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Khadem M, Arenas C, Balanyà J, Mestres F. Long-term changes in the inversion chromosomal polymorphism: Drosophila subobscura population from Rasht (north of Iran). J Genet 2022. [DOI: 10.1007/s12041-022-01387-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Zivanovic G, Arenas C, Mestres F. Adaptation of Drosophila subobscura chromosomal inversions to climatic variables: the Balkan natural population of Avala. Genetica 2021; 149:155-169. [PMID: 34129131 DOI: 10.1007/s10709-021-00125-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/10/2021] [Indexed: 11/26/2022]
Abstract
The adaptive value of chromosomal inversions continues raising relevant questions in evolutionary biology. In many species of the Drosophila genus, different inversions have been recognized to be related to thermal adaptation, but it is necessary to determine to which specific climatic variables the inversions are adaptive. With this aim, the behavior of thermal adapted inversions of Drosophila subobscura regarding climatic variables was studied in the natural population of Avala (Serbia) during the 2014-2017 period. The results obtained were compared with those previously reported in the Font Groga (Barcelona, Spain) population, which presents different climatic and environmental conditions. In both populations, it was observed that most thermal adapted inversions were significantly associated with the first, second or both principal components, which were related with maximum, minimum and mean temperatures. Moreover, a significant increase over years (2004-2017) for the minimum temperature was detected. In parallel, a significant variation over time in Avala was only observed for the frequencies of 'warm' and 'non-thermal' adapted inversions of the U chromosome. However, stability in the chromosomal inversion polymorphism was observed for the 2014-2017 period which might result from the temporal span of the study and/or selective process acting on the population.
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Affiliation(s)
- Goran Zivanovic
- Department of Genetics, Institute for Biological Research "Sinisa Stankovic" - National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Concepció Arenas
- Departament de Genètica, Microbiologia i Estadística, Secció d'Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Francesc Mestres
- Departament de Genètica, Microbiologia i Estadística, Secció de Genètica Biomèdica, Evolutiva i Desenvolupament - IRBio (Institut de Recerca per la Biodiversitat), Universitat de Barcelona, Barcelona, Spain.
- Departament de Genètica, Microbiologia i Estadística, Secció Genètica Biomèdica, Evolució i Desenvolupament, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain.
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Ilan Y. Overcoming randomness does not rule out the importance of inherent randomness for functionality. J Biosci 2019. [DOI: 10.1007/s12038-019-9958-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Rate of change for the thermal adapted inversions in Drosophila subobscura. Genetica 2019; 147:401-409. [PMID: 31625005 DOI: 10.1007/s10709-019-00078-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/05/2019] [Indexed: 10/25/2022]
Abstract
The changes of chromosomal inversion polymorphism composition of Drosophila subobscura in samples from Apatin (Serbia) were studied in a 24-years interval (1994-2018). The variation was significant for all autosomes and directional, increasing the inversions considered as 'warm', whereas those reported as 'cold' decreased. Furthermore, the Chromosomal Thermal Index (CTI), which allows studying the thermal adaptation of the whole karyotype increased significantly in that period of time. These results were in agreement with the indicators of global warming in Apatin: a trend to increase of the mean, maximum and minimum (this latter even significant) temperatures, and an erratic pattern of rainfall (also usual in global warming). The deviations from the Wright-Fisher model of genetic drift were used to consider the possible effect of migration or selection as evolutionary factors responsible for the change in inversion frequencies. To quantify approximately the rate of change in the frequencies, for each kind of inversions ('cold', 'warm' and 'non-thermal adapted'), the difference in frequency between the Apatin samples obtained in 1994 and 2018 was computed and then it was divided by the number of years elapsed. This rate was always higher (from twice as many as thirty times more depending on the autosome) for thermal adapted inversions ('cold' or 'warm') than the 'non-thermal' adapted. From this study, it could be concluded that the chromosomal inversions of D. subobscura could change (in composition and frequencies) in a predictable direction and a rather 'rapid' rhythm to adapt to the global warming scenario.
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Karageorgiou C, Gámez-Visairas V, Tarrío R, Rodríguez-Trelles F. Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects. BMC Genomics 2019; 20:223. [PMID: 30885123 PMCID: PMC6423853 DOI: 10.1186/s12864-019-5590-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/06/2019] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Drosophila subobscura has long been a central model in evolutionary genetics. Presently, its use is hindered by the lack of a reference genome. To bridge this gap, here we used PacBio long-read technology, together with the available wealth of genetic marker information, to assemble and annotate a high-quality nuclear and complete mitochondrial genome for the species. With the obtained assembly, we performed the first synteny analysis of genome structure evolution in the subobscura subgroup. RESULTS We generated a highly-contiguous ~ 129 Mb-long nuclear genome, consisting of six pseudochromosomes corresponding to the six chromosomes of a female haploid set, and a complete 15,764 bp-long mitogenome, and provide an account of their numbers and distributions of codifying and repetitive content. All 12 identified paracentric inversion differences in the subobscura subgroup would have originated by chromosomal breakage and repair, with some associated duplications, but no evidence of direct gene disruptions by the breakpoints. Between lineages, inversion fixation rates were 10 times higher in continental D. subobscura than in the two small oceanic-island endemics D. guanche and D. madeirensis. Within D. subobscura, we found contrasting ratios of chromosomal divergence to polymorphism between the A sex chromosome and the autosomes. CONCLUSIONS We present the first high-quality, long-read sequencing of a D. subobscura genome. Our findings generally support genome structure evolution in this species being driven indirectly, through the inversions' recombination-suppression effects in maintaining sets of adaptive alleles together in the face of gene flow. The resources developed will serve to further establish the subobscura subgroup as model for comparative genomics and evolutionary indicator of global change.
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Affiliation(s)
- Charikleia Karageorgiou
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Bellaterra, Barcelona, Spain
| | - Víctor Gámez-Visairas
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Bellaterra, Barcelona, Spain
| | - Rosa Tarrío
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Bellaterra, Barcelona, Spain
| | - Francisco Rodríguez-Trelles
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Bellaterra, Barcelona, Spain
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Galludo M, Canals J, Pineda-Cirera L, Esteve C, Rosselló M, Balanyà J, Arenas C, Mestres F. Climatic adaptation of chromosomal inversions in Drosophila subobscura. Genetica 2018; 146:433-441. [PMID: 30151609 DOI: 10.1007/s10709-018-0035-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 08/21/2018] [Indexed: 01/12/2023]
Abstract
Drosophila subobscura is a species with a rich chromosomal polymorphism which is adaptive to different climatic conditions. Five samples of the Font Groga population (Barcelona, Spain) were sampled in autumn during 5 consecutive years (2011-2015) to obtain their inversion chromosomal polymorphism, and climatic data of several meteorological variables were also collected. The aim was to analyze the adaptive potential of inversions with regard to climatic variables, being the most relevant: mean temperature (Tmean), maximum temperature (Tmax), minimum temperature (Tmin), humidity (Hm) and rainfall (Rf). As expected, no significant variation in inversion frequencies were detected over this short period of time. However, from a climatic point of view it was possible to differentiate 'warm' and 'dry' from 'cold' and 'humid' samples. The joint study of maximum (Tmax) and minimum (Tmin) temperatures was a key element to understand the effect on adaptation of many inversions. It was also observed that temperature had to be considered in conjunction with humidity and rainfall. All these factors would condition the biota of D. subobscura habitat, and chromosomal inversions could provide an adaptive response to it.
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Affiliation(s)
- Maria Galludo
- Departament de Genètica, Microbiologia i Estadística, Secció Genètica Biomèdica, Evolució i Desenvolupament, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain
| | - Jordi Canals
- Departament de Genètica, Microbiologia i Estadística, Secció Genètica Biomèdica, Evolució i Desenvolupament, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain
| | - Laura Pineda-Cirera
- Departament de Genètica, Microbiologia i Estadística, Secció Genètica Biomèdica, Evolució i Desenvolupament, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain
| | - Carla Esteve
- Departament de Genètica, Microbiologia i Estadística, Secció Genètica Biomèdica, Evolució i Desenvolupament, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain
| | - Maria Rosselló
- Departament de Genètica, Microbiologia i Estadística, Secció Genètica Biomèdica, Evolució i Desenvolupament, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain
| | - Joan Balanyà
- Departament de Genètica, Microbiologia i Estadística, Secció Genètica Biomèdica, Evolució i Desenvolupament, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain
- IRBio-Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
| | - Conxita Arenas
- Departament de Genètica, Microbiologia i Estadística, Secció Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Francesc Mestres
- Departament de Genètica, Microbiologia i Estadística, Secció Genètica Biomèdica, Evolució i Desenvolupament, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain.
- IRBio-Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain.
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Arenas C, Zivanovic G, Mestres F. Chromosomal Thermal Index: a comprehensive way to integrate the thermal adaptation of Drosophila subobscura whole karyotype. Genome 2017; 61:73-78. [PMID: 29190121 DOI: 10.1139/gen-2017-0124] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Drosophila has demonstrated to be an excellent model to study the adaptation of organisms to global warming, with inversion chromosomal polymorphism having a key role in this adaptation. Here, we introduce a new index (Chromosomal Thermal Index or CTI) to quantify the thermal adaptation of a population according to its composition of "warm" and "cold" adapted inversions. This index is intuitive, has good statistical properties, and can be used to hypothesis on the effect of global warming on natural populations. We show the usefulness of CTI using data from European populations of D. subobscura, sampled in different years. Out of 15 comparisons over time, nine showed significant increase of CTI, in accordance with global warming expectations. Although large regions of the genome outside inversions contain thermal adaptation genes, our results show that the total amount of warm or cold inversions in populations seems to be directly involved in thermal adaptation, whereas the interactions between the inversions content of homologous and non-homologous chromosomes are not relevant.
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Affiliation(s)
- Conxita Arenas
- a Departament de Genètica, Microbiologia i Estadística, Secció d'Estadística, Universitat de Barcelona, Av. Diagonal, 643, 08028-Barcelona, Spain
| | - Goran Zivanovic
- b Department of Genetics, Institute for Biological Research "Sinisa Stankovic", University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia
| | - Francesc Mestres
- c Departament de Genètica, Microbiologia i Estadística, Secció de Genètica Biomèdica, Evolutiva i del Desenvolupament, Universitat de Barcelona, Av. Diagonal, 643, 08028-Barcelona, Spain; IRBio (Institut de Recerca per la Biodiversitat), Universitat de Barcelona, Av. Diagonal, 643, 08028-Barcelona, Spain
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