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Yusuf LH, Tyukmaeva V, Hoikkala A, Ritchie MG. Divergence and introgression among the virilis group of Drosophila. Evol Lett 2022; 6:537-551. [PMID: 36579165 PMCID: PMC9783487 DOI: 10.1002/evl3.301] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 09/23/2022] [Accepted: 10/12/2022] [Indexed: 12/03/2022] Open
Abstract
Speciation with gene flow is now widely regarded as common. However, the frequency of introgression between recently diverged species and the evolutionary consequences of gene flow are still poorly understood. The virilis group of Drosophila contains 12 species that are geographically widespread and show varying levels of prezygotic and postzygotic isolation. Here, we use de novo genome assemblies and whole-genome sequencing data to resolve phylogenetic relationships and describe patterns of introgression and divergence across the group. We suggest that the virilis group consists of three, rather than the traditional two, subgroups. Some genes undergoing rapid sequence divergence across the group were involved in chemical communication and desiccation tolerance, and may be related to the evolution of sexual isolation and adaptation. We found evidence of pervasive phylogenetic discordance caused by ancient introgression events between distant lineages within the group, and more recent gene flow between closely related species. When assessing patterns of genome-wide divergence in species pairs across the group, we found no consistent genomic evidence of a disproportionate role for the X chromosome as has been found in other systems. Our results show how ancient and recent introgressions confuse phylogenetic reconstruction, but may play an important role during early radiation of a group.
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Affiliation(s)
- Leeban H. Yusuf
- Centre for Biological Diversity, School of BiologyUniversity of St AndrewsSt AndrewsKY16 9THUnited Kingdom
| | - Venera Tyukmaeva
- Centre for Biological Diversity, School of BiologyUniversity of St AndrewsSt AndrewsKY16 9THUnited Kingdom,Department of Evolution, Ecology and BehaviourUniversity of LiverpoolLiverpoolL69 7ZBUnited Kingdom
| | - Anneli Hoikkala
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskylä40014Finland
| | - Michael G. Ritchie
- Centre for Biological Diversity, School of BiologyUniversity of St AndrewsSt AndrewsKY16 9THUnited Kingdom
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2
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Hoikkala A, Poikela N. Adaptation and ecological speciation in seasonally varying environments at high latitudes: Drosophila virilis group. Fly (Austin) 2022; 16:85-104. [PMID: 35060806 PMCID: PMC8786326 DOI: 10.1080/19336934.2021.2016327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Living in high latitudes and altitudes sets specific requirements on species’ ability to forecast seasonal changes and to respond to them in an appropriate way. Adaptation into diverse environmental conditions can also lead to ecological speciation through habitat isolation or by inducing changes in traits that influence assortative mating. In this review, we explain how the unique time-measuring systems of Drosophila virilis group species have enabled the species to occupy high latitudes and how the traits involved in species reproduction and survival exhibit strong linkage with latitudinally varying photoperiodic and climatic conditions. We also describe variation in reproductive barriers between the populations of two species with overlapping distributions and show how local adaptation and the reinforcement of prezygotic barriers have created partial reproductive isolation between conspecific populations. Finally, we consider the role of species-specific chromosomal inversions and the X chromosome in the development of reproductive barriers between diverging lineages.
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Affiliation(s)
- Anneli Hoikkala
- Department of Biological and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Noora Poikela
- Department of Biological and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
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3
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Wiberg RAW, Tyukmaeva V, Hoikkala A, Ritchie MG, Kankare M. Cold adaptation drives population genomic divergence in the ecological specialist, Drosophila montana. Mol Ecol 2021; 30:3783-3796. [PMID: 34047417 DOI: 10.1111/mec.16003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/10/2021] [Accepted: 05/20/2021] [Indexed: 12/18/2022]
Abstract
Detecting signatures of ecological adaptation in comparative genomics is challenging, but analysing population samples with characterised geographic distributions, such as clinal variation, can help identify genes showing covariation with important ecological variation. Here, we analysed patterns of geographic variation in the cold-adapted species Drosophila montana across phenotypes, genotypes and environmental conditions and tested for signatures of cold adaptation in population genomic divergence. We first derived the climatic variables associated with the geographic distribution of 24 populations across two continents to trace the scale of environmental variation experienced by the species, and measured variation in the cold tolerance of the flies of six populations from different geographic contexts. We then performed pooled whole genome sequencing of these six populations, and used Bayesian methods to identify SNPs where genetic differentiation is associated with both climatic variables and the population phenotypic measurements, while controlling for effects of demography and population structure. The top candidate SNPs were enriched on the X and fourth chromosomes, and they also lay near genes implicated in other studies of cold tolerance and population divergence in this species and its close relatives. We conclude that ecological adaptation has contributed to the divergence of D. montana populations throughout the genome and in particular on the X and fourth chromosomes, which also showed highest interpopulation FST . This study demonstrates that ecological selection can drive genomic divergence at different scales, from candidate genes to chromosome-wide effects.
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Affiliation(s)
- R A W Wiberg
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK
| | - V Tyukmaeva
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - A Hoikkala
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - M G Ritchie
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK
| | - M Kankare
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
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4
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Erickson PA, Weller CA, Song DY, Bangerter AS, Schmidt P, Bergland AO. Unique genetic signatures of local adaptation over space and time for diapause, an ecologically relevant complex trait, in Drosophila melanogaster. PLoS Genet 2020; 16:e1009110. [PMID: 33216740 PMCID: PMC7717581 DOI: 10.1371/journal.pgen.1009110] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 12/04/2020] [Accepted: 09/10/2020] [Indexed: 02/07/2023] Open
Abstract
Organisms living in seasonally variable environments utilize cues such as light and temperature to induce plastic responses, enabling them to exploit favorable seasons and avoid unfavorable ones. Local adapation can result in variation in seasonal responses, but the genetic basis and evolutionary history of this variation remains elusive. Many insects, including Drosophila melanogaster, are able to undergo an arrest of reproductive development (diapause) in response to unfavorable conditions. In D. melanogaster, the ability to diapause is more common in high latitude populations, where flies endure harsher winters, and in the spring, reflecting differential survivorship of overwintering populations. Using a novel hybrid swarm-based genome wide association study, we examined the genetic basis and evolutionary history of ovarian diapause. We exposed outbred females to different temperatures and day lengths, characterized ovarian development for over 2800 flies, and reconstructed their complete, phased genomes. We found that diapause, scored at two different developmental cutoffs, has modest heritability, and we identified hundreds of SNPs associated with each of the two phenotypes. Alleles associated with one of the diapause phenotypes tend to be more common at higher latitudes, but these alleles do not show predictable seasonal variation. The collective signal of many small-effect, clinally varying SNPs can plausibly explain latitudinal variation in diapause seen in North America. Alleles associated with diapause are segregating in Zambia, suggesting that variation in diapause relies on ancestral polymorphisms, and both pro- and anti-diapause alleles have experienced selection in North America. Finally, we utilized outdoor mesocosms to track diapause under natural conditions. We found that hybrid swarms reared outdoors evolved increased propensity for diapause in late fall, whereas indoor control populations experienced no such change. Our results indicate that diapause is a complex, quantitative trait with different evolutionary patterns across time and space.
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Affiliation(s)
- Priscilla A. Erickson
- Department of Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Cory A. Weller
- Department of Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Daniel Y. Song
- Department of Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Alyssa S. Bangerter
- Department of Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Paul Schmidt
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Alan O. Bergland
- Department of Biology, University of Virginia, Charlottesville, Virginia, United States of America
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5
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Kristensen TN, Ketola T, Kronholm I. Adaptation to environmental stress at different timescales. Ann N Y Acad Sci 2018; 1476:5-22. [PMID: 30259990 DOI: 10.1111/nyas.13974] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 08/24/2018] [Accepted: 09/08/2018] [Indexed: 12/21/2022]
Abstract
Environments are changing rapidly, and to cope with these changes, organisms have to adapt. Adaptation can take many shapes and occur at different speeds, depending on the type of response, the trait, the population, and the environmental conditions. The biodiversity crisis that we are currently facing illustrates that numerous species and populations are not capable of adapting with sufficient speed to ongoing environmental changes. Here, we discuss current knowledge on the ability of animals and plants to adapt to environmental stress on different timescales, mainly focusing on thermal stress and ectotherms. We discuss within-generation responses that can be fast and induced within minutes or hours, evolutionary adaptations that are often slow and take several generations, and mechanisms that lay somewhere in between and that include epigenetic transgenerational effects. To understand and predict the impacts of environmental change and stress on biodiversity, we suggest that future studies should (1) have an increased focus on understanding the type and speed of responses to fast environmental changes; (2) focus on the importance of environmental fluctuations and the predictability of environmental conditions on adaptive capabilities, preferably in field studies encompassing several fitness components; and (3) look at ecosystem responses to environmental stress and their resilience when disturbed.
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Affiliation(s)
- Torsten Nygaard Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.,Department of Bioscience, University of Aarhus, Aarhus, Denmark
| | - Tarmo Ketola
- Department of Biology and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Ilkka Kronholm
- Department of Biology and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
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6
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Parker DJ, Wiberg RAW, Trivedi U, Tyukmaeva VI, Gharbi K, Butlin RK, Hoikkala A, Kankare M, Ritchie MG. Inter and Intraspecific Genomic Divergence in Drosophila montana Shows Evidence for Cold Adaptation. Genome Biol Evol 2018; 10:2086-2101. [PMID: 30010752 PMCID: PMC6107330 DOI: 10.1093/gbe/evy147] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2018] [Indexed: 12/25/2022] Open
Abstract
The genomes of species that are ecological specialists will likely contain signatures of genomic adaptation to their niche. However, distinguishing genes related to ecological specialism from other sources of selection and more random changes is a challenge. Here, we describe the genome of Drosophila montana, which is the most extremely cold-adapted Drosophila species known. We use branch tests to identify genes showing accelerated divergence in contrasts between cold- and warm-adapted species and identify about 250 genes that show differences, possibly driven by a lower synonymous substitution rate in cold-adapted species. We also look for evidence of accelerated divergence between D. montana and D. virilis, a previously sequenced relative, but do not find strong evidence for divergent selection on coding sequence variation. Divergent genes are involved in a variety of functions, including cuticular and olfactory processes. Finally, we also resequenced three populations of D. montana from across its ecological and geographic range. Outlier loci were more likely to be found on the X chromosome and there was a greater than expected overlap between population outliers and those genes implicated in cold adaptation between Drosophila species, implying some continuity of selective process at these different evolutionary scales.
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Affiliation(s)
- Darren J Parker
- Department of Biological and Environmental Science, University of Jyväskylä, Finland
- Center for Biological Diversity, School of Biology, University of St. Andrews, Fife, United Kingdom
- Department of Ecology and Evolution, University of Lausanne, Biophore, Switzerland
| | - R Axel W Wiberg
- Center for Biological Diversity, School of Biology, University of St. Andrews, Fife, United Kingdom
| | - Urmi Trivedi
- Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, United Kingdom
| | - Venera I Tyukmaeva
- Department of Biological and Environmental Science, University of Jyväskylä, Finland
| | - Karim Gharbi
- Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, United Kingdom
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Roger K Butlin
- Department of Animal and Plant Sciences, The University of Sheffield, UK
- Department of Marine Sciences, University of Gothenburg, Göteborg, Sweden
| | - Anneli Hoikkala
- Department of Biological and Environmental Science, University of Jyväskylä, Finland
| | - Maaria Kankare
- Department of Biological and Environmental Science, University of Jyväskylä, Finland
| | - Michael G Ritchie
- Center for Biological Diversity, School of Biology, University of St. Andrews, Fife, United Kingdom
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Cui M, Hu P, Wang T, Tao J, Zong S. Differential transcriptome analysis reveals genes related to cold tolerance in seabuckthorn carpenter moth, Eogystia hippophaecolus. PLoS One 2017; 12:e0187105. [PMID: 29131867 PMCID: PMC5683614 DOI: 10.1371/journal.pone.0187105] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 10/15/2017] [Indexed: 01/27/2023] Open
Abstract
Seabuckthorn carpenter moth, Eogystia hippophaecolus (Lepidoptera: Cossidae), is an important pest of sea buckthorn (Hippophae rhamnoides), which is a shrub that has significant ecological and economic value in China. E. hippophaecolus is highly cold tolerant, but limited studies have been conducted to elucidate the molecular mechanisms underlying its cold resistance. Here we sequenced the E. hippophaecolus transcriptome using RNA-Seq technology and performed de novo assembly from the short paired-end reads. We investigated the larval response to cold stress by comparing gene expression profiles between treatments. We obtained 118,034 unigenes, of which 22,161 were annotated with gene descriptions, conserved domains, gene ontology terms, and metabolic pathways. These resulted in 57 GO terms and 193 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. By comparing transcriptome profiles for differential gene expression, we identified many differentially expressed proteins and genes, including heat shock proteins and cuticular proteins which have previously been reported to be involved in cold resistance of insects. This study provides a global transcriptome analysis and an assessment of differential gene expression in E. hippophaecolus under cold stress. We found seven differential expressed genes in common between developmental stages, which were verified with qPCR. Our findings facilitate future genomic studies aimed at improving our understanding of the molecular mechanisms underlying the response of insects to low temperatures.
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Affiliation(s)
- Mingming Cui
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, P.R. China
| | - Ping Hu
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, P.R. China
| | - Tao Wang
- Mentougou Forestry Station, Beijing, China
| | - Jing Tao
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, P.R. China
- * E-mail: (JT); (SXZ)
| | - Shixiang Zong
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, P.R. China
- * E-mail: (JT); (SXZ)
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Roulin AC, Bourgeois Y, Stiefel U, Walser JC, Ebert D. A Photoreceptor Contributes to the Natural Variation of Diapause Induction inDaphnia magna. Mol Biol Evol 2016; 33:3194-3204. [DOI: 10.1093/molbev/msw200] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Kankare M, Parker DJ, Merisalo M, Salminen TS, Hoikkala A. Transcriptional Differences between Diapausing and Non-Diapausing D. montana Females Reared under the Same Photoperiod and Temperature. PLoS One 2016; 11:e0161852. [PMID: 27571415 PMCID: PMC5003386 DOI: 10.1371/journal.pone.0161852] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 08/13/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND A wide range of insects living at higher latitudes enter diapause at the end of the warm season, which increases their chances of survival through harsh winter conditions. In this study we used RNA sequencing to identify genes involved in adult reproductive diapause in a northern fly species, Drosophila montana. Both diapausing and non-diapausing flies were reared under a critical day length and temperature, where about half of the emerging females enter diapause enabling us to eliminate the effects of varying environmental conditions on gene expression patterns of the two types of female flies. RESULTS RNA sequencing revealed large differences between gene expression patterns of diapausing and non-diapausing females, especially in genes involved with metabolism, fatty acid biosynthesis, and metal and nucleotide binding. Differently expressed genes included several gene groups, including myosin, actin and cytochromeP450 genes, which have been previously associated with diapause. This study also identified new candidate genes, including some involved in cuticular hydrocarbon synthesis or regulation (desat1 and desat2), and acyl-CoA Δ11-desaturase activity (CG9747), and few odorant-binding protein genes (e.g. Obp44A). Also, several transposable elements (TEs) showed differential expression between the two female groups motivating future research on their roles in diapause. CONCLUSIONS Our results demonstrate that the adult reproductive diapause in D. montana involves changes in the expression level of a variety of genes involved in key processes (e.g. metabolism and fatty acid biosynthesis) which help diapausing females to cope with overwintering. This is consistent with the view that diapause is a complex adaptive phenotype where not only sexual maturation is arrested, but also changes in adult physiology are required in order to survive over the winter.
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Affiliation(s)
- Maaria Kankare
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, Jyväskylä, Finland
| | - Darren J. Parker
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, Jyväskylä, Finland
- Centre for Biological Diversity, School of Biology, University of St Andrews, Fife, KY16 9TH, St Andrews, United Kingdom
| | - Mikko Merisalo
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, Jyväskylä, Finland
| | - Tiina S. Salminen
- BioMediTech, Biokatu 6, F1-33014, University of Tampere, Tampere, Finland
| | - Anneli Hoikkala
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, Jyväskylä, Finland
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