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1. As the crow, flies : identifying genomic loci contributing to adaptation in Drosophila and the corvid radiation

Author

Wiberg, R. Axel W. and Ritchie, Michael G.

Subjects
576.8
Abstract

Identifying loci that contribute to adaptive traits is an important goal of evolutionary biology. I take a comparative genomic approach to identify loci that have responded to divergent selection. First I consider the challenges of identifying consistent genomic responses to selection during experimental evolution. I use population genetic simulations to show that commonly applied statistical tests perform poorly and identify superior methods. These will also be useful in comparing allele frequencies in other contexts. Next I analyse whole genome data from an experimental evolution study of Drosophila pseudoobscura evolving under altered mating systems. I find that around 300 SNPs show consistent allele frequency differences between experimental treatments. These are clustered in genomic regions which also show signatures of selective sweeps or background selection. These regions contain genes with mutant phenotypes related to changes already documented in this system. In another chapter I use a novel approach to identify markers potentially influencing female re-mating rate among lines of D. pseudoobscura. I use simulations to show that there are more fixed differences between extreme pairs of isofemale lines from different populations than expected by chance. Many of the genes are implicated in female mating behaviour in other studies. I then focus on local adaptation in wild Drosophila montana populations. I use Bayesian methods to relate genetic and environmental differentiation among populations. Finally, I take a broader comparative approach using multiple genomes from 14 species of crow to identify potential signatures of selection in the New Caledonian (NC) (Corvus moneduloides) and Hawai'ian crow (Corvus hawaiiensis) lineages. The NC and, more recently, Hawai'ian crows are of great interest for their unusual tool-using foraging behaviour. I find only modest evidence for greater rates of molecular evolution at coding regions within these lineages. This thesis applies novel techniques to genomic data to identify candidate loci for evolutionary divergence in these different systems and highlight analytical methods that will be generally useful in other systems.

Published
2019
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7. Experimental Life History Evolution Results in Sex-specific Evolution of Gene Expression in Seed Beetles

Author

Immonen, Elina, Sayadi, Ahmed, Stojkovic, Biljana, Savkovic, Uros, Dordevic, Mirko, Liljestrand-Rönn, Johanna, Wiberg, R. Axel W., Arnqvist, Göran, Immonen, Elina, Sayadi, Ahmed, Stojkovic, Biljana, Savkovic, Uros, Dordevic, Mirko, Liljestrand-Rönn, Johanna, Wiberg, R. Axel W., and Arnqvist, Göran

Abstract

The patterns of reproductive timing and senescence vary within and across species owing to differences in reproductive strategies, but our understanding of the molecular underpinnings of such variation is incomplete. This is perhaps particularly true for sex differences. We investigated the evolution of sex-specific gene expression associated with life history divergence in replicated populations of the seed beetle Acanthoscelides obtectus, experimentally evolving under (E)arly or (L)ate life reproduction for >200 generations which has resulted in strongly divergent life histories. We detected 1,646 genes that were differentially expressed in E and L lines, consistent with a highly polygenic basis of life history evolution. Only 30% of differentially expressed genes were similarly affected in males and females. The evolution of long life was associated with significantly reduced sex differences in expression, especially in non-reproductive tissues. The expression differences were overall more pronounced in females, in accordance with their greater phenotypic divergence in lifespan. Functional enrichment analysis revealed differences between E and L beetles in gene categories previously implicated in aging, such as mitochondrial function and defense response. The results show that divergent life history evolution can be associated with profound changes in gene expression that alter the transcriptome in a sex-specific way, highlighting the importance of understanding the mechanisms of aging in each sex.

Published
2023
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8. Y-Linked Copy Number Polymorphism of Target of Rapamycin Is Associated with Sexual Size Dimorphism in Seed Beetles

Author

Kaufmann, Philipp, Wiberg, R. Axel W., Papachristos, Konstantinos, Scofield, Douglas G., Tellgren-Roth, Christian, Immonen, Elina, Kaufmann, Philipp, Wiberg, R. Axel W., Papachristos, Konstantinos, Scofield, Douglas G., Tellgren-Roth, Christian, and Immonen, Elina

Abstract

The Y chromosome is theorized to facilitate evolution of sexual dimorphism by accumulating sexually antagonistic loci, but empirical support is scarce. Due to the lack of recombination, Y chromosomes are prone to degenerative processes, which poses a constraint on their adaptive potential. Yet, in the seed beetle, Callosobruchus maculatus segregating Y linked variation affects male body size and thereby sexual size dimorphism (SSD). Here, we assemble C. maculatus sex chromosome sequences and identify molecular differences associated with Y-linked SSD variation. The assembled Y chromosome is largely euchromatic and contains over 400 genes, many of which are ampliconic with a mixed autosomal and X chromosome ancestry. Functional annotation suggests that the Y chromosome plays important roles in males beyond primary reproductive functions. Crucially, we find that, besides an autosomal copy of the gene target of rapamycin (TOR), males carry an additional TOR copy on the Y chromosome. TOR is a conserved regulator of growth across taxa, and our results suggest that a Y-linked TOR provides a male specific opportunity to alter body size. A comparison of Y haplotypes associated with male size difference uncovers a copy number variation for TOR, where the haplotype associated with decreased male size, and thereby increased sexual dimorphism, has two additional TOR copies. This suggests that sexual conflict over growth has been mitigated by autosome to Y translocation of TOR followed by gene duplications. Our results reveal that despite of suppressed recombination, the Y chromosome can harbor adaptive potential as a male-limited supergene.

Published
2023
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11. The genetic basis and adult reproductive consequences of developmental thermal plasticity

Author

Rodrigues, Leonor R., Zwoinska, Martyna K., Wiberg, R. Axel W., Snook, Rhonda R., Rodrigues, Leonor R., Zwoinska, Martyna K., Wiberg, R. Axel W., and Snook, Rhonda R.

Abstract

Increasing temperature and thermal variability generate profound selection on populations. Given the fast rate of environmental change, understanding the role of plasticity and genetic adaptation in response to increasing temperatures is critical. This may be especially true for thermal effects on reproductive traits in which thermal fertility limits at high temperatures may be lower than for survival traits. Consequences of changing environments during development on adult phenotypes may be particularly problematic for core traits such as reproduction that begin early in development. Here we examine the consequences of developmental thermal plasticity on subsequent adult reproductive traits and its genetic basis. We used a panel of Drosophila melanogaster (the Drosophila Genetic Reference Panel; DGRP) in which male fertility performance was previously defined as either showing relatively little (status = ‘high’-performing lines) or substantial (‘low’-performing lines) decline when exposed to increasing developmental temperatures. We used a thermal reaction norm approach to quantify variation in the consequences of developmental thermal plasticity on multiple adult reproductive traits, including sex-specific responses, and to identify candidate genes underlying such variation. Developmental thermal stress impacted the means and thermal reaction norms of all reproductive traits except offspring sex ratio. Mating success declined as temperature increased with no difference between high and low lines, whereas increasing temperature resulted in declines for both male and female fertility and productivity but depended on line status. Fertility and offspring number were positively correlated within and between the sexes across lines, but males were more affected than females. We identified 933 SNPs with significant evolved genetic differentiation between high and low lines. In all, 54 of these lie within genomic windows of overall high differentiation, have significant ef

Published
2022
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12. Mating strategy predicts gene presence/absence patterns in a genus of simultaneously hermaphroditic flatworms

Author

Wiberg, R. Axel W., Viktorin, Gudrun, Scharer, Lukas, Wiberg, R. Axel W., Viktorin, Gudrun, and Scharer, Lukas

Abstract

Gene repertoire turnover is a characteristic of genome evolution. However, we lack well-replicated analyses of presence/absence patterns associated with different selection contexts. Here, we study similar to 100 transcriptome assemblies across Macrostomum, a genus of simultaneously hermaphroditic flatworms exhibiting multiple convergent shifts in mating strategy and associated reproductive morphologies. Many species mate reciprocally, with partners donating and receiving sperm at the same time. Other species convergently evolved to mate by hypodermic injection of sperm into the partner. We find that for orthologous transcripts annotated as expressed in the body region containing the testes, sequences from hypodermically inseminating species diverge more rapidly from the model species, Macrostomum lignano, and have a lower probability of being observed in other species. For other annotation categories, simpler models with a constant rate of similarity decay with increasing genetic distance from M. lignano match the observed patterns well. Thus, faster rates of sequence evolution for hypodermically inseminating species in testis-region genes result in higher rates of homology detection failure, yielding a signal of rapid evolution in sequence presence/absence patterns. Our results highlight the utility of considering appropriate null models for unobserved genes, as well as associating patterns of gene presence/absence with replicated evolutionary events in a phylogenetic context.

Published
2022
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16. Pool-seq DrosEU 2014 samples VCF file

Author

Agencia Estatal de Investigación (España), University of Freiburg, Academy of Finland, Russian Foundation for Basic Research, Danish Natural Science Research Council, Ministerio de Economía y Competitividad (España), European Commission, Centre National de la Recherche Scientifique (France), Swedish Research Council, German Research Foundation, National Institutes of Health (US), Ministerio de Ciencia, Innovación y Universidades (España), The Scientific and Technological Research Council of Turkey, Agence Nationale de la Recherche (France), Israel Science Foundation, Austrian Science Fund, Biotechnology and Biological Sciences Research Council (UK), Swiss National Science Foundation, Kapun, Martin [0000-0002-3810-0504], Barrón, Maite G. [0000-0001-6146-6259], Staubach, Fabian [0000-0002-8097-2349], Vieira, Jorge [0000-0001-7032-5220], Obbard, Darren, J. [0000-0001-5392-8142], Rota-Stabelli, Omar [0000-0002-0030-7788], Kankare, Maaria [0000-0003-1541-9050], Haudry, Annabelle [0000-0001-6088-0909], Wiberg, R. Axel W. [0000-0002-8074-8670], Waidele, Lena [0000-0002-6323-6438], Kozeretska, Iryna [0000-0002-6485-1408], Pasyukova, Elena G. [0000-0002-6491-8561], Loeschcke, Volker [0000-0003-1450-0754], Pascual, Marta [0000-0002-6189-0612], Vieira, Cristina P. [0000-0002-7139-2107], Serga, Svitlana [0000-0003-1875-3185], Montchamp-Moreau, Catherine [0000-0002-5044-9709], Abbott, Jessica [0000-0002-8743-2089], Gibert, Patricia [0000-0002-9461-6820], Porcelli, Damiano [0000-0002-9019-5758], Posnien, Nico [0000-0003-0700-5595], Grath, Sonja [0000-0003-3621-736X], Sucena, Élio [0000-0001-8810-870X], Bergland, Alan O. [0000-0001-7145-7575], Onder, Banu Sebnem [0000-0002-3003-248X], Argyridou, Eliza [0000-0002-6890-4642], Guio, Lain [0000-0002-5481-5200], Schou, Mads Fristrup [0000-0001-5521-5269], Deplancke, Bart [0000-0001-9935-843X], Vieira, Cristina [0000-0003-3414-3993], Ritchie, Michael G. [0000-0001-7913-8675], Zwaan, Blas J. [0000-0002-8221-4998], Tauber, Eran [0000-0003-4018-6535], Orengo, Dorcas J. [0000-0001-7911-3224], Puerma, Eva [0000-0001-7261-187X], Aguadé i Porres, Montserrat [0000-0002-3884-7800], Schmidt, Paul S. [0000-0002-8076-6705], Parsch, John [0000-0001-9068-5549], Betancourt, Andrea J. [0000-0001-9351-1413], Flatt, Thomas [0000-0002-5990-1503], González Pérez, Josefa [0000-0001-9824-027X], González Pérez, Josefa [josefa.gonzalez@ibe.upf-csic.es], Kapun, Martin, Barrón, Maite G., Staubach, Fabian, Vieira, Jorge, Obbard, Darren, J., Rota-Stabelli, Omar, Kankare, Maaria, Haudry, Annabelle, Wiberg, R. Axel W., Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G., Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P., Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico, Grath, Sonja, Sucena, Élio, Bergland, Alan O., Garcia Guerreiro, Maria Pilar, Onder, Banu Sebnem, Argyridou, Eliza, Guio, Lain, Schou, Mads Fristrup, Deplancke, Bart, Vieira, Cristina, Ritchie, Michael G., Zwaan, Blas J., Tauber, Eran, Orengo, Dorcas J., Puerma, Eva, Aguadé i Porres, Montserrat, Schmidt, Paul S., Parsch, John, Betancourt, Andrea J., Flatt, Thomas, González Pérez, Josefa, Agencia Estatal de Investigación (España), University of Freiburg, Academy of Finland, Russian Foundation for Basic Research, Danish Natural Science Research Council, Ministerio de Economía y Competitividad (España), European Commission, Centre National de la Recherche Scientifique (France), Swedish Research Council, German Research Foundation, National Institutes of Health (US), Ministerio de Ciencia, Innovación y Universidades (España), The Scientific and Technological Research Council of Turkey, Agence Nationale de la Recherche (France), Israel Science Foundation, Austrian Science Fund, Biotechnology and Biological Sciences Research Council (UK), Swiss National Science Foundation, Kapun, Martin [0000-0002-3810-0504], Barrón, Maite G. [0000-0001-6146-6259], Staubach, Fabian [0000-0002-8097-2349], Vieira, Jorge [0000-0001-7032-5220], Obbard, Darren, J. [0000-0001-5392-8142], Rota-Stabelli, Omar [0000-0002-0030-7788], Kankare, Maaria [0000-0003-1541-9050], Haudry, Annabelle [0000-0001-6088-0909], Wiberg, R. Axel W. [0000-0002-8074-8670], Waidele, Lena [0000-0002-6323-6438], Kozeretska, Iryna [0000-0002-6485-1408], Pasyukova, Elena G. [0000-0002-6491-8561], Loeschcke, Volker [0000-0003-1450-0754], Pascual, Marta [0000-0002-6189-0612], Vieira, Cristina P. [0000-0002-7139-2107], Serga, Svitlana [0000-0003-1875-3185], Montchamp-Moreau, Catherine [0000-0002-5044-9709], Abbott, Jessica [0000-0002-8743-2089], Gibert, Patricia [0000-0002-9461-6820], Porcelli, Damiano [0000-0002-9019-5758], Posnien, Nico [0000-0003-0700-5595], Grath, Sonja [0000-0003-3621-736X], Sucena, Élio [0000-0001-8810-870X], Bergland, Alan O. [0000-0001-7145-7575], Onder, Banu Sebnem [0000-0002-3003-248X], Argyridou, Eliza [0000-0002-6890-4642], Guio, Lain [0000-0002-5481-5200], Schou, Mads Fristrup [0000-0001-5521-5269], Deplancke, Bart [0000-0001-9935-843X], Vieira, Cristina [0000-0003-3414-3993], Ritchie, Michael G. [0000-0001-7913-8675], Zwaan, Blas J. [0000-0002-8221-4998], Tauber, Eran [0000-0003-4018-6535], Orengo, Dorcas J. [0000-0001-7911-3224], Puerma, Eva [0000-0001-7261-187X], Aguadé i Porres, Montserrat [0000-0002-3884-7800], Schmidt, Paul S. [0000-0002-8076-6705], Parsch, John [0000-0001-9068-5549], Betancourt, Andrea J. [0000-0001-9351-1413], Flatt, Thomas [0000-0002-5990-1503], González Pérez, Josefa [0000-0001-9824-027X], González Pérez, Josefa [josefa.gonzalez@ibe.upf-csic.es], Kapun, Martin, Barrón, Maite G., Staubach, Fabian, Vieira, Jorge, Obbard, Darren, J., Rota-Stabelli, Omar, Kankare, Maaria, Haudry, Annabelle, Wiberg, R. Axel W., Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G., Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P., Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico, Grath, Sonja, Sucena, Élio, Bergland, Alan O., Garcia Guerreiro, Maria Pilar, Onder, Banu Sebnem, Argyridou, Eliza, Guio, Lain, Schou, Mads Fristrup, Deplancke, Bart, Vieira, Cristina, Ritchie, Michael G., Zwaan, Blas J., Tauber, Eran, Orengo, Dorcas J., Puerma, Eva, Aguadé i Porres, Montserrat, Schmidt, Paul S., Parsch, John, Betancourt, Andrea J., Flatt, Thomas, and González Pérez, Josefa

Published
2019

19. Transcriptome assemblies, gene alignments and phylogenetic trees supporting Brand et al. 2021. Large-scale phylogenomics of the genus Macrostomum (Platyhelminthes) reveals cryptic diversity and novel sexual traits

Author

Brand, Jeremias N., Viktorin, Gudrun, Wiberg, R. Axel W. Wiberg, Beisel, Christin, and Schärer, Lukas

Subjects
Macrostomum, Phylogeny
Abstract

The deposited folders contain results of the computations performed in: Brand, J. N., G. Viktorin, R. A. W. Wiberg, C. Beisel, and L. Schärer. 2021. Large-scale phylogenomics of the genus Macrostomum (Platyhelminthes) reveals cryptic diversity and novel sexual traits. Primer and noPrimer contain the alignments and transcriptomes, with and without the SMARTseq primers. We recommend you only use the noPrimer data. Naming follows the description in Brand et al. 2021. fa: Trinity transcriptome assembly pep: protein sequence predicted by TransDecoder cds: coding sequence predicted by TransDecoder The trees directory contains both ultrametric (UM) and non ultrametric species trees. 28S_C.aln: Alignment of 28S sequences used for the C-IQ-TREE phylogenetic inference. 28S_delim.aln: Aligment of 28S sequences used for species delimitation using haplotype networks (after filtering from missing data, 28S_delim_nogap.aln) &nbsp

Published
2021
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22. Experimental evolution supports signatures of sexual selection in genomic divergence

Author

Wiberg, R. Axel W., Veltsos, Paris, Snook, Rhonda R., Ritchie, Michael G., Wiberg, R. Axel W., Veltsos, Paris, Snook, Rhonda R., and Ritchie, Michael G.

Abstract

Comparative genomics has contributed to the growing evidence that sexual selection is an important component of evolutionary divergence and speciation. Divergence by sexual selection is implicated in faster rates of divergence of the X chromosome and of genes thought to underlie sexually selected traits, including genes that are sex biased in expression. However, accurately inferring the relative importance of complex and interacting forms of natural selection, demography, and neutral processes that occurred in the evolutionary past is challenging. Experimental evolution provides an opportunity to apply controlled treatments for multiple generations and examine the consequent genomic divergence. Here, we altered sexual selection intensity, elevating sexual selection in polyandrous lines and eliminating it in monogamous lines, and examined patterns of allele frequency divergence in the genome of Drosophila pseudoobscura after more than 160 generations of experimental evolution. Divergence is not uniform across the genome but concentrated in islands, many of which contain candidate genes implicated in mating behaviors and other sexually selected phenotypes. These are more often seen on the X chromosome, which also shows greater divergence in F-ST than neutral expectations. There are characteristic signatures of selection seen in these regions, with lower diversity on the X chromosome than the autosomes, and differences in diversity on the autosomes between selection regimes. Reduced Tajima's D within some of the divergent regions may imply that selective sweeps have occurred, despite considerable recombination. These changes are associated with both differential gene expression between the lines and sex-biased gene expression within the lines. Our results are very similar to those thought to implicate sexual selection in divergence between species and natural populations, and hence provide experimental support for the likely role of sexual selection in driving such ty

Published
2021
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23. A genome-wide investigation of adaptive signatures in protein-coding genes related to tool behaviour in New Caledonian and Hawaiian crows

Author

Dussex, Nicolas, Kutschera, Verena E., Wiberg, R. Axel W., Parker, Darren J., Hunt, Gavin R., Gray, Russell D., Rutherford, Kim, Abe, Hideaki, Fleischer, Robert C., Ritchie, Michael G., Rutz, Christian, Wolf, Jochen B. W., Gemmell, Neil J., Dussex, Nicolas, Kutschera, Verena E., Wiberg, R. Axel W., Parker, Darren J., Hunt, Gavin R., Gray, Russell D., Rutherford, Kim, Abe, Hideaki, Fleischer, Robert C., Ritchie, Michael G., Rutz, Christian, Wolf, Jochen B. W., and Gemmell, Neil J.

Abstract

Very few animals habitually manufacture and use tools. It has been suggested that advanced tool behaviour co-evolves with a suite of behavioural, morphological and life history traits. In fact, there are indications for such an adaptive complex in tool-using crows (genus Corvus species). Here, we sequenced the genomes of two habitually tool-using and ten non-tool-using crow species to search for genomic signatures associated with a tool-using lifestyle. Using comparative genomic and population genetic approaches, we screened for signals of selection in protein-coding genes in the tool-using New Caledonian and Hawaiian crows. While we detected signals of recent selection in New Caledonian crows near genes associated with bill morphology, our data indicate that genetic changes in these two lineages are surprisingly subtle, with little evidence at present for convergence. We explore the biological explanations for these findings, such as the relative roles of gene regulation and protein-coding changes, as well as the possibility that statistical power to detect selection in recently diverged lineages may have been insufficient. Our study contributes to a growing body of literature aiming to decipher the genetic basis of recently evolved complex behaviour.

Published
2021
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24. Genomic analysis of European Drosophila populations reveals longitudinal structure and continent-wide selection

Author

Kapun, Martin, Barrón, Maite G., Staubach, Fabian, Vieira, Jorge, Obbard, Darren, J., Rota-Stabelli, Omar, Kankare, Maaria, Haudry, Annabelle, Wiberg, R. Axel W., Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G., Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P., Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico, Grath, Sonja, Sucena, Élio, Bergland, Alan O., Garcia Guerreiro, Maria Pilar, Onder, Banu Sebnem, Argyridou, Eliza, Guio, Lain, Schou, Mads Fristrup, Deplancke, Bart, Vieira, Cristina, Ritchie, Michael G., Zwaan, Blas J., Tauber, Eran, Orengo, Dorcas J., Puerma, Eva, Aguadé i Porres, Montserrat, Schmidt, Paul S., Parsch, John, Betancourt, Andrea J., Flatt, Thomas, González Pérez, Josefa, Agencia Estatal de Investigación (España), University of Freiburg, Academy of Finland, Russian Foundation for Basic Research, Danish Natural Science Research Council, Ministerio de Economía y Competitividad (España), European Commission, Centre National de la Recherche Scientifique (France), Swedish Research Council, German Research Foundation, National Institutes of Health (US), Ministerio de Ciencia, Innovación y Universidades (España), Agence Nationale de la Recherche (France), Israel Science Foundation, Austrian Science Fund, Biotechnology and Biological Sciences Research Council (UK), Swiss National Science Foundation, Kapun, Martin [0000-0002-3810-0504], Barrón, Maite G. [0000-0001-6146-6259], Staubach, Fabian [0000-0002-8097-2349], Vieira, Jorge [0000-0001-7032-5220], Obbard, Darren, J. [0000-0001-5392-8142], Rota-Stabelli, Omar [0000-0002-0030-7788], Kankare, Maaria [0000-0003-1541-9050], Haudry, Annabelle [0000-0001-6088-0909], Wiberg, R. Axel W. [0000-0002-8074-8670], Waidele, Lena [0000-0002-6323-6438], Kozeretska, Iryna [0000-0002-6485-1408], Pasyukova, Elena G. [0000-0002-6491-8561], Loeschcke, Volker [0000-0003-1450-0754], Pascual, Marta [0000-0002-6189-0612], Vieira, Cristina P. [0000-0002-7139-2107], Serga, Svitlana [0000-0003-1875-3185], Montchamp-Moreau, Catherine [0000-0002-5044-9709], Abbott, Jessica [0000-0002-8743-2089], Gibert, Patricia [0000-0002-9461-6820], Porcelli, Damiano [0000-0002-9019-5758], Posnien, Nico [0000-0003-0700-5595], Grath, Sonja [0000-0003-3621-736X], Sucena, Élio [0000-0001-8810-870X], Bergland, Alan O. [0000-0001-7145-7575], Onder, Banu Sebnem [0000-0002-3003-248X], Argyridou, Eliza [0000-0002-6890-4642], Guio, Lain [0000-0002-5481-5200], Schou, Mads Fristrup [0000-0001-5521-5269], Deplancke, Bart [0000-0001-9935-843X], Vieira, Cristina [0000-0003-3414-3993], Ritchie, Michael G. [0000-0001-7913-8675], Zwaan, Blas J. [0000-0002-8221-4998], Tauber, Eran [0000-0003-4018-6535], Orengo, Dorcas J. [0000-0001-7911-3224], Puerma, Eva [0000-0001-7261-187X], Aguadé i Porres, Montserrat [0000-0002-3884-7800], Schmidt, Paul S. [0000-0002-8076-6705], Parsch, John [0000-0001-9068-5549], Betancourt, Andrea J. [0000-0001-9351-1413], Flatt, Thomas [0000-0002-5990-1503], González Pérez, Josefa [0000-0001-9824-027X], Kapun, Martin, Barrón, Maite G., Staubach, Fabian, Vieira, Jorge, Obbard, Darren, J., Rota-Stabelli, Omar, Kankare, Maaria, Haudry, Annabelle, Wiberg, R. Axel W., Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G., Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P., Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico, Grath, Sonja, Sucena, Élio, Bergland, Alan O., Onder, Banu Sebnem, Argyridou, Eliza, Guio, Lain, Schou, Mads Fristrup, Deplancke, Bart, Vieira, Cristina, Ritchie, Michael G., Zwaan, Blas J., Tauber, Eran, Orengo, Dorcas J., Puerma, Eva, Aguadé i Porres, Montserrat, Schmidt, Paul S., Parsch, John, Betancourt, Andrea J., Flatt, Thomas, and González Pérez, Josefa

Abstract

Genetic variation is the fuel of evolution. However, analyzing evolutionary dynamics in natural populations is challenging, sequencing of entire populations remains costly and comprehensive sampling logistically difficult. To tackle this issue and to define relevant spatial and temporal scales of variation, we have founded the European Drosophila Population Genomics Consortium (DrosEU). Here we present the first analysis of 48 D. melanogaster population samples collected across Europe in 2014. Our analysis uncovers novel patterns of variation at multiple levels: genome-wide neutral SNPs, mtDNA haplotypes, inversions, and TEs showing previously cryptic longitudinal population structure; signatures of selective sweeps shared among populations; presumably adaptive clines in inversions; and geographic variation in TEs. Additionally, we document highly variable microbiota and identify several new Drosophila viruses. Our study reveals novel aspects of the population biology of D. melanogaster and illustrates the power of extensive sampling and pooled sequencing of populations on a continent-wide scale.

Published
2018

26. Genomic analysis of European Drosophila populations reveals longitudinal structure and continent-wide selection

Author

Agencia Estatal de Investigación (España), University of Freiburg, Academy of Finland, Russian Foundation for Basic Research, Danish Natural Science Research Council, Ministerio de Economía y Competitividad (España), European Commission, Centre National de la Recherche Scientifique (France), Swedish Research Council, German Research Foundation, National Institutes of Health (US), Ministerio de Ciencia, Innovación y Universidades (España), Agence Nationale de la Recherche (France), Israel Science Foundation, Austrian Science Fund, Biotechnology and Biological Sciences Research Council (UK), Swiss National Science Foundation, Kapun, Martin [0000-0002-3810-0504], Barrón, Maite G. [0000-0001-6146-6259], Staubach, Fabian [0000-0002-8097-2349], Vieira, Jorge [0000-0001-7032-5220], Obbard, Darren, J. [0000-0001-5392-8142], Rota-Stabelli, Omar [0000-0002-0030-7788], Kankare, Maaria [0000-0003-1541-9050], Haudry, Annabelle [0000-0001-6088-0909], Wiberg, R. Axel W. [0000-0002-8074-8670], Waidele, Lena [0000-0002-6323-6438], Kozeretska, Iryna [0000-0002-6485-1408], Pasyukova, Elena G. [0000-0002-6491-8561], Loeschcke, Volker [0000-0003-1450-0754], Pascual, Marta [0000-0002-6189-0612], Vieira, Cristina P. [0000-0002-7139-2107], Serga, Svitlana [0000-0003-1875-3185], Montchamp-Moreau, Catherine [0000-0002-5044-9709], Abbott, Jessica [0000-0002-8743-2089], Gibert, Patricia [0000-0002-9461-6820], Porcelli, Damiano [0000-0002-9019-5758], Posnien, Nico [0000-0003-0700-5595], Grath, Sonja [0000-0003-3621-736X], Sucena, Élio [0000-0001-8810-870X], Bergland, Alan O. [0000-0001-7145-7575], Onder, Banu Sebnem [0000-0002-3003-248X], Argyridou, Eliza [0000-0002-6890-4642], Guio, Lain [0000-0002-5481-5200], Schou, Mads Fristrup [0000-0001-5521-5269], Deplancke, Bart [0000-0001-9935-843X], Vieira, Cristina [0000-0003-3414-3993], Ritchie, Michael G. [0000-0001-7913-8675], Zwaan, Blas J. [0000-0002-8221-4998], Tauber, Eran [0000-0003-4018-6535], Orengo, Dorcas J. [0000-0001-7911-3224], Puerma, Eva [0000-0001-7261-187X], Aguadé i Porres, Montserrat [0000-0002-3884-7800], Schmidt, Paul S. [0000-0002-8076-6705], Parsch, John [0000-0001-9068-5549], Betancourt, Andrea J. [0000-0001-9351-1413], Flatt, Thomas [0000-0002-5990-1503], González Pérez, Josefa [0000-0001-9824-027X], Kapun, Martin, Barrón, Maite G., Staubach, Fabian, Vieira, Jorge, Obbard, Darren, J., Rota-Stabelli, Omar, Kankare, Maaria, Haudry, Annabelle, Wiberg, R. Axel W., Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G., Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P., Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico, Grath, Sonja, Sucena, Élio, Bergland, Alan O., Garcia Guerreiro, Maria Pilar, Onder, Banu Sebnem, Argyridou, Eliza, Guio, Lain, Schou, Mads Fristrup, Deplancke, Bart, Vieira, Cristina, Ritchie, Michael G., Zwaan, Blas J., Tauber, Eran, Orengo, Dorcas J., Puerma, Eva, Aguadé i Porres, Montserrat, Schmidt, Paul S., Parsch, John, Betancourt, Andrea J., Flatt, Thomas, González Pérez, Josefa, Agencia Estatal de Investigación (España), University of Freiburg, Academy of Finland, Russian Foundation for Basic Research, Danish Natural Science Research Council, Ministerio de Economía y Competitividad (España), European Commission, Centre National de la Recherche Scientifique (France), Swedish Research Council, German Research Foundation, National Institutes of Health (US), Ministerio de Ciencia, Innovación y Universidades (España), Agence Nationale de la Recherche (France), Israel Science Foundation, Austrian Science Fund, Biotechnology and Biological Sciences Research Council (UK), Swiss National Science Foundation, Kapun, Martin [0000-0002-3810-0504], Barrón, Maite G. [0000-0001-6146-6259], Staubach, Fabian [0000-0002-8097-2349], Vieira, Jorge [0000-0001-7032-5220], Obbard, Darren, J. [0000-0001-5392-8142], Rota-Stabelli, Omar [0000-0002-0030-7788], Kankare, Maaria [0000-0003-1541-9050], Haudry, Annabelle [0000-0001-6088-0909], Wiberg, R. Axel W. [0000-0002-8074-8670], Waidele, Lena [0000-0002-6323-6438], Kozeretska, Iryna [0000-0002-6485-1408], Pasyukova, Elena G. [0000-0002-6491-8561], Loeschcke, Volker [0000-0003-1450-0754], Pascual, Marta [0000-0002-6189-0612], Vieira, Cristina P. [0000-0002-7139-2107], Serga, Svitlana [0000-0003-1875-3185], Montchamp-Moreau, Catherine [0000-0002-5044-9709], Abbott, Jessica [0000-0002-8743-2089], Gibert, Patricia [0000-0002-9461-6820], Porcelli, Damiano [0000-0002-9019-5758], Posnien, Nico [0000-0003-0700-5595], Grath, Sonja [0000-0003-3621-736X], Sucena, Élio [0000-0001-8810-870X], Bergland, Alan O. [0000-0001-7145-7575], Onder, Banu Sebnem [0000-0002-3003-248X], Argyridou, Eliza [0000-0002-6890-4642], Guio, Lain [0000-0002-5481-5200], Schou, Mads Fristrup [0000-0001-5521-5269], Deplancke, Bart [0000-0001-9935-843X], Vieira, Cristina [0000-0003-3414-3993], Ritchie, Michael G. [0000-0001-7913-8675], Zwaan, Blas J. [0000-0002-8221-4998], Tauber, Eran [0000-0003-4018-6535], Orengo, Dorcas J. [0000-0001-7911-3224], Puerma, Eva [0000-0001-7261-187X], Aguadé i Porres, Montserrat [0000-0002-3884-7800], Schmidt, Paul S. [0000-0002-8076-6705], Parsch, John [0000-0001-9068-5549], Betancourt, Andrea J. [0000-0001-9351-1413], Flatt, Thomas [0000-0002-5990-1503], González Pérez, Josefa [0000-0001-9824-027X], Kapun, Martin, Barrón, Maite G., Staubach, Fabian, Vieira, Jorge, Obbard, Darren, J., Rota-Stabelli, Omar, Kankare, Maaria, Haudry, Annabelle, Wiberg, R. Axel W., Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G., Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P., Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico, Grath, Sonja, Sucena, Élio, Bergland, Alan O., Garcia Guerreiro, Maria Pilar, Onder, Banu Sebnem, Argyridou, Eliza, Guio, Lain, Schou, Mads Fristrup, Deplancke, Bart, Vieira, Cristina, Ritchie, Michael G., Zwaan, Blas J., Tauber, Eran, Orengo, Dorcas J., Puerma, Eva, Aguadé i Porres, Montserrat, Schmidt, Paul S., Parsch, John, Betancourt, Andrea J., Flatt, Thomas, and González Pérez, Josefa

Abstract

Genetic variation is the fuel of evolution. However, analyzing evolutionary dynamics in natural populations is challenging, sequencing of entire populations remains costly and comprehensive sampling logistically difficult. To tackle this issue and to define relevant spatial and temporal scales of variation, we have founded the European Drosophila Population Genomics Consortium (DrosEU). Here we present the first analysis of 48 D. melanogaster population samples collected across Europe in 2014. Our analysis uncovers novel patterns of variation at multiple levels: genome-wide neutral SNPs, mtDNA haplotypes, inversions, and TEs showing previously cryptic longitudinal population structure; signatures of selective sweeps shared among populations; presumably adaptive clines in inversions; and geographic variation in TEs. Additionally, we document highly variable microbiota and identify several new Drosophila viruses. Our study reveals novel aspects of the population biology of D. melanogaster and illustrates the power of extensive sampling and pooled sequencing of populations on a continent-wide scale.

Published
2018

27. Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses

Author

Kapun, Martin, Barrón, Maite G, Staubach, Fabian, Obbard, Darren J, Wiberg, R Axel W, Vieira, Jorge, Goubert, Clément, Rota-Stabelli, Omar, Kankare, Maaria, Bogaerts-Márquez, María, Haudry, Annabelle, Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G, Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P, Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico, Sánchez-Gracia, Alejandro, Grath, Sonja, Sucena, Élio, Bergland, Alan O, Guerreiro, Maria Pilar Garcia, Onder, Banu Sebnem, Argyridou, Eliza, University of Zurich, Falush, Daniel, and Kapun, Martin

Subjects
10127 Institute of Evolutionary Biology and Environmental Studies, 1105 Ecology, Evolution, Behavior and Systematics, 1311 Genetics, Ecology, Behavior and Systematics, Evolution, 1312 Molecular Biology, Genetics, 570 Life sciences, biology, 590 Animals (Zoology), Molecular Biology
Published
2020

28. Purifying Selection in Corvids Is Less Efficient on Islands

Author

Kutschera, Verena E., Poelstra, Jelmer W., Botero-Castro, Fidel, Dussex, Nicolas, Gennnnell, Neil J., Hunt, Gavin R., Ritchie, Michael G., Rutz, Christian, Wiberg, R. Axel W., Wolf, Jochen B. W., Kutschera, Verena E., Poelstra, Jelmer W., Botero-Castro, Fidel, Dussex, Nicolas, Gennnnell, Neil J., Hunt, Gavin R., Ritchie, Michael G., Rutz, Christian, Wiberg, R. Axel W., and Wolf, Jochen B. W.

Abstract

Theory predicts that deleterious mutations accumulate more readily in small populations. As a consequence, mutation load is expected to be elevated in species where life-history strategies and geographic or historical contingencies reduce the number of reproducing individuals. Yet, few studies have empirically tested this prediction using genome-wide data in a comparative framework. We collected whole-genome sequencing data for 147 individuals across seven crow species (Corvus spp.). For each species, we estimated the distribution of fitness effects of deleterious mutations and compared it with proxies of the effective population size N-e. Island species with comparatively smaller geographic range sizes had a significantly increased mutation load. These results support the view that small populations have an elevated risk of mutational meltdown, which may contribute to the higher extinction rates observed in island species.

Published
2020
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29. Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses

Author

CSIC - Unidad de Recursos de Información Científica para la Investigación (URICI), Stanford University, European Society for Evolutionary Biology, Wellcome Trust, University of Freiburg, German Research Foundation, Academy of Finland, Russian Foundation for Basic Research, Danish Natural Science Research Council, Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Centre National de la Recherche Scientifique (France), Swedish Research Council, National Institutes of Health (US), The Scientific and Technological Research Council of Turkey, Agence Nationale de la Recherche (France), European Commission, Israel Science Foundation, Austrian Science Fund, Biotechnology and Biological Sciences Research Council (UK), Swiss National Science Foundation, European Research Council, Generalitat de Catalunya, Kapun, Martin, Barrón, Maite G., Staubach, Fabian, Obbard, Darren, J., Wiberg, R. Axel W., Vieira, Jorge, Goubert, Clément, Rota-Stabelli, Omar, Kankare, Maaria, Bogaerts-Márquez, María, Haudry, Annabelle, Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G., Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P., Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico, Sánchez-Gracia, Alejandro, Grath, Sonja, Sucena, Élio, Bergland, Alan O., Garcia Guerreiro, Maria Pilar, Onder, Banu Sebnem, Argyridou, Eliza, Guio, Lain, Schou, Mads Fristrup, Deplancke, Bart, Vieira, Cristina, Ritchie, Michael G., Zwaan, Blas J., Tauber, Eran, Orengo, Dorcas J., Puerma, Eva, Aguadé i Porres, Montserrat, Schmidt, Paul S., Parsch, John, Betancourt, Andrea J., Flatt, Thomas, González Pérez, Josefa, CSIC - Unidad de Recursos de Información Científica para la Investigación (URICI), Stanford University, European Society for Evolutionary Biology, Wellcome Trust, University of Freiburg, German Research Foundation, Academy of Finland, Russian Foundation for Basic Research, Danish Natural Science Research Council, Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Centre National de la Recherche Scientifique (France), Swedish Research Council, National Institutes of Health (US), The Scientific and Technological Research Council of Turkey, Agence Nationale de la Recherche (France), European Commission, Israel Science Foundation, Austrian Science Fund, Biotechnology and Biological Sciences Research Council (UK), Swiss National Science Foundation, European Research Council, Generalitat de Catalunya, Kapun, Martin, Barrón, Maite G., Staubach, Fabian, Obbard, Darren, J., Wiberg, R. Axel W., Vieira, Jorge, Goubert, Clément, Rota-Stabelli, Omar, Kankare, Maaria, Bogaerts-Márquez, María, Haudry, Annabelle, Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G., Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P., Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico, Sánchez-Gracia, Alejandro, Grath, Sonja, Sucena, Élio, Bergland, Alan O., Garcia Guerreiro, Maria Pilar, Onder, Banu Sebnem, Argyridou, Eliza, Guio, Lain, Schou, Mads Fristrup, Deplancke, Bart, Vieira, Cristina, Ritchie, Michael G., Zwaan, Blas J., Tauber, Eran, Orengo, Dorcas J., Puerma, Eva, Aguadé i Porres, Montserrat, Schmidt, Paul S., Parsch, John, Betancourt, Andrea J., Flatt, Thomas, and González Pérez, Josefa

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.

Published
2020

30. Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses

Author

Falush, Daniel, Falush, D ( Daniel ), Kapun, Martin; https://orcid.org/0000-0002-3810-0504, Barrón, Maite G, Staubach, Fabian, Obbard, Darren J, Wiberg, R Axel W; https://orcid.org/0000-0001-5392-8142, Vieira, Jorge, Goubert, Clément, Rota-Stabelli, Omar, Kankare, Maaria; https://orcid.org/0000-0003-1541-9050, Bogaerts-Márquez, María, Haudry, Annabelle, Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G, Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P, Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico; https://orcid.org/0000-0003-0700-5595, Sánchez-Gracia, Alejandro, Grath, Sonja, Sucena, Élio, Bergland, Alan O, Guerreiro, Maria Pilar Garcia, Onder, Banu Sebnem, Argyridou, Eliza, Falush, Daniel, Falush, D ( Daniel ), Kapun, Martin; https://orcid.org/0000-0002-3810-0504, Barrón, Maite G, Staubach, Fabian, Obbard, Darren J, Wiberg, R Axel W; https://orcid.org/0000-0001-5392-8142, Vieira, Jorge, Goubert, Clément, Rota-Stabelli, Omar, Kankare, Maaria; https://orcid.org/0000-0003-1541-9050, Bogaerts-Márquez, María, Haudry, Annabelle, Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G, Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P, Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico; https://orcid.org/0000-0003-0700-5595, Sánchez-Gracia, Alejandro, Grath, Sonja, Sucena, Élio, Bergland, Alan O, Guerreiro, Maria Pilar Garcia, Onder, Banu Sebnem, and Argyridou, Eliza

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.

Published
2020

31. A genome‐wide investigation of adaptive signatures in protein‐coding genes related to tool behaviour in New Caledonian and Hawaiian crows

Author

Dussex, Nicolas, primary, Kutschera, Verena E., additional, Wiberg, R. Axel W., additional, Parker, Darren J., additional, Hunt, Gavin R., additional, Gray, Russell D., additional, Rutherford, Kim, additional, Abe, Hideaki, additional, Fleischer, Robert C., additional, Ritchie, Michael G., additional, Rutz, Christian, additional, Wolf, Jochen B. W., additional, and Gemmell, Neil J., additional

Published
2020
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33. Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses

Author

Kapun, Martin, primary, Barrón, Maite G, additional, Staubach, Fabian, additional, Obbard, Darren J, additional, Wiberg, R Axel W, additional, Vieira, Jorge, additional, Goubert, Clément, additional, Rota-Stabelli, Omar, additional, Kankare, Maaria, additional, Bogaerts-Márquez, María, additional, Haudry, Annabelle, additional, Waidele, Lena, additional, Kozeretska, Iryna, additional, Pasyukova, Elena G, additional, Loeschcke, Volker, additional, Pascual, Marta, additional, Vieira, Cristina P, additional, Serga, Svitlana, additional, Montchamp-Moreau, Catherine, additional, Abbott, Jessica, additional, Gibert, Patricia, additional, Porcelli, Damiano, additional, Posnien, Nico, additional, Sánchez-Gracia, Alejandro, additional, Grath, Sonja, additional, Sucena, Élio, additional, Bergland, Alan O, additional, Guerreiro, Maria Pilar Garcia, additional, Onder, Banu Sebnem, additional, Argyridou, Eliza, additional, Guio, Lain, additional, Schou, Mads Fristrup, additional, Deplancke, Bart, additional, Vieira, Cristina, additional, Ritchie, Michael G, additional, Zwaan, Bas J, additional, Tauber, Eran, additional, Orengo, Dorcas J, additional, Puerma, Eva, additional, Aguadé, Montserrat, additional, Schmidt, Paul, additional, Parsch, John, additional, Betancourt, Andrea J, additional, Flatt, Thomas, additional, and González, Josefa, additional

Published
2020
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37. Selection for reproduction under short photoperiods changes diapause-associated traits and induces widespread genomic divergence

Author

Kauranen, H. (Hannele), Kinnunen, J. (Johanna), Hiillos, A.-L. (Anna-Lotta), Lankinen, P. (Pekka), Hopkins, D. (David), Wiberg, R. A. (R. Axel W.), Ritchie, M. G. (Michael G.), Hoikkala, A. (Anneli), Kauranen, H. (Hannele), Kinnunen, J. (Johanna), Hiillos, A.-L. (Anna-Lotta), Lankinen, P. (Pekka), Hopkins, D. (David), Wiberg, R. A. (R. Axel W.), Ritchie, M. G. (Michael G.), and Hoikkala, A. (Anneli)

Abstract

The incidence of reproductive diapause is a critical aspect of life history in overwintering insects from temperate regions. Much has been learned about the timing, physiology and genetics of diapause in a range of insects, but how the multiple changes involved in this and other photoperiodically regulated traits are inter-related is not well understood. We performed quasinatural selection on reproduction under short photoperiods in a northern fly species, Drosophila montana, to trace the effects of photoperiodic selection on traits regulated by the photoperiodic timer and/or by a circadian clock system. Selection changed several traits associated with reproductive diapause, including the critical day length for diapause (CDL), the frequency of diapausing females under photoperiods that deviate from daily 24 h cycles and cold tolerance, towards the phenotypes typical of lower latitudes. However, selection had no effect on the period of free-running locomotor activity rhythm regulated by the circadian clock in fly brain. At a genomic level, selection induced extensive divergence from the control line in 16 gene clusters involved in signal transduction, membrane properties, immunologlobulins and development. These changes resembled those detected between latitudinally divergent D. montana populations in the wild and involved SNP divergence associated with several genes linked with diapause induction. Overall, our study shows that photoperiodic selection for reproduction under short photoperiods affects diapause-associated traits without disrupting the central clock network generating circadian rhythms in fly locomotor activity.

Published
2019

38. Purifying Selection in Corvids Is Less Efficient on Islands

Author

Kutschera, Verena E, primary, Poelstra, Jelmer W, additional, Botero-Castro, Fidel, additional, Dussex, Nicolas, additional, Gemmell, Neil J, additional, Hunt, Gavin R, additional, Ritchie, Michael G, additional, Rutz, Christian, additional, Wiberg, R Axel W, additional, and Wolf, Jochen B W, additional

Published
2019
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40. Identifying consistent allele frequency differences in studies of stratified populations

Author

Wiberg, R. Axel W., Gaggiotti, Oscar E., Morrissey, Michael B., Ritchie, Michael G., NERC, University of St Andrews. School of Biology, University of St Andrews. Centre for Biological Diversity, University of St Andrews. Marine Alliance for Science & Technology Scotland, University of St Andrews. Scottish Oceans Institute, and University of St Andrews. Institute of Behavioural and Neural Sciences

Subjects
QA75, Evolutionary Biology, Pool-seq, QA75 Electronic computers. Computer science, QH301 Biology, Quaibinomial GLM, CMH-test, selection, CMH‐test, DAS, QH426 Genetics, allele frequency differences, Allele frequency differences, pool‐seq, QH301, Experimental evolution, quasibinomial GLM, experimental evolution, Selection, QH426, Research Article
Abstract

This work was supported by a combined NERC and St Andrews 600th Anniversary PhD Studentship [grant NE/L501852/1] to RAWW and also supported by a NERC grant [grant NE/I027800/1] to MGR and Rhonda R. Snook. MBM was supported by The Royal Society. OEG was supported by MASTS (Marine Alliance for Science and Technology for Scotland). Computational analyses were supported by the University of St Andrews Bioinformatics Unit which is funded by a Wellcome Trust ISSF award [grant 105621/Z/14/Z]. 1. With increasing application of pooled-sequencing approaches to population genomics robust methods are needed to accurately quantify allele frequency differences between populations. Identifying consistent differences across stratified populations can allow us to detect genomic regions under selection and that differ between populations with different histories or attributes. Current popular statistical tests are easily implemented in widely available software tools which make them simple for researchers to apply. However, there are potential problems with the way such tests are used,which means that underlying assumptions about the data are frequently violated. 2. These problems are highlighted by simulation of simple but realistic population genetic models of neutral evolution and the performance of different tests are assessed. We present alternative tests (including GLMs with quasibinomial error structure) with attractive properties for the analysis of allele frequency differences and re-analyse a published dataset. 3. The simulations show that common statistical tests for consistent allele frequency differences perform poorly, with high false positive rates. Applying tests that do not confound heterogeneity and main effects significantly improves inference. Variation in sequencing coverage likely produces many false positives and re-scaling allele frequencies to counts out of a common value or an effective sample size reduces this effect. 4. Many researchers are interested in identifying allele frequencies that vary consistently across replicates to identify loci underlying phenotypic responses to selection or natural variation in phenotypes. Popular methods that have been suggested for this task perform poorly in simulations. Overall, quasibinomial GLMs perform better and also have the attractive feature of allowing correction for multiple testing by standard procedures and are easily extended to other designs. Publisher PDF

Published
2017

41. Purifying Selection in Corvids Is Less Efficient on Islands.

Author

Kutschera, Verena E, Poelstra, Jelmer W, Botero-Castro, Fidel, Dussex, Nicolas, Gemmell, Neil J, Hunt, Gavin R, Ritchie, Michael G, Rutz, Christian, Wiberg, R Axel W, and Wolf, Jochen B W

Abstract

Theory predicts that deleterious mutations accumulate more readily in small populations. As a consequence, mutation load is expected to be elevated in species where life-history strategies and geographic or historical contingencies reduce the number of reproducing individuals. Yet, few studies have empirically tested this prediction using genome-wide data in a comparative framework. We collected whole-genome sequencing data for 147 individuals across seven crow species (Corvus spp.). For each species, we estimated the distribution of fitness effects of deleterious mutations and compared it with proxies of the effective population size N e. Island species with comparatively smaller geographic range sizes had a significantly increased mutation load. These results support the view that small populations have an elevated risk of mutational meltdown, which may contribute to the higher extinction rates observed in island species. [ABSTRACT FROM AUTHOR]

Published
2020
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43. Genomic analysis of EuropeanDrosophila melanogasterpopulations reveals longitudinal structure, continent-wide selection, and previously unknown DNA viruses

Author

Kapun, Martin, primary, Barrón, Maite G., additional, Staubach, Fabian, additional, Obbard, Darren J., additional, Wiberg, R. Axel W., additional, Vieira, Jorge, additional, Goubert, Clément, additional, Rota-Stabelli, Omar, additional, Kankare, Maaria, additional, Bogaerts-Márquez, María, additional, Haudry, Annabelle, additional, Waidele, Lena, additional, Kozeretska, Iryna, additional, Pasyukova, Elena G., additional, Loeschcke, Volker, additional, Pascual, Marta, additional, Vieira, Cristina P., additional, Serga, Svitlana, additional, Montchamp-Moreau, Catherine, additional, Abbott, Jessica, additional, Gibert, Patricia, additional, Porcelli, Damiano, additional, Posnien, Nico, additional, Sánchez-Gracia, Alejandro, additional, Grath, Sonja, additional, Sucena, Élio, additional, Bergland, Alan O., additional, Guerreiro, Maria Pilar Garcia, additional, Onder, Banu Sebnem, additional, Argyridou, Eliza, additional, Guio, Lain, additional, Schou, Mads Fristrup, additional, Deplancke, Bart, additional, Vieira, Cristina, additional, Ritchie, Michael G., additional, Zwaan, Bas J., additional, Tauber, Eran, additional, Orengo, Dorcas J., additional, Puerma, Eva, additional, Aguadé, Montserrat, additional, Schmidt, Paul S., additional, Parsch, John, additional, Betancourt, Andrea J., additional, Flatt, Thomas, additional, and González, Josefa, additional

Published
2018
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47. The Genome and Methylome of a Beetle with Complex Social Behavior,Nicrophorus vespilloides(Coleoptera: Silphidae)

Author

Cunningham, Christopher B., primary, Ji, Lexiang, additional, Wiberg, R. Axel W., additional, Shelton, Jennifer, additional, McKinney, Elizabeth C., additional, Parker, Darren J., additional, Meagher, Richard B., additional, Benowitz, Kyle M., additional, Roy-Zokan, Eileen M., additional, Ritchie, Michael G., additional, Brown, Susan J., additional, Schmitz, Robert J., additional, and Moore, Allen J., additional

Published
2015
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49. The Nicrophorus vespilloides genome and methylome, a beetle with complex social behavior

Author

Cunningham, Christopher B, primary, Ji, Lexiang, additional, Wiberg, R. Axel W, additional, Shelton, Jennifer M, additional, McKinney, Elizabeth C, additional, Parker, Darren J, additional, Meagher, Richard B, additional, Benowitz, Kyle M, additional, Roy-Zokan, Eileen M, additional, Ritchie, Michael G, additional, Brown, Susan J, additional, Schmitz, Robert J, additional, and Moore, Allen J, additional

Published
2015
Full Text
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50. The Genome and Methylome of a Beetle with Complex Social Behavior, Nicrophorus vespilloides (Coleoptera: Silphidae).

Author

Cunningham, Christopher B., Lexiang Ji, Wiberg, R. Axel W., Shelton, Jennifer, McKinney, Elizabeth C., Parker, Darren J., Meagher, Richard B., Benowitz, Kyle M., Roy-Zokan, Eileen M., Ritchie, Michael G., Brown, Susan J., Schmitz, Robert J., and Moore, Allen J.

Subjects
GENOMICS, BEETLE behavior, ANIMAL social behavior, BURYING beetles, DNA methylation, ANIMAL behavior
Abstract

Testing for conserved and novel mechanisms underlying phenotypic evolution requires a diversity of genomes available for comparison spanning multiple independent lineages. For example, complex social behavior in insects has been investigated primarily with eusocial lineages, nearly all of which are Hymenoptera. If conserved genomic influences on sociality do exist, we need data from a wider range of taxa that also vary in their levels of sociality. Here, we present the assembled and annotated genome of the subsocial beetle Nicrophorus vespilloides, a species long used to investigate evolutionary questions of complex social behavior. We used this genome to address two questions. First, do aspects of life history, such as using a carcass to breed, predict overlap in gene models more strongly than phylogeny? We found that the overlap in gene models was similar between N. vespilloides and all other insect groups regardless of life history. Second, like other insects with highly developed social behavior but unlike other beetles, does N. vespilloides have DNA methylation? We found strong evidence for an active DNA methylation system. The distribution of meth-ylation was similar to other insects with exons having the most methylated CpGs. Methylation status appears highly conserved; 85% of the methylated genes in N. vespilloides are also methylated in the hymentopteran Nasonia vitripennis. The addition of this genome adds a coleopteran resource to answer questions about the evolution and mechanistic basis of sociality and to address questions about the potential role of methylation in social behavior. [ABSTRACT FROM AUTHOR]

Published
2015
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