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Chung MY, Merilä J, Li J, Mao K, López-Pujol J, Tsumura Y, Chung MG. Neutral and adaptive genetic diversity in plants: An overview. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1116814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Genetic diversity is a prerequisite for evolutionary change in all kinds of organisms. It is generally acknowledged that populations lacking genetic variation are unable to evolve in response to new environmental conditions (e.g., climate change) and thus may face an increased risk of extinction. Although the importance of incorporating genetic diversity into the design of conservation measures is now well understood, less attention has been paid to the distinction between neutral (NGV) and adaptive (AGV) genetic variation. In this review, we first focus on the utility of NGV by examining the ways to quantify it, reviewing applications of NGV to infer ecological and evolutionary processes, and by exploring its utility in designing conservation measures for plant populations and species. Against this background, we then summarize the ways to identify and estimate AGV and discuss its potential use in plant conservation. After comparing NGV and AGV and considering their pros and cons in a conservation context, we conclude that there is an urgent need for a better understanding of AGV and its role in climate change adaptation. To date, however, there are only a few AGV studies on non-model plant species aimed at deciphering the genetic and genomic basis of complex trait variation. Therefore, conservation researchers and practitioners should keep utilizing NGV to develop relevant strategies for rare and endangered plant species until more estimates of AGV are available.
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Zhao W, Wang X, Li L, Li J, Yin H, Zhao Y, Chen X. Evaluation of environmental factors affecting the genetic diversity, genetic structure, and the potential distribution of Rhododendron aureum Georgi under changing climate. Ecol Evol 2021; 11:12294-12306. [PMID: 34594500 PMCID: PMC8462154 DOI: 10.1002/ece3.7803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 04/19/2021] [Accepted: 05/27/2021] [Indexed: 11/29/2022] Open
Abstract
Understanding genetic variation and structure, adaptive genetic variation, and its relationship with environmental factors is of great significance to understand how plants adapt to climate change and design effective conservation and management strategies. The objective of this study was to (I) investigate the genetic diversity and structure by AFLP markers in 36 populations of R. aureum from northeast China, (Ⅱ) reveal the relative contribution of geographical and environmental impacts on the distribution and genetic differentiation of R. aureum, (Ⅲ) identify outlier loci under selection and evaluate the association between outlier loci and environmental factors, and (Ⅳ) exactly calculate the development trend of population of R. aureum, as it is confronted with severe climate change and to provide information for designing effective conservation and management strategies. We found high genetic variation (I = 0.584) and differentiation among populations (ΦST = 0.703) and moderate levels of genetic diversity within populations of R. aureum. A significant relationship between genetic distance and environmental distance was identified, which suggested that the differentiation of different populations was caused by environmental factors. Using BayeScan and Dfdist, 42 outlier loci are identified and most of the outlier loci are associated with climate or relief factors, suggesting that these loci are linked to genes that are involved in the adaptability of R. aureum to the environment. Species distribution models (SDMs) showed that climate warming will cause a significant reduction in suitable areas for R. aureum, especially under the RCP 85 scenario. Our results help to understand the potential response of R. aureum to climatic changes and provide new perspectives for R. aureum resource management and conservation strategies.
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Affiliation(s)
- Wei Zhao
- National & Local United Engineering Laboratory for Chinese Herbal Medicine Breeding and CultivationJilin UniversityChangchunChina
- School of Life ScienceJilin UniversityChangchunChina
| | - Xiaolong Wang
- Medical Technology DepartmentQiqihar Medical UniversityQiqiharChina
| | - Lin Li
- Medical Technology DepartmentQiqihar Medical UniversityQiqiharChina
| | - Jiangnan Li
- National & Local United Engineering Laboratory for Chinese Herbal Medicine Breeding and CultivationJilin UniversityChangchunChina
- School of Life ScienceJilin UniversityChangchunChina
| | - Hang Yin
- Jilin Provincial Joint Key Laboratory of Changbai Mountain Biocoenosis and BiodiversityAntuChina
- Academy of Sciences of Changbai MountainChangbaishanChina
| | - Ying Zhao
- Jilin Provincial Joint Key Laboratory of Changbai Mountain Biocoenosis and BiodiversityAntuChina
- Academy of Sciences of Changbai MountainChangbaishanChina
| | - Xia Chen
- National & Local United Engineering Laboratory for Chinese Herbal Medicine Breeding and CultivationJilin UniversityChangchunChina
- School of Life ScienceJilin UniversityChangchunChina
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Shiflett SA, Zinnert JC, Young DR. Functional traits of expanding, thicket‐forming shrubs: contrasting strategies between exotic and native species. Ecosphere 2017. [DOI: 10.1002/ecs2.1918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Sheri A. Shiflett
- Department of Biology Virginia Commonwealth University Richmond Virginia 23284 USA
| | - Julie C. Zinnert
- Department of Biology Virginia Commonwealth University Richmond Virginia 23284 USA
| | - Donald R. Young
- Department of Biology Virginia Commonwealth University Richmond Virginia 23284 USA
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Zinnert JC, Stallins JA, Brantley ST, Young DR. Crossing Scales: The Complexity of Barrier-Island Processes for Predicting Future Change. Bioscience 2016. [DOI: 10.1093/biosci/biw154] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Sujii PS, Martins K, Wadt LHDO, Azevedo VCR, Solferini VN. Genetic structure of Bertholletia excelsa populations from the Amazon at different spatial scales. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0714-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Trapnell DW, Hamrick JL, Ishibashi CD, Kartzinel TR. Genetic inference of epiphytic orchid colonization; it may only take one. Mol Ecol 2013; 22:3680-92. [DOI: 10.1111/mec.12338] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 03/20/2013] [Accepted: 03/26/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Dorset W. Trapnell
- Department of Plant Biology; University of Georgia; Athens Georgia 30602 USA
| | - J. L. Hamrick
- Department of Plant Biology; University of Georgia; Athens Georgia 30602 USA
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Helsen K, Jacquemyn H, Hermy M, Vandepitte K, Honnay O. Rapid Buildup of Genetic Diversity in Founder Populations of the Gynodioecious Plant Species Origanum vulgare after Semi-Natural Grassland Restoration. PLoS One 2013; 8:e67255. [PMID: 23840642 PMCID: PMC3686717 DOI: 10.1371/journal.pone.0067255] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 05/15/2013] [Indexed: 11/18/2022] Open
Abstract
In most landscapes the success of habitat restoration is largely dependent on spontaneous colonization of plant species. This colonization process, and the outcome of restoration practices, can only be considered successful if the genetic makeup of founding populations is not eroded through founder effects and subsequent genetic drift. Here we used 10 microsatellite markers to investigate the genetic effects of recent colonization of the long-lived gynodioecious species Origanum vulgare in restored semi-natural grassland patches. We compared the genetic diversity and differentiation of fourteen recent populations with that of thirteen old, putative source populations, and we evaluated the effects of spatial configuration of the populations on colonization patterns. We did not observe decreased genetic diversity in recent populations, or inflated genetic differentiation among them. Nevertheless, a significantly higher inbreeding coefficient was observed in recent populations, although this was not associated with negative fitness effects. Overall population genetic differentiation was low (FST = 0.040). Individuals of restored populations were assigned to on average 6.1 different source populations (likely following the 'migrant pool' model). Gene flow was, however, affected by the spatial configuration of the grasslands, with gene flow into the recent populations mainly originating from nearby source populations. This study demonstrates how spontaneous colonization after habitat restoration can lead to viable populations in a relatively short time, overcoming pronounced founder effects, when several source populations are nearby. Restored populations can therefore rapidly act as stepping stones and sources of genetic diversity, likely increasing overall metapopulation viability of the study species.
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Affiliation(s)
- Kenny Helsen
- Plant Conservation and Population Biology, Department of Biology, University of Leuven, Leuven, Belgium
- * E-mail:
| | - Hans Jacquemyn
- Plant Conservation and Population Biology, Department of Biology, University of Leuven, Leuven, Belgium
| | - Martin Hermy
- Division Forest, Nature and Landscape Research, Department of Earth and Environmental Sciences, University of Leuven, Leuven, Belgium
| | - Katrien Vandepitte
- Plant Conservation and Population Biology, Department of Biology, University of Leuven, Leuven, Belgium
| | - Olivier Honnay
- Plant Conservation and Population Biology, Department of Biology, University of Leuven, Leuven, Belgium
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VANDEPITTE K, GRISTINA AS, DE HERT K, MEEKERS T, ROLDÁN-RUIZ I, HONNAY O. Recolonization after habitat restoration leads to decreased genetic variation in populations of a terrestrial orchid. Mol Ecol 2012; 21:4206-15. [DOI: 10.1111/j.1365-294x.2012.05698.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Hamrick J, Trapnell DW. Using population genetic analyses to understand seed dispersal patterns. ACTA OECOLOGICA-INTERNATIONAL JOURNAL OF ECOLOGY 2011. [DOI: 10.1016/j.actao.2011.05.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Sujii P, Martins K, Wadt L, Azevedo V, Solferini V. Genetic diversity of Bertholletia excelsa, an Amazonian species of wide distribution. BMC Proc 2011. [PMCID: PMC3240071 DOI: 10.1186/1753-6561-5-s7-p5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Ramakrishnan AP, Musial T, Cruzan MB. Shifting dispersal modes at an expanding species' range margin. Mol Ecol 2010; 19:1134-46. [PMID: 20456225 DOI: 10.1111/j.1365-294x.2010.04543.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
While it is generally recognized that noncontiguous (long-distance) dispersal of small numbers of individuals is important for range expansion over large geographic areas, it is often assumed that colonization on more local scales proceeds by population expansion and diffusion dispersal (larger numbers of individuals colonizing adjacent sites). There are few empirical studies of dispersal modes at the front of expanding ranges, and very little information is available on dispersal dynamics at smaller geographic scales where we expect contiguous (diffusion) dispersal to be prevalent. We used highly polymorphic genetic markers to characterize dispersal modes at a local geographic scale for populations at the edge of the range of a newly invasive grass species (Brachypodium sylvaticum) that is undergoing rapid range expansion in the Pacific Northwest of North America. Comparisons of Bayesian clustering of populations, patterns of genetic diversity, and gametic disequilibrium indicate that new populations are colonized ahead of the invasion front by noncontiguous dispersal from source populations, with admixture occurring as populations age. This pattern of noncontiguous colonization was maintained even at a local scale. Absence of evidence for dispersal among adjacent pioneer sites at the edge of the expanding range of this species suggests that pioneer populations undergo an establishment phase during which they do not contribute emigrants for colonization of neighbouring sites. Our data indicate that dispersal modes change as the invasion matures: initial colonization processes appear to be dominated by noncontiguous dispersal from only a few sources, while contiguous dispersal may play a greater role once populations become established.
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Affiliation(s)
- Alisa P Ramakrishnan
- Department of Biology, Portland State University, PO Box 751, Portland, OR 97207-0751, USA.
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Chun YJ, Fumanal B, Laitung B, Bretagnolle F. Gene flow and population admixture as the primary post-invasion processes in common ragweed (Ambrosia artemisiifolia) populations in France. THE NEW PHYTOLOGIST 2010; 185:1100-7. [PMID: 20028474 DOI: 10.1111/j.1469-8137.2009.03129.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
*An improved inference of the evolutionary history of invasive species may be achieved by analyzing the genetic variation and population differentiation of recently established populations and their ancestral (historical) populations. Employing this approach, we investigated the role of gene flow in the post-invasion evolution of common ragweed (Ambrosia artemisiifolia). *Using eight microsatellite loci, we compared genetic diversity and structure among nine pairs of historical and recent populations in France. Historical populations were reconstructed from herbarium specimens dated from the late 19th to early 20th century, whereas recent populations were collected within the last 5 yr. *Recent populations showed greater allelic and genetic diversity than did historical populations. Recent populations exhibited a lower level of population differentiation, shorter genetic distances among populations and more weakly structured populations than did historical populations. *Our results suggest that currently invasive populations have arisen from active gene flow and the subsequent admixture of historical populations, incorporating new alleles from multiple introductions.
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Affiliation(s)
- Young Jin Chun
- INRA, UMR 1210 Biologie et Gestion des Adventices, Dijon, France.
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González-Pérez MA, Sosa PA, Rivero E, González-González EA, Naranjo A. Molecular markers reveal no genetic differentiation between Myrica rivas-martinezii and M. faya (Myricaceae). ANNALS OF BOTANY 2009; 103:79-86. [PMID: 19008254 PMCID: PMC2707291 DOI: 10.1093/aob/mcn222] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Revised: 09/11/2008] [Accepted: 10/14/2008] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Myrica rivas-martinezii is a critically endangered endemic of the laurel forest of the Canary Islands and co-occurs very close to M. faya. Some authors suggest that M. rivas-martinezii and M. faya are two morphs of the same species, so molecular markers were used to estimate the levels and structuring of genetic variation within and among natural populations in order to evaluate genetic relationships between these two congeners. METHODS Six polymorphic microsatellite (simple sequence repeat, SSR) markers were used to determine the genetic diversity and the genetic relationship between both Myrica species. KEY RESULTS Most of the natural populations analysed were in Hardy-Weinberg equilibrium for both taxa. Analysis of molecular variance (AMOVA) for both species revealed that most of the genetic variability detected was contained within populations (92.48 and 85.91 % for M. faya and M. rivas-martinezii, respectively), which it is consistent with outcrossing and dioecious plants. Estimates of interpopulation genetic variation, calculated from F(ST) and G'(ST), were quite low in the two taxa, and these values did not increase substantially when M. rivas-martinezii and M. faya populations were compared. The UPGMA dendrogram based on Nei's genetic distance clustered the populations by their island origin, independently of taxon. In fact, the mixture of individuals of both taxa did not appreciably disrupt the intrapopulational genetic cohesion, and only 3.76 % variation existed between species. CONCLUSIONS All the results obtained using molecular markers indicate clearly that both taxa share the same genetic pool, and they are probably the same taxa. Considering that M. rivas-martinezii is classified as at risk of extinction, there should be a change of focus of the current management actions for the conservation of this putatively endangered Canarian endemic.
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Affiliation(s)
- Miguel A González-Pérez
- Departamento de Biología, Universidad de Las Palmas de Gran Canaria, Campus Universitario de Tafira, Las Palmas de Gran Canaria, Canary Islands, Spain.
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Born C, Kjellberg F, Chevallier MH, Vignes H, Dikangadissi JT, Sanguié J, Wickings EJ, Hossaert-McKey M. Colonization processes and the maintenance of genetic diversity: insights from a pioneer rainforest tree, Aucoumea klaineana. Proc Biol Sci 2008; 275:2171-9. [PMID: 18559325 DOI: 10.1098/rspb.2008.0446] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Despite recurrent episodes of range expansion and contraction, forest trees often harbour high genetic diversity. Studies of temperate forest trees suggest that prolonged juvenile phase and high pollen flow are the main factors limiting founder effects. Here, we studied the local colonization process of a pioneer rainforest tree in central Africa, Aucoumea klaineana. We identified 87% of parents among trees up to 20-25 years old and could thus compare direct parentage structure data with classical population genetics estimators. In this species, genetic diversity was maintained during colonization. The absence of founder effects was explained by (i) local random mating and (ii) local recruitment, as we showed that 75% of the trees in the close neighbourhood participated in the recruitment of new saplings. Long-distance pollen flow contributed little to genetic diversity: pollen and seed dispersal was mainly within stand (128 and 118 m, respectively). Spatial genetic structure was explained by aggregated seed dispersal rather than by mother-offspring proximity as assumed in classical isolation-by-distance models. Hence, A. klaineana presents a genetic diversity pattern typical of forest trees but does not follow the classical rules by which this diversity is generally achieved. We suggest that while high local genetic variability is of general importance to forest tree survival, the proximate mechanisms by which it is achieved may follow very different scenarios.
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PARDINI EA, HAMRICK JL. Inferring recruitment history from spatial genetic structure within populations of the colonizing tree Albizia julibrissin (Fabaceae). Mol Ecol 2008; 17:2865-79. [DOI: 10.1111/j.1365-294x.2008.03807.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Yang S, Bishop JG, Webster MS. Colonization genetics of an animal-dispersed plant (Vaccinium membranaceum) at Mount St Helens, Washington. Mol Ecol 2008; 17:731-40. [PMID: 18194163 DOI: 10.1111/j.1365-294x.2007.03625.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- S Yang
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA 99164-4236, USA.
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OKADA MIKI, AHMAD RIAZ, JASIENIUK MARIE. Microsatellite variation points to local landscape plantings as sources of invasive pampas grass (Cortaderia selloana) in California. Mol Ecol 2007; 16:4956-71. [DOI: 10.1111/j.1365-294x.2007.03568.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Raffl C, Schönswetter P, Erschbamer B. ‘Sax-sess’- genetics of primary succession in a pioneer species on two parallel glacier forelands. Mol Ecol 2006; 15:2433-40. [PMID: 16842417 DOI: 10.1111/j.1365-294x.2006.02964.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The primary succession on glacier forelands is characterized by a sequence of early and late successional species, but whether there is also a chronosequence at the intraspecific, genetic level is a matter of debate. Two opposing hypotheses differ in their prediction of genetic diversity in colonizing populations due to founder effects and postcolonization gene immigration. The development of genetic diversity in the pioneer Saxifraga aizoides was investigated along a successional gradient on two parallel glacier forelands, in order to test whether populations from older successional stages were less genetically diverse than populations from younger successional stages, and to locate the sources of the propagules that originally colonized new glacier foreland. Genetic diversity was determined with amplified fragment length polymorphisms, and potential sources of colonizing propagules were assessed via assignment tests. Our results indicate considerable postcolonization gene flow among populations on glacier forelands, since population differentiation was low and genetic diversity within populations was significantly higher. Molecular diversity and differentiation of populations did not develop linearly. Dispersal events within the glacier foreland, from the adjacent valley slopes, and from parallel glacier valleys were identified. In summary, it seems that the colonization of glacier forelands in the European Alps is highly dynamic and stochastic.
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Affiliation(s)
- C Raffl
- Institute of Botany, University of Innsbruck, Sternwartestrasse 15, 6020 Innsbruck, Austria.
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