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Ye H, Wu J, Wang Z, Hou H, Gao Y, Han W, Ru W, Sun G, Wang Y. Population genetic variation characterization of the boreal tree Acer ginnala in Northern China. Sci Rep 2020; 10:13515. [PMID: 32782277 PMCID: PMC7419535 DOI: 10.1038/s41598-020-70444-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: 02/25/2020] [Accepted: 07/24/2020] [Indexed: 11/09/2022] Open
Abstract
Genetic diversity and differentiation are revealed particularly through spatio-temporal environmental heterogeneity. Acer ginnala, as a deciduous shrub/small tree, is a foundation species in many terrestrial ecosystems of Northern China. Owing to its increased use as an economic resource, this species has been in the vulnerability. Therefore, the elucidations of the genetic differentiation and influence of environmental factors on A. ginnala are very critical for its management and future utilization strategies. In this study, high genetic diversity and differentiation occurred in A. ginnala, which might be resulted from its pollination mechanism and species characteristics. Compared with the species level, relatively low genetic diversity was detected at the population level that might be the cause for its vulnerability. There was no significant relationship between genetic and geographical distances, while a significant correlation existed between genetic and environmental distances. Among nineteen climate variables, Annual Mean Temperature (bio1), Mean Diurnal Range (bio2), Isothermality (bio3), Temperature Seasonality (bio4), Precipitation of Wettest Month (bio13), Precipitation Seasonality (bio15), and Precipitation of Warmest Quarter (bio18) could explain the substantial levels of genetic variation (> 40%) in this species. The A. ginnala populations were isolated into multi-subpopulations by the heterogeneous climate conditions, which subsequently promoted the genetic divergence. Climatic heterogeneity played an important role in the pattern of genetic differentiation and population distribution of A. ginnala across a relatively wide range in Northern China. These would provide some clues for the conservation and management of this vulnerable species.
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Affiliation(s)
- Hang Ye
- College of Life Science, Shanxi Normal University, Linfen, 041000, Shanxi, China
| | - Jiahui Wu
- College of Life Science, Shanxi Normal University, Linfen, 041000, Shanxi, China.,Changzhi University, Changzhi, 046011, Shanxi, China
| | - Zhi Wang
- College of Life Science, Shanxi Normal University, Linfen, 041000, Shanxi, China
| | - Huimin Hou
- College of Life Science, Shanxi Normal University, Linfen, 041000, Shanxi, China
| | - Yue Gao
- College of Life Science, Shanxi Normal University, Linfen, 041000, Shanxi, China
| | - Wei Han
- College of Life Science, Shanxi Normal University, Linfen, 041000, Shanxi, China
| | - Wenming Ru
- Changzhi University, Changzhi, 046011, Shanxi, China.
| | - Genlou Sun
- Department of Biology, Saint Mary's University, Halifax, NS, B3H3C3, Canada.
| | - Yiling Wang
- College of Life Science, Shanxi Normal University, Linfen, 041000, Shanxi, China.
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The genetic diversity and population structure of Sophora alopecuroides (Faboideae) as determined by microsatellite markers developed from transcriptome. PLoS One 2019; 14:e0226100. [PMID: 31805153 PMCID: PMC6894834 DOI: 10.1371/journal.pone.0226100] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 11/18/2019] [Indexed: 11/19/2022] Open
Abstract
Sophora alopecuroides (Faboideae) is an endemic species, mainly distributed in northwest China. However, the limited molecular markers range for this species hinders breeding and genetic studies. A total of 20,324 simple sequence repeat (SSR) markers were identified from 118,197 assembled transcripts and 18 highly polymorphic SSR markers were used to explore the genetic diversity and population structure of S. alopecuroides from 23 different geographical populations. A relatively low genetic diversity was found in S. alopecuroides based on mean values of the number of effective alleles (Ne = 1.81), expected heterozygosity (He = 0.39) and observed heterozygosity (Ho = 0.55). The results of AMOVA indicated higher levels of variation within populations than between populations. Bayesian-based cluster analysis, principal coordinates analysis and Neighbor-Joining phylogeny analysis roughly divided all genotypes into four major groups with some admixtures. Meanwhile, geographic barriers would have restricted gene flow between the northern and southern regions (separated by Tianshan Mountains), wherein the two relatively ancestral and independent clusters of S. alopecuroides occur. History trade and migration along the Silk Road would together have promoted the spread of S. alopecuroides from the western to the eastern regions of the northwest plateau in China, resulting in the current genetic diversity and population structure. The transcriptomic SSR markers provide a valuable resource for understanding the genetic diversity and population structure of S. alopecuroides, and will assist effective conservation management.
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From depth to regional spatial genetic differentiation of Eunicella cavolini in the NW Mediterranean. C R Biol 2018; 341:421-432. [PMID: 30318420 DOI: 10.1016/j.crvi.2018.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 09/12/2018] [Accepted: 09/15/2018] [Indexed: 11/23/2022]
Abstract
Connectivity studies in the marine realm are of great importance to understand the evolutionary potential of populations in a context of growing pressures on the marine environment. Here, we investigated the effect of the local, regional, and depth spatial scale on the population genetic structure of the yellow gorgonian Eunicella cavolini, one of the most common octocoral species of the Mediterranean hard-bottom communities. This species, along with other sessile metazoans typical of coralligenous ecosystems, plays an important role in supporting biodiversity, but is also impacted by direct and indirect consequences of human activities, such as physical destruction or mortality events due to thermal anomalies. Samples were taken from 15 sites located in the Ligurian Sea (NW Mediterranean) in two adjacent regions 100 kilometres apart, i.e. from the areas of Marseille (France) and Portofino (Genoa, Italy), and were analysed using six microsatellite loci. A pattern of isolation by distance was observed at the regional as well as the local scales. Although E. cavolini showed less genetic structure than other Mediterranean octocorallian species, we observed a significant genetic differentiation between populations a few kilometres apart. A low genetic differentiation was also observed between shallow and deep populations. The occurrence of genetically differentiated populations of E. cavolini at the scale of kilometres has important consequences for the management of this species and of the associated communities.
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De Novo Transcriptome Assembly and Population Genetic Analyses for an Endangered Chinese Endemic Acer miaotaiense (Aceraceae). Genes (Basel) 2018; 9:genes9080378. [PMID: 30060522 PMCID: PMC6115825 DOI: 10.3390/genes9080378] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 12/17/2022] Open
Abstract
Acer miaotaiense (P. C. Tsoong) is a rare and highly endangered plant in China. Because of the lack of genomic information and the limited number of available molecular markers, there are insufficient tools to determine the genetic diversity of this species. Here, 93,305 unigenes were obtained by multiple assembled contigs with a transcriptome sequencing program. Furthermore, 12,819 expressed sequence tag-derived simple sequence repeat (EST-SSR) markers were generated, 300 were randomly selected and synthesized, 19 primer pairs were identified as highly polymorphic (average number of alleles (Na) = 8, expected heterozygosity (He) = 0.635, polymorphism information content (PIC) = 0.604) and were further used for population genetic analysis. All 261 samples were grouped into two genetic clusters by UPGMA, a principal component analyses and a STRUCTURE analyses. A moderate level of genetic differentiation (genetic differentiation index (Fst) = 0.059–0.116, gene flow = 1.904–3.993) among the populations and the major genetic variance (81.01%) within populations were revealed by the AMOVA. Based on the results, scientific conservation strategies should be established using in situ and ex situ conservation strategies. The study provides useful genetic information for the protection of precious wild resources and for further research on the origin and evolution of this endangered plant and its related species.
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Cahill AE, De Jode A, Dubois S, Bouzaza Z, Aurelle D, Boissin E, Chabrol O, David R, Egea E, Ledoux JB, Mérigot B, Weber AAT, Chenuil A. A multispecies approach reveals hot spots and cold spots of diversity and connectivity in invertebrate species with contrasting dispersal modes. Mol Ecol 2017; 26:6563-6577. [PMID: 29087018 DOI: 10.1111/mec.14389] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 09/18/2017] [Indexed: 12/18/2022]
Abstract
Genetic diversity is crucial for species' maintenance and persistence, yet is often overlooked in conservation studies. Species diversity is more often reported due to practical constraints, but it is unknown if these measures of diversity are correlated. In marine invertebrates, adults are often sessile or sedentary and populations exchange genes via dispersal of gametes and larvae. Species with a larval period are expected to have more connected populations than those without larval dispersal. We assessed the relationship between measures of species and genetic diversity, and between dispersal ability and connectivity. We compiled data on genetic patterns and life history traits in nine species across five phyla. Sampling sites spanned 600 km in the northwest Mediterranean Sea and focused on a 50-km area near Marseilles, France. Comparative population genetic approaches yielded three main results. (i) Species without larvae showed higher levels of genetic structure than species with free-living larvae, but the role of larval type (lecithotrophic or planktotrophic) was negligible. (ii) A narrow area around Marseilles, subject to offshore advection, limited genetic connectivity in most species. (iii) We identified sites with significant positive contributions to overall genetic diversity across all species, corresponding with areas near low human population densities. In contrast, high levels of human activity corresponded with a negative contribution to overall genetic diversity. Genetic diversity within species was positively and significantly linearly related to local species diversity. Our study suggests that local contribution to overall genetic diversity should be taken into account for future conservation strategies.
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Affiliation(s)
- Abigail E Cahill
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France.,Biology Department, Albion College, Albion, MI, USA
| | - Aurélien De Jode
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France
| | - Sophie Dubois
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France
| | - Zoheir Bouzaza
- Département de Biologie, Faculté des Sciences de la Nature et de la Vie, Université Abdelhamid Ibn Badis, Mostaganem, Algérie
| | - Didier Aurelle
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France
| | - Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France
| | - Olivier Chabrol
- CNRS, Centrale Marseille, I2M, UMR7373, Aix-Marseille Université, Marseille, France
| | - Romain David
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France
| | - Emilie Egea
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France
| | - Jean-Baptiste Ledoux
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Porto, Portugal.,Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain
| | - Bastien Mérigot
- UMR MARBEC (CNRS, Ifremer, IRD, UM), Université de Montpellier, Sète, France
| | - Alexandra Anh-Thu Weber
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France.,Zoological Institute, University of Basel, Basel, Switzerland
| | - Anne Chenuil
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France
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El Ayari T, Trigui El Menif N, Saavedra C, Cordero D, Viard F, Bierne N. Unexpected mosaic distribution of two hybridizing sibling lineages in the teleplanically dispersing snail Stramonita haemastoma suggests unusual postglacial redistribution or cryptic invasion. Ecol Evol 2017; 7:9016-9026. [PMID: 29177037 PMCID: PMC5689492 DOI: 10.1002/ece3.3418] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 08/04/2017] [Accepted: 08/11/2017] [Indexed: 01/29/2023] Open
Abstract
Molecular approaches have proven efficient to identify cryptic lineages within single taxonomic entities. Sometimes these cryptic lineages maybe previously unreported or unknown invasive taxa. The genetic structure of the marine gastropod Stramonita haemastoma has been examined in the Western Mediterranean and North‐Eastern Atlantic populations with mtDNA COI sequences and three newly developed microsatellite markers. We identified two cryptic lineages, differentially fixed for alternative mtDNA COI haplogroups and significantly differentiated at microsatellite loci. The mosaic distribution of the two lineages is unusual for a warm‐temperate marine invertebrate with a teleplanic larval stage. The Atlantic lineage was unexpectedly observed as a patch enclosed in the north of the Western Mediterranean Sea between eastern Spain and the French Riviera, and the Mediterranean lineage was found in Macronesian Islands. Although cyto‐nuclear disequilibrium is globally maintained, asymmetric introgression occurs in the Spanish region where the two lineages co‐occur in a hybrid zone. A first interpretation of our results is mito‐nuclear discordance in a stable postglacial hybrid zone. Under this hypothesis, though, the location of genetic discontinuities would be unusual among planktonic dispersers. An alternative interpretation is that the Atlantic lineage, also found in Senegal and Venezuela, has been introduced by human activities in the Mediterranean area and is introgressing Mediterranean genes during its propagation, as theoretically expected. This second hypothesis would add an additional example to the growing list of cryptic marine invasions revealed by molecular studies.
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Affiliation(s)
- Tahani El Ayari
- Université de Montpellier Montpellier Cedex 5 France.,ISEM - CNRS UMR 5554 Station Marine OREME Sète France.,Laboratory of Environment Bio-monitoring Faculty of Sciences of Bizerta University of Carthage Bizerta Tunisia
| | - Najoua Trigui El Menif
- Laboratory of Environment Bio-monitoring Faculty of Sciences of Bizerta University of Carthage Bizerta Tunisia
| | - Carlos Saavedra
- Instituto de Acuicultura Torre de la Sal Consejo Superior de Investigaciones Cientίficas Ribera de Cabanes (Castellόn) Spain
| | - David Cordero
- Instituto de Acuicultura Torre de la Sal Consejo Superior de Investigaciones Cientίficas Ribera de Cabanes (Castellόn) Spain
| | - Frédérique Viard
- UPMC Université Paris 6CNRS UMR 7144 Adaptation et Diversité en Milieu Marin Equipe DIVCO Station Biologique de Roscoff Sorbonne Université Roscoff France
| | - Nicolas Bierne
- Université de Montpellier Montpellier Cedex 5 France.,ISEM - CNRS UMR 5554 Station Marine OREME Sète France
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Contrasting patterns of population structure and gene flow facilitate exploration of connectivity in two widely distributed temperate octocorals. Heredity (Edinb) 2017; 119:35-48. [PMID: 28295035 PMCID: PMC5520136 DOI: 10.1038/hdy.2017.14] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 02/03/2017] [Accepted: 02/17/2017] [Indexed: 12/13/2022] Open
Abstract
Connectivity is an important component of metapopulation dynamics in marine systems and can influence population persistence, migration rates and conservation decisions associated with Marine Protected Areas (MPAs). In this study, we compared the genetic diversity, gene flow and population structure of two octocoral species, Eunicella verrucosa and Alcyonium digitatum, in the northeast Atlantic (ranging from the northwest of Ireland and the southern North Sea, to southern Portugal), using two panels of 13 and 8 microsatellite loci, respectively. Our results identified regional genetic structure in E. verrucosa partitioned between populations from southern Portugal, northwest Ireland and Britain/France; subsequent hierarchical analysis of population structure also indicated reduced gene flow between southwest Britain and northwest France. However, over a similar geographical area, A. digitatum showed little evidence of population structure, suggesting high gene flow and/or a large effective population size; indeed, the only significant genetic differentiation detected in A. digitatum occurred between North Sea samples and those from the English Channel/northeast Atlantic. In both species the vast majority of gene flow originated from sample sites within regions, with populations in southwest Britain being the predominant source of contemporary exogenous genetic variants for the populations studied. Overall, historical patterns of gene flow appeared more complex, though again southwest Britain appeared to be an important source of genetic variation for both species. Our findings have major conservation implications, particularly for E. verrucosa, a protected species in UK waters and listed by the IUCN as ‘Vulnerable’, and for the designation and management of European MPAs.
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Masmoudi MB, Chaoui L, Topçu NE, Hammami P, Kara MH, Aurelle D. Contrasted levels of genetic diversity in a benthic Mediterranean octocoral: Consequences of different demographic histories? Ecol Evol 2016; 6:8665-8678. [PMID: 28035258 PMCID: PMC5192949 DOI: 10.1002/ece3.2490] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 08/17/2016] [Accepted: 08/18/2016] [Indexed: 01/17/2023] Open
Abstract
Understanding the factors explaining the observed patterns of genetic diversity is an important question in evolutionary biology. We provide the first data on the genetic structure of a Mediterranean octocoral, the yellow gorgonian Eunicella cavolini, along with insights into the demographic history of this species. We sampled populations in four areas of the Mediterranean Sea: continental France, Algeria, Turkey, and the Balearic and Corsica islands. Along French coasts, three sites were sampled at two depths (20 and 40 m). We demonstrated a high genetic structure in this species (overall FST = 0.13), and most pairwise differentiation tests were significant. We did not detect any difference between depths at the same site. Clustering analyses revealed four differentiated groups corresponding to the main geographical areas. The levels of allelic richness and heterozygosity were significantly different between regions, with highest diversity in Algeria and lowest levels in Turkey. The highest levels of private allelic richness were observed in Algeria followed by Turkey. Such contrasted patterns of genetic diversity were not observed in other Mediterranean octocorals and could be the result of different evolutionary histories. We also provide new empirical evidence of contrasting results between tests and model‐based studies of demographic history. Our results have important consequences for the management of this species.
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Affiliation(s)
- Moutassem Billah Masmoudi
- Aix Marseille Univ Univ Avignon CNRS IRD IMBE Marseille France; Laboratoire Bioressources Marines Université d'Annaba Badji Mokhtar Annaba Algérie
| | - Lamya Chaoui
- Laboratoire Bioressources Marines Université d'Annaba Badji Mokhtar Annaba Algérie
| | - Nur Eda Topçu
- İstanbul Üniversitesi Su Ürünleri Fakültesi İstanbul Turkey
| | - Pachka Hammami
- Aix Marseille UnivUniv Avignon CNRS IRD IMBE Marseille France; CIRAD UMR CMAEE Montpellier France
| | - Mohamed Hichem Kara
- Laboratoire Bioressources Marines Université d'Annaba Badji Mokhtar Annaba Algérie
| | - Didier Aurelle
- Aix Marseille Univ Univ Avignon CNRS IRD IMBE Marseille France
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