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Booker TR, Yeaman S, Whiting JR, Whitlock MC. The WZA: A window-based method for characterizing genotype-environment associations. Mol Ecol Resour 2024; 24:e13768. [PMID: 36785926 DOI: 10.1111/1755-0998.13768] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 01/17/2023] [Accepted: 01/23/2023] [Indexed: 02/15/2023]
Abstract
Genotype-environment association (GEA) studies have the potential to identify the genetic basis of local adaptation in natural populations. Specifically, GEA approaches look for a correlation between allele frequencies and putatively selective features of the environment. Genetic markers with extreme evidence of correlation with the environment are presumed to be tagging the location of alleles that contribute to local adaptation. In this study, we propose a new method for GEA studies called the Weighted-Z Analysis (WZA) that combines information from closely linked sites into analysis windows in a way that was inspired by methods for calculating FST . Performing GEA methods in analysis windows has the advantage that it takes advantage of the increased linkage disequilibrium expected surrounding sites subject to local adaptation. We analyse simulations modelling local adaptation to heterogeneous environments to compare the WZA with existing methods. In the majority of cases we tested, the WZA either outperformed single-SNP (single nucleotide polymorphism)-based approaches or performed similarly. In particular, the WZA outperformed individual SNP approaches when a small number of individuals or demes were sampled. Particularly troubling, we found that some GEA methods exhibit very high false positive rates. We applied the WZA to previously published data from lodgepole pine and identified candidate loci that were identified in the original study alongside numerous loci that were not found in the original study.
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Affiliation(s)
- Tom R Booker
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - James R Whiting
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Michael C Whitlock
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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2
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Wambulwa MC, Luo YH, Zhu GF, Milne R, Wachira FN, Wu ZY, Wang H, Gao LM, Li DZ, Liu J. Determinants of Genetic Structure in a Highly Heterogeneous Landscape in Southwest China. FRONTIERS IN PLANT SCIENCE 2022; 13:779989. [PMID: 35574120 PMCID: PMC9097793 DOI: 10.3389/fpls.2022.779989] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 04/04/2022] [Indexed: 06/15/2023]
Abstract
Intra-specific genetic diversity is a fundamental component of biodiversity, and is key to species adaptation and persistence. However, significant knowledge gaps still exist in our understanding of the patterns of genetic diversity and their key determinants. Most previous investigations mainly utilized single-species and/or a limited number of explanatory variables; so here we mapped the patterns of plastid genetic diversity within 15 plant species, and explored the key determinants shaping these patterns using a wide range of variables. Population-level cpDNA sequence data for 15 plant species from the Longitudinal Range Gorge Region (LRGR), southwest China, were retrieved from literature and used to estimate haplotype diversity (H D) and population pairwise genetic differentiation (F ST) indices. Genetic diversity and divergence landscape surfaces were then generated based on the H D and F ST, respectively, to clarify the patterns of genetic structure in the region. Subsequently, we analyzed the relationships between plastid genetic diversity and 16 explanatory variables (classified as anthropogenic, climatic, and topographic). We found that the highest genetic diversity occurred in the Yulong Mountain region, with a significant proportion (~74.81%) of the high diversity land area being located outside of protected areas. The highest genetic divergence was observed approximately along the 25°N latitudinal line, with notable peaks in the western and eastern edges of the LRGR. Genetic diversity (H D) was weakly but significantly positively correlated with both Latitude (lat) and Annual Mean Wet Day Frequency (wet), yet significantly negatively correlated with all of Longitude (long), Annual Mean Cloud Cover Percent (cld), Annual Mean Anthropogenic Flux (ahf), and Human Footprint Index (hfp). A combination of climatic, topographic, and anthropogenic factors explained a significant proportion (78%) of genetic variation, with topographic factors (lat and long) being the best predictors. Our analysis identified areas of high genetic diversity (genetic diversity "hotspots") and divergence in the region, and these should be prioritized for conservation. This study contributes to a better understanding of the features that shape the distribution of plastid genetic diversity in the LRGR and thus would inform conservation management efforts in this species-rich, but vulnerable region.
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Affiliation(s)
- Moses C. Wambulwa
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Department of Life Sciences, School of Science and Computing, South Eastern Kenya University, Kitui, Kenya
| | - Ya-Huang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Guang-Fu Zhu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Richard Milne
- School of Biological Sciences, Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Francis N. Wachira
- Department of Life Sciences, School of Science and Computing, South Eastern Kenya University, Kitui, Kenya
| | - Zeng-Yuan Wu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Hong Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, China
| | - De-Zhu Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, China
| | - Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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3
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Zacharias M, Pampuch T, Heer K, Avanzi C, Würth DG, Trouillier M, Bog M, Wilmking M, Schnittler M. Population structure and the influence of microenvironment and genetic similarity on individual growth at Alaskan white spruce treelines. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 798:149267. [PMID: 34332391 DOI: 10.1016/j.scitotenv.2021.149267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Knowledge on the adaptation of trees to rapid environmental changes is essential to preserve forests and their ecosystem services under climate change. Treeline populations are particularly suitable for studying adaptation processes in trees, as environmental stress together with reduced gene flow can enhance local adaptation. We investigated white spruce (Picea glauca) populations in Alaska on one moisture-limited and two cold-limited treeline sites with a paired plot design of one forest and one treeline population each, resulting in six plots. Additionally, one forest plot in the middle of the distribution range complements the study design. We combined spatial, climatic and dendrochronological data with neutral genetic marker of 2203 trees to investigate population genetic structure and drivers of tree growth. We used several individual-based approaches including random slope mixed-effects models to test the influence of genetic similarity and microenvironment on growth performance. A high degree of genetic diversity was found within each of the seven plots associated with high rates of gene flow. We discovered a low genetic differentiation between the three sites which was better explained by geographic distances than by environmental differences, indicating genetic drift as the main driver of population differentiation. Our findings indicated that microenvironmental features had an overall larger influence on growth performances than genetic similarity among individuals. The effects of climate on growth differed between sites but were smaller than the effect of tree size. Overall, our results suggest that the high genetic diversity of white spruce may result in a wider range of phenotypes which enhances the efficiency of selection when the species is facing rapid climatic changes. In addition, the large intra-individual variability in growth responses may indicate the high phenotypic plasticity of white spruce which can buffer short-term environmental changes and, thus, allow enduring the present changing climate conditions.
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Affiliation(s)
- Melanie Zacharias
- Institute of Botany und Landscape Ecology, University of Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany.
| | - Timo Pampuch
- Institute of Botany und Landscape Ecology, University of Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany.
| | - Katrin Heer
- Conservation Biology, University of Marburg, Karl-von-Frisch-Strasse 8, 35043 Marburg, Germany.
| | - Camilla Avanzi
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy.
| | - David G Würth
- Institute of Botany und Landscape Ecology, University of Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany
| | - Mario Trouillier
- Institute of Botany und Landscape Ecology, University of Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany.
| | - Manuela Bog
- Institute of Botany und Landscape Ecology, University of Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany.
| | - Martin Wilmking
- Institute of Botany und Landscape Ecology, University of Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany.
| | - Martin Schnittler
- Institute of Botany und Landscape Ecology, University of Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany.
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Zhao W, Wang X, Li L, Li J, Yin H, Zhao Y, Chen X. Evaluation of environmental factors affecting the genetic diversity, genetic structure, and the potential distribution of Rhododendron aureum Georgi under changing climate. Ecol Evol 2021; 11:12294-12306. [PMID: 34594500 PMCID: PMC8462154 DOI: 10.1002/ece3.7803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 04/19/2021] [Accepted: 05/27/2021] [Indexed: 11/29/2022] Open
Abstract
Understanding genetic variation and structure, adaptive genetic variation, and its relationship with environmental factors is of great significance to understand how plants adapt to climate change and design effective conservation and management strategies. The objective of this study was to (I) investigate the genetic diversity and structure by AFLP markers in 36 populations of R. aureum from northeast China, (Ⅱ) reveal the relative contribution of geographical and environmental impacts on the distribution and genetic differentiation of R. aureum, (Ⅲ) identify outlier loci under selection and evaluate the association between outlier loci and environmental factors, and (Ⅳ) exactly calculate the development trend of population of R. aureum, as it is confronted with severe climate change and to provide information for designing effective conservation and management strategies. We found high genetic variation (I = 0.584) and differentiation among populations (ΦST = 0.703) and moderate levels of genetic diversity within populations of R. aureum. A significant relationship between genetic distance and environmental distance was identified, which suggested that the differentiation of different populations was caused by environmental factors. Using BayeScan and Dfdist, 42 outlier loci are identified and most of the outlier loci are associated with climate or relief factors, suggesting that these loci are linked to genes that are involved in the adaptability of R. aureum to the environment. Species distribution models (SDMs) showed that climate warming will cause a significant reduction in suitable areas for R. aureum, especially under the RCP 85 scenario. Our results help to understand the potential response of R. aureum to climatic changes and provide new perspectives for R. aureum resource management and conservation strategies.
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Affiliation(s)
- Wei Zhao
- National & Local United Engineering Laboratory for Chinese Herbal Medicine Breeding and CultivationJilin UniversityChangchunChina
- School of Life ScienceJilin UniversityChangchunChina
| | - Xiaolong Wang
- Medical Technology DepartmentQiqihar Medical UniversityQiqiharChina
| | - Lin Li
- Medical Technology DepartmentQiqihar Medical UniversityQiqiharChina
| | - Jiangnan Li
- National & Local United Engineering Laboratory for Chinese Herbal Medicine Breeding and CultivationJilin UniversityChangchunChina
- School of Life ScienceJilin UniversityChangchunChina
| | - Hang Yin
- Jilin Provincial Joint Key Laboratory of Changbai Mountain Biocoenosis and BiodiversityAntuChina
- Academy of Sciences of Changbai MountainChangbaishanChina
| | - Ying Zhao
- Jilin Provincial Joint Key Laboratory of Changbai Mountain Biocoenosis and BiodiversityAntuChina
- Academy of Sciences of Changbai MountainChangbaishanChina
| | - Xia Chen
- National & Local United Engineering Laboratory for Chinese Herbal Medicine Breeding and CultivationJilin UniversityChangchunChina
- School of Life ScienceJilin UniversityChangchunChina
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5
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Steele SE, Ryder OA, Maschinski J. RNA-Seq reveals adaptive genetic potential of the rare Torrey pine (Pinus torreyana) in the face of Ips bark beetle outbreaks. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01394-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Li S, Wang Z, Su Y, Wang T. EST-SSR-based landscape genetics of Pseudotaxus chienii, a tertiary relict conifer endemic to China. Ecol Evol 2021; 11:9498-9515. [PMID: 34306638 PMCID: PMC8293779 DOI: 10.1002/ece3.7769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/04/2021] [Accepted: 05/19/2021] [Indexed: 12/12/2022] Open
Abstract
Pseudotaxus chienii, belonging to the monotypic genus Pseudotaxus (Taxaceae), is a relict conifer endemic to China. Its populations are usually small and patchily distributed, having a low capacity of natural regeneration. To gain a clearer understanding of how landscape variables affect the local adaptation of P. chienii, we applied EST-SSR markers in conjunction with landscape genetics methods: (a) to examine the population genetic pattern and spatial genetic structure; (b) to perform genome scan and selection scan to identify outlier loci and the associated landscape variables; and (c) to model the ecological niche under climate change. As a result, P. chienii was found to have a moderate level of genetic variation and a high level of genetic differentiation. Its populations displayed a significant positive relationship between the genetic and geographical distance (i.e., "isolation by distance" pattern) and a strong fine-scale spatial genetic structure within 2 km. A putatively adaptive locus EMS6 (functionally annotated to cellulose synthase A catalytic subunit 7) was identified, which was found significantly associated with soil Cu, K, and Pb content and the combined effects of temperature and precipitation. Moreover, P. chienii was predicted to experience significant range contractions in future climate change scenarios. Our results highlight the potential of specific soil metal content and climate variables as the driving force of adaptive genetic differentiation in P. chienii. The data would also be useful to develop a conservation action plan for P. chienii.
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Affiliation(s)
- Shufeng Li
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Zhen Wang
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Yingjuan Su
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
- Research Institute of Sun Yat‐sen University in ShenzhenShenzhenChina
| | - Ting Wang
- Research Institute of Sun Yat‐sen University in ShenzhenShenzhenChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
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7
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Ye H, Wang Z, Hou H, Wu J, Gao Y, Han W, Ru W, Sun G, Wang Y. Localized environmental heterogeneity drives the population differentiation of two endangered and endemic Opisthopappus Shih species. BMC Ecol Evol 2021; 21:56. [PMID: 33858342 PMCID: PMC8050911 DOI: 10.1186/s12862-021-01790-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 04/08/2021] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Climate heterogeneity not only indirectly shapes the genetic structures of plant populations, but also drives adaptive divergence by impacting demographic dynamics. The variable localized climates and topographic complexity of the Taihang Mountains make them a major natural boundary in Northern China that influences the divergence of organisms distributed across this region. Opisthopappus is an endemic genus of the Taihang Mountains that includes only two spatially partitioned species Opisthopappus longilobus and Opisthopappus taihangensis. For this study, the mechanisms behind the genetic variations in Opisthopappus populations were investigated. RESULTS Using SNP and InDel data coupled with geographic and climatic information, significant genetic differentiation was found to exist either between Opisthopappus populations or two species. All studied populations were divided into two genetic groups with the differentiation of haplotypes between the groups. At approximately 17.44 Ma of the early Miocene, O. taihangensis differentiated from O. longilobus under differing precipitation regimes due to the intensification of the Asian monsoon. Subsequently, intraspecific divergence might be induced by the dramatic climatic transformation from the mid- to late Miocene. During the Pleistocene period, the rapid uplift of the Taihang Mountains coupled with violent climatic oscillations would further promote the diversity of the two species. Following the development of the Taihang Mountains, its complex topography created geographical and ecological heterogeneity, which could lead to spatiotemporal isolation between the Opisthopappus populations. Thus the adaptive divergence might occur within these intraspecific populations in the localized heterogeneous environment of the Taihang Mountains. CONCLUSIONS The localized environmental events through the integration of small-scale spatial effects impacted the demographic history and differentiation mechanism of Opisthopappus species in the Taihang Mountains. The results provide useful information for us to understand the ecology and evolution of organisms in the mountainous environment from population and species perspective.
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Affiliation(s)
- Hang Ye
- College of Life Science, Shanxi Normal University, Linfen, China
| | - Zhi Wang
- College of Life Science, Shanxi Normal University, Linfen, China
| | - Huimin Hou
- College of Life Science, Shanxi Normal University, Linfen, China
| | - Jiahui Wu
- College of Life Science, Shanxi Normal University, Linfen, China
- Changzhi University, Changzhi, China
| | - Yue Gao
- College of Life Science, Shanxi Normal University, Linfen, China
| | - Wei Han
- College of Life Science, Shanxi Normal University, Linfen, China
| | | | - Genlou Sun
- Saint Mary's University, Halifax, Canada
| | - Yiling Wang
- College of Life Science, Shanxi Normal University, Linfen, China.
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8
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Csilléry K, Buchmann N, Fady B. Adaptation to drought is coupled with slow growth, but independent from phenology in marginal silver fir ( Abies alba Mill.) populations. Evol Appl 2020; 13:2357-2376. [PMID: 33042220 PMCID: PMC7539328 DOI: 10.1111/eva.13029] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 05/01/2020] [Accepted: 05/05/2020] [Indexed: 12/20/2022] Open
Abstract
Drought is one of the most important selection pressures for forest trees in the context of climate change. Yet, the different evolutionary mechanisms, and their environmental drivers, by which certain populations become more drought tolerant than others is still little understood. We studied adaptation to drought in 16 silver fir (Abies alba Mill.) populations from the French Mediterranean Alps by combining observations on seedlings from a greenhouse experiment (N = 8,199) and on adult tress in situ (N = 315). In the greenhouse, we followed half-sib families for four growing seasons for growth and phenology traits, and tested their water stress response in a "drought until death" experiment. Adult trees in the field were assessed for δ 13C, a proxy for water use efficiency, and genotyped at 357 SNP loci. SNP data was used to generate a null expectation for seedling trait divergence between populations in order to detect the signature of selection, and 31 environmental variables were used to identify the selective environment. We found that seedlings originating from populations with low soil water capacity grew more slowly, attained a smaller stature, and resisted water stress for a longer period of time in the greenhouse. Additionally, adult trees of these populations exhibited a higher water use efficiency as evidenced by their δ 13C. These results suggest a correlated evolution of the growth-drought tolerance trait complex. Population divergence in bud break phenology was adaptive only in the second growing season, and evolved independently from the growth-drought tolerance trait complex. Adaptive divergence in bud break phenology was principally driven by the inter- and intra-annual variation in temperature at the geographic origin of the population. Our results illustrate the different evolutionary strategies used by populations to cope with drought stress at the range limits across a highly heterogeneous landscape, and can be used to inform assisted migration programs.
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Affiliation(s)
- Katalin Csilléry
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZürichZürichSwitzerland
- Biodiversity & Conservation BiologySwiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Nina Buchmann
- Institute of Agricultural SciencesETH ZürichZürichSwitzerland
| | - Bruno Fady
- INRAEcology of Mediterranean Forests (URFM)UR629AvignonFrance
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9
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Castilla AR, Méndez-Vigo B, Marcer A, Martínez-Minaya J, Conesa D, Picó FX, Alonso-Blanco C. Ecological, genetic and evolutionary drivers of regional genetic differentiation in Arabidopsis thaliana. BMC Evol Biol 2020; 20:71. [PMID: 32571210 PMCID: PMC7310121 DOI: 10.1186/s12862-020-01635-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Disentangling the drivers of genetic differentiation is one of the cornerstones in evolution. This is because genetic diversity, and the way in which it is partitioned within and among populations across space, is an important asset for the ability of populations to adapt and persist in changing environments. We tested three major hypotheses accounting for genetic differentiation-isolation-by-distance (IBD), isolation-by-environment (IBE) and isolation-by-resistance (IBR)-in the annual plant Arabidopsis thaliana across the Iberian Peninsula, the region with the largest genomic diversity. To that end, we sampled, genotyped with genome-wide SNPs, and analyzed 1772 individuals from 278 populations distributed across the Iberian Peninsula. RESULTS IBD, and to a lesser extent IBE, were the most important drivers of genetic differentiation in A. thaliana. In other words, dispersal limitation, genetic drift, and to a lesser extent local adaptation to environmental gradients, accounted for the within- and among-population distribution of genetic diversity. Analyses applied to the four Iberian genetic clusters, which represent the joint outcome of the long demographic and adaptive history of the species in the region, showed similar results except for one cluster, in which IBR (a function of landscape heterogeneity) was the most important driver of genetic differentiation. Using spatial hierarchical Bayesian models, we found that precipitation seasonality and topsoil pH chiefly accounted for the geographic distribution of genetic diversity in Iberian A. thaliana. CONCLUSIONS Overall, the interplay between the influence of precipitation seasonality on genetic diversity and the effect of restricted dispersal and genetic drift on genetic differentiation emerges as the major forces underlying the evolutionary trajectory of Iberian A. thaliana.
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Affiliation(s)
- Antonio R Castilla
- Centre for Applied Ecology "Prof. Baeta Neves", InBIO, School of Agriculture, University of Lisbon, Lisbon, Portugal
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Arnald Marcer
- CREAF, Centre de Recerca Ecològica i Aplicacions Forestals, Bellaterra, E08193, Cerdanyola de Vallès, Catalonia, Spain
- Universitat Autònoma de Barcelona, Bellaterra, E08193, Cerdanyola de Vallès, Catalonia, Spain
| | | | - David Conesa
- Departament d'Estadística i Investigació Operativa, Universitat de València, Valencia, Spain
| | - F Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain.
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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10
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Coelho GM, Santos AS, de Menezes IPP, Tarazi R, Souza FMO, Silva MDGCPC, Gaiotto FA. Genetic structure among morphotypes of the endangered Brazilian palm Euterpe edulis Mart (Arecaceae). Ecol Evol 2020; 10:6039-6048. [PMID: 32607211 PMCID: PMC7319139 DOI: 10.1002/ece3.6348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/04/2020] [Accepted: 04/14/2020] [Indexed: 11/07/2022] Open
Abstract
Euterpe edulis (Arecaceae) Mart has high ecological and economic importance providing food resources for more than 58 species of birds and 20 species of mammals, including humans. E. edulis is the second most exploited nontimber product from Brazilian Atlantic Forest. Due to overexploitation and destruction of habitats, E. edulis is threatened by extinction. Euterpe edulis populations have large morphological variations, with individuals having green, red, or yellow leaf sheath. However, no study has related phenotypic distinctions between populations and their levels of genetic structure. Thus, this study aimed to evaluate the diversity and genetic structure of different E. edulis morphotypes. We sampled 250 adult individuals in eight populations with the different morphotypes. Using 14 microsatellite markers, we access genetic diversity through population genetic parameters calculated in the GenAlex program and the diveRsity package in R. We used the Wilcoxon test to verify population bottlenecks and the genetic distance of Nei and Bayesian analysis for genetic clusters. The eight populations showed low allele richness, low observed heterozygosity, and high inbreeding values (f). In addition, six of the eight populations experienced genetic bottlenecks, which would partly explain the low genetic diversity in populations. Cluster analysis identified two clusters (K = 2), with green morphotype genetically distinguishing from yellow and red morphotypes. Thus, we show, for the first time, a strong genetic structure among E. edulis morphotypes even for geographically close populations.
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Affiliation(s)
- Gislaine Mendes Coelho
- Departamento de Ciências BiológicasCentro de Biotecnologia e GenéticaUniversidade Estadual de Santa CruzIlhéusBrazil
| | - Alesandro Souza Santos
- Departamento de Ciências BiológicasCentro de Biotecnologia e GenéticaUniversidade Estadual de Santa CruzIlhéusBrazil
- Laboratório de Ecologia Aplicada à ConservaçãoUniversidade Estadual de Santa CruzIlhéusBrazil
| | | | | | - Fernanda Maria Oliveira Souza
- Departamento de Ciências BiológicasCentro de Biotecnologia e GenéticaUniversidade Estadual de Santa CruzIlhéusBrazil
| | | | - Fernanda Amato Gaiotto
- Departamento de Ciências BiológicasCentro de Biotecnologia e GenéticaUniversidade Estadual de Santa CruzIlhéusBrazil
- Laboratório de Ecologia Aplicada à ConservaçãoUniversidade Estadual de Santa CruzIlhéusBrazil
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11
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Knowledge status and sampling strategies to maximize cost-benefit ratio of studies in landscape genomics of wild plants. Sci Rep 2020; 10:3706. [PMID: 32111897 PMCID: PMC7048820 DOI: 10.1038/s41598-020-60788-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 02/11/2020] [Indexed: 11/27/2022] Open
Abstract
To avoid local extinction due to the changes in their natural ecosystems, introduced by anthropogenic activities, species undergo local adaptation. Landscape genomics approach, through genome–environment association studies, has helped evaluate the local adaptation in natural populations. Landscape genomics, is still a developing discipline, requiring refinement of guidelines in sampling design, especially for studies conducted in the backdrop of stark socioeconomic realities of the rainforest ecologies, which are global biodiversity hotspots. In this study we aimed to devise strategies to improve the cost-benefit ratio of landscape genomics studies by surveying sampling designs and genome sequencing strategies used in existing studies. We conducted meta-analyses to evaluate the importance of sampling designs, in terms of (i) number of populations sampled, (ii) number of individuals sampled per population, (iii) total number of individuals sampled, and (iv) number of SNPs used in different studies, in discerning the molecular mechanisms underlying local adaptation of wild plant species. Using the linear mixed effects model, we demonstrated that the total number of individuals sampled and the number of SNPs used, significantly influenced the detection of loci underlying the local adaptation. Thus, based on our findings, in order to optimize the cost-benefit ratio of landscape genomics studies, we suggest focusing on increasing the total number of individuals sampled and using a targeted (e.g. sequencing capture) Pool-Seq approach and/or a random (e.g. RAD-Seq) Pool-Seq approach to detect SNPs and identify SNPs under selection for a given environmental cline. We also found that the existing molecular evidences are inadequate in predicting the local adaptations to climate change in tropical forest ecosystems.
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Mosca E, Cruz F, Gómez-Garrido J, Bianco L, Rellstab C, Brodbeck S, Csilléry K, Fady B, Fladung M, Fussi B, Gömöry D, González-Martínez SC, Grivet D, Gut M, Hansen OK, Heer K, Kaya Z, Krutovsky KV, Kersten B, Liepelt S, Opgenoorth L, Sperisen C, Ullrich KK, Vendramin GG, Westergren M, Ziegenhagen B, Alioto T, Gugerli F, Heinze B, Höhn M, Troggio M, Neale DB. A Reference Genome Sequence for the European Silver Fir ( Abies alba Mill.): A Community-Generated Genomic Resource. G3 (BETHESDA, MD.) 2019; 9:2039-2049. [PMID: 31217262 PMCID: PMC6643874 DOI: 10.1534/g3.119.400083] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/11/2019] [Indexed: 02/08/2023]
Abstract
Silver fir (Abies alba Mill.) is a keystone conifer of European montane forest ecosystems that has experienced large fluctuations in population size during during the Quaternary and, more recently, due to land-use change. To forecast the species' future distribution and survival, it is important to investigate the genetic basis of adaptation to environmental change, notably to extreme events. For this purpose, we here provide a first draft genome assembly and annotation of the silver fir genome, established through a community-based initiative. DNA obtained from haploid megagametophyte and diploid needle tissue was used to construct and sequence Illumina paired-end and mate-pair libraries, respectively, to high depth. The assembled A. alba genome sequence accounted for over 37 million scaffolds corresponding to 18.16 Gb, with a scaffold N50 of 14,051 bp. Despite the fragmented nature of the assembly, a total of 50,757 full-length genes were functionally annotated in the nuclear genome. The chloroplast genome was also assembled into a single scaffold (120,908 bp) that shows a high collinearity with both the A. koreana and A. sibirica complete chloroplast genomes. This first genome assembly of silver fir is an important genomic resource that is now publicly available in support of a new generation of research. By genome-enabling this important conifer, this resource will open the gate for new research and more precise genetic monitoring of European silver fir forests.
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Affiliation(s)
- Elena Mosca
- C3A - Centro Agricoltura Alimenti Ambiente, University of Trento, via E. Mach 1, 38010 S. Michele a/Adige (TN), Italy
| | - Fernando Cruz
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, BaldiriReixac 4, 08028 Barcelona, Spain
| | - Jèssica Gómez-Garrido
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, BaldiriReixac 4, 08028 Barcelona, Spain
| | - Luca Bianco
- Fondazione Edmund Mach, Via Mach 1, 38010 S. Michele a/Adige (TN), Italy
| | - Christian Rellstab
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Sabine Brodbeck
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Katalin Csilléry
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- University of Zürich, Department of Evolutionary Biology and Environmental Studies, Winterthurerstrasse 190, CH-8057 Zurich
| | - Bruno Fady
- Institut National de la Recherche Agronomique (INRA), Unité de Recherche Ecologie des Forêts Méditerranéennes (URFM), Site Agroparc, Domaine Saint Paul, 84914 Avignon, France
| | - Matthias Fladung
- Thünen-Institute of Forest Genetics, Sieker Landstr, 2, 22927 Grosshansdorf, Germany
| | - Barbara Fussi
- Bavarian Office for Forest Seeding and Planting (ASP), Applied Forest Genetics, Forstamtsplatz 1, 83317 Teisendorf, Germany
| | - Dušan Gömöry
- Technical University in Zvolen, TG Masaryka 24, 96053 Zvolen, Slovakia
| | - Santiago C González-Martínez
- Institut National de la Recherche Agronomique (INRA), UMR1202 Biodiversity, Genes & Communities (BIOGECO), University of Bordeaux, 69, route d'Arcachon, 33610 Cestas, France
| | - Delphine Grivet
- INIA Forest Research Centre, Carretera de la Coruña km 7.5, 28040 Madrid, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, BaldiriReixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Plaça de la Mercè, 10, 08002 Barcelona, Spain
| | - Ole Kim Hansen
- Department of Geosciences and Natural Resource Management (IGN), University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg C, Denmark
| | - Katrin Heer
- Philipps-Universität Marburg, Faculty of Biology (PUM), Karl-von-Frisch-Str. 8, 35032 Marburg, Germany
| | - Zeki Kaya
- Department of Biological Sciences (METU), Middle East Technical University, 06800 Çankaya/Ankara, Turkey
| | - Konstantin V Krutovsky
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
- Laboratory of Population Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina Str. 3, 11991 Moscow, Russia
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 50a/2 Akademgorodok, 660036 Krasnoyarsk, Russia
| | - Birgit Kersten
- Thünen-Institute of Forest Genetics, Sieker Landstr, 2, 22927 Grosshansdorf, Germany
| | - Sascha Liepelt
- Philipps-Universität Marburg, Faculty of Biology (PUM), Karl-von-Frisch-Str. 8, 35032 Marburg, Germany
| | - Lars Opgenoorth
- Philipps-Universität Marburg, Faculty of Biology (PUM), Karl-von-Frisch-Str. 8, 35032 Marburg, Germany
| | - Christoph Sperisen
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Kristian K Ullrich
- Department of Biological Sciences (METU), Middle East Technical University, 06800 Çankaya/Ankara, Turkey
| | - Giovanni G Vendramin
- Institute of Biosciences and BioResources, National Research Council, Via Madonna del Piano 10,50019 Sesto Fiorentino (Firenze), Italy
| | - Marjana Westergren
- Slovenian Forestry Institute (SFI), Gozdarskiinštitut Slovenije), Večna pot 2, 1000 Ljubljana, Slovenia
| | - Birgit Ziegenhagen
- Philipps-Universität Marburg, Faculty of Biology (PUM), Karl-von-Frisch-Str. 8, 35032 Marburg, Germany
| | - Tyler Alioto
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, BaldiriReixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Plaça de la Mercè, 10, 08002 Barcelona, Spain
| | - Felix Gugerli
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Berthold Heinze
- Federal Research and Training Centre for Forests, Natural Hazards and Landscape (BFW), Seckendorff-Gudent Weg 8, 1130 Wien, Austria
| | - Maria Höhn
- Max Planck Institute for Evolutionary Biology, Department for Evolutionary Genetics (MPI), August Thienemann Str. 2, 24306 Ploen, Germany
| | - Michela Troggio
- Fondazione Edmund Mach, Via Mach 1, 38010 S. Michele a/Adige (TN), Italy
| | - David B Neale
- Department of Plant Sciences, University of California at Davis (UCD), Davis 95616
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Acosta JJ, Fahrenkrog AM, Neves LG, Resende MFR, Dervinis C, Davis JM, Holliday JA, Kirst M. Exome Resequencing Reveals Evolutionary History, Genomic Diversity, and Targets of Selection in the Conifers Pinus taeda and Pinus elliottii. Genome Biol Evol 2019; 11:508-520. [PMID: 30689841 PMCID: PMC6385631 DOI: 10.1093/gbe/evz016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2019] [Indexed: 12/22/2022] Open
Abstract
Loblolly pine (Pinus taeda) and slash pine (Pinus elliottii) are ecologically and economically important pine species that dominate many forest ecosystems in the southern United States, but like all conifers, the study of their genetic diversity and demographic history has been hampered by their large genome size. A small number of studies mainly based on candidate-gene sequencing have been reported for P. taeda to date, whereas none are available for P. elliottii. Targeted exome resequencing has recently enabled population genomics studies for conifers, approach used here to assess genomic diversity, signatures of selection, population structure, and demographic history of P. elliottii and P. taeda. Extensive similarities were revealed between these species: both species feature rapid linkage disequilibrium decay and high levels of genetic diversity. Moreover, genome-wide positive correlations for measures of genetic diversity between the species were also observed, likely due to shared structural genomic constraints. Also, positive selection appears to be targeting a common set of genes in both pines. Demographic history differs between both species, with only P. taeda being affected by a dramatic bottleneck during the last glacial period. The ability of P. taeda to recover from a dramatic reduction in population size while still retaining high levels of genetic diversity shows promise for other pines facing environmental stressors associated with climate change, indicating that these too may be able to adapt successfully to new future conditions even after a drastic population size contraction.
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Affiliation(s)
- Juan J Acosta
- School of Forest Resources and Conservation, University of Florida.,University of Florida Genetics Institute, University of Florida.,Camcore, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC
| | - Annette M Fahrenkrog
- School of Forest Resources and Conservation, University of Florida.,Plant Molecular and Cellular Biology Graduate Program, University of Florida
| | - Leandro G Neves
- School of Forest Resources and Conservation, University of Florida.,Plant Molecular and Cellular Biology Graduate Program, University of Florida.,RAPiD Genomics, Gainesville, FL
| | | | | | - John M Davis
- School of Forest Resources and Conservation, University of Florida
| | - Jason A Holliday
- Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University
| | - Matias Kirst
- School of Forest Resources and Conservation, University of Florida.,Plant Molecular and Cellular Biology Graduate Program, University of Florida.,University of Florida Genetics Institute, University of Florida
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Cisneros‐de la Cruz DJ, Martínez‐Castillo J, Herrera‐Silveira J, Yáñez‐Espinosa L, Ortiz‐García M, Us‐Santamaria R, Andrade JL. Short-distance barriers affect genetic variability of Rhizophora mangle L. in the Yucatan Peninsula. Ecol Evol 2018; 8:11083-11099. [PMID: 30519427 PMCID: PMC6262909 DOI: 10.1002/ece3.4575] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 08/13/2018] [Accepted: 08/28/2018] [Indexed: 11/22/2022] Open
Abstract
The environmental variability at local scale results in different physiognomic types of mangrove forest. However, this variability has never been considered in studies of mangrove genetic variability. This study analyzed the genetic and morphological variability and structure of Rhizophora mangle at regional and local scales in the Yucatan Peninsula. Thirteen mangrove populations (eight scrub and five tall), located in seven sites, were sampled, and their morphological variability and relationship with the availability of phosphorus and salinity were analyzed. The diversity and genetic structure were estimated at different hierarchical levels with nine microsatellites, also Bayesian inference and Principal Coordinates Analysis were used. We found a great morphological variability of R. mangle that responded to local environmental variability and not to the precipitation gradient of the peninsula. The genetic diversity found in the peninsula was greater than that reported for other populations in Mexico and was grouped into two regions: the Gulf of Mexico and the Caribbean Sea. At a local scale, tall and scrub mangroves had significant genetic differentiation suggesting that ecological barriers promote genetic differentiation within sites. These results need to be considered in future population genetic studies and for mangrove management and conservation.
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Affiliation(s)
| | | | | | - Laura Yáñez‐Espinosa
- Instituto de Investigaciones de Zonas DesérticasUniversidad Autónoma de San Luis Potosí (UASLP)San Luis PotosíMexico
| | | | | | - José L. Andrade
- Centro de Investigación Científica de Yucatán (CICY)MéridaMéxico
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15
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From America to Eurasia: a multigenomes history of the genus Abies. Mol Phylogenet Evol 2018; 125:14-28. [DOI: 10.1016/j.ympev.2018.03.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 03/05/2018] [Accepted: 03/07/2018] [Indexed: 11/24/2022]
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16
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The Tanggula Mountains enhance population divergence in Carex moorcroftii: a dominant sedge on the Qinghai-Tibetan Plateau. Sci Rep 2018; 8:2741. [PMID: 29426823 PMCID: PMC5807306 DOI: 10.1038/s41598-018-21129-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 01/30/2018] [Indexed: 11/08/2022] Open
Abstract
High-altitude mountains are often geographic barriers to gene flow and play important roles in shaping population divergence. The central Qinghai-Tibetan Plateau (QTP) stands the location of the Tanggula Mountains (TM). We use the TM as a case, using Carex moorcroftii, a dominant species on the QTP to test the effects of geographic barriers on plant population divergence. We sampled 18 C. moorcroftii populations along a north-south transect crossing the TM to investigate the correlations of genetic variation and morphological traits with climate variables. The results showed this species holds high genetic diversity (He = 0.58) and the surveyed populations can be genetically clustered into two groups: populations from the north face of TM, and the other from the south. Gene flow between populations within groups is higher than those between groups. The traits, number and mass of seeds, mass of root and infructescence significantly varied among populations. Mantel-tests detected a weak but significantly positive correlation between genetic and geographic (R2 = 0.107, p = 0.032) and climatic distance (R2 = 0.162, p = 0.005), indicating both isolation by distance and isolation by environment. These findings together suggest high-altitude mountains of TM interrupt habitat continuity, result in distinct climatic conditions on both sides, increasing population divergence of plant species.
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17
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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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18
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Morente-López J, García C, Lara-Romero C, García-Fernández A, Draper D, Iriondo JM. Geography and Environment Shape Landscape Genetics of Mediterranean Alpine Species Silene ciliata Poiret. (Caryophyllaceae). FRONTIERS IN PLANT SCIENCE 2018; 9:1698. [PMID: 30538712 PMCID: PMC6277476 DOI: 10.3389/fpls.2018.01698] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 10/31/2018] [Indexed: 05/22/2023]
Abstract
The study of the drivers that shape spatial genetic structure across heterogeneous landscapes is one of the main approaches used to understand population dynamics and responses in changing environments. While the Isolation-by-Distance model (IBD) assumes that genetic differentiation increases among populations with geographical distance, the Isolation-by-Resistance model (IBR) also considers geographical barriers and other landscape features that impede gene flow. On the other hand, the Isolation-by-Environment model (IBE) explains genetic differentiation through environmental differences between populations. Although spatial genetic studies have increased significantly in recent years, plants from alpine ecosystems are highly underrepresented, even though they are great suitable systems to disentangle the role of the different factors that structure genetic variation across environmental gradients. Here, we studied the spatial genetic structure of the Mediterranean alpine specialist Silene ciliata across its southernmost distribution limit. We sampled three populations across an altitudinal gradient from 1850 to 2400 m, and we replicated this sample over three mountain ranges aligned across an E-W axis in the central part of the Iberian Peninsula. We genotyped 20 individuals per population based on eight microsatellite markers and used different landscape genetic tools to infer the role of topographic and environmental factors in shaping observed patterns along the altitudinal gradient. We found a significant genetic structure among the studied Silene ciliata populations which was related to the orography and E-W configuration of the mountain ranges. IBD pattern arose as the main factor shaping population genetic differentiation. Geographical barriers between mountain ranges also affected the spatial genetic structure (IBR pattern). Although environmental variables had a significant effect on population genetic diversity parameters, no IBE pattern was found on genetic structure. Our study reveals that IBD was the driver that best explained the genetic structure, whereas environmental factors also played a role in determining genetic diversity values of this dominant plant of Mediterranean alpine environments.
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Affiliation(s)
- Javier Morente-López
- Área de Biodiversidad y Conservación, Escuela Superior de Ciencias Experimentales y Tecnología (ESCET), Universidad Rey Juan Carlos, Madrid, Spain
- *Correspondence: Javier Morente-López, José María Iriondo,
| | - Cristina García
- Department of Evolution, Ecology and Behaviour, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Plant Biology Group, CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Laboratório Associado, Universidade do Porto, Porto, Portugal
| | - Carlos Lara-Romero
- Área de Biodiversidad y Conservación, Escuela Superior de Ciencias Experimentales y Tecnología (ESCET), Universidad Rey Juan Carlos, Madrid, Spain
- Global Change Research Group, Mediterranean Institute for Advanced Studies (IMEDEA), Consejo Superior de Investigaciones Científicas (CSIC), Esporles, Spain
| | - Alfredo García-Fernández
- Área de Biodiversidad y Conservación, Escuela Superior de Ciencias Experimentales y Tecnología (ESCET), Universidad Rey Juan Carlos, Madrid, Spain
| | - David Draper
- Natural History and Systematics Research Group, cE3c, Centro de Ecologia, Evolução e Alterações Ambientais, Universidade de Lisboa, Lisbon, Portugal
- UBC Botanical Garden and Centre for Plant Research, Department of Botany, The University of British Columbia, Vancouver, BC, Canada
| | - José María Iriondo
- Área de Biodiversidad y Conservación, Escuela Superior de Ciencias Experimentales y Tecnología (ESCET), Universidad Rey Juan Carlos, Madrid, Spain
- *Correspondence: Javier Morente-López, José María Iriondo,
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Landscape Genomics: Understanding Relationships Between Environmental Heterogeneity and Genomic Characteristics of Populations. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/13836_2017_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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20
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Wang X, Li L, Zhao W, Zhao J, Chen X. Rhododendron aureum Georgi formed a special soil microbial community and competed with above-ground plants on the tundra of the Changbai Mountain, China. Ecol Evol 2017; 7:7503-7514. [PMID: 28944034 PMCID: PMC5606866 DOI: 10.1002/ece3.3307] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 06/25/2017] [Accepted: 07/15/2017] [Indexed: 01/22/2023] Open
Abstract
Rhododendron aureum Georgi is a perennial evergreen dwarf shrub that grows at all elevations within the alpine tundra of northern China. Previous research has investigated the plant communities of R. aureum; however, little information is available regarding interspecific competition and underground soil microbial community composition. The objective of our study was to determine whether the presence of R. aureum creates a unique soil microbiome and to investigate the relationship between R. aureum and other plant species. Our study site ranged from 1,800 to 2,600 m above sea level on the northern slope of the Changbai Mountain. The results show that the soil from sites with an R. aureum community had a higher abundance of nitrogen-fixing bacteria and a higher resistance to pathogens than soils from sites without R. aureum. We emphasize that R. aureum promotes a unique soil microbial community structure that is distinct from those associated with other plants. Elevation and microbial biomass were the main influencing factors for plant community structure. Analysis of interspecific relationships reveals that R. aureum is negatively associated with most other dominant shrubs and herbs, suggesting interspecific competition. It is necessary to focus on other dominant species if protection and restoration of the R. aureum competition is to occur. In the future, more is needed to prove whether R. aureum decreases species diversity in the tundra ecosystems of Changbai Mountain.
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Affiliation(s)
- Xiaolong Wang
- National and Local United Engineering Laboratory for Chinese Herbal Medicine Breeding and Cultivation School of Life Sciences Jilin University Changchun China
| | - Lin Li
- National and Local United Engineering Laboratory for Chinese Herbal Medicine Breeding and Cultivation School of Life Sciences Jilin University Changchun China
| | - Wei Zhao
- National and Local United Engineering Laboratory for Chinese Herbal Medicine Breeding and Cultivation School of Life Sciences Jilin University Changchun China
| | - Jiaxin Zhao
- National and Local United Engineering Laboratory for Chinese Herbal Medicine Breeding and Cultivation School of Life Sciences Jilin University Changchun China
| | - Xia Chen
- National and Local United Engineering Laboratory for Chinese Herbal Medicine Breeding and Cultivation School of Life Sciences Jilin University Changchun China
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21
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Mousavi S, Mariotti R, Bagnoli F, Costantini L, Cultrera NGM, Arzani K, Pandolfi S, Vendramin GG, Torkzaban B, Hosseini-Mazinani M, Baldoni L. The eastern part of the Fertile Crescent concealed an unexpected route of olive (Olea europaea L.) differentiation. ANNALS OF BOTANY 2017; 119:1305-1318. [PMID: 28387783 PMCID: PMC5604562 DOI: 10.1093/aob/mcx027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 02/28/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Olive is considered a native plant of the eastern side of the Mediterranean basin, from where it should have spread westward along the Mediterranean shores, while little is known about its diffusion in the eastern direction. METHODS Genetic diversity levels and population genetic structure of a wide set of olive ecotypes and varieties collected from several provinces of Iran, representing a high percentage of the entire olive resources present in the area, was screened with 49 chloroplast and ten nuclear simple sequence repeat markers, and coupled with archaeo-botanical and historical data on Mediterranean olive varieties. Approximate Bayesian Computation was applied to define the demographic history of olives including Iranian germplasm, and species distribution modelling was performed to understand the impact of the Late Quaternary on olive distribution. KEY RESULTS The results of the present study demonstrated that: (1) the climatic conditions of the last glacial maximum had an important role on the actual olive distribution, (2) all Iranian olive samples had the same maternal inheritance as Mediterranean cultivars, and (3) the nuclear gene flow from the Mediterranean basin to the Iranian plateau was almost absent, as well as the contribution of subspecies cuspidata to the diversity of Iranian olives. CONCLUSIONS Based on this evidence, a new scenario for the origin and distribution of this important fruit crop has been traced. The evaluation of olive trees growing in the eastern part of the Levant highlighted a new perspective on the spread and distribution of olive, suggesting two routes of olive differentiation, one westward, spreading along the Mediterranean basin, and another moving towards the east and reaching the Iranian plateau before its domestication.
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Affiliation(s)
- Soraya Mousavi
- CNR - Institute for Agricultural and Forest Systems in the Mediterranean, via Madonna Alta, 128, 06128 Perugia, Italy
- Tarbiat Modares University, Department of Horticultural Science, Jalal Ale Ahmad Highway, PO Box 14115111, Tehran, Iran
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-e Pajoohesh, Km 15, Tehran - Karaj Highway, PO Box 14965161, Tehran, Iran
- Co-first authors: These authors contributed equally to this work
| | - Roberto Mariotti
- CNR - Institute of Biosciences and Bioresources, via Madonna Alta, 130, 06128 Perugia, Italy
- Co-first authors: These authors contributed equally to this work
| | - Francesca Bagnoli
- CNR - Institute of Biosciences and Bioresources, Via Madonna del Piano, 10, 50019 Sesto Fiorentino, Florence, Italy
| | - Lorenzo Costantini
- ISMEO - International Association of Mediterranean and Oriental Studies, Corso Vittorio Emanuele II, 244, 00186 Rome, Italy
| | - Nicolò G. M. Cultrera
- CNR - Institute of Biosciences and Bioresources, via Madonna Alta, 130, 06128 Perugia, Italy
| | - Kazem Arzani
- Tarbiat Modares University, Department of Horticultural Science, Jalal Ale Ahmad Highway, PO Box 14115111, Tehran, Iran
| | - Saverio Pandolfi
- CNR - Institute of Biosciences and Bioresources, via Madonna Alta, 130, 06128 Perugia, Italy
| | - Giovanni Giuseppe Vendramin
- CNR - Institute of Biosciences and Bioresources, Via Madonna del Piano, 10, 50019 Sesto Fiorentino, Florence, Italy
| | - Bahareh Torkzaban
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-e Pajoohesh, Km 15, Tehran - Karaj Highway, PO Box 14965161, Tehran, Iran
| | - Mehdi Hosseini-Mazinani
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-e Pajoohesh, Km 15, Tehran - Karaj Highway, PO Box 14965161, Tehran, Iran
- For correspondence. E-mail or
| | - Luciana Baldoni
- CNR - Institute of Biosciences and Bioresources, via Madonna Alta, 130, 06128 Perugia, Italy
- For correspondence. E-mail or
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22
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Nadeau S, Meirmans PG, Aitken SN, Ritland K, Isabel N. The challenge of separating signatures of local adaptation from those of isolation by distance and colonization history: The case of two white pines. Ecol Evol 2016; 6:8649-8664. [PMID: 28035257 PMCID: PMC5192886 DOI: 10.1002/ece3.2550] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/25/2016] [Accepted: 09/06/2016] [Indexed: 01/13/2023] Open
Abstract
Accurately detecting signatures of local adaptation using genetic‐environment associations (GEAs) requires controlling for neutral patterns of population structure to reduce the risk of false positives. However, a high degree of collinearity between climatic gradients and neutral population structure can greatly reduce power, and the performance of GEA methods in such case is rarely evaluated in empirical studies. In this study, we attempted to disentangle the effects of local adaptation and isolation by environment (IBE) from those of isolation by distance (IBD) and isolation by colonization from glacial refugia (IBC) using range‐wide samples in two white pine species. For this, SNPs from 168 genes, including 52 candidate genes for growth and phenology, were genotyped in 133 and 61 populations of Pinus strobus and P. monticola, respectively. For P. strobus and using all 153 SNPs, climate (IBE) did not significantly explained among‐population variation when controlling for IBD and IBC in redundancy analyses (RDAs). However, 26 SNPs were significantly associated with climate in single‐locus GEA analyses (Bayenv2 and LFMM), suggesting that local adaptation took place in the presence of high gene flow. For P. monticola, we found no evidence of IBE using RDAs and weaker signatures of local adaptation using GEA and FST outlier tests, consistent with adaptation via phenotypic plasticity. In both species, the majority of the explained among‐population variation (69 to 96%) could not be partitioned between the effects of IBE, IBD, and IBC. GEA methods can account differently for this confounded variation, and this could explain the small overlap of SNPs detected between Bayenv2 and LFMM. Our study illustrates the inherent difficulty of taking into account neutral structure in natural populations and the importance of sampling designs that maximize climatic variation, while minimizing collinearity between climatic gradients and neutral structure.
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Affiliation(s)
- Simon Nadeau
- Natural Resources Canada Canadian Forest Service Laurentian Forestry Centre Québec QC Canada; Department of Forest and Conservation Sciences The University of British Columbia Vancouver BC Canada
| | - Patrick G Meirmans
- Institute for Biodiversity and Ecosystem Dynamics University of Amsterdam Amsterdam The Netherlands
| | - Sally N Aitken
- Department of Forest and Conservation Sciences The University of British Columbia Vancouver BC Canada
| | - Kermit Ritland
- Department of Forest and Conservation Sciences The University of British Columbia Vancouver BC Canada
| | - Nathalie Isabel
- Natural Resources Canada Canadian Forest Service Laurentian Forestry Centre Québec QC Canada
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23
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Brousseau L, Postolache D, Lascoux M, Drouzas AD, Källman T, Leonarduzzi C, Liepelt S, Piotti A, Popescu F, Roschanski AM, Zhelev P, Fady B, Vendramin GG. Local Adaptation in European Firs Assessed through Extensive Sampling across Altitudinal Gradients in Southern Europe. PLoS One 2016; 11:e0158216. [PMID: 27392065 PMCID: PMC4938419 DOI: 10.1371/journal.pone.0158216] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 06/13/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Local adaptation is a key driver of phenotypic and genetic divergence at loci responsible for adaptive traits variations in forest tree populations. Its experimental assessment requires rigorous sampling strategies such as those involving population pairs replicated across broad spatial scales. METHODS A hierarchical Bayesian model of selection (HBM) that explicitly considers both the replication of the environmental contrast and the hierarchical genetic structure among replicated study sites is introduced. Its power was assessed through simulations and compared to classical 'within-site' approaches (FDIST, BAYESCAN) and a simplified, within-site, version of the model introduced here (SBM). RESULTS HBM demonstrates that hierarchical approaches are very powerful to detect replicated patterns of adaptive divergence with low false-discovery (FDR) and false-non-discovery (FNR) rates compared to the analysis of different sites separately through within-site approaches. The hypothesis of local adaptation to altitude was further addressed by analyzing replicated Abies alba population pairs (low and high elevations) across the species' southern distribution range, where the effects of climatic selection are expected to be the strongest. For comparison, a single population pair from the closely related species A. cephalonica was also analyzed. The hierarchical model did not detect any pattern of adaptive divergence to altitude replicated in the different study sites. Instead, idiosyncratic patterns of local adaptation among sites were detected by within-site approaches. CONCLUSION Hierarchical approaches may miss idiosyncratic patterns of adaptation among sites, and we strongly recommend the use of both hierarchical (multi-site) and classical (within-site) approaches when addressing the question of adaptation across broad spatial scales.
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Affiliation(s)
- Louise Brousseau
- INRA, UR629 URFM Ecologie des Forêts Méditerranéennes, Domaine Saint Paul, Site Agroparc CS 40509, 84914 Avignon Cedex 9, France
- Institute of Biosciences and BioResources, National Research Council (IBBR-CNR), Division of Florence, Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy
| | - Dragos Postolache
- Institute of Biosciences and BioResources, National Research Council (IBBR-CNR), Division of Florence, Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy
- Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127 Pisa, Italy
- National Institute of Forest Research and Development (INCDS), Research Station Simeria, Str. Biscaria 1, 335900 Simeria, Romania
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Center and Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden
| | - Andreas D. Drouzas
- School of Biology, Aristotle University of Thessaloniki, GR-54124, Thessaloniki, Greece
| | - Thomas Källman
- Department of Ecology and Genetics, Evolutionary Biology Center and Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden
| | - Cristina Leonarduzzi
- Institute of Biosciences and BioResources, National Research Council (IBBR-CNR), Division of Florence, Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy
- Institute of Biosciences and BioResources, National Research Council (IBBR-CNR), Division of Palermo, National 3. Research Council—Corso Calatafimi, 414—I-90129, Palermo (PA), Italy
| | - Sascha Liepelt
- University of Marburg, Faculty of Biology, Conservation Biology, Karl-von-Frisch-Straße 35032 Marburg, Germany
| | - Andrea Piotti
- Institute of Biosciences and BioResources, National Research Council (IBBR-CNR), Division of Florence, Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy
| | - Flaviu Popescu
- National Institute of Forest Research and Development (INCDS), Research Station Simeria, Str. Biscaria 1, 335900 Simeria, Romania
| | - Anna M. Roschanski
- University of Marburg, Faculty of Biology, Conservation Biology, Karl-von-Frisch-Straße 35032 Marburg, Germany
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank Collections North, Inselstrasse 9, D-23999 Malchow/Poel, Germany
| | - Peter Zhelev
- University of Forestry, 10, Kl. Ohridsky Blvd., 1797 Sofia, Bulgaria
| | - Bruno Fady
- INRA, UR629 URFM Ecologie des Forêts Méditerranéennes, Domaine Saint Paul, Site Agroparc CS 40509, 84914 Avignon Cedex 9, France
| | - Giovanni Giuseppe Vendramin
- Institute of Biosciences and BioResources, National Research Council (IBBR-CNR), Division of Florence, Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy
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24
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He SL, Wang YS, Li DZ, Yi TS. Environmental and Historical Determinants of Patterns of Genetic Differentiation in Wild Soybean (Glycine soja Sieb. et Zucc). Sci Rep 2016; 6:22795. [PMID: 26952904 PMCID: PMC4782138 DOI: 10.1038/srep22795] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 02/18/2016] [Indexed: 11/09/2022] Open
Abstract
Wild soybean, the direct progenitor of cultivated soybean, inhabits a wide distribution range across the mainland of East Asia and the Japanese archipelago. A multidisciplinary approach combining analyses of population genetics based on 20 nuclear microsatellites and one plastid locus were applied to reveal the genetic variation of wild soybean, and the contributions of geographical, environmental factors and historic climatic change on its patterns of genetic differentiation. High genetic diversity and significant genetic differentiation were revealed in wild soybean. Wild soybean was inferred to be limited to southern and central China during the Last Glacial Maximum (LGM) and experienced large-scale post-LGM range expansion into northern East Asia. A substantial northward range shift has been predicted to occur by the 2080s. A stronger effect of isolation by environment (IBE) versus isolation by geographical distance (IBD) was found for genetic differentiation in wild soybean, which suggested that environmental factors were responsible for the adaptive eco-geographical differentiation. This study indicated that IBE and historical climatic change together shaped patterns of genetic variation and differentiation of wild soybean. Different conservation measures should be implemented on different populations according to their adaptive potential to future changes in climate and human-induced environmental changes.
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Affiliation(s)
- Shui-Lian He
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, 650201, China
| | - Yun-Sheng Wang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- School of Environmental and life Science, Kaili University, Kaili, 650201, China
| | - De-Zhu Li
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Ting-Shuang Yi
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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25
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Roschanski AM, Csilléry K, Liepelt S, Oddou-Muratorio S, Ziegenhagen B, Huard F, Ullrich KK, Postolache D, Vendramin GG, Fady B. Evidence of divergent selection for drought and cold tolerance at landscape and local scales inAbies albaMill. in the French Mediterranean Alps. Mol Ecol 2016; 25:776-94. [DOI: 10.1111/mec.13516] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 11/20/2015] [Accepted: 12/09/2015] [Indexed: 01/13/2023]
Affiliation(s)
- Anna M. Roschanski
- Conservation Biology; Faculty of Biology; University of Marburg; Karl-von-Frisch-Straße Marburg 35032 Germany
| | - Katalin Csilléry
- INRA, UR629; Ecologie des Forêts Méditerranéennes (URFM); Avignon Cedex 9 84914 France
| | - Sascha Liepelt
- Conservation Biology; Faculty of Biology; University of Marburg; Karl-von-Frisch-Straße Marburg 35032 Germany
| | | | - Birgit Ziegenhagen
- Conservation Biology; Faculty of Biology; University of Marburg; Karl-von-Frisch-Straße Marburg 35032 Germany
| | | | - Kristian K. Ullrich
- Cell Biology; Faculty of Biology; University of Marburg; Karl-von-Frisch-Straße Marburg 35032 Germany
| | - Dragos Postolache
- Scuola Superiore Sant'Anna; Piazza Martiri della Libertà 33 Pisa 56127 Italy
- Institute of Biosciences and Bioresources; National Research Council (CNR); Via Madonna del Piano 10 Sesto Fiorentino (Firenze) 50019 Italy
- National Institute of Forest Research and Development (INCDS); Simeria Research Station; Str. Biscaria 1 Simeria 335900 Romania
| | - Giovanni G. Vendramin
- Institute of Biosciences and Bioresources; National Research Council (CNR); Via Madonna del Piano 10 Sesto Fiorentino (Firenze) 50019 Italy
| | - Bruno Fady
- INRA, UR629; Ecologie des Forêts Méditerranéennes (URFM); Avignon Cedex 9 84914 France
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26
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Mayol M, Riba M, González-Martínez SC, Bagnoli F, de Beaulieu JL, Berganzo E, Burgarella C, Dubreuil M, Krajmerová D, Paule L, Romšáková I, Vettori C, Vincenot L, Vendramin GG. Adapting through glacial cycles: insights from a long-lived tree (Taxus baccata). THE NEW PHYTOLOGIST 2015; 208:973-986. [PMID: 26096330 DOI: 10.1111/nph.13496] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/30/2015] [Indexed: 06/04/2023]
Abstract
Despite the large body of research devoted to understanding the role of Quaternary glacial cycles in the genetic divergence of European trees, the differential contribution of geographic isolation and/or environmental adaptation in creating population genetic divergence remains unexplored. In this study, we used a long-lived tree (Taxus baccata) as a model species to investigate the impact of Quaternary climatic changes on genetic diversity via neutral (isolation-by-distance) and selective (isolation-by-adaptation) processes. We applied approximate Bayesian computation to genetic data to infer its demographic history, and combined this information with past and present climatic data to assess the role of environment and geography in the observed patterns of genetic structure. We found evidence that yew colonized Europe from the East, and that European samples diverged into two groups (Western, Eastern) at the beginning of the Quaternary glaciations, c. 2.2 Myr before present. Apart from the expected effects of geographical isolation during glacials, we discovered a significant role of environmental adaptation during interglacials at the origin of genetic divergence between both groups. This process may be common in other organisms, providing new research lines to explore the effect of Quaternary climatic factors on present-day patterns of genetic diversity.
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Affiliation(s)
| | - Miquel Riba
- CREAF, Cerdanyola del Vallès, 08193, Spain
- Univ Autonòma Barcelona, Cerdanyola del Vallès, 08193, Spain
| | | | - Francesca Bagnoli
- Plant Protection Institute, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino (FI), Italy
| | | | | | - Concetta Burgarella
- Université Montpellier 2, CNRS UMR, Institut de Sciences de l'Evolution de Montpellier, Montpellier, 5554, France
| | | | - Diana Krajmerová
- Faculty of Forestry, Technical University, SK-96053, Zvolen, Slovakia
| | - Ladislav Paule
- Faculty of Forestry, Technical University, SK-96053, Zvolen, Slovakia
| | - Ivana Romšáková
- Faculty of Forestry, Technical University, SK-96053, Zvolen, Slovakia
| | - Cristina Vettori
- Institute of Biosciences and Bioresources, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino (FI), Italy
| | | | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino (FI), Italy
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27
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Micro- and macro-geographic scale effect on the molecular imprint of selection and adaptation in Norway spruce. PLoS One 2014; 9:e115499. [PMID: 25551624 PMCID: PMC4281139 DOI: 10.1371/journal.pone.0115499] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 11/19/2014] [Indexed: 11/19/2022] Open
Abstract
Forest tree species of temperate and boreal regions have undergone a long history of demographic changes and evolutionary adaptations. The main objective of this study was to detect signals of selection in Norway spruce (Picea abies [L.] Karst), at different sampling-scales and to investigate, accounting for population structure, the effect of environment on species genetic diversity. A total of 384 single nucleotide polymorphisms (SNPs) representing 290 genes were genotyped at two geographic scales: across 12 populations distributed along two altitudinal-transects in the Alps (micro-geographic scale), and across 27 populations belonging to the range of Norway spruce in central and south-east Europe (macro-geographic scale). At the macrogeographic scale, principal component analysis combined with Bayesian clustering revealed three major clusters, corresponding to the main areas of southern spruce occurrence, i.e. the Alps, Carpathians, and Hercynia. The populations along the altitudinal transects were not differentiated. To assess the role of selection in structuring genetic variation, we applied a Bayesian and coalescent-based FST-outlier method and tested for correlations between allele frequencies and climatic variables using regression analyses. At the macro-geographic scale, the FST-outlier methods detected together 11 FST-outliers. Six outliers were detected when the same analyses were carried out taking into account the genetic structure. Regression analyses with population structure correction resulted in the identification of two (micro-geographic scale) and 38 SNPs (macro-geographic scale) significantly correlated with temperature and/or precipitation. Six of these loci overlapped with FST-outliers, among them two loci encoding an enzyme involved in riboflavin biosynthesis and a sucrose synthase. The results of this study indicate a strong relationship between genetic and environmental variation at both geographic scales. It also suggests that an integrative approach combining different outlier detection methods and population sampling at different geographic scales is useful to identify loci potentially involved in adaptation.
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28
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Csilléry K, Lalagüe H, Vendramin GG, González-Martínez SC, Fady B, Oddou-Muratorio S. Detecting short spatial scale local adaptation and epistatic selection in climate-related candidate genes in European beech (Fagus sylvatica) populations. Mol Ecol 2014; 23:4696-708. [PMID: 25156570 DOI: 10.1111/mec.12902] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 08/20/2014] [Accepted: 08/22/2014] [Indexed: 01/17/2023]
Abstract
Detecting signatures of selection in tree populations threatened by climate change is currently a major research priority. Here, we investigated the signature of local adaptation over a short spatial scale using 96 European beech (Fagus sylvatica L.) individuals originating from two pairs of populations on the northern and southern slopes of Mont Ventoux (south-eastern France). We performed both single and multilocus analysis of selection based on 53 climate-related candidate genes containing 546 SNPs. FST outlier methods at the SNP level revealed a weak signal of selection, with three marginally significant outliers in the northern populations. At the gene level, considering haplotypes as alleles, two additional marginally significant outliers were detected, one on each slope. To account for the uncertainty of haplotype inference, we averaged the Bayes factors over many possible phase reconstructions. Epistatic selection offers a realistic multilocus model of selection in natural populations. Here, we used a test suggested by Ohta based on the decomposition of the variance of linkage disequilibrium. Overall populations, 0.23% of the SNP pairs (haplotypes) showed evidence of epistatic selection, with nearly 80% of them being within genes. One of the between gene epistatic selection signals arose between an FST outlier and a nonsynonymous mutation in a drought response gene. Additionally, we identified haplotypes containing selectively advantageous allele combinations which were unique to high or low elevations and northern or southern populations. Several haplotypes contained nonsynonymous mutations situated in genes with known functional importance for adaptation to climatic factors.
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Affiliation(s)
- Katalin Csilléry
- UR629, Écologie Forestière Méditerranéenne, INRA, Domaine Saint Paul, Avignon, F-84914, France
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29
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Dillon S, McEvoy R, Baldwin DS, Rees GN, Parsons Y, Southerton S. Characterisation of adaptive genetic diversity in environmentally contrasted populations of Eucalyptus camaldulensis Dehnh. (river red gum). PLoS One 2014; 9:e103515. [PMID: 25093589 PMCID: PMC4122390 DOI: 10.1371/journal.pone.0103515] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 06/30/2014] [Indexed: 12/02/2022] Open
Abstract
As an increasing number of ecosystems face departures from long standing environmental conditions under climate change, our understanding of the capacity of species to adapt will become important for directing conservation and management of biodiversity. Insights into the potential for genetic adaptation might be gained by assessing genomic signatures of adaptation to historic or prevailing environmental conditions. The river red gum (Eucalyptus camaldulensis Dehnh.) is a widespread Australian eucalypt inhabiting riverine and floodplain habitats which spans strong environmental gradients. We investigated the effects of adaptation to environment on population level genetic diversity of E. camaldulensis, examining SNP variation in candidate gene loci sampled across 20 climatically diverse populations approximating the species natural distribution. Genetic differentiation among populations was high (F(ST) = 17%), exceeding previous estimates based on neutral markers. Complementary statistical approaches identified 6 SNP loci in four genes (COMT, Dehydrin, ERECTA and PIP2) which, after accounting for demographic effects, exhibited higher than expected levels of genetic differentiation among populations and whose allelic variation was associated with local environment. While this study employs but a small proportion of available diversity in the eucalyptus genome, it draws our attention to the potential for application of wide spread eucalypt species to test adaptive hypotheses.
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Affiliation(s)
| | - Rachel McEvoy
- Department of Genetics, La Trobe University, Bundoora, VIC, Australia
| | - Darren S. Baldwin
- Murray Darling Freshwater Research Centre, Wodonga, VIC, Australia
- CSIRO Land and Water Flagship, Wodonga, VIC, Australia
| | - Gavin N. Rees
- Murray Darling Freshwater Research Centre, Wodonga, VIC, Australia
- CSIRO Land and Water Flagship, Wodonga, VIC, Australia
| | - Yvonne Parsons
- Department of Genetics, La Trobe University, Bundoora, VIC, Australia
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