| 1. |
- Kapun, Martin, et al.
(författare)
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Genomic analysis of european drosophila melanogaster populations reveals longitudinal structure, continent-wide selection, and previously unknown DNA viruses
- 2020
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 37:9, s. 2661-2678
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Tidskriftsartikel (refereegranskat)abstract
- Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatiotemporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterize variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.
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| 2. |
- Nowell, Reuben W., et al.
(författare)
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A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana
- 2017
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Ingår i: GigaScience. - : Oxford University Press (OUP). - 2047-217X. ; 6:7
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Tidskriftsartikel (refereegranskat)abstract
- The mycalesine butterfly Bicyclus anynana, the Squinting bush brown, is a model organism in the study of lepidopteran ecology, development, and evolution. Here, we present a draft genome sequence for B. anynana to serve as a genomics resource for current and future studies of this important model species. Seven libraries with insert sizes ranging from 350 bp to 20 kb were constructed using DNA from an inbred female and sequenced using both Illumina and PacBio technology; 128 Gb of raw Illumina data was filtered to 124 Gb and assembled to a final size of 475 Mb (similar to x260 assembly coverage). Contigs were scaffolded using mate-pair, transcriptome, and PacBio data into 10 800 sequences with an N50 of 638 kb (longest scaffold 5 Mb). The genome is comprised of 26% repetitive elements and encodes a total of 22 642 predicted protein-coding genes. Recovery of a BUSCO set of core metazoan genes was almost complete (98%). Overall, these metrics compare well with other recently published lepidopteran genomes. We report a high-quality draft genome sequence for Bicyclus anynana. The genome assembly and annotated gene models are available at LepBase (http://ensembl.lepbase.org/index.html).
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| 3. |
- Oostra, Vicencio, et al.
(författare)
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Strong phenotypic plasticity limits potential for evolutionary responses to climate change
- 2018
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Phenotypic plasticity, the expression of multiple phenotypes from one genome, is a wide-spread adaptation to short-term environmental fluctuations, but whether it facilitates evolutionary adaptation to climate change remains contentious. Here, we investigate seasonal plasticity and adaptive potential in an Afrotropical butterfly expressing distinct phenotypes in dry and wet seasons. We assess the transcriptional architecture of plasticity in a full-factorial analysis of heritable and environmental effects across 72 individuals, and reveal pervasive gene expression differences between the seasonal phenotypes. Strikingly, intra-population genetic variation for plasticity is largely absent, consistent with specialisation to a particular environmental cue reliably predicting seasonal transitions. Under climate change, deteriorating accuracy of predictive cues will likely aggravate maladaptive phenotype-environment mismatches and increase selective pressures on reaction norms. However, the observed paucity of genetic variation for plasticity limits evolutionary responses, potentially weakening prospects for population persistence. Thus, seasonally plastic species may be especially vulnerable to climate change.
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| 4. |
- Tobi, Elmar W., et al.
(författare)
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Selective Survival of Embryos Can Explain DNA Methylation Signatures of Adverse Prenatal Environments
- 2018
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Ingår i: Cell Reports. - : Elsevier BV. - 2211-1247. ; 25:10, s. 4-2667
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Tidskriftsartikel (refereegranskat)abstract
- An adverse intrauterine environment is associated with long-term physiological changes in offspring. These are believed to be mediated by epigenomic marks, including DNA methylation (DNAm). Changes in DNAm are often interpreted as damage or plastic responses of the embryo. Here, we propose that stochastic DNAm variation, generated during remodeling of the epigenome after fertilization, contributes to DNAm signatures of prenatal adversity through differential survival of embryos. Using a mathematical model of re-methylation in the early embryo, we demonstrate that selection, but not plasticity, will generate a characteristic reduction in DNAm variance at loci that contribute to survival. Such a reduction in DNAm variance was apparent in a human cohort prenatally exposed to the Dutch famine, illustrating that it is possible to detect a signature of selection on epigenomic variation. Selection should be considered as a possible mechanism linking prenatal adversity to subsequent health and may have implications when evaluating interventions. Tobi et al. hypothesize that prenatal adversity can cause selection on epigenomic profiles in utero. Their model predicts that such selection reduces the variance in DNA methylation at genomic regions that contribute to survival, which is testable and detectable in empirical data from the Dutch famine.
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