scholarly journals Temporal sampling helps unravel the genetic structure of naturally occurring populations of a phytoparasitic nematode. 1. Insights from the estimation of effective population sizes

2016 ◽  
Vol 9 (3) ◽  
pp. 489-501 ◽  
Author(s):  
Pierre‐Loup Jan ◽  
Cécile Gracianne ◽  
Sylvain Fournet ◽  
Eric Olivier ◽  
Jean‐François Arnaud ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Effective Population ◽  
Temporal Sampling ◽  
Naturally Occurring ◽  
Population Sizes ◽  
Phytoparasitic Nematode

scholarly journals Temporal sampling helps unravel the genetic structure of naturally occurring populations of a phytoparasitic nematode. 2. Separating the relative effects of gene flow and genetic drift

2016 ◽  
Vol 9 (8) ◽  
pp. 1005-1016 ◽  
Author(s):  
Cécile Gracianne ◽  
Pierre-Loup Jan ◽  
Sylvain Fournet ◽  
Eric Olivier ◽  
Jean-François Arnaud ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Drift ◽  
Temporal Sampling ◽  
Naturally Occurring ◽  
Phytoparasitic Nematode

scholarly journals The Genetic History of France

2019 ◽  
Author(s):  
Aude Saint Pierre ◽  
Joanna Giemza ◽  
Matilde Karakachoff ◽  
Isabel Alves ◽  
Philippe Amouyel ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Demographic History ◽  
Migration Routes ◽  
Effective Population ◽  
Genetic Studies ◽  
Independent Population ◽  
Genome Wide Data ◽  
Population Sizes ◽  
History Of ◽  
Exhaustive Study

ABSTRACTThe study of the genetic structure of different countries within Europe has provided significant insights into their demographic history and their actual stratification. Although France occupies a particular location at the end of the European peninsula and at the crossroads of migration routes, few population genetic studies have been conducted so far with genome-wide data. In this study, we analyzed SNP-chip genetic data from 2 184 individuals born in France who were enrolled in two independent population cohorts. Using FineStructure, six different genetic clusters of individuals were found that were very consistent between the two cohorts. These clusters match extremely well the geography and overlap with historical and linguistic divisions of France. By modeling the relationship between genetics and geography using EEMS software, we were able to detect gene flow barriers that are similar in the two cohorts and corresponds to major French rivers or mountains. Estimations of effective population sizes using IBDNe program also revealed very similar patterns in both cohorts with a rapid increase of effective population sizes over the last 150 generations similar to what was observed in other European countries. A marked bottleneck is also consistently seen in the two datasets starting in the fourteenth century when the Black Death raged in Europe. In conclusion, by performing the first exhaustive study of the genetic structure of France, we fill a gap in the genetic studies in Europe that would be useful to medical geneticists but also historians and archeologists.

scholarly journals Genetic diversity in migratory bats: Results from RADseq data for three tree bat species at an Ohio windfarm

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1647 ◽  
Author(s):  
Michael G. Sovic ◽  
Bryan C. Carstens ◽  
H. Lisle Gibbs
Keyword(s):  
Genetic Structure ◽  
Wind Farm ◽  
Nuclear Dna ◽  
Effective Population ◽  
Genetic Analyses ◽  
Lasiurus Cinereus ◽  
Time Migration ◽  
Show Evidence ◽  
Population Sizes ◽  
Wind Facility

Genetic analyses can identify the scale at which wildlife species are impacted by human activities, and provide demographic information useful for management. Here, we use thousands of nuclear DNA genetic loci to assess whether genetic structure occurs withinLasiurus cinereus(Hoary Bat),L. borealis(Red Bat), andLasionycteris noctivagans(Silver-Haired Bat) bats found at a wind turbine site in Ohio, and to also estimate demographic parameters in each of these three groups. Our specific goals are to: 1) demonstrate the feasibility of isolating RADseq loci from these tree bat species, 2) test for genetic structure within each species, including any structure that may be associated with time (migration period), and 3) use coalescent-based modeling approaches to estimate genetically-effective population sizes and patterns of population size changes over evolutionary timescales. Thousands of loci were successfully genotyped for each species, demonstrating the value of RADseq for generating polymorphic loci for population genetic analyses in these bats. There was no evidence for genetic differentiation between groups of samples collected at different times throughout spring and fall migration, suggesting that individuals from each species found at the wind facility are from single panmictic populations. Estimates of present-day effective population sizes varied across species, but were consistently large, on the order of 105–106. All populations show evidence of expansions that date to the Pleistocene. These results, along with recent work also suggesting limited genetic structure in bats across North America, argue that additional biomarker systems such as stable-isotopes or trace elements should be investigated as alternative and/or complementary approaches to genetics for sourcing individuals collected at single wind farm sites.

scholarly journals Range-wide neutral and adaptive genetic structure of an endemic herb from Amazonian Savannas

AoB Plants ◽  
2020 ◽  
Vol 12 (1) ◽  
Author(s):  
Amanda R Silva ◽  
Luciana C Resende-Moreira ◽  
Carolina S Carvalho ◽  
Eder C M Lanes ◽  
Mabel P Ortiz-Vera ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Extinction Risk ◽  
Clustering Methods ◽  
Effective Population ◽  
Evolutionary Potential ◽  
Management Actions ◽  
Temperature And Precipitation ◽  
Population Sizes ◽  
Genetic Clustering

Abstract Conserving genetic diversity in rare and narrowly distributed endemic species is essential to maintain their evolutionary potential and minimize extinction risk under future environmental change. In this study we assess neutral and adaptive genetic structure and genetic diversity in Brasilianthus carajensis (Melastomataceae), an endemic herb from Amazonian Savannas. Using RAD sequencing we identified a total of 9365 SNPs in 150 individuals collected across the species’ entire distribution range. Relying on assumption-free genetic clustering methods and environmental association tests we then compared neutral with adaptive genetic structure. We found three neutral and six adaptive genetic clusters, which could be considered management units (MU) and adaptive units (AU), respectively. Pairwise genetic differentiation (FST) ranged between 0.024 and 0.048, and even though effective population sizes were below 100, no significant inbreeding was found in any inferred cluster. Nearly 10 % of all analysed sequences contained loci associated with temperature and precipitation, from which only 25 sequences contained annotated proteins, with some of them being very relevant for physiological processes in plants. Our findings provide a detailed insight into genetic diversity, neutral and adaptive genetic structure in a rare endemic herb, which can help guide conservation and management actions to avoid the loss of unique genetic variation.

scholarly journals Hierarchical genetic structure and effective population sizes in Phalacrus substriatus

Heredity ◽  
1997 ◽  
Vol 79 (2) ◽  
pp. 153-161 ◽  
Author(s):  
Pär K Ingvarsson ◽  
Katarina Olsson
Keyword(s):  
Genetic Structure ◽  
Effective Population ◽  
Population Sizes

scholarly journals Genetic characterization of ninety elite soybean cultivars using coefficient of parentage

2007 ◽  
Vol 42 (3) ◽  
pp. 363-369 ◽  
Author(s):  
Zilda de Fátima Sgobero Miranda ◽  
Carlos Alberto Arrabal Arias ◽  
Cássio Egidio Cavenaghi Prete ◽  
Romeu Afonso de Souza Kiihl ◽  
Leones Alves de Almeida ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Genetic Characterization ◽  
High Similarity ◽  
Effective Population ◽  
Coefficient Of Parentage ◽  
Soybean Cultivars ◽  
Cultivar Groups ◽  
Weighted Means ◽  
Population Sizes

The objective of this work was to estimate the coefficient of parentage and to understand the genetic structure of 90 elite soybean cultivars, which are adapted to different Brazilian environments. A total of 4,005 coefficients of parentage (f) were obtained and used to group the cultivars by UPGMA method. The constructed dendrogram showed several related cultivar groups which shared similar ancestors and clearly showed the genetic structure of the main Brazilian cultivars. Effective population sizes (Ne) were also estimated for cultivars in different generations. The average f = 0.2124 value, obtained from cultivars classified into four decades according to the release year, suggested effective soybean population sizes of 11 and 13 calculated using arithmetic and weighted means, respectively. The relatively small Ne and the high parentage coefficient support the conclusion that there is a high similarity degree among the main soybean cultivars in Brazil.

scholarly journals Genetic Structure and Effective Population Sizes in European Red Deer (Cervus elaphus) at a Continental Scale: Insights from Microsatellite DNA

2016 ◽  
Vol 107 (4) ◽  
pp. 318-326 ◽  
Author(s):  
Frank E. Zachos ◽  
Alain C. Frantz ◽  
Ralph Kuehn ◽  
Sabine Bertouille ◽  
Marc Colyn ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Cervus Elaphus ◽  
Microsatellite Dna ◽  
Red Deer ◽  
Effective Population ◽  
Continental Scale ◽  
Population Sizes
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