The origin of chromosomal inversions as a source of segmental duplications in the Sophophora subgenus of Drosophila

The origin and maintenance of supergenes contributing to ecological adaptation in Atlantic herring

Chromosomal inversions are associated with local adaptation in many species. However, questions regarding how they are formed, maintained and impact various other evolutionary processes remain elusive. Here, using a large genomic dataset of long-read and short-read sequencing, we ask these questions in one of the most abundant vertebrates on Earth, the Atlantic herring. This species has four megabase-sized inversions associated with ecological adaptation that correlate with water temperature. The S and N inversion alleles at these four loci dominate in the southern and northern parts, respectively, of the species distribution in the North Atlantic Ocean. By determining breakpoint coordinates of the four inversions and the structural variations surrounding them, we hypothesize that these inversions are formed by ectopic recombination between duplicated sequences immediately outside of the inversions. We show that these are old inversions (>1 MY), albeit formed after the split between the Atlantic herring and its sister species, the Pacific herring. There is evidence for extensive gene flux between inversion alleles at all four loci. The large Ne of herring combined with the common occurrence of opposite homozygotes across the species distribution has allowed effective purifying selection to prevent the accumulation of genetic load and repeats within the inversions.

Genomics of natural populations: gene conversion events reveal selected genes within the inversions of Drosophila pseudoobscura

When adaptive phenotypic variation or quantitative trait loci map within an inverted segment of a chromosome, researchers often despair because the suppression of crossing over will prevent the discovery of selective target genes that established the rearrangement. If an inversion polymorphism is old enough, then the accumulation of gene conversion tracts offers the promise that quantitative trait loci or selected loci within inversions can be mapped. The inversion polymorphism of Drosophila pseudoobscura is a model system to show that gene conversion analysis is a useful tool for mapping selected loci within inversions. D. pseudoobscura has over 30 different chromosomal arrangements on the third chromosome (Muller C) in natural populations and their frequencies vary with changes in environmental habitats. Statistical tests of five D. pseudoobscura gene arrangements identified outlier genes within inverted regions that had potentially heritable variation, either fixed amino acid differences or differential expression patterns. We use genome sequences of the inverted third chromosome (Muller C) to infer 98,443 gene conversion tracts for a total coverage of 142 Mb or 7.2× coverage of the 19.7 Mb chromosome. We estimated gene conversion tract coverage in the 2,668 genes on Muller C and tested whether gene conversion coverage was similar among arrangements for outlier vs non-outlier loci. Outlier genes had lower gene conversion tract coverage among arrangements than the non-outlier genes suggesting that selection removes exchanged DNA in the outlier genes. These data support the hypothesis that the third chromosome in D. pseudoobscura captured locally adapted combinations of alleles prior to inversion mutation events.

Population History Shapes Responses to Different Temperature Regimes in Drosophila subobscura

Drosophila subobscura is considered a good model species for investigation of a population's ability to adapt and cope with climate changes. Decade long research has shown that inversion frequencies change in response to environmental factors indicating their role in adaptation to novel environments. The mechanisms behind organisms' responses to temperature are complex, involving changes in physiology, behavior, gene expression and regulation. On the other hand, a population's ability to respond to suboptimal conditions depends on standing genetic variation and population history. In order to elucidate the role of local adaptation in population response to the changing temperature, we investigated the response to temperature in D. subobscura individuals originating from two different altitudes by combining traditional cytogenetic techniques with assessing the levels of Hsp70 protein expression. Inversion polymorphism was assessed in the flies sampled from natural populations and in flies reared in laboratory conditions at three different temperatures after five and sixteen generations and Hsp70 protein expression profile in 12th generation flies at the basal level and after heat shock induction. Our results indicate that local adaptation and population history influence population response to the changing temperature.

Fine-Scale Position Effects Shape the Distribution of Inversion Breakpoints in Drosophila melanogaster

Chromosomal inversions are among the primary drivers of genome structure evolution in a wide range of natural populations. Although there is an impressive array of theory and empirical analyses that have identified conditions under which inversions can be positively selected, comparatively little data are available on the fitness impacts of these genome structural rearrangements themselves. Because inversion breakpoints can disrupt functional elements and alter chromatin domains, the precise positioning of an inversion’s breakpoints can strongly affect its fitness. Here, we compared the fine-scale distribution of low-frequency inversion breakpoints with those of high-frequency inversions and inversions that have gone to fixation between Drosophila species. We identified a number of differences among frequency classes that may influence inversion fitness. In particular, breakpoints that are proximal to insulator elements, generate large tandem duplications, and minimize impacts on gene coding spans which are more prevalent in high-frequency and fixed inversions than in rare inversions. The data suggest that natural selection acts to preserve both genes and larger cis-regulatory networks in the occurrence and spread of rearrangements. These factors may act to limit the availability of high-fitness arrangements when suppressed recombination is favorable.

The Cyclically Seasonal Drosophila subobscura Inversion O7 Originated From Fragile Genomic Sites and Relocated Immunity and Metabolic Genes

Chromosome inversions are important contributors to standing genetic variation in Drosophila subobscura. Presently, the species is experiencing a rapid replacement of high-latitude by low-latitude inversions associated with global warming. Yet not all low-latitude inversions are correlated with the ongoing warming trend. This is particularly unexpected in the case of O7 because it shows a regular seasonal cycle that peaks in summer and rose with a heatwave. The inconsistent behavior of O7 across components of the ambient temperature suggests that is causally more complex than simply due to temperature alone. In order to understand the dynamics of O7, high-quality genomic data are needed to determine both the breakpoints and the genetic content. To fill this gap, here we generated a PacBio long read-based chromosome-scale genome assembly, from a highly homozygous line made isogenic for an O3 + 4 + 7 chromosome. Then we isolated the complete continuous sequence of O7 by conserved synteny analysis with the available reference genome. Main findings include the following: (i) the assembled O7 inversion stretches 9.936 Mb, containing > 1,000 annotated genes; (ii) O7 had a complex origin, involving multiple breaks associated with non-B DNA-forming motifs, formation of a microinversion, and ectopic repair in trans with the two homologous chromosomes; (iii) the O7 breakpoints carry a pre-inversion record of fragility, including a sequence insertion, and transposition with later inverted duplication of an Attacin immunity gene; and (iv) the O7 inversion relocated the major insulin signaling forkhead box subgroup O (foxo) gene in tight linkage with its antagonistic regulatory partner serine/threonine-protein kinase B (Akt1) and disrupted concerted evolution of the two inverted Attacin duplicates, reattaching them to dFOXO metabolic enhancers. Our findings suggest that O7 exerts antagonistic pleiotropic effects on reproduction and immunity, setting a framework to understand its relationship with climate change. Furthermore, they are relevant for fragility in genome rearrangement evolution and for current views on the contribution of breakage versus repair in shaping inversion-breakpoint junctions.

Computational Sequence Analysis of Inversion Breakpoint Regions in the Cactophilic Drosophila mojavensis Lineage

We investigated rates of chromosomal evolution in Drosophila mojavensis using whole-genome sequence information from D. mojavensis, Drosophila buzzatii, and Drosophila virilis. Drosophila mojavensis is a cactophilic species of the repleta group living under extreme ecological conditions in the deserts of the Southwestern United States and Northwestern México. The genome of D. buzzatii, another member of the repleta group, was recently sequenced and the largest scaffolds anchored to all chromosomes using diverse procedures. Chromosome organization between D. mojavensis and D. buzzatii was compared using MUMmer and GRIMM software. Our results corroborate previous cytological analyses that indicated chromosome 2 differed between these 2 species by 10 inversions, chromosomes X and 5 differed by one inversion each, and chromosome 4 was homosequential. In contrast, we found that chromosome 3 differed by 5 inversions instead of the expected 2 that were previously inferred by cytological analyses. Thirteen of these inversions occurred in the D. mojavensis lineage: 12 are fixed and one of them is a polymorphic inversion previously described in populations from Sonora and Baja California, México. We previously investigated the breakpoints of chromosome 2 inversions fixed in D. mojavensis. Here we characterized the breakpoint regions of the 5 inversions found in chromosome 3 in order to infer the molecular mechanism that generated each inversion and its putative functional consequences. Overall, our results reveal a number of gene alterations at the inversion breakpoints with putative adaptive consequences that point to natural selection as the cause for fast chromosomal evolution in D. mojavensis.

The molecular genealogy of sequential overlapping inversions implies both homologous chromosomes of a heterokaryotype in an inversion origin

Cytological and molecular studies have revealed that inversion chromosomal polymorphism is widespread across taxa and that inversions are among the most common structural changes fixed between species. Two major mechanisms have been proposed for the origin of inversions considering that breaks occur at either repetitive or non-homologous sequences. While inversions originating through the first mechanism might have a multiple origin, those originating through the latter mechanism would have a unique origin. Variation at regions flanking inversion breakpoints can be informative on the origin and history of inversions given the reduced recombination in heterokaryotypes. Here, we have analyzed nucleotide variation at a fragment flanking the most centromere-proximal shared breakpoint of several sequential overlapping inversions of the E chromosome of Drosophila subobscura —inversions E₁, E₂, E₉ and E₃. The molecular genealogy inferred from variation at this shared fragment does not exhibit the branching pattern expected according to the sequential origin of inversions. The detected discordance between the molecular and cytological genealogies has led us to consider a novel possibility for the origin of an inversion, and more specifically that one of these inversions originated on a heterokaryotype for chromosomal arrangements. Based on this premise, we propose three new models for inversions origin.

The molecular characterization of fixed inversions breakpoints unveils the ancestral character of the Drosophila guanche chromosomal arrangements

Cytological studies revealed that the number of chromosomes and their organization varies across species. The increasing availability of whole genome sequences of multiple species across specific phylogenies has confirmed and greatly extended these cytological observations. In the Drosophila genus, the ancestral karyotype consists of five rod-like acrocentric chromosomes (Muller elements A to E) and one dot-like chromosome (element F), each exhibiting a generally conserved gene content. Chromosomal fusions and paracentric inversions are thus the major contributors, respectively, to chromosome number variation among species and to gene order variation within chromosomal element. The subobscura cluster of Drosophila consists in three species that retain the genus ancestral karyotype and differ by a reduced number of fixed inversions. Here, we have used cytological information and the D. guanche genome sequence to identify and molecularly characterize the breakpoints of inversions that became fixed since the D. guanche-D. subobscura split. Our results have led us to propose a modified version of the D. guanche cytological map of its X chromosome, and to establish that (i) most inversions became fixed in the D. subobscura lineage and (ii) the order in which the four X chromosome overlapping inversions occurred and became fixed.

Inversion evolutionary rates might limit the experimental identification of inversion breakpoints in non-model species

Chromosomal inversions are structural changes that alter gene order but generally not gene content in the affected region. In Drosophila, extensive cytological studies revealed the widespread character of inversion polymorphism, with evidence for its adaptive character. In Drosophila subobscura, polymorphism affects both its four large autosomal elements and its X (A) chromosome. The characterization of eight of these autosomal inversions breakpoints revealed that most of them originated through the staggered-breaks mechanism. Here, we have performed chromosomal walks to identify the breakpoints of two X-chromosome widely distributed inversions -A₂ and A₁- of D. subobscura. Inversion A₂ is considered a warm-adapted arrangement that exhibits parallel latitudinal clines in the species ancestral distribution area and in both American subcontinents, whereas inversion A₁ is only present in the Palearctic region where it presents an east-west cline. The duplication detected at the A₂ inversion breakpoints is consistent with its origin by the staggered-breaks mechanism. Inversion A₁ breakpoints could not be molecularly identified even though they could be narrowly delimited. This result points to chromosome walking limitations when using as a guide the genome of other species. Limitations stem from the rate of evolution by paracentric inversions, which in Drosophila is highest for the X chromosome.

An easy route to the massive karyotyping of complex chromosomal arrangements in Drosophila

Inversion polymorphism is widespread in the Drosophila genus as well as in other dipteran genera. The presence of polytene chromosomes in some insect organs and, thus, the possibility to observe the different arrangements generated by inversions through a microscope enhanced the cytological study of this structural polymorphism. In several Drosophila species, these studies provided evidence for the adaptive character of this polymorphism, which together with the standing interest to uncover targets of natural selection has led to a renewed interest for inversion polymorphism. Our recent molecular characterization of the breakpoint regions of five inversions of the E chromosome of D. subobscura has allowed us to design a PCR-based strategy to molecularly identify the different chromosomal arrangements and, most importantly, to determine the E chromosome karyotype of medium- and large-sized samples from natural populations. Individuals of a test sample that were both cytologically and molecularly karyotyped were used to establish the strategy that was subsequently applied to karyotype a larger sample. Our strategy has proved to be robust and time efficient, and it lays therefore the groundwork for future studies of the E chromosome structural polymorphism through space and time, and of its putative contribution to adaptation.

Dense gene physical maps of the non-model species Drosophila subobscura

The comparative analysis of genetic and physical maps as well as of whole genome sequences had revealed that in the Drosophila genus, most structural rearrangements occurred within chromosomal elements as a result of paracentric inversions. Genome sequence comparison would seem the best method to estimate rates of chromosomal evolution, but the high-quality reference genomes required for this endeavor are still scanty. Here, we have obtained dense physical maps for Muller elements A, C, and E of Drosophila subobscura, a species with an extensively studied rich and adaptive chromosomal polymorphism. These maps are based on 462 markers: 115, 236, and 111 markers for elements A, C, and E, respectively. The availability of these dense maps will facilitate genome assembly and will thus greatly contribute to obtaining a good reference genome, which is a required step for D. subobscura to attain the model species status. The comparative analysis of these physical maps and those obtained from the D. pseudoobscura and D. melanogaster genomes allowed us to infer the number of fixed inversions and chromosomal evolutionary rates for each pairwise comparison. For all three elements, rates inferred from the more closely related species were higher than those inferred from the more distantly related species, which together with results of relative-rate tests point to an acceleration in the D. subobscura lineage at least for elements A and E.

Multiple and diverse structural changes affect the breakpoint regions of polymorphic inversions across the Drosophila genus

Chromosomal polymorphism is widespread in the Drosophila genus, with extensive evidence supporting its adaptive character in diverse species. Moreover, inversions are the major contributors to the genus chromosomal evolution. The molecular characterization of a reduced number of polymorphic inversion breakpoints in Drosophila melanogaster and Drosophila subobscura supports that their inversions would have mostly originated through a mechanism that generates duplications —staggered double-strand breaks— and has thus the potential to contribute to their adaptive character. There is also evidence for inversion breakpoint reuse at different time scales. Here, we have characterized the breakpoints of two inversions of D. subobscura —O₄ and O₈— involved in complex arrangements that are frequent in the warm parts of the species distribution area. The duplications detected at their breakpoints are consistent with their origin through the staggered-break mechanism, which further supports it as the prevalent mechanism in D. subobscura. The comparative analysis of inversions breakpoint regions across the Drosophila genus has revealed several genes affected by multiple disruptions due not only to inversions but also to single-gene transpositions and duplications.