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Zhao W, Gao J, Hall D, Andersson BA, Bruxaux J, Tomlinson KW, Drouzas AD, Suyama Y, Wang XR. Evolutionary radiation of the Eurasian Pinus species under pervasive gene flow. New Phytol 2024. [PMID: 38515228 DOI: 10.1111/nph.19694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 03/04/2024] [Indexed: 03/23/2024]
Abstract
Evolutionary radiation, a pivotal aspect of macroevolution, offers valuable insights into evolutionary processes. The genus Pinus is the largest genus in conifers withc . $$ c. $$ 90% of the extant species emerged in the Miocene, which signifies a case of rapid diversification. Despite this remarkable history, our understanding of the mechanisms driving radiation within this expansive genus has remained limited. Using exome capture sequencing and a fossil-calibrated phylogeny, we investigated the divergence history, niche diversification, and introgression among 13 closely related Eurasian species spanning climate zones from the tropics to the boreal Arctic. We detected complex introgression among lineages in subsection Pinus at all stages of the phylogeny. Despite this widespread gene exchange, each species maintained its genetic identity and showed clear niche differentiation. Demographic analysis unveiled distinct population histories among these species, which further influenced the nucleotide diversity and efficacy of purifying and positive selection in each species. Our findings suggest that radiation in the Eurasian pines was likely fueled by interspecific recombination and further reinforced by their adaptation to distinct environments. Our study highlights the constraints and opportunities for evolutionary change, and the expectations of future adaptation in response to environmental changes in different lineages.
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Affiliation(s)
- Wei Zhao
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, SE-90187, Sweden
| | - Jie Gao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
| | - David Hall
- Forestry Research Institute of Sweden (Skogforsk), Sävar, SE-91833, Sweden
| | - Bea Angelica Andersson
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, SE-90187, Sweden
| | - Jade Bruxaux
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, SE-90187, Sweden
| | - Kyle W Tomlinson
- Center for Integrative Conservation & Yunnan Key Laboratory for Conservation of Tropical Rainforests and Asian Elephant, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
| | - Andreas D Drouzas
- Laboratory of Systematic Botany and Phytogeography, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Yoshihisa Suyama
- Graduate School of Agricultural Science, Tohoku University, Miyagi, 989-6711, Japan
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, SE-90187, Sweden
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
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Bruxaux J, Zhao W, Hall D, Curtu AL, Androsiuk P, Drouzas AD, Gailing O, Konrad H, Sullivan AR, Semerikov V, Wang XR. Scots pine - panmixia and the elusive signal of genetic adaptation. New Phytol 2024. [PMID: 38308133 DOI: 10.1111/nph.19563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/14/2024] [Indexed: 02/04/2024]
Abstract
Scots pine is the foundation species of diverse forested ecosystems across Eurasia and displays remarkable ecological breadth, occurring in environments ranging from temperate rainforests to arid tundra margins. Such expansive distributions can be favored by various demographic and adaptive processes and the interactions between them. To understand the impact of neutral and selective forces on genetic structure in Scots pine, we conducted range-wide population genetic analyses on 2321 trees from 202 populations using genotyping-by-sequencing, reconstructed the recent demography of the species and examined signals of genetic adaptation. We found a high and uniform genetic diversity across the entire range (global FST 0.048), no increased genetic load in expanding populations and minor impact of the last glacial maximum on historical population sizes. Genetic-environmental associations identified only a handful of single-nucleotide polymorphisms significantly linked to environmental gradients. The results suggest that extensive gene flow is predominantly responsible for the observed genetic patterns in Scots pine. The apparent missing signal of genetic adaptation is likely attributed to the intricate genetic architecture controlling adaptation to multi-dimensional environments. The panmixia metapopulation of Scots pine offers a good study system for further exploration into how genetic adaptation and plasticity evolve under gene flow and changing environment.
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Affiliation(s)
- Jade Bruxaux
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
| | - Wei Zhao
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
| | - David Hall
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
- Forestry Research Institute of Sweden (Skogforsk), 918 21, Sävar, Sweden
| | | | - Piotr Androsiuk
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719, Olsztyn, Poland
| | - Andreas D Drouzas
- Laboratory of Systematic Botany and Phytogeography, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Oliver Gailing
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, 37077, Göttingen, Germany
| | - Heino Konrad
- Department of Forest Biodiversity and Nature Conservation, Unit of Ecological Genetics, Austrian Research Centre for Forests (BFW), 1140, Vienna, Austria
| | - Alexis R Sullivan
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
| | - Vladimir Semerikov
- Institute of Plant and Animal Ecology, Ural Division of Russian Academy of Sciences, 620144, Ekaterinburg, Russia
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, 901 87, Umeå, Sweden
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Lo Y, Bruxaux J, Rodríguez de la Vega RC, O'Donnell S, Snirc A, Coton M, Le Piver M, Le Prieur S, Roueyre D, Dupont J, Houbraken J, Debuchy R, Ropars J, Giraud T, Branca A. Domestication in dry-cured meat Penicillium fungi: Convergent specific phenotypes and horizontal gene transfers without strong genetic subdivision. Evol Appl 2023; 16:1637-1660. [PMID: 37752962 PMCID: PMC10519415 DOI: 10.1111/eva.13591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/17/2023] [Accepted: 08/18/2023] [Indexed: 09/28/2023] Open
Abstract
Some fungi have been domesticated for food production, with genetic differentiation between populations from food and wild environments, and food populations often acquiring beneficial traits through horizontal gene transfers (HGTs). Studying their adaptation to human-made substrates is of fundamental and applied importance for understanding adaptation processes and for further strain improvement. We studied here the population structures and phenotypes of two distantly related Penicillium species used for dry-cured meat production, P. nalgiovense, the most common species in the dry-cured meat food industry, and P. salamii, used locally by farms. Both species displayed low genetic diversity, lacking differentiation between strains isolated from dry-cured meat and those from other environments. Nevertheless, the strains collected from dry-cured meat within each species displayed slower proteolysis and lipolysis than their wild conspecifics, and those of P. nalgiovense were whiter. Phenotypically, the non-dry-cured meat strains were more similar to their sister species than to their conspecific dry-cured meat strains, indicating an evolution of specific phenotypes in dry-cured meat strains. A comparison of available Penicillium genomes from various environments revealed HGTs, particularly between P. nalgiovense and P. salamii (representing almost 1.5 Mb of cumulative length). HGTs additionally involved P. biforme, also found in dry-cured meat products. We further detected positive selection based on amino acid changes. Our findings suggest that selection by humans has shaped the P. salamii and P. nalgiovense populations used for dry-cured meat production, which constitutes domestication. Several genetic and phenotypic changes were similar in P. salamii, P. nalgiovense and P. biforme, indicating convergent adaptation to the same human-made environment. Our findings have implications for fundamental knowledge on adaptation and for the food industry: the discovery of different phenotypes and of two mating types paves the way for strain improvement by conventional breeding, to elucidate the genomic bases of beneficial phenotypes and to generate diversity.
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Affiliation(s)
- Ying‐Chu Lo
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Jade Bruxaux
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
- Department of Ecology and Environmental ScienceUmeå UniversityUmeåSweden
| | | | - Samuel O'Donnell
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Alodie Snirc
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Monika Coton
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie MicrobiennePlouzanéFrance
| | - Mélanie Le Piver
- Laboratoire Interprofessionnel de Production – SAS L.I.PAurillacFrance
| | - Stéphanie Le Prieur
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Daniel Roueyre
- Laboratoire Interprofessionnel de Production – SAS L.I.PAurillacFrance
| | - Joëlle Dupont
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS‐MNHN, Muséum National d'Histoire NaturelleParis Cedex 05France
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity InstituteUtrechtThe Netherlands
| | - Robert Debuchy
- Université Paris‐Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
| | - Jeanne Ropars
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Tatiana Giraud
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Antoine Branca
- IDEEV – Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTechUniversité Paris‐SaclayGif‐sur‐YvetteFrance
- IDEEV – Laboratoire Evolution, Génomes Comportement, EcologieCNRS Université Paris Saclay UMR 9191, IRD UMR 247Gif‐sur‐YvetteFrance
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Bruxaux J, Gabrielli M, Ashari H, Prŷs-Jones R, Joseph L, Milá B, Besnard G, Thébaud C. Recovering the evolutionary history of crowned pigeons (Columbidae: Goura): Implications for the biogeography and conservation of New Guinean lowland birds. Mol Phylogenet Evol 2018; 120:248-258. [DOI: 10.1016/j.ympev.2017.11.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 11/27/2022]
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Bourgeois YXC, Delahaie B, Gautier M, Lhuillier E, Malé PJG, Bertrand JAM, Cornuault J, Wakamatsu K, Bouchez O, Mould C, Bruxaux J, Holota H, Milá B, Thébaud C. A novel locus on chromosome 1 underlies the evolution of a melanic plumage polymorphism in a wild songbird. R Soc Open Sci 2017; 4:160805. [PMID: 28386436 PMCID: PMC5367300 DOI: 10.1098/rsos.160805] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/12/2017] [Indexed: 06/07/2023]
Abstract
Understanding the mechanisms responsible for phenotypic diversification within and among species ultimately rests with linking naturally occurring mutations to functionally and ecologically significant traits. Colour polymorphisms are of great interest in this context because discrete colour patterns within a population are often controlled by just a few genes in a common environment. We investigated how and why phenotypic diversity arose and persists in the Zosterops borbonicus white-eye of Reunion (Mascarene archipelago), a colour polymorphic songbird in which all highland populations contain individuals belonging to either a brown or a grey plumage morph. Using extensive phenotypic and genomic data, we demonstrate that this melanin-based colour polymorphism is controlled by a single locus on chromosome 1 with two large-effect alleles, which was not previously described as affecting hair or feather colour. Differences between colour morphs appear to rely upon complex cis-regulatory variation that either prevents the synthesis of pheomelanin in grey feathers, or increases its production in brown ones. We used coalescent analyses to show that, from a 'brown' ancestral population, the dominant 'grey' allele spread quickly once it arose from a new mutation. Since colour morphs are always found in mixture, this implies that the selected allele does not go to fixation, but instead reaches an intermediate frequency, as would be expected under balancing selection.
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Affiliation(s)
- Yann X. C. Bourgeois
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Boris Delahaie
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Mathieu Gautier
- INRA, UMR 1062 CBGP (INRA, IRD, Cirad, Montpellier SupAgro), Campus de Baillarguet, 34988 Montferrier-sur-Lez, France
| | - Emeline Lhuillier
- INRA, GeT-PlaGe, Genotoul, 24 chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan, France
- INRA, UAR1209, 24 chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan, France
| | - Pierre-Jean G. Malé
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Joris A. M. Bertrand
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Josselin Cornuault
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Kazumasa Wakamatsu
- Department of Chemistry, Fujita Health University, School of Health Sciences, Toyoake Aichi 470-1192, Japan
| | - Olivier Bouchez
- INRA, GeT-PlaGe, Genotoul, 24 chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan, France
- GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, 24 chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan, France
| | - Claire Mould
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Jade Bruxaux
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Hélène Holota
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), 28006 Madrid, Spain
| | - Christophe Thébaud
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
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