1
|
Li YR, Fritsch PW, Zhao GG, Cheng XJ, Ding ZL, Lu L. Population differentiation and dynamics of five pioneer species of Gaultheria from the secondary forests in subtropical China. BMC PLANT BIOLOGY 2024; 24:516. [PMID: 38851686 PMCID: PMC11161945 DOI: 10.1186/s12870-024-05189-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Accepted: 05/23/2024] [Indexed: 06/10/2024]
Abstract
BACKGROUND The influence of native secondary succession associated with anthropogenic disturbance on the biodiversity of the forests in subtropical China remains uncertain. In particular, the evolutionary response of small understory shrubs, particularly pioneer species inhabiting continuously disturbed habitats, to topographic heterogeneity and climate change is poorly understood. This study aimed to address this knowledge gap by focusing on the Gaultheria crenulata group, a clade of small pioneer shrubs in subtropical China. RESULTS We examined the genetic structure and demographic history of all five species of the G. crenulata group with two maternally inherited chloroplast DNA (cpDNA) fragments and two biparentally inherited low-copy nuclear genes (LCG) over 89 natural populations. We found that the genetic differentiation of this group was influenced by the geomorphological boundary between different regions of China in association with Quaternary climatic events. Despite low overall genetic diversity, we observed an isolation-by-distance (IBD) pattern at a regional scale, rather than isolation-by-environment (IBE), which was attributed to ongoing human disturbance in the region. CONCLUSION Our findings suggest that the genetic structure of the G. crenulata group reflects the interplay of geological topography, historical climates, and anthropogenic disturbance during the Pliocene-Pleistocene-Holocene periods in subtropical China. The observed IBD pattern, particularly prominent in western China, highlights the role of limited dispersal and gene flow, possibly influenced by physical barriers or decreased connectivity over geographic distance. Furthermore, the east-to-west trend of gene flow, potentially facilitated by the East Asian monsoon system, underscores the complex interplay of biotic and abiotic factors shaping the genetic dynamics of pioneer species in subtropical China's secondary forests. These findings can be used to assess the impact of environmental changes on the adaptation and persistence of biodiversity in subtropical forest ecosystems.
Collapse
Affiliation(s)
- Yi-Rong Li
- School of Pharmaceutical Sciences, Yunnan Key Laboratory of Pharmacology for Natural Products, Yunnan College of Modern Biomedical Industry, Kunming Medical University, Kunming, 650500, Yunnan, China
| | - Peter W Fritsch
- Botanical Research Institute of Texas, 1700 University Drive, Fort Worth, TX, 76017, USA
| | - Gui-Gang Zhao
- Genome Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Science, Kunming, 650223, China
| | - Xiao-Juan Cheng
- School of Pharmaceutical Sciences, Yunnan Key Laboratory of Pharmacology for Natural Products, Yunnan College of Modern Biomedical Industry, Kunming Medical University, Kunming, 650500, Yunnan, China
| | - Zhao-Li Ding
- Genome Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Science, Kunming, 650223, China.
- Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Science, Kunming, 650223, China.
| | - Lu Lu
- School of Pharmaceutical Sciences, Yunnan Key Laboratory of Pharmacology for Natural Products, Yunnan College of Modern Biomedical Industry, Kunming Medical University, Kunming, 650500, Yunnan, China.
| |
Collapse
|
2
|
Huang WC, Liao B, Liu H, Liang YY, Chen XY, Wang B, Xia H. A chromosome-scale genome assembly of Castanopsis hystrix provides new insights into the evolution and adaptation of Fagaceae species. FRONTIERS IN PLANT SCIENCE 2023; 14:1174972. [PMID: 37215286 PMCID: PMC10197965 DOI: 10.3389/fpls.2023.1174972] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 03/22/2023] [Indexed: 05/24/2023]
Abstract
Fagaceae species dominate forests and shrublands throughout the Northern Hemisphere, and have been used as models to investigate the processes and mechanisms of adaptation and speciation. Compared with the well-studied genus Quercus, genomic data is limited for the tropical-subtropical genus Castanopsis. Castanopsis hystrix is an ecologically and economically valuable species with a wide distribution in the evergreen broad-leaved forests of tropical-subtropical Asia. Here, we present a high-quality chromosome-scale reference genome of C. hystrix, obtained using a combination of Illumina and PacBio HiFi reads with Hi-C technology. The assembled genome size is 882.6 Mb with a contig N50 of 40.9 Mb and a BUSCO estimate of 99.5%, which are higher than those of recently published Fagaceae species. Genome annotation identified 37,750 protein-coding genes, of which 97.91% were functionally annotated. Repeat sequences constituted 50.95% of the genome and LTRs were the most abundant repetitive elements. Comparative genomic analysis revealed high genome synteny between C. hystrix and other Fagaceae species, despite the long divergence time between them. Considerable gene family expansion and contraction were detected in Castanopsis species. These expanded genes were involved in multiple important biological processes and molecular functions, which may have contributed to the adaptation of the genus to a tropical-subtropical climate. In summary, the genome assembly of C. hystrix provides important genomic resources for Fagaceae genomic research communities, and improves understanding of the adaptation and evolution of forest trees.
Collapse
Affiliation(s)
- Wei-Cheng Huang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Borong Liao
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Hui Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Yi-Ye Liang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Xue-Yan Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Baosheng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Hanhan Xia
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| |
Collapse
|
3
|
Daco L, Matthies D, Hermant S, Colling G. Genetic diversity and differentiation of populations of Anthyllis vulneraria along elevational and latitudinal gradients. Ecol Evol 2022; 12:e9167. [PMID: 35949527 PMCID: PMC9351329 DOI: 10.1002/ece3.9167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 11/09/2022] Open
Abstract
The abundant centre model (ACM) predicts that the suitability of environmental conditions for a species decreases from the centre of its distribution toward its range periphery and, consequently, its populations will become scarcer, smaller and more isolated, resulting in lower genetic diversity and increased differentiation. However, little is known about whether genetic diversity shows similar patterns along elevational and latitudinal gradients with similar changes in important environmental conditions. Using microsatellite markers, we studied the genetic diversity and structure of 20 populations each of Anthyllis vulneraria along elevational gradients in the Alps from the valleys to the elevational limit (2500 m) and along a latitudinal gradient (2500 km) from Central Europe to the range margin in northern Scandinavia. Both types of gradients corresponded to an 11.5°C difference in mean annual temperature. Genetic diversity strongly declined and differentiation increased with latitude in line with the predictions of the ACM. However, as population size did not decline with latitude and genetic diversity was not related to population size in A. vulneraria, this pattern is not likely to be due to less favorable conditions in the North, but due to serial founder effects during the post-glacial recolonization process. Genetic diversity was not related to elevation, but we found significant isolation by distance along both gradients, although the elevational gradient was shorter by orders of magnitude. Subarctic populations differed genetically from alpine populations indicating that the northern populations did not originate from high elevational Alpine ones. Our results support the notion that postglacial latitudinal colonization over large distances resulted in a larger loss of genetic diversity than elevational range shifts. The lack of genetic diversity in subarctic populations may threaten their long-term persistence in the face of climate change, whereas alpine populations could benefit from gene flow from low-elevation populations.
Collapse
Affiliation(s)
- Laura Daco
- Musée national d'histoire naturelleLuxembourgLuxembourg
- University of Marburg, Department of BiologyMarburgGermany
- Fondation faune‐floreLuxembourgLuxembourg
| | | | | | - Guy Colling
- Musée national d'histoire naturelleLuxembourgLuxembourg
| |
Collapse
|
4
|
Fuentes G, González F, Saavedra J, López-Sepúlveda P, Victoriano PF, Stuessy TF, Ruiz-Ponce E. Assessing signals of selection and historical demography to develop conservation strategies in the Chilean emblematic Araucaria araucana. Sci Rep 2021; 11:20504. [PMID: 34654850 PMCID: PMC8521589 DOI: 10.1038/s41598-021-98662-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 08/27/2021] [Indexed: 11/25/2022] Open
Abstract
Loss of genetic diversity reduces the ability of species to evolve and respond to environmental change. Araucaria araucana is an emblematic conifer species from southern South America, with important ethnic value for the Mapuche people (Pehuenche); the Chilean Government has catalogued its conservation status as vulnerable. Climatic fluctuations were potentially a major impact in the genetic variation within many tree species. In this context, the restricted geographic distribution of A. araucana in Chile appears to be a consequence of the Last Glacial Maximum (LGM). During the past two centuries, strong human intervention has also affected the geographical distribution and population sizes of A. araucana. Reduction of population size may cause loss of genetic diversity, which could affect frequency of adaptive loci. The aims of this study were to know the existence of potential loci under selection and populations with genetic, demographic disequilibrium in the Chilean distribution of A. araucana. Based on 268 polymorphic AFLP loci, we have investigated potential loci under selection and genetic, demographic disequilibrium within seven Chilean populations of Araucaria araucana. Correlation of 41 outlier loci with the environmental variables of precipitation and temperature reveals signatures of selection, whereas 227 neutral loci provide estimates of demographic equilibrium and genetic population structure. Three populations are recommended as priorities for conservation.
Collapse
Affiliation(s)
- Glenda Fuentes
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Fidelina González
- Departamento de Biología Celular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.
| | - Javier Saavedra
- Departamento de Agronomia, Universidade Estadual de Maringá, Av. Colombo 5790, Maringá, PR, Brasil
| | - Patricio López-Sepúlveda
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Pedro F Victoriano
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Tod F Stuessy
- Herbarium and Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, 43210, USA.,Department of Botany and Biodiversity Research, University of Vienna, 1030, Vienna, Austria
| | - Eduardo Ruiz-Ponce
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| |
Collapse
|
5
|
Vega-Polo P, Cobo MM, Argudo A, Gutierrez B, Rowntree J, Torres MDL. Characterizing the genetic diversity of the Andean blueberry (Vaccinium floribundum Kunth.) across the Ecuadorian Highlands. PLoS One 2020; 15:e0243420. [PMID: 33284832 PMCID: PMC7721170 DOI: 10.1371/journal.pone.0243420] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/22/2020] [Indexed: 11/18/2022] Open
Abstract
The Ecuadorian páramo, a high altitude tundra-like ecosystem, is a unique source of various ecosystem services and distinct biodiversity. Anthropogenic activities are associated with its fragmentation, which alters ecological factors and directly threatens resident species. Vaccinium floribundum Kunth., commonly known as Andean blueberry or mortiño, is a wild shrub endemic to the Andean region and highly valued in Ecuador for its berries, which are widely used in food preparations and hold an important cultural value. Since it is a wild species, mortiño could be vulnerable to environmental changes, resulting in a reduction of the size and distribution of its populations. To evaluate the extent of these effects on the mortiño populations, we assessed the genetic diversity and population structure of the species along the Ecuadorian highlands. We designed and developed a set of 30 species-specific SSR (simple sequence repeats) markers and used 16 of these to characterize 100 mortiño individuals from 27 collection sites. Our results revealed a high degree of genetic diversity (HE = 0.73) for the Ecuadorian mortiño, and a population structure analyses suggested the existence of distinct genetic clusters present in the northern, central and southern highlands. A fourth, clearly differentiated cluster was also found and included individuals from locations at higher elevations. We suggest that the population structure of the species could be explained by an isolation-by-distance model and can be associated with the geological history of the Andean region. Our results suggest that elevation could also be a key factor in the differentiation of mortiño populations. This study provides an extensive overview of the species across its distribution range in Ecuador, contributing to a better understanding of its conservation status. These results can assist in the development of conservation programs for this valuable biological and cultural resource and for the páramo ecosystem as a whole.
Collapse
Affiliation(s)
- Pamela Vega-Polo
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Maria Mercedes Cobo
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Andrea Argudo
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Bernardo Gutierrez
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Jennifer Rowntree
- Department of Natural Sciences, Ecology and Environment Research Centre, Manchester Metropolitan University, Oxford, United Kingdom
| | - Maria de Lourdes Torres
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- * E-mail:
| |
Collapse
|
6
|
Linck EB, Celi JE, Sheldon KS. Panmixia across elevation in thermally sensitive Andean dung beetles. Ecol Evol 2020; 10:4143-4155. [PMID: 32489637 PMCID: PMC7244805 DOI: 10.1002/ece3.6185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 11/17/2022] Open
Abstract
Janzen's seasonality hypothesis predicts that organisms inhabiting environments with limited climatic variability will evolve a reduced thermal tolerance breadth compared with organisms experiencing greater climatic variability. In turn, narrow tolerance breadth may select against dispersal across strong temperature gradients, such as those found across elevation. This can result in narrow elevational ranges and generate a pattern of isolation by environment or neutral genetic differentiation correlated with environmental variables that are independent of geographic distance. We tested for signatures of isolation by environment across elevation using genome-wide SNP data from five species of Andean dung beetles (subfamily Scarabaeinae) with well-characterized, narrow thermal physiologies, and narrow elevational distributions. Contrary to our expectations, we found no evidence of population genetic structure associated with elevation and little signal of isolation by environment. Further, elevational ranges for four of five species appear to be at equilibrium and show no decay of genetic diversity at range limits. Taken together, these results suggest physiological constraints on dispersal may primarily operate outside of a stable realized niche and point to a lower bound on the spatial scale of local adaptation.
Collapse
Affiliation(s)
- Ethan B. Linck
- Department of Ecology & Evolutionary BiologyUniversity of Tennessee, KnoxvilleKnoxvilleTNUSA
| | - Jorge E. Celi
- Biogeography and Spatial Ecology Research GroupUniversidad Regional Amazónica IkiamTenaEcuador
| | - Kimberly S. Sheldon
- Department of Ecology & Evolutionary BiologyUniversity of Tennessee, KnoxvilleKnoxvilleTNUSA
| |
Collapse
|
7
|
Wind pollination over 70 years reduces the negative genetic effects of severe forest fragmentation in the tropical oak Quercus bambusifolia. Heredity (Edinb) 2019; 124:156-169. [PMID: 31431738 DOI: 10.1038/s41437-019-0258-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 07/05/2019] [Accepted: 07/09/2019] [Indexed: 11/08/2022] Open
Abstract
Whether wind pollination in trees can offset the negative genetic consequences of anthropogenic forest fragmentation is not clearly established. To answer this question, we examined the demographic genetics of Quercus bambusifolia over a 70-year recovery period in highly fragmented forests in Hong Kong. We sampled 1138 individuals from 37 locations, and genetically analysed the chronosequence through the classification of tree diameters from the same populations using 13 microsatellite markers. Our study reveals that severe fragmentation caused a significant genetic bottleneck with very few remaining but genetically diverse individuals. We observed an enhanced genetic diversity during demographic recovery. We found full-sibs within populations and half-sibs across the study range. This reflects a limited seed dispersal and extensive pollen flow. Despite reduced genetic structure both among and within populations, overall a strong persisting genetic differentiation (F'ST = 0.240, P < 0.01) and significant small-scale spatial genetic structure (F(1) = 0.13, Sp = 0.024, P < 0.01) were observed. Existing bottlenecks and low effective population sizes within the temporal chronosequence suggest that the long-term effect of severe fragmentation cannot be entirely eliminated by wind pollination with demographic recovery in the absence of effective seed dispersal. Our results lead to recommendations for forest management.
Collapse
|
8
|
Thongkumkoon P, Chomdej S, Kampuansai J, Pradit W, Waikham P, Elliott S, Chairuangsri S, Shannon DP, Wangpakapattanawong P, Liu A. Genetic assessment of three Fagaceae species in forest restoration trials. PeerJ 2019; 7:e6958. [PMID: 31179177 PMCID: PMC6544010 DOI: 10.7717/peerj.6958] [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: 01/25/2019] [Accepted: 04/14/2019] [Indexed: 11/20/2022] Open
Abstract
Restoring isolated patches of forest ecosystems in degraded landscapes could potentially lead to genetic loss and inbreeding. Therefore, this study determined the occurrence of genetic diversity among the tree species Castanopsis tribuloides, C. calathiformis, and Lithocarpus polystachyus all of which were proven previously to be effective native tree species in the restoration of upland evergreen forests in northern Thailand when using the seed sample collection method. We tested our hypothesis as to whether the genetic diversity of a plant population that had been planted from the seeds of 4–6 adult trees would be lower and whether incidences of fixation index (Fis) would be higher among the second generation seedlings of these three Fagaceae species in isolated forest restoration trial plots. Microsatellite primers were selected from the entire genome sequence of C. tribuloides and the genetic sequences of C. tribuloides, L. polystachyus, and C. calathiformis were analyzed. Our results indicated a high degree of genetic diversity (He) in C. tribuloides (0.736) and C. calathiformis (0.481); however, a low level of genetic diversity was observed in L. polystachyus (0.281) within the restored forest. The fixation index for the second generation of L. polystachyus and C. calathiformis in the restored forest showed evidence of inbreeding. These results imply the efficiency of the seed sample collection method and verify that it does not reduce the level of genetic diversity in C. tribuloides and C. calathiformis. However, it may result in incidences of an inbreeding phenomena, suggesting the need to increase the number of adult trees used at the seed collection stage.
Collapse
Affiliation(s)
- Patcharawadee Thongkumkoon
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Environmental Science Research Center, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Siriwadee Chomdej
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Jatupol Kampuansai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Waranee Pradit
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Pimubon Waikham
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Stephen Elliott
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Forest Restoration Research Unit, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Sutthathorn Chairuangsri
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Forest Restoration Research Unit, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Dia Panitnard Shannon
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Forest Restoration Research Unit, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Prasit Wangpakapattanawong
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Environmental Science Research Center, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Aizhong Liu
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China (Ministry of Education), Southwest Forestry University, Kunming, China
| |
Collapse
|
9
|
Sakaguchi S, Horie K, Ishikawa N, Nagano AJ, Yasugi M, Kudoh H, Ito M. Simultaneous evaluation of the effects of geographic, environmental and temporal isolation in ecotypic populations of Solidago virgaurea. THE NEW PHYTOLOGIST 2017; 216:1268-1280. [PMID: 28833204 DOI: 10.1111/nph.14744] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 07/07/2017] [Indexed: 05/14/2023]
Abstract
Early stages of ecological speciation can create populations with an ecology and reproduction timing distinct from those of related populations. Landscape genetic models incorporating environmental heterogeneity and population-specific reproductive traits enable the processes of population genetic differentiation to be inferred. We investigated genome-wide genetic variation in ecotypic populations of Solidago virgaurea sensu lato, a herbaceous plant inhabiting a wide range of habitats (woodlands, serpentine barrens and alpine grasslands) and displaying remarkable variation in flowering time. Simultaneous evaluation of environmental factors revealed an overwhelming effect of soil type differences on neutral genetic differentiation, compared with elevational differences. This result probably reflects the abrupt environmental changes generated by geological boundaries, whereas mountain slopes exhibit clinal changes, facilitating gene exchange between neighbouring populations. Temporal isolation was positively associated with genetic differentiation, with some early-flowering serpentine populations having allele frequencies distinct from adjacent nonserpentine populations. Overall, this study highlights the importance of ecological processes and of evolution of flowering time to promote genetic differentiation of S. virgaurea populations in a complex landscape.
Collapse
Affiliation(s)
- Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Kenji Horie
- Asahikawa City Northern Wild Plants Garden, Asahikawa, 071-1200, Japan
| | - Naoko Ishikawa
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Shiga, 520-2194, Japan
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2113, Japan
- JST CREST, Honcho 4-1-8, Kawaguchi, Saitama, 332-0012, Japan
| | - Masaki Yasugi
- National Institute for Basic Biology, Higashiyama 5-1, Myodaiji, Okazaki, 444-8787, Aichi, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2113, Japan
| | - Motomi Ito
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan
| |
Collapse
|
10
|
Genetic structure and isolation by altitude in rice landraces of Yunnan, China revealed by nucleotide and microsatellite marker polymorphisms. PLoS One 2017; 12:e0175731. [PMID: 28423046 PMCID: PMC5396909 DOI: 10.1371/journal.pone.0175731] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 03/30/2017] [Indexed: 11/30/2022] Open
Abstract
Rice landraces, a genetic reservoir for varietal improvement, are developed by farmers through artificial selection during the long-term domestication process. To efficiently conserve, manage, and use such germplasm resources, an understanding of the genetic structure and differentiation of local rice landraces is required. In this study, we analyzed 188 accessions of rice landraces collected from localities across an altitudinal gradient from 425 to 2, 274 m above sea level in Yunnan Province, China using ten target genes and 48 SSR markers. We detected clear differentiation of the rice landraces into indica and japonica groups and further separation of the accessions in each group into two subgroups according to altitude, including a lower altitude subgroup and higher altitude subgroup. The AMOVA results showed significant genetic differentiation among altitude zones at SSRs and most genes, except Os1977 and STS22. We further determined that differentiation among landrace populations followed a model of isolation by altitude, in which gene flow was higher among populations at similar altitude levels than across different altitude levels. Our findings demonstrated that both adaptation to altitude and altitude-dependent gene flow played key roles in the genetic differentiation of rice landraces in Yunnan, China.
Collapse
|
11
|
Peng Y, Morales L, Hensen I, Renison D. No effect of elevation and fragmentation on genetic diversity and structure inPolylepis australistrees from central Argentina. AUSTRAL ECOL 2016. [DOI: 10.1111/aec.12432] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yanling Peng
- Institute of Biology/Geobotany and Botanical Garden; Martin Luther University of Halle-Wittenberg; Halle/Saale Germany
| | - Laura Morales
- Department of Plant Sciences and Graduate Group in Ecology; University of California; Davis California USA
| | - Isabell Hensen
- Institute of Biology/Geobotany and Botanical Garden; Martin Luther University of Halle-Wittenberg; Halle/Saale Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Leipzig Germany
| | - Daniel Renison
- Instituto de Investigaciones Biológicas y Tecnológicas; Centro de Ecología y Recursos Naturales Renovables (CONICET - Universidad Nacional de Córdoba); Córdoba Argentina
| |
Collapse
|
12
|
Castilla AR, Pope N, Jaffé R, Jha S. Elevation, Not Deforestation, Promotes Genetic Differentiation in a Pioneer Tropical Tree. PLoS One 2016; 11:e0156694. [PMID: 27280872 PMCID: PMC4900633 DOI: 10.1371/journal.pone.0156694] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 04/28/2016] [Indexed: 11/22/2022] Open
Abstract
The regeneration of disturbed forest is an essential part of tropical forest ecology, both with respect to natural disturbance regimes and large-scale human-mediated logging, grazing, and agriculture. Pioneer tree species are critical for facilitating the transition from deforested land to secondary forest because they stabilize terrain and enhance connectivity between forest fragments by increasing matrix permeability and initiating disperser community assembly. Despite the ecological importance of early successional species, little is known about their ability to maintain gene flow across deforested landscapes. Utilizing highly polymorphic microsatellite markers, we examined patterns of genetic diversity and differentiation for the pioneer understory tree Miconia affinis across the Isthmus of Panama. Furthermore, we investigated the impact of geographic distance, forest cover, and elevation on genetic differentiation among populations using circuit theory and regression modeling within a landscape genetics framework. We report marked differences in historical and contemporary migration rates and moderately high levels of genetic differentiation in M. affinis populations across the Isthmus of Panama. Genetic differentiation increased significantly with elevation and geographic distance among populations; however, we did not find that forest cover enhanced or reduced genetic differentiation in the study region. Overall, our results reveal strong dispersal for M. affinis across human-altered landscapes, highlighting the potential use of this species for reforestation in tropical regions. Additionally, this study demonstrates the importance of considering topography when designing programs aimed at conserving genetic diversity within degraded tropical landscapes.
Collapse
Affiliation(s)
- Antonio R. Castilla
- Department of Integrative Biology, 401 Biological Laboratories, University of Texas, Austin, TX, 78712, United States of America
| | - Nathaniel Pope
- Department of Integrative Biology, 401 Biological Laboratories, University of Texas, Austin, TX, 78712, United States of America
| | - Rodolfo Jaffé
- Vale Institute of Technology–Sustainable Development, Rua Boaventura da Silva 955, Belém, PA 66055–090, Brazil
- Department of Ecology, University of São Paulo, Rua do Matão 321, São Paulo, SP 05508–090, Brazil
| | - Shalene Jha
- Department of Integrative Biology, 401 Biological Laboratories, University of Texas, Austin, TX, 78712, United States of America
- * E-mail:
| |
Collapse
|
13
|
Durka W, Michalski SG, Berendzen KW, Bossdorf O, Bucharova A, Hermann JM, Hölzel N, Kollmann J. Genetic differentiation within multiple common grassland plants supports seed transfer zones for ecological restoration. J Appl Ecol 2016. [DOI: 10.1111/1365-2664.12636] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Walter Durka
- Department of Community Ecology (BZF); Helmholtz Centre for Environmental Research - UFZ; Theodor-Lieser-Str. 4 06120 Halle Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Deutscher Platz 5e 04103 Leipzig Germany
| | - Stefan G. Michalski
- Department of Community Ecology (BZF); Helmholtz Centre for Environmental Research - UFZ; Theodor-Lieser-Str. 4 06120 Halle Germany
| | - Kenneth W. Berendzen
- ZMBP - Central Facilities; University of Tübingen; Auf der Morgenstelle 32 72076 Tübingen Germany
| | - Oliver Bossdorf
- Plant Evolutionary Ecology; Institute of Evolution & Ecology; University of Tübingen; Auf der Morgenstelle 5 72076 Tübingen Germany
| | - Anna Bucharova
- Plant Evolutionary Ecology; Institute of Evolution & Ecology; University of Tübingen; Auf der Morgenstelle 5 72076 Tübingen Germany
| | - Julia-Maria Hermann
- Restoration Ecology; Department of Ecology & Ecosystem Management; Technical University Munich; Emil-Ramann-Str. 6 85354 Freising Germany
| | - Norbert Hölzel
- Biodiversity and Ecosystem Research Group; Institute of Landscape Ecology; University of Münster; Heisenbergstr. 2 48149 Münster Germany
| | - Johannes Kollmann
- Restoration Ecology; Department of Ecology & Ecosystem Management; Technical University Munich; Emil-Ramann-Str. 6 85354 Freising Germany
| |
Collapse
|
14
|
Wu Z, Yu D, Wang Z, Li X, Xu X. Great influence of geographic isolation on the genetic differentiation of Myriophyllum spicatum under a steep environmental gradient. Sci Rep 2015; 5:15618. [PMID: 26494202 PMCID: PMC4616052 DOI: 10.1038/srep15618] [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: 03/30/2015] [Accepted: 09/28/2015] [Indexed: 11/01/2022] Open
Abstract
Understanding how natural processes affect population genetic structures is an important issue in evolutionary biology. One effective method is to assess the relative importance of environmental and geographical factors in the genetic structure of populations. In this study, we examined the spatial genetic variation of thirteen Myriophyllum spicatum populations from the Qinghai-Tibetan Plateau (QTP) and adjacent highlands (Yunnan-Guizhou Plateau, YGP) by using microsatellite loci and environmental and geographical factors. Bioclim layers, hydrological properties and elevation were considered as environmental variables and reduced by principal component analysis. The genetic isolation by geographic distance (IBD) was tested by Mantel tests and the relative importance of environmental variables on population genetic differentiation was determined by a partial Mantel test and multiple matrix regression with randomization (MMRR). Two genetic clusters corresponding to the QTP and YGP were identified. Both tests and MMRR revealed a significant and strong correlation between genetic divergence and geographic isolation under the influence of environmental heterogeneity at the overall and finer spatial scales. Our findings suggested the dominant role of geography on the evolution of M. spicatum under a steep environmental gradient in the alpine landscape as a result of dispersal limitation and genetic drift.
Collapse
Affiliation(s)
- Zhigang Wu
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Dan Yu
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Zhong Wang
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Xing Li
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Xinwei Xu
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| |
Collapse
|
15
|
Funk WC, Murphy MA, Hoke KL, Muths E, Amburgey SM, Lemmon EM, Lemmon AR. Elevational speciation in action? Restricted gene flow associated with adaptive divergence across an altitudinal gradient. J Evol Biol 2015; 29:241-52. [DOI: 10.1111/jeb.12760] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/28/2015] [Accepted: 09/08/2015] [Indexed: 01/15/2023]
Affiliation(s)
- W. C. Funk
- Department of Biology Colorado State University Fort Collins CO USA
- Graduate Degree Program in Ecology Colorado State University Fort Collins CO USA
| | - M. A. Murphy
- Department of Ecosystem Science and Management University of Wyoming Laramie WY USA
- Program in Ecology University of Wyoming Laramie WY USA
| | - K. L. Hoke
- Department of Biology Colorado State University Fort Collins CO USA
| | - E. Muths
- U.S. Geological Survey Fort Collins Science Center Fort Collins CO USA
| | - S. M. Amburgey
- Department of Ecosystem Science and Management Pennsylvania State University University Park PA USA
- Intercollege Graduate Degree Program in Ecology Pennsylvania State University University Park PA USA
| | - E. M. Lemmon
- Department of Biology Florida State University Tallahassee FL USA
| | - A. R. Lemmon
- Department of Scientific Computing Florida State University Tallahassee FL USA
| |
Collapse
|
16
|
Reis TS, Ciampi-Guillardi M, Bajay MM, de Souza AP, Dos Santos FAM. Elevation as a barrier: genetic structure for an Atlantic rain forest tree (Bathysa australis) in the Serra do Mar mountain range, SE Brazil. Ecol Evol 2015; 5:1919-31. [PMID: 26140207 PMCID: PMC4485972 DOI: 10.1002/ece3.1501] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 03/10/2015] [Accepted: 03/11/2015] [Indexed: 12/02/2022] Open
Abstract
Distance and discrete geographic barriers play a role in isolating populations, as seed and pollen dispersal become limited. Nearby populations without any geographic barrier between them may also suffer from ecological isolation driven by habitat heterogeneity, which may promote divergence by local adaptation and drift. Likewise, elevation gradients may influence the genetic structure and diversity of populations, particularly those marginally distributed. Bathysa australis (Rubiaceae) is a widespread tree along the elevation gradient of the Serra do Mar, SE Brazil. This self-compatible species is pollinated by bees and wasps and has autochoric seeds, suggesting restricted gene dispersal. We investigated the distribution of genetic diversity in six B. australis populations at two extreme sites along an elevation gradient: a lowland site (80–216 m) and an upland site (1010–1100 m.a.s.l.). Nine microsatellite loci were used to test for genetic structure and to verify differences in genetic diversity between sites. We found a marked genetic structure on a scale as small as 6 km (FST = 0.21), and two distinct clusters were identified, each corresponding to a site. Although B. australis is continuously distributed along the elevation gradient, we have not observed a gene flow between the extreme populations. This might be related to B. australis biological features and creates a potential scenario for adaptation to the different conditions imposed by the elevation gradient. We failed to find an isolation-by-distance pattern; although on the fine scale, all populations showed spatial autocorrelation until ∼10-20 m. Elevation difference was a relevant factor though, but we need further sampling effort to check its correlation with genetic distance. The lowland populations had a higher allelic richness and showed higher rare allele counts than the upland ones. The upland site may be more selective, eliminating rare alleles, as we did not find any evidence for bottleneck.
Collapse
Affiliation(s)
- Talita Soares Reis
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas - UNICAMP CP 6109, 13083-970, Campinas, SP, Brazil
| | - Maísa Ciampi-Guillardi
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas - UNICAMP CP 6010, 13083-970, Campinas, SP, Brazil
| | - Miklos Maximiliano Bajay
- Departamento de Genética, ESALQ/Universidade de São Paulo - USP 12418-900, Piracicaba, SP, Brazil
| | - Anete Pereira de Souza
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas - UNICAMP CP 6109, 13083-970, Campinas, SP, Brazil ; Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas - UNICAMP CP 6010, 13083-970, Campinas, SP, Brazil
| | - Flavio Antonio Maës Dos Santos
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas - UNICAMP CP 6109, 13083-970, Campinas, SP, Brazil
| |
Collapse
|
17
|
A unifying study of phenotypic and molecular genetic variability in natural populations of Anadenanthera colubrina var. cebil from Yungas and Paranaense biogeographic provinces in Argentina. J Genet 2015; 93:123-32. [PMID: 24840829 DOI: 10.1007/s12041-014-0347-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Anadenanthera colubrina var. cebil is a discontinuously distributed native tree species in South American subtropical forests. Thirteen quantitative traits and eight nuclear microsatellite loci were examined in individuals from two biogeographic provinces of Argentina to determine the number and composition of genetically distinguishable groups of individuals and explore possible spatial patterns of the phenotypic and genetic variability. Means of reproductive traits were higher in the Yungas than in the Paranaense biogeographic province, whereas five out of eight nonreproductive quantitative traits showed higher mean values in the latter. Variance coefficients were moderate, and there were significant differences between and within provinces. Three clusters were defined based on spatial model for cluster membership for quantitative traits. One cluster grouped the individuals from the Paranaense biogeographic province whereas the individuals from the Yungas biogeographic province grouped regarding its population of origin. Parameters of molecular genetic variability showed higher values in the Yungas than in the Paranaense biogeographic province. Observed heterozygosity was lower than expected heterozygosity in both biogeographic provinces, indicating an excess of homozygosity. The homozygosity test by Watterson and the exact test by Slatkin suggested diversifying selection for locus Ac41.1. Bayesian clustering spatial model for microsatellites loci data were performed for both all loci and for all loci excluding locus Ac41.1. In both analyses two clusters were inferred. Analysis of molecular variance revealed similar results for all genotypes and for all genotypes defined excluding locus Ac41.1. Most of the total variance is attributable to genetic variation within clusters. The presence of homogeneous clusters was detected for both the phenotypic and molecular genetic variability. Two Bayesian clustering analyses were performed according to molecular genetic data, and two clusters were inferred. Individuals were assigned to their provinces of origin. Genetic molecular variation was higher in the populations of the Yungas biogeographic province which translates into highly qualified populations for conservation. Populations from the Paranaense biogeographic province showed the highest mean value of number of seeds per fruit making them valuable as well with regard to the exploitation of management strategies as a means to recover the impacted areas where these populations are located.
Collapse
|
18
|
Isolation and characterization of thirteen polymorphic microsatellite loci for Lithocarpus glaber. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.02.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
19
|
Orsini L, Vanoverbeke J, Swillen I, Mergeay J, De Meester L. Drivers of population genetic differentiation in the wild: isolation by dispersal limitation, isolation by adaptation and isolation by colonization. Mol Ecol 2013; 22:5983-99. [DOI: 10.1111/mec.12561] [Citation(s) in RCA: 310] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 10/08/2013] [Accepted: 10/11/2013] [Indexed: 02/01/2023]
Affiliation(s)
- Luisa Orsini
- Laboratory of Aquatic Ecology, Evolution and Conservation; University of Leuven; Ch. Deberiotstraat 32 Leuven 3000 Belgium
| | - Joost Vanoverbeke
- Laboratory of Aquatic Ecology, Evolution and Conservation; University of Leuven; Ch. Deberiotstraat 32 Leuven 3000 Belgium
| | - Ine Swillen
- Laboratory of Aquatic Ecology, Evolution and Conservation; University of Leuven; Ch. Deberiotstraat 32 Leuven 3000 Belgium
| | - Joachim Mergeay
- Laboratory of Aquatic Ecology, Evolution and Conservation; University of Leuven; Ch. Deberiotstraat 32 Leuven 3000 Belgium
- Research Institute for Nature and Forest; Gaverstraat 4 Geraardsbergen B-9500 Belgium
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation; University of Leuven; Ch. Deberiotstraat 32 Leuven 3000 Belgium
| |
Collapse
|
20
|
Hamasha HR, Schmidt-Lebuhn AN, Durka W, Schleuning M, Hensen I. Bioclimatic regions influence genetic structure of four Jordanian Stipa species. PLANT BIOLOGY (STUTTGART, GERMANY) 2013; 15:882-891. [PMID: 23369254 DOI: 10.1111/j.1438-8677.2012.00689.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 09/11/2012] [Indexed: 06/01/2023]
Abstract
Strong environmental gradients can affect the genetic structure of plant populations, but little is known as to whether closely related species respond similarly or idiosyncratically to ecogeographic variation. We analysed the extent to which gradients in temperature and rainfall shape the genetic structure of four Stipa species in four bioclimatic regions in Jordan. Genetic diversity, differentiation and structure of Stipa species were investigated using amplified fragment length polymorphism (AFLP) molecular markers. For each of the four study species, we sampled 120 individuals from ten populations situated in distinct bioclimatic regions and assessed the degree of genetic diversity and genetic differentiation within and among populations. The widespread ruderals Stipa capensis and S. parviflora had higher genetic diversity than the geographically restricted semi-desert species S. arabica and S. lagascae. In three of the four species, genetic diversity strongly decreased with precipitation, while genetic diversity increased with temperature in S. capensis. Most genetic diversity resided among populations in the semi-desert species (Φ(ST) = 0.572/0.595 in S. arabica/lagascae) but within populations in the ruderal species (Φ(ST) = 0.355/0.387 S. capensis/parviflora). Principal coordinate analysis (PCoA) and STRUCTURE analysis showed that Stipa populations of all species clustered ecogeographically. A genome scan revealed that divergent selection at particular AFLP loci contributed to genetic differentiation. Irrespective of their different life histories, Stipa species responded similarly to the bioclimatic gradient in Jordan. We conclude that, in addition to predominant random processes, steep climatic gradients might shape the genetic structure of plant populations.
Collapse
Affiliation(s)
- H R Hamasha
- Institute of Biology/Geobotany and Botanical Garden, Martin-Luther-University Halle-Wittenberg, Halle/Saale, Germany.
| | | | | | | | | |
Collapse
|
21
|
Wei X, Meng H, Jiang M. Landscape genetic structure of a Streamside tree species Euptelea pleiospermum (Eupteleaceae): contrasting roles of river valley and mountain ridge. PLoS One 2013; 8:e66928. [PMID: 23825588 PMCID: PMC3692547 DOI: 10.1371/journal.pone.0066928] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 05/13/2013] [Indexed: 11/25/2022] Open
Abstract
We used landscape genetics and statistical models to test how landscape features influence connectivity or create barriers to dispersal for a mountain riparian tree species, Euptelea pleiospermum. Young leaves from 1078 individuals belonging to 36 populations at elevations of 900-2000 m along upper reaches of four rivers were genotyped using eight nuclear microsatellite markers. We found no evidence for the unidirectional dispersal hypothesis in E. pleiospermum within each river. The linear dispersal pattern along each river valley is mostly consistent with the "classical metapopulaton" model. Mountain ridges separating rivers were genetic barriers for this wind-pollinated tree species with anemochorous seeds, whereas river valleys provided important corridors for dispersal. Gene flow among populations along elevational gradients within each river prevails over gene flow among populations at similar elevations but from different rivers. This pattern of gene flow is likely to promote elevational range shifts of plant populations and to hinder local adaptation along elevational gradients. This study provides a paradigm to determine which of the two strategies (migration or adaptation) will be adopted by mountain riparian plants under climate warming.
Collapse
Affiliation(s)
- Xinzeng Wei
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, People’s Republic of China
| | - Hongjie Meng
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Mingxi Jiang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, People’s Republic of China
| |
Collapse
|
22
|
Forest fragmentation and edge effects on the genetic structure ofClusia sphaerocarpaandC. lechleri(Clusiaceae) in tropical montane forests. JOURNAL OF TROPICAL ECOLOGY 2013. [DOI: 10.1017/s0266467413000345] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Abstract:Fragmentation of tropical forests influences abiotic and biotic processes that affect the genetic structure of plant populations. In forest fragments, edge effects, i.e. changes of abiotic and biotic factors at forest edges, may be prevalent. In two forest fragments (c. 200 ha atc. 2450 m asl) of tropical montane forest in Bolivia, sympatric populations of the dioecious tree speciesClusia sphaerocarpaandC. lechleriwere used as case study species to compare genetic diversity and small-scale genetic structure (SGS) between edge and interior habitats. Eight microsatellite markers were employed to genotype 343 individuals including adults, juveniles and seedlings ofC. sphaerocarpaand 196 ofC. lechleri. Genetic differentiation was found between habitats in both species (ΦRT= 0.071 forC. sphaerocarpaand ΦRT= 0.028 forC. lechleri) and among ages inC. sphaerocarpa(ΦRT= 0.016). Overall, SGS was weak but significant with more pronounced SGS inC. lechleri(Sp= 0.0128) than inC. sphaerocarpa(Sp= 0.0073). However, positive spatial genetic autocorrelation extended only up to 10 m. ForC. sphaerocarpa, SGS was stronger in seedling and juvenile stages than in adults and in the forest interior than at forest edges. Our results show that edge effects can extend to the genetic level by breaking-up local genetic structures, probably due to increased gene flow and enhanced pollination and seed-dispersal interactions at forest edges.
Collapse
|
23
|
Soto-Cerda BJ, Cloutier S. Outlier Loci and Selection Signatures of Simple Sequence Repeats (SSRs) in Flax ( Linum usitatissimum L.). PLANT MOLECULAR BIOLOGY REPORTER 2013; 31:978-990. [PMID: 24415843 PMCID: PMC3881565 DOI: 10.1007/s11105-013-0568-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Genomic microsatellites (gSSRs) and expressed sequence tag-derived SSRs (EST-SSRs) have gained wide application for elucidating genetic diversity and population structure in plants. Both marker systems are assumed to be selectively neutral when making demographic inferences, but this assumption is rarely tested. In this study, three neutrality tests were assessed for identifying outlier loci among 150 SSRs (85 gSSRs and 65 EST-SSRs) that likely influence estimates of population structure in three differentiated flax sub-populations (FST = 0.19). Moreover, the utility of gSSRs, EST-SSRs, and the combined sets of SSRs was also evaluated in assessing genetic diversity and population structure in flax. Six outlier loci were identified by at least two neutrality tests showing footprints of balancing selection. After removing the outlier loci, the STRUCTURE analysis and the dendrogram topology of EST-SSRs improved. Conversely, gSSRs and combined SSRs results did not change significantly, possibly as a consequence of the higher number of neutral loci assessed. Taken together, the genetic structure analyses established the superiority of gSSRs to determine the genetic relationships among flax accessions, although the combined SSRs produced the best results. Genetic diversity parameters did not differ statistically (P > 0.05) between gSSRs and EST-SSRs, an observation partially explained by the similar number of repeat motifs. Our study provides new insights into the ability of gSSRs and EST-SSRs to measure genetic diversity and structure in flax and confirms the importance of testing for the occurrence of outlier loci to properly assess natural and breeding populations, particularly in studies considering only few loci.
Collapse
Affiliation(s)
- Braulio J. Soto-Cerda
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB Canada R3T 2M9
- Agriaquaculture Nutritional Genomic Center, Genomics and Bioinformatics Unit, CGNA, Km 10 Camino Cajón-Vilcún, INIA, Temuco, Chile
| | - Sylvie Cloutier
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB Canada R3T 2M9
| |
Collapse
|
24
|
Hahn T, Kettle CJ, Ghazoul J, Frei ER, Matter P, Pluess AR. Patterns of genetic variation across altitude in three plant species of semi-dry grasslands. PLoS One 2012; 7:e41608. [PMID: 22870236 PMCID: PMC3411590 DOI: 10.1371/journal.pone.0041608] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 06/22/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Environmental gradients caused by altitudinal gradients may affect genetic variation within and among plant populations and inbreeding within populations. Populations in the upper range periphery of a species may be important source populations for range shifts to higher altitude in response to climate change. In this study we investigate patterns of population genetic variation at upper peripheral and lower more central altitudes in three common plant species of semi-dry grasslands in montane landscapes. METHODOLOGY/PRINCIPAL FINDINGS In Briza media, Trifolium montanum and Ranunculus bulbosus genetic diversity, inbreeding and genetic relatedness of individuals within populations and genetic differentiation among populations was characterized using AFLP markers. Populations were sampled in the Swiss Alps at 1800 (upper periphery of the study organisms) and at 1200 m a.s.l. Genetic diversity was not affected by altitude and only in B. media inbreeding was greater at higher altitudes. Genetic differentiation was slightly greater among populations at higher altitudes in B. media and individuals within populations were more related to each other compared to individuals in lower altitude populations. A similar but less strong pattern of differentiation and relatedness was observed in T. montanum, while in R. bulbosus there was no effect of altitude. Estimations of population size and isolation of populations were similar, both at higher and lower altitudes. CONCLUSIONS/SIGNIFICANCE Our results suggest that altitude does not affect genetic diversity in the grassland species under study. Genetic differentiation of populations increased only slightly at higher elevation, probably due to extensive (historic) gene flow among altitudes. Potentially pre-adapted genes might therefore spread easily across altitudes. Our study indicates that populations at the upper periphery are not genetically depauperate or isolated and thus may be important source populations for migration under climate change.
Collapse
Affiliation(s)
- Thomas Hahn
- Institute of Terrestrial Ecosystems, Ecosystem Management, ETH Zurich, Zurich, Switzerland.
| | | | | | | | | | | |
Collapse
|
25
|
Shi MM, Chen XY. Leading-edge populations do not show low genetic diversity or high differentiation in a wind-pollinated tree. POPUL ECOL 2012. [DOI: 10.1007/s10144-012-0332-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
26
|
Roderick GK, Croucher PJP, Vandergast AG, Gillespie RG. Species Differentiation on a Dynamic Landscape: Shifts in Metapopulation Genetic Structure Using the Chronology of the Hawaiian Archipelago. Evol Biol 2012; 39:192-206. [PMID: 22707805 PMCID: PMC3364410 DOI: 10.1007/s11692-012-9184-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 04/06/2012] [Indexed: 11/20/2022]
Abstract
Species formation during adaptive radiation often occurs in the context of a changing environment. The establishment and arrangement of populations, in space and time, sets up ecological and genetic processes that dictate the rate and pattern of differentiation. Here, we focus on how a dynamic habitat can affect genetic structure, and ultimately, differentiation among populations. We make use of the chronology and geographical history provided by the Hawaiian archipelago to examine the initial stages of population establishment and genetic divergence. We use data from a set of 6 spider lineages that differ in habitat affinities, some preferring low elevation habitats with a longer history of connection, others being more specialized for high elevation and/or wet forest, some with more general habitat affinities. We show that habitat preferences associated with lineages are important in ecological and genetic structuring. Lineages that have more restricted habitat preferences are subject to repeated episodes of isolation and fragmentation as a result of lava flows and vegetation succession. The initial dynamic set up by the landscape translates over time into discrete lineages. Further work is needed to understand how genetic changes interact with a changing set of ecological interactions amongst a shifting mosaic of landscapes to achieve species formation.
Collapse
Affiliation(s)
- George K. Roderick
- Department of Environmental Science, Policy, and Management, University of California, 130 Mulford Hall, Berkeley, CA 94720-3114 USA
| | - Peter J. P. Croucher
- Department of Environmental Science, Policy, and Management, University of California, 130 Mulford Hall, Berkeley, CA 94720-3114 USA
| | - Amy G. Vandergast
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, 4165 Spruance Road, Suite 200, San Diego, CA 92101 USA
| | - Rosemary G. Gillespie
- Department of Environmental Science, Policy, and Management, University of California, 130 Mulford Hall, Berkeley, CA 94720-3114 USA
| |
Collapse
|
27
|
Assessment of provenance delineation by genetic differentiation patterns and estimates of gene flow in the common grassland plant Geranium pratense. CONSERV GENET 2012. [DOI: 10.1007/s10592-011-0309-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
|