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Patterns of geographic variation of thermal adapted candidate genes in Drosophila subobscura sex chromosome arrangements. BMC Evol Biol 2018; 18:60. [PMID: 29699488 PMCID: PMC5921438 DOI: 10.1186/s12862-018-1178-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 04/11/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The role of chromosomal arrangements in adaptation is supported by the repeatable clinal variation in inversion frequencies across continents in colonizing species such as Drosophila subobscura. However, there is a lack of knowledge on the genetic variation in genes within inversions, possibly targets of climatic selection, across a geographic latitudinal gradient. In the present study we analysed four candidate loci for thermal adaptation, located close to the breakpoints, in two chromosomal arrangements of the sex (A) chromosome of Drosophila subobscura with different thermal preferences. Individual chromosomes with A2 (the inverted arrangement considered warm adapted) or AST (the standard ancestral arrangement considered cold adapted) were sequenced across four European localities at varying latitudes, up to ~ 2500 Kms apart. RESULTS Importantly, we found very low differentiation for each specific arrangement across populations as well as no clinal patterns of genomic variation. This suggests wide gene exchange along the cline. Differentiation between the sex chromosome arrangements was significant in the two more proximal regions relative to the AST orientation but not in the distal ones, independently of their location inside or outside the inversion. This can be possibly due to variation in the levels of gene flux and/or selection acting in these regions. CONCLUSIONS Gene flow appears to have homogenized the genetic content within-arrangement at a wide geographical scale, despite the expected diverse selective pressures in the specific natural environments of the different populations sampled. It is thus likely that the inversion frequency clines in this species are being maintained by local adaptation in face of gene flow. The differences between arrangements at non-coding regions might be associated with the previously observed differential gene expression in different thermal regimes. Higher resolution genomic scans for individual chromosomal arrangements performed over a large environmental gradient are needed to find the targets of selection and further elucidate the adaptive mechanisms maintaining chromosomal inversion polymorphisms.
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Santos J, Pascual M, Fragata I, Simões P, Santos MA, Lima M, Marques A, Lopes-Cunha M, Kellen B, Balanyà J, Rose MR, Matos M. Tracking changes in chromosomal arrangements and their genetic content during adaptation. J Evol Biol 2016; 29:1151-67. [PMID: 26969850 DOI: 10.1111/jeb.12856] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 02/23/2016] [Accepted: 02/25/2016] [Indexed: 12/13/2022]
Abstract
There is considerable evidence for an adaptive role of inversions, but how their genetic content evolves and affects the subsequent evolution of chromosomal polymorphism remains controversial. Here, we track how life-history traits, chromosomal arrangements and 22 microsatellites, within and outside inversions, change in three replicated populations of Drosophila subobscura for 30 generations of laboratory evolution since founding from the wild. The dynamics of fitness-related traits indicated adaptation to the new environment concomitant with directional evolution of chromosomal polymorphism. Evidence of selective changes in frequency of inversions was obtained for seven of 23 chromosomal arrangements, corroborating a role for inversions in adaptation. The evolution of linkage disequilibrium between some microsatellites and chromosomes suggested that adaptive changes in arrangements involved changes in their genetic content. Several microsatellite alleles increased in frequency more than expected by drift in targeted inversions in all replicate populations. In particular, there were signs of selection in the O3+4 arrangement favouring a combination of alleles in two loci linked to the inversion and changing along with it, although the lack of linkage disequilibrium between these loci precludes epistatic selection. Seven other alleles increased in frequency within inversions more than expected by drift, but were not in linkage disequilibrium with them. Possibly these alleles were hitchhiking along with alleles under selection that were not specific to those inversions. Overall, the selection detected on the genetic content of inversions, despite limited coverage of the genome, suggests that genetic changes within inversions play an important role in adaptation.
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Affiliation(s)
- J Santos
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - M Pascual
- Department of Genetics and IrBio, Facultat de Biologia, Universitat de Barcelona, Barcelona, España
| | - I Fragata
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - P Simões
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - M A Santos
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - M Lima
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - A Marques
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - M Lopes-Cunha
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - B Kellen
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - J Balanyà
- Department of Genetics and IrBio, Facultat de Biologia, Universitat de Barcelona, Barcelona, España
| | - M R Rose
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - M Matos
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
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Fragata I, Lopes-Cunha M, Bárbaro M, Kellen B, Lima M, Santos MA, Faria GS, Santos M, Matos M, Simões P. How much can history constrain adaptive evolution? A real-time evolutionary approach of inversion polymorphisms in Drosophila subobscura. J Evol Biol 2014; 27:2727-38. [PMID: 25430492 DOI: 10.1111/jeb.12533] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 10/10/2014] [Accepted: 10/20/2014] [Indexed: 12/24/2022]
Abstract
Chromosomal inversions are present in a wide range of animals and plants, having an important role in adaptation and speciation. Although empirical evidence of their adaptive value is abundant, the role of different processes underlying evolution of chromosomal polymorphisms is not fully understood. History and selection are likely to shape inversion polymorphism variation to an extent yet largely unknown. Here, we perform a real-time evolution study addressing the role of historical constraints and selection in the evolution of these polymorphisms. We founded laboratory populations of Drosophila subobscura derived from three locations along the European cline and followed the evolutionary dynamics of inversion polymorphisms throughout the first 40 generations. At the beginning, populations were highly differentiated and remained so throughout generations. We report evidence of positive selection for some inversions, variable between foundations. Signs of negative selection were more frequent, in particular for most cold-climate standard inversions across the three foundations. We found that previously observed convergence at the phenotypic level in these populations was not associated with convergence in inversion frequencies. In conclusion, our study shows that selection has shaped the evolutionary dynamics of inversion frequencies, but doing so within the constraints imposed by previous history. Both history and selection are therefore fundamental to predict the evolutionary potential of different populations to respond to global environmental changes.
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Affiliation(s)
- I Fragata
- CE3C - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
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Pegueroles C, Aquadro CF, Mestres F, Pascual M. Gene flow and gene flux shape evolutionary patterns of variation in Drosophila subobscura. Heredity (Edinb) 2013; 110:520-9. [PMID: 23321709 PMCID: PMC3656635 DOI: 10.1038/hdy.2012.118] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 10/11/2012] [Accepted: 12/17/2012] [Indexed: 12/12/2022] Open
Abstract
Gene flow (defined as allele exchange between populations) and gene flux (defined as allele exchange during meiosis in heterokaryotypic females) are important factors decreasing genetic differentiation between populations and inversions. Many chromosomal inversions are under strong selection and their role in recombination reduction enhances the maintenance of their genetic distinctness. Here we analyze levels and patterns of nucleotide diversity, selection and demographic history, using 37 individuals of Drosophila subobscura from Mount Parnes (Greece) and Barcelona (Spain). Our sampling focused on two frequent O-chromosome arrangements that differ by two overlapping inversions (OST and O(3+4)), which are differentially adapted to the environment as observed by their opposing latitudinal clines in inversion frequencies. The six analyzed genes (Pif1A, Abi, Sqd, Yrt, Atpα and Fmr1) were selected for their location across the O-chromosome and their implication in thermal adaptation. Despite the extensive gene flux detected outside the inverted region, significant genetic differentiation between both arrangements was found inside it. However, high levels of gene flow were detected for all six genes when comparing the same arrangement among populations. These results suggest that the adaptive value of inversions is maintained, regardless of the lack of genetic differentiation within arrangements from different populations, and thus favors the Local Adaptation hypothesis over the Coadapted Genome hypothesis as the basis of the selection acting on inversions in these populations.
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Affiliation(s)
- C Pegueroles
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Spain.
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Simões P, Calabria G, Picão-Osório J, Balanyà J, Pascual M. The genetic content of chromosomal inversions across a wide latitudinal gradient. PLoS One 2012; 7:e51625. [PMID: 23272126 PMCID: PMC3525579 DOI: 10.1371/journal.pone.0051625] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 11/02/2012] [Indexed: 12/23/2022] Open
Abstract
There is increasing evidence regarding the role of chromosomal inversions in relevant biological processes such as local adaptation and speciation. A classic example of the adaptive role of chromosomal polymorphisms is given by the clines of inversion frequencies in Drosophila subobscura, repeatable across continents. Nevertheless, not much is known about the molecular variation associated with these polymorphisms. We characterized the genetic content of ca. 600 individuals from nine European populations following a latitudinal gradient by analysing 19 microsatellite loci from two autosomes (J and U) and the sex chromosome (A), taking into account their chromosomal inversions. Our results clearly demonstrate the molecular genetic uniformity within a given chromosomal inversion across a large latitudinal gradient, particularly from Groningen (Netherlands) in the north to Málaga (Spain) in the south, experiencing highly diverse environmental conditions. This low genetic differentiation within the same gene arrangement across the nine European populations is consistent with the local adaptation hypothesis for th evolutionof chromosomal polymorphisms. We also show the effective role of chromosomal inversions in maintaining different genetic pools within these inverted genomic regions even in the presence of high gene flow. Inversions represent thus an important barrier to gene flux and can help maintain specific allelic combinations with positive effects on fitness. Consistent patterns of microsatellite allele-inversion linkage disequilibrium particularly in loci within inversions were also observed. Finally, we identified areas within inversions presenting clinal variation that might be under selection.
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Affiliation(s)
- Pedro Simões
- Grup de Biologia Evolutiva/IRBio, Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.
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Papaceit M, Segarra C, Aguadé M. Structure and population genetics of the breakpoints of a polymorphic inversion in Drosophila subobscura. Evolution 2012; 67:66-79. [PMID: 23289562 DOI: 10.1111/j.1558-5646.2012.01731.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Drosophila subobscura is a paleartic species of the obscura group with a rich chromosomal polymorphism. To further our understanding on the origin of inversions and on how they regain variation, we have identified and sequenced the two breakpoints of a polymorphic inversion of D. subobscura--inversion 3 of the O chromosome--in a population sample. The breakpoints could be identified as two rather short fragments (∼300 bp and 60 bp long) with no similarity to any known transposable element family or repetitive sequence. The presence of the ∼300-bp fragment at the two breakpoints of inverted chromosomes implies its duplication, an indication of the inversion origin via staggered double-strand breaks. Present results and previous findings support that the mode of origin of inversions is neither related to the inversion age nor species-group specific. The breakpoint regions do not consistently exhibit the lower level of variation within and stronger genetic differentiation between arrangements than more internal regions that would be expected, even in moderately small inversions, if gene conversion were greatly restricted at inversion breakpoints. Comparison of the proximal breakpoint region in species of the obscura group shows that this breakpoint lies in a small high-turnover fragment within a long collinear region (∼300 kb).
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Affiliation(s)
- Montserrat Papaceit
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, i Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
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Araúz PA, Peris-Bondia F, Latorre A, Serra L, Mestres F. Molecular evidence to suggest the origin of a colonization: Drosophila subobscura in America. Genetica 2012; 139:1477-86. [PMID: 22481521 DOI: 10.1007/s10709-012-9647-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 03/26/2012] [Indexed: 10/28/2022]
Abstract
The recent colonization of America by Drosophila subobscura represents a great opportunity for evolutionary biology studies. Knowledge of the populations from which the colonization started would provide an understanding of how genetic composition changed during adaptation to the new environment. Thus, a 793 nucleotide fragment of the Odh (Octanol dehydrogenase) gene was sequenced in 66 chromosomal lines from Barcelona (western Mediterranean) and in 66 from Mt. Parnes (Greece, eastern Mediterranean). No sequence of Odh fragment in Barcelona or Mt. Parnes was identical to any of those previously detected in America. However, an Odh sequence from Barcelona differed in only one nucleotide from another found in American populations. In both cases, the chromosomal lines presented the same inversion: O(7), and the Odh gene was located within this inversion. This evidence suggests a possible western Mediterranean origin for the colonization. Finally, the molecular and inversion data indicate that the colonization was not characterized by multiple reintroductions.
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Affiliation(s)
- Pedro A Araúz
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 643, Barcelona, Spain
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KHADEM M, MUNTÉ A, CAMACHO R, AGUADÉ M, SEGARRA C. Multilocus analysis of nucleotide variation in Drosophila madeirensis, an endemic species of the Laurisilva forest in Madeira. J Evol Biol 2012; 25:726-39. [DOI: 10.1111/j.1420-9101.2012.02467.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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9
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Arboleda-Bustos CE, Segarra C. The Dca Gene Involved in Cold Adaptation in Drosophila melanogaster Arose by Duplication of the Ancestral regucalcin Gene. Mol Biol Evol 2011; 28:2185-95. [DOI: 10.1093/molbev/msr040] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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10
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Mestres F, Serra L. The Va/Ba balanced lethal strain: thirty years of research in Drosophila subobscura (1977–2007). J ZOOL SYST EVOL RES 2008. [DOI: 10.1111/j.1439-0469.2008.00463.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Rašić G, Stamenković -Radak M, Savić T, Andjelković M. Inbreeding reveals interpopulation differences in inversion polymorphism of Drosophila subobscura. J ZOOL SYST EVOL RES 2007. [DOI: 10.1111/j.1439-0469.2007.00428.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Khadem M, Rozas J, Segarra C, Aguade M. DNA variation at the rp49 gene region in Drosophila madeirensis and D. subobscura from Madeira: inferences about the origin of an insular endemic species. J Evol Biol 2001. [DOI: 10.1046/j.1420-9101.2001.00293.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Zapata C, Alvarez G, Rodríguez-Trelles F, Maside X. A long-term study on seasonal changes of gametic disequilibrium between allozymes and inversions in Drosophila subobscura. Evolution 2000; 54:1673-9. [PMID: 11108594 DOI: 10.1111/j.0014-3820.2000.tb00711.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Seasonal variation (spring, early summer, late summer, and autumn) of gametic disequilibrium between gene arrangements (OST and O3+4) of the O chromosome and Lap, Pept-1, and Acph allozyme loci, located inside these inversions, has been recorded in a natural population of Drosophila subobscura during seven years over a 15-year period. The length of the study allowed us to investigate the temporal variation of the allozyme-inversion associations by statistical methods of time series analysis. Cyclic seasonal changes of allozyme-inversion associations for both Lap and Pept-1 are detected in the natural population. In both cases, the patterns of seasonal change are due to the seasonal change of frequency of Lap and Pept-1 allozymes occurring exclusively within the OST gene arrangement. In contrast, the allozyme frequencies at these loci within the O3+4 gene arrangement are stable along seasons. The patterns of temporal variation of allozyme-inversion associations for Lap and Pept-1 in the natural population are contrasted with those previously published that correspond to gene arrangements of the O chromosome and nucleotide polymorphism at the rp49 region located inside these inversions, suggesting that natural selection is operating on these allozyme-inversion associations.
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Affiliation(s)
- C Zapata
- Departamento de Biología Fundamental, Facultad de Biología, Universidad de Santiago de Compostela, Spain.
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Zapata C, Alvarez G, Rodríguez-Trelles F, Maside X. A LONG-TERM STUDY ON SEASONAL CHANGES OF GAMETIC DISEQUILIBRIUM BETWEEN ALLOZYMES AND INVERSIONS IN DROSOPHILA SUBOBSCURA. Evolution 2000. [DOI: 10.1554/0014-3820(2000)054[1673:altsos]2.0.co;2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Navarro-Sabaté A, Aguadé M, Segarra C. The relationship between allozyme and chromosomal polymorphism inferred from nucleotide variation at the Acph-1 gene region of Drosophila subobscura. Genetics 1999; 153:871-89. [PMID: 10511564 PMCID: PMC1460765 DOI: 10.1093/genetics/153.2.871] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Acph-1 gene region was sequenced in 51 lines of Drosophila subobscura. Lines differ in their chromosomal arrangement for segment I of the O chromosome (O(st) and O(3+4)) and in the Acph-1 electrophoretic allele (Acph-1(100), Acph-1(054), and Acph-1(>100)). The ACPH-1 protein exhibits much more variation than previously detected by electrophoresis. The amino acid replacements responsible for the Acph-1(054) and Acph-1(>100) electrophoretic variants are different within O(st) and within O(3+4), which invalidates all previous studies on linkage disequilibrium between chromosomal and allozyme polymorphisms at this locus. The Acph-1(>100) allele within O(3+4) has a recent origin, while both Acph-1(054) alleles are rather old. Levels of nucleotide variation are higher within the O(3+4) than within the O(st) arrangement except for nonsynonymous sites. The McDonald and Kreitman test shows a significant excess of nonsynonymous polymorphisms within O(st) when D. guanche is used as the outgroup. According to the nearly neutral model of molecular evolution, this excess is consistent with a smaller effective size of O(st) relative to O(3+4) arrangements. A smaller population size, a lower recombination, and a more recent bottleneck might be contributing to the smaller effective size of O(st).
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Affiliation(s)
- A Navarro-Sabaté
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, 08071 Barcelona, Spain
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16
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Rozas J, Segarra C, Ribó G, Aguadé M. Molecular population genetics of the rp49 gene region in different chromosomal inversions of Drosophila subobscura. Genetics 1999; 151:189-202. [PMID: 9872959 PMCID: PMC1460452 DOI: 10.1093/genetics/151.1.189] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Nucleotide variation at the ribosomal protein 49 (rp49) gene region has been studied in 75 lines of Drosophila subobscura belonging to four chromosomal arrangements (Ost, O3+4, O3+4+8, and O3+4+23). The location of the rp49 gene region within the inversion loop differs among heterokaryotypes: it is very close to one of the breakpoints in heterozygotes involving Ost chromosomes, while it is in a more central position in all other heterokaryotypes. The distribution of nucleotide polymorphism in the different arrangements is consistent with a monophyletic origin of the inversions. The data also provide evidence that gene conversion and possibly double crossover are involved in shuffling nucleotide variation among gene arrangements. The analyses reveal that the level of genetic exchange is higher when the region is located in a more central position of the inverted fragment than when it is close to the breakpoints. The pairwise difference distributions as well as the negative values of Tajima's and Fu and Li's statistics further support the hypothesis that nucleotide variation within chromosomal arrangements still reflects expansion after the origin of the inversions. Under the expansion model, we have estimated the time of origin of the studied inversions.
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Affiliation(s)
- J Rozas
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, 08071 Barcelona, Spain.
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Rodríguez-Trelles F, Rodríguez MA. Rapid micro-evolution and loss of chromosomal diversity in Drosophila in response to climate warming. Evol Ecol 1998. [DOI: 10.1023/a:1006546616462] [Citation(s) in RCA: 119] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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