Molecular population genetics of the OBP83 genomic region in Drosophila subobscura and D. guanche: contrasting the effects of natural selection and gene arrangement expansion in the patterns of nucleotide variation

Sánchez-Gracia, Alejandro; Rozas, Julio

doi:10.1038/hdy.2010.26

Cited by 9 publications

(14 citation statements)

References 65 publications

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“…1). Markers AbdA 11 and Obp83a/Obp83b 29 that are located at section 94E and 98D, respectively, were used as starting points to identify the inversion breakpoints in non-inverted chromosomes.…”

Section: Resultsmentioning

confidence: 99%

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

Puerma

Orengo

Aguadé

2016

Sci Rep

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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.

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Section: Resultsmentioning

confidence: 99%

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

Puerma

Orengo

Aguadé

2016

Sci Rep

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“…Interestingly, the O chromosome is the largest in this species (Laayouni et al ., ; Santos et al ., ) and presents the highest level of inversion polymorphisms (Krimbas, , ). Additionally, the O chromosome has been amply studied at the molecular level, with reports of high linkage disequilibrium of genes within inversions (Munté et al ., ; Pegueroles et al ., ; Sánchez‐Gracia & Rozas, ). Linkage within these inversions may facilitate the association between inversions and phenotypic traits.…”

Section: Discussionmentioning

confidence: 99%

Wing trait–inversion associations in Drosophila subobscura can be generalized within continents, but may change through time

Simões

Fragata

Lopes‐Cunha

et al. 2015

J of Evolutionary Biology

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Clinal variation is one of the most emblematic examples of the action of natural selection at a wide geographical range. In Drosophila subobscura, parallel clines in body size and inversions, but not in wing shape, were found in Europe and South and North America. Previous work has shown that a bottleneck effect might be largely responsible for differences in wing trait-inversion association between one European and one South American population. One question still unaddressed is whether the associations found before are present across other populations of the European and South American clines. Another open question is whether evolutionary dynamics in a new environment can lead to relevant changes in wing traits-inversion association. To analyse geographical variation in these associations, we characterized three recently laboratory founded D. subobscura populations from both the European and South American latitudinal clines. To address temporal variation, we also characterized the association at a later generation in the European populations. We found that wing size and shape associations can be generalized across populations of the same continent, but may change through time for wing size. The observed temporal changes are probably due to changes in the genetic content of inversions, derived from adaptation to the new, laboratory environment. Finally, we show that it is not possible to predict clinal variation from intrapopulation associations. All in all this suggests that, at least in the present, wing traits-inversion associations are not responsible for the maintenance of the latitudinal clines in wing shape and size.

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“…As suggested in previous studies and concordant with recovery from the last glaciations, the three models considered (Fig. ) incorporate changes in species size at different time intervals, and they all share a final population size expansion: (i) the expansion model (M1) is a simple stepwise expansion model (Rozas & Aguadé ; Sánchez‐Gracia & Rozas ); (ii) the bottleneck model (M2) is a simple stepwise reduction plus expansion model that incorporates the possible size changes due to past glacial periods (Castro et al . ); and (iii) the admixture model (M3) is a bottleneck and subdivision model that incorporates the possible isolation in glacial refugia (Menozzi & Krimbas ).…”

Section: Methodsmentioning

confidence: 62%

“…; Navarro‐Sabaté et al . ; Sánchez‐Gracia & Rozas ). However, these studies used as null model the SNM and were, thus, unable to discriminate between the proposed scenario, and one considering that the detected pattern mainly reflects the population demographic history.…”

Section: Introductionmentioning

confidence: 98%

“…; Stevison et al . ; Sánchez‐Gracia & Rozas ). To infer the demographic history of D. subobscura from levels and patterns of variation, we have sequenced multiple noncoding regions distributed along the J chromosome of this species, which in the geographical area studied as well as in most of its European and North African range only harbours the J st and J 1 arrangements that differ by the rather small J 1 inversion (Krimbas ).…”

Section: Introductionmentioning

confidence: 98%

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Inferring the demographic history of Drosophila subobscura from nucleotide variation at regions not affected by chromosomal inversions

2015

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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 as previous information indicated that its nucleotide variation is not at mutation-drift equilibrium. For that purpose, we sequenced 16 noncoding 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 origin and frequency increase of inversions. Among the simple demographic models considered in our Approximate Bayesian Computation analysis of variation at the 16 regions, the model best supported by the data implies a population size expansion soon after the penultimate glacial period. This model constitutes a better null model, and it is therefore an important resource for subsequent studies aiming among others to uncover selective events across the species genome. Our results also highlight the importance of introducing the possibility of multiple hits in the coalescent simulations with an outgroup.

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Molecular population genetics of the OBP83 genomic region in Drosophila subobscura and D. guanche: contrasting the effects of natural selection and gene arrangement expansion in the patterns of nucleotide variation

Cited by 9 publications

References 65 publications

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

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

Wing trait–inversion associations in Drosophila subobscura can be generalized within continents, but may change through time

Inferring the demographic history of Drosophila subobscura from nucleotide variation at regions not affected by chromosomal inversions

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