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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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2
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Sprengelmeyer QD, Lack JB, Braun DT, Monette MJ, Pool JE. The evolution of larger size in high-altitude Drosophila melanogaster has a variable genetic architecture. G3 GENES|GENOMES|GENETICS 2022; 12:6493269. [PMID: 35100377 PMCID: PMC8895999 DOI: 10.1093/g3journal/jkab454] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 12/21/2021] [Indexed: 11/12/2022]
Abstract
Important uncertainties persist regarding the genetic architecture of adaptive trait evolution in natural populations, including the number of genetic variants involved, whether they are drawn from standing genetic variation, and whether directional selection drives them to complete fixation. Here, we take advantage of a unique natural population of Drosophila melanogaster from the Ethiopian highlands, which has evolved larger body size than any other known population of this species. We apply a bulk segregant quantitative trait locus mapping approach to 4 unique crosses between highland Ethiopian and lowland Zambian populations for both thorax length and wing length. Results indicated a persistently variable genetic basis for these evolved traits (with largely distinct sets of quantitative trait loci for each cross), and at least a moderately polygenic architecture with relatively strong effects present. We complemented these mapping experiments with population genetic analyses of quantitative trait locus regions and gene ontology enrichment analysis, generating strong hypotheses for specific genes and functional processes that may have contributed to these adaptive trait changes. Finally, we find that the genetic architectures indicated by our quantitative trait locus mapping results for size traits mirror those from similar experiments on other recently evolved traits in this species. Collectively, these studies suggest a recurring pattern of polygenic adaptation in this species, in which causative variants do not approach fixation and moderately strong effect loci are present.
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Affiliation(s)
| | - Justin B Lack
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Dylan T Braun
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Matthew J Monette
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - John E Pool
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
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3
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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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4
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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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5
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García‐Roa R, Chirinos V, Carazo P. The ecology of sexual conflict: Temperature variation in the social environment can drastically modulate male harm to females. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13275] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Roberto García‐Roa
- Behaviour and Evolution Group, Ethology Lab, Cavanilles Institute of Biodiversity and Evolutionary Biology University of Valencia Valencia Spain
| | - Valeria Chirinos
- Behaviour and Evolution Group, Ethology Lab, Cavanilles Institute of Biodiversity and Evolutionary Biology University of Valencia Valencia Spain
| | - Pau Carazo
- Behaviour and Evolution Group, Ethology Lab, Cavanilles Institute of Biodiversity and Evolutionary Biology University of Valencia Valencia Spain
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6
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Bowman LL, Kondrateva ES, Timofeyev MA, Yampolsky LY. Temperature gradient affects differentiation of gene expression and SNP allele frequencies in the dominant Lake Baikal zooplankton species. Mol Ecol 2018; 27:2544-2559. [PMID: 29691934 DOI: 10.1111/mec.14704] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/20/2018] [Accepted: 03/27/2018] [Indexed: 12/13/2022]
Abstract
Local adaptation and phenotypic plasticity are main mechanisms of organisms' resilience in changing environments. Both are affected by gene flow and are expected to be weak in zooplankton populations inhabiting large continuous water bodies and strongly affected by currents. Lake Baikal, the deepest and one of the coldest lakes on Earth, experienced epilimnion temperature increase during the last 100 years, exposing Baikal's zooplankton to novel selective pressures. We obtained a partial transcriptome of Epischura baikalensis (Copepoda: Calanoida), the dominant component of Baikal's zooplankton, and estimated SNP allele frequencies and transcript abundances in samples from regions of Baikal that differ in multiyear average surface temperatures. The strongest signal in both SNP and transcript abundance differentiation is the SW-NE gradient along the 600+ km long axis of the lake, suggesting isolation by distance. SNP differentiation is stronger for nonsynonymous than synonymous SNPs and is paralleled by differential survival during a laboratory exposure to increased temperature, indicating directional selection operating on the temperature gradient. Transcript abundance, generally collinear with the SNP differentiation, shows samples from the warmest, less deep location clustering together with the southernmost samples. Differential expression is more frequent among transcripts orthologous to candidate thermal response genes previously identified in model arthropods, including genes encoding cytoskeleton proteins, heat-shock proteins, proteases, enzymes of central energy metabolism, lipid and antioxidant pathways. We conclude that the pivotal endemic zooplankton species in Lake Baikal exists under temperature-mediated selection and possesses both genetic variation and plasticity to respond to novel temperature-related environmental pressures.
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Affiliation(s)
- Larry L Bowman
- Department of Biological Sciences, East Tennessee State University, Johnson City, Tennessee
| | - Elizaveta S Kondrateva
- Institute of Biology, Irkutsk State University, Irkutsk, Russia.,Baikal Research Centre, Irkutsk, Russia
| | - Maxim A Timofeyev
- Siberian Institute of Plant Physiology and Biochemistry SB RAS, Irkutsk, Russia
| | - Lev Y Yampolsky
- Department of Biological Sciences, East Tennessee State University, Johnson City, Tennessee
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7
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Caddy-Retalic S, Andersen AN, Aspinwall MJ, Breed MF, Byrne M, Christmas MJ, Dong N, Evans BJ, Fordham DA, Guerin GR, Hoffmann AA, Hughes AC, van Leeuwen SJ, McInerney FA, Prober SM, Rossetto M, Rymer PD, Steane DA, Wardle GM, Lowe AJ. Bioclimatic transect networks: Powerful observatories of ecological change. Ecol Evol 2017; 7:4607-4619. [PMID: 28690791 PMCID: PMC5496522 DOI: 10.1002/ece3.2995] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 03/21/2017] [Indexed: 01/02/2023] Open
Abstract
Transects that traverse substantial climate gradients are important tools for climate change research and allow questions on the extent to which phenotypic variation associates with climate, the link between climate and species distributions, and variation in sensitivity to climate change among biomes to be addressed. However, the potential limitations of individual transect studies have recently been highlighted. Here, we argue that replicating and networking transects, along with the introduction of experimental treatments, addresses these concerns. Transect networks provide cost‐effective and robust insights into ecological and evolutionary adaptation and improve forecasting of ecosystem change. We draw on the experience and research facilitated by the Australian Transect Network to demonstrate our case, with examples, to clarify how population‐ and community‐level studies can be integrated with observations from multiple transects, manipulative experiments, genomics, and ecological modeling to gain novel insights into how species and systems respond to climate change. This integration can provide a spatiotemporal understanding of past and future climate‐induced changes, which will inform effective management actions for promoting biodiversity resilience.
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Affiliation(s)
- Stefan Caddy-Retalic
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,School of Biological Sciences and Environment InstituteUniversity of Adelaide Adelaide SA Australia
| | - Alan N Andersen
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,Charles Darwin University Darwin NT Australia
| | - Michael J Aspinwall
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,Hawkesbury Institute for the Environment Western Sydney University Parramatta NSW Australia
| | - Martin F Breed
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,School of Biological Sciences and Environment InstituteUniversity of Adelaide Adelaide SA Australia
| | - Margaret Byrne
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,Science and Conservation Division Western Australian Department of Parks and Wildlife Kensington WA Australia
| | - Matthew J Christmas
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,School of Biological Sciences and Environment InstituteUniversity of Adelaide Adelaide SA Australia
| | - Ning Dong
- Department of Biological Sciences Macquarie University North Ryde NSW Australia.,Ecosystem Modelling and Scaling Infrastructure Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia
| | - Bradley J Evans
- Ecosystem Modelling and Scaling Infrastructure Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,School Life and Environmental Sciences University of Sydney Sydney NSW Australia
| | - Damien A Fordham
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,School of Biological Sciences and Environment InstituteUniversity of Adelaide Adelaide SA Australia
| | - Greg R Guerin
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,School of Biological Sciences and Environment InstituteUniversity of Adelaide Adelaide SA Australia
| | - Ary A Hoffmann
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,School of BioSciences, Bio 21 InstituteThe University of Melbourne Parkville VIC Australia
| | - Alice C Hughes
- Centre for Integrative Conservation Xishuangbanna Tropical Botanic Garden Chinese Academy of Sciences Menglun, Mengla County Yunnan China
| | - Stephen J van Leeuwen
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,Science and Conservation Division Western Australian Department of Parks and Wildlife Kensington WA Australia
| | - Francesca A McInerney
- Sprigg Geobiology Centre and School of Physical Sciences University of Adelaide Adelaide SA Australia
| | - Suzanne M Prober
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,CSIRO Land and Water Wembley WA Australia
| | - Maurizio Rossetto
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,National Herbarium of NSW Royal Botanic Gardens and Domain Trust Sydney NSW Australia
| | - Paul D Rymer
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,Hawkesbury Institute for the Environment Western Sydney University Parramatta NSW Australia
| | - Dorothy A Steane
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,CSIRO Land and Water Wembley WA Australia.,School of Biological Sciences University of Tasmania Private Bag 55 Hobart Tasmania 7001 Australia.,Faculty of Science, Health, Education and Engineering University of the Sunshine Coast Maroochydore QLD Australia
| | - Glenda M Wardle
- School Life and Environmental Sciences University of Sydney Sydney NSW Australia.,Long Term Ecological Research Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia
| | - Andrew J Lowe
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,School of Biological Sciences and Environment InstituteUniversity of Adelaide Adelaide SA Australia
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8
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Juneja P, Quinn A, Jiggins FM. Latitudinal clines in gene expression and cis-regulatory element variation in Drosophila melanogaster. BMC Genomics 2016; 17:981. [PMID: 27894253 PMCID: PMC5126864 DOI: 10.1186/s12864-016-3333-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/23/2016] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Organisms can rapidly adapt to their environment when colonizing a new habitat, and this could occur by changing protein sequences or by altering patterns of gene expression. The importance of gene expression in driving local adaptation is increasingly being appreciated, and cis-regulatory elements (CREs), which control and modify the expression of the nearby genes, are predicted to play an important role. Here we investigate genetic variation in gene expression in immune-challenged Drosophila melanogaster from temperate and tropical or sub-tropical populations in Australia and United States. RESULTS We find parallel latitudinal changes in gene expression, with genes involved in immunity, insecticide resistance, reproduction, and the response to the environment being especially likely to differ between latitudes. By measuring allele-specific gene expression (ASE), we show that cis-regulatory variation also shows parallel latitudinal differences between the two continents and contributes to the latitudinal differences in gene expression. CONCLUSIONS Both Australia and United States were relatively recently colonized by D. melanogaster, and it was recently shown that introductions of both African and European flies occurred, with African genotypes contributing disproportionately to tropical populations. Therefore, both the demographic history of the populations and local adaptation may be causing the patterns that we see.
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Affiliation(s)
- Punita Juneja
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Andrew Quinn
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Francis M Jiggins
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK.
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9
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Porcelli D, Westram AM, Pascual M, Gaston KJ, Butlin RK, Snook RR. Gene expression clines reveal local adaptation and associated trade-offs at a continental scale. Sci Rep 2016; 6:32975. [PMID: 27599812 PMCID: PMC5013434 DOI: 10.1038/srep32975] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/18/2016] [Indexed: 01/03/2023] Open
Abstract
Local adaptation, where fitness in one environment comes at a cost in another, should lead to spatial variation in trade-offs between life history traits and may be critical for population persistence. Recent studies have sought genomic signals of local adaptation, but often have been limited to laboratory populations representing two environmentally different locations of a species’ distribution. We measured gene expression, as a proxy for fitness, in males of Drosophila subobscura, occupying a 20° latitudinal and 11 °C thermal range. Uniquely, we sampled six populations and studied both common garden and semi-natural responses to identify signals of local adaptation. We found contrasting patterns of investment: transcripts with expression positively correlated to latitude were enriched for metabolic processes, expressed across all tissues whereas negatively correlated transcripts were enriched for reproductive processes, expressed primarily in testes. When using only the end populations, to compare our results to previous studies, we found that locally adaptive patterns were obscured. While phenotypic trade-offs between metabolic and reproductive functions across widespread species are well-known, our results identify underlying genetic and tissue responses at a continental scale that may be responsible for this. This may contribute to understanding population persistence under environmental change.
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Affiliation(s)
- Damiano Porcelli
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Anja M Westram
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Marta Pascual
- Departament de Genètica, Microbiologia I Estabdistica and IrBio, Universitat de Barcelona, Barcelona 08028, ES
| | - Kevin J Gaston
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall TR10 9FE, UK
| | - Roger K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Rhonda R Snook
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
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10
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Affiliation(s)
- Steven L. Chown
- School of Biological Sciences Monash University Melbourne Vic.3800 Australia
| | - Kevin J. Gaston
- Environment and Sustainability Institute University of Exeter Penryn Cornwall TR10 9FE UK
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11
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Zhao L, Wit J, Svetec N, Begun DJ. Parallel Gene Expression Differences between Low and High Latitude Populations of Drosophila melanogaster and D. simulans. PLoS Genet 2015; 11:e1005184. [PMID: 25950438 PMCID: PMC4423912 DOI: 10.1371/journal.pgen.1005184] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 03/27/2015] [Indexed: 11/19/2022] Open
Abstract
Gene expression variation within species is relatively common, however, the role of natural selection in the maintenance of this variation is poorly understood. Here we investigate low and high latitude populations of Drosophila melanogaster and its sister species, D. simulans, to determine whether the two species show similar patterns of population differentiation, consistent with a role for spatially varying selection in maintaining gene expression variation. We compared at two temperatures the whole male transcriptome of D. melanogaster and D. simulans sampled from Panama City (Panama) and Maine (USA). We observed a significant excess of genes exhibiting differential expression in both species, consistent with parallel adaptation to heterogeneous environments. Moreover, the majority of genes showing parallel expression differentiation showed the same direction of differential expression in the two species and the magnitudes of expression differences between high and low latitude populations were correlated across species, further bolstering the conclusion that parallelism for expression phenotypes results from spatially varying selection. However, the species also exhibited important differences in expression phenotypes. For example, the genomic extent of genotype × environment interaction was much more common in D. melanogaster. Highly differentiated SNPs between low and high latitudes were enriched in the 3’ UTRs and CDS of the geographically differently expressed genes in both species, consistent with an important role for cis-acting variants in driving local adaptation for expression-related phenotypes. While gene expression variation in natural populations is common, the population genetic processes responsible for the maintenance of this variation remain obscure. Here we study geographic differences in gene expression in recently established low and high latitude populations of two closely related species of Drosophila. We observe substantial parallelism in expression differences and expression plasticity between populations, which supports the idea that spatially varying selection correlated with latitude contributes to the maintenance of gene expression variation in these species. Comparison of inter-population sequence differentiation and expression differentiation suggests that cis-acting variants play a role in geographic expression differentiation.
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Affiliation(s)
- Li Zhao
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
- * E-mail:
| | - Janneke Wit
- Department of Bioscience, Section of Integrative Ecology and Evolution, Aarhus University, Aarhus C, Denmark
| | - Nicolas Svetec
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
| | - David J. Begun
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
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12
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Multiple regulatory safeguards confine the expression of the GATA factor Serpent to the hemocyte primordium within the Drosophila mesoderm. Dev Biol 2013; 386:272-9. [PMID: 24360907 DOI: 10.1016/j.ydbio.2013.12.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 12/03/2013] [Accepted: 12/05/2013] [Indexed: 11/23/2022]
Abstract
serpent (srp) encodes a GATA-factor that controls various aspects of embryogenesis in Drosophila, such as fatbody development, gut differentiation and hematopoiesis. During hematopoiesis, srp expression is required in the embryonic head mesoderm and the larval lymph gland, the two known hematopoietic tissues of Drosophila, to obtain mature hemocytes. srp expression in the hemocyte primordium is known to depend on snail and buttonhead, but the regulatory complexity that defines the primordium has not been addressed yet. Here, we find that srp is sufficient to transform trunk mesoderm into hemocytes. We identify two disjoint cis-regulatory modules that direct the early expression in the hemocyte primordium and the late expression in mature hemocytes and lymph gland, respectively. During embryonic hematopoiesis, a combination of snail, buttonhead, empty spiracles and even-skipped confines the mesodermal srp expression to the head region. This restriction to the head mesoderm is crucial as ectopic srp in mesodermal precursors interferes with the development of mesodermal derivates and promotes hemocytes and fatbody development. Thus, several genes work in a combined fashion to restrain early srp expression to the head mesoderm in order to prevent expansion of the hemocyte primordium.
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13
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Lee SF, Eyre-Walker YC, Rane RV, Reuter C, Vinti G, Rako L, Partridge L, Hoffmann AA. Polymorphism in the neurofibromin gene, Nf1, is associated with antagonistic selection on wing size and development time in Drosophila melanogaster. Mol Ecol 2013; 22:2716-25. [PMID: 23506114 DOI: 10.1111/mec.12301] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 02/10/2013] [Accepted: 02/16/2013] [Indexed: 12/14/2022]
Abstract
In many invertebrates, body size shows genetically based clines, with size increasing in colder climates. Large body size is typically associated with prolonged development times. We consider variation in the CNS-specific gene neurofibromin 1 (Nf1) and its association with body size and development time. We identified two major Nf1 haplotypes in natural populations, Nf1-insertion-A and Nf1-deletion-G. These haplotypes are characterized by a 45-base insertion/deletion (INDEL) in Nf1 intron 2 and an A/G synonymous substitution (locus L17277). Linkage disequilibrium (LD) between the INDEL and adjacent sites is high but appears to be restricted within the Nf1 gene interval. In Australia, the frequency of the Nf1-insertion-A haplotype increases with latitude where wing size is larger, independent of the chromosomal inversion In(3R)Payne. Unexpectedly, the Nf1-insertion-A haplotype is negatively associated with wing size. We found that the Nf1-insertion-A haplotype is enriched in females with shorter development time. This suggests that the Nf1 haplotype cline may be driven by selection for development time rather than size; females from southern (higher latitude) D. melanogaster populations maintain a rapid development time despite being relatively larger, and the higher incidence of Nf1-insertion-A in Southern Australia may contribute to this pattern, whereas the effects of the Nf1 haplotypes on size may be countered by other loci with antagonistic effects on size and development time. Our results point to the potential complexity involved in identifying selection on genetic variants exhibiting pleiotropic effects when studies are based on spatial patterns or association studies.
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Affiliation(s)
- Siu F Lee
- Department of Genetics and Bio21 Institute, The University of Melbourne, Parkville, Melbourne, VIC, Australia.
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