OptiMAS: A Decision Support Tool for Marker-Assisted Assembly of Diverse Alleles

Valente, Fabio; Gauthier, Franck; Bardol, Nicolas; Blanc, Guylaine; Joets, Johann; Charcosset, Alain; Moreau, Laurence

doi:10.1093/jhered/est020

Cited by 25 publications

(23 citation statements)

References 17 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Expected heterozygosity65 and allele number per locus and populations were calculated with the program Arlequin ver 3.548. Allelic richness per locus, population and overall populations, was obtained with the program Fstat v.2.9.375. A linkage disequilibrium test was done for each pair of loci in each population and across all populations by means of a G-test implemented in the program Genepop ‘00772.…”

Section: Methodsmentioning

confidence: 99%

Population genetics of the Manila clam (Ruditapes philippinarum) introduced in North America and Europe

Cordero

Delgado

Liu

et al. 2017

Sci Rep

View full text Add to dashboard Cite

Globally, the Manila clam (Ruditapes philippinarum) stands as the second most important bivalve species in fisheries and aquaculture. Native to the Pacific coast of Asia, it is now well-established in North America and Europe, where its on-going management reflects local economic interests. The historic record of transfers spans the 20th century and suggests sequential movement from Japan to North America, as a hitch-hiker on oysters, and then intentional introduction in Europe, but global genetic data are missing. We have studied mitochondrial DNA and microsatellite markers in nine populations from Asia, North America and Europe. The results from the two types of markers indicated a good concordance of present-day genetic structure with the reported history of clam transfers across continents, and no evidence of relevant concealed introductions from continental Asia in Europe and North America. However, European populations showed a loss of genetic variability and significant genetic differentiation as compared to their American counterparts. Our study shows that in spite of the increasing ease for species to spread out of their native range, in the case of the Manila clam this has not resulted in new invasion waves in the two studied continents.

show abstract

Section: Methodsmentioning

confidence: 99%

Population genetics of the Manila clam (Ruditapes philippinarum) introduced in North America and Europe

Cordero

Delgado

Liu

et al. 2017

Sci Rep

View full text Add to dashboard Cite

show abstract

“…The mean number of alleles per locus ( A ), allelic richness ( R s) [31] and gene diversity ( H e) [32] were estimated using the software Fstat 2.9.3.2 [33]. The presence of group-specific alleles (hereafter referred to as private alleles) was examined for each group.…”

Section: Methodsmentioning

confidence: 99%

Dissecting maize diversity in lowland South America: genetic structure and geographic distribution models

et al. 2016

View full text Add to dashboard Cite

BackgroundMaize landraces from South America have traditionally been assigned to two main categories: Andean and Tropical Lowland germplasm. However, the genetic structure and affiliations of the lowland gene pools have been difficult to assess due to limited sampling and the lack of comparative analysis. Here, we examined SSR and Adh2 sequence variation in a diverse sample of maize landraces from lowland middle South America, and performed a comprehensive integrative analysis of population structure and diversity including already published data of archaeological and extant specimens from the Americas. Geographic distribution models were used to explore the relationship between environmental factors and the observed genetic structure.ResultsBayesian and multivariate analyses of population structure showed the existence of two previously overlooked lowland gene pools associated with Guaraní indigenous communities of middle South America. The singularity of this germplasm was also evidenced by the frequency distribution of microsatellite repeat motifs of the Adh2 locus and the distinct spatial pattern inferred from geographic distribution models.ConclusionOur results challenge the prevailing view that lowland middle South America is just a contact zone between Andean and Tropical Lowland germplasm and highlight the occurrence of a unique, locally adapted gene pool. This information is relevant for the conservation and utilization of maize genetic resources, as well as for a better understanding of environment-genotype associations.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0874-5) contains supplementary material, which is available to authorized users.

show abstract

“…GENALEX v6.501 (Peakall and Smouse 2006) was used to calculate measures of genetic diversity, such as mean number of alleles per locus (Na), observed (Ho), expected (He) and unbiased expected (uHe) heterozygosities, as well as F-statistics (F IS -inbreeding coefficient, F IT -total fixation index and F ST -fixation index). Allelic richness (AR) was calculated in FSTAT v2.9.3.2 (Goudet 1995).…”

Section: Microsatellite Genotyping and Data Analysesmentioning

confidence: 99%

Differentiation of North African foxes and population genetic dynamics in the desert—insights into the evolutionary history of two sister taxa, Vulpes rueppellii and Vulpes vulpes

et al. 2015

View full text Add to dashboard Cite

The effects of Pleistocene glaciations on moulding biodiversity have been extensively investigated within temperate biomes, yet arid ecosystems are largely neglected. A clear example comes from North Africa and the successive range of expansion/contraction cycles of the Sahara desert. This study focuses on North African foxes (genus Vulpes), in particular two sister taxa, Vulpes rueppellii and Vulpes vulpes, but also Vulpes zerda and Vulpes pallida. A set of two mitochondrial markers (Cyt-b and D-loop) and 31-33 autosomal microsatellites were used to conduct phylogenetic and population analyses, as well as to investigate the possible occurrence of hybridisation events. Phylogenetic analysis revealed V. rueppellii to be more closely related to North African V. vulpes than the latter with Eurasian V. vulpes, along with the occurrence of two sub-clades of V. vulpes within the Maghreb. In contrast, microsatellite analysis identified V. rueppellii and V. vulpes as clearly separate entities, and no sign of population structure was observed for both species within North Africa. Both mitochondrial and nuclear markers separated North African and Eurasian V. vulpes in two distinct groups. We propose two explanatory scenarios, both influenced by past climatic shifts: (1) past introgression of V. vulpes mitochondrial genome into V. rueppellii and (2) V. rueppellii represents an arid ecotype of V. vulpes trapped in the Sahara during a humid/arid transition. The successive expansions/contractions of the Sahara were also likely responsible for the mitochondrial structure of North African V. vulpes. We unveil intriguing insights on the genetic structure of carnivore species in North Africa, suggesting that further integrative research is needed.

show abstract

OptiMAS: A Decision Support Tool for Marker-Assisted Assembly of Diverse Alleles

Cited by 25 publications

References 17 publications

Population genetics of the Manila clam (Ruditapes philippinarum) introduced in North America and Europe

Population genetics of the Manila clam (Ruditapes philippinarum) introduced in North America and Europe

Dissecting maize diversity in lowland South America: genetic structure and geographic distribution models

Differentiation of North African foxes and population genetic dynamics in the desert—insights into the evolutionary history of two sister taxa, Vulpes rueppellii and Vulpes vulpes

Contact Info

Product

Resources

About