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Gargiulo R, Decroocq V, González‐Martínez SC, Paz‐Vinas I, Aury J, Lesur Kupin I, Plomion C, Schmitt S, Scotti I, Heuertz M. Estimation of contemporary effective population size in plant populations: Limitations of genomic datasets. Evol Appl 2024; 17:e13691. [PMID: 38707994 PMCID: PMC11069024 DOI: 10.1111/eva.13691] [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: 08/21/2023] [Revised: 03/22/2024] [Accepted: 04/03/2024] [Indexed: 05/07/2024] Open
Abstract
Effective population size (N e) is a pivotal evolutionary parameter with crucial implications in conservation practice and policy. Genetic methods to estimate N e have been preferred over demographic methods because they rely on genetic data rather than time-consuming ecological monitoring. Methods based on linkage disequilibrium (LD), in particular, have become popular in conservation as they require a single sampling and provide estimates that refer to recent generations. A software program based on the LD method, GONE, looks particularly promising to estimate contemporary and recent-historical N e (up to 200 generations in the past). Genomic datasets from non-model species, especially plants, may present some constraints to the use of GONE, as linkage maps and reference genomes are seldom available, and SNP genotyping is usually based on reduced-representation methods. In this study, we use empirical datasets from four plant species to explore the limitations of plant genomic datasets when estimating N e using the algorithm implemented in GONE, in addition to exploring some typical biological limitations that may affect N e estimation using the LD method, such as the occurrence of population structure. We show how accuracy and precision of N e estimates potentially change with the following factors: occurrence of missing data, limited number of SNPs/individuals sampled, and lack of information about the location of SNPs on chromosomes, with the latter producing a significant bias, previously unexplored with empirical data. We finally compare the N e estimates obtained with GONE for the last generations with the contemporary N e estimates obtained with the programs currentNe and NeEstimator.
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Affiliation(s)
| | | | | | - Ivan Paz‐Vinas
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
- CNRS, ENTPE, UMR5023 LEHNAUniversité Claude Bernard Lyon 1VilleurbanneFrance
| | - Jean‐Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris‐SaclayEvryFrance
| | | | | | - Sylvain Schmitt
- AMAPUniv. Montpellier, CIRAD, CNRS, INRAE, IRDMontpellierFrance
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2
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Ju T, Han ZT, Ruhsam M, Li JL, Tao WJ, Tso S, Miehe G, Mao KS. Reproduction and genetic diversity of Juniperus squamata along an elevational gradient in the Hengduan Mountains. PLANT DIVERSITY 2022; 44:369-376. [PMID: 35967254 PMCID: PMC9363649 DOI: 10.1016/j.pld.2021.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 12/06/2021] [Accepted: 12/06/2021] [Indexed: 06/15/2023]
Abstract
Elevation plays a crucial factor in the distribution of plants, as environmental conditions become increasingly harsh at higher elevations. Previous studies have mainly focused on the effects of large-scale elevational gradients on plants, with little attention on the impact of smaller-scale gradients. In this study we used 14 microsatellite loci to survey the genetic structure of 332 Juniperus squamata plants along elevation gradient from two sites in the Hengduan Mountains. We found that the genetic structure (single, clonal, mosaic) of J. squamata shrubs is affected by differences in elevational gradients of only 150 m. Shrubs in the mid-elevation plots rarely have a clonal or mosaic structure compared to shrubs in lower- or higher-elevation plots. Human activity can significantly affect genetic structure, as well as reproductive strategy and genetic diversity. Sub-populations at mid-elevations had the highest yield of seed cones, lower levels of asexual reproduction and higher levels of genetic diversity. This may be due to the trade-off between elevational stress and anthropogenic disturbance at mid-elevation since there is greater elevational stress at higher-elevations and greater intensity of anthropogenic disturbance at lower-elevations. Our findings provide new insights into the finer scale genetic structure of alpine shrubs, which may improve the conservation and management of shrublands, a major vegetation type on the Hengduan Mountains and the Qinghai-Tibet Plateau.
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Affiliation(s)
- Tsam Ju
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Zhi-Tong Han
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Jia-Liang Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Wen-Jing Tao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Sonam Tso
- College of Science, Tibet University, Lhasa, Tibet 850000, China
| | - Georg Miehe
- Department of Geography, Philipps-Universität Marburg, Deutschhausstraße 10, Marburg 35032, Hessen, Germany
| | - Kang-Shan Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan 610065, China
- College of Science, Tibet University, Lhasa, Tibet 850000, China
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3
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Schmitt S, Tysklind N, Heuertz M, Hérault B. Selection in space and time: Individual tree growth is adapted to tropical forest gap dynamics. Mol Ecol 2022. [PMID: 35152482 DOI: 10.1111/mec.16392] [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: 07/08/2021] [Revised: 01/07/2022] [Accepted: 02/07/2022] [Indexed: 10/19/2022]
Abstract
Tropical forest dynamics are driven by growth and survival strategies of tree species in relation to treefall gaps; however, the ecological and evolutionary roles of intraspecific variation in the response to forest gaps remain unexplored. Here, we associated genomic data of three related tree species of the genus Symphonia in a French Guiana forest with (1) each individual tree's growth potential, and (2) with its light and competition environment estimated based on 33 years of forest monitoring in plots covering 120 ha. We show that individual trees within species have genetically determined growth strategies that are adapted to the local light and competition environments, which are shaped by the time since the last treefall. Within species, fast-growing genotypes are more frequent in light-enriched environments and slow-growing genotypes in more shaded environments. Forest gap dynamics is thus a strong selection driver that shapes adaptive strategies and maintains genetic variation within tropical tree species.
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Affiliation(s)
- Sylvain Schmitt
- CNRS, UMR EcoFoG (Agroparistech, CIRAD, INRAE, Université des Antilles, Université de la Guyane), Campus Agronomique, Kourou, French Guiana
- Univ Bordeaux, INRAE, BIOGECO, Cestas, France
| | - Niklas Tysklind
- INRAE, UMR EcoFoG (Agroparistech, CNRS, CIRAD, Université des Antilles, Université de la Guyane), Campus Agronomique, Kourou, French Guiana
| | | | - Bruno Hérault
- CIRAD, UR Forêts et Sociétés, Yamoussoukro, Côte d'Ivoire
- CIRAD, Univ Montpellier, UR Forêts et Sociétés, Montpellier, France
- Institut National Polytechnique Félix Houphouët-Boigny, INP-HB, Yamoussoukro, Côte d'Ivoire
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4
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O'Brien MJ, Escudero A. Topography in tropical forests enhances growth and survival differences within and among species via water availability and biotic interactions. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13977] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Michael J. O'Brien
- Área de Biodiversidad y Conservación Universidad Rey Juan Carlos Móstoles Spain
- Southeast Asia Rainforest Research Partnership (SEARRP) Kota Kinabalu Sabah Malaysia
| | - Adrián Escudero
- Área de Biodiversidad y Conservación Universidad Rey Juan Carlos Móstoles Spain
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5
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Schmitt S, Tysklind N, Hérault B, Heuertz M. Topography drives microgeographic adaptations of closely related species in two tropical tree species complexes. Mol Ecol 2021; 30:5080-5093. [PMID: 34387001 DOI: 10.1111/mec.16116] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 11/27/2022]
Abstract
Closely related tree species that grow in sympatry are abundant in rainforests. However, little is known of the eco-evolutionary processes that govern their niches and local coexistence. We assessed genetic species delimitation in closely related sympatric species belonging to two Neotropical tree species complexes and investigated their genomic adaptation to a fine-scale topographic gradient with associated edaphic and hydrologic features. Combining LiDAR-derived topography, tree inventories, and single nucleotide polymorphisms (SNPs) from gene capture experiments, we explored genome-wide population genetic structure, covariation of environmental variables, and genotype-environment association to assess microgeographic adaptations to topography within the species complexes Symphonia (Clusiaceae), and Eschweilera (Lecythidaceae) with three species per complex and 385 and 257 individuals genotyped, respectively. Within species complexes, closely related tree species had different realized optima for topographic niches defined through the topographic wetness index or the relative elevation, and species displayed genetic signatures of adaptations to these niches. Symphonia species were genetically differentiated along water and nutrient distribution particularly in genes responding to water deprivation, whereas Eschweilera species were genetically differentiated according to soil chemistry. Our results suggest that varied topography represents a powerful driver of processes modulating tropical forest biodiversity with differential adaptations that stabilize local coexistence of closely related tree species.
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Affiliation(s)
- Sylvain Schmitt
- CNRS, UMR EcoFoG (Agroparistech, Cirad, INRAE, Université des Antilles, Université de la Guyane), Campus Agronomique, 97310, Kourou, French Guiana, France.,Univ. Bordeaux, INRAE, BIOGECO, 69 route d'Arcachon, 33610, Cestas, France
| | - Niklas Tysklind
- INRAE, UMR EcoFoG (Agroparistech, CNRS, Cirad, Université des Antilles, Université de la Guyane), Campus Agronomique, 97310, Kourou, French Guiana, France
| | - Bruno Hérault
- CIRAD, UR Forêts et Sociétés, Yamoussoukro Côte d'Ivoire, France.,Forêts et Sociétés, Univ Montpellier, CIRAD, Montpellier, France.,Institut National Polytechnique Félix Houphouët-Boigny, INP-HB, Yamoussoukro Côte d'Ivoire, France
| | - Myriam Heuertz
- Univ. Bordeaux, INRAE, BIOGECO, 69 route d'Arcachon, 33610, Cestas, France
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Major EI, Höhn M, Avanzi C, Fady B, Heer K, Opgenoorth L, Piotti A, Popescu F, Postolache D, Vendramin GG, Csilléry K. Fine-scale spatial genetic structure across the species range reflects recent colonization of high elevation habitats in silver fir (Abies alba Mill.). Mol Ecol 2021; 30:5247-5265. [PMID: 34365696 PMCID: PMC9291806 DOI: 10.1111/mec.16107] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 07/07/2021] [Accepted: 07/16/2021] [Indexed: 12/03/2022]
Abstract
Variation in genetic diversity across species ranges has long been recognized as highly informative for assessing populations’ resilience and adaptive potential. The spatial distribution of genetic diversity within populations, referred to as fine‐scale spatial genetic structure (FSGS), also carries information about recent demographic changes, yet it has rarely been connected to range scale processes. We studied eight silver fir (Abies alba Mill.) population pairs (sites), growing at high and low elevations, representative of the main genetic lineages of the species. A total of 1,368 adult trees and 540 seedlings were genotyped using 137 and 116 single nucleotide polymorphisms (SNPs), respectively. Sites revealed a clear east‐west isolation‐by‐distance pattern consistent with the post‐glacial colonization history of the species. Genetic differentiation among sites (FCT = 0.148) was an order of magnitude greater than between elevations within sites (FSC = 0.031), nevertheless high elevation populations consistently exhibited a stronger FSGS. Structural equation modelling revealed that elevation and, to a lesser extent, post‐glacial colonization history, but not climatic and habitat variables, were the best predictors of FSGS across populations. These results suggest that high elevation habitats have been colonized more recently across the species range. Additionally, paternity analysis revealed a high reproductive skew among adults and a stronger FSGS in seedlings than in adults, suggesting that FSGS may conserve the signature of demographic changes for several generations. Our results emphasize that spatial patterns of genetic diversity within populations provide information about demographic history complementary to non‐spatial statistics, and could be used for genetic diversity monitoring, especially in forest trees.
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Affiliation(s)
- Enikő I Major
- Department of Botany, Hungarian University of Agronomy and Life Sciences, Budapest, Hungary
| | - Mária Höhn
- Department of Botany, Hungarian University of Agronomy and Life Sciences, Budapest, Hungary
| | - Camilla Avanzi
- Institute of Biosciences and Bioresources, National Research Council of Italy (IBBR-CNR), Sesto Fiorentino (Firenze), Italy
| | - Bruno Fady
- Ecology of Mediterranean Forests (URFM), INRAE, UR629, Avignon, France
| | - Katrin Heer
- Conservation Biology, Philipps Universität Marburg, Marburg, Germany
| | - Lars Opgenoorth
- Plant Ecology and Geobotany, Philipps Universität Marburg, Marburg, Germany.,Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Andrea Piotti
- Institute of Biosciences and Bioresources, National Research Council of Italy (IBBR-CNR), Sesto Fiorentino (Firenze), Italy
| | - Flaviu Popescu
- National Institute for Research and Development in Forestry "Marin Drăcea", Ilfov County, Romania
| | - Dragos Postolache
- National Institute for Research and Development in Forestry "Marin Drăcea", Ilfov County, Romania
| | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources, National Research Council of Italy (IBBR-CNR), Sesto Fiorentino (Firenze), Italy
| | - Katalin Csilléry
- Land Change Science, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
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7
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Schmitt S, Tysklind N, Derroire G, Heuertz M, Hérault B. Topography shapes the local coexistence of tree species within species complexes of Neotropical forests. Oecologia 2021; 196:389-398. [PMID: 33978831 DOI: 10.1007/s00442-021-04939-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/05/2021] [Indexed: 11/26/2022]
Abstract
Forest inventories in Amazonia include around 5000 described tree species belonging to more than 800 genera. Numerous species-rich genera share genetic variation among species because of recent speciation and/or recurrent hybridisation, forming species complexes. Despite the key role that tree species complexes play in understanding Neotropical diversification, and their need to exploit a diversity of niches, little is known about the mechanisms that allow local coexistence of tree species complexes and their species in sympatry. In this study, we explored the fine-scale distribution of five tree species complexes and 22 species within these complexes. Combining forest inventories, botanical determination, and LiDAR-derived topographic data over 120 ha of permanent plots in French Guiana, we used a Bayesian modelling framework to test the role of fine-scale topographic wetness and tree neighbourhood on the occurrence of species complexes and the relative distribution of species within complexes. Species complexes of Neotropical trees were widely spread across the topographic wetness gradient at the local scale. Species within complexes showed pervasive niche differentiation along with topographic wetness and competition gradients. Similar patterns of species-specific habitat preferences were observed within several species complexes: species more tolerant to competition for resources grow in drier and less fertile plateaus and slopes. If supported by partial reproductive isolation of species and adaptive introgression at the species complex level, our results suggest that both species-specific habitat specialisation within species complexes and the broad ecological distribution of species complexes might explain the success of these species complexes at the regional scale.
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Affiliation(s)
- Sylvain Schmitt
- CNRS, UMR EcoFoG (Agroparistech, Cirad, INRAE, Université Des Antilles, Université de La Guyane), Campus Agronomique, 97310, Kourou, French Guiana.
- University of Bordeaux, INRAE, BIOGECO, 69 route d'Arcachon, 33610, Cestas, France.
| | - Niklas Tysklind
- INRAE, UMR EcoFoG (Agroparistech, CNRS, Cirad, Université Des Antilles, Université de La Guyane), Campus Agronomique, 97310, Kourou, French Guiana
| | - Géraldine Derroire
- Cirad, UMR EcoFoG (Agroparistech, CNRS, INRAE, Université Des Antilles, Université de La Guyane), Campus Agronomique, 97310, Kourou, French Guiana
| | - Myriam Heuertz
- University of Bordeaux, INRAE, BIOGECO, 69 route d'Arcachon, 33610, Cestas, France
| | - Bruno Hérault
- CIRAD, UPR Forêts Et Sociétés, Yamoussoukro, Côte d'Ivoire
- Forêts Et Sociétés, University of Montpellier, CIRAD, Montpellier, France
- Institut National Polytechnique Félix Houphouët-Boigny, INP-HB, Yamoussoukro, Côte d'Ivoire
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8
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Tysklind N, Etienne MP, Scotti-Saintagne C, Tinaut A, Casalis M, Troispoux V, Cazal SO, Brousseau L, Ferry B, Scotti I. Microgeographic local adaptation and ecotype distributions: The role of selective processes on early life-history traits in sympatric, ecologically divergent Symphonia populations. Ecol Evol 2020; 10:10735-10753. [PMID: 33072293 PMCID: PMC7548183 DOI: 10.1002/ece3.6731] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/29/2020] [Accepted: 08/01/2020] [Indexed: 11/11/2022] Open
Abstract
Trees are characterized by the large number of seeds they produce. Although most of those seeds will never germinate, plenty will. Of those which germinate, many die young, and eventually, only a minute fraction will grow to adult stage and reproduce. Is this just a random process? Do variations in germination and survival at very young stages rely on variations in adaptations to microgeographic heterogeneity? and do these processes matter at all in determining tree species distribution and abundance? We have studied these questions with the Neotropical Symphonia tree species. In the Guiana shield, Symphonia are represented by at least two sympatric taxa or ecotypes, Symphonia globulifera found almost exclusively in bottomlands, and a yet undescribed more generalist taxon/ecotype, Symphonia sp1. A reciprocal transplantation experiment (510 seeds, 16 conditions) was set up and followed over the course of 6 years to evaluate the survival and performance of individuals from different ecotypes and provenances. Germination, survival, growth, and herbivory showed signs of local adaptation, with some combinations of ecotypes and provenances growing faster and surviving better in their own habitat or provenance region. S. globulifera was strongly penalized when planted outside its home habitat but showed the fastest growth rates when planted in its home habitat, suggesting it is a specialist of a high‐risk high‐gain strategy. Conversely, S. sp1 behaved as a generalist, performing well in a variety of environments. The differential performance of seeds and seedlings in the different habitats matches the known distribution of both ecotypes, indicating that environmental filtering at the very early stages can be a key determinant of tree species distributions, even at the microgeographic level and among very closely related taxa. Furthermore, such differential performance also contributes to explain, in part, the maintenance of the different Symphonia ecotypes living in intimate sympatry despite occasional gene flow.
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Affiliation(s)
- Niklas Tysklind
- INRAE UMR0745 EcoFoG AgroParisTech Cirad CNRS Université des Antilles Université de Guyane Kourou Cedex France
| | | | | | - Alexandra Tinaut
- INRAE UMR0745 EcoFoG AgroParisTech Cirad CNRS Université des Antilles Université de Guyane Kourou Cedex France.,Université de Guyane UMR0745 EcoFoG INRAE AgroParisTech Cirad CNRS Université des Antilles Kourou Cedex France
| | - Maxime Casalis
- INRAE UMR0745 EcoFoG AgroParisTech Cirad CNRS Université des Antilles Université de Guyane Kourou Cedex France.,Université de Guyane UMR0745 EcoFoG INRAE AgroParisTech Cirad CNRS Université des Antilles Kourou Cedex France
| | - Valerie Troispoux
- INRAE UMR0745 EcoFoG AgroParisTech Cirad CNRS Université des Antilles Université de Guyane Kourou Cedex France
| | - Saint-Omer Cazal
- INRAE UMR0745 EcoFoG AgroParisTech Cirad CNRS Université des Antilles Université de Guyane Kourou Cedex France
| | - Louise Brousseau
- INRAE UMR0745 EcoFoG AgroParisTech Cirad CNRS Université des Antilles Université de Guyane Kourou Cedex France.,Present address: UMR AMAP IRD Cirad CNRS INRAE Université Montpellier Montpellier France
| | - Bruno Ferry
- AgroParisTech INRAE UMR SILVA Université de Lorraine Nancy France
| | - Ivan Scotti
- INRAE UR629 Ecologie des Forêts Méditerranéennes (URFM) Avignon France
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9
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Brousseau L, Fine PVA, Dreyer E, Vendramin GG, Scotti I. Genomic and phenotypic divergence unveil microgeographic adaptation in the Amazonian hyperdominant tree Eperua falcata Aubl. (Fabaceae). Mol Ecol 2020; 30:1136-1154. [PMID: 32786115 DOI: 10.1111/mec.15595] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 06/19/2020] [Accepted: 07/31/2020] [Indexed: 01/04/2023]
Abstract
Plant populations can undergo very localized adaptation, allowing widely distributed populations to adapt to divergent habitats in spite of recurrent gene flow. Neotropical trees-whose large and undisturbed populations often span a variety of environmental conditions and local habitats-are particularly good models to study this process. Here, we explore patterns of adaptive divergence from large (i.e., regional) to small (i.e., microgeographic) spatial scales in the hyperdominant Amazonian tree Eperua falcata Aubl. (Fabaceae) under a replicated design involving two microhabitats (~300 m apart) in two study sites (~300 km apart). A three-year reciprocal transplant illustrates that, beyond strong maternal effects and phenotypic plasticity, genetically driven divergence in seedling growth and leaf traits was detected both between seedlings originating from different regions, and between seedlings from different microhabitats. In parallel, a complementary genome scan for selection was carried out through whole-genome sequencing of tree population pools. A set of 290 divergence outlier SNPs was detected at the regional scale (between study sites), while 185 SNPs located in the vicinity of 106 protein-coding genes were detected as replicated outliers between microhabitats within regions. Outlier-surrounding genomic regions are involved in a variety of physiological processes, including plant responses to stress (e.g., oxidative stress, hypoxia and metal toxicity) and biotic interactions. Together with evidence of microgeographic divergence in functional traits, the discovery of genomic candidates for microgeographic adaptive divergence represents a promising advance in our understanding of local adaptation, which probably operates across multiple spatial scales and underpins divergence and diversification in Neotropical trees.
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Affiliation(s)
- Louise Brousseau
- UMR EcoFoG, AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles, Kourou Cedex, France.,AMAP, Univ. Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France
| | - Paul V A Fine
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Erwin Dreyer
- Université de Lorraine, AgroParisTech, INRAE, Silva, Nancy, France
| | - Giovanni G Vendramin
- Institute of Biosciences and BioResources (IBBR-CNR), National Research Council, Division of Florence, Sesto Fiorentino, Italy
| | - Ivan Scotti
- UR629 Ecologie des Forêts Méditerranéennes (URFM), INRAE, Avignon, France
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10
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Schmitt S, Hérault B, Ducouret É, Baranger A, Tysklind N, Heuertz M, Marcon É, Cazal SO, Derroire G. Topography consistently drives intra‐ and inter‐specific leaf trait variation within tree species complexes in a Neotropical forest. OIKOS 2020. [DOI: 10.1111/oik.07488] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Sylvain Schmitt
- Univ. Bordeaux, INRAE, BIOGECO 69 route d'Arcachon FR‐33610 Cestas France
| | - Bruno Hérault
- CIRAD, UPR Forêts et Sociétés, Yamoussoukro, Côte d'Ivoire, and: Forêts et Sociétés, Univ Montpellier, CIRAD Montpellier France
| | - Émilie Ducouret
- Cirad, UMR EcoFoG (Agroparistech, CNRS, INRAE, Université des Antilles, Univ. de la Guyane) Kourou French Guiana
| | - Anne Baranger
- Univ. Bordeaux, INRAE, BIOGECO 69 route d'Arcachon FR‐33610 Cestas France
| | - Niklas Tysklind
- INRAE, UMR EcoFoG (Agroparistech, CNRS, Cirad, Université des Antilles, Univ. de la Guyane) Kourou French Guiana
| | - Myriam Heuertz
- Univ. Bordeaux, INRAE, BIOGECO 69 route d'Arcachon FR‐33610 Cestas France
| | - Éric Marcon
- Agroparistech, UMR EcoFoG (CNRS, Cirad, INRAE, Université des Antilles, Univ. de la Guyane) Kourou French Guiana
| | - Saint Omer Cazal
- INRAE, UMR EcoFoG (Agroparistech, CNRS, Cirad, Université des Antilles, Univ. de la Guyane) Kourou French Guiana
| | - Géraldine Derroire
- Cirad, UMR EcoFoG (Agroparistech, CNRS, INRAE, Université des Antilles, Univ. de la Guyane) Kourou French Guiana
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11
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Sujii PS, Cozzolino S, Pinheiro F. Hybridization and geographic distribution shapes the spatial genetic structure of two co-occurring orchid species. Heredity (Edinb) 2019; 123:458-469. [PMID: 31391556 PMCID: PMC6781141 DOI: 10.1038/s41437-019-0254-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/11/2019] [Accepted: 07/17/2019] [Indexed: 11/09/2022] Open
Abstract
Multiple ecological and life-history traits shape the fine-scale spatial genetic structure (FSGS) of a given population. The occurrence in core versus peripheral populations, levels of outcrossing, pollen and seed dispersal, and hybridization are important biological properties that influence the kinship of individuals within populations. We examined spatial genetic structure within 15 populations of Epidendrum fulgens and E. puniceoluteum distributed along a linear gradient of Brazilian coastal vegetation, including both allopatric and sympatric populations where the two orchid species hybridize. We analyzed 581 mapped specimens using nine simple sequence repeat loci, aiming to investigate how geographic distribution and hybridization shape within-population FSGS. A significant increase in FSGS was found towards peripheral populations, compared to core populations. Analysis of short-distance and long-distance components of FSGS identified biparental inbreeding and higher levels of FSGS at peripheral populations, when compared to core populations. In contrast, the relatively high density of reproductive adults in core populations potentially leads to highly overlapping seed and pollen movement, decreasing FSGS. Hybridization was an important factor shaping within-population spatial genetic structure at sympatric sites, decreasing the FSGS observed in parental species. Our results indicate that different ecological forces act in concert to create a gradient of FSGS along species distribution ranges, shaped by extensive levels of intraspecific and interspecific gene exchange.
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Affiliation(s)
| | - Salvatore Cozzolino
- Department of Biology, Complesso Universitario di Monte S. Angelo, Università degli Studi di Napoli Federico II, 80126, Napoli, Italy
| | - Fábio Pinheiro
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, Instituto de Biologia, Campinas, Brazil.
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Nagamitsu T, Shuri K, Kikuchi S, Koike S, Naoe S, Masaki T. Multiscale spatial genetic structure within and between populations of wild cherry trees in nuclear genotypes and chloroplast haplotypes. Ecol Evol 2019; 9:11266-11276. [PMID: 31641471 PMCID: PMC6802027 DOI: 10.1002/ece3.5628] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 07/31/2019] [Accepted: 08/07/2019] [Indexed: 11/10/2022] Open
Abstract
Spatial genetic structure (SGS) of plants mainly depends on the effective population size and gene dispersal. Maternally inherited loci are expected to have higher genetic differentiation between populations and more intensive SGS within populations than biparentally inherited loci because of smaller effective population sizes and fewer opportunities of gene dispersal in the maternally inherited loci. We investigated biparentally inherited nuclear genotypes and maternally inherited chloroplast haplotypes of microsatellites in 17 tree populations of three wild cherry species under different conditions of tree distribution and seed dispersal. As expected, interpopulation genetic differentiation was 6-9 times higher in chloroplast haplotypes than in nuclear genotypes. This difference indicated that pollen flow 4-7 times exceeded seed flow between populations. However, no difference between nuclear and chloroplast loci was detected in within-population SGS intensity due to their substantial variation among the populations. The SGS intensity tended to increase as trees became more aggregated, suggesting that tree aggregation biased pollen and seed dispersal distances toward shorter. The loss of effective seed dispersers, Asian black bears, did not affect the SGS intensity probably because of mitigation of the bear loss by other vertebrate dispersers and too few tree generations after the bear loss to alter SGS. The findings suggest that SGS is more variable in smaller spatial scales due to various ecological factors in local populations.
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Affiliation(s)
- Teruyoshi Nagamitsu
- Hokkaido Research CenterForestry and Forest Products Research InstituteForest Research and Management OrganizationSapporoJapan
| | - Kato Shuri
- Tama Forest Science GardenForestry and Forest Products Research InstituteForest Research and Management OrganizationHachiojiJapan
| | - Satoshi Kikuchi
- Forestry and Forest Products Research InstituteForest Research and Management OrganizationTsukubaJapan
| | - Shinsuke Koike
- Institute of AgricultureTokyo University of Agriculture and TechnologyFuchuJapan
| | - Shoji Naoe
- Tohoku Research CenterForestry and Forest Products Research InstituteForest Research and Management OrganizationMoriokaJapan
| | - Takashi Masaki
- Forestry and Forest Products Research InstituteForest Research and Management OrganizationTsukubaJapan
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Smith JR, Ghazoul J, Burslem DFRP, Itoh A, Khoo E, Lee SL, Maycock CR, Nanami S, Ng KKS, Kettle CJ. Are patterns of fine-scale spatial genetic structure consistent between sites within tropical tree species? PLoS One 2018; 13:e0193501. [PMID: 29547644 PMCID: PMC5856272 DOI: 10.1371/journal.pone.0193501] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 02/12/2018] [Indexed: 11/18/2022] Open
Abstract
Documenting the scale and intensity of fine-scale spatial genetic structure (FSGS), and the processes that shape it, is relevant to the sustainable management of genetic resources in timber tree species, particularly where logging or fragmentation might disrupt gene flow. In this study we assessed patterns of FSGS in three species of Dipterocarpaceae (Parashorea tomentella, Shorea leprosula and Shorea parvifolia) across four different tropical rain forests in Malaysia using nuclear microsatellite markers. Topographic heterogeneity varied across the sites. We hypothesised that forests with high topographic heterogeneity would display increased FSGS among the adult populations driven by habitat associations. This hypothesis was not supported for S. leprosula and S. parvifolia which displayed little variation in the intensity and scale of FSGS between sites despite substantial variation in topographic heterogeneity. Conversely, the intensity of FSGS for P. tomentella was greater at a more topographically heterogeneous than a homogeneous site, and a significant difference in the overall pattern of FSGS was detected between sites for this species. These results suggest that local patterns of FSGS may in some species be shaped by habitat heterogeneity in addition to limited gene flow by pollen and seed dispersal. Site factors can therefore contribute to the development of FSGS. Confirming consistency in species’ FSGS amongst sites is an important step in managing timber tree genetic diversity as it provides confidence that species specific management recommendations based on species reproductive traits can be applied across a species’ range. Forest managers should take into account the interaction between reproductive traits and site characteristics, its consequences for maintaining forest genetic resources and how this might influence natural regeneration across species if management is to be sustainable.
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Affiliation(s)
- James R. Smith
- Institute for Terrestrial Ecology, ETH Zurich, Zurich, Switzerland
| | - Jaboury Ghazoul
- Institute for Terrestrial Ecology, ETH Zurich, Zurich, Switzerland
| | | | - Akira Itoh
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka, Japan
| | - Eyen Khoo
- Forest Research Centre, Sabah Forestry Department, Sabah, Malaysia
| | - Soon Leong Lee
- Forest Research Institute Malaysia, Kepong, Selangor, Malaysia
| | - Colin R. Maycock
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Sabah, Malaysia
| | - Satoshi Nanami
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka, Japan
| | | | - Chris J. Kettle
- Institute for Terrestrial Ecology, ETH Zurich, Zurich, Switzerland
- * E-mail:
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Mosca E, Di Pierro EA, Budde KB, Neale DB, González-Martínez SC. Environmental effects on fine-scale spatial genetic structure in four Alpine keystone forest tree species. Mol Ecol 2018; 27:647-658. [PMID: 29274175 DOI: 10.1111/mec.14469] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 11/15/2017] [Accepted: 11/22/2017] [Indexed: 12/22/2022]
Abstract
Genetic responses to environmental changes take place at different spatial scales. While the effect of environment on the distribution of species' genetic diversity at large geographical scales has been the focus of several recent studies, its potential effects on genetic structure at local scales are understudied. Environmental effects on fine-scale spatial genetic structure (FSGS) were investigated in four Alpine conifer species (five to eight populations per species) from the eastern Italian Alps. Significant FSGS was found for 11 of 25 populations. Interestingly, we found no significant differences in FSGS across species but great variation among populations within species, highlighting the importance of local environmental factors. Interannual variability in spring temperature had a small but significant effect on FSGS of Larix decidua, probably related to species-specific life history traits. For Abies alba, Picea abies and Pinus cembra, linear models identified spring precipitation as a potentially relevant climate factor associated with differences in FSGS across populations; however, models had low explanatory power and were strongly influenced by a P. cembra outlier population from a very dry site. Overall, the direction of the identified effects is according to expectations, with drier and more variable environments increasing FSGS. Underlying mechanisms may include climate-related changes in the variance of reproductive success and/or environmental selection of specific families. This study provides new insights on potential changes in local genetic structure of four Alpine conifers in the face of environmental changes, suggesting that new climates, through altering FSGS, may also have relevant impacts on plant microevolution.
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Affiliation(s)
- Elena Mosca
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), S. Michele all'Adige, Italy.,Faculty of Science and Technology, Free University of Bolzano, Bolzano, Italy
| | - Erica A Di Pierro
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), S. Michele all'Adige, Italy
| | | | - David B Neale
- Department of Plant Sciences, University of California at Davis, Davis, CA, USA
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Gelmi-Candusso TA, Heymann EW, Heer K. Effects of zoochory on the spatial genetic structure of plant populations. Mol Ecol 2017; 26:5896-5910. [PMID: 28921766 DOI: 10.1111/mec.14351] [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] [Received: 04/21/2016] [Revised: 08/30/2017] [Accepted: 09/05/2017] [Indexed: 01/17/2023]
Abstract
Spatial genetic structure (SGS) of plants results from the nonrandom distribution of related individuals. SGS provides information on gene flow and spatial patterns of genetic diversity within populations. Seed dispersal creates the spatial template for plant distribution. Thus, in zoochorous plants, dispersal mode and disperser behaviour might have a strong impact on SGS. However, many studies only report the taxonomic group of seed dispersers, without further details. The recent increase in studies on SGS provides the opportunity to review findings and test for the influence of dispersal mode, taxonomic affiliation of dispersers and their behaviour. We compared the proportions of studies with SGS among groups and tested for differences in strength of SGS using Sp statistics. The presence of SGS differed among taxonomic groups, with reduced presence in plants dispersed by birds. Strength of SGS was instead significantly influenced by the behaviour of seed dispersal vectors, with higher SGS in plant species dispersed by animals with behavioural traits that result in short seed dispersal distances. We observed high variance in the strength of SGS in plants dispersed by animals that actively or passively accumulate seeds. Additionally, we found SGS was also affected by pollination and marker type used. Our study highlights the importance of vector behaviour on SGS even in the presence of variance created by other factors. Thus, more detailed information on the behaviour of seed dispersers would contribute to better understand which factors shape the spatial scale of gene flow in animal-dispersed plant species.
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Affiliation(s)
- Tiziana A Gelmi-Candusso
- Verhaltensökologie & Soziobiologie, Deutsches Primatenzentrum - Leibniz-Institut für Primatenforschung, Göttingen, Germany
| | - Eckhard W Heymann
- Verhaltensökologie & Soziobiologie, Deutsches Primatenzentrum - Leibniz-Institut für Primatenforschung, Göttingen, Germany
| | - Katrin Heer
- Naturschutzbiologie, Phillips-Universität Marburg, Marburg, Germany
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