DYNADIV Team

The main focus of DYNADIV Team is
tounderstand how biodiversity of tropical plants is shaped through evolutionary forces resulting from human and environmental impacts.

Its activity is essentially based on population genetics but also integrates a multidisciplinary approach including ecology, botany, molecular phylogenetics and anthropology. It is structured around three axes:

Evolutionary history & domestication;
Diversity & conservation;
Global changes, diversity & adaptation.

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81 to 90 of 114 Results

S4_Introduction_GenomeWideAssociationStudy_GWAS.pdf May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) Adobe PDF - 912.5 KB - MD5: da9c01bfb9ae62fefc2a5b288cc9889d Documentation Introduction to the core concept of genome wide association studies.
S4_script_GWAS_basic_Rcode.pdf May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) Adobe PDF - 73.2 KB - MD5: 17bd3bb83031e7349c5d4730581569e8 Documentation This file comments on the R script for GWAS analysis.
S4_Script_GWAS_Introduction.pdf May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) Adobe PDF - 574.9 KB - MD5: b3bd4b806a6968e50f665cd4e34e832b Documentation This file presents a script for GWAS analysis using R. We used a dataset of pearl millet accessions (Varshney et al. 2017).
sample_metadata.tab May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) Tabular Data - 2.5 KB - 5 Variables, 55 Observations - UNF:6:LNg1C4IBq05VUN9bbZDOeQ== Data Table containing the passport data of the pearl millet accessions. This data file is associated with the script "S1_Introduction_to_R_Passport.html". These data are published in Berthouly-Salazar et al. (2016).
Called genotypes (chromosome 1) from Illumina whole-genome sequencing of an Indica x Japonica rice F2 population Apr 29, 2024 Lorieux, Mathias; Triay, Cécile, 2024, "Called genotypes (chromosome 1) from Illumina whole-genome sequencing of an Indica x Japonica rice F2 population", https://doi.org/10.23708/8FXUNC, DataSuds, V1 Motivation: Genotyping of bi-parental populations can be performed with low-coverage next-generation sequencing (LC-NGS). This allows the creation of highly saturated genetic maps at reasonable cost, precisely localized recombination breakpoints (i.e., the crossovers), and minimi...
DiscriminantSitesOnly_biallelic_freebayes_bcftools_snps_on_AZUwithOrganelles_chr01.vcf.gz Apr 29, 2024 - Called genotypes (chromosome 1) from Illumina whole-genome sequencing of an Indica x Japonica rice F2 population Gzip Archive - 206.7 MB - MD5: 161bb7f90f38757bd830bc5e005cd453 Data Called genotypes (chromosome 1) from Illumina whole-genome sequencing of an Indica x Japonica rice F2 population
ReadMe.txt Apr 29, 2024 - Called genotypes (chromosome 1) from Illumina whole-genome sequencing of an Indica x Japonica rice F2 population Plain Text - 1.0 KB - MD5: 91fe283277eff5f80f7fb8e3703d8c40 Documentation ReadMe file - data citation, description and terms of use.
Supplementary data for: Ethnolinguistic and genetic diversity of fonio (Digitaria exilis - Kippist - Stapf) in Senegal Dec 6, 2023 Diop, Baye Magatte; Barnaud, Adeline; Billot, Claire; Guèye, Mame Codou, 2023, "Supplementary data for: Ethnolinguistic and genetic diversity of fonio (Digitaria exilis - Kippist - Stapf) in Senegal", https://doi.org/10.23708/5WDKS1, DataSuds, V1, UNF:6:NeauNrptcRyq6NeGtIhJqg== [fileUNF] This data on fonio highlighted that social factors are pivotal in structuring diversity and should be taken into greater consideration in research and conservation projects to dovetail local and regional scales. It also showed that neglected species such as fonio - which are seld...
Fonio_Genotype_Senegal_2013_2015.tab Dec 6, 2023 - Supplementary data for: Ethnolinguistic and genetic diversity of fonio (Digitaria exilis - Kippist - Stapf) in Senegal Tabular Data - 26.1 KB - 20 Variables, 158 Observations - UNF:6:NeauNrptcRyq6NeGtIhJqg== Data This dataset is the most comprehensive collection on fonio in Senegal. It includes the individuals, regions, villages, ethnic groups of the farmers interviewed, their linguistic group, the cycle of fonio accessions reported by the farmers and SSR data.
Genotyping data for field samples from Haitian coffee agroforestry systems and international collection accessions Nov 29, 2023 Millet, Claude Patrick; Allinne, Clémentine; Vi, Tram; Marraccini, Pierre; Verleysen, Lauren; Couderc, Marie; Ruttink, Tom; Zhang, Dapeng; Solano Sánchez, William; Christine, Tranchant-Dubreuil; Jeune, Wesly; Poncet, Valérie, 2023, "Genotyping data for field samples from Haitian coffee agroforestry systems and international collection accessions", https://doi.org/10.23708/T6YZML, DataSuds, V1, UNF:6:4wzzOYlt0nsxd5jgI0e5Eg== [fileUNF] Though facing significant challenges, Coffee (Coffea arabica) grown in Haitian agroforestry systems are important contributors to rural livelihoods and provide several ecosystem services. There has been little work done on their genetic diversity and the variety mixtures used, an...

S4_Introduction_GenomeWideAssociationStudy_GWAS.pdf

May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)

Adobe PDF - 912.5 KB -

Documentation

Introduction to the core concept of genome wide association studies.

S4_script_GWAS_basic_Rcode.pdf

May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)

Adobe PDF - 73.2 KB -

Documentation

This file comments on the R script for GWAS analysis.

S4_Script_GWAS_Introduction.pdf

May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)

Adobe PDF - 574.9 KB -

Documentation

This file presents a script for GWAS analysis using R. We used a dataset of pearl millet accessions (Varshney et al. 2017).

sample_metadata.tab

May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)

Tabular Data - 2.5 KB - 5 Variables, 55 Observations -

Data

Table containing the passport data of the pearl millet accessions. This data file is associated with the script "S1_Introduction_to_R_Passport.html". These data are published in Berthouly-Salazar et al. (2016).

Called genotypes (chromosome 1) from Illumina whole-genome sequencing of an Indica x Japonica rice F2 population

Apr 29, 2024

Lorieux, Mathias; Triay, Cécile, 2024, "Called genotypes (chromosome 1) from Illumina whole-genome sequencing of an Indica x Japonica rice F2 population", https://doi.org/10.23708/8FXUNC, DataSuds, V1

Motivation: Genotyping of bi-parental populations can be performed with low-coverage next-generation sequencing (LC-NGS). This allows the creation of highly saturated genetic maps at reasonable cost, precisely localized recombination breakpoints (i.e., the crossovers), and minimi...

DiscriminantSitesOnly_biallelic_freebayes_bcftools_snps_on_AZUwithOrganelles_chr01.vcf.gz

Apr 29, 2024 - Called genotypes (chromosome 1) from Illumina whole-genome sequencing of an Indica x Japonica rice F2 population

Gzip Archive - 206.7 MB -

Data

Called genotypes (chromosome 1) from Illumina whole-genome sequencing of an Indica x Japonica rice F2 population

ReadMe.txt

Apr 29, 2024 - Called genotypes (chromosome 1) from Illumina whole-genome sequencing of an Indica x Japonica rice F2 population

Plain Text - 1.0 KB -

Documentation

ReadMe file - data citation, description and terms of use.

Supplementary data for: Ethnolinguistic and genetic diversity of fonio (Digitaria exilis - Kippist - Stapf) in Senegal

Dec 6, 2023

Diop, Baye Magatte; Barnaud, Adeline; Billot, Claire; Guèye, Mame Codou, 2023, "Supplementary data for: Ethnolinguistic and genetic diversity of fonio (Digitaria exilis - Kippist - Stapf) in Senegal", https://doi.org/10.23708/5WDKS1, DataSuds, V1, UNF:6:NeauNrptcRyq6NeGtIhJqg== [fileUNF]

This data on fonio highlighted that social factors are pivotal in structuring diversity and should be taken into greater consideration in research and conservation projects to dovetail local and regional scales. It also showed that neglected species such as fonio - which are seld...

Fonio_Genotype_Senegal_2013_2015.tab

Dec 6, 2023 - Supplementary data for: Ethnolinguistic and genetic diversity of fonio (Digitaria exilis - Kippist - Stapf) in Senegal

Tabular Data - 26.1 KB - 20 Variables, 158 Observations -

Data

This dataset is the most comprehensive collection on fonio in Senegal. It includes the individuals, regions, villages, ethnic groups of the farmers interviewed, their linguistic group, the cycle of fonio accessions reported by the farmers and SSR data.

Genotyping data for field samples from Haitian coffee agroforestry systems and international collection accessions

Nov 29, 2023

Millet, Claude Patrick; Allinne, Clémentine; Vi, Tram; Marraccini, Pierre; Verleysen, Lauren; Couderc, Marie; Ruttink, Tom; Zhang, Dapeng; Solano Sánchez, William; Christine, Tranchant-Dubreuil; Jeune, Wesly; Poncet, Valérie, 2023, "Genotyping data for field samples from Haitian coffee agroforestry systems and international collection accessions", https://doi.org/10.23708/T6YZML, DataSuds, V1, UNF:6:4wzzOYlt0nsxd5jgI0e5Eg== [fileUNF]

Though facing significant challenges, Coffee (Coffea arabica) grown in Haitian agroforestry systems are important contributors to rural livelihoods and provide several ecosystem services. There has been little work done on their genetic diversity and the variety mixtures used, an...

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