticity increased in 75% of these genes, which were strongly enriched for several well-defined functional categories (e.g., chitin metabolism, glycolysis, and oxidative phosphorylation). Furthermore, we show that plasticity in gene expression of populations exposed to different temperatures is rather similar across species. We conclude that most of the ancestral plasticity can evolve further in more extreme environments.
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Affiliation(s)
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Austria
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24
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Hague MTJ, Caldwell CN, Cooper BS. Pervasive Effects of Wolbachia on Host Temperature Preference. mBio 2020; 11:e01768-20. [PMID: 33024036 PMCID: PMC7542361 DOI: 10.1128/mbio.01768-20] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023] Open
Abstract
Heritable symbionts can modify a range of ecologically important host traits, including behavior. About half of all insect species are infected with maternally transmitted Wolbachia, a bacterial endosymbiont known to alter host reproduction, nutrient acquisition, and virus susceptibility. Here, we broadly test the hypothesis that Wolbachia modifies host behavior by assessing the effects of eight different Wolbachia strains on the temperature preference of six Drosophila melanogaster subgroup species. Four of the seven host genotypes infected with A-group Wolbachia strains (wRi in Drosophila simulans, wHa in D. simulans, wSh in Drosophila sechellia, and wTei in Drosophila teissieri) prefer significantly cooler temperatures relative to uninfected genotypes. Contrastingly, when infected with divergent B-group wMau, Drosophila mauritiana prefers a warmer temperature. For most strains, changes to host temperature preference do not alter Wolbachia titer. However, males infected with wSh and wTei tend to experience an increase in titer when shifted to a cooler temperature for 24 h, suggesting that Wolbachia-induced changes to host behavior may promote bacterial replication. Our results indicate that Wolbachia modifications to host temperature preference are likely widespread, which has important implications for insect thermoregulation and physiology. Understanding the fitness consequences of these Wolbachia effects is crucial for predicting evolutionary outcomes of host-symbiont interactions, including how Wolbachia spreads to become common.IMPORTANCE Microbes infect a diversity of species, influencing the performance and fitness of their hosts. Maternally transmitted Wolbachia bacteria infect most insects and other arthropods, making these bacteria some of the most common endosymbionts in nature. Despite their global prevalence, it remains mostly unknown how Wolbachia influence host physiology and behavior to proliferate. We demonstrate pervasive effects of Wolbachia on Drosophila temperature preference. Most hosts infected with A-group Wolbachia prefer cooler temperatures, whereas the one host species infected with divergent B-group Wolbachia prefers warmer temperatures, relative to uninfected genotypes. Changes to host temperature preference generally do not alter Wolbachia abundance in host tissues, but for some A-group strains, adult males have increased Wolbachia titer when shifted to a cooler temperature. This suggests that Wolbachia-induced changes to host behavior may promote bacterial replication. Our results help elucidate the impact of endosymbionts on their hosts amid the global Wolbachia pandemic.
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Affiliation(s)
- Michael T J Hague
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Chelsey N Caldwell
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Brandon S Cooper
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
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25
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Edelsparre AH, Fitzpatrick MJ, Rodríguez MA, Sokolowski MB. Tracking dispersal across a patchy landscape reveals a dynamic interaction between genotype and habitat structure. OIKOS 2020. [DOI: 10.1111/oik.07368] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Allan H. Edelsparre
- Dept of Ecology and Evolutionary Biology, Univ. of Toronto Toronto ON M5S 56 3B2 Canada
- Dept of Biological Sciences, Univ. of Toronto Scarborough Toronto ON M1C 1A4 Canada
| | - Mark J. Fitzpatrick
- Dept of Ecology and Evolutionary Biology, Univ. of Toronto Toronto ON M5S 56 3B2 Canada
- Dept of Cells and Systems Biology, Univ. of Toronto Totonto ON Canada
| | - Marco A. Rodríguez
- Dépt des sciences de l'environnement, Univ. du Québec à Trois‐Rivières Trois‐Rivières QC Canada
| | - Marla B. Sokolowski
- Dept of Ecology and Evolutionary Biology, Univ. of Toronto Toronto ON M5S 56 3B2 Canada
- Program in Child and Brain Development, Canadina Institute for Advanced Reserach Toronto ON Canada
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26
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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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27
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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: 66] [Impact Index Per Article: 16.5] [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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28
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Rejection of the beneficial acclimation hypothesis (BAH) for short term heat acclimation in Drosophila nepalensis. Genetica 2020; 148:173-182. [PMID: 32789784 DOI: 10.1007/s10709-020-00100-8] [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: 04/04/2020] [Accepted: 08/08/2020] [Indexed: 10/23/2022]
Abstract
Beneficial acclimation hypothesis (BAH) is the phenotypic plasticity in response to changing environments which enables organisms to enhance their fitness. In recent years, however, BAH has received vigorous criticism and is still debatable. In this study, we tested thermal hardiness phenotypes (melanization, chill coma recovery, heat knockdown and percentage survival) on adult and pre-adult stages of Drosophila nepalensis, reared in different thermal environments (14, 17, 21 and 25 °C) to check whether increasing natural surrounding temperature and acclimation limit towards environmental change is detrimental or beneficial. Results showed that rearing D. nepalensis at higher temperatures (21 and 25 °C) reduces its melanization and cold hardiness but improves heat knockdown times. When temperature was raised to 26.2 °C (0.6 °C above the upper thermal maxima), to determine the short-term acclimation effects, survival and fitness of adults diminished approximately 1.5 to 2 folds. These results suggest that D. nepalensis has long-term developmental acclimation to both heat and cold which would be extremely beneficial as temperatures and climates alter in the region due to global warming. However, a lack of short-term heat acclimation suggests that rapid shifts in thermal extreme could be detrimental to D. nepalensis.
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29
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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: 66] [Impact Index Per Article: 16.5] [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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30
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Ragland GJ, Armbruster PA, Meuti ME. Evolutionary and functional genetics of insect diapause: a call for greater integration. CURRENT OPINION IN INSECT SCIENCE 2019; 36:74-81. [PMID: 31539788 PMCID: PMC7212789 DOI: 10.1016/j.cois.2019.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 07/29/2019] [Accepted: 08/07/2019] [Indexed: 06/10/2023]
Abstract
Diapause in response to seasonality is an important model for rapid evolutionary adaptation that is highly genetically variable, and experiences strong natural selection. Forward genetic methods using various genomic and transcriptomic approaches have begun to characterize the genetic architecture and candidate genes underlying diapause evolution. Largely in parallel, reverse genetic studies have identified functional roles for candidate genes that may or may not be genetically variable. We illustrate the disconnect between the evolutionary and physiological literature using a suite of studies of the role of the circadian clock in diapause regulation. These extensive studies in two different disciplines provide excellent opportunities for integration, which should facilitate rapid progress in understanding both the regulation and evolution of diapause.
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Affiliation(s)
- Gregory J Ragland
- Department of Integrative Biology, University of Colorado, Denver, 1151 Arapahoe St., SI 2071, Denver, CO 80204, USA.
| | - Peter A Armbruster
- Department of Biology, Georgetown University, Reiss Science Building, Room 406 37th and O Streets, NW Washington DC 20057, USA
| | - Megan E Meuti
- Department of Entomology, The Ohio State University, 216 Kottman Hall 2021 Coffey Road, Columbus, OH 43210, USA
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31
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Prober SM, Raisbeck-Brown N, Porter NB, Williams KJ, Leviston Z, Dickson F. Recent climate-driven ecological change across a continent as perceived through local ecological knowledge. PLoS One 2019; 14:e0224625. [PMID: 31756177 PMCID: PMC6874335 DOI: 10.1371/journal.pone.0224625] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 10/17/2019] [Indexed: 01/06/2023] Open
Abstract
Documenting effects of climate change is an important step towards designing mitigation and adaptation responses. Impacts of climate change on terrestrial biodiversity and ecosystems have been well-documented in the Northern Hemisphere, but long-term data to detect change in the Southern Hemisphere are limited, and some types of change are generally difficult to measure. Here we present a novel approach using local ecological knowledge to facilitate a continent-scale view of climate change impacts on terrestrial biodiversity and ecosystems that people have perceived in Australia. We sought local knowledge using a national web-based survey, targeting respondents with close links to the environment (e.g. farmers, ecologists), and using a custom-built mapping tool to ask respondents to describe and attribute recent changes they had observed within an area they knew well. Results drawn from 326 respondents showed that people are already perceiving simple and complex climate change impacts on hundreds of species and ecosystems across Australia, significantly extending the detail previously reported for the continent. While most perceived trends and attributions remain unsubstantiated, >35 reported anecdotes concurred with examples in the literature, and >20 were reported more than once. More generally, anecdotes were compatible with expectations from global climate change impact frameworks, including examples across the spectrum from organisms (e.g. increased mortality in >75 species), populations (e.g. changes in recruitment or abundance in >100 species, phenological change in >50 species), and species (e.g. >80 species newly arriving or disappearing), to communities and landscapes (e.g. >50 examples of altered ecological interactions). The overarching pattern indicated by the anecdotes suggests that people are more often noticing climate change losers (typically native species) than winners in their local areas, but with observations of potential ‘adaptation in action’ via compositional and phenological change and through arrivals and range shifts (particularly for native birds and exotic plants). A high proportion of climate change-related anecdotes also involved cumulative or interactive effects of land use. We conclude that targeted elicitation of local ecological knowledge about climate change impacts can provide a valuable complement to data-derived knowledge, substantially extending the volume of explicit examples and offering a foundation for further investigation.
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Affiliation(s)
- Suzanne M. Prober
- CSIRO Land and Water, Wembley, Western Australia, Australia
- * E-mail:
| | | | | | | | - Zoe Leviston
- School of Arts and Humanities, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Fiona Dickson
- Department of the Environment and Energy, Canberra, Australian Capital Territory, Australia
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32
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Austin CJ, Moehring AJ. Local thermal adaptation detected during multiple life stages across populations of
Drosophila melanogaster. J Evol Biol 2019; 32:1342-1351. [DOI: 10.1111/jeb.13530] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/19/2019] [Accepted: 08/23/2019] [Indexed: 11/30/2022]
Affiliation(s)
| | - Amanda J. Moehring
- Department of Biology The University of Western Ontario London ON Canada
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33
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Hangartner S, Lasne C, Sgrò CM, Connallon T, Monro K. Genetic covariances promote climatic adaptation in Australian
Drosophila
*. Evolution 2019; 74:326-337. [DOI: 10.1111/evo.13831] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 07/12/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Sandra Hangartner
- School of Biological Sciences Monash University Building 18 Melbourne Victoria 3800 Australia
| | - Clementine Lasne
- School of Biological Sciences Monash University Building 18 Melbourne Victoria 3800 Australia
| | - Carla M. Sgrò
- School of Biological Sciences Monash University Building 18 Melbourne Victoria 3800 Australia
| | - Tim Connallon
- School of Biological Sciences Monash University Building 18 Melbourne Victoria 3800 Australia
| | - Keyne Monro
- School of Biological Sciences Monash University Building 18 Melbourne Victoria 3800 Australia
- Centre for Geometric Biology Monash University Melbourne Victoria 3800 Australia
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34
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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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35
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Connallon T, Débarre F, Li XY. Linking local adaptation with the evolution of sex differences. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0414. [PMID: 30150215 DOI: 10.1098/rstb.2017.0414] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2018] [Indexed: 01/21/2023] Open
Abstract
Many conspicuous forms of evolutionary diversity occur within species. Two prominent examples include evolutionary divergence between populations differentially adapted to their local environments (local adaptation), and divergence between females and males in response to sex differences in selection (sexual dimorphism sensu lato). These two forms of diversity have inspired vibrant research programmes, yet these fields have largely developed in isolation from one another. Nevertheless, conceptual parallels between these research traditions are striking. Opportunities for local adaptation strike a balance between local selection, which promotes divergence, and gene flow-via dispersal and interbreeding between populations-which constrains it. Sex differences are similarly constrained by fundamental features of inheritance that mimic gene flow. Offspring of each sex inherit genes from same-sex and opposite-sex parents, leading to gene flow between each differentially selected half of the population, and raising the question of how sex differences arise and are maintained. This special issue synthesizes and extends emerging research at the interface between the research traditions of local adaptation and sex differences. Each field can promote understanding of the other, and interactions between local adaptation and sex differences can generate new empirical predictions about the evolutionary consequences of selection that varies across space, time, and between the sexes.This article is part of the theme issue 'Linking local adaptation with the evolution of sex differences'.
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Affiliation(s)
- Tim Connallon
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Florence Débarre
- CNRS, UMR 7241 Centre Interdisciplinaire de Recherche en Biologie (CIRB), Collège de France, Paris, France
| | - Xiang-Yi Li
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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36
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Ko L, Harshman L, Hangartner S, Hoffmann A, Kachman S, Black P. Changes in lipid classes of Drosophila melanogaster in response to selection for three stress traits. JOURNAL OF INSECT PHYSIOLOGY 2019; 117:103890. [PMID: 31153895 DOI: 10.1016/j.jinsphys.2019.103890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 05/29/2019] [Accepted: 05/29/2019] [Indexed: 06/09/2023]
Abstract
Laboratory selection on environmental stress traits is an evolutionary approach that is informative in the context of understanding stress adaptation. Here we characterize changes in a lipidome of Drosophila melanogaster in lines selected for increased heat (elevated heat knockdown refractoriness), cold (decreased time to recover from chill-coma) and desiccation survival. Selection for desiccation resistance resulted in changes in multiple lipid classes used to characterize a lipidome. This included a decrease in triacylglycerols (TAGs) which is relevant to interpretation of storage lipid levels in previous D. melanogaster desiccation survival selection experiments. Chill-coma recovery rate selection was expected to show extensive changes in lipid classes, but only phosphatidic acids exhibited significant change. Selection for increased heat knockdown resistance resulted in a substantial change in the abundance of a class of lipids (diacylglycerols) which could play a role in mediating the heat shock response or result in an increase in neutral lipid mobilization.
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Affiliation(s)
- Li Ko
- School of Biological Sciences, University of Nebraska Lincoln, 1104 T St, Lincoln, NE 68588, USA.
| | - Lawrence Harshman
- School of Biological Sciences, University of Nebraska Lincoln, 1104 T St, Lincoln, NE 68588, USA
| | - Sandra Hangartner
- School of Biological Sciences, The University of Melbourne, 30 Flemington Road, Parkville 3010, Australia
| | - Ary Hoffmann
- School of Biological Sciences, The University of Melbourne, 30 Flemington Road, Parkville 3010, Australia
| | - Steve Kachman
- Department of Statistics, University of Nebraska Lincoln, 340 Hardin Hall North Wing, Lincoln, NE 68583, USA
| | - Paul Black
- Department of Biochemistry, University of Nebraska Lincoln, 1901 Vince Street, Lincoln, NE 68588, USA
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Walters RJ, Berger D. Implications of existing local (mal)adaptations for ecological forecasting under environmental change. Evol Appl 2019; 12:1487-1502. [PMID: 31417629 PMCID: PMC6691230 DOI: 10.1111/eva.12840] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 06/22/2019] [Accepted: 06/24/2019] [Indexed: 01/31/2023] Open
Abstract
Standing genetic variation represents a genetic load on population fitness but can also support a rapid response to short-term environmental change, and the greatest potential source of such standing genetic variation typically exists among locally adapted populations living along an environmental gradient. Here, we develop a spatially explicit simulation model to quantify the contribution of existing genetic variation arising from migration-mutation-selection-drift balance to time to extinction under environmental change. Simulations reveal that local adaptation across a species range associated with an underlying environmental gradient could extend time to extinction by nearly threefold irrespective of the rate of environmental change. The potential for preadapted alleles to increase the rate of adaptation changes the relative importance of established extinction risk factors; in particular, it reduced the importance of the breadth of environmental tolerance and it increased the relative importance of fecundity. Although migration of preadapted alleles generally increased persistence time, it decreased it at rates of environmental change close to the critical rate of change by creating a population bottleneck, which ultimately limited the rate at which de novo mutations could arise. An analysis of the extinction dynamics further revealed that one consequence of gene flow is the potential to maximize population growth rate in at least part of the species range, which is likely to have consequences for forecasting the consequences of ecological interactions. Our study shows that predictions of persistence time change fundamentally when existing local adaptations are explicitly taken into account, underscoring the need to preserve and manage genetic diversity.
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Affiliation(s)
- Richard J. Walters
- Centre for Environmental and Climate ResearchLund UniversityLundSweden
- School of Biological SciencesUniversity of ReadingReadingUK
| | - David Berger
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSweden
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Rödin‐Mörch P, Luquet E, Meyer‐Lucht Y, Richter‐Boix A, Höglund J, Laurila A. Latitudinal divergence in a widespread amphibian: Contrasting patterns of neutral and adaptive genomic variation. Mol Ecol 2019; 28:2996-3011. [DOI: 10.1111/mec.15132] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/17/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Patrik Rödin‐Mörch
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - Emilien Luquet
- CNRS, ENTPE, UMR5023 LEHNA Univ Lyon, Université Claude Bernard Lyon 1 Villeurbanne France
| | - Yvonne Meyer‐Lucht
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - Alex Richter‐Boix
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - Jacob Höglund
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - Anssi Laurila
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
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39
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Angilletta MJ, Condon C, Youngblood JP. Thermal acclimation of flies from three populations of Drosophila melanogaster fails to support the seasonality hypothesis. J Therm Biol 2019; 81:25-32. [DOI: 10.1016/j.jtherbio.2019.02.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 02/03/2019] [Accepted: 02/03/2019] [Indexed: 12/29/2022]
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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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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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42
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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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43
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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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44
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Kapun M, Flatt T. The adaptive significance of chromosomal inversion polymorphisms inDrosophila melanogaster. Mol Ecol 2018; 28:1263-1282. [DOI: 10.1111/mec.14871] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/01/2018] [Accepted: 09/10/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Martin Kapun
- Department of BiologyUniversity of Fribourg Fribourg Switzerland
| | - Thomas Flatt
- Department of BiologyUniversity of Fribourg Fribourg Switzerland
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45
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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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46
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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: 30] [Impact Index Per Article: 5.0] [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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47
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Bauerfeind SS, Schäfer MA, Berger D, Blanckenhorn WU, Fox CW. Replicated latitudinal clines in reproductive traits of European and North American yellow dung flies. OIKOS 2018. [DOI: 10.1111/oik.05421] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Martin A. Schäfer
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich; Zurich Switzerland
| | - David Berger
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich; Zurich Switzerland
- Dept of Ecology and Genetics, Univ. of Uppsala; Uppsala Sweden
| | - Wolf U. Blanckenhorn
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich; Zurich Switzerland
| | - Charles W. Fox
- Dept of Entomology, Univ. of Kentucky; S225 Ag Science Center North Lexington KY 40546-0091 USA
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48
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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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49
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Shi M, White VL, Schlub T, Eden JS, Hoffmann AA, Holmes EC. No detectable effect of Wolbachia wMel on the prevalence and abundance of the RNA virome of Drosophila melanogaster. Proc Biol Sci 2018; 285:20181165. [PMID: 30051873 PMCID: PMC6083246 DOI: 10.1098/rspb.2018.1165] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/02/2018] [Indexed: 12/11/2022] Open
Abstract
Wolbachia is an endosymbiotic bacterium that can block viral infections in arthropods, generating interest in its potential to control the spread of mosquito-borne disease. Drosophila melanogaster is model organism for Wolbachia infection, and the wMel strain of Wolbachia can improve host survival following viral infection. However, it is unclear whether wMel induces anti-viral blocking against the broader native virome of D. melanogaster, or whether the major effect of Wolbachia is a reduction in viral abundance rather than viral clearance. We examined the effect of Wolbachia on viral abundance by comparing the total transcriptome of wMel-positive and wMel-negative D. melanogaster populations sampled from six locations in Australia. In addition, we examined the impact of wMel on individual flies by obtaining transcriptome data from 20 wMel-positive and 20 wMel-negative D. melanogaster from the location (Melbourne) with highest density of wMel. These data revealed high viral abundance in both Wolbachia-positive and -negative populations and individuals. Notably, none of the viral species identified, representing RNA viruses from at least nine families/floating genera, showed evidence of protection by wMel. Although the viral loads of picorna-like viruses are reduced by wMel under experimental conditions, we observed no such effect here. These data show that D. melanogaster can harbour abundant RNA viruses regardless of its Wolbachia status and imply that the interaction between Wolbachia and viruses in nature is more complex than simple blocking.
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Affiliation(s)
- Mang Shi
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Vanessa L White
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Timothy Schlub
- Sydney School of Public Health, Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia
| | - John-Sebastian Eden
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia
- The Westmead Institute for Medical Research, Centre for Virus Research, Sydney, New South Wales 2145, Australia
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia
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50
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Telonis-Scott M, Hoffmann AA. Enhancing Ebony? Common Associations With a cis-Regulatory Haplotype for Drosophila melanogaster Thoracic Pigmentation in a Japanese Population and Australian Populations. Front Physiol 2018; 9:822. [PMID: 30042686 PMCID: PMC6048255 DOI: 10.3389/fphys.2018.00822] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/12/2018] [Indexed: 12/30/2022] Open
Abstract
The molecular underpinnings of pigmentation diversity in Drosophila have recently emerged as a model for understanding how the evolution of different cis-regulatory variants results in common adaptive phenotypes within species. We compared sequence variation in a 5' regulatory region harboring a modular enhancer containing a ∼0.7-kb core element contributing to abdominal melanisation in African, and a ∼0.5-kb core element contributing to thoracic pigmentation in D. melanogaster from Japan, to tropical and temperate populations from eastern Australia previously shown to be divergent in thoracic pigmentation and ebony expression. The Australian populations exhibited strong association with the core enhancer polymorphism cluster in complete association with Dark and Light phenotypes from Iriomote, Japan. Moreover, the Iriomote Light and Dark core enhancer haplotypes are common to the Australian populations in the direction predicted by pigmentation phenotype. We also confirmed the Japanese patterns of linkage disequilibrium and association of the tropical inversion In(3R)Payne with the Light enhancer haplotype in the Australian tropical light population. A worldwide survey of the ∼0.5-kb ebony control region SNPs and haplotypes in a subset of the Drosophila Genome Nexus (DGN) populations suggest origins in the sub-Saharan ancestral region surrounding Zambia and subsequent invasion following colonization out of Africa. A previous study demonstrated complex within and between population genetic architecture for abdominal pigmentation which is also correlated with thoracic pigmentation in melanized DGN sub-Saharan populations; however, the ∼0.5-kb ebony control region was not associated and both haplotypes are common even in the most intensely pigmented D. melanogaster from high altitude Ethiopia. In the Australian populations, the strong phenotypic association with the enhancer SNPs and haplotypes that at least partly regulates ebony expression in the Iriomote population, our previous work demonstrating opposing clines for thoracic pigmentation and ebony expression, where the expression cline parallels the In(3R)Payne cline, and the concerted evolution of pigmentation intensity and ebony expression under rapid experimental evolution, all point to a common adaptive evolutionary pathway in distinct populations.
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Affiliation(s)
- Marina Telonis-Scott
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Ary A. Hoffmann
- Pest and Environmental Adaptation Group, School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, VIC, Australia
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