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Aihara T, Araki K, Onuma Y, Cai Y, Paing AMM, Goto S, Hisamoto Y, Tomaru N, Homma K, Takagi M, Yoshida T, Iio A, Nagamatsu D, Kobayashi H, Hirota M, Uchiyama K, Tsumura Y. Divergent mechanisms of reduced growth performance in Betula ermanii saplings from high-altitude and low-latitude range edges. Heredity (Edinb) 2023; 131:387-397. [PMID: 37940658 PMCID: PMC10673911 DOI: 10.1038/s41437-023-00655-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023] Open
Abstract
The reduced growth performance of individuals from range edges is a common phenomenon in various taxa, and considered to be an evolutionary factor that limits the species' range. However, most studies did not distinguish between two mechanisms that can lead to this reduction: genetic load and adaptive selection to harsh conditions. To address this lack of understanding, we investigated the climatic and genetic factors underlying the growth performance of Betula ermanii saplings transplanted from 11 populations including high-altitude edge and low-latitude edge population. We estimated the climatic position of the populations within the overall B. ermanii's distribution, and the genetic composition and diversity using restriction-site associated DNA sequencing, and measured survival, growth rates and individual size of the saplings. The high-altitude edge population (APW) was located below the 95% significance interval for the mean annual temperature range, but did not show any distinctive genetic characteristics. In contrast, the low-latitude edge population (SHK) exhibited a high level of linkage disequilibrium, low genetic diversity, a distinct genetic composition from the other populations, and a high relatedness coefficient. Both APW and SHK saplings displayed lower survival rates, heights and diameters, while SHK saplings also exhibited lower growth rates than the other populations' saplings. The low heights and diameters of APW saplings was likely the result of adaptive selection to harsh conditions, while the low survival and growth rates of SHK saplings was likely the result of genetic load. Our findings shed light on the mechanisms underlying the reduced growth performance of range-edge populations.
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Affiliation(s)
- Takaki Aihara
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Kyoko Araki
- Garden Division, Maintenance and Works Department, the Imperial Household Agency, 1-1, Chiyoda, Chiyoda-ku, Tokyo, 100-8111, Japan
- Graduate School of Science and Technology, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Yunosuke Onuma
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Yihan Cai
- Graduate School of Environmental Science, Hokkaido University, Kita 10 Nishi 5, Kita-ku, Sapporo, 060-0810, Japan
| | - Aye Myat Myat Paing
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Susumu Goto
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yoko Hisamoto
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Nobuhiro Tomaru
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Cikusa-ku, Nagoya, Aichi, 464-0804, Japan
| | - Kosuke Homma
- Sado Island Center for Ecological Sustainability, Niigata University, 1101-1, Niibokatagami, Sado, Niigata, 952-0103, Japan
| | - Masahiro Takagi
- Faculty of Agriculture, University of Miyazaki, 1-1, Gakuen kibanadai nishi, Miyazaki, Miyazaki, 889-2192, Japan
| | - Toshiya Yoshida
- Field Science Center for Northern Biosphere, Hokkaido University, Kita 10 Nishi 5, Kita-ku, Sapporo, 060-0810, Japan
| | - Atsuhiro Iio
- Graduate School of Integrated Science and Technology, Shizuoka University, 836, Ohtani, Suruga-ku, Shizuoka, Shizuoka, 422-8017, Japan
| | - Dai Nagamatsu
- Faculty of Agriculture, Tottori University, 4-101, Koyama-cho, Tottori, Tottori, 680-8553, Japan
| | - Hajime Kobayashi
- Faculty of Agriculture, Shinshu University, 8304, Minamiminowa-mura, Kamiina-gun, Nagano, 399-4598, Japan
| | - Mitsuru Hirota
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Kentaro Uchiyama
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, 1, Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan
| | - Yoshihiko Tsumura
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki, 305-8577, Japan.
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Su Y, Liu L, Deng Q, Lü Z, Wang Z, He Z, Wang T. Epigenetic architecture of Pseudotaxus chienii: Revealing the synergistic effects of climate and soil variables. Ecol Evol 2023; 13:e10511. [PMID: 37701023 PMCID: PMC10493196 DOI: 10.1002/ece3.10511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 07/27/2023] [Accepted: 08/07/2023] [Indexed: 09/14/2023] Open
Abstract
Whether conifers can withstand environmental changes especially temperature fluctuations has been controversial. Epigenetic analysis may provide new perspectives for solving the issue. Pseudotaxus chienii is an endangered gymnosperm species endemic to China. In this study, we have examined the genetic and epigenetic variations in its natural populations aiming to disentangle the synergistic effects of climate and soil on its population (epi)genetic differentiation by using amplified fragment length polymorphism (AFLP) and methylation-sensitive AFLP (MSAP) techniques. We identified 23 AFLP and 26, 7, and 5 MSAP outliers in P. chienii. Twenty-one of the putative adaptive AFLP loci were found associated with climate and/or soil variables including precipitation, temperature, K, Fe, Zn, and Cu, whereas 21, 7, and 4 MSAP outliers were significantly related to precipitation of wettest month (Bio13), precipitation driest of month (Bio14), percent tree cover (PTC), and soil Fe, Mn, and Cu compositions. Total precipitation and precipitation in the driest seasons were the most influential factors for genetic and epigenetic variation, respectively. In addition, a high full-methylation level and a strong correlation between genetic and epigenetic variation were detected in P. chienii. Climate is found of greater importance than soil in shaping adaptive (epi)genetic differentiation, and the synergistic effects of climate and climate-soil variables were also observed. The identified climate and soil variables should be considered when applying ex situ conservation.
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Affiliation(s)
- Yingjuan Su
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
- Research Institute of Sun Yat‐sen University in ShenzhenShenzhenChina
| | - Li Liu
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Qi Deng
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
- School of MedicineGuangxi University of Science and TechnologyLiuzhouChina
| | - Zhuyan Lü
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Zhen Wang
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Ziqing He
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Ting Wang
- Research Institute of Sun Yat‐sen University in ShenzhenShenzhenChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
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Zhang Y, Qi S, Liu L, Bao Q, Wu T, Liu W, Zhang Y, Zhao W, Xu Q, Chen G. Genetic Diversity Analysis and Breeding of Geese Based on the Mitochondrial ND6 Gene. Genes (Basel) 2023; 14:1605. [PMID: 37628656 PMCID: PMC10454708 DOI: 10.3390/genes14081605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
To explore the differences in body-weight traits of five goose breeds and analyze their genetic diversity and historical dynamics, we collected body-weight data statistics and used Sanger sequencing to determine the mitochondrial DNA of 100 samples of five typical goose breeds in China and abroad. The results indicated that Lion-Head, Hortobagy, and Yangzhou geese have great breeding potential for body weight. Thirteen polymorphic sites were detected in the corrected 505 bp sequence of the mitochondrial DNA (mtDNA) ND6 gene, accounting for approximately 2.57% of the total number of sites. The guanine-cytosine (GC) content (51.7%) of the whole sequence was higher than the adenine-thymine (AT) content (48.3%), showing a certain GC base preference. There were 11 haplotypes among the five breeds, including one shared haplotype. We analyzed the differences in the distribution of base mismatches among the five breeds and conducted Tajima's D and Fu's Fs neutral tests on the historical dynamics of the populations. The distribution of the mismatch difference presented an unsmooth single peak and the Tajima's D value of the neutral test was negative (D < 0) and reached a significant level, which proves that the population of the three species had expanded; the Lion-Head goose population tends to be stable. The genetic diversity of Lion-Head, Zhedong White, Yangzhou, and Taihu geese was equal to the average diversity of Chinese goose breeds. The Hortobagy goose is a foreign breed with differences in mating line breeding and hybrid advantage utilization.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Guohong Chen
- Key Laboratory for Evaluation and Utilization of Poultry Genetic Resources of Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China; (Y.Z.); (S.Q.); (L.L.); (Q.B.); (T.W.); (W.L.); (Y.Z.); (W.Z.); (Q.X.)
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García-García I, Méndez-Cea B, González de Andrés E, Gazol A, Sánchez-Salguero R, Manso-Martínez D, Horreo JL, Camarero JJ, Linares JC, Gallego FJ. Climate and Soil Microsite Conditions Determine Local Adaptation in Declining Silver Fir Forests. PLANTS (BASEL, SWITZERLAND) 2023; 12:2607. [PMID: 37514222 PMCID: PMC10384727 DOI: 10.3390/plants12142607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/15/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023]
Abstract
Ongoing climatic change is threatening the survival of drought-sensitive tree species, such as silver fir (Abies alba). Drought-induced dieback had been previously explored in this conifer, although the role played by tree-level genetic diversity and its relationship with growth patterns and soil microsite conditions remained elusive. We used double digest restriction-site-associated DNA sequencing (ddRADseq) to describe different genetic characteristics of five silver fir forests in the Spanish Pyrenees, including declining and non-declining trees. Single nucleotide polymorphisms (SNPs) were used to investigate the relationships between genetics, dieback, intraspecific trait variation (functional dendrophenotypic traits and leaf traits), local bioclimatic conditions, and rhizosphere soil properties. While there were no noticeable genetic differences between declining and non-declining trees, genome-environment associations with selection signatures were abundant, suggesting a strong influence of climate, soil physicochemical properties, and soil microbial diversity on local adaptation. These results provide novel insights into how genetics and diverse environmental factors are interrelated and highlight the need to incorporate genetic data into silver fir forest dieback studies to gain a better understanding of local adaptation.
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Affiliation(s)
- Isabel García-García
- Departamento de Genética, Fisiología y Microbiología, Unidad de Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Belén Méndez-Cea
- Departamento de Genética, Fisiología y Microbiología, Unidad de Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | | | - Antonio Gazol
- Instituto Pirenaico de Ecología (IPE-CSIC), 50059 Zaragoza, Spain
| | - Raúl Sánchez-Salguero
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - David Manso-Martínez
- Departamento de Genética, Fisiología y Microbiología, Unidad de Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Jose Luis Horreo
- Departamento de Genética, Fisiología y Microbiología, Unidad de Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - J Julio Camarero
- Instituto Pirenaico de Ecología (IPE-CSIC), 50059 Zaragoza, Spain
| | - Juan Carlos Linares
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Francisco Javier Gallego
- Departamento de Genética, Fisiología y Microbiología, Unidad de Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
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Ji R, Yu X, Ren T, Chang Y, Li Z, Xia X, Yin W, Liu C. Genetic diversity and population structure of Caryopteris mongholica revealed by reduced representation sequencing. BMC PLANT BIOLOGY 2022; 22:297. [PMID: 35710341 PMCID: PMC9205053 DOI: 10.1186/s12870-022-03681-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Caryopteris mongholica Bunge is a rare broad-leaved shrub distributed in the desert and arid regions of Mongol and North China. Due to land reclamation, natural habitat deterioration and anthropogenic activities in recent years, the wild resources have sharply reduced. To effectively protect and rationally use it, we investigated the genetic diversity and population structure from 18 populations across the range of C. mongholica in China by reduced representation sequencing technology. RESULTS We found the overall average values of observed heterozygosity (Ho), expected heterozygosity (He), and average nucleotide diversity (π) were 0.43, 0.35 and 0.135, respectively. Furthermore, the NM17 population exhibited higher genetic diversity than other populations. The phylogenetic tree, principal component analysis (PCA) and structure analysis showed the sampled individuals clustered into two main groups. The NM03 population, with individuals clustered in both groups, may be a transitional population located between the two groups. In addition, most genetic variation existed within populations (90.97%) compared to that among the populations (9.03%). Interestingly, geographic and environmental distances were almost equally important to the observed genetic differences. Redundancy analysis (RDA) identified optical radiation (OR), minimum temperature (MIT) and mean annual precipitation (MAP) related variables as the most important environment factors influencing genetic variation, and the importance of MIT was also confirmed in the latent factor mixed models (LFMM). CONCLUSIONS The results of this study facilitate research on the genetic diversity of C. mongholica. These genetic features provided vital information for conserving and sustainably developing the C. mongholica genetic resources.
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Affiliation(s)
- Ruoxuan Ji
- College of Biological Sciences and Biotechnology, National Engineering Research Center of Tree Breeding, Beijing Forestry University, Beijing, China
| | - Xiao Yu
- College of Biological Sciences and Biotechnology, National Engineering Research Center of Tree Breeding, Beijing Forestry University, Beijing, China
| | - Tianmeng Ren
- College of Biological Sciences and Biotechnology, National Engineering Research Center of Tree Breeding, Beijing Forestry University, Beijing, China
| | - Yuan Chang
- College of Biological Sciences and Biotechnology, National Engineering Research Center of Tree Breeding, Beijing Forestry University, Beijing, China
| | - Zheng Li
- College of Biological Sciences and Biotechnology, National Engineering Research Center of Tree Breeding, Beijing Forestry University, Beijing, China
| | - Xinli Xia
- College of Biological Sciences and Biotechnology, National Engineering Research Center of Tree Breeding, Beijing Forestry University, Beijing, China
| | - Weilun Yin
- College of Biological Sciences and Biotechnology, National Engineering Research Center of Tree Breeding, Beijing Forestry University, Beijing, China
| | - Chao Liu
- College of Biological Sciences and Biotechnology, National Engineering Research Center of Tree Breeding, Beijing Forestry University, Beijing, China.
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Candidate Genes for the High-Altitude Adaptations of Two Mountain Pine Taxa. Int J Mol Sci 2021; 22:ijms22073477. [PMID: 33801727 PMCID: PMC8036860 DOI: 10.3390/ijms22073477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 01/26/2023] Open
Abstract
Mountain plants, challenged by vegetation time contractions and dynamic changes in environmental conditions, developed adaptations that help them to balance their growth, reproduction, survival, and regeneration. However, knowledge regarding the genetic basis of species adaptation to higher altitudes remain scarce for most plant species. Here, we attempted to identify such corresponding genomic regions of high evolutionary importance in two closely related European pines, Pinus mugo and P. uncinata, contrasting them with a reference lowland relative—P. sylvestris. We genotyped 438 samples at thousands of single nucleotide polymorphism (SNP) markers, tested their genetic differentiation and population structure followed by outlier detection and gene ontology annotations. Markers clearly differentiated the species and uncovered patterns of population structure in two of them. In P. uncinata three Pyrenean sites were grouped together, while two outlying populations constituted a separate cluster. In P. sylvestris, Spanish population appeared distinct from the remaining four European sites. Between mountain pines and the reference species, 35 candidate genes for altitude-dependent selection were identified, including such encoding proteins responsible for photosynthesis, photorespiration and cell redox homeostasis, regulation of transcription, and mRNA processing. In comparison between two mountain pines, 75 outlier SNPs were found in proteins involved mainly in the gene expression and metabolism.
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Yang Y, Zhou T, Qian Z, Zhao G. Phylogenetic relationships in Chinese oaks (Fagaceae, Quercus): Evidence from plastid genome using low-coverage whole genome sequencing. Genomics 2021; 113:1438-1447. [PMID: 33744343 DOI: 10.1016/j.ygeno.2021.03.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 01/19/2021] [Accepted: 03/05/2021] [Indexed: 01/29/2023]
Abstract
China is a second center of oak diversity but with less intensively systematic studies. Here, with 49 species representing all four sections in China, we firstly gave insight into the comprehensive phylogenetic relationships of Chinese oaks based on 54 complete plastid genomes. Our results recovered a robust phylogenetic framework and provided strong support for most nodes. The phylogenetic tree supported Quercus section Ilex as not monophyletic, in which Quercus section Cyclobalanopsis and Quercus section Cerris were nested. Most likely, incomplete lineage sorting and/or introgression among ancestral lineages in these three sections resulted in this complex pattern. The current distribution, diversification and molecular differentiation of Q. sect. Ilex in China are likely consequences of local adaptation to the geographic and paleoclimatic changes, which were driven by the uplift of Tibetan Plateau, the Hengduan Mountains and the Himalayas.
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Affiliation(s)
- Yanci Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, China; School of Biological Science and Technology, Baotou Teachers' College, Baotou, China
| | - Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Zengqiang Qian
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Guifang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, China.
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Cruz-Nicolás J, Villarruel-Arroyo A, Gernandt DS, Fonseca RM, Aguirre-Planter E, Eguiarte LE, Jaramillo-Correa JP. Non-adaptive evolutionary processes governed the diversification of a temperate conifer lineage after its migration into the tropics. Mol Phylogenet Evol 2021; 160:107125. [PMID: 33636326 DOI: 10.1016/j.ympev.2021.107125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 11/16/2022]
Abstract
Constructing phylogenetic relationships among closely related species is a recurrent challenge in evolutionary biology, particularly for long-lived taxa with large effective population sizes and uncomplete reproductive isolation, like conifers. Conifers further have slow evolutionary rates, which raises the question of whether adaptive or non/adaptive processes were predominantly involved when they rapidly diversified after migrating from temperate regions into the tropical mountains. Indeed, fine-scale phylogenetic relationships within several conifer genus remain under debate. Here, we studied the phylogenetic relationships of endemic firs (Abies, Pinaceae) discontinuously distributed in the montane forests from the Southwestern United States to Guatemala, and addressed several hypotheses related to adaptive and non-adaptive radiations. We derived over 80 K SNPs from genotyping by sequencing (GBS) for 45 individuals of nine Mesoamerican species to perform phylogenetic analyses. Both Maximum Likelihood and quartets-inference phylogenies resulted in a well-resolved topology, showing a single fir lineage divided in four subgroups that coincided with the main mountain ranges of Mesoamerica; thus having important taxonomic implications. Such subdivision fitted a North-South isolation by distance framework, in which non-adaptive allopatric processes seemed the rule. Interestingly, several reticulations were observed within subgroups, especially in the central-south region, which may explain past difficulties for generating infrageneric phylogenies. Further evidence for non-adaptive processes was obtained from analyses of 21 candidate-gene regions, which exhibited diminishing values of πa/πs and Ka/Ks with latitude, thus indicating reduced efficiency of purifying selection towards the Equator. Our study indicates that non-adaptive allopatric processes may be key generators of species diversity and endemism in the tropics.
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Affiliation(s)
- Jorge Cruz-Nicolás
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, Mexico City CDMX 04510, Mexico
| | - Alfredo Villarruel-Arroyo
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, Mexico City CDMX 04510, Mexico
| | - David S Gernandt
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, AP 70-233, Mexico City CDMX 04510, Mexico
| | - Rosa María Fonseca
- Laboratorio de Plantas Vasculares, Facultad de Ciencias, Universidad Nacional Autónoma de México, AP 70-282, Mexico City CDMX 04510, Mexico
| | - Erika Aguirre-Planter
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, Mexico City CDMX 04510, Mexico
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, Mexico City CDMX 04510, Mexico
| | - Juan P Jaramillo-Correa
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, Mexico City CDMX 04510, Mexico.
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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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Perry A, Wachowiak W, Downing A, Talbot R, Cavers S. Development of a single nucleotide polymorphism array for population genomic studies in four European pine species. Mol Ecol Resour 2020; 20:1697-1705. [PMID: 32633888 DOI: 10.1111/1755-0998.13223] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 06/03/2020] [Accepted: 06/25/2020] [Indexed: 02/06/2023]
Abstract
Pines are some of the most ecologically and economically important tree species in the world, and many have enormous natural distributions or have been extensively planted. However, a lack of rapid genotyping capability is hampering progress in understanding the molecular basis of genetic variation in these species. Here, we deliver an efficient tool for genotyping thousands of single nucleotide polymorphism (SNP) markers across the genome that can be applied to genetic studies in pines. Polymorphisms from resequenced candidate genes and transcriptome sequences of P. sylvestris, P. mugo, P. uncinata, P. uliginosa and P. radiata were used to design a 49,829 SNP array (Axiom_PineGAP, Thermo Fisher). Over a third (34.68%) of the unigenes identified from the P. sylvestris transcriptome were represented on the array, which was used to screen samples of four pine species. The conversion rate for the array on all samples was 42% (N = 20,795 SNPs) and was similar for SNPs sourced from resequenced candidate gene and transcriptome sequences. The broad representation of gene ontology terms by unigenes containing converted SNPs reflected their coverage across the full transcriptome. Over a quarter of successfully converted SNPs were polymorphic among all species, and the data were successful in discriminating among the species and some individual populations. The SNP array provides a valuable new tool to advance genetic studies in these species and demonstrates the effectiveness of the technology for rapid genotyping in species with large and complex genomes.
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Affiliation(s)
- Annika Perry
- UK Centre for Ecology & Hydrology Edinburgh, Penicuik, UK
| | - Witold Wachowiak
- Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Alison Downing
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
| | - Richard Talbot
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
| | - Stephen Cavers
- UK Centre for Ecology & Hydrology Edinburgh, Penicuik, UK
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Jia K, Zhao W, Maier PA, Hu X, Jin Y, Zhou S, Jiao S, El‐Kassaby YA, Wang T, Wang X, Mao J. Landscape genomics predicts climate change-related genetic offset for the widespread Platycladus orientalis (Cupressaceae). Evol Appl 2020; 13:665-676. [PMID: 32211059 PMCID: PMC7086053 DOI: 10.1111/eva.12891] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 10/30/2019] [Accepted: 11/03/2019] [Indexed: 12/22/2022] Open
Abstract
Understanding and quantifying populations' adaptive genetic variation and their response to climate change are critical to reforestation's seed source selection, forest management decisions, and gene conservation. Landscape genomics combined with geographic and environmental information provide an opportunity to interrogate forest populations' genome-wide variation for understanding the extent to which evolutionary forces shape past and contemporary populations' genetic structure, and identify those populations that may be most at risk under future climate change. Here, we used genotyping by sequencing to generate over 11,000 high-quality variants from Platycladus orientalis range-wide collection to evaluate its diversity and to predict genetic offset under future climate scenarios. Platycladus orientalis is a widespread conifer in China with significant ecological, timber, and medicinal values. We found population structure and evidences of isolation by environment, indicative of adaptation to local conditions. Gradient forest modeling identified temperature-related variables as the most important environmental factors influencing genetic variation and predicted areas with higher risk under future climate change. This study provides an important reference for forest resource management and conservation for P. orientalis.
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Affiliation(s)
- Kai‐Hua Jia
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingKey Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Wei Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingKey Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | | | - Xian‐Ge Hu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingKey Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yuqing Jin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingKey Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Shan‐Shan Zhou
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingKey Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Si‐Qian Jiao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingKey Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yousry A El‐Kassaby
- Department of Forest and Conservation SciencesFaculty of ForestryThe University of British ColumbiaVancouverBCCanada
| | - Tongli Wang
- Department of Forest and Conservation SciencesFaculty of ForestryThe University of British ColumbiaVancouverBCCanada
| | - Xiao‐Ru Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingKey Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Department of Ecology and Environmental ScienceUPSCUmeå UniversityUmeåSweden
| | - Jian‐Feng Mao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignNational Engineering Laboratory for Tree BreedingKey Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
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12
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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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13
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Silva AR, Resende-Moreira LC, Carvalho CS, Lanes ECM, Ortiz-Vera MP, Viana PL, Jaffé R. Range-wide neutral and adaptive genetic structure of an endemic herb from Amazonian Savannas. AOB PLANTS 2020; 12:plaa003. [PMID: 32128104 PMCID: PMC7043808 DOI: 10.1093/aobpla/plaa003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/28/2020] [Indexed: 05/05/2023]
Abstract
Conserving genetic diversity in rare and narrowly distributed endemic species is essential to maintain their evolutionary potential and minimize extinction risk under future environmental change. In this study we assess neutral and adaptive genetic structure and genetic diversity in Brasilianthus carajensis (Melastomataceae), an endemic herb from Amazonian Savannas. Using RAD sequencing we identified a total of 9365 SNPs in 150 individuals collected across the species' entire distribution range. Relying on assumption-free genetic clustering methods and environmental association tests we then compared neutral with adaptive genetic structure. We found three neutral and six adaptive genetic clusters, which could be considered management units (MU) and adaptive units (AU), respectively. Pairwise genetic differentiation (F ST) ranged between 0.024 and 0.048, and even though effective population sizes were below 100, no significant inbreeding was found in any inferred cluster. Nearly 10 % of all analysed sequences contained loci associated with temperature and precipitation, from which only 25 sequences contained annotated proteins, with some of them being very relevant for physiological processes in plants. Our findings provide a detailed insight into genetic diversity, neutral and adaptive genetic structure in a rare endemic herb, which can help guide conservation and management actions to avoid the loss of unique genetic variation.
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Affiliation(s)
- Amanda R Silva
- Universidade Federal Rural da Amazônia/Museu Paraense Emílio Goeldi, Programa de Pós-graduação em Ciências Biológicas - Botânica Tropical, Belém-PA, Brazil
- Museu Paraense Emílio Goeldi, Programa de Capacitação Institucional (PCI), Belém-PA, Brazil
| | | | | | - Eder C M Lanes
- Instituto Tecnológico Vale, Desenvolvimento Sustentável, Belém-PA, Brazil
| | - Mabel P Ortiz-Vera
- Instituto Tecnológico Vale, Desenvolvimento Sustentável, Belém-PA, Brazil
- Universidade Federal do Pará, Instituto de Ciências Biológicas, Programa de Pós-Graduação em Genética e Biologia Molecular, Belém-PA, Brazil
| | - Pedro L Viana
- Universidade Federal Rural da Amazônia/Museu Paraense Emílio Goeldi, Programa de Pós-graduação em Ciências Biológicas - Botânica Tropical, Belém-PA, Brazil
| | - Rodolfo Jaffé
- Instituto Tecnológico Vale, Desenvolvimento Sustentável, Belém-PA, Brazil
- Universidade de São Paulo, Departamento de Ecologia, São Paulo-SP, Brazil
- Corresponding author’s email address:
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14
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Low genetic differentiation despite high fragmentation in the endemic serpentinophyte Minuartia smejkalii (M. verna agg., Caryophyllaceae) revealed by RADSeq SNP markers. CONSERV GENET 2020. [DOI: 10.1007/s10592-019-01239-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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15
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Yan M, Liu R, Li Y, Hipp AL, Deng M, Xiong Y. Ancient events and climate adaptive capacity shaped distinct chloroplast genetic structure in the oak lineages. BMC Evol Biol 2019; 19:202. [PMID: 31684859 PMCID: PMC6829957 DOI: 10.1186/s12862-019-1523-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 10/01/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Understanding the origin of genetic variation is the key to predict how species will respond to future climate change. The genus Quercus is a species-rich and ecologically diverse woody genus that dominates a wide range of forests and woodland communities of the Northern Hemisphere. Quercus thus offers a unique opportunity to investigate how adaptation to environmental changes has shaped the spatial genetic structure of closely related lineages. Furthermore, Quercus provides a deep insight into how tree species will respond to future climate change. This study investigated whether closely related Quercus lineages have similar spatial genetic structures and moreover, what roles have their geographic distribution, ecological tolerance, and historical environmental changes played in the similar or distinct genetic structures. RESULTS Despite their close relationships, the three main oak lineages (Quercus sections Cyclobalanopsis, Ilex, and Quercus) have different spatial genetic patterns and occupy different climatic niches. The lowest level and most homogeneous pattern of genetic diversity was found in section Cyclobalanopsis, which is restricted to warm and humid climates. The highest genetic diversity and strongest geographic genetic structure were found in section Ilex, which is due to their long-term isolation and strong local adaptation. The widespread section Quercus is distributed across the most heterogeneous range of environments; however, it exhibited moderate haplotype diversity. This is likely due to regional extinction during Quaternary climatic fluctuation in Europe and North America. CONCLUSIONS Genetic variations of sections Ilex and Quercus were significantly predicted by geographic and climate variations, while those of section Cyclobalanopsis were poorly predictable by geographic or climatic diversity. Apart from the different historical environmental changes experienced by different sections, variation of their ecological or climatic tolerances and physiological traits induced varying responses to similar environment changes, resulting in distinct spatial genetic patterns.
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Affiliation(s)
- Mengxiao Yan
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, 05282, Myanmar
| | - Ruibin Liu
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Ying Li
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- The Ecological Technique and Engineering College, Shanghai Institute of Technology, Shanghai, 201418, China
| | - Andrew L Hipp
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL, 60532, USA
- The Field Museum, 1400 S Lake Shore Drive, Chicago, IL, 60605, USA
| | - Min Deng
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, 05282, Myanmar.
| | - Yanshi Xiong
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
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16
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Tóth EG, Tremblay F, Housset JM, Bergeron Y, Carcaillet C. Geographic isolation and climatic variability contribute to genetic differentiation in fragmented populations of the long-lived subalpine conifer Pinus cembra L. in the western Alps. BMC Evol Biol 2019; 19:190. [PMID: 31623551 PMCID: PMC6798344 DOI: 10.1186/s12862-019-1510-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 09/09/2019] [Indexed: 11/13/2022] Open
Abstract
Background Genetic processes shape the modern-day distribution of genetic variation within and between populations and can provide important insights into the underlying mechanisms of evolution. The resulting genetic variation is often unequally partitioned within species’ distribution range and especially large differences can manifest at the range limit, where population fragmentation and isolation play a crucial role in species survival. Despite several molecular studies investigating the genetic diversity and differentiation of European Alpine mountain forests, the climatic and demographic constrains which influence the genetic processes are often unknown. Here, we apply non-coding microsatellite markers to evaluate the sporadic peripheral and continuous populations of cembra pine (Pinus cembra L.), a long-lived conifer species that inhabits the subalpine treeline ecotone in the western Alps to investigate how the genetic processes contribute to the modern-day spatial distribution. Moreover, we corroborate our findings with paleoecological records, micro and macro-remains, to infer the species’ possible glacial refugia and expansion scenarios. Results Four genetically distinct groups were identified, with Bayesian and FST based approaches, across the range of the species, situated in the northern, inner and south-western Alps. We found that genetic differentiation is substantially higher in marginal populations than at the center of the range, and marginal stands are characterized by geographic and genetic isolation due to spatial segregation and restricted gene flow. Moreover, multiple matrix regression approaches revealed effects of climatic heterogeneity in species’ spatial genetic pattern. Also, population stability tests indicated that all populations had experienced a severe historical bottleneck, no heterozygosity excess was detected, suggesting that more recently population sizes have remained relatively stable. Conclusions Our study demonstrated that cembra pine might have survived in multiple glacial refugia and subsequently recolonized the Alps by different routes. Modern-day marginal populations, at the edge of the species’ range, could maintain stable sizes over long periods without inbreeding depression and preserve high amounts of genetic variation. Moreover, our analyses indicate that climatic variability has played a major role in shaping differentiation, in addition to past historical events such as migration and demographic changes.
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Affiliation(s)
- Endre Gy Tóth
- Forest Research Institute (IRF), University of Quebec in Abitibi-Témiscamingue (UQAT), 445 Boul. de l'Université, Rouyn-Noranda, QC, J9X 5E4, Canada. .,National Agricultural Research and Innovation Center (NARIC), Forest Research Institute (FRI), Várkerület u. 30/A, Sárvár, 9600, Hungary.
| | - Francine Tremblay
- Forest Research Institute (IRF), University of Quebec in Abitibi-Témiscamingue (UQAT), 445 Boul. de l'Université, Rouyn-Noranda, QC, J9X 5E4, Canada
| | - Johann M Housset
- Centre for Forest Research (CEF), University of Québec in Montréal (UQAM), C.P. 8888, succ. Centre-ville, Montréal, QC, H3C 3P8, Canada.,Ecole Pratique des Hautes Etudes (EPHE), Paris Sciences & Lettres University (PSL), Paris, France.,Alcina, 10 rue des Amaryllis, 34070, Montpellier, France
| | - Yves Bergeron
- Forest Research Institute (IRF), University of Quebec in Abitibi-Témiscamingue (UQAT), 445 Boul. de l'Université, Rouyn-Noranda, QC, J9X 5E4, Canada.,Centre for Forest Research (CEF), University of Québec in Montréal (UQAM), C.P. 8888, succ. Centre-ville, Montréal, QC, H3C 3P8, Canada
| | - Christopher Carcaillet
- Ecole Pratique des Hautes Etudes (EPHE), Paris Sciences & Lettres University (PSL), Paris, France.,Laboratory for Ecology of Natural and Anthropised Hydrosystems (UMR 5023 CNRS UCBL ENTPE), Université Lyon 1, Villeurbanne Cedex, France
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17
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A Reference Genome Sequence for the European Silver Fir ( Abies alba Mill.): A Community-Generated Genomic Resource. G3-GENES GENOMES GENETICS 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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [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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18
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Csilléry K, Ovaskainen O, Sperisen C, Buchmann N, Widmer A, Gugerli F. Adaptation to local climate in multi-trait space: evidence from silver fir (Abies alba Mill.) populations across a heterogeneous environment. Heredity (Edinb) 2019; 124:77-92. [PMID: 31182819 DOI: 10.1038/s41437-019-0240-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/08/2019] [Accepted: 05/22/2019] [Indexed: 01/13/2023] Open
Abstract
Heterogeneous environments, such as mountainous landscapes, create spatially varying selection pressure that potentially affects several traits simultaneously across different life stages, yet little is known about the general patterns and drivers of adaptation in such complex settings. We studied silver fir (Abies alba Mill.) populations across Switzerland and characterized its mountainous landscape using downscaled historical climate data. We sampled 387 trees from 19 populations and genotyped them at 374 single-nucleotide polymorphisms (SNPs) to estimate their demographic distances. Seedling morphology, growth and phenology traits were recorded in a common garden, and a proxy for water use efficiency was estimated for adult trees. We tested whether populations have more strongly diverged at quantitative traits than expected based on genetic drift alone in a multi-trait framework, and identified potential environmental drivers of selection. We found two main responses to selection: (i) populations from warmer and more thermally stable locations have evolved towards a taller stature, and (ii) the growth timing of populations evolved towards two extreme strategies, 'start early and grow slowly' or 'start late and grow fast', driven by precipitation seasonality. Populations following the 'start early and grow slowly' strategy had higher water use efficiency and came from inner Alpine valleys characterized by pronounced summer droughts. Our results suggest that contrasting adaptive life-history strategies exist in silver fir across different life stages (seedling to adult), and that some of the characterized populations may provide suitable seed sources for tree growth under future climatic conditions.
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Affiliation(s)
- Katalin Csilléry
- Center for Adaptation to a Changing Environment, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland. .,Swiss Federal Research Institute WSL, Birmensdorf, Switzerland. .,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
| | - Otso Ovaskainen
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | | | - Nina Buchmann
- Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Alex Widmer
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Felix Gugerli
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
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19
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Finsinger W, Schwörer C, Heiri O, Morales-Molino C, Ribolini A, Giesecke T, Haas JN, Kaltenrieder P, Magyari EK, Ravazzi C, Rubiales JM, Tinner W. Fire on ice and frozen trees? Inappropriate radiocarbon dating leads to unrealistic reconstructions. THE NEW PHYTOLOGIST 2019; 222:657-662. [PMID: 30019412 DOI: 10.1111/nph.15354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/29/2018] [Indexed: 06/08/2023]
Affiliation(s)
- Walter Finsinger
- Palaeoecology, ISEM, CNRS, EPHE, IRD, Univ. Montpellier, F-34095, Montpellier, France
| | - Christoph Schwörer
- Institute of Plant Sciences and Oeschger Centre for Climate Change Research, University of Bern, Altenbergrain 21, CH-3013, Bern, Switzerland
| | - Oliver Heiri
- Institute of Plant Sciences and Oeschger Centre for Climate Change Research, University of Bern, Altenbergrain 21, CH-3013, Bern, Switzerland
| | - César Morales-Molino
- Institute of Plant Sciences and Oeschger Centre for Climate Change Research, University of Bern, Altenbergrain 21, CH-3013, Bern, Switzerland
- Palaeoclimate, EPOC (UMR 5805 CNRS/University of Bordeaux), University of Bordeaux, F-33615, Pessac, France
| | - Adriano Ribolini
- Dipartimento di Scienze della Terra, University of Pisa, via S. Maria 53, 56126, Pisa, Italy
| | - Thomas Giesecke
- Department of Palynology and Climate Dynamics, University of Göttingen, Wilhelm-Weber-Str. 2a, D-37073, Göttingen, Germany
| | - Jean Nicolas Haas
- Institute of Botany, Division of Systematics, Palynology and Geobotany, University of Innsbruck, Sternwartestrasse 15, A-6020, Innsbruck, Austria
| | - Petra Kaltenrieder
- Institute of Plant Sciences and Oeschger Centre for Climate Change Research, University of Bern, Altenbergrain 21, CH-3013, Bern, Switzerland
| | - Enikő K Magyari
- MTA-MTM-ELTE Research Group for Paleontology and Department of Environmental and Landscape Geography, Eötvös Lóránd University, Pázmány Péter stny. 1/C, H-1117, Budapest, Hungary
| | - Cesare Ravazzi
- CNR - Institute for the Dynamics of Environmental Processes, U1 - DISAT - Università Milano Bicocca, Piazza della Scienza 1, I-20126, Milano, Italy
| | - Juan Manuel Rubiales
- Departamento de Sistemas y Recursos Naturales, Escuela Técnica Superior de Ingeniería de Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, E-28040, Madrid, Spain
- Departamento de Biodiversidad, Ecología y Evolución, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, C/José Antonio Novais, E-28040, Madrid, Spain
| | - Willy Tinner
- Institute of Plant Sciences and Oeschger Centre for Climate Change Research, University of Bern, Altenbergrain 21, CH-3013, Bern, Switzerland
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20
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Bessega C, Pometti C, López RP, Larrea‐Alcázar D, Fortunato RH, Saidman B, Vilardi JC. Genetic diversity and differentiation among Prosopis alba (Leguminosae) populations from dry valleys of Bolivia with different levels of human disturbance and altitude. Ecol Evol 2018; 8:11309-11321. [PMID: 30519445 PMCID: PMC6262908 DOI: 10.1002/ece3.4610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 07/16/2018] [Accepted: 09/13/2018] [Indexed: 12/13/2022] Open
Abstract
The fast expansion of human population around La Paz, Bolivia (3,200-4,100 m.a.s.l.) triggered new suburban settlements in nearby areas in valleys and mountain feet. The white mesquite, Prosopis alba Griseb. (Leguminosae), is a resource (originally used by native communities) that is strongly affected by changes in land use. A gradient in the level of disturbance is found moving away from the La Paz city toward less altitude areas. The main objective of this study was to characterize genetically three P. alba populations with different levels of human disturbance located at different altitudes in Bolivia, in order to provide some guidelines for management and conservation of these species. Based on 10 SSR loci, the populations showed high level of genetic diversity in comparison with other forest species. The population less disturbed and situated at the lowest altitude was the most variable (H e = 0.51-0.42), whereas the less variable was the most disturbed and situated at the highest altitude. Heterozygote excess was observed in all populations. Most of genetic diversity (99%) is contained within populations. Genetic differentiation among populations is low (1%), suggesting low gene flow among populations. No evidence of recent bottlenecks events was detected. The estimates of the effective population size were low in all populations. The results are in agreement with the hypothesis that genetic diversity is reduced by the impact of anthropic disturbance in the population located at higher altitude in comparison with the lightly disturbed situated at lower altitude and farther from urban settlements.
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Affiliation(s)
- Cecilia Bessega
- Departamento Ecología, Genética y Evolución, Facultad de Ciencias Exactas y NaturalesUniversidad de Buenos AiresBuenos AiresArgentina
- Instituto de Ecología, Genética y Evolución (IEGEBA)CONICET‐Universidad de Buenos AiresBuenos AiresArgentina
| | - Carolina Pometti
- Departamento Ecología, Genética y Evolución, Facultad de Ciencias Exactas y NaturalesUniversidad de Buenos AiresBuenos AiresArgentina
- Instituto de Ecología, Genética y Evolución (IEGEBA)CONICET‐Universidad de Buenos AiresBuenos AiresArgentina
| | - Ramiro Pablo López
- Facultad de Ciencias Puras y Naturales, Carrera de BiologíaUniversidad Mayor de San AndrésLa PazBolivia
| | - Daniel Larrea‐Alcázar
- Asociación Boliviana para la Investigación y Conservación de Ecosistemas Andino‐Amazónicos (ACEAA)La PazBolivia
| | - Reneé H. Fortunato
- N. Repetto y Los Reseros s.n., Hurlingham (1686)Argentina ‐ Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)Instituto de Recursos Biológicos (CIRN–CNIA, INTA)Buenos AiresArgentina
| | - Beatriz Saidman
- Departamento Ecología, Genética y Evolución, Facultad de Ciencias Exactas y NaturalesUniversidad de Buenos AiresBuenos AiresArgentina
- Instituto de Ecología, Genética y Evolución (IEGEBA)CONICET‐Universidad de Buenos AiresBuenos AiresArgentina
| | - Juan Cesar Vilardi
- Departamento Ecología, Genética y Evolución, Facultad de Ciencias Exactas y NaturalesUniversidad de Buenos AiresBuenos AiresArgentina
- Instituto de Ecología, Genética y Evolución (IEGEBA)CONICET‐Universidad de Buenos AiresBuenos AiresArgentina
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21
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Stojanova B, Šurinová M, Klápště J, Koláříková V, Hadincová V, Münzbergová Z. Adaptive differentiation of Festuca rubra along a climate gradient revealed by molecular markers and quantitative traits. PLoS One 2018; 13:e0194670. [PMID: 29617461 PMCID: PMC5884518 DOI: 10.1371/journal.pone.0194670] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/07/2018] [Indexed: 12/02/2022] Open
Abstract
Species response to climate change is influenced by predictable (selective) and unpredictable (random) evolutionary processes. To understand how climate change will affect present-day species, it is necessary to assess their adaptive potential and distinguish it from the effects of random processes. This will allow predicting how different genotypes will respond to forecasted environmental change. Space for time substitution experiments are an elegant way to test the response of present day populations to climate variation in real time. Here we assess neutral and putatively adaptive variation in 11 populations of Festuca rubra situated along crossed gradients of temperature and moisture using molecular markers and phenotypic measurements, respectively. By comparing population differentiation in putatively neutral molecular markers and phenotypic traits (QST-FST comparisons), we show the existence of adaptive differentiation in phenotypic traits and their plasticity across the climatic gradient. The observed patterns of differentiation are due to the high genotypic and phenotypic differentiation of the populations from the coldest (and wettest) environment. Finally, we observe statistically significant covariation between markers and phenotypic traits, which is likely caused by isolation by adaptation. These results contribute to a better understanding of the current adaptation and evolutionary potential to face climate change of a widespread species. They can also be extrapolated to understand how the studied populations will adjust to upcoming climate change without going through the lengthy process of phenotyping.
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Affiliation(s)
- Bojana Stojanova
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Mária Šurinová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic
| | - Jaroslav Klápště
- Scion (New Zealand Forest Research Institute Ltd.), Whakarewarewa, Rotorua, New Zealand
| | - Veronika Koláříková
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Věroslava Hadincová
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic
| | - Zuzana Münzbergová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic
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22
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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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23
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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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24
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Conlisk E, Castanha C, Germino MJ, Veblen TT, Smith JM, Moyes AB, Kueppers LM. Seed origin and warming constrain lodgepole pine recruitment, slowing the pace of population range shifts. GLOBAL CHANGE BIOLOGY 2018; 24:197-211. [PMID: 28746786 DOI: 10.1111/gcb.13840] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 06/21/2017] [Indexed: 06/07/2023]
Abstract
Understanding how climate warming will affect the demographic rates of different ecotypes is critical to predicting shifts in species distributions. Here, we present results from a common garden, climate change experiment in which we measured seedling recruitment of lodgepole pine, a widespread North American conifer that is also planted globally. Seeds from a low-elevation provenance had more than three-fold greater recruitment to their third year than seeds from a high-elevation provenance across sites within and above its native elevation range and across climate manipulations. Heating halved recruitment to the third year of both low- and high-elevation seed sources across the elevation gradient, while watering more than doubled recruitment, alleviating some of the negative effects of heating. Demographic models based on recruitment data from the climate manipulations and long-term observations of adult populations revealed that heating could effectively halt modeled upslope range expansion except when combined with watering. Simulating fire and rapid postfire forest recovery at lower elevations accelerated lodgepole pine expansion into the alpine, but did not alter final abundance rankings among climate scenarios. Regardless of climate scenario, greater recruitment of low-elevation seeds compensated for longer dispersal distances to treeline, assuming colonization was allowed to proceed over multiple centuries. Our results show that ecotypes from lower elevations within a species' range could enhance recruitment and facilitate upslope range shifts with climate change.
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Affiliation(s)
- Erin Conlisk
- Energy and Resources Group, University of California, Berkeley, CA, USA
| | - Cristina Castanha
- Lawrence Berkeley National Laboratory, Climate and Ecosystem Sciences Division, Berkeley, CA, USA
- Sierra Nevada Research Institute, University of California, Merced, CA, USA
| | - Matthew J Germino
- US Geological Survey, Forest and Rangeland Ecosystem Science Center, Boise, ID, USA
| | - Thomas T Veblen
- Department of Geography, University of Colorado, Boulder, CO, USA
| | - Jeremy M Smith
- Department of Geography, University of Colorado, Boulder, CO, USA
| | - Andrew B Moyes
- Lawrence Berkeley National Laboratory, Climate and Ecosystem Sciences Division, Berkeley, CA, USA
- Sierra Nevada Research Institute, University of California, Merced, CA, USA
| | - Lara M Kueppers
- Energy and Resources Group, University of California, Berkeley, CA, USA
- Lawrence Berkeley National Laboratory, Climate and Ecosystem Sciences Division, Berkeley, CA, USA
- Sierra Nevada Research Institute, University of California, Merced, CA, USA
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25
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Moran E, Lauder J, Musser C, Stathos A, Shu M. The genetics of drought tolerance in conifers. THE NEW PHYTOLOGIST 2017; 216:1034-1048. [PMID: 28895167 DOI: 10.1111/nph.14774] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 07/27/2017] [Indexed: 05/20/2023]
Abstract
Contents 1034 I. 1034 II. 1035 III. 1037 IV. 1038 V. 1042 VI. 1043 VII. 1045 References 1045 SUMMARY: As temperatures warm and precipitation patterns shift as a result of climate change, interest in the identification of tree genotypes that will thrive under more arid conditions has grown. In this review, we discuss the multiple definitions of 'drought tolerance' and the biological processes involved in drought responses. We describe the three major approaches taken in the study of genetic variation in drought responses, the advantages and shortcomings of each, and what each of these approaches has revealed about the genetic basis of adaptation to drought in conifers. Finally, we discuss how a greater knowledge of the genetics of drought tolerance may aid forest management, and provide recommendations for how future studies may overcome the limitations of past approaches. In particular, we urge a more direct focus on survival, growth and the traits that directly predict them (rather than on proxies, such as water use efficiency), combining research approaches with complementary strengths and weaknesses, and the inclusion of a wider range of taxa and life stages.
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Affiliation(s)
- Emily Moran
- UC Merced, 5200 N Lake Rd, Merced, CA, 95343, USA
| | | | - Cameron Musser
- Yale School of Forestry & Environmental Studies, 195 Prospect Street, New Haven, CT, 06511, USA
| | | | - Mengjun Shu
- UC Merced, 5200 N Lake Rd, Merced, CA, 95343, USA
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26
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Carcaillet C, Blarquez O. Fire ecology of a tree glacial refugium on a nunatak with a view on Alpine glaciers. THE NEW PHYTOLOGIST 2017; 216:1281-1290. [PMID: 28805959 DOI: 10.1111/nph.14721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/26/2017] [Indexed: 06/07/2023]
Abstract
In paleoecology, the function of biomass as a fire driver has become a focus of attention in cold ecosystems, and concerns have been raised about climate in this context. Little is known about the fire frequency and fire-plant relationships during glaciation when woodlands were limited and the climate was cold. Fire history and tree biomass were reconstructed from sedimentary charcoal and macroremains, respectively, archived in lake sediments from the western Alps. Two nunataks were investigated, both with lacustrine sediments covering the last 21 000 yr at least. During the Last Glacial Maximum (LGM) and the Lateglacial, fires occurred only on the nunatak sheltering woody plants. Cembra pine (Pinus cembra) and larch (Larix decidua) survived above glaciers during the LGM, thus evidencing a biological refugium and supporting the nunatak theory. We highlighted a long-term relationship between fires and dominant trees over the last 21 000 yr, where fire frequencies track the global climate and the local changes in tree biomass. Glacial climate (dry, cold) does not rule out fires. Fuel load and composition were significant fire drivers, with cembra pine dominating during colder periods with rare fires, and larch during the warmer Holocene with frequent fires. These findings increase knowledge of fire ecology in cold environments, and open perspectives in tree population genetics by considering new areas of tree glacial refugia in Europe.
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Affiliation(s)
- Christopher Carcaillet
- PSL Research University Paris, Ecole Pratique des Hautes Etudes, 4-14 rue Ferrus, Paris, F-75014, France
- Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (UMR5023 CNRS), Université Lyon 1, Villeurbanne Cedex, F-69622, France
- LTER Zone Atelier Alpes, Grenoble, F-38000, France
- International Associated Laboratory (LIA France-Canada MONTABOR), Montpellier, F-34000, France
| | - Olivier Blarquez
- International Associated Laboratory (LIA France-Canada MONTABOR), Montpellier, F-34000, France
- Département de Géographie, Université de Montréal, C.P. 6128 Succ. Centre Ville, Montréal, QC, H3C 3J7, Canada
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27
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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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28
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Steane DA, Potts BM, McLean EH, Collins L, Holland BR, Prober SM, Stock WD, Vaillancourt RE, Byrne M. Genomic Scans across Three Eucalypts Suggest that Adaptation to Aridity is a Genome-Wide Phenomenon. Genome Biol Evol 2017; 9:253-265. [PMID: 28391293 PMCID: PMC5381606 DOI: 10.1093/gbe/evw290] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2016] [Indexed: 01/01/2023] Open
Abstract
Widespread species spanning strong environmental (e.g., climatic) gradients frequently display morphological and physiological adaptations to local conditions. Some adaptations are common to different species that occupy similar environments. However, the genomic architecture underlying such convergent traits may not be the same between species. Using genomic data from previous studies of three widespread eucalypt species that grow along rainfall gradients in southern Australia, our probabilistic approach provides evidence that adaptation to aridity is a genome-wide phenomenon, likely to involve multiple and diverse genes, gene families and regulatory regions that affect a multitude of complex genetic and biochemical processes.
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Affiliation(s)
- Dorothy A. Steane
- School of Biological Sciences and ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania, Australia
- CSIRO Land and Water, Wembley, Western Australia, Australia
| | - Brad M. Potts
- School of Biological Sciences and ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania, Australia
| | - Elizabeth H. McLean
- CSIRO Land and Water, Wembley, Western Australia, Australia
- Science and Conservation Division, Department of Parks and Wildlife, Bentley Delivery Centre, Western Australia, Australia
| | - Lesley Collins
- Faculty of Health Science, Universal College of Learning, Palmerston North, New Zealand
| | - Barbara R. Holland
- School of Physical Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | | | - William D. Stock
- Centre for Ecosystem Management, School of Natural Sciences, Edith Cowan University, Perth, Western Australia, Australia
| | - René E. Vaillancourt
- School of Biological Sciences and ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania, Australia
| | - Margaret Byrne
- Science and Conservation Division, Department of Parks and Wildlife, Bentley Delivery Centre, Western Australia, Australia
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29
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Dzialuk A, Boratyńska K, Romo A, Boratyński A. Taxonomic and geographic variation of the Pinus mugo complex on chloroplast microsatellite markers. SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1257518] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Artur Dzialuk
- Kazimierz Wielki University, Department of Genetics, Powstańców Wielkopolskich 10, 85-090 Bydgoszcz, Poland
| | - Krystyna Boratyńska
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 63-036 Kórnik, Poland
| | - Angel Romo
- Institute of Botany, Consejo Superior de Investigaciones Cientificas, Passeig del Migdia, s/n 08038 Barcelona, Spain
| | - Adam Boratyński
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 63-036 Kórnik, Poland
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30
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Rubol S, Dutta T, Rocchini D. 2D visualization captures the local heterogeneity of oxidative metabolism across soils from diverse land-use. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 572:713-723. [PMID: 27575428 DOI: 10.1016/j.scitotenv.2016.06.252] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/30/2016] [Accepted: 06/30/2016] [Indexed: 06/06/2023]
Abstract
Fine-scale processes in soils affect large-scale phenomena by controlling mixing and reaction rates, yet technological constraints have hampered the collection of micro-scale kinetic data. As a result, limited information is available on the magnitude of fine-scale biogeochemical rates and their temporal and spatial pattern in response to environmental perturbations. In this work we investigate the spatio-temporal dynamics in oxidative microbial activity and the development of anoxic micro zones (i.e., anoxic hot-spots) at the microscopic level (μm - cm). These analyses rely on novel non-invasive & non-destructive optodes, which are able to capture real-time imaging of oxygen concentrations over time at an interval of twenty seconds. Results showed that labile carbon addition resulted in maximum rates of local metabolic activity within a few minutes (5 to 15) and led to the subsequent formation of anoxic hot-spots. Different areas within a given soil sample presented up to one order of magnitude variation in metabolic rate values. As a result, oxic and anoxic micro-zones coexisted closely. The relationship between oxygen concentrations and heterogeneity of oxidative metabolism resulted in an initial increase in metabolic heterogeneity over time followed by a decrease when anoxic conditions dominated. A similar link was found by comparing metabolic activity and its heterogeneity across a range of soil types. These results demonstrate that the microbial activity and hot-spot development can be monitored by using a non-invasive quantitative imaging system that allows real-time monitoring of spatial oxygen distribution. We conclude that local dynamics of heterogeneity in space and time at the fine-scale present the same functional behavior encountered in most ecosystems at the landscape-scale.
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Affiliation(s)
- Simonetta Rubol
- Department of Biological Sciences, Marine Environmental Biology Section, University of Southern California, Los Angeles, CA 90089, USA.
| | - Tanushree Dutta
- Department of Civil & Environmental Engineering, Hanyang University, 222 Wangsimni-Ro, Seoul 04763, Republic of Korea
| | - Duccio Rocchini
- Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, Research and Innovation Centre, S. Michele all'Adige Trento, Italy
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31
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Jordan R, Dillon SK, Prober SM, Hoffmann AA. Landscape genomics reveals altered genome wide diversity within revegetated stands of Eucalyptus microcarpa (Grey Box). THE NEW PHYTOLOGIST 2016; 212:992-1006. [PMID: 27440730 DOI: 10.1111/nph.14084] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 05/31/2016] [Indexed: 05/22/2023]
Abstract
In order to contribute to evolutionary resilience and adaptive potential in highly modified landscapes, revegetated areas should ideally reflect levels of genetic diversity within and across natural stands. Landscape genomic analyses enable such diversity patterns to be characterized at genome and chromosomal levels. Landscape-wide patterns of genomic diversity were assessed in Eucalyptus microcarpa, a dominant tree species widely used in revegetation in Southeastern Australia. Trees from small and large patches within large remnants, small isolated remnants and revegetation sites were assessed across the now highly fragmented distribution of this species using the DArTseq genomic approach. Genomic diversity was similar within all three types of remnant patches analysed, although often significantly but only slightly lower in revegetation sites compared with natural remnants. Differences in diversity between stand types varied across chromosomes. Genomic differentiation was higher between small, isolated remnants, and among revegetated sites compared with natural stands. We conclude that small remnants and revegetated sites of our E. microcarpa samples largely but not completely capture patterns in genomic diversity across the landscape. Genomic approaches provide a powerful tool for assessing restoration efforts across the landscape.
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Affiliation(s)
- Rebecca Jordan
- Bio21 Institute, School of BioSciences, University of Melbourne, 30 Flemington Rd, Parkville, Vic, 3010, Australia
- CSIRO Land and Water, 147 Underwood Ave, Floreat, WA, 6014, Australia
| | - Shannon K Dillon
- CSIRO Agriculture, Clunies Ross Street, Black Mountain, ACT, 2601, Australia
| | - Suzanne M Prober
- CSIRO Land and Water, 147 Underwood Ave, Floreat, WA, 6014, Australia
| | - Ary A Hoffmann
- Bio21 Institute, School of BioSciences, University of Melbourne, 30 Flemington Rd, Parkville, Vic, 3010, Australia
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32
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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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33
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Huang CC, Hsu TW, Wang HV, Liu ZH, Chen YY, Chiu CT, Huang CL, Hung KH, Chiang TY. Multilocus Analyses Reveal Postglacial Demographic Shrinkage of Juniperus morrisonicola (Cupressaceae), a Dominant Alpine Species in Taiwan. PLoS One 2016; 11:e0161713. [PMID: 27561108 PMCID: PMC4999204 DOI: 10.1371/journal.pone.0161713] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 08/10/2016] [Indexed: 11/18/2022] Open
Abstract
Postglacial climate changes alter geographical distributions and diversity of species. Such ongoing changes often force species to migrate along the latitude/altitude. Altitudinal gradients represent assemblage of environmental, especially climatic, variable factors that influence the plant distributions. Global warming that triggered upward migrations has therefore impacted the alpine plants on an island. In this study, we examined the genetic structure of Juniperus morrisonicola, a dominant alpine species in Taiwan, and inferred historical, demographic dynamics based on multilocus analyses. Lower levels of genetic diversity in north indicated that populations at higher latitudes were vulnerable to climate change, possibly related to historical alpine glaciers. Neither organellar DNA nor nuclear genes displayed geographical subdivisions, indicating that populations were likely interconnected before migrating upward to isolated mountain peaks, providing low possibilities of seed/pollen dispersal across mountain ranges. Bayesian skyline plots suggested steady population growth of J. morrisonicola followed by recent demographic contraction. In contrast, most lower-elevation plants experienced recent demographic expansion as a result of global warming. The endemic alpine conifer may have experienced dramatic climate changes over the alternation of glacial and interglacial periods, as indicated by a trend showing decreasing genetic diversity with the altitudinal gradient, plus a fact of upward migration.
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Affiliation(s)
| | - Tsai-Wen Hsu
- Endemic Species Research Institute, Nantou, Taiwan
| | - Hao-Ven Wang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Zin-Huang Liu
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Yen Chen
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Chi-Te Chiu
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Chao-Li Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Kuo-Hsiang Hung
- Graduate Institute of Bioresources, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Tzen-Yuh Chiang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
- University Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan
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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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Cocozza C, Palombo C, Tognetti R, La Porta N, Anichini M, Giovannelli A, Emiliani G. Monitoring intra-annual dynamics of wood formation with microcores and dendrometers in Picea abies at two different altitudes. TREE PHYSIOLOGY 2016; 36:832-846. [PMID: 26941291 DOI: 10.1093/treephys/tpw009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/27/2016] [Indexed: 06/05/2023]
Abstract
Seasonal analyses of cambial cell production and day-by-day stem radial increment can help to elucidate how climate modulates wood formation in conifers. Intra-annual dynamics of wood formation were determined with microcores and dendrometers and related to climatic signals in Norway spruce (Picea abies (L.) Karst.). The seasonal dynamics of these processes were observed at two sites of different altitude, Savignano (650 m a.s.l.) and Lavazè (1800 m a.s.l.) in the Italian Alps. Seasonal dynamics of cambial activity were found to be site specific, indicating that the phenology of cambial cell production is highly variable and plastic with altitude. There was a site-specific trend in the number of cells in the wall thickening phase, with the maximum cell production in early July (DOY 186) at Savignano and in mid-July (DOY 200) at Lavazè. The formation of mature cells showed similar trends at the two sites, although different numbers of cells and timing of cell differentiation were visible in the model shapes; at the end of ring formation in 2010, the number of cells was four times higher at Savignano (106.5 cells) than at Lavazè (26.5 cells). At low altitudes, microcores and dendrometers described the radial growth patterns comparably, though the dendrometer function underlined the higher upper asymptote of maximum growth in comparison with the cell production function. In contrast, at high altitude, these functions exhibited different trends. The best model was obtained by fitting functions of the Gompertz model to the experimental data. By combining radial growth and cambial activity indices we defined a model system able to synchronize these processes. Processes of adaptation of the pattern of xylogenesis occurred, enabling P. abies to occupy sites with contrasting climatic conditions. The use of daily climatic variables in combination with plant functional traits obtained by sensors and/or destructive sampling could provide a suitable tool to better investigate the effect of disturbances on response strategies in trees and, consequently, contribute to improving our prediction of tree growth and species resilience based on climate scenarios.
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Affiliation(s)
- Claudia Cocozza
- Istituto per la Protezione Sostenibile delle Piante (IPSP), Consiglio Nazionale delle Ricerche, I-50019 Sesto Fiorentino, Italy
| | - Caterina Palombo
- Dipartimento di Bioscienze e Territorio, Università del Molise, I-86090 Pesche, Italy
| | - Roberto Tognetti
- Dipartimento di Bioscienze e Territorio, Università del Molise, I-86090 Pesche, Italy The EFI Project Centre on Mountain Forests (MOUNTFOR), Edmund Mach Foundation, I-38010 San Michele all'Adige, Italy
| | - Nicola La Porta
- The EFI Project Centre on Mountain Forests (MOUNTFOR), Edmund Mach Foundation, I-38010 San Michele all'Adige, Italy Department of Sustainable Agro-Ecosystems and Bioresources, IASMA Research and Innovation Centre, Edmund Mach Foundation, I-38010 San Michele all'Adige, Italy
| | - Monica Anichini
- Laboratorio di Xilogenesi, Istituto per la Valorizzazione Legno e delle Specie Arboree (IVALSA), Consiglio Nazionale delle Ricerche, I-50019 Sesto Fiorentino, Italy
| | - Alessio Giovannelli
- Laboratorio di Xilogenesi, Istituto per la Valorizzazione Legno e delle Specie Arboree (IVALSA), Consiglio Nazionale delle Ricerche, I-50019 Sesto Fiorentino, Italy
| | - Giovanni Emiliani
- Laboratorio di Xilogenesi, Istituto per la Valorizzazione Legno e delle Specie Arboree (IVALSA), Consiglio Nazionale delle Ricerche, I-50019 Sesto Fiorentino, Italy
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Wang T, Wang Z, Xia F, Su Y. Local adaptation to temperature and precipitation in naturally fragmented populations of Cephalotaxus oliveri, an endangered conifer endemic to China. Sci Rep 2016; 6:25031. [PMID: 27113970 PMCID: PMC4844950 DOI: 10.1038/srep25031] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/04/2016] [Indexed: 01/02/2023] Open
Abstract
Cephalotaxus oliveri is an endangered tertiary relict conifer endemic to China. The species survives in a wide range from west to east with heterogeneous climatic conditions. Precipitation and temperature are main restrictive factors for distribution of C. oliveri. In order to comprehend the mechanism of adaptive evolution to climate variation, we employed ISSR markers to detect adaptive evolution loci, to identify the association between variation in temperature and precipitation and adaptive loci, and to investigate the genetic structure for 22 C. oliveri natural populations. In total, 14 outlier loci were identified, of which five were associated with temperature and precipitation. Among outlier loci, linkage disequilibrium (LD) was high (42.86%), which also provided strong evidence for selection. In addition, C. oliveri possessed high genetic variation (93.31%) and population differentiation, which may provide raw material to evolution and accelerate local adaptation, respectively. Ecological niche modeling showed that global warming will cause a shift for populations of C. oliveri from south to north with a shrinkage of southern areas. Our results contribute to understand the potential response of conifers to climatic changes, and provide new insights for conifer resource management and conservation strategies.
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Affiliation(s)
- Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zhen Wang
- College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Fan Xia
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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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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38
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Moran EV, Ormond RA. Simulating the Interacting Effects of Intraspecific Variation, Disturbance, and Competition on Climate-Driven Range Shifts in Trees. PLoS One 2015; 10:e0142369. [PMID: 26560869 PMCID: PMC4641630 DOI: 10.1371/journal.pone.0142369] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 10/21/2015] [Indexed: 11/18/2022] Open
Abstract
Climate change is expected to favor shifts in plant distributions; some such shifts are already being observed along elevation gradients. However, the rate of such shifts may be limited by their ability to reach newly suitable areas and by competition from resident species. The degree of local adaptation and genetic variation may also play a role in the interaction between migrants and residents by affecting relative fitness. We used a simulation model to explore the interacting effects of dispersal, fecundity, disturbance, and genetic variation on range-edge dynamics between a pair of demographically similar tree species. Ideal climate for an individual is determined by genotype. The simulated landscape undergoes an 80-year period of climate change in which climate bands shift upslope; subsequently, climate is held constant for 300 years. The presence of a high-elevation competitor caused a significant lag in the range shift of the low-elevation species relative to competition-free scenarios. Increases in fecundity and dispersal distance both helped to speed up the replacement of the high-elevation species by the low-elevation species at their range boundary. While some disturbance scenarios facilitated this transition, frequent canopy disturbance inhibited colonization by removing reproductive adults and led to range contractions in both species. Differences between dispersal scenarios were more pronounced when disturbance was frequent (15 vs. 25 year return interval) and dispersal was limited. When the high-elevation species lacked genetic variation, its range was more-easily invaded by the low-elevation species, while a similar lack of variation in the low-elevation species inhibited colonization-but only when this lack of variation decreased the fitness of the affected species near the range boundary. Our model results support the importance of measuring and including dispersal/fecundity, disturbance type and frequency, and genetic variation when assessing the potential for range shifts and species vulnerability to climate change.
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Affiliation(s)
- Emily V. Moran
- School of Natural Sciences, University of California Merced, Merced, California, United States of America
| | - Rhys A. Ormond
- School of Natural Sciences, University of California Merced, Merced, California, United States of America
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Rellstab C, Gugerli F, Eckert AJ, Hancock AM, Holderegger R. A practical guide to environmental association analysis in landscape genomics. Mol Ecol 2015; 24:4348-70. [DOI: 10.1111/mec.13322] [Citation(s) in RCA: 441] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 07/10/2015] [Accepted: 07/13/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Christian Rellstab
- WSL Swiss Federal Research Institute; Zürcherstrasse 111 8903 Birmensdorf Switzerland
| | - Felix Gugerli
- WSL Swiss Federal Research Institute; Zürcherstrasse 111 8903 Birmensdorf Switzerland
| | - Andrew J. Eckert
- Department of Biology; Virginia Commonwealth University; Richmond VA 23284 USA
| | - Angela M. Hancock
- Faculty of Molecular Biology; Max F. Perutz Laboratories and University of Vienna; Oskar-Morgenstern-Platz 1 1090 Vienna Austria
| | - Rolf Holderegger
- WSL Swiss Federal Research Institute; Zürcherstrasse 111 8903 Birmensdorf Switzerland
- ETH Zürich; Institute of Integrative Biology; Universitätstrasse 16 8092 Zürich Switzerland
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40
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Boratyńska K, Jasińska AK, Boratyński A. Taxonomic and geographic differentiation ofPinus mugocomplex on the needle characteristics. SYST BIODIVERS 2015. [DOI: 10.1080/14772000.2015.1058300] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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41
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Wachowiak W, Trivedi U, Perry A, Cavers S. Comparative transcriptomics of a complex of four European pine species. BMC Genomics 2015; 16:234. [PMID: 25887584 PMCID: PMC4458023 DOI: 10.1186/s12864-015-1401-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 02/24/2015] [Indexed: 11/25/2022] Open
Abstract
Background Pinus sylvestris, P. mugo, P. uliginosa and P. uncinata are closely related but phenotypically and ecologically very distinct European pine species providing an excellent study system for analysis of the genetic basis of adaptive variation and speciation. For comparative genomic analysis of the species, transcriptome sequence was generated for 17 samples collected across the European distribution range using Illumina paired-end sequencing technology. Results De novo transcriptome assembly of a reference sample of P. sylvestris contained 40968 unigenes, of which fewer than 0.5% were identified as putative retrotransposon sequences. Based on gene annotation approaches, 19659 contigs were identified and assigned to unique genes covering a broad range of gene ontology categories. About 80% of the reads from each sample were successfully mapped to the reference transcriptome of P. sylvestris. Single nucleotide polymorphisms were identified in 22041-24096 of the unigenes providing a set of ~220-262 k SNPs identified for each species. Very similar levels of nucleotide polymorphism were observed across species (π=0.0044-0.0053) and highest pairwise nucleotide divergence (0.006) was found between P. mugo and P. sylvestris at a common set of unigenes. Conclusions The study provides whole transcriptome sequence and a large set of SNPs to advance population and association genetic studies in pines. Our study demonstrates that transcriptome sequencing can be a very useful approach for development of novel genomic resources in species with large and complex genomes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1401-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Witold Wachowiak
- Centre for Ecology and Hydrology Edinburgh, Bush Estate, Penicuik, Midlothian, EH26 0QB, UK. .,Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035, Kórnik, Poland.
| | - Urmi Trivedi
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, Edinburgh, EH9 3JT, UK.
| | - Annika Perry
- Centre for Ecology and Hydrology Edinburgh, Bush Estate, Penicuik, Midlothian, EH26 0QB, UK.
| | - Stephen Cavers
- Centre for Ecology and Hydrology Edinburgh, Bush Estate, Penicuik, Midlothian, EH26 0QB, UK.
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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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Molecular proxies for climate maladaptation in a long-lived tree (Pinus pinaster Aiton, Pinaceae). Genetics 2014; 199:793-807. [PMID: 25549630 DOI: 10.1534/genetics.114.173252] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Understanding adaptive genetic responses to climate change is a main challenge for preserving biological diversity. Successful predictive models for climate-driven range shifts of species depend on the integration of information on adaptation, including that derived from genomic studies. Long-lived forest trees can experience substantial environmental change across generations, which results in a much more prominent adaptation lag than in annual species. Here, we show that candidate-gene SNPs (single nucleotide polymorphisms) can be used as predictors of maladaptation to climate in maritime pine (Pinus pinaster Aiton), an outcrossing long-lived keystone tree. A set of 18 SNPs potentially associated with climate, 5 of them involving amino acid-changing variants, were retained after performing logistic regression, latent factor mixed models, and Bayesian analyses of SNP-climate correlations. These relationships identified temperature as an important adaptive driver in maritime pine and highlighted that selective forces are operating differentially in geographically discrete gene pools. The frequency of the locally advantageous alleles at these selected loci was strongly correlated with survival in a common garden under extreme (hot and dry) climate conditions, which suggests that candidate-gene SNPs can be used to forecast the likely destiny of natural forest ecosystems under climate change scenarios. Differential levels of forest decline are anticipated for distinct maritime pine gene pools. Geographically defined molecular proxies for climate adaptation will thus critically enhance the predictive power of range-shift models and help establish mitigation measures for long-lived keystone forest trees in the face of impending climate change.
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Wang IJ, Bradburd GS. Isolation by environment. Mol Ecol 2014; 23:5649-62. [DOI: 10.1111/mec.12938] [Citation(s) in RCA: 505] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 09/07/2014] [Accepted: 09/21/2014] [Indexed: 12/15/2022]
Affiliation(s)
- Ian J. Wang
- Department of Environmental Science, Policy, and Management; University of California; 130 Mulford Hall #3114 Berkeley CA 94705 USA
| | - Gideon S. Bradburd
- Center for Population Biology; Department of Evolution and Ecology; University of California; 2320 Storer Hall 1 Shields Ave Davis CA 95616 USA
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Zhou Y, Zhang L, Liu J, Wu G, Savolainen O. Climatic adaptation and ecological divergence between two closely related pine species in Southeast China. Mol Ecol 2014; 23:3504-22. [PMID: 24935279 DOI: 10.1111/mec.12830] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 05/09/2014] [Accepted: 05/21/2014] [Indexed: 02/04/2023]
Abstract
Climate is one of the most important drivers for adaptive evolution in forest trees. Climatic selection contributes greatly to local adaptation and intraspecific differentiation, but this kind of selection could also have promoted interspecific divergence through ecological speciation. To test this hypothesis, we examined intra- and interspecific genetic variation at 25 climate-related candidate genes and 12 reference loci in two closely related pine species, Pinus massoniana Lamb. and Pinus hwangshanensis Hisa, using population genetic and landscape genetic approaches. These two species occur in Southeast China but have contrasting ecological preferences in terms of several environmental variables, notably altitude, although hybrids form where their distributions overlap. One or more robust tests detected signals of recent and/or ancient selection at two-thirds (17) of the 25 candidate genes, at varying evolutionary timescales, but only three of the 12 reference loci. The signals of recent selection were species specific, but signals of ancient selection were mostly shared by the two species likely because of the shared evolutionary history. FST outlier analysis identified six SNPs in five climate-related candidate genes under divergent selection between the two species. In addition, a total of 24 candidate SNPs representing nine candidate genes showed significant correlation with altitudinal divergence in the two species based on the covariance matrix of population history derived from reference SNPs. Genetic differentiation between these two species was higher at the candidate genes than at the reference loci. Moreover, analysis using the isolation-with-migration model indicated that gene flow between the species has been more restricted for climate-related candidate genes than the reference loci, in both directions. Taken together, our results suggest that species-specific and divergent climatic selection at the candidate genes might have counteracted interspecific gene flow and played a key role in the ecological divergence of these two closely related pine species.
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Affiliation(s)
- Yongfeng Zhou
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, China; Plant Genetics Group, Department of Biology, University of Oulu, 90014, Oulu, Finland
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Shen D, Bo W, Xu F, Wu R. Genetic diversity and population structure of the Tibetan poplar (Populus szechuanica var. tibetica) along an altitude gradient. BMC Genet 2014; 15 Suppl 1:S11. [PMID: 25079034 PMCID: PMC4118629 DOI: 10.1186/1471-2156-15-s1-s11] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background The Tibetan poplar (Populus szechuanica var. tibetica Schneid), which is distributed at altitudes of 2,000-4,500 m above sea level, is an ecologically important species of the Qinghai-Tibet Plateau and adjacent areas. However, the genetic adaptations responsible for its ability to cope with the harsh environment remain unknown. Results In this study, a total of 24 expressed sequence tag microsatellite (EST-SSR) markers were used to evaluate the genetic diversity and population structure of Tibetan poplars along an altitude gradient. The 172 individuals were of genotypes from low-, medium- and high-altitude populations, and 126 alleles were identified. The expected heterozygosity (HE) value ranged from 0.475 to 0.488 with the highest value found in low-altitude populations and the lowest in high-altitude populations. Genetic variation was low among populations, indicating a limited influence of altitude on microsatellite variation. Low genetic differentiation and high levels of gene flow were detected both between and within the populations along the altitude gradient. An analysis of molecular variance (AMOVA) showed that 6.38% of the total molecular variance was attributed to diversity between populations, while 93.62% variance was associated with differences within populations. There was no clear correlation between genetic variation and altitude, and a Mantel test between genetic distance and altitude resulted in a coefficient of association of r = 0.001, indicating virtually no correlation. Conclusion Microsatellite genotyping results showing genetic diversity and low differentiation suggest that extensive gene flow may have counteracted local adaptations imposed by differences in altitude. The genetic analyses carried out in this study provide new insight for conservation and optimization of future arboriculture.
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López de Heredia U, López R, Collada C, Emerson BC, Gil L. Signatures of volcanism and aridity in the evolution of an insular pine (Pinus canariensis Chr. Sm. Ex DC in Buch). Heredity (Edinb) 2014; 113:240-9. [PMID: 24619181 DOI: 10.1038/hdy.2014.22] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 01/21/2014] [Accepted: 02/07/2014] [Indexed: 01/15/2023] Open
Abstract
Oceanic islands of volcanic origin provide useful templates for the study of evolution because they are subjected to recurrent perturbations that generate steep environmental gradients that may promote adaptation. Here we combine population genetic data from nuclear genes with the analysis of environmental variation and phenotypic data from common gardens to disentangle the confounding effects of demography and selection to identify the factors of importance for the evolution of the insular pine P. canariensis. Eight nuclear genes were partially sequenced in a survey covering the entire species range, and phenotypic traits were measured in four common gardens from contrasting environments. The explanatory power of population substrate age and environmental indices were assessed against molecular and phenotypic diversity estimates. In addition, neutral genetic variability (FST) and the genetic differentiation of phenotypic variation (QST) were compared in order to identify the evolutionary forces acting on these traits. Two key factors in the evolution of the species were identified: (1) recurrent volcanic activity has left an imprint in the genetic diversity of the nuclear genes; (2) aridity in southern slopes promotes local adaptation in the driest localities of P. canariensis, despite high levels of gene flow among populations.
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Affiliation(s)
- U López de Heredia
- Forest Genetics and Physiology Research Group, Technical University of Madrid (UPM), Ciudad Universitaria s/n, Madrid, Spain
| | - R López
- Forest Genetics and Physiology Research Group, Technical University of Madrid (UPM), Ciudad Universitaria s/n, Madrid, Spain
| | - C Collada
- Forest Genetics and Physiology Research Group, Technical University of Madrid (UPM), Ciudad Universitaria s/n, Madrid, Spain
| | - B C Emerson
- Island Ecology and Evolution Research Group, IPNA-CSIC, Tenerife, Canary Islands, Spain
| | - L Gil
- Forest Genetics and Physiology Research Group, Technical University of Madrid (UPM), Ciudad Universitaria s/n, Madrid, Spain
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Budde KB, Heuertz M, Hernández-Serrano A, Pausas JG, Vendramin GG, Verdú M, González-Martínez SC. In situ genetic association for serotiny, a fire-related trait, in Mediterranean maritime pine (Pinus pinaster). THE NEW PHYTOLOGIST 2014; 201:230-241. [PMID: 24015853 DOI: 10.1111/nph.12483] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 07/28/2013] [Indexed: 05/28/2023]
Abstract
Wildfire is a major ecological driver of plant evolution. Understanding the genetic basis of plant adaptation to wildfire is crucial, because impending climate change will involve fire regime changes worldwide. We studied the molecular genetic basis of serotiny, a fire-related trait, in Mediterranean maritime pine using association genetics. A single nucleotide polymorphism (SNP) set was used to identify genotype : phenotype associations in situ in an unstructured natural population of maritime pine (eastern Iberian Peninsula) under a mixed-effects model framework. RR-BLUP was used to build predictive models for serotiny in this region. Model prediction power outside the focal region was tested using independent range-wide serotiny data. Seventeen SNPs were potentially associated with serotiny, explaining approximately 29% of the trait phenotypic variation in the eastern Iberian Peninsula. Similar prediction power was found for nearby geographical regions from the same maternal lineage, but not for other genetic lineages. Association genetics for ecologically relevant traits evaluated in situ is an attractive approach for forest trees provided that traits are under strong genetic control and populations are unstructured, with large phenotypic variability. This will help to extend the research focus to ecological keystone non-model species in their natural environments, where polymorphisms acquired their adaptive value.
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Affiliation(s)
- Katharina B Budde
- Department of Forest Ecology and Genetics, INIA Forest Research Centre, 28040, Madrid, Spain
| | - Myriam Heuertz
- Department of Forest Ecology and Genetics, INIA Forest Research Centre, 28040, Madrid, Spain
| | - Ana Hernández-Serrano
- Centro de Investigaciones sobre Desertificación (CIDE-CSIC/UV/GV), 46113, Moncada, Valencia, Spain
| | - Juli G Pausas
- Centro de Investigaciones sobre Desertificación (CIDE-CSIC/UV/GV), 46113, Moncada, Valencia, Spain
| | - Giovanni G Vendramin
- Plant Genetics Institute, National Research Council, 50019, Sesto Fiorentino, Florence, Italy
| | - Miguel Verdú
- Centro de Investigaciones sobre Desertificación (CIDE-CSIC/UV/GV), 46113, Moncada, Valencia, Spain
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Mosca E, González-Martínez SC, Neale DB. Environmental versus geographical determinants of genetic structure in two subalpine conifers. THE NEW PHYTOLOGIST 2014; 201:180-192. [PMID: 24102203 DOI: 10.1111/nph.12476] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 07/30/2013] [Indexed: 06/02/2023]
Abstract
Alpine ecosystems are facing rapid human-induced environmental changes, and so more knowledge about tree adaptive potential is needed. This study investigated the relative role of isolation by distance (IBD) versus isolation by adaptation (IBA) in explaining population genetic structure in Abies alba and Larix decidua, based on 231 and 233 single nucleotide polymorphisms (SNPs) sampled across 36 and 22 natural populations, respectively, in the Alps and Apennines. Genetic structure was investigated for both geographical and environmental groups, using analysis of molecular variance (AMOVA). For each species, nine environmental groups were defined using climate variables selected from a multiple factor analysis. Complementary methods were applied to identify outliers based on these groups, and to test for IBD versus IBA. AMOVA showed weak but significant genetic structure for both species, with higher values in L. decidua. Among the potential outliers detected, up to two loci were found for geographical groups and up to seven for environmental groups. A stronger effect of IBD than IBA was found in both species; nevertheless, once spatial effects had been removed, temperature and soil in A. alba, and precipitation in both species, were relevant factors explaining genetic structure. Based on our findings, in the Alpine region, genetic structure seems to be affected by both geographical isolation and environmental gradients, creating opportunities for local adaptation.
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Affiliation(s)
- Elena Mosca
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, S. Michele all'Adige, 38010, Italy
| | | | - David B Neale
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, S. Michele all'Adige, 38010, Italy
- Department of Plant Sciences, University of California at Davis, Davis, CA, 95616, USA
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Bradburd GS, Ralph PL, Coop GM. Disentangling the effects of geographic and ecological isolation on genetic differentiation. Evolution 2013; 67:3258-73. [PMID: 24102455 DOI: 10.1111/evo.12193] [Citation(s) in RCA: 181] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 06/05/2013] [Indexed: 11/30/2022]
Abstract
Populations can be genetically isolated both by geographic distance and by differences in their ecology or environment that decrease the rate of successful migration. Empirical studies often seek to investigate the relationship between genetic differentiation and some ecological variable(s) while accounting for geographic distance, but common approaches to this problem (such as the partial Mantel test) have a number of drawbacks. In this article, we present a Bayesian method that enables users to quantify the relative contributions of geographic distance and ecological distance to genetic differentiation between sampled populations or individuals. We model the allele frequencies in a set of populations at a set of unlinked loci as spatially correlated Gaussian processes, in which the covariance structure is a decreasing function of both geographic and ecological distance. Parameters of the model are estimated using a Markov chain Monte Carlo algorithm. We call this method Bayesian Estimation of Differentiation in Alleles by Spatial Structure and Local Ecology (BEDASSLE), and have implemented it in a user-friendly format in the statistical platform R. We demonstrate its utility with a simulation study and empirical applications to human and teosinte data sets.
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Affiliation(s)
- Gideon S Bradburd
- Department of Evolution and Ecology, Center for Population Biology, University of California, Davis, California, 95616.
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