1
|
Valverde J, Medrano M, Herrera CM, Alonso C. Comparative epigenetic and genetic spatial structure in Mediterranean mountain plants: a multispecies study. Heredity (Edinb) 2024; 132:106-116. [PMID: 38233486 PMCID: PMC10844209 DOI: 10.1038/s41437-024-00668-3] [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: 06/06/2023] [Revised: 12/26/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024] Open
Abstract
Changes in epigenetic states can allow individuals to cope with environmental changes. If such changes are heritable, this may lead to epigenetic adaptation. Thus, it is likely that in sessile organisms such as plants, part of the spatial epigenetic variation found across individuals will reflect the environmental heterogeneity within populations. The departure of the spatial epigenetic structure from the baseline genetic variation can help in understanding the value of epigenetic regulation in species with different breadth of optimal environmental requirements. Here, we hypothesise that in plants with narrow environmental requirements, epigenetic variability should be less structured in space given the lower variability in suitable environmental conditions. We performed a multispecies study that considered seven pairs of congeneric plant species, each encompassing a narrow endemic with habitat specialisation and a widespread species. In three populations per species we used AFLP and methylation-sensitive AFLP markers to characterise the spatial genetic and epigenetic structures. Narrow endemics showed a significantly lower epigenetic than genetic differentiation between populations. Within populations, epigenetic variation was less spatially structured than genetic variation, mainly in narrow endemics. In these species, structural equation models revealed that such pattern was associated to a lack of correlation between epigenetic and genetic information. Altogether, these results show a greater decoupling of the spatial epigenetic variation from the baseline spatial genetic pattern in endemic species. These findings highlight the value of studying genetic and epigenetic spatial variation to better understand habitat specialisation in plants.
Collapse
Affiliation(s)
- Javier Valverde
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain.
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain.
| | - Mónica Medrano
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Carlos M Herrera
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Conchita Alonso
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain.
| |
Collapse
|
2
|
Danusevičius D, Rajora OP, Kavaliauskas D, Baliuckas V, Augustaitis A. Stronger genetic differentiation among within-population genetic groups than among populations in Scots pine provides new insights into within-population genetic structuring. Sci Rep 2024; 14:2713. [PMID: 38302512 PMCID: PMC10834436 DOI: 10.1038/s41598-024-52769-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 01/23/2024] [Indexed: 02/03/2024] Open
Abstract
We investigated the presence of spatial genetic groups within forest tree populations and determined if the genetic divergence among these groups is greater than that between populations using Scots pine (Pinus sylvestris) as a model species. We genotyped 890 adult trees of Scots pine in six natural populations in Lithuania at 11 nuclear microsatellite loci. We used a Bayesian clustering approach to identify the within-population genetic groups within each of the six populations. We calculated the differentiation indexes among the genetic groups within each population and among the six populations by ignoring the genetic groups. The Bayesian clustering revealed 2 to 6 distinct genetic groups of varying size as the most likely genetic structures within populations. The genetic differentiation indexes among the genetic groups within populations were nearly tenfold greater (FST = 0.012-0.070) than those between the populations (FST = 0.003). We conclude on the existence of markedly stronger structuring of genetic variation within populations than between populations of Scots pine in large forest tracts of northern Europe. Such genetic structures serve as a contributing factor to large within population genetic diversity in northern conifers. We assume that within population mating in Scots pine is not completely random but rather is stratified into genetic clusters. Our study provides pioneering novel key insights into structuring of genetic variation within populations. Our findings have implications for examining within-population genetic diversity and genetic structure, conservation, and management of genetic resources.
Collapse
Affiliation(s)
- Darius Danusevičius
- Vytautas Magnus University, K. Donelaičio Str. 58, 44248, Kaunas, Lithuania.
| | - Om P Rajora
- Faculty of Forestry and Environmental Management, University of New Brunswick, PO Box 4400, 28 Dineen Drive, Fredericton, NB, E3B 5A3, Canada.
| | - Darius Kavaliauskas
- Vytautas Magnus University, K. Donelaičio Str. 58, 44248, Kaunas, Lithuania
- Lithuanian Research Centre for Agriculture and Forestry, Forestry Institute, Liepu Str. 1, 53101, Kaunas Reg., Lithuania
| | - Virgilijus Baliuckas
- Vytautas Magnus University, K. Donelaičio Str. 58, 44248, Kaunas, Lithuania
- Lithuanian Research Centre for Agriculture and Forestry, Forestry Institute, Liepu Str. 1, 53101, Kaunas Reg., Lithuania
| | | |
Collapse
|
3
|
Weithmann G, Paligi SS, Schuldt B, Leuschner C. Branch xylem vascular adjustments in European beech in response to decreasing water availability across a precipitation gradient. TREE PHYSIOLOGY 2022; 42:2224-2238. [PMID: 35861677 DOI: 10.1093/treephys/tpac080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/02/2022] [Indexed: 06/15/2023]
Abstract
Crucial for the climate adaptation of trees is a xylem anatomical structure capable of adjusting to changing water regimes. Although species comparisons across climate zones have demonstrated anatomical change in response to altered water availability and tree height, less is known about the adaptability of tree vascular systems to increasing water deficits at the intraspecific level. Information on the between-population and within-population variability of xylem traits helps assessing a species' ability to cope with climate change. We investigated the variability of wood anatomical and related hydraulic traits in terminal branches of European beech (Fagus sylvatica L.) trees across a precipitation gradient (520-890 mm year-1) and examined the influence of climatic water balance (CWB), soil water capacity (AWC), neighborhood competition (CI), tree height and branch age on these traits. Furthermore, the relationship between xylem anatomical traits and embolism resistance (P50) was tested. Within-population trait variation was larger than between-population variation. Vessel diameter, lumen-to-sapwood area ratio and potential conductivity of terminal branches decreased with decreasing CWB, but these traits were not affected by AWC, whereas vessel density increased with an AWC decrease. In contrast, none of the studied anatomical traits were influenced by variation in tree height (21-34 m) or CI. Branch age was highly variable (2-22 years) despite equal diameter and position in the flow path, suggesting different growth trajectories in the past. Vessel diameter decreased, and vessel density increased, with increasing branch age, reflecting negative annual radial growth trends. Although vessel diameter was not related to P50, vessel grouping index and lumen-to-sapwood area ratio showed a weak, though highly significant, positive relationship to P50. We conclude that the xylem anatomy of terminal tree-top branches in European beech is modified in response to increasing climatic aridity and/or decreasing soil water availability, independent of a tree height effect.
Collapse
Affiliation(s)
- Greta Weithmann
- Plant Ecology, Albrecht von Haller Institute for Plant Sciences, University of Goettingen, Untere Karspüle 2, 37073 Goettingen, Germany
| | - Sharath Shyamappa Paligi
- Plant Ecology, Albrecht von Haller Institute for Plant Sciences, University of Goettingen, Untere Karspüle 2, 37073 Goettingen, Germany
| | - Bernhard Schuldt
- Plant Ecology, Albrecht von Haller Institute for Plant Sciences, University of Goettingen, Untere Karspüle 2, 37073 Goettingen, Germany
- Ecophysiology and Vegetation Ecology, Julius-von-Sachs-Institute of Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz, 97082 Würzburg, Germany
| | - Christoph Leuschner
- Plant Ecology, Albrecht von Haller Institute for Plant Sciences, University of Goettingen, Untere Karspüle 2, 37073 Goettingen, Germany
- Centre for Biodiversity and Sustainable Land Use (CBL), University of Goettingen, 37075 Goettingen, Germany
| |
Collapse
|
4
|
Mattera MG, Pastorino MJ, Lantschner MV, Marchelli P, Soliani C. Genetic diversity and population structure in Nothofagus pumilio, a foundation species of Patagonian forests: defining priority conservation areas and management. Sci Rep 2020; 10:19231. [PMID: 33159157 PMCID: PMC7648826 DOI: 10.1038/s41598-020-76096-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 10/23/2020] [Indexed: 11/08/2022] Open
Abstract
Patagonian forests are the southernmost temperate forests in the world, and Nothofagus pumilio is one of their most ecologically important tree species (i.e., a foundation species). It presents great adaptability and a wide distribution range, making it a suitable model for predicting the performance of trees facing global climate change. N. pumilio forests are increasingly threatened by extreme climatic events and anthropogenic activities. This study aims to identify priority conservation areas and Genetic Zones (GZs) for N. pumilio, promoting the implementation of specific practices to ensure its management and long-term preservation. Thirty-five populations (965 trees) sampled across its distribution (more than 2200 km latitudinally) were genotyped with SSRs, and geographical patterns of genetic variation were identified using Bayesian approaches. The phylogeographic patterns of the species and geomorphological history of the region were also considered. Six priority conservation areas were identified, which hold high allelic richness and/or exclusive allelic variants. Eighteen GZs were delineated based on the genetic structure of this species, and maps showing their distributional range were drawn up. Overall, this study defines management units based on genetic data for N. pumilio for the first time, which will facilitate the establishment of sustainable practices and highlight priorities for investment of conservation funding.
Collapse
Affiliation(s)
- M Gabriela Mattera
- Grupo de Genética Ecológica y Mejoramiento Forestal del Instituto de Investigaciones Forestales y Agropecuarias Bariloche (IFAB) INTA EEA Bariloche -CONICET, Modesta Victoria 4450, CP: 8400,, S. C. Bariloche, Río Negro, Argentina.
| | - Mario J Pastorino
- Grupo de Genética Ecológica y Mejoramiento Forestal del Instituto de Investigaciones Forestales y Agropecuarias Bariloche (IFAB) INTA EEA Bariloche -CONICET, Modesta Victoria 4450, CP: 8400,, S. C. Bariloche, Río Negro, Argentina
| | - M Victoria Lantschner
- Grupo de Ecología de Poblaciones de Insectos del Instituto de Investigaciones Forestales y Agropecuarias Bariloche (IFAB) INTA EEA Bariloche -CONICET, Modesta Victoria 4450, CP: 8400, S. C. Bariloche, Río Negro, Argentina
| | - Paula Marchelli
- Grupo de Genética Ecológica y Mejoramiento Forestal del Instituto de Investigaciones Forestales y Agropecuarias Bariloche (IFAB) INTA EEA Bariloche -CONICET, Modesta Victoria 4450, CP: 8400,, S. C. Bariloche, Río Negro, Argentina
| | - Carolina Soliani
- Grupo de Genética Ecológica y Mejoramiento Forestal del Instituto de Investigaciones Forestales y Agropecuarias Bariloche (IFAB) INTA EEA Bariloche -CONICET, Modesta Victoria 4450, CP: 8400,, S. C. Bariloche, Río Negro, Argentina
| |
Collapse
|
5
|
Borges D, Mariano-Neto E, Caribé D, Corrêa R, Gaiotto F. Changes in fine-scale spatial genetic structure related to protection status in Atlantic Rain Forest fragment. J Nat Conserv 2020. [DOI: 10.1016/j.jnc.2019.125784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
6
|
Pruvost O, Boyer K, Ravigné V, Richard D, Vernière C. Deciphering how plant pathogenic bacteria disperse and meet: Molecular epidemiology of Xanthomonas citri pv. citri at microgeographic scales in a tropical area of Asiatic citrus canker endemicity. Evol Appl 2019; 12:1523-1538. [PMID: 31462912 PMCID: PMC6708428 DOI: 10.1111/eva.12788] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/25/2019] [Accepted: 02/24/2019] [Indexed: 12/15/2022] Open
Abstract
Although some plant pathogenic bacteria represent a significant threat to agriculture, the determinants of their ecological success and evolutionary potential are still poorly understood. Refining our understanding of bacterial strain circulation at small spatial scales and the biological significance and evolutionary consequences of co-infections are key questions. The study of bacterial population biology can be challenging, because it requires high-resolution markers that can be genotyped with a high throughput. Here, we overcame this difficulty for Xanthomonas citri pv. citri, a genetically monomorphic bacterium causing Asiatic citrus canker (ACC). Using a genotyping method that did not require cultivating the bacterium or purifying DNA, we deciphered the pathogen's spatial genetic structure at several microgeographic scales, down to single lesion, in a situation of ACC endemicity. In a grove where copper was recurrently applied for ACC management, copper-susceptible and copper-resistant X. citri pv. citri coexisted and the bacterial population structured as three genetic clusters, suggesting a polyclonal contamination. The range of spatial dependency, estimated for the two largest clusters, was four times greater for the cluster predominantly composed of copper-resistant bacteria. Consistently, the evenness value calculated for this cluster was indicative of increased transmission. Linkage disequilibrium was high even at a tree scale, probably due to a combination of clonality and admixture. Approximately 1% of samples exhibited within-lesion multilocus polymorphism, explained at least in part by polyclonal infections. Canker lesions, which are of major biological significance as an inoculum source, may also represent a preferred niche for horizontal gene transfer. This study points out the potential of genotyping data for estimating the range of spatial dependency of plant bacterial pathogens, an important parameter for guiding disease management strategies.
Collapse
Affiliation(s)
| | | | | | - Damien Richard
- CIRADUMR PVBMTSaint Pierre, La RéunionFrance
- ANSESSaint Pierre, La RéunionFrance
- Université de la RéunionUMR PVBMTSaint Denis, La RéunionFrance
| | - Christian Vernière
- CIRADUMR PVBMTSaint Pierre, La RéunionFrance
- CIRADUMR BGPIMontpellierFrance
| |
Collapse
|
7
|
Investigating the genetic diversity and differentiation patterns in the Penstemon scariosus species complex under different sample sizes using AFLPs and SSRs. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1103-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
8
|
Rezaie N, D'Andrea E, Bräuning A, Matteucci G, Bombi P, Lauteri M. Do atmospheric CO2 concentration increase, climate and forest management affect iWUE of common beech? Evidences from carbon isotope analyses in tree rings. TREE PHYSIOLOGY 2018; 38:1110-1126. [PMID: 29579292 DOI: 10.1093/treephys/tpy025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 02/13/2018] [Indexed: 06/08/2023]
Abstract
Beech is one of the most important forest tree species in Europe, hence possible adverse factors affecting its physiology and productivity can have strong ecological and economic impacts. In this context, four beech forests along a latitudinal gradient from southern Apennines to middle European lowlands were selected for chronological determinations of carbon isotope composition (δ13C) in tree-ring cellulose. The main objectives of this study were to assess (i) the effect of climate on the carbon signature of tree-ring cellulose (δ13C); (ii) the physiological response to recent CO2 concentration increment and to climatic variation; and (iii) the relationship between intrinsic water-use efficiency (iWUE, here the average long-term ratio of net photosynthesis to stomatal conductance) and growth of trees in different sites since 1950. Our results demonstrated that site climatic conditions peculiarly affect δ13C. In northern sites, a climatic control of summer precipitation and temperature on stomatal conductance was demonstrated by their opposite correlations with δ13C, negative and positive, respectively. Furthermore, an 'earliness effect' was suggested by a significant relationship between spring temperature and δ13C in the coldest sites and by a positive one between winter temperature and δ13C in the warmest ones. In all the study sites, during the maturity phase, a positive correlation between the increment of CO2 and iWUE was observed, due to an active response of trees to CO2 increment. This increment of CO2 was the main driver of the long term increasing trend of iWUE, resulting by an active response of trees to CO2 fertilization. Moreover, precipitation mostly influences positively and negatively the inter-annual variations of iWUE of the southernmost and northernmost sites, respectively. Overall, we observed a mean increment of 40% of iWUE. Moreover, the sensitivity of iWUE to the increase of CO2 was different between the northernmost and southernmost sites. Increasing iWUE was correlated to growth in the two sites during the release phase and we hypothesize a positive effect of silvicultural treatments.
Collapse
Affiliation(s)
- Negar Rezaie
- Istituto di Biologia Agroambientale e Forestale (IBAF), Consiglio Nazionale delle Ricerche (CNR), Via Salaria km 29,300, Monterotondo Scalo (RM), Italy
| | - Ettore D'Andrea
- Istituto di Biologia Agroambientale e Forestale (IBAF), Consiglio Nazionale delle Ricerche (CNR), Via Salaria km 29,300, Monterotondo Scalo (RM), Italy
| | - Achim Bräuning
- Institute of Geography, Friedrich Alexander University Erlangen Nürnberg, Erlangen, Germany
| | - Giorgio Matteucci
- Istituto per i Sistemi Agricoli e Forestali del Mediterraneo (ISAFoM), Consiglio Nazionale delle Ricerche (CNR), Via Patacca, 85 Ercolano (NA) Italy
| | - Pierluigi Bombi
- Istituto di Biologia Agroambientale e Forestale (IBAF), Consiglio Nazionale delle Ricerche (CNR), Via Salaria km 29,300, Monterotondo Scalo (RM), Italy
| | - Marco Lauteri
- Istituto di Biologia Agroambientale e Forestale (IBAF), Consiglio Nazionale delle Ricerche (CNR), Viale G. Marconi 2, Porano (TR), Italy
| |
Collapse
|
9
|
Lowe AJ, Breed MF, Caron H, Colpaert N, Dick C, Finegan B, Gardner M, Gheysen G, Gribel R, Harris JBC, Kremer A, Lemes MR, Margis R, Navarro CM, Salgueiro F, Villalobos-Barrantes HM, Cavers S. Standardized genetic diversity-life history correlates for improved genetic resource management of Neotropical trees. DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12716] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Andrew J. Lowe
- Environment Institute and School of Biological Sciences; University of Adelaide; Adelaide SA Australia
| | - Martin F. Breed
- Environment Institute and School of Biological Sciences; University of Adelaide; Adelaide SA Australia
| | | | - Nathalie Colpaert
- Faculty of Bioscience Engineering; Department of Molecular Biotechnology; Ghent University; Ghent Belgium
| | - Christopher Dick
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor MI USA
- Smithsonian Tropical Research Institute; Balboa Panama
| | - Bryan Finegan
- Tropical Agricultural Research and Higher Education Center; Turrialba Cartago Costa Rica
| | - Mike Gardner
- Environment Institute and School of Biological Sciences; University of Adelaide; Adelaide SA Australia
- Biological Sciences; Flinders University; Adelaide SA Australia
| | - Godelieve Gheysen
- Faculty of Bioscience Engineering; Department of Molecular Biotechnology; Ghent University; Ghent Belgium
| | - Rogério Gribel
- Coordenação de Biodiversidade; Instituto Nacional de Pesquisas da Amazônia - INPA; Manaus Brazil
| | - J. Berton C. Harris
- Environment Institute and School of Biological Sciences; University of Adelaide; Adelaide SA Australia
- Rainforest Trust; Warrenton VA USA
| | | | - Maristerra R. Lemes
- Laboratório de Genética e Biologia Reprodutiva de Plantas (LabGen); Instituto Nacional de Pesquisas da Amazônia; Manaus Amazonas Brazil
| | - Rogerio Margis
- Centro de Biotecnologia; Universidade Federal do Rio Grande do Sul (UFRGS); Porto Alegre Brazil
| | - Carlos M. Navarro
- Tropical Agricultural Research and Higher Education Center; Turrialba Cartago Costa Rica
| | - Fabiano Salgueiro
- Programa de Pós-graduação em Ciências Biológicas (Biodiversidade Neotropical); Universidade Federal do Estado do Rio de Janeiro (UNIRIO); Rio de Janeiro Brazil
| | - Heidy M. Villalobos-Barrantes
- Centro de Investigación en Biología Celular y Molecular and Escuela de Química; Universidad de Costa Rica; San José Costa Rica
| | - Stephen Cavers
- Centre for Ecology and Hydrology; CEH Edinburgh; Penicuik UK
| |
Collapse
|
10
|
Herrera CM, Medrano M, Bazaga P. Comparative epigenetic and genetic spatial structure of the perennial herb Helleborus foetidus: Isolation by environment, isolation by distance, and functional trait divergence. AMERICAN JOURNAL OF BOTANY 2017; 104:1195-1204. [PMID: 28814406 DOI: 10.3732/ajb.1700162] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/27/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY Epigenetic variation can play a role in local adaptation; thus, there should be associations among epigenetic variation, environmental variation, and functional trait variation across populations. This study examines these relationships in the perennial herb Helleborus foetidus (Ranunculaceae). METHODS Plants from 10 subpopulations were characterized genetically (AFLP, SSR markers), epigenetically (MSAP markers), and phenotypically (20 functional traits). Habitats were characterized using six environmental variables. Isolation-by-distance (IBD) and isolation-by-environment (IBE) patterns of genetic and epigenetic divergence were assessed, as was the comparative explanatory value of geographical and environmental distance as predictors of epigenetic, genetic, and functional differentiation. KEY RESULTS Subpopulations were differentiated genetically, epigenetically, and phenotypically. Genetic differentiation was best explained by geographical distance, while epigenetic differentiation was best explained by environmental distance. Divergence in functional traits was correlated with environmental and epigenetic distances, but not with geographical and genetic distances. CONCLUSIONS Results are compatible with the hypothesis that epigenetic IBE and functional divergence reflected responses to environmental variation. Spatial analyses simultaneously considering epigenetic, genetic, phenotypic and environmental information provide a useful tool to evaluate the role of environmental features as drivers of natural epigenetic variation between populations.
Collapse
Affiliation(s)
- Carlos M Herrera
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Americo Vespucio 26, 41092 Sevilla, Spain
| | - Mónica Medrano
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Americo Vespucio 26, 41092 Sevilla, Spain
| | - Pilar Bazaga
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Americo Vespucio 26, 41092 Sevilla, Spain
| |
Collapse
|
11
|
Araki KS, Kubo T, Kudoh H. Genet-specific DNA methylation probabilities detected in a spatial epigenetic analysis of a clonal plant population. PLoS One 2017; 12:e0178145. [PMID: 28542457 PMCID: PMC5439711 DOI: 10.1371/journal.pone.0178145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 05/08/2017] [Indexed: 12/21/2022] Open
Abstract
In sessile organisms such as plants, spatial genetic structures of populations show long-lasting patterns. These structures have been analyzed across diverse taxa to understand the processes that determine the genetic makeup of organismal populations. For many sessile organisms that mainly propagate via clonal spread, epigenetic status can vary between clonal individuals in the absence of genetic changes. However, fewer previous studies have explored the epigenetic properties in comparison to the genetic properties of natural plant populations. Here, we report the simultaneous evaluation of the spatial structure of genetic and epigenetic variation in a natural population of the clonal plant Cardamine leucantha. We applied a hierarchical Bayesian model to evaluate the effects of membership of a genet (a group of individuals clonally derived from a single seed) and vegetation cover on the epigenetic variation between ramets (clonal plants that are physiologically independent individuals). We sampled 332 ramets in a 20 m × 20 m study plot that contained 137 genets (identified using eight SSR markers). We detected epigenetic variation in DNA methylation at 24 methylation-sensitive amplified fragment length polymorphism (MS-AFLP) loci. There were significant genet effects at all 24 MS-AFLP loci in the distribution of subepiloci. Vegetation cover had no statistically significant effect on variation in the majority of MS-AFLP loci. The spatial aggregation of epigenetic variation is therefore largely explained by the aggregation of ramets that belong to the same genets. By applying hierarchical Bayesian analyses, we successfully identified a number of genet-specific changes in epigenetic status within a natural plant population in a complex context, where genotypes and environmental factors are unevenly distributed. This finding suggests that it requires further studies on the spatial epigenetic structure of natural populations of diverse organisms, particularly for sessile clonal species.
Collapse
Affiliation(s)
- Kiwako S. Araki
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
- Department of Biotechnology, Faculty of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Takuya Kubo
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| |
Collapse
|
12
|
Bodare S, Ravikanth G, Ismail SA, Patel MK, Spanu I, Vasudeva R, Shaanker RU, Vendramin GG, Lascoux M, Tsuda Y. Fine- and local- scale genetic structure of Dysoxylum malabaricum, a late-successional canopy tree species in disturbed forest patches in the Western Ghats, India. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0877-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
13
|
Herrera CM, Medrano M, Bazaga P. Comparative spatial genetics and epigenetics of plant populations: heuristic value and a proof of concept. Mol Ecol 2016; 25:1653-64. [PMID: 26850938 DOI: 10.1111/mec.13576] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 01/29/2016] [Accepted: 02/01/2016] [Indexed: 11/26/2022]
Abstract
Despite the recent upsurge of interest on natural epigenetic variation of nonmodel organisms, factors conditioning the spatial structure of epigenetic diversity in wild plant populations remain virtually unexplored. We propose that information on processes shaping natural epigenetic variation can be gained using the spatial structure of genetic diversity as null model. Departures of epigenetic isolation-by-distance (IBD) patterns from genetic IBD patterns for the same sample, particularly differences in slope of similarity-distance regressions, will reflect the action of factors that operate specifically on epigenetic variation, including imperfect transgenerational inheritance and responsiveness to environmental factors of epigenetic marks. As a proof of concept, we provide a comparative analysis of spatial genetic and epigenetic structure of 200 mapped individuals of the perennial herb Helleborus foetidus. Plants were fingerprinted using nuclear microsatellites, amplified fragment length polymorphisms (AFLP) and methylation-sensitive AFLP markers. Expectations from individual-level IBD patterns were tested by means of kinship-distance regressions. Both genetic and epigenetic similarity between H. foetidus individuals conformed to theoretical expectations under individual-level IBD models. Irrespective of marker type, there were significant negative linear relationships between the kinship coefficient for plant pairs and their spatial separation. Regression slopes were significantly steeper for epigenetic markers. Epigenetic similarity between individuals was much greater than genetic similarity at shortest distances, such epigenetic 'kinship excess' tending to decrease as plant separation increased. Results suggest that moderate-to-high heritability and responsiveness to local environments are major drivers of epigenetic spatial structure in H. foetidus, and illustrate the heuristic value of comparing genetic and epigenetic spatial structure for formulating and testing hypotheses on forces shaping epigenetic diversity in wild plant populations.
Collapse
Affiliation(s)
- Carlos M Herrera
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Américo Vespucio s/n, Isla de La Cartuja, 41092, Sevilla, Spain
| | - Mónica Medrano
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Américo Vespucio s/n, Isla de La Cartuja, 41092, Sevilla, Spain
| | - Pilar Bazaga
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Américo Vespucio s/n, Isla de La Cartuja, 41092, Sevilla, Spain
| |
Collapse
|
14
|
Brousseau L, Foll M, Scotti-Saintagne C, Scotti I. Neutral and adaptive drivers of microgeographic genetic divergence within continuous populations: the case of the neotropical tree Eperua falcata (Aubl.). PLoS One 2015; 10:e0121394. [PMID: 25807272 PMCID: PMC4373894 DOI: 10.1371/journal.pone.0121394] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 01/31/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In wild plant populations, genetic divergence within continuous stands is common, sometimes at very short geographical scales. While restrictions to gene flow combined with local inbreeding and genetic drift may cause neutral differentiation among subpopulations, microgeographical variations in environmental conditions can drive adaptive divergence through natural selection at some targeted loci. Such phenomena have recurrently been observed in plant populations occurring across sharp environmental boundaries, but the interplay between selective processes and neutral genetic divergence has seldom been studied. METHODS We assessed the extent of within-stand neutral and environmentally-driven divergence in the Neotropical tree Eperua falcate Aubl. (Fabaceae) through a genome-scan approach. Populations of this species grow in dense stands that cross the boundaries between starkly contrasting habitats. Within-stand phenotypic and candidate-gene divergence have already been proven, making this species a suitable model for the study of genome-wide microgeographic divergence. Thirty trees from each of two habitats (seasonally flooded swamps and well-drained plateaus) in two separate populations were genotyped using thousands of AFLPs markers. To avoid genotyping errors and increase marker reliability, each sample was genotyped twice and submitted to a rigorous procedure for data cleaning, which resulted in 1196 reliable and reproducible markers. RESULTS Despite the short spatial distances, we detected within-populations genetic divergence, probably caused by neutral processes, such as restrictions in gene flow. Moreover, habitat-structured subpopulations belonging to otherwise continuous stands also diverge in relation to environmental variability and habitat patchiness: we detected convincing evidence of divergent selection at the genome-wide level and for a fraction of the analyzed loci (comprised between 0.25% and 1.6%). Simulations showed that the levels of differentiation for these outliers are compatible with scenarios of strong divergent selection.
Collapse
Affiliation(s)
- Louise Brousseau
- INRA, UMR745 EcoFoG Ecologie des forêts de Guyane, Campus Agronomique BP316, 97379 Kourou Cedex, France
- INRA—Université de Lorraine, UMR1137 EEF Ecologie et Ecophysiologie Forestière, allée de l’Arboretum, 54280 Champenoux, France
- INRA, UR629 URFM Ecologie des Forêts Méditerranéennes, Domaine Saint Paul, Site Agroparc CS 40509, 84914 Avignon Cedex 9, France
| | - Matthieu Foll
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 15, CH-1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Caroline Scotti-Saintagne
- INRA, UMR745 EcoFoG Ecologie des forêts de Guyane, Campus Agronomique BP316, 97379 Kourou Cedex, France
- INRA, UR629 URFM Ecologie des Forêts Méditerranéennes, Domaine Saint Paul, Site Agroparc CS 40509, 84914 Avignon Cedex 9, France
| | - Ivan Scotti
- INRA, UMR745 EcoFoG Ecologie des forêts de Guyane, Campus Agronomique BP316, 97379 Kourou Cedex, France
- INRA, UR629 URFM Ecologie des Forêts Méditerranéennes, Domaine Saint Paul, Site Agroparc CS 40509, 84914 Avignon Cedex 9, France
| |
Collapse
|
15
|
Nistelberger HM, Coates DJ, Llorens TM, Yates CJ, Byrne M. A cryptic genetic boundary in remnant populations of a long-lived, bird-pollinated shrubBanksia sphaerocarpavar.caesia(Proteaceae). Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12521] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Heidi M. Nistelberger
- Science and Conservation Division; Department of Parks and Wildlife; Bentley Delivery Centre; Locked Bag 104 Perth WA 6983 Australia
| | - David J. Coates
- Science and Conservation Division; Department of Parks and Wildlife; Bentley Delivery Centre; Locked Bag 104 Perth WA 6983 Australia
| | - Tanya M. Llorens
- Science and Conservation Division; Department of Parks and Wildlife; Bentley Delivery Centre; Locked Bag 104 Perth WA 6983 Australia
| | - Colin J. Yates
- Science and Conservation Division; Department of Parks and Wildlife; Bentley Delivery Centre; Locked Bag 104 Perth WA 6983 Australia
| | - Margaret Byrne
- Science and Conservation Division; Department of Parks and Wildlife; Bentley Delivery Centre; Locked Bag 104 Perth WA 6983 Australia
| |
Collapse
|
16
|
Broadhurst L. Pollen dispersal in fragmented populations of the dioecious wind-pollinated tree, Allocasuarina verticillata (drooping sheoak, drooping she-oak; Allocasuarinaceae). PLoS One 2015; 10:e0119498. [PMID: 25742183 PMCID: PMC4350918 DOI: 10.1371/journal.pone.0119498] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 01/21/2015] [Indexed: 11/28/2022] Open
Abstract
Vegetation clearing, land modification and agricultural intensification have impacted on many ecological communities around the world. Understanding how species respond to fragmentation and the scales over which functionality is retained, can be critical for managing biodiversity in agricultural landscapes. Allocasuarina verticillata (drooping sheoak, drooping she-oak) is a dioecious, wind-pollinated and -dispersed species with key conservation values across southeastern Australia. But vegetation clearing associated with agricultural expansion has reduced the abundance and spatial distribution of this species in many regions. Spatial genetic structure, relatedness among trees, pollen dispersal and mating patterns were examined in fragmented A. verticillata populations selected to represent the types of remnants that now characterise this species. Short scale spatial genetic structure (5-25 m) and relatedness among trees were observed in most populations. Unexpectedly, the two male trees closest to each female did not have a reproductive advantage accounting for only 4-15% of the seed produced in larger populations. Biparental inbreeding was also generally low (<4%) with limited evidence of seed crop domination by some male trees. More male trees contributed to seed crops in linear remnants (mean 17) compared to those from patch remnants (mean 11.3) which may reflect differences in pollen dispersal within the two remnant types. On average, pollen travels ~100 m irrespective of remnant type but was also detected to have dispersed as far as 1 km in open landscapes. Low biparental inbreeding, limited reproductive assurance for near-neighbour and probably related males and variability in the distances over which females sample pollen pools suggest that some mechanism to prevent matings between relatives exists in this species.
Collapse
Affiliation(s)
- Linda Broadhurst
- Centre for Australian National Biodiversity Research, National Research Collections, CSIRO, Canberra, Australia
| |
Collapse
|
17
|
Carsjens C, Nguyen Ngoc Q, Guzy J, Knutzen F, Meier IC, Müller M, Finkeldey R, Leuschner C, Polle A. Intra-specific variations in expression of stress-related genes in beech progenies are stronger than drought-induced responses. TREE PHYSIOLOGY 2014; 34:1348-61. [PMID: 25430883 DOI: 10.1093/treephys/tpu093] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Rapidly decreasing water availability as a consequence of climate change is likely to endanger the range of long-lived tree species. A pressing question is, therefore, whether adaptation to drought exists in important temperate tree species like European beech (Fagus sylvatica L.), a wide-spread, dominant forest tree in Central Europe. Here, five beech stands were selected along a precipitation gradient from moist to dry conditions. Neutral genetic markers revealed strong variation within and little differentiation between the populations. Natural regeneration from these stands was transferred to a common garden and used to investigate the expression of genes for abscisic acid (ABA)-related drought signaling [9-cis-epoxy-dioxygenase (NCED), protein phosphatase 2C (PP2C), early responsive to dehydration (ERD)] and stress protection [ascorbate peroxidase (APX), superoxide dismutase (SOD), aldehyde dehydrogenase (ALDH), glutamine amidotransferase (GAT)] that are involved in drought acclimation. We hypothesized that progenies from dry sites exhibit constitutively higher expression levels of ABA- and stress-related genes and are less drought responsive than progenies from moist sites. Transcript levels and stress responses (leaf area loss, membrane integrity) of well-irrigated and drought-stressed plants were measured during the early, mid- and late growing season. Principal component (PC) analysis ordered the beech progenies according to the mean annual precipitation at tree origin by the transcript levels of SOD, ALDH, GAT and ERD as major loadings along PC1. PC2 separated moist and drought treatments with PP2C levels as important loading. These results suggest that phosphatase-mediated signaling is flexibly acclimated to the current requirements, whereas stress compensatory measures exhibited genotypic variation, apparently underlying climate selection. In contrast to expectation, the drought responses were less pronounced than the progeny-related differences and the transcript levels were constitutively lower in beeches from dry than from moist sites. These results imply that beeches from dry origins may have evolved mechanisms to avoid oxidative stress.
Collapse
Affiliation(s)
- Caroline Carsjens
- Forstbotanik und Baumphysiologie, Büsgen-Institute, Georg-August Universität Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - Quynh Nguyen Ngoc
- Forstbotanik und Baumphysiologie, Büsgen-Institute, Georg-August Universität Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - Jonas Guzy
- Forstbotanik und Baumphysiologie, Büsgen-Institute, Georg-August Universität Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - Florian Knutzen
- Plant Ecology, Albrecht von Haller Institute for Plant Sciences, Georg-August Universität Göttingen, Untere Karspüle 2, 37073 Göttingen, Germany
| | - Ina Christin Meier
- Plant Ecology, Albrecht von Haller Institute for Plant Sciences, Georg-August Universität Göttingen, Untere Karspüle 2, 37073 Göttingen, Germany
| | - Markus Müller
- Forstgenetik und Forstpflanzenzüchtung, Büsgen-Institute, Georg-August Universität Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - Reiner Finkeldey
- Forstgenetik und Forstpflanzenzüchtung, Büsgen-Institute, Georg-August Universität Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - Christoph Leuschner
- Plant Ecology, Albrecht von Haller Institute for Plant Sciences, Georg-August Universität Göttingen, Untere Karspüle 2, 37073 Göttingen, Germany
| | - Andrea Polle
- Forstbotanik und Baumphysiologie, Büsgen-Institute, Georg-August Universität Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
| |
Collapse
|
18
|
Within-population genetic structure in beech (Fagus sylvatica L.) stands characterized by different disturbance histories: does forest management simplify population substructure? PLoS One 2013; 8:e73391. [PMID: 24039930 PMCID: PMC3764177 DOI: 10.1371/journal.pone.0073391] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 07/17/2013] [Indexed: 11/24/2022] Open
Abstract
The fine-scale assessment of both spatially and non-spatially distributed genetic variation is crucial to preserve forest genetic resources through appropriate forest management. Cryptic within-population genetic structure may be more common than previously thought in forest tree populations, which has strong implications for the potential of forests to adapt to environmental change. The present study was aimed at comparing within-population genetic structure in European beech (Fagus sylvatica L.) plots experiencing different disturbance levels. Five plot pairs made up by disturbed and undisturbed plots having the same biogeographic history were sampled throughout Europe. Overall, 1298 individuals were analyzed using four highly polymorphic nuclear microsatellite markers (SSRs). Bayesian clustering within plots identified 3 to 11 genetic clusters (within-plot θST ranged from 0.025 to 0.124). The proportion of within-population genetic variation due to genetic substructuring (FCluPlot = 0.067) was higher than the differentiation among the 10 plots (FPlotTot = 0.045). Focusing on the comparison between managed and unmanaged plots, disturbance mostly explains differences in the complexity of within-population genetic structure, determining a reduction of the number of genetic clusters present in a standardized area. Our results show that: i) genetic substructuring needs to be investigated when studying the within-population genetic structure in forest tree populations, and ii) indices describing subtle characteristics of the within-population genetic structure are good candidates for providing early signals of the consequences of forest management, and of disturbance events in general.
Collapse
|
19
|
Mathiasen P, Premoli AC. Fine-scale genetic structure of Nothofagus pumilio (lenga) at contrasting elevations of the altitudinal gradient. Genetica 2013; 141:95-105. [PMID: 23456320 DOI: 10.1007/s10709-013-9709-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 02/21/2013] [Indexed: 10/27/2022]
Abstract
Montane forests provide the natural framework to test for various ecological settings at distinct elevations as they may affect population demography, which in turn will affect the spatial genetic structure (SGS). We analyzed the fine-scale SGS of Nothofagus pumilio, which dominates mountain areas of Patagonia, in three pairs of sites at contrasting elevations (low- vs. high-elevation). Within a total area of 1 ha fresh leaf tissue from 90 individuals was collected at each of the six studied stands following a spatially explicit sampling design. Population genetic diversity parameters were analyzed for all sampled individuals using five polymorphic isozyme loci, and a subset of 50 individuals per stand were also screened for five microsatellite loci. The SGS was assessed on 50 individuals/stand, using the combined datasets of isozymes and microsatellites. Most low-elevation stands consisted of older individuals with complex age structures and genetically diverse plots. In contrast, high-elevation stands and one post-fire low-elevation population yielded even-aged structures with evidence of growth suppression, and were genetically homogeneous. All stands yielded significant SGS. Similarly to mature stands of the non-sprouter congener Nothofagus dombeyi, multi-age low-altitude N. pumilio yielded significant SGS weakened by competing species of the understory and the formation of seedling banks. Alike the sprouter Nothofagus antarctica, high-altitude stands produced significant SGS as a consequence of occasional seedling establishment reinforced by vegetative spread.
Collapse
Affiliation(s)
- Paula Mathiasen
- Laboratorio Ecotono, Instituto de Investigaciones en Biodiversidad y Medioambiente, CONICET, Universidad Nacional del Comahue, Quintral 1250, Bariloche, Argentina
| | | |
Collapse
|
20
|
Millerón M, López de Heredia U, Lorenzo Z, Alonso J, Dounavi A, Gil L, Nanos N. Assessment of spatial discordance of primary and effective seed dispersal of European beech (Fagus sylvatica L.) by ecological and genetic methods. Mol Ecol 2013; 22:1531-45. [PMID: 23379310 DOI: 10.1111/mec.12200] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 11/29/2012] [Accepted: 11/29/2012] [Indexed: 11/28/2022]
Abstract
Spatial discordance between primary and effective dispersal in plant populations indicates that postdispersal processes erase the seed rain signal in recruitment patterns. Five different models were used to test the spatial concordance of the primary and effective dispersal patterns in a European beech (Fagus sylvatica) population from central Spain. An ecological method was based on classical inverse modelling (SSS), using the number of seed/seedlings as input data. Genetic models were based on direct kernel fitting of mother-to-offspring distances estimated by a parentage analysis or were spatially explicit models based on the genotype frequencies of offspring (competing sources model and Moran-Clark's Model). A fully integrated mixed model was based on inverse modelling, but used the number of genotypes as input data (gene shadow model). The potential sources of error and limitations of each seed dispersal estimation method are discussed. The mean dispersal distances for seeds and saplings estimated with these five methods were higher than those obtained by previous estimations for European beech forests. All the methods show strong discordance between primary and effective dispersal kernel parameters, and for dispersal directionality. While seed rain was released mostly under the canopy, saplings were established far from mother trees. This discordant pattern may be the result of the action of secondary dispersal by animals or density-dependent effects; that is, the Janzen-Connell effect.
Collapse
Affiliation(s)
- M Millerón
- Forest Genetics and Physiology Research Group, E.T.S. Forestry Engineering Technical University of Madrid (UPM), Ciudad Universitaria s/n, 28040, Madrid, Spain
| | | | | | | | | | | | | |
Collapse
|
21
|
Lopez L, Barreiro R. Genetic guidelines for the conservation of the endangered polyploid Centaurea borjae (Asteraceae). JOURNAL OF PLANT RESEARCH 2013; 126:81-93. [PMID: 22678690 DOI: 10.1007/s10265-012-0497-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 04/30/2012] [Indexed: 06/01/2023]
Abstract
Appropriate management of species of conservation concern requires designing strategies that should include genetic information as small population size and restricted geographic range can reduce genetic variation. We used AFLPs to investigate genetic variation within and among populations of the endangered narrow endemic Centaurea borjae, and found no evidence for genetic impoverishment despite its <40 km range and potential for vegetative propagation. Genetic variation was comparable to other plants with similar life history (88 % occurring within populations) and potential clone mates were less frequent than expected. Nonetheless, populations separated by few hundred meters showed signs of significant genetic differentiation suggesting low gene flow between them. Our results suggested that the three geographically closer populations located at the center of the range might be treated as a single management unit, while the remaining ones could be considered independent units. We found evidence of fine-scale spatial genetic structure up to 80 m indicating that the collection of germplasm for ex-situ conservation should focus on individuals separated >80 m to maximize genetic variation.
Collapse
Affiliation(s)
- Lua Lopez
- Área de Ecología, Facultad de Ciencias, Universidad da Coruña, Campus A Zapateira s/n, 15071 A Coruña, Spain.
| | | |
Collapse
|
22
|
Wang ZF, Lian JY, Huang GM, Ye WH, Cao HL, Wang ZM. Genetic groups in the common plant speciesCastanopsischinensis and their associations with topographic habitats. OIKOS 2012. [DOI: 10.1111/j.1600-0706.2012.20483.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
23
|
Jump AS, Rico L, Coll M, Peñuelas J. Wide variation in spatial genetic structure between natural populations of the European beech (Fagus sylvatica) and its implications for SGS comparability. Heredity (Edinb) 2012; 108:633-9. [PMID: 22354112 DOI: 10.1038/hdy.2012.1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Identification and quantification of spatial genetic structure (SGS) within populations remains a central element of understanding population structure at the local scale. Understanding such structure can inform on aspects of the species' biology, such as establishment patterns and gene dispersal distance, in addition to sampling design for genetic resource management and conservation. However, recent work has identified that variation in factors such as sampling methodology, population characteristics and marker system can all lead to significant variation in SGS estimates. Consequently, the extent to which estimates of SGS can be relied on to inform on the biology of a species or differentiate between experimental treatments is open to doubt. Following on from a recent report of unusually extensive SGS when assessed using amplified fragment length polymorphisms in the tree Fagus sylvatica, we explored whether this marker system led to similarly high estimates of SGS extent in other apparently similar populations of this species. In the three populations assessed, SGS extent was even stronger than this previously reported maximum, extending up to 360 m, an increase in up to 800% in comparison with the generally accepted maximum of 30-40 m based on the literature. Within this species, wide variation in SGS estimates exists, whether quantified as SGS intensity, extent or the Sp parameter. Consequently, we argue that greater standardization should be applied in sample design and SGS estimation and highlight five steps that can be taken to maximize the comparability between SGS estimates.
Collapse
Affiliation(s)
- A S Jump
- Biological and Environmental Sciences, School of Natural Sciences, University of Stirling, Stirling, UK.
| | | | | | | |
Collapse
|
24
|
LEFÈVRE S, WAGNER S, PETIT RJ, De LAFONTAINE G. Multiplexed microsatellite markers for genetic studies of beech. Mol Ecol Resour 2011; 12:484-91. [DOI: 10.1111/j.1755-0998.2011.03094.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- S. LEFÈVRE
- INRA, UMR 1202 BIOGECO, F‐33610 Cestas, France
- Université de Bordeaux, UMR 1202 BIOGECO, F‐33400 Talence, France
| | - S. WAGNER
- INRA, UMR 1202 BIOGECO, F‐33610 Cestas, France
- Université de Bordeaux, UMR 1202 BIOGECO, F‐33400 Talence, France
- University of Bonn, Steinmann Institut, D‐53115 Bonn, Germany
| | - R. J. PETIT
- INRA, UMR 1202 BIOGECO, F‐33610 Cestas, France
- Université de Bordeaux, UMR 1202 BIOGECO, F‐33400 Talence, France
| | - G. De LAFONTAINE
- INRA, UMR 1202 BIOGECO, F‐33610 Cestas, France
- Université de Bordeaux, UMR 1202 BIOGECO, F‐33400 Talence, France
| |
Collapse
|
25
|
Increased inbreeding and strong kinship structure in Taxus baccata estimated from both AFLP and SSR data. Heredity (Edinb) 2011; 107:589-600. [PMID: 21712844 DOI: 10.1038/hdy.2011.51] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Habitat fragmentation can have severe genetic consequences for trees, such as increased inbreeding and decreased effective population size. In effect, local populations suffer from reduction of genetic variation, and thus loss of adaptive capacity, which consequently increases their risk of extinction. In Europe, Taxus baccata is among a number of tree species experiencing strong habitat fragmentation. However, there is little empirical data on the population genetic consequences of fragmentation for this species. This study aimed to characterize local genetic structure in two natural remnants of English yew in Poland based on both amplified fragment length polymorphism (AFLP) and microsatellite (SSR) markers. We introduced a Bayesian approach that estimates the average inbreeding coefficient using AFLP (dominant) markers. Results showed that, in spite of high dispersal potential (bird-mediated seed dispersal and wind-mediated pollen dispersal), English yew populations show strong kinship structure, with a spatial extent of 50-100 m, depending on the population. The estimated inbreeding levels ranged from 0.016 to 0.063, depending on the population and marker used. Several patterns were evident: (1) AFLP markers showed stronger kinship structure than SSRs; (2) AFLP markers provided higher inbreeding estimates than SSRs; and (3) kinship structure and inbreeding were more pronounced in denser populations regardless of the marker used. Our results suggest that, because both kinship structure and (bi-parental) inbreeding exist in populations of English yew, gene dispersal can be fairly limited in this species. Furthermore, at a local scale, gene dispersal intensity can be more limited in a dense population.
Collapse
|
26
|
HAMPE ARNDT, EL MASRI LEILA, PETIT RÉMYJ. Origin of spatial genetic structure in an expanding oak population. Mol Ecol 2010; 19:459-71. [DOI: 10.1111/j.1365-294x.2009.04492.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
27
|
Chaput-Bardy A, Lemaire C, Picard D, Secondi J. In-stream and overland dispersal across a river network influences gene flow in a freshwater insect, Calopteryx splendens. Mol Ecol 2009; 17:3496-505. [PMID: 19160477 DOI: 10.1111/j.1365-294x.2008.03856.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gene flow in riverine species is constrained by the dendritic (branching) structure of the river network. Spatial genetic structure (SGS) of freshwater insects is particularly influenced by catchment characteristics and land use in the surroundings of the river. Gene flow also depends on the life cycle of organisms. Aquatic larvae mainly drift downstream whereas flying adults can disperse actively overland and along watercourses. In-stream movements can generate isolation by distance (IBD) at a local scale and differentiation between subcatchments. However, these patterns can be disrupted by overland dispersal. We studied SGS across the Loire River in the damselfly Calopteryx splendens which is able to disperse along and between watercourses. Our sampling design allowed us to test for overland dispersal effects on genetic differentiation between watercourses. Amplified fragment length polymorphism markers revealed high genetic differentiation at the catchment scale but the genetic structure did not reflect the geographical structure of sampling sites. We observed IBD patterns when considering the distance following the watercourse but also the Euclidean distance, i.e. the shortest distance, between pairs of sites. Altogether, our results support the hypothesis of overland dispersal between watercourses. From a conservation perspective, attention should be paid to the actual pathways of gene flow across complex landscapes such as river networks.
Collapse
Affiliation(s)
- A Chaput-Bardy
- Laboratoire Paysages et Biodiversité, UFR Sciences, 2 Bd Lavoisier, 49045 Angers cedex 01, France.
| | | | | | | |
Collapse
|
28
|
Jump AS, Rico L, Lloret F, Peñuelas J. Microspatial population genetic structure of the Mediterranean shrub Fumana thymifolia. PLANT BIOLOGY (STUTTGART, GERMANY) 2009; 11:152-160. [PMID: 19228322 DOI: 10.1111/j.1438-8677.2008.00109.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Fumana thymifolia (Cistaceae) is an insect-pollinated, gravity-dispersed evergreen shrub, which is a common component of fire-prone Mediterranean shrubland ecosystems. Despite the availability of basic knowledge on its ecology, little is known of its breeding system and no information is available on its population genetic structure. We explored the within-population genetic structure of this species using amplified fragment length polymorphism (AFLP) molecular markers and related this to predictions based on its breeding system, pollen and seed dispersal. Existing information on the reproductive ecology of F. thymifolia was supplemented by artificial pollination experiments. We determined that self-fertilisation can occur in F. thymifolia but results in reduced fruit set. Significant genetic structuring was detected within the population, a likely consequence of localised seed dispersal in combination with a mixed mating system. In a study site covering approximately 0.5 ha, amova revealed that approximately 9% of genetic variability was distributed among population subsamples. Significant spatial genetic structure was detected, with kinship coefficients being significantly elevated above the null expectation in the first six distance classes (maximum 5 m), and a value of Sp of up to 0.0342, comparable with species having similar ecological characteristics. Weak isolation by distance at the plot scale was detected, suggesting that insect-mediated pollen flow is non-random, despite being more extensive than seed dispersal. Fumana thymifolia provides a promising model for the investigation of both short- and long-term population dynamics in relation to fire frequency within this plant community.
Collapse
Affiliation(s)
- A S Jump
- Unitat d'Ecofisiologia i Canvi Global CSIC-CEAB-CREAF, CREAF (Centre de Recerca Ecològica i Aplicacions Forestals), Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain.
| | | | | | | |
Collapse
|
29
|
Chybicki IJ, Burczyk J. Simultaneous Estimation of Null Alleles and Inbreeding Coefficients. J Hered 2008; 100:106-13. [DOI: 10.1093/jhered/esn088] [Citation(s) in RCA: 455] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
30
|
PARDINI EA, HAMRICK JL. Inferring recruitment history from spatial genetic structure within populations of the colonizing tree Albizia julibrissin (Fabaceae). Mol Ecol 2008; 17:2865-79. [DOI: 10.1111/j.1365-294x.2008.03807.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
31
|
Stefenon VM, Gailing O, Finkeldey R. The role of gene flow in shaping genetic structures of the subtropical conifer species Araucaria angustifolia. PLANT BIOLOGY (STUTTGART, GERMANY) 2008; 10:356-364. [PMID: 18426482 DOI: 10.1111/j.1438-8677.2008.00048.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The morphological features of pollen and seed of Araucaria angustifolia have led to the proposal of limited gene dispersal for this species. We used nuclear microsatellite and AFLP markers to assess patterns of genetic variation in six natural populations at the intra- and inter-population level, and related our findings to gene dispersal in this species. Estimates of both fine-scale spatial genetic structure (SGS) and migration rate suggest relatively short-distance gene dispersal. However, gene dispersal differed among populations, and effects of more efficient dispersal within population were observed in at least one stand. In addition, even though some seed dispersal may be aggregated in this principally barochorous species, reasonable secondary seed dispersal, presumably facilitated by animals, and overlap of seed shadows within populations is suggested. Overall, no correlation was observed between levels of SGS and inbreeding, density or age structure, except that a higher level of SGS was revealed for the population with a higher number of juvenile individuals. A low estimate for the number of migrants per generation between two neighbouring populations implies limited gene flow. We expect that stepping-stone pollen flow may have contributed to low genetic differentiation among populations observed in a previous survey. Thus, strategies for maintenance of gene flow among remnant populations should be considered in order to avoid degrading effects of population fragmentation on the evolution of A. angustifolia.
Collapse
Affiliation(s)
- V M Stefenon
- Institute of Forest Genetics and Forest Tree Breeding, Georg-August-University, Göttingen, Germany.
| | | | | |
Collapse
|
32
|
Tang S, Dai W, Li M, Zhang Y, Geng Y, Wang L, Zhong Y. Genetic diversity of relictual and endangered plant Abies ziyuanensis (Pinaceae) revealed by AFLP and SSR markers. Genetica 2007; 133:21-30. [PMID: 17661154 DOI: 10.1007/s10709-007-9178-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2006] [Accepted: 07/16/2007] [Indexed: 10/23/2022]
Abstract
Abies ziyuanensis is a highly endangered fir species endemic to South China. Unlike other Abies species that are distributed in areas with cold climates, A. ziyuanensis is restricted to several isolated island-like localities at subtropical mountains. In this study, we used dominant amplified fragment length polymorphism (AFLP) and co-dominant simple sequence repeats (SSR) markers to infer the genetic structure of A. ziyuanensis. Seven populations consisting of 139 individuals were sampled across their whole distribution. A. ziyuanenesis has a relatively low level of genetic variation, with a mean genetic diversity per population (He) of 0.136 (AFLP) and 0.337 (SSR), which is lower than that of other reported endemic species based on the same kind of marker. We observed high population differentiation, with Gst = 0.482 (AFLP) and Fst = 0.250 (SSR), among the seven populations. AMOVA also detected significant differentiation among populations (Phist (AFLP) = 0.550 and Phist (SSR) = 0.289) and among regions (Phict (AFLP) = 0.139 and Phict (SSR) = 0.135) in both marker types. Both ongoing evolutionary forces (e.g., genetic drift resulting from small population size) and historical events (e.g., population contraction and fragmentation during and after the Quaternary glacial cycles) may have contributed to the genetic structure in A. ziyuanensis.
Collapse
Affiliation(s)
- Shaoqing Tang
- School of Life Sciences, Guangxi Normal Univertsity, Guilin 541004, China
| | | | | | | | | | | | | |
Collapse
|