Infectious Diseases and Vectors: Ecology, Genetics, Evolution and Control

The aims of the group MIVEGEC are to develop integrative and transdisciplinary research to the mechanisms that maintain, amplify and transmit pathogenic agents, along with their genetic and epigenetic determinants, in order to better understand how these systems evolve and to improve their control.
L’UMR MIVEGEC "Maladies Infectieuses et Vecteurs : Ecologie, Génétique, Evolution et Contrôle" a pour mission de comprendre, via des recherches intégratives et transdisciplinaires, les mécanismes de maintenance, d’amplification et de transmission d’agents pathogènes, leurs déterminants génétiques et non génétiques, afin de pouvoir mieux appréhender l’évolution de ces systèmes infectieux et contribuer à en améliorer le contrôle.
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181 to 190 of 203 Results
1_TtmappednewTtvar_biallelic.vcf.gz
Sep 2, 2021 - Replication Data for: Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins
Gzip Archive - 704.4 MB - MD5: 4461877afe51bc505f570808593aa7c0
Data
Variant calling format (VCF) file including the biallelic single nucleotide variants (SNVs or SNPs) used in Louis et al. The sample names are in the vcf file header. See the materials and methods and supplementary material of the manuscript for details on data generation.
2_Tursiops_unlinkedSNPs.beagle.gz
Sep 2, 2021 - Replication Data for: Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins
Gzip Archive - 85.1 MB - MD5: 8fe3f103955bdd7dd145c316dc008fe6
Data
Genotype likelihood LD pruned input file in Beagle format. Note that Sample order (Ind0 to Ind55) is given in the file Tursiops_samples_no7Tt182.bamlist. Sample 7Tt182 is not included in the beagle file due to its low coverage but clusters with the other NWAp. See materials and...
3_Tursiops_ALL.haplo.gz
Sep 2, 2021 - Replication Data for: Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins
Gzip Archive - 108.0 MB - MD5: e7909efb3649e2ac35f3cb17268be917
Data
haplo file (pseudo-haploid random call): samples order is given in Tursiops_samples_ALL.bamlist. Note that 7Tt182 is included, but was not included in the analyses, which are based on subset of individuals (one coastal individual and all allopatric pelagic individuals except from...
4_GhostAncestry-master.tar.gz
Sep 2, 2021 - Replication Data for: Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins
Gzip Archive - 8.8 KB - MD5: d5234dbb967ad08679ed0eb346e3308e
Code
GhostAncestry-master contains the codes written by Benoit Simon-Bouhet to generate the input files for the ghost ancestry analyses - also available at https://github.com/besibo/GhostAncestry ## The folder 1_One Scaffold contains the code to test the script on one scaffold only #...
Tursiop_samples_ALL.bamlist.txt
Sep 2, 2021 - Replication Data for: Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins
Unknown - 351 B - MD5: 8b7e2ce3192a5f460626c00d41c18f65
Data
Names of the samples and their order. See materials and methods and supplementary material for details on data generation
Tursiop_samples_no7Tt182.bamlist.txt
Sep 2, 2021 - Replication Data for: Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins
Unknown - 344 B - MD5: 734cebd2c7212d5a5b48cead8ebd0d42
Data
Names of the samples and their order, after excluding sample 7Tt182. See materials and methods and supplementary material for details on data generation
Porpoises_NA_All_mtDNA_sequences.fasta
Mar 11, 2021 - Replication data for: No leading-edge effect in North Atlantic harbor porpoises: Evolutionary and conservation implications
Unknown - 655.4 KB - MD5: da4517956b1ba25a2647dd804c0a3a3a
Data
Fasta alignment of 150 mitochondrial DNA sequences (148 harbor porpoises and 2 Dall's porpoises, see Table S3 in Ben Chehida et al. 2021 Evol. App.). This alignment includes five mitochondrial coding regions (CytB, ATP6, ATP8, ND5, and COX-I). These sequences were used in all the...
Porpoises_NA_Microsatellite_data_cleaned.tab
Mar 11, 2021 - Replication data for: No leading-edge effect in North Atlantic harbor porpoises: Evolutionary and conservation implications
Tabular Data - 100.6 KB - 25 Variables, 925 Observations - UNF:6:j1jcc4A1Rs+FEedPbYzYIQ==
Data
File providing the identifier, geographical group, local sub-group, latitude, longitude, and the genotypes at the 10 microsatellites for 925 harbor porpoises (i.e. individuals with ≤40% of missing data). This dataset was used in all the analyses but the sPCA. The sPCA analysis us...
Porpoises_NA_Unique_haplotypes.fasta
Mar 11, 2021 - Replication data for: No leading-edge effect in North Atlantic harbor porpoises: Evolutionary and conservation implications
Unknown - 469.4 KB - MD5: a82b8e6724f8492893f54daf714c9543
Data
Fasta alignment of 111 unique mitochondrial DNA haplotypes (110 harbor porpoises and 1 Dall's porpoise). This alignment contains five mitochondrial coding regions (CytB, ATP6, ATP8, ND5, and COXI). These unique sequences were used to infer the phylogenetic tree. For further detai...
Divergence_time_beast.sh
Sep 4, 2020 - Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum
Shell Script - 852 B - MD5: 3da14ba7c072d5b354c04f98edba3cc8
Code
Bash script used to infer the chronogram with BEAST software. See details in Ben Chehida et al. (2020, Scientific Reports, DOI: 10.1038/s41598-020-71603-9)
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