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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71 to 80 of 101 Results

S3_GeneticDiversity.pdf May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) Adobe PDF - 8.0 MB - MD5: b221ac40593882f7deb0a1a3d35b3a17 Documentation Introduction to Population Genetics for analysing the genetic diversity of crops
S3_Genetic_diversity+structure.html May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) HTML - 4.3 MB - MD5: 828d31d700d62f10b8f9fbf120f7883a CodeDocumentation In this R tutorial, we we will take a processed VCF. First, we will explore diversity through: polymorphic SNPs (required packages: adegenet), allele frequencies (required packages: adegenet), private and shared alleles (required packages: poppr), allelic richness (required packa...
S3_install.packages.R May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) R Syntax - 975 B - MD5: c7a6dda8fc71fd10aebe8212eb9edbdf Code List of packages to install for session 3 on diversity and structure analysis. To be opened with RStudio.
S3_Structure.pdf May 16, 2024 - High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa) Adobe PDF - 3.8 MB - MD5: f5d2b43e2d5a5eefd051c29b2c68833e Documentation Introduction to Population Genetics for analysing the genetic structure of crops.
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).
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.

S3_GeneticDiversity.pdf

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

Adobe PDF - 8.0 MB -

Documentation

Introduction to Population Genetics for analysing the genetic diversity of crops

S3_Genetic_diversity+structure.html

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

HTML - 4.3 MB -

CodeDocumentation

In this R tutorial, we we will take a processed VCF. First, we will explore diversity through: polymorphic SNPs (required packages: adegenet), allele frequencies (required packages: adegenet), private and shared alleles (required packages: poppr), allelic richness (required packa...

S3_install.packages.R

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

R Syntax - 975 B -

Code

List of packages to install for session 3 on diversity and structure analysis. To be opened with RStudio.

S3_Structure.pdf

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

Adobe PDF - 3.8 MB -

Documentation

Introduction to Population Genetics for analysing the genetic structure of crops.

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).

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.

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