Drosophila subobscura presents a rich and complex chromosomal inversion polymorphism. It can thus be considered a model system i) to study the mechanisms originating inversions and how inversions affect the levels and patterns of variation in the inverted regions, and ii) to study adaptation at both the single-gene and chromosomal inversion levels. It is therefore important to infer its demographic history since previous information indicated that its nucleotide variation is not at mutation-drift equilibrium. For that purpose, we sequenced 16 non-coding regions distributed across those parts of the J chromosome not affected by inversions in the studied population and possibly either by other selective events. The pattern of variation detected in these 16 regions is similar to that previously reported within different chromosomal arrangements, suggesting that the latter results would, thus, mainly reflect recent demographic events rather than the partial selective sweep imposed by the or...

The demographic structure is an important factor influencing the development of the services industry. As the country with the world’s most serious aging problem, China’s service industry structure is likely to undergo profound changes in response to the rapid demographic transition. Therefore, this paper examines the effect of population aging on the development of the service industry in the context of China’s accelerating population aging. The study found that: (1) Population aging has a significant "inverted U" effect on the development of the services industry. (2) The impact of population aging on the development of the service industry has obvious regional and industry heterogeneity. The study of regional heterogeneity found that population aging in economically developed regions has a more obvious effect on the development of the service industry than in economically less developed regions. Industry heterogeneity studies found that population aging has an obvious promotional effect on the development of medical and other rigid demand industries, while the effect on other non-rigid demand industries is not significant. (3) The threshold effect test found that when the degree of population aging exceeds the threshold, the stimulating effect of population aging on the development of the services industry is no longer significant. The research in this paper provides useful insights into the likely response to changes in the industrial structure of the services industry, and offers some implications for countries with similar demographic profiles to China.

Chromosomal inversions have been an enduring interest of population geneticists since their discovery in Drosophila melanogaster. Numerous lines of evidence suggest powerful selective pressures govern the distributions of polymorphic inversions, and these observations have spurred the development of many explanatory models. However, due to a paucity of nucleotide data, little progress has been made towards investigating selective hypotheses or towards inferring the genealogical histories of inversions, which can inform models of inversion evolution and suggest selective mechanisms. Here, we utilize population genomic data to address persisting gaps in our knowledge of D. melanogaster's inversions. We develop a method, termed Reference-Assisted Reassembly, to assemble unbiased, highly accurate sequences near inversion breakpoints, which we use to estimate the age and the geographic origins of polymorphic inversions. We find that inversions are young, and most are African in origin, which is consistent with the demography of the species. The data suggest that inversions interact with polymorphism not only in breakpoint regions but also chromosome-wide. Inversions remain differentiated at low levels from standard haplotypes even in regions that are distant from breakpoints. Although genetic exchange appears fairly extensive, we identify numerous regions that are qualitatively consistent with selective hypotheses. Finally, we show that In(1)Be, which we estimate to be ∼60 years old (95% CI 5.9 to 372.8 years), has likely achieved high frequency via sex-ratio segregation distortion in males. With deeper sampling, it will be possible to build on our inferences of inversion histories to rigorously test selective models—particularly those that postulate that inversions achieve a selective advantage through the maintenance of co-adapted allele complexes.

Chromosome-level genome assemblies of Drosophila montana and Drosophila flavomontana that are associated with the publication "Chromosomal inversions and the demography of speciation in Drosophila montana and Drosophila flavomontana" by Poikela et al. (2024).

Dmontana_chromosomes = only D. montana scaffolds assigned to chromosomes

Dmontana_all_regions = all genomic D. montana regions

Dflavomontana_chromosomes = only D. flavomontana scaffolds assigned to chromosomes

Dflavomontana_all_regions = all genomic D. flavomontana regions

Chromosomal inversions are important structural changes that may facilitate divergent selection when they capture co-adaptive loci in the face of gene flow. However, identifying selection targets within inversions can be challenging. The high degrees of differentiation between heterokaryotypes, as well as the differences in demographic histories of collinear regions compared with inverted ones, reduce the power of traditional outlier analyses for detecting selected loci. Here, we develop a new approach that uses discriminant functions informed from inversion-specific expectations to classify loci that are under selection (or drift). Analysis of RAD sequencing data we collected in a classic dipteran species with polymorphic inversion clines-Anopheles gambiae, a malaria vector species from sub-Saharan Africa-demonstrates the benefits of the approach compared with traditional outlier analyses. We focus specifically on two polymorphic inversions, the 2La and 2Rb arrangements that predominat...

Chromosomal rearrangement polymorphisms are common and increasingly found to be associated with adaptive ecological divergence and speciation. Rearrangements, such as inversions, reduce recombination in heterozygous individuals and thus can protect favorable allelic combinations at linked loci, facilitating their spread in the presence of gene flow. Recently, we identified a chromosomal inversion polymorphism that contributes to ecological adaptation and reproductive isolation between annual and perennial ecotypes of the yellow monkeyflower, Mimulus guttatus. Here we evaluate the population genetic structure of this inverted region in comparison with the collinear regions of the genome across the M. guttatus species complex. We tested whether annual and perennial M. guttatus exhibit different patterns of divergence for loci in the inverted and noninverted regions of the genome. We then evaluated whether there are contrasting climate associations with these genomic regions through redundancy analysis. We found that the inversion exhibits broadly different patterns of divergence among annual and perennial M. guttatus and is associated with environmental variation across population accessions. This study is the first widespread population genetic survey of the diversity of the M. guttatus species complex. Our findings contribute to a greater understanding of morphological, ecological, and genetic evolutionary divergence across this highly diverse group of closely related ecotypes and species. Finally, understanding species relationships among M. guttatus sp. has hitherto been stymied by accumulated evidence of substantial gene flow among populations as well as designated species. Nevertheless, our results shed light on these relationships and provide insight into adaptation in life history traits within the complex.

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Inversions---in which the popular vote winner loses the election---have occurred in four US presidential races. We show that rather than being statistical flukes, inversions have been ex ante likely since the early 1800s. In elections yielding a popular vote margin within one point (one-eighth of presidential elections), about 40% will be inversions in expectation. We show this conditional probability is remarkably stable across historical periods---despite differences in which groups voted, which states existed, and which parties participated. Our findings imply that the US has experienced so few inversions merely because there have been so few elections (and fewer close elections).

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Scripts and manual for bioinformatic analysesRVR_pipeline.shChr 3L -> Population - Is [Alignment Files]3LIs_crams.tar.bz2Chr 3L -> Population - Ys [Alignment Files]3LYs_crams.tar.bz2Chr 3L -> Population - Ii [Alignment Files]3LIi_crams.tar.bz2Chr 3R -> Population - Is [Alignment Files]3RIs_crams.tar.bz2Chr 3R -> Population - Ys [Alignment Files]3RYs_crams.tar.bz2Chr 3R -> Population - Ii [Alignment Files]3RIi_crams.tar.bz2Imputed and combined variant call filesVCF files for 3 populations after data imputation3L-3R_Imputed_Merged_Variant_calls.tar.gzRaw variant calls from alignment filesVCF files created using GATK UnifiedGenotyper from alignment files3L-3R_Raw_variant_calls.tar.gzFst calculationsFST calculations for all comparisons per SNP and in 200kb windows sliding every 20kb, using VCFTOOLSFst_calculations_VCFTOOLS.tar.gz

Drosophila subobscura karyotypesData on D. subobscura karyotypes from Mt. Avala. Jun-July 2014Zivanovic et al. Karyotypes.xlsxDrosophila subobscura polymorphismData on Drosophila subobscura polymorphism for the whole chromosomal set. Data are from Mt. Avala, Serbia.Zivanovic et al. Polymorphism.xlsx

Large structural variants in the genome, such as inversions, may play an important role in producing population structure and local adaptation to the environment through suppression of recombination. However, relatively few studies have linked inversions to phenotypic traits that are sexually selected and may play a role in reproductive isolation. Here we found that geographic differences in the sexually-selected plumage of a warbler, the common yellowthroat (Geothlypis trichas), are largely due to differences on the Z (sex) chromosome (males are ZZ), which contains at least one putative inversion spanning 40% (31/77 Mb) of its length. The inversions on the Z chromosome vary dramatically east and west of the Appalachian mountains, which provides evidence of cryptic population structure within the range of the most widespread eastern subspecies (G. t. trichas). In an eastern (New York) and western (Wisconsin) population of this subspecies, female prefer different male ornaments; larger ..., , , # Data from: Sexually-selected differences in warbler plumage are related to a putative inversion on the Z chromosome

https://doi.org/10.5061/dryad.g1jwstqxd

Description of the data and file structure

Files and variables

Files on Dryad

1. Table S1.doc – A copy of this MSWord file is also on the publisher’s website. The file contains a summary of sample sizes and type of sequence data for each yellowthroat population.
2. Supporting Data Table S1_WINY_20kb_Fst_Autosome_Genes.xls (807 rows, 11 columns). -- Outlier genes (top 1% of Fst in 20kb windows) between NY (New York) and WI (Wisconsin) populations on the autosomes from pool-seq samples (based on analysis of VCF pool-seq files; see #5 below). The pooled sequences are at Bioproject PRJNA734331 and the reference genome is Genbank Assembly GCA_009764595.1. There were 763 annotated genes and 43 with unknown function. Empty cells under Gene Symbol and Pigment indicate that ...

• Values are the number of patients/number of controls.Demographic distribution of the individuals in the study*.

The demographic structure is an important factor influencing the development of the services industry. As the country with the world’s most serious aging problem, China’s service industry structure is likely to undergo profound changes in response to the rapid demographic transition. Therefore, this paper examines the effect of population aging on the development of the service industry in the context of China’s accelerating population aging. The study found that: (1) Population aging has a significant "inverted U" effect on the development of the services industry. (2) The impact of population aging on the development of the service industry has obvious regional and industry heterogeneity. The study of regional heterogeneity found that population aging in economically developed regions has a more obvious effect on the development of the service industry than in economically less developed regions. Industry heterogeneity studies found that population aging has an obvious promotional effect on the development of medical and other rigid demand industries, while the effect on other non-rigid demand industries is not significant. (3) The threshold effect test found that when the degree of population aging exceeds the threshold, the stimulating effect of population aging on the development of the services industry is no longer significant. The research in this paper provides useful insights into the likely response to changes in the industrial structure of the services industry, and offers some implications for countries with similar demographic profiles to China.

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Multiple forms of balancing selection maintain inversion polymorphism

Dataset DOI: 10.5061/dryad.bvq83bkn7

Description of the data and file structure

The main aim of our study (Paris et al. 2025) was to investigate the effects of the In(3R)Payne inversion polymorphism on a suite of fitness-related traits in the vinegar fly, Drosophila melanogaster. Here we present the raw data of our study (see: Paris_et_al_2025_Heredity_raw_data.xlsx). For further details see our paper Paris et al. 2025, entitled "Multiple Forms of Balancing Selection Maintain Inversion Polymorphism", published in Heredity. For additional details please contact the first author, Margot Paris (margot.paris@unifr.ch), or the corresponding author, Thomas Flatt (thomas.flatt@unifr.ch).

Files and variables

File: Paris_et_al_2025_Heredity_raw_data.xlsx

Description: Each tab of the excel file provides t...

Recent advances in sequencing allow population-genomic data to be generated for virtually any species. However, approaches to analyse such data lag behind the ability to generate it, particularly in nonmodel species. Linkage disequilibrium (LD, the nonrandom association of alleles from different loci) is a highly sensitive indicator of many evolutionary phenomena including chromosomal inversions, local adaptation and geographical structure. Here, we present linkage disequilibrium network analysis (LDna), which accesses information on LD shared between multiple loci genomewide. In LD networks, vertices represent loci, and connections between vertices represent the LD between them. We analysed such networks in two test cases: a new restriction-site-associated DNA sequence (RAD-seq) data set for Anopheles baimaii, a Southeast Asian malaria vector; and a well-characterized single nucleotide polymorphism (SNP) data set from 21 three-spined stickleback individuals. In each case, we readily identified five distinct LD network clusters (single-outlier clusters, SOCs), each comprising many loci connected by high LD. In A. baimaii, further population-genetic analyses supported the inference that each SOC corresponds to a large inversion, consistent with previous cytological studies. For sticklebacks, we inferred that each SOC was associated with a distinct evolutionary phenomenon: two chromosomal inversions, local adaptation, population-demographic history and geographic structure. LDna is thus a useful exploratory tool, able to give a global overview of LD associated with diverse evolutionary phenomena and identify loci potentially involved. LDna does not require a linkage map or reference genome, so it is applicable to any population-genomic data set, making it especially valuable for nonmodel species.

Local adaptation to environmental stress at different levels of genetic polymorphism in various plants and animals has been documented through evolution of heavy metal tolerance. We used samples of Drosophila subobscura populations from two differently polluted environments to analyze the change of chromosomal inversion polymorphism as genetic marker during laboratory exposure to lead. Exposure to environmental contamination can affect the genetic content within a particular inversion and produce targets for selection in populations from different environments. The aims were to discover whether the inversion polymorphism is shaped by the local natural environments, and if lead as a selection pressure would cause adaptive divergence of two populations during the multigenerational laboratory experiment. The results showed that populations retain signatures from past contamination events, and that heavy metal pollution can cause adaptive changes in population. Differences in inversion polymorphism between the two populations increased over generations under lead contamination in the laboratory. The inversion polymorphism of population originating from the more polluted natural environment was more stable during the experiment, both under conditions with and without lead. Therefore, results showed that inversion polymorphism as a genetic marker reflects a strong signature of adaptation to the local environment, and that historical demographic events and selection are important for both prediction of evolutionary potential and long-term viability of natural populations.

Anopheles gambiae s.l. are important malaria vectors, but little is known about their genomic variation in the wild. Here we present inter- and intra- species analysis of genome-wide RADseq data, in three Anopheles gambiae s.l. species collected from East Africa. The mosquitoes fall into three genotypic clusters representing described species (An. gambiae, An. arabiensis, and An. merus) with no evidence of cryptic breeding units. An. merus is the most divergent of the three species, supporting a recent new phylogeny based on chromosomal inversions. Even though the species clusters are well separated, there is extensive shared polymorphism, particularly between An. gambiae and An. arabiensis. Divergence between An. gambiae and An. arabiensis does not vary across the autosomes, but is higher in X-linked inversions than elsewhere on X or on the autosomes, consistent with the suggestion that this inversion (or a gene within it) is important in reproductive isolation between the species. The 2La/2L+a inversion shows no more evidence of introgression between An. gambiae and An. arabiensis than the rest of the autosomes. Population differentiation within An. gambiae and An. arabiensis is weak over ~190-270km, implying no strong barriers to dispersal. Analysis of Tajima's D and the allele frequency spectrum is consistent with modest population increases in An. arabiensis and An. merus, but a more complex demographic history of expansion followed by contraction in An. gambiae. Although they are less than 200km apart, the two An. gambiae populations show evidence of different demographic histories.