Conservation genomics reveals low genetic diversity and multiple parentage in the threatened freshwater mussel, Margaritifera hembeli

2020 ◽  
Author(s):  
Nicole L. Garrison ◽  
Paul D. Johnson ◽  
Nathan V. Whelan
Keyword(s):  
Genetic Diversity ◽  
Multiple Paternity ◽  
Freshwater Mussel ◽  
Population Level ◽  
Conservation Genomics ◽  
The North ◽  
Low Genetic Diversity ◽  
Genetic Diversity And Structure ◽  
Genetic Patterns ◽  
Genomic Approach

AbstractMargaritifera hembeli is a federally threatened freshwater mussel species restricted to three central Louisiana drainages. Currently, management efforts are being formulated without an understanding of population-level genetic patterns, which could result in sub-optimal conservation outcomes. In particular, information about riverscape genetic patterns is needed to design effective propagation and reintroduction plans. We apply a genomic approach (RADseq) to assess genetic diversity and structure among four wild populations sampled from across the species range. We also assess the genetic diversity of a captively reared cohort produced from a single female. We recovered population differentiation between individuals sampled to the north and south of the Red River. All sites had similarly low levels of heterogeneity and other measures of genetic diversity. The captive cohort displayed higher levels of genetic diversity than expected and likely represents a case of multiple paternity. Future propagation efforts will likely be able to produce genetically diverse cohorts from a small number of wild-caught females, and we recommend future reintroduction efforts utilize brooders within the sub-drainage closest to the reintroduction effort.

scholarly journals How diverse can rare species be on the margins of genera distribution?

AoB Plants ◽  
2019 ◽  
Vol 11 (4) ◽  
Author(s):  
Alice Backes ◽  
Geraldo Mäder ◽  
Caroline Turchetto ◽  
Ana Lúcia Segatto ◽  
Jeferson N Fregonezi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Variability ◽  
Habitat Loss ◽  
Evolutionary History ◽  
Founder Effects ◽  
Geographical Isolation ◽  
Genetic Diversity And Structure ◽  
Genetic Patterns

Abstract Different genetic patterns have been demonstrated for narrowly distributed taxa, many of them linking rarity to evolutionary history. Quite a few species in young genera are endemics and have several populations that present low variability, sometimes attributed to geographical isolation or dispersion processes. Assessing the genetic diversity and structure of such species may be important for protecting them and understanding their diversification history. In this study, we used microsatellite markers and plastid sequences to characterize the levels of genetic variation and population structure of two endemic and restricted species that grow in isolated areas on the margin of the distribution of their respective genera. Plastid and nuclear diversities were very low and weakly structured in their populations. Evolutionary scenarios for both species are compatible with open-field expansions during the Pleistocene interglacial periods and genetic variability supports founder effects to explain diversification. At present, both species are suffering from habitat loss and changes in the environment can lead these species towards extinction.

scholarly journals Genetic studies of human diversity in East Asia

2007 ◽  
Vol 362 (1482) ◽  
pp. 987-996 ◽  
Author(s):  
Feng Zhang ◽  
Bing Su ◽  
Ya-ping Zhang ◽  
Li Jin
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
East Asia ◽  
Pacific Islands ◽  
East Asian ◽  
Human Populations ◽  
Genetic Studies ◽  
The North ◽  
Asian Populations ◽  
Genetic Diversity And Structure

East Asia is one of the most important regions for studying evolution and genetic diversity of human populations. Recognizing the relevance of characterizing the genetic diversity and structure of East Asian populations for understanding their genetic history and designing and interpreting genetic studies of human diseases, in recent years researchers in China have made substantial efforts to collect samples and generate data especially for markers on Y chromosomes and mtDNA. The hallmark of these efforts is the discovery and confirmation of consistent distinction between northern and southern East Asian populations at genetic markers across the genome. With the confirmation of an African origin for East Asian populations and the observation of a dominating impact of the gene flow entering East Asia from the south in early human settlement, interpretation of the north–south division in this context poses the challenge to the field. Other areas of interest that have been studied include the gene flow between East Asia and its neighbouring regions (i.e. Central Asia, the Sub-continent, America and the Pacific Islands), the origin of Sino-Tibetan populations and expansion of the Chinese.

scholarly journals Seascape Genomics of the Sugar Kelp Saccharina latissima along the North Eastern Atlantic Latitudinal Gradient

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1503
Author(s):  
Jaromir Guzinski ◽  
Paolo Ruggeri ◽  
Marion Ballenghien ◽  
Stephane Mauger ◽  
Bertrand Jacquemin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Climatic Changes ◽  
Statistical Correlation ◽  
Limiting Factors ◽  
Saccharina Latissima ◽  
Nucleotide Polymorphisms ◽  
Marker Allele ◽  
The North ◽  
Distribution Ranges ◽  
Genetic Diversity And Structure

Temperature is one of the most important range-limiting factors for many seaweeds. Driven by the recent climatic changes, rapid northward shifts of species’ distribution ranges can potentially modify the phylogeographic signature of Last Glacial Maximum. We explored this question in detail in the cold-tolerant kelp species Saccharina latissima, using microsatellites and double digest restriction site-associated DNA sequencing ( ddRAD-seq) derived single nucleotide polymorphisms (SNPs) to analyze the genetic diversity and structure in 11 sites spanning the entire European Atlantic latitudinal range of this species. In addition, we checked for statistical correlation between genetic marker allele frequencies and three environmental proxies (sea surface temperature, salinity, and water turbidity). Our findings revealed that genetic diversity was significantly higher for the northernmost locality (Spitsbergen) compared to the southern ones (Northern Iberia), which we discuss in light of the current state of knowledge on phylogeography of S. latissima and the potential influence of the recent climatic changes on the population structure of this species. Seven SNPs and 12 microsatellite alleles were found to be significantly associated with at least one of the three environmental variables. We speculate on the putative adaptive functions of the genes associated with the outlier markers and the importance of these markers for successful conservation and aquaculture strategies for S. latissima in this age of rapid global change.

Genetic consequences of long-term isolation for the last French population of Eryngium viviparum (Apiaceae)

2019 ◽  
Vol 191 (2) ◽  
pp. 285-298 ◽  
Author(s):  
Pauline Rascle ◽  
Elodie Flaven ◽  
Frédéric Bioret ◽  
Sylvie Magnanon ◽  
Erwan Glemarec ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Conservation Status ◽  
Disjunct Distribution ◽  
French Population ◽  
Endemic Plant ◽  
Evolutionary Potential ◽  
The North ◽  
Low Genetic Diversity ◽  
Geographical Regions ◽  
Seasonally Flooded

Abstract Eryngium viviparum (Apiaceae) is an endangered endemic plant of the Atlantic region of Europe, growing in seasonally flooded sites, and is characterized by a highly disjunct distribution. It occurs in just a few sites in the north-western part of the Iberian Peninsula and in a single locality in France. To improve the conservation status of E. viviparum in France, a conservation programme has been implemented to reintroduce the species. Before considering such an operation, genetic studies were conducted to determine the genetic status of the last French population and to identify the genetic source that should be considered for the best reintroduction strategy. Using microsatellite markers, we documented the genetic structure of the last French population and compared its genetic diversity with that of ten Iberian populations, which cover the three geographical regions where the species occurs. As expected, the French population of E. viviparum shows low genetic diversity due to a bottleneck and geographical isolation. The evolutionary potential appears low, with no private alleles in this population. Furthermore, this population is highly differentiated from the Iberian populations in terms of genetic variation and ecological niche. These results bring new questions regarding the conservation of E. viviparum in France, especially for management and reintroduction aimed at favouring genetic diversity and avoiding extinction.

scholarly journals Microsatellite analysis of genetic diversity and structure of Bruguiera gymnorrhiza and Kandelia obovate

2018 ◽  
Vol 52 ◽  
pp. 00027 ◽  
Author(s):  
Mohammad Basyuni ◽  
Shigeyuki Baba ◽  
Hirosuke Oku
Keyword(s):  
Genetic Diversity ◽  
Allelic Diversity ◽  
Geographic Range ◽  
Microsatellite Analysis ◽  
Bruguiera Gymnorrhiza ◽  
Low Genetic Diversity ◽  
Genetic Diversity And Structure ◽  
Low Levels ◽  
High Level ◽  
F Statistics

Microsatellite loci were used for estimating genetic diversity and structure for three populations of B. gymnorrhiza and K. obovata (Rhizophoracea) in Okinawa, Japan. Thirty propagules of individual samples representing the population of both species were genotyped at five microsatellites. The level of observed heterozygosity (HO) was observed for several population, overall loci, ranged 0.422-0.800 with an average 0.627 for B. gymnorrhiza and 0.477-0.822 with an average 0.665 for K. obovata, indicating both species had relatively low genetic diversity. Both species showed low levels of allelic diversity, 3-5 and 3-5 alleles per locus, respectively. Gene diversitywas also maintained within populations (HS: 0.741 and 0.954). Additionally, an analysis of molecular variance (AMOVA) based on the immeasurable alleles model (F-statistics), for B. gymnorrhiza and K. obovata found that most of the variation resided within individuals in the total populations, i.e. 79.78 % and 69.90 % respectively, and among individuals within populations, i.e.14.30 % and 27.95 % respectively. There was little variation between populations, i.e. 5.92 % and 2.15 % for B. gymnorrhiza and K. obovata, respectively. The high-level genetic differentiation within individuals and populations both species may be due to the geographic range of the species, mating system, and environmental factors.

Assessing genetic diversity of protected coho salmon (Oncorhynchus kisutch) populations in California

2007 ◽  
Vol 64 (1) ◽  
pp. 30-42 ◽  
Author(s):  
Katherine A Bucklin ◽  
Michael A Banks ◽  
Dennis Hedgecock
Keyword(s):  
Genetic Diversity ◽  
Coho Salmon ◽  
Random Mating ◽  
Oncorhynchus Kisutch ◽  
Legal Protection ◽  
Population Level ◽  
Population Subdivision ◽  
Minimal Impact ◽  
Low Genetic Diversity ◽  
Microsatellite Dna Markers

California coho salmon (Oncorhynchus kisutch) are under legal protection owing to significant declines in abundance over the last decades. Previously, California coho salmon were characterized as having low genetic diversity and weak population subdivision, attributable potentially to homogenization by out-of-basin hatchery releases. Here, diversity at seven highly polymorphic microsatellite DNA markers is assessed within and among 32 collections of coho salmon from 16 California watersheds. In 71% of local populations, genotypic composition deviates significantly from that expected under the assumption of random mating. We develop and apply methods to adjust for two potential causes of deviation from random mating expectations: (i) Wahlund effects, owing to heterogeneous collections of individuals, and (ii) the "Allendorf–Phelp's effect", owing to closely related juveniles in samples. Such population-level "adjustments" reduce within-region and increase among-region variance; after adjustment, we find strong concordance of genetic and geographic distances. We conclude that stock transfers have had minimal impact on population structure and that California coho salmon populations likely comprise small numbers of endemic breeders, potentially experiencing high levels of genetic drift and inbreeding.

scholarly journals Genetic diversity and structure in hill rice (Oryza sativa L.) landraces from the North-Eastern Himalayas of India

BMC Genetics ◽  
2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Somnath Roy ◽  
B. C. Marndi ◽  
B. Mawkhlieng ◽  
A. Banerjee ◽  
R. M. Yadav ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Oryza Sativa ◽  
Oryza Sativa L ◽  
Eastern Himalayas ◽  
The North ◽  
Genetic Diversity And Structure ◽  
North Eastern

scholarly journals A Disjunctive Marginal Edge of Evergreen Broad-Leaved Oak (Quercus gilva) in East Asia: The High Genetic Distinctiveness and Unusual Diversity of Jeju Island Populations and Insight into a Massive, Independent Postglacial Colonization

Genes ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1114
Author(s):  
Eun-Kyeong Han ◽  
Won-Bum Cho ◽  
Jong-Soo Park ◽  
In-Su Choi ◽  
Myounghai Kwak ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ecological Niche Modeling ◽  
East Asian ◽  
Glacial Refugia ◽  
Jeju Island ◽  
Evolutionary Potential ◽  
Postglacial Colonization ◽  
Low Genetic Diversity ◽  
Genetic Diversity And Structure ◽  
Edge Populations

Jeju Island is located at a marginal edge of the distributional range of East Asian evergreen broad-leaved forests. The low genetic diversity of such edge populations is predicted to have resulted from genetic drift and reduced gene flow when compared to core populations. To test this hypothesis, we examined the levels of genetic diversity of marginal-edge populations of Quercus gilva, restricted to a few habitats on Jeju Island, and compared them with the southern Kyushu populations. We also evaluated their evolutionary potential and conservation value. The genetic diversity and structure were analyzed using 40 polymorphic microsatellite markers developed in this study. Ecological Niche Modeling (ENM) has been employed to develop our insights, which can be inferred from historical distribution changes. Contrary to our expectations, we detected a similar level of genetic diversity in the Jeju populations, comparable to that of the southern Kyushu populations, which have been regarded as long-term glacial refugia with a high genetic variability of East Asian evergreen trees. We found no signatures of recent bottlenecks in the Jeju populations. The results of STRUCTURE, neighbor-joining phylogeny, and Principal Coordinate Analysis (PCoA) with a significant barrier clearly demonstrated that the Jeju and Kyushu regions are genetically distinct. However, ENM showed that the probability value for the distribution of the trees on Jeju Island during the Last Glacial Maximum (LGM) converge was zero. In consideration of these results, we hypothesize that independent massive postglacial colonization from a separate large genetic source, other than Kyushu, could have led to the current genetic diversity of Jeju Island. Therefore, we suggest that the Jeju populations deserve to be separately managed and designated as a level of management unit (MU). These findings improve our understanding of the paleovegetation of East Asian evergreen forests, and the microevolution of oaks.

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