Genetics of Natural Populations Ix. Temporal Changes in the Composition of Populations of Drosophila Pseudoobscura

Dobzhansky, Th.

doi:10.1093/genetics/28.2.162

Cited by 201 publications

(29 citation statements)

References 9 publications

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“…Seasonal change in Drosophila inversion frequencies is a long-standing topic of study ( Dobzhansky 1943 ). We therefore asked whether inversion frequencies varied seasonally between our fall and spring samples ( supplementary table S5, Supplementary Material online).…”

Section: Resultsmentioning

confidence: 99%

A Population Genomic Assessment of Three Decades of Evolution in a Natural Drosophila Population

Lange

Bastide

Lack

et al. 2021

Molecular Biology and Evolution

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Population genetics seeks to illuminate the forces shaping genetic variation, often based on a single snapshot of genomic variation. However, utilizing multiple sampling times to study changes in allele frequencies can help clarify the relative roles of neutral and non-neutral forces on short time scales. This study compares whole-genome sequence variation of recently collected natural population samples of Drosophila melanogaster against a collection made approximately 35 years prior from the same locality—encompassing roughly 500 generations of evolution. The allele frequency changes between these time points would suggest a relatively small local effective population size on the order of 10,000, significantly smaller than the global effective population size of the species. Some loci display stronger allele frequency changes than would be expected anywhere in the genome under neutrality—most notably the tandem paralogs Cyp6a17 and Cyp6a23, which are impacted by structural variation associated with resistance to pyrethroid insecticides. We find a genome-wide excess of outliers for high genetic differentiation between old and new samples, but a larger number of adaptation targets may have affected SNP-level differentiation versus window differentiation. We also find evidence for strengthening latitudinal allele frequency clines: northern-associated alleles have increased in frequency by an average of nearly 2.5% at SNPs previously identified as clinal outliers, but no such pattern is observed at random SNPs. This project underscores the scientific potential of using multiple sampling time points to investigate how evolution operates in natural populations, by quantifying how genetic variation has changed over ecologically relevant timescales.

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Section: Resultsmentioning

confidence: 99%

A Population Genomic Assessment of Three Decades of Evolution in a Natural Drosophila Population

Lange

Bastide

Lack

et al. 2021

Molecular Biology and Evolution

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“…For instance, theory suggests that linked selection can cause the spread of an initially rare inversion when it captures a locally adaptive haplotype, protects it from recombination load and/or maladaptive gene flow from neighboring populations, and then ‘hitchhikes’ with it to high frequency; alternatively, a new inversion might be favored by direct positive selection when the breakpoints of the inversion fortuitously induce a beneficial mutation (Charlesworth and Charlesworth 1973; Charlesworth 1974; Kirkpatrick and Barton 2006; Kirkpatrick 2010; Guerrero et al 2012; Charlesworth and Barton 2018; Kapun and Flatt 2019; Durmaz et al 2020; Mackintosh et al 2022). Indeed, beginning with Dobzhansky’s seminal observations in Drosophila pseudoobscura (Dobzhansky 1943, 1947, 1948, 1950; Wright and Dobzhansky 1946), many inversion polymorphisms subject to spatially and/or temporally varying selection have been identified, from plants to humans (Krimbas and Powell 1992; Hoffmann et al 2004; Stefansson et al 2005; Hoffmann and Rieseberg 2008; Lowry and Willis 2010; Kapun et al 2016a; Wellenreuther and Bernatchez 2018; Faria et al 2019; Kapun and Flatt 2019; Machado et al 2021; Lange et al 2022).…”

Section: Introductionmentioning

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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“…Adaptation can occur at remarkably short timescales in natural populations, leading to drastic changes in genotype frequencies and phenotypes over a few generations only (Buffalo and Coop, 2019). This rapid pace of adaptation has motivated the use of temporal data to understand neutral (Prout, 1954; Wallace, 1956; Nei and Tajima, 1981; Pollak, 1983; Mueller et al, 1985b; Waples, 1989; Wang and Whitlock, 2003) and under-selection genetic evolution over time (Dobzhansky, 1943; Fisher and Ford, 1947; Kettlewell, 1958, 1961; Mueller et al, 1985a). However, such time series studies remain rare compared to the amount of work focusing on one contemporary sample to trace back its genetic history (Buffalo and Coop, 2019, 2020; Pavinato et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Approximate Bayesian Computation applied to time series of population genetic data disentangles rapid genetic changes and demographic variations in a pathogen population

Saubin¹,

Tellier

Stoeckel³

et al. 2022

Preprint

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Adaptation can occur at remarkably short timescales in natural populations, leading to drastic changes in phenotypes and genotype frequencies over a few generations only. The inference of demographic parameters can allow understanding how evolutionary forces interact and shape the genetic trajectories of populations during rapid adaptation. Here we propose a new Approximate Bayesian Computation (ABC) framework that couples a forward and individual-based model with temporal genetic data to disentangle genetic changes and demographic variations in a case of rapid adaptation. We test the accuracy of our inferential framework and evaluate the benefit of considering the full trajectory compared to few time samples. Theoretical investigations demonstrate high accuracy in both model and parameter estimations, even if a strong thinning is applied to time series data. Then, we apply our ABC inferential framework to empirical data describing the population genetics changes of the poplar rust pathogen following a major event of resistance overcoming. We successfully estimate key demographic and genetic parameters, including the proportion of resistant hosts deployed in the landscape and the level of standing genetic variation from which selection occurred. Inferred values are in accordance with our empirical knowledge of this biological system. This new inferential framework, which contrasts with coalescent-based ABC analyses, is promising for a better understanding of evolutionary trajectories of populations subjected to rapid adaptation.

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Genetics of Natural Populations Ix. Temporal Changes in the Composition of Populations of Drosophila Pseudoobscura

Cited by 201 publications

References 9 publications

A Population Genomic Assessment of Three Decades of Evolution in a Natural Drosophila Population

A Population Genomic Assessment of Three Decades of Evolution in a Natural Drosophila Population

An Ancestral Balanced Inversion Polymorphism Confers Global Adaptation

Approximate Bayesian Computation applied to time series of population genetic data disentangles rapid genetic changes and demographic variations in a pathogen population

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