Demographic analyses of a new sample of haploid genomes from a Swedish population of Drosophila melanogaster

Kapopoulou, Adamandia; Kapun, Martin; Pieper, Bjorn; Pavlidis, Pavlos; Wilches, Ricardo; Duchen, Pablo; Stephan, Wolfgang; Laurent, Stefan

doi:10.1038/s41598-020-79720-1

Cited by 15 publications

(22 citation statements)

References 47 publications

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“…We decided to mimic the conditions of a typical summer day in Oulu, Finland (65° North) for two reasons. First, Drosophila melanogaster populate Northern Scandinavian regions in this latitude and overwinter here (e.g., 37 ). Second, from mid-May to the end of June day length varies from 19 to 22 h, and the rest of the “night” corresponds to civil twilight, where the sun does not set more than 6° below the horizon and general activities can be performed without artificial light (‘white nights’, maximum darkness between 1–3 lux).…”

Section: Resultsmentioning

confidence: 99%

A natural timeless polymorphism allowing circadian clock synchronization in “white nights”

et al. 2022

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Daily temporal organisation offers a fitness advantage and is determined by an interplay between environmental rhythms and circadian clocks. While light:dark cycles robustly synchronise circadian clocks, it is not clear how animals experiencing only weak environmental cues deal with this problem. Like humans, Drosophila originate in sub-Saharan Africa and spread North up to the polar circle, experiencing long summer days or even constant light (LL). LL disrupts clock function, due to constant activation of CRYPTOCHROME, which induces degradation of the clock protein TIMELESS (TIM), but temperature cycles are able to overcome these deleterious effects of LL. We show here that for this to occur a recently evolved natural timeless allele (ls-tim) is required, encoding the less light-sensitive L-TIM in addition to S-TIM, the only form encoded by the ancient s-tim allele. We show that only ls-tim flies can synchronise their behaviour to semi-natural conditions typical for Northern European summers, suggesting that this functional gain is driving the Northward ls-tim spread.

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Section: Resultsmentioning

confidence: 99%

A natural timeless polymorphism allowing circadian clock synchronization in “white nights”

et al. 2022

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“…In our simulations, we simulated 436 gene trees within the fixed species tree (see below) and three different population sizes: 100,000 diploid individuals, 1,000,000 diploid individuals and 10,000,000 diploid individuals. The chosen population sizes for the simulations were based on known insect effective population sizes (Keightley et al 2015; Crossley et al 2019; Arguello et al 2019; Kapopoulou et al 2020) and were conservatively large to explore the potential effect.…”

Section: Methods and Datamentioning

confidence: 99%

A Time-calibrated Firefly (Coleoptera: Lampyridae) Phylogeny: Using Genomic Data for Divergence Time Estimation

Höhna

Lower

Duchen

et al. 2021

Preprint

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Fireflies (Coleoptera: Lampyridae) consist of over 2,000 described extant species. A well-resolved phylogeny of fireflies is important for the study of their bioluminescence, evolution, and conservation. We used a recently published anchored hybrid enrichment dataset (AHE; 436 loci for 88 Lampyridae species and 10 outgroup species) and state-of-the-art statistical methods (the fossilized birth-death-range process implemented in a Bayesian framework) to estimate a time-calibrated phylogeny of Lampyridae. Unfortunately, estimating calibrated phylogenies using AHE and the latest and most robust time-calibration strategies is not possible because of computational constraints. As a solution, we subset the full dataset and applied three different strategies: using the most complete loci, the most homogeneous loci, and the loci with the highest accuracy to infer the well established Photinus clade. The estimated topology using the three data subsets agreed on almost all major clades and only showed minor discordance with less supported nodes. The estimated divergence times overlapped for all nodes that are shared between the topologies. Thus, divergence time estimation is robust as long as the topology inference is robust and any well selected data subset suffices. Additionally, we observed an unexpected amount of gene tree discordance between the 436 AHE loci. Our assessment of model adequacy showed that standard phylogenetic substitution models are not adequate for any of the 436 AHE loci which is likely to bias phylogenetic inferences. We performed a simulation study to explore the impact of (a) incomplete lineage sorting, (b) uniformly distributed and systematic missing data, and (c) systematic bias in the position of highly variable and conserved sites. For our simulated data, we observed less gene tree variation and hence the empirically observed amount of gene tree discordance for the AHE dataset is unexpected.

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“…In addition to 7 strains carrying In(3R)Payne, we randomly picked an equal number of strains with standard arrangement on the third chromosome and obtained the genomic data from Dryad (http://doi.org/10.5061/dryad.403b2). In addition to this European low-latitude sample from Portugal, we integrated phased sequencing data from 14 non-inverted strains from a highlatitude population in Umeå (Sweden) into our analyses, which were sequenced as haploid embryos (Kapopoulou et al 2020), similar to the African samples mentioned above. Kapun et al (2016a), Rane et al (2015) found that Australian flies from tropical Queensland (where the polymorphism is segregating) do not exhibit elevated genetic differentiation between inverted and standard karyotypes within the genomic region spanned by In(3R)Payne.…”

Section: Additional Sequencing Data From Other Continentsmentioning

confidence: 99%

An Ancestral Balanced Inversion Polymorphism Confers Global Adaptation

Kapun¹,

Mitchell²,

Kawecki³

et al. 2023

Preprint

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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 non-inverted 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-seq we identify overlap between inversion-linked SNPs and loci that are differentially expressed between inverted and non-inverted 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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Demographic analyses of a new sample of haploid genomes from a Swedish population of Drosophila melanogaster

Cited by 15 publications

References 47 publications

A natural timeless polymorphism allowing circadian clock synchronization in “white nights”

A natural timeless polymorphism allowing circadian clock synchronization in “white nights”

A Time-calibrated Firefly (Coleoptera: Lampyridae) Phylogeny: Using Genomic Data for Divergence Time Estimation

An Ancestral Balanced Inversion Polymorphism Confers Global Adaptation

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