1
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Bock DG, Baeckens S, Kolbe JJ, Losos JB. When adaptation is slowed down: Genomic analysis of evolutionary stasis in thermal tolerance during biological invasion in a novel climate. Mol Ecol 2024; 33:e17075. [PMID: 37489260 DOI: 10.1111/mec.17075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 06/25/2023] [Accepted: 07/04/2023] [Indexed: 07/26/2023]
Abstract
Research conducted during the past two decades has demonstrated that biological invasions are excellent models of rapid evolution. Even so, characteristics of invasive populations such as a short time for recombination to assemble optimal combinations of alleles may occasionally limit adaptation to new environments. Here, we investigated such genetic constraints to adaptation in the invasive brown anole (Anolis sagrei)-a tropical ectotherm that was introduced to the southeastern United States, a region with a much colder climate than in its native Caribbean range. We examined thermal physiology for 30 invasive populations and tested for a climatic cline in cold tolerance. Also, we used genomics to identify mechanisms that may limit adaptation. We found no support for a climatic cline, indicating that thermal tolerance did not shift adaptively. Concomitantly, population genomic results were consistent with the occurrence of recombination cold spots that comprise more than half of the genome and maintain long-range associations among alleles in invasive populations. These genomic regions overlap with both candidate thermal tolerance loci that we identified using a standard genome-wide association test. Moreover, we found that recombination cold spots do not have a large contribution to population differentiation in the invasive range, contrary to observations in the native range. We suggest that limited recombination is constraining the contribution of large swaths of the genome to adaptation in invasive brown anoles. Our study provides an example of evolutionary stasis during invasion and highlights the possibility that reduced recombination occasionally slows down adaptation in invasive populations.
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Affiliation(s)
- Dan G Bock
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - Simon Baeckens
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Evolution and Optics of Nanostructures Lab, Department of Biology, Ghent University, Ghent, Belgium
- Functional Morphology Lab, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Jason J Kolbe
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Jonathan B Losos
- Department of Biology, Washington University, St. Louis, Missouri, USA
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2
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Cheek RG, McLaughlin JF, Gamboa MP, Marshall CA, Johnson BM, Silver DB, Mauro AA, Ghalambor CK. A lack of genetic diversity and minimal adaptive evolutionary divergence in introduced Mysis shrimp after 50 years. Evol Appl 2024; 17:e13637. [PMID: 38283609 PMCID: PMC10818135 DOI: 10.1111/eva.13637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 11/17/2023] [Accepted: 12/07/2023] [Indexed: 01/30/2024] Open
Abstract
The successes of introduced populations in novel habitats often provide powerful examples of evolution and adaptation. In the 1950s, opossum shrimp (Mysis diluviana) individuals from Clearwater Lake in Minnesota, USA were transported and introduced to Twin Lakes in Colorado, USA by fisheries managers to supplement food sources for trout. Mysis were subsequently introduced from Twin Lakes into numerous lakes throughout Colorado. Because managers kept detailed records of the timing of the introductions, we had the opportunity to test for evolutionary divergence within a known time interval. Here, we used reduced representation genomic data to investigate patterns of genetic diversity, test for genetic divergence between populations, and for evidence of adaptive evolution within the introduced populations in Colorado. We found very low levels of genetic diversity across all populations, with evidence for some genetic divergence between the Minnesota source population and the introduced populations in Colorado. There was little differentiation among the Colorado populations, consistent with the known provenance of a single founding population, with the exception of the population from Gross Reservoir, Colorado. Demographic modeling suggests that at least one undocumented introduction from an unknown source population hybridized with the population in Gross Reservoir. Despite the overall low genetic diversity we observed, F ST outlier and environmental association analyses identified multiple loci exhibiting signatures of selection and adaptive variation related to elevation and lake depth. The success of introduced species is thought to be limited by genetic variation, but our results imply that populations with limited genetic variation can become established in a wide range of novel environments. From an applied perspective, the observed patterns of divergence between populations suggest that genetic analysis can be a useful forensic tool to determine likely sources of invasive species.
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Affiliation(s)
- Rebecca G. Cheek
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColoradoUSA
| | - Jessica F. McLaughlin
- Department of Environmental Science, Policy, and ManagementUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Maybellene P. Gamboa
- Department of Organismal Biology and EcologyColorado CollegeColorado SpringsColoradoUSA
| | - Craig A. Marshall
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
- Council on Science and TechnologyPrinceton UniversityPrincetonNew JerseyUSA
| | - Brett M. Johnson
- Department of Fish, Wildlife and Conservation BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Douglas B. Silver
- Department of Fish, Wildlife and Conservation BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Alexander A. Mauro
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColoradoUSA
- Department of Biology, Centre for Biodiversity Dynamics (CBD)Norwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Cameron K. Ghalambor
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColoradoUSA
- Department of Biology, Centre for Biodiversity Dynamics (CBD)Norwegian University of Science and Technology (NTNU)TrondheimNorway
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3
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Zivanovic G, Arenas C, Mestres F. The Adaptive Value of Chromosomal Inversions and Climatic Change-Studies on the Natural Populations of Drosophila subobscura from the Balkans. INSECTS 2023; 14:596. [PMID: 37504602 PMCID: PMC10380441 DOI: 10.3390/insects14070596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/29/2023]
Abstract
The adaptive value of the Drosophila subobscura chromosomal inversion polymorphism with regard to environmental effects is well-known. However, the specific details of the inversion adaptations to the global warming scenario deserve to be analyzed. Toward this aim, polymorphism and karyotypes were studied in 574 individuals from Petnica (Serbia) in annual samples taken in June for the period 2019-2022. Comparing the results of Petnica (Cfa: humid subtropical climate) with those from Avala (Serbia: Cfb, temperate oceanic climate) and Font Groga (Barcelona, Spain; Csa: hot-summer Mediterranean climate), significant differences were observed for their chromosomal polymorphism. In Petnica, inversions from U and E chromosomes mainly reacted significantly with regard to temperature, humidity, and rainfall. Moreover, the inversion polymorphism from Petnica (2019-2022) was compared with that from 1995. In this period, a significant increase in mean and maximum temperature was observed. However, to properly explain the observed variations of inversions over time, it was necessary to carefully analyze annual seasonal changes and particular heat wave episodes. Interestingly, yearly fluctuations of U chromosome 'warm'-adapted inversions corresponded with opposite changes in 'non-thermal' inversions. Perhaps these types of inversions were not correctly defined with regard to thermal adaptation, or these fluctuations were also due to adaptations to other physical and/or biological variables. Finally, a joint study of chromosomal inversion polymorphism from many Balkan populations of D. subobscura indicated that different climatic regions presented distinct composition, including thermal-adapted inversions.
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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, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia
| | - Concepció Arenas
- Departament de Genètica, Microbiologia i Estadística, Secció d'Estadística, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
| | - Francesc Mestres
- Departament de Genètica, Microbiologia i Estadística, Secció de Genètica Biomèdica, Evolutiva i Desenvolupament and IRBio (Institut de Recerca per la Biodiversitat), Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
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4
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Erić K, Veselinović MS, Patenković A, Davidović S, Erić P, Stamenković-Radak M, Tanasković M. Population History Shapes Responses to Different Temperature Regimes in Drosophila subobscura. Life (Basel) 2023; 13:1333. [PMID: 37374116 DOI: 10.3390/life13061333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/12/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
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.
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Affiliation(s)
- Katarina Erić
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research "Siniša Stanković"-National Institute of the Republic of Serbia, University of Belgrade, Despot Stefan Blvd. 142, 11060 Belgrade, Serbia
| | | | - Aleksandra Patenković
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research "Siniša Stanković"-National Institute of the Republic of Serbia, University of Belgrade, Despot Stefan Blvd. 142, 11060 Belgrade, Serbia
| | - Slobodan Davidović
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research "Siniša Stanković"-National Institute of the Republic of Serbia, University of Belgrade, Despot Stefan Blvd. 142, 11060 Belgrade, Serbia
| | - Pavle Erić
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research "Siniša Stanković"-National Institute of the Republic of Serbia, University of Belgrade, Despot Stefan Blvd. 142, 11060 Belgrade, Serbia
| | | | - Marija Tanasković
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research "Siniša Stanković"-National Institute of the Republic of Serbia, University of Belgrade, Despot Stefan Blvd. 142, 11060 Belgrade, Serbia
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5
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Santos MA, Antunes MA, Grandela A, Carromeu-Santos A, Quina AS, Santos M, Matos M, Simões P. Past history shapes evolution of reproductive success in a global warming scenario. J Therm Biol 2023; 112:103478. [PMID: 36796921 DOI: 10.1016/j.jtherbio.2023.103478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/10/2022] [Accepted: 01/06/2023] [Indexed: 01/13/2023]
Abstract
Adaptive evolution is critical for animal populations to thrive in the fast-changing natural environments. Ectotherms are particularly vulnerable to global warming and, although their limited coping ability has been suggested, few real-time evolution experiments have directly accessed their evolutionary potential. Here, we report a long-term experimental evolution study addressing the evolution of Drosophila thermal reaction norms, after ∼30 generations under different dynamic thermal regimes: fluctuating (daily variation between 15 and 21 °C) or warming (daily fluctuation with increases in both thermal mean and variance across generations). We analyzed the evolutionary dynamics of Drosophila subobscura populations as a function of the thermally variable environments in which they evolved and their distinct background. Our results showed clear differences between the historically differentiated populations: high latitude D. subobscura populations responded to selection, improving their reproductive success at higher temperatures whereas their low latitude counterparts did not. This suggests population variation in the amount of genetic variation available for thermal adaptation, an aspect that needs to be considered to allow for better predictions of future climate change responses. Our results highlight the complex nature of thermal responses in face of environmental heterogeneity and emphasize the importance of considering inter-population variation in thermal evolution studies.
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Affiliation(s)
- Marta A Santos
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Lisboa, Portugal; Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Marta A Antunes
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Lisboa, Portugal; Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Afonso Grandela
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Lisboa, Portugal; Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Ana Carromeu-Santos
- CESAM - Centre for Environmental and Marine Studies, Universidade de Aveiro and Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Ana S Quina
- CESAM - Centre for Environmental and Marine Studies, Universidade de Aveiro and Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Mauro Santos
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Lisboa, Portugal; Departament de Genètica i de Microbiologia, Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GBBE), Universitat Autònoma de Barcelona, Spain
| | - Margarida Matos
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Lisboa, Portugal; Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Pedro Simões
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Lisboa, Portugal; Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal.
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6
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Daly EZ, Chabrerie O, Massol F, Facon B, Hess MC, Tasiemski A, Grandjean F, Chauvat M, Viard F, Forey E, Folcher L, Buisson E, Boivin T, Baltora‐Rosset S, Ulmer R, Gibert P, Thiébaut G, Pantel JH, Heger T, Richardson DM, Renault D. A synthesis of biological invasion hypotheses associated with the introduction–naturalisation–invasion continuum. OIKOS 2023. [DOI: 10.1111/oik.09645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Ella Z. Daly
- Univ. of Rennes, CNRS, ECOBIO (Ecosystèmes, Biodiversité, Evolution), UMR 6553 Rennes France
| | - Olivier Chabrerie
- Univ. de Picardie Jules Verne, UMR 7058 CNRS EDYSAN Amiens Cedex 1 France
| | - Francois Massol
- Univ. Lille, CNRS, Inserm, CHU Lille, Inst. Pasteur de Lille, U1019 – UMR 9017 – CIIL – Center for Infection and Immunity of Lille Lille France
| | - Benoit Facon
- CBGP, INRAE, CIRAD, IRD, Montpellier Institut Agro, Univ. Montpellier Montpellier France
| | - Manon C.M. Hess
- Inst. Méditerranéen de Biodiversité et d'Ecologie Marine et Continentale (IMBE), UMR: Aix Marseille Univ., Avignon Université, CNRS, IRD France
- Inst. de Recherche pour la Conservation des zones Humides Méditerranéennes Tour du Valat, Le Sambuc Arles France
| | - Aurélie Tasiemski
- Univ. Lille, CNRS, Inserm, CHU Lille, Inst. Pasteur de Lille, U1019 – UMR 9017 – CIIL – Center for Infection and Immunity of Lille Lille France
| | - Frédéric Grandjean
- Univ. de Poitiers, UMR CNRS 7267 EBI‐Ecologie et Biologie des Interactions, équipe EES Poitiers Cedex 09 France
| | | | | | - Estelle Forey
- Normandie Univ., UNIROUEN, INRAE, USC ECODIV Rouen France
| | - Laurent Folcher
- ANSES – Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Laboratoire de la Santé des Végétaux – Unité de Nématologie Le Rheu France
| | - Elise Buisson
- Inst. Méditerranéen de Biodiversité et d'Ecologie Marine et Continentale (IMBE), UMR: Aix Marseille Univ., Avignon Université, CNRS, IRD France
| | - Thomas Boivin
- INRAE, UR629 Écologie des Forêts Méditerranéennes, Centre de Recherche Provence‐Alpes‐Côte d'Azur Avignon France
| | | | - Romain Ulmer
- Univ. de Picardie Jules Verne, UMR 7058 CNRS EDYSAN Amiens Cedex 1 France
| | - Patricia Gibert
- UMR 5558 CNRS – Univ. Claude Bernard Lyon 1, Biométrie et Biologie Evolutive, Bât. Gregor Mendel Villeurbanne Cedex France
| | - Gabrielle Thiébaut
- Univ. of Rennes, CNRS, ECOBIO (Ecosystèmes, Biodiversité, Evolution), UMR 6553 Rennes France
| | - Jelena H. Pantel
- Ecological Modelling, Faculty of Biology, Univ. of Duisburg‐Essen Essen Germany
| | - Tina Heger
- Leibniz Inst. of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Technical Univ. of Munich, Restoration Ecology Freising Germany
| | - David M. Richardson
- Centre for Invasion Biology, Dept. Botany & Zoology, Stellenbosch University Stellenbosch South Africa
- Inst. of Botany, Czech Academy of Sciences Průhonice Czech Republic
| | - David Renault
- Univ. of Rennes, CNRS, ECOBIO (Ecosystèmes, Biodiversité, Evolution), UMR 6553 Rennes France
- Inst. Universitaire de France Paris Cedex 05 France
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7
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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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8
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Santos MA, Carromeu-Santos A, Quina AS, Santos M, Matos M, Simões P. No evidence for short-term evolutionary response to a warming environment in Drosophila. Evolution 2021; 75:2816-2829. [PMID: 34617283 DOI: 10.1111/evo.14366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 07/28/2021] [Accepted: 09/10/2021] [Indexed: 11/29/2022]
Abstract
Adaptive evolution is key in mediating responses to global warming and may sometimes be the only solution for species to survive. Such evolution will expectedly lead to changes in the populations' thermal reaction norm and improve their ability to cope with stressful conditions. Conversely, evolutionary constraints might limit the adaptive response. Here, we test these expectations by performing a real-time evolution experiment in historically differentiated Drosophila subobscura populations. We address the phenotypic change after nine generations of evolution in a daily fluctuating environment with average constant temperature, or in a warming environment with increasing average and amplitude temperature across generations. Our results showed that (1) evolution under a global warming scenario does not lead to a noticeable change in the thermal response; (2) historical background appears to be affecting responses under the warming environment, particularly at higher temperatures; and (3) thermal reaction norms are trait dependent: although lifelong exposure to low temperature decreases fecundity and productivity but not viability, high temperature causes negative transgenerational effects on productivity and viability, even with high fecundity. These findings in such an emblematic organism for thermal adaptation studies raise concerns about the short-term efficiency of adaptive responses to the current rising temperatures.
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Affiliation(s)
- Marta A Santos
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal, 1749-016.,Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal, 1749-016
| | - Ana Carromeu-Santos
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal, 1749-016.,CESAM, Centre for Environmental and Marine Studies, Universidade de Aveiro, Aveiro, Portugal, 3810-193
| | - Ana S Quina
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal, 1749-016.,CESAM, Centre for Environmental and Marine Studies, Universidade de Aveiro, Aveiro, Portugal, 3810-193
| | - Mauro Santos
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal, 1749-016.,Departament de Genètica i de Microbiologia, Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GBBE), Universitat Autònoma de Barcelona, Bellaterra, Spain, 08193
| | - Margarida Matos
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal, 1749-016.,Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal, 1749-016
| | - Pedro Simões
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal, 1749-016.,Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal, 1749-016
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9
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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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10
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Santos MA, Carromeu-Santos A, Quina AS, Santos M, Matos M, Simões P. High developmental temperature leads to low reproduction despite adult temperature. J Therm Biol 2020; 95:102794. [PMID: 33454035 DOI: 10.1016/j.jtherbio.2020.102794] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/25/2020] [Accepted: 11/23/2020] [Indexed: 10/22/2022]
Abstract
Phenotypic plasticity can help organisms cope with changing thermal conditions and it may depend on which life-stage the thermal stress is imposed: for instance, exposure to stressful temperatures during development can trigger a positive plastic response in adults. Here, we analyze the thermal plastic response of laboratory populations of Drosophila subobscura, derived from two contrasting latitudes of the European cline. We measured reproductive performance through fecundity characters, after the experimental populations were exposed to five thermal treatments, with different combinations of developmental and adult temperatures (14 °C, 18 °C, or 26 °C). Our questions were whether (1) adult performance changes with exposure to higher (or lower) temperatures during development; (2) flies raised at lower temperatures outperform those developed at higher ones, supporting the "colder is better" hypothesis; (3) there is a cumulative effect on adult performance of exposing both juveniles and adults to higher (or lower) temperatures; (4) there is evidence for biogeographical effects on adult performance. Our main findings were that (1) higher developmental temperatures led to low reproductive performance regardless of adult temperature, while at lower temperatures reduced performance only occurred when colder conditions were persistent across juvenile and adult stages; (2) flies raised at lower temperatures did not always outperform those developed at other temperatures; (3) there were no harmful cumulative effects after exposing both juveniles and adults to higher temperatures; (4) both latitudinal populations showed similar thermal plasticity patterns. The negative effect of high developmental temperature on reproductive performance, regardless of adult temperature, highlights the developmental stage as very critical and most vulnerable to climate change and associated heat waves.
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Affiliation(s)
- Marta A Santos
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Ana Carromeu-Santos
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Ana S Quina
- CESAM, Centre for Environmental and Marine Studies, Universidade de Aveiro and Faculdade de Ciências, Universidade de Lisboa, Portugal
| | - Mauro Santos
- Departament de Genètica i de Microbiologia, Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Universitat Autonòma de Barcelona, Spain
| | - Margarida Matos
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Pedro Simões
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal.
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11
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Esteve C, Lagares C, Mestres F. First detection of chromosomal inversions in a natural population of the invasive pest species Drosophila suzukii. J Genet 2020. [DOI: 10.1007/s12041-020-01238-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Nowling RJ, Manke KR, Emrich SJ. Detecting inversions with PCA in the presence of population structure. PLoS One 2020; 15:e0240429. [PMID: 33119626 PMCID: PMC7595445 DOI: 10.1371/journal.pone.0240429] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 09/28/2020] [Indexed: 12/26/2022] Open
Abstract
Chromosomal inversions can lead to reproductive isolation and adaptation in insects such as Drosophila melanogaster and the non-model malaria vector Anopheles gambiae. Inversions can be detected and characterized using principal component analysis (PCA) of single nucleotide polymorphisms (SNPs). To aid in developing such methods, we formed a new benchmark derived from three publicly-available insect data. We then used this benchmark to perform an extended validation of our software for inversion analysis (Asaph). Through that process, we identified and characterized several problematic test cases liable to misinterpretation that can help guide PCA-based inversion detection. Lastly, we re-analyzed the 2R chromosome arm of 150 An. gambiae and coluzzii samples and observed two inversions (2Rc and 2Rd) that were previously known but not annotated in these particular individuals. The resulting benchmark data set and methods will be useful for future inversion detection based solely on SNP data.
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Affiliation(s)
- Ronald J. Nowling
- Electrical Engineering and Computer Science, Milwaukee School of Engineering, Milwaukee, WI
| | - Krystal R. Manke
- Physics and Chemistry, Milwaukee School of Engineering, Milwaukee, WI
| | - Scott J. Emrich
- Electrical Engineering and Computer Science, University of Tennessee–Knoxville, Knoxville, TN
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13
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Karageorgiou C, Tarrío R, Rodríguez-Trelles F. The Cyclically Seasonal Drosophila subobscura Inversion O 7 Originated From Fragile Genomic Sites and Relocated Immunity and Metabolic Genes. Front Genet 2020; 11:565836. [PMID: 33193649 PMCID: PMC7584159 DOI: 10.3389/fgene.2020.565836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/09/2020] [Indexed: 11/28/2022] Open
Abstract
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.
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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, Barcelona, Spain
| | - Rosa Tarrío
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Barcelona, Spain
| | - Francisco Rodríguez-Trelles
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Barcelona, Spain
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14
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Sillero N, Huey RB, Gilchrist G, Rissler L, Pascual M. Distribution modelling of an introduced species: do adaptive genetic markers affect potential range? Proc Biol Sci 2020; 287:20201791. [PMID: 32933443 DOI: 10.1098/rspb.2020.1791] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Biological invasions have increased in the last few decades mostly due to anthropogenic causes such as globalization of trade. Because invaders sometimes cause large economic losses and ecological disturbances, estimating their origin and potential geographical ranges is useful. Drosophila subobscura is native to the Old World but was introduced in the New World in the late 1970s and spread widely. We incorporate information on adaptive genetic markers into ecological niche modelling and then estimate the most probable geographical source of colonizers; evaluate whether the genetic bottleneck experienced by founders affects their potential distribution; and finally test whether this species has spread to all its potential suitable habitats worldwide. We find the environmental space occupied by this species in its native and introduced distributions are notably the same, although the introduced niche has shifted slightly towards higher temperature and lower precipitation. The genetic bottleneck of founding individuals was a key factor limiting the spread of this introduced species. We also find that regions in the Mediterranean and north-central Portugal show the highest probability of being the origin of the colonizers. Using genetically informed environmental niche modelling can enhance our understanding of the initial colonization and spread of invasive species, and also elucidate potential areas of future expansions worldwide.
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Affiliation(s)
- Neftalí Sillero
- CICGE Centro de Investigação em Ciências Geo-Espaciais, Faculdade de Ciências da Universidade do Porto (FCUP), Observatório Astronómico Prof. Manuel de Barros, Alameda do Monte da Virgem, 4430-146 Vila Nova de Gaia, Portugal
| | - Raymond B Huey
- Department of Biology, University of Washington, Seattle, WA, USA
| | - George Gilchrist
- Division of Environmental Biology, National Science Foundation, Alexandria, VA, USA.,Department of Biology, The College of William and Mary, Williamsburg, VA, USA
| | - Leslie Rissler
- Division of Environmental Biology, National Science Foundation, Alexandria, VA, USA
| | - Marta Pascual
- Departament de Genètica, Microbiologia i Estadística and IRBio, Universitat de Barcelona, Diagonal 643, 08028 Barcelona, Spain
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15
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Wang J, Gaughan S, Lamer JT, Deng C, Hu W, Wachholtz M, Qin S, Nie H, Liao X, Ling Q, Li W, Zhu L, Bernatchez L, Wang C, Lu G. Resolving the genetic paradox of invasions: Preadapted genomes and postintroduction hybridization of bigheaded carps in the Mississippi River Basin. Evol Appl 2020; 13:263-277. [PMID: 31993075 PMCID: PMC6976960 DOI: 10.1111/eva.12863] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/07/2019] [Accepted: 07/15/2019] [Indexed: 12/23/2022] Open
Abstract
The genetic paradox of biological invasions is complex and multifaceted. In particular, the relative role of disparate propagule sources and genetic adaptation through postintroduction hybridization has remained largely unexplored. To add resolution to this paradox, we investigate the genetic architecture responsible for the invasion of two invasive Asian carp species, bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix) (bigheaded carps) that experience extensive hybridization in the Mississippi River Basin (MRB). We sequenced the genomes of bighead and silver carps (~1.08G bp and ~1.15G bp, respectively) and their hybrids collected from the MRB. We found moderate-to-high heterozygosity in bighead (0.0021) and silver (0.0036) carps, detected significantly higher dN/dS ratios of single-copy orthologous genes in bigheaded carps versus 10 other species of fish, and identified genes in both species potentially associated with environmental adaptation and other invasion-related traits. Additionally, we observed a high genomic similarity (96.3% in all syntenic blocks) between bighead and silver carps and over 90% embryonic viability in their experimentally induced hybrids. Our results suggest intrinsic genomic features of bigheaded carps, likely associated with life history traits that presumably evolved within their native ranges, might have facilitated their initial establishment of invasion, whereas ex-situ interspecific hybridization between the carps might have promoted their range expansion. This study reveals an alternative mechanism that could resolve one of the genetic paradoxes in biological invasions and provides invaluable genomic resources for applied research involving bigheaded carps.
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Affiliation(s)
- Jun Wang
- Department of BiologyUniversity of Nebraska at OmahaOmahaUSA
- Key Laboratory of Freshwater Fisheries Germplasm ResourcesMinistry of AgricultureNational Demonstration Center for Experimental Fisheries ScienceEducation/Shanghai Engineering Research Center of AquacultureShanghai Ocean UniversityShanghaiChina
| | - Sarah Gaughan
- Department of BiologyUniversity of Nebraska at OmahaOmahaUSA
| | - James T. Lamer
- Department of Biological SciencesWestern Illinois UniversityMacombILUSA
| | - Cao Deng
- DNA Stories Bioinformatics CenterChengduChina
| | - Wanting Hu
- College of Life of SciencesNanjing Normal UniversityNanjingChina
| | | | | | - Hu Nie
- DNA Stories Bioinformatics CenterChengduChina
| | - Xiaolin Liao
- Institute of HydroecologyMinistry of Water Resources & Chinese Academy of SciencesWuhanChina
| | - Qufei Ling
- Department of BiologyUniversity of Nebraska at OmahaOmahaUSA
- Aquaculture InstituteSchool of Biology and Basic Medical SciencesSoochow UniversitySuzhouChina
| | - Weitao Li
- Institute of HydroecologyMinistry of Water Resources & Chinese Academy of SciencesWuhanChina
| | - Lifeng Zhu
- College of Life of SciencesNanjing Normal UniversityNanjingChina
| | - Louis Bernatchez
- IBIS (Institut de Biologie Intégrative et des Systèmes)Université LavalQuébecQCCanada
| | - Chenghui Wang
- Key Laboratory of Freshwater Fisheries Germplasm ResourcesMinistry of AgricultureNational Demonstration Center for Experimental Fisheries ScienceEducation/Shanghai Engineering Research Center of AquacultureShanghai Ocean UniversityShanghaiChina
| | - Guoqing Lu
- Department of BiologyUniversity of Nebraska at OmahaOmahaUSA
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16
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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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17
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Castañeda LE, Romero‐Soriano V, Mesas A, Roff DA, Santos M. Evolutionary potential of thermal preference and heat tolerance in
Drosophila subobscura. J Evol Biol 2019; 32:818-824. [DOI: 10.1111/jeb.13483] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/16/2019] [Accepted: 04/22/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Luis E. Castañeda
- Programa de Genética Humana Facultad de Medicina Instituto de Ciencias Biomédicas Universidad de Chile Santiago Chile
| | | | - Andrés Mesas
- Facultad de Ciencias Instituto de Ciencias Ambientales y Evolutivas Universidad Austral de Chile Valdivia Valdivia Chile
| | - Derek A. Roff
- Department of Evolution, Ecology and Organismal Biology University of California Riverside California
| | - Mauro Santos
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE) Departament de Genètica i de Microbiologia Universitat Autònoma de Barcelona Barcelona Spain
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18
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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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19
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Moghadam NN, Kurbalija Novicic Z, Pertoldi C, Kristensen TN, Bahrndorff S. Effects of photoperiod on life-history and thermal stress resistance traits across populations of Drosophila subobscura. Ecol Evol 2019; 9:2743-2754. [PMID: 30891213 PMCID: PMC6405525 DOI: 10.1002/ece3.4945] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/29/2018] [Accepted: 01/08/2019] [Indexed: 11/05/2022] Open
Abstract
INTRODUCTION Organisms use environmental cues to match their phenotype with the future availability of resources and environmental conditions. Changes in the magnitude and frequency of environmental cues such as photoperiod and temperature along latitudes can be used by organisms to predict seasonal changes. While the role of temperature variation on the induction of plastic and seasonal responses is well established, the importance of photoperiod for predicting seasonal changes is less explored. MATERIALS AND METHODS Here we studied changes in life-history and thermal stress resistance traits in Drosophila subobscura in response to variation in photoperiod (6:18, 12:12 and 18:6 light:dark cycles) mimicking seasonal variations in day length. The populations of D. subobscura were collected from five locations along a latitudinal gradient (from North Africa and Europe). These populations were exposed to different photoperiods for two generations, whereafter egg-to-adult viability, productivity, dry body weight, thermal tolerance, and starvation resistance were assessed. RESULTS We found strong effects of photoperiod, origin of populations, and their interactions on life-history and stress resistance traits. Thermal resistance varied between the populations and the effect of photoperiod depended on the trait and the method applied for the assessment of thermal resistance. PERSPECTIVES Our results show a strong effect of the origin of population and photoperiod on a range of fitness-related traits and provide evidence for local adaptation to environmental cues (photoperiod by population interaction). The findings emphasize an important and often neglected role of photoperiod in studies on thermal resistance and suggest that cues induced by photoperiod may provide some buffer enabling populations to cope with a more variable and unpredictable future climate.
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Affiliation(s)
- Neda N. Moghadam
- Department of Chemistry and BioscienceAalborg UniversityAalborg EDenmark
- Department of Biological and Environmental Science, Centre of Excellence in Biological InteractionsUniversity of JyvaskylaJyväskyläFinland
| | - Zorana Kurbalija Novicic
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology CenterUppsala UniversityUppsalaSweden
| | - Cino Pertoldi
- Department of Chemistry and BioscienceAalborg UniversityAalborg EDenmark
- Aalborg ZooAalborgDenmark
| | - Torsten N. Kristensen
- Department of Chemistry and BioscienceAalborg UniversityAalborg EDenmark
- Department of BioscienceAarhus UniversityAarhus CDenmark
| | - Simon Bahrndorff
- Department of Chemistry and BioscienceAalborg UniversityAalborg EDenmark
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20
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The molecular characterization of fixed inversions breakpoints unveils the ancestral character of the Drosophila guanche chromosomal arrangements. Sci Rep 2019; 9:1706. [PMID: 30737415 PMCID: PMC6368638 DOI: 10.1038/s41598-018-37121-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 12/04/2018] [Indexed: 12/20/2022] Open
Abstract
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.
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21
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Christmas MJ, Wallberg A, Bunikis I, Olsson A, Wallerman O, Webster MT. Chromosomal inversions associated with environmental adaptation in honeybees. Mol Ecol 2018; 28:1358-1374. [DOI: 10.1111/mec.14944] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 11/07/2018] [Accepted: 11/07/2018] [Indexed: 01/03/2023]
Affiliation(s)
- Matthew J. Christmas
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory Uppsala University Uppsala Sweden
| | - Andreas Wallberg
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory Uppsala University Uppsala Sweden
| | - Ignas Bunikis
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala University Uppsala Sweden
| | - Anna Olsson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory Uppsala University Uppsala Sweden
| | - Ola Wallerman
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory Uppsala University Uppsala Sweden
| | - Matthew T. Webster
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory Uppsala University Uppsala Sweden
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22
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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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23
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Yadav JP, Singh P. Effect of metabolites on stress, adaptation and longevity in laboratory populations of
Drosophila
flies. J Zool (1987) 2018. [DOI: 10.1111/jzo.12535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- J. P. Yadav
- Department of Zoology Bundelkhand University Jhansi India
| | - P. Singh
- Department of Zoology Bundelkhand University Jhansi India
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24
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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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Puerma E, Orengo DJ, Aguadé M. Inversion evolutionary rates might limit the experimental identification of inversion breakpoints in non-model species. Sci Rep 2017; 7:17281. [PMID: 29222501 PMCID: PMC5722822 DOI: 10.1038/s41598-017-17650-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 11/29/2017] [Indexed: 11/09/2022] Open
Abstract
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.
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Affiliation(s)
- Eva Puerma
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Dorcas J Orengo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Montserrat Aguadé
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.
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An easy route to the massive karyotyping of complex chromosomal arrangements in Drosophila. Sci Rep 2017; 7:12717. [PMID: 28983092 PMCID: PMC5629216 DOI: 10.1038/s41598-017-13043-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 09/12/2017] [Indexed: 01/09/2023] Open
Abstract
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.
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Seabra SG, Fragata I, Antunes MA, Faria GS, Santos MA, Sousa VC, Simões P, Matos M. Different Genomic Changes Underlie Adaptive Evolution in Populations of Contrasting History. Mol Biol Evol 2017; 35:549-563. [PMID: 29029198 DOI: 10.1093/molbev/msx247] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Experimental evolution is a powerful tool to understand the adaptive potential of populations under environmental change. Here, we study the importance of the historical genetic background in the outcome of evolution at the genome-wide level. Using the natural clinal variation of Drosophila subobscura, we sampled populations from two contrasting latitudes (Adraga, Portugal and Groningen, Netherlands) and introduced them in a new common environment in the laboratory. We characterized the genome-wide temporal changes underlying the evolutionary dynamics of these populations, which had previously shown fast convergence at the phenotypic level, but not at chromosomal inversion frequencies. We found that initially differentiated populations did not converge either at genome-wide level or at candidate SNPs with signs of selection. In contrast, populations from Portugal showed convergence to the control population that derived from the same geographical origin and had been long-established in the laboratory. Candidate SNPs showed a variety of different allele frequency change patterns across generations, indicative of an underlying polygenic basis. We did not detect strong linkage around candidate SNPs, but rather a small but long-ranging effect. In conclusion, we found that history played a major role in genomic variation and evolution, with initially differentiated populations reaching the same adaptive outcome through different genetic routes.
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Affiliation(s)
- Sofia G Seabra
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Inês Fragata
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal.,Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Marta A Antunes
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Gonçalo S Faria
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal.,School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Marta A Santos
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal.,CEDOC - Centro de Estudos de Doenças Crónicas, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Vitor C Sousa
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Pedro Simões
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Margarida Matos
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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Romero ML, Colombo PC, Remis MI. Microsatellite DNA analysis of population structure in Cornops aquaticum (Orthoptera: Acrididae), over a cline for three Robertsonian translocations. Evol Ecol 2017. [DOI: 10.1007/s10682-017-9915-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Graves JL, Hertweck KL, Phillips MA, Han MV, Cabral LG, Barter TT, Greer LF, Burke MK, Mueller LD, Rose MR. Genomics of Parallel Experimental Evolution in Drosophila. Mol Biol Evol 2017; 34:831-842. [PMID: 28087779 PMCID: PMC5400383 DOI: 10.1093/molbev/msw282] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
What are the genomic foundations of adaptation in sexual populations? We address this question using fitness–character and whole-genome sequence data from 30 Drosophila laboratory populations. These 30 populations are part of a nearly 40-year laboratory radiation featuring 3 selection regimes, each shared by 10 populations for up to 837 generations, with moderately large effective population sizes. Each of 3 sets of the 10 populations that shared a selection regime consists of 5 populations that have long been maintained under that selection regime, paired with 5 populations that had only recently been subjected to that selection regime. We find a high degree of evolutionary parallelism in fitness phenotypes when most-recent selection regimes are shared, as in previous studies from our laboratory. We also find genomic parallelism with respect to the frequencies of single-nucleotide polymorphisms, transposable elements, insertions, and structural variants, which was expected. Entirely unexpected was a high degree of parallelism for linkage disequilibrium. The evolutionary genetic changes among these sexual populations are rapid and genomically extensive. This pattern may be due to segregating functional genetic variation that is abundantly maintained genome-wide by selection, variation that responds immediately to changes of selection regime.
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Affiliation(s)
- J L Graves
- Joint School of Nanoscience and Nanoengineering, North Carolina A&T State University and UNC Greensboro, Greensboro, NC
| | - K L Hertweck
- Department of Biology, The University of Texas at Tyler, Tyler, TX
| | - M A Phillips
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
| | - M V Han
- School of Life Sciences, University of Nevada, Las Vegas, NV
| | - L G Cabral
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
| | - T T Barter
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
| | - L F Greer
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
| | - M K Burke
- Department of Integrative Biology, Oregon State University, Corvallis, OR
| | - L D Mueller
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
| | - M R Rose
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
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Pascual M, Serra L, Ayala FJ. INTERSPECIFIC LABORATORY COMPETITION OF THE RECENTLY SYMPATRIC SPECIES DROSOPHILA SUBOBSCURA AND DROSOPHILA PSEUDOOBSCURA. Evolution 2017; 52:269-274. [PMID: 28568145 DOI: 10.1111/j.1558-5646.1998.tb05162.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/1997] [Accepted: 09/12/1997] [Indexed: 11/29/2022]
Abstract
-Drosophila subobscura and D. pseudoobscura are closely related species coexisting on the West Coast of North America, which was recently colonized by D. subobscura. In competition experiments with overlapping generations, D. subobscura is eliminated by D. pseudoobscura in a few generations at all four temperatures and two initial frequencies tested. Yet in one-species cultures, D. subobscura thrives at all experimental conditions. Single-generation competition experiments reveal lower survivorship and productivity of D. subobscura at all temperatures and frequencies. Productivity per female is dependent on the initial frequencies: greater for D. subobscura as its initial frequency becomes higher, but lower for D. pseudoobscura as its frequency becomes higher. Strains of D. subobscura from three disparate geographic origins yield similar results.
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Affiliation(s)
- Marta Pascual
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, 92717
| | - Luis Serra
- Departament de Genètica, Universitat de Barcelona, 08071, Barcelona, Spain
| | - Francisco J Ayala
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, 92717
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Prevosti A, Serra L, Segarra C, Aguade M, Ribo G, Monclus M. CLINES OF CHROMOSOMAL ARRANGEMENTS OF DROSOPHILA SUBOBSCURA
IN SOUTH AMERICA EVOLVE CLOSER TO OLD WORLD PATTERNS. Evolution 2017; 44:218-221. [DOI: 10.1111/j.1558-5646.1990.tb04294.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/1989] [Accepted: 10/16/1989] [Indexed: 11/26/2022]
Affiliation(s)
- Antonio Prevosti
- Department of Genetics, Faculty of Biology; University of Barcelona; 08028 Barcelona SPAIN
| | - Luis Serra
- Department of Genetics, Faculty of Biology; University of Barcelona; 08028 Barcelona SPAIN
| | - Carmen Segarra
- Department of Genetics, Faculty of Biology; University of Barcelona; 08028 Barcelona SPAIN
| | - Montserrat Aguade
- Department of Genetics, Faculty of Biology; University of Barcelona; 08028 Barcelona SPAIN
| | - Griselda Ribo
- Department of Genetics, Faculty of Biology; University of Barcelona; 08028 Barcelona SPAIN
| | - Maria Monclus
- Department of Genetics, Faculty of Biology; University of Barcelona; 08028 Barcelona SPAIN
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Mestres F, Pegueroles G, Prevosti A, Serra L. COLONIZATION OF AMERICA BY DROSOPHILA SUBOBSCURA: LETHAL GENES AND THE PROBLEM OF THE O 5 INVERSION. Evolution 2017; 44:1823-1836. [PMID: 28567803 DOI: 10.1111/j.1558-5646.1990.tb05253.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/1989] [Accepted: 01/29/1990] [Indexed: 11/29/2022]
Abstract
In this work, the process of colonization of North and South America by the species Drosophila subobscura has been studied by analyzing the variability of lethal genes. The genetic structures of a Palearctic natural central population (Bordils, Spain) and a colonizer population from America (Gilroy, California) have been compared. The frequencies of lethal chromosomes and their allelism are 29.007% and 0.0069 in the first population and 14.414% and 0.0526 in the American population. A founder effect is detected after the computation of some population parameters (Ne , h, he and the lethal load). Furthermore, the allelism of lethal chromosomes has revealed a strong association between a lethal gene and the O5 inversion both in Gilroy and in the population of Puerto Montt (Chile). The interpopulation allelism shows that the O5 arrangement from the USA and Chile is the same, confirming that the colonizing processes of North and South America are correlated. The O5 arrangement can also be useful as a genetic marker to trace the origin of the colonization. The frequency of the O5 arrangement in the original population of the colonization could be used to estimate the number of colonizers. This population is still unknown, but taking the extreme values of the frequency of the O5 inversion in natural Palearctic populations (1-15%), the number of colonizers could vary between 9 and 149 individuals.
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Affiliation(s)
- F Mestres
- Department of Genetics, Faculty of Biology, University of Barcelona, 08071, Barcelona, SPAIN
| | - G Pegueroles
- Department of Genetics, Faculty of Biology, University of Barcelona, 08071, Barcelona, SPAIN
| | - A Prevosti
- Department of Genetics, Faculty of Biology, University of Barcelona, 08071, Barcelona, SPAIN
| | - L Serra
- Department of Genetics, Faculty of Biology, University of Barcelona, 08071, Barcelona, SPAIN
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Orengo DJ, Prevosti A. TEMPORAL CHANGES IN CHROMOSOMAL POLYMORPHISM OF DROSOPHILA SUBOBSCURA RELATED TO CLIMATIC CHANGES. Evolution 2017; 50:1346-1350. [PMID: 28565278 DOI: 10.1111/j.1558-5646.1996.tb02376.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/1994] [Accepted: 06/20/1995] [Indexed: 11/28/2022]
Affiliation(s)
- Dorcas-J Orengo
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Avda. Diagonal, 645, 08071, Barcelona, Spain
| | - Antonio Prevosti
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Avda. Diagonal, 645, 08071, Barcelona, Spain
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Mestres F, Balañá J, Segarra C, Prevosti A, Serra L. COLONIZATION OF AMERICA BY DROSOPHILA SUBOBSCURA: ANALYSIS OF THE O 5 INVERSIONS FROM EUROPE AND AMERICA AND THEIR IMPLICATIONS FOR THE COLONIZING PROCESS. Evolution 2017; 46:1564-1568. [PMID: 28568991 DOI: 10.1111/j.1558-5646.1992.tb01147.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/1991] [Accepted: 01/24/1992] [Indexed: 11/28/2022]
Affiliation(s)
- F Mestres
- Department of Genetics, Faculty of Biology, University of Barcelona, 08071, Barcelona, SPAIN
| | - J Balañá
- Department of Genetics, Faculty of Biology, University of Barcelona, 08071, Barcelona, SPAIN
| | - C Segarra
- Department of Genetics, Faculty of Biology, University of Barcelona, 08071, Barcelona, SPAIN
| | - A Prevosti
- Department of Genetics, Faculty of Biology, University of Barcelona, 08071, Barcelona, SPAIN
| | - L Serra
- Department of Genetics, Faculty of Biology, University of Barcelona, 08071, Barcelona, SPAIN
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Orengo DJ, Puerma E, Papaceit M, Segarra C, Aguadé M. Dense gene physical maps of the non-model species Drosophila subobscura. Chromosome Res 2017; 25:145-154. [PMID: 28078516 DOI: 10.1007/s10577-016-9549-1] [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] [Received: 11/10/2016] [Revised: 12/20/2016] [Accepted: 12/22/2016] [Indexed: 11/29/2022]
Abstract
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.
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Affiliation(s)
- Dorcas J Orengo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Eva Puerma
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Montserrat Papaceit
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Carmen Segarra
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Montserrat Aguadé
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.
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Multiple and diverse structural changes affect the breakpoint regions of polymorphic inversions across the Drosophila genus. Sci Rep 2016; 6:36248. [PMID: 27782210 PMCID: PMC5080602 DOI: 10.1038/srep36248] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/12/2016] [Indexed: 12/20/2022] Open
Abstract
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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Puerma E, Orengo DJ, Aguadé M. The origin of chromosomal inversions as a source of segmental duplications in the Sophophora subgenus of Drosophila. Sci Rep 2016; 6:30715. [PMID: 27470196 PMCID: PMC4965816 DOI: 10.1038/srep30715] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 07/05/2016] [Indexed: 01/06/2023] Open
Abstract
Chromosomal inversions can contribute to the adaptation of organisms to their environment by capturing particular advantageous allelic combinations of a set of genes included in the inverted fragment and also by advantageous functional changes due to the inversion process itself that might affect not only the expression of flanking genes but also their dose and structure. Of the two mechanisms originating inversions —ectopic recombination, and staggered double-strand breaks and subsequent repair— only the latter confers the inversion the potential to have dosage effects and/or to generate advantageous chimeric genes. In Drosophila subobscura, there is ample evidence for the adaptive character of its chromosomal polymorphism, with an important contribution of some warm-climate arrangements such as E1+2+9+12. Here, we have characterized the breakpoints of inversion E12 and established that it originated through the staggered-break mechanism like four of the five inversions of D. subobscura previously studied. This mechanism that also predominates in the D. melanogaster lineage might be prevalent in the Sophophora subgenus and contribute to the adaptive character of the polymorphic and fixed inversions of its species. Finally, we have shown that the D. subobscura inversion breakpoint regions have generally been disrupted by additional structural changes occurred at different time scales.
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Affiliation(s)
- Eva Puerma
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Dorcas J Orengo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Montserrat Aguadé
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
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Kirkpatrick M. The Evolution of Genome Structure by Natural and Sexual Selection. J Hered 2016; 108:3-11. [PMID: 27388336 DOI: 10.1093/jhered/esw041] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 06/28/2016] [Indexed: 11/13/2022] Open
Abstract
Progress on understanding how genome structure evolves is accelerating with the arrival of new genomic, comparative, and theoretical approaches. This article reviews progress in understanding how chromosome inversions and sex chromosomes evolve, and how their evolution affects species' ecology. Analyses of clines in inversion frequencies in flies and mosquitoes imply strong local adaptation, and roles for both over- and under dominant selection. Those results are consistent with the hypothesis that inversions become established when they capture locally adapted alleles. Inversions can carry alleles that are beneficial to closely related species, causing them to introgress following hybridization. Models show that this "adaptive cassette" scenario can trigger large range expansions, as recently happened in malaria mosquitoes. Sex chromosomes are the most rapidly evolving genome regions of some taxa. Sexually antagonistic selection may be the key force driving transitions of sex determination between different pairs of chromosomes and between XY and ZW systems. Fusions between sex-chromosomes and autosomes most often involve the Y chromosome, a pattern that can be explained if fusions are mildly deleterious and fix by drift. Sexually antagonistic selection is one of several hypotheses to explain the recent discovery that the sex determination system has strong effects on the adult sex ratios of tetrapods. The emerging view of how genome structure evolves invokes a much richer constellation of forces than was envisioned during the Golden Age of research on Drosophila karyotypes.
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Affiliation(s)
- Mark Kirkpatrick
- From the Department of Integrative Biology C-0990, University of Texas, Austin, TX 78712 USA (Kirkpatrick).
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40
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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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41
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Pegueroles C, Ferrés-Coy A, Martí-Solano M, Aquadro CF, Pascual M, Mestres F. Inversions and adaptation to the plant toxin ouabain shape DNA sequence variation within and between chromosomal inversions of Drosophila subobscura. Sci Rep 2016; 6:23754. [PMID: 27029337 PMCID: PMC4815013 DOI: 10.1038/srep23754] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 03/14/2016] [Indexed: 12/14/2022] Open
Abstract
Adaptation is defined as an evolutionary process allowing organisms to succeed in certain habitats or conditions. Chromosomal inversions have the potential to be key in the adaptation processes, since they can contribute to the maintenance of favoured combinations of adaptive alleles through reduced recombination between individuals carrying different inversions. We have analysed six genes (Pif1A, Abi, Sqd, Yrt, Atpα and Fmr1), located inside and outside three inversions of the O chromosome in European populations of Drosophila subobscura. Genetic differentiation was significant between inversions despite extensive recombination inside inverted regions, irrespective of gene distance to the inversion breakpoints. Surprisingly, the highest level of genetic differentiation between arrangements was found for the Atpα gene, which is located outside the O1 and O7 inversions. Two derived unrelated arrangements (O3+4+1 and O3+4+7) are nearly fixed for several amino acid substitutions at the Atpα gene that have been described to confer resistance in other species to the cardenolide ouabain, a plant toxin capable of blocking ATPases. Similarities in the Atpα variants, conferring ouabain resistance in both arrangements, may be the result of convergent substitution and be favoured in response to selective pressures presumably related to the presence of plants containing ouabain in the geographic locations where both inversions are present.
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Affiliation(s)
- Cinta Pegueroles
- Departament de Genètica and IRBio, Facultat de Biologia, Universitat de Barcelona, Barcelona 08028, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Albert Ferrés-Coy
- Department of Neurochemistry and Neuropharmacology, IIBB-CSIC, Barcelona, Spain
| | - Maria Martí-Solano
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute), Dr. Aiguader, 88, 08003 Barcelona, Spain
| | - Charles F Aquadro
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Marta Pascual
- Departament de Genètica and IRBio, Facultat de Biologia, Universitat de Barcelona, Barcelona 08028, Spain
| | - Francesc Mestres
- Departament de Genètica and IRBio, Facultat de Biologia, Universitat de Barcelona, Barcelona 08028, Spain
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Foucaud J, Moreno C, Pascual M, Rezende EL, Castañeda LE, Gibert P, Mery F. Introduced Drosophila subobscura populations perform better than native populations during an oviposition choice task due to increased fecundity but similar learning ability. Ecol Evol 2016; 6:1725-36. [PMID: 26925216 PMCID: PMC4755011 DOI: 10.1002/ece3.2015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 01/25/2016] [Accepted: 01/27/2016] [Indexed: 12/13/2022] Open
Abstract
The success of invasive species is tightly linked to their fitness in a putatively novel environment. While quantitative components of fitness have been studied extensively in the context of invasive species, fewer studies have looked at qualitative components of fitness, such as behavioral plasticity, and their interaction with quantitative components, despite intuitive benefits over the course of an invasion. In particular, learning is a form of behavioral plasticity that makes it possible to finely tune behavior according to environmental conditions. Learning can be crucial for survival and reproduction of introduced organisms in novel areas, for example, for detecting new predators, or finding mates or oviposition sites. Here we explored how oviposition performance evolved in relation to both fecundity and learning during an invasion, using native and introduced Drosophila subobscura populations performing an ecologically relevant task. Our results indicated that, under comparable conditions, invasive populations performed better during our oviposition task than did native populations. This was because invasive populations had higher fecundity, together with similar cognitive performance when compared to native populations, and that there was no interaction between learning and fecundity. Unexpectedly, our study did not reveal an allocation trade‐off (i.e., a negative relationship) between learning and fecundity. On the contrary, the pattern we observed was more consistent with an acquisition trade‐off, meaning that fecundity could be limited by availability of resources, unlike cognitive ability. This pattern might be the consequence of escaping natural enemies and/or competitors during the introduction. The apparent lack of evolution of learning may indicate that the introduced population did not face novel cognitive challenges in the new environment (i.e., cognitive “pre‐adaptation”). Alternatively, the evolution of learning may have been transient and therefore not detected.
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Affiliation(s)
- Julien Foucaud
- Laboratoire Evolution, Génomes, Comportement et Ecologie UMR-CNRS 9191 Gif/Yvette France
| | - Céline Moreno
- Laboratoire Evolution, Génomes, Comportement et Ecologie UMR-CNRS 9191 Gif/Yvette France
| | - Marta Pascual
- Department of Genetics and IrBio Universitat de Barcelona Av. Diagonal 643 08028 Barcelona Spain
| | - Enrico L Rezende
- Department of Life Sciences University of Roehampton Holybourne Avenue London SW15 4JD UK
| | - Luis E Castañeda
- Instituto de Ciencias Ambientales y Evolutivas Universidad Austral de Chile PO 5090000 Valdivia Chile
| | - Patricia Gibert
- Université de Lyon Université Lyon1 Laboratoire de Biométrie et Biologie Evolutive UMR CNRS 5558 43 Bd du 11 Novembre 1918 69622 Villeurbanne Cedex France
| | - Frederic Mery
- Laboratoire Evolution, Génomes, Comportement et Ecologie UMR-CNRS 9191 Gif/Yvette France
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43
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Gibert P, Hill M, Pascual M, Plantamp C, Terblanche JS, Yassin A, Sgrò CM. Drosophila as models to understand the adaptive process during invasion. Biol Invasions 2016. [DOI: 10.1007/s10530-016-1087-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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44
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Zivanovic G, Arenas C, Mestres F. Individual inversions or their combinations: which is the main selective target in a natural population of Drosophila subobscura? J Evol Biol 2015; 29:657-64. [PMID: 26644367 DOI: 10.1111/jeb.12800] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 11/20/2015] [Indexed: 12/30/2022]
Abstract
It is generally accepted that chromosomal inversions have been key elements in adaptation and speciation processes. In this context, Drosophila subobscura has been, and still is, an excellent model species due to its rich chromosomal polymorphism. In this species, many analyses from natural populations have demonstrated the adaptive potential of individual inversions (and their overlapped combinations, the so-called arrangements). However, little information is available on the evolutionary role of combinations generated by inversions located in homologous and nonhomologous chromosomes. The aim of this research was to ascertain whether these combinations are also a target for natural selection. For this objective, we have studied the inversion composition of homologous and nonhomologous chromosomes from a D. subobscura sample collected in a well-studied population, Mount Avala (Serbia). No significant deviation from H-W expectations was detected, and when comparing particular karyotypic combinations, likelihood ratios close to 1 were obtained. Thus, it seems that for each pair of homologous chromosomes inversions no deviation from randomness was detected. Finally, no linkage disequilibrium was observed between inversions located in different chromosomes of the karyotype. For all these reasons, it can be assumed that, at the cytological level, the individual inversions rather than their combinations in different chromosomes are the main target of selection.
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Affiliation(s)
- G Zivanovic
- Department of Genetics, Institute for Biological Research "Sinisa Stankovic", University of Belgrade, Belgrade, Serbia
| | - C Arenas
- Departament d'Estadística, Universitat de Barcelona, Barcelona, Spain
| | - F Mestres
- Departament de Genètica, Universitat de Barcelona, Barcelona, Spain.,IRBio (Institut de Recerca per la Biodiversitat), Universitat de Barcelona, Barcelona, Spain
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45
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Simões P, Fragata I, Lopes-Cunha M, Lima M, Kellen B, Bárbaro M, Santos M, Matos M. Wing trait-inversion associations in Drosophila subobscura can be generalized within continents, but may change through time. J Evol Biol 2015; 28:2163-74. [PMID: 26302686 DOI: 10.1111/jeb.12739] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 07/28/2015] [Accepted: 08/18/2015] [Indexed: 01/14/2023]
Abstract
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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Affiliation(s)
- P Simões
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - I Fragata
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - M Lopes-Cunha
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - M Lima
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - B Kellen
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - M Bárbaro
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - M Santos
- Departament de Genètica i de Microbiologia, Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Universitat Autonòma de Barcelona, Bellaterra (Barcelona), Spain
| | - M Matos
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
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46
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Adrion JR, Hahn MW, Cooper BS. Revisiting classic clines in Drosophila melanogaster in the age of genomics. Trends Genet 2015; 31:434-44. [PMID: 26072452 PMCID: PMC4526433 DOI: 10.1016/j.tig.2015.05.006] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/11/2015] [Accepted: 05/12/2015] [Indexed: 12/16/2022]
Abstract
Adaptation to spatially varying environments has been studied for decades, but advances in sequencing technology are now enabling researchers to investigate the landscape of genetic variation underlying this adaptation genome wide. In this review we highlight some of the decades-long research on local adaptation in Drosophila melanogaster from well-studied clines in North America and Australia. We explore the evidence for parallel adaptation and identify commonalities in the genes responding to clinal selection across continents as well as discussing instances where patterns differ among clines. We also investigate recent studies utilizing whole-genome data to identify clines in D. melanogaster and several other systems. Although connecting segregating genomic variation to variation in phenotypes and fitness remains challenging, clinal genomics is poised to increase our understanding of local adaptation and the selective pressures that drive the extensive phenotypic diversity observed in nature.
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Affiliation(s)
- Jeffrey R Adrion
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN 47405, USA; School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Brandon S Cooper
- Center for Population Biology, University of California, Davis, CA 95616, USA; Department of Evolution and Ecology, University of California, Davis, CA 95616, USA.
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47
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Dlugosch KM, Anderson SR, Braasch J, Cang FA, Gillette HD. The devil is in the details: genetic variation in introduced populations and its contributions to invasion. Mol Ecol 2015; 24:2095-111. [PMID: 25846825 DOI: 10.1111/mec.13183] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 03/26/2015] [Accepted: 03/27/2015] [Indexed: 12/14/2022]
Abstract
The influence of genetic variation on invasion success has captivated researchers since the start of the field of invasion genetics 50 years ago. We review the history of work on this question and conclude that genetic variation-as surveyed with molecular markers-appears to shape invasion rarely. Instead, there is a significant disconnect between marker assays and ecologically relevant genetic variation in introductions. We argue that the potential for adaptation to facilitate invasion will be shaped by the details of genotypes affecting phenotypes, and we highlight three areas in which we see opportunities to make powerful new insights. (i) The genetic architecture of adaptive variation. Traits shaped by large-effect alleles may be strongly impacted by founder events yet more likely to respond to selection when genetic drift is strong. Large-effect loci may be especially relevant for traits involved in biotic interactions. (ii) Cryptic genetic variation exposed during invasion. Introductions have strong potential to uncover masked variation due to alterations in genetic and ecological environments. (iii) Genetic interactions during admixture of multiple source populations. As divergence among sources increases, positive followed by increasingly negative effects of admixture should be expected. Although generally hypothesized to be beneficial during invasion, admixture is most often reported among sources of intermediate divergence, supporting the possibility that incompatibilities among divergent source populations might be limiting their introgression. Finally, we note that these details of invasion genetics can be coupled with comparative demographic analyses to link genetic changes to the evolution of invasiveness itself.
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Affiliation(s)
- Katrina M Dlugosch
- Department of Ecology & Evolutionary Biology, University of Arizona, PO Box 210088, Tucson, AZ, 85721, USA
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48
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Pratdesaba R, Segarra C, Aguadé M. Inferring the demographic history of Drosophila subobscura from nucleotide variation at regions not affected by chromosomal inversions. Mol Ecol 2015; 24:1729-41. [PMID: 25776124 DOI: 10.1111/mec.13155] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 03/09/2015] [Accepted: 03/11/2015] [Indexed: 11/29/2022]
Abstract
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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Affiliation(s)
- Roser Pratdesaba
- Departament de Genètica, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Diagonal 643, 08028, Barcelona, Spain
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49
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Cristescu ME. Genetic reconstructions of invasion history. Mol Ecol 2015; 24:2212-25. [DOI: 10.1111/mec.13117] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Revised: 02/11/2015] [Accepted: 02/12/2015] [Indexed: 12/14/2022]
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50
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Lizé A, Price TAR, Heys C, Lewis Z, Hurst GDD. Extreme cost of rivalry in a monandrous species: male-male interactions result in failure to acquire mates and reduced longevity. Proc Biol Sci 2015; 281:rspb.2014.0631. [PMID: 24827446 DOI: 10.1098/rspb.2014.0631] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mating system variation is profound in animals. In insects, female willingness to remate varies from mating with hundreds of males (extreme polyandry) to never remating (monandry). This variation in female behaviour is predicted to affect the pattern of selection on males, with intense pre-copulatory sexual selection under monandry compared to a mix of pre- and post-copulatory forces affecting fitness under polyandry. We tested the hypothesis that differences in female mating biology would be reflected in different costs of pre-copulatory competition between males. We observed that exposure to rival males early in life was highly costly for males of a monandrous species, but had lower costs in the polyandrous species. Males from the monandrous species housed with competitors showed reduced ability to obtain a mate and decreased longevity. These effects were specific to exposure to rivals compared with other types of social interactions (heterospecific male and mated female) and were either absent or weaker in males of the polyandrous species. We conclude that males in monandrous species suffer severe physiological costs from interactions with rivals and note the significance of male-male interactions as a source of stress in laboratory culture.
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Affiliation(s)
- Anne Lizé
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Thomas A R Price
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Chloe Heys
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Zenobia Lewis
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Gregory D D Hurst
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
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