UMR MIVEGEC

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.

Porpoises genetics and genomics

REACT Project

REACT2 Project

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61 to 70 of 167 Results

REACT2 Project Aug 29, 2023 Malaria control : Improving access to pREventive, diAgnostical and CuraTive arsenal among rural and vulnerable communities (REACT2 project) The fight against malaria faces now the challenge of the emergence and expansion of the resistance to both curative (treatment) and preventi...
Taconet_2023_input_data_dictionary.pdf Aug 4, 2023 - Data and code for: Physiological and behavioural resistance of malaria vectors in rural West-Africa: a data mining study to adress their fine-scale spatiotemporal heterogeneity, drivers, and predictability Adobe PDF - 32.6 KB - MD5: 71a610ee7b81a01506a4bcc432e867a2 Documentation Data dictionary (i.e. labels of the columns of the input data)
Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters Jun 9, 2023 - Porpoises genetics and genomics Louis, Marie; Korlević, Petra; Nykänen, Milaja; Archer, Frederick; Berrow, Simon; Brownlow, Andrew; Lorenzen, Eline; O'brien, Joanne; Post, Klaas; Racimo, Fernando; Rogan, Emer; Rosel, Patricia; Sinding, Mikkel; Van Der Es, Henry; Wales, Nathan; Fontaine, Michael C.; Gaggiotti, Oscar; Foote, Andrew, 2023, "Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters", https://doi.org/10.23708/DABAWD, DataSuds, V1 This dataset includes the data and scripts supporting the replicability of the paper: Louis M., Korlević P., Nykänen M.*, Archer F., Berrow S., Brownload A., Lorenzen E. D., O’Brien J., Post K., Racimo F., Rogan E., Rosel P. E., Sinding M.-H. S., van der Es H., Wales N., Fontai...
Louis_et_al2023_3.1.1.smartpca_fromvcf.tar.gz Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters Gzip Archive - 41.6 MB - MD5: edeb5067263a9c6545e0ebbf479817d1 CodeData Input file and scripts to format a vcf file and run smartpca (Figure S4). To uncompress, type "tar xzvf 3.1.1.smartpca_fromvcf.tar.gz"
Louis_et_al2023_3.1.2.smartpca_fromhaplo.tar.gz Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters Gzip Archive - 29.7 MB - MD5: 7f3a8762ab2f1393f629b9061ed84167 CodeData Scripts and input files to format an haplo file and run smartpca both for the data mapped to the killer whale reference genome and bottlenose dolphin reference genome (see subfolder mapped_Ttruncatus) (Figures 1c, S5 and S6). To uncompress, type "tar xzvf 3.1.2.smartpca_fromhaplo...
Louis_et_al2023_3.2.single_read_PCA.tar.gz Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters Gzip Archive - 16.2 KB - MD5: 38529e12e86c2043ba0147206cb23475 CodeData Scripts and input files to run and plot a single-read PCA (Figure S8). To uncompress, type "tar xzvf 3.2.single_read_PCA.tar.gz"
Louis_et_al2023_3.3.tfa.tar.gz Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters Gzip Archive - 1.1 MB - MD5: 1d4689415c6c66efd15ac30ad8866e16 CodeData Scripts and input file to run and plot the tfa - factor analysis (Figures 1d and S7). To uncompress, type "tar xzvf 3.3.tfa.tar.gz"
Louis_et_al2023_3.4.PCA_downsampling_modern.tar.gz Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters Gzip Archive - 13.1 MB - MD5: 39d6bc3f6db277efe72dc0fb0dd72e8d CodeData Scripts and input files to run smartpca (subfolder 3.4.1.smartpca) and the single read PCA (subfolder 3.4.2.single_read) on the modern data including one individual downsampled to 0.03x (Figure S3). To uncompress, type "tar xzvf 3.4.PCA_downsampling_modern.tar.gz"
Louis_et_al2023_4.1.D_statistics.tar.gz Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters Gzip Archive - 12.8 KB - MD5: 068eb49f9c9aaeb60632c4cde49783ca CodeData Scripts and input files to run D-statistics (Figures S9 and S10). To uncompress, type "tar xzvf 4.1.D_statistics.tar.gz"
Louis_et_al2023_4.2.qpbrute.tar.gz Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters Gzip Archive - 21.9 MB - MD5: 823c1555aa862779e58967acee925a6c CodeData Scripts and input file to format the files and run qprbute from an haplo file (subfolder 4.2.1.pseudohaploid_withSP1060) or a vcf file (subfolder 4.2.2.genotypes_modern) (Figure 2 and S11). To uncompress, type "tar xzvf 4.2.qpbrute.tar.gz"

REACT2 Project

Aug 29, 2023

Malaria control : Improving access to pREventive, diAgnostical and CuraTive arsenal among rural and vulnerable communities (REACT2 project) The fight against malaria faces now the challenge of the emergence and expansion of the resistance to both curative (treatment) and preventi...

Taconet_2023_input_data_dictionary.pdf

Aug 4, 2023 - Data and code for: Physiological and behavioural resistance of malaria vectors in rural West-Africa: a data mining study to adress their fine-scale spatiotemporal heterogeneity, drivers, and predictability

Adobe PDF - 32.6 KB -

Documentation

Data dictionary (i.e. labels of the columns of the input data)

Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Jun 9, 2023 - Porpoises genetics and genomics

Louis, Marie; Korlević, Petra; Nykänen, Milaja; Archer, Frederick; Berrow, Simon; Brownlow, Andrew; Lorenzen, Eline; O'brien, Joanne; Post, Klaas; Racimo, Fernando; Rogan, Emer; Rosel, Patricia; Sinding, Mikkel; Van Der Es, Henry; Wales, Nathan; Fontaine, Michael C.; Gaggiotti, Oscar; Foote, Andrew, 2023, "Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters", https://doi.org/10.23708/DABAWD, DataSuds, V1

This dataset includes the data and scripts supporting the replicability of the paper: Louis M.*, Korlević P.*, Nykänen M.*, Archer F., Berrow S., Brownload A., Lorenzen E. D., O’Brien J., Post K., Racimo F., Rogan E., Rosel P. E., Sinding M.-H. S., van der Es H., Wales N., Fontai...

Louis_et_al2023_3.1.1.smartpca_fromvcf.tar.gz

Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Gzip Archive - 41.6 MB -

CodeData

Input file and scripts to format a vcf file and run smartpca (Figure S4). To uncompress, type "tar xzvf 3.1.1.smartpca_fromvcf.tar.gz"

Louis_et_al2023_3.1.2.smartpca_fromhaplo.tar.gz

Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Gzip Archive - 29.7 MB -

CodeData

Scripts and input files to format an haplo file and run smartpca both for the data mapped to the killer whale reference genome and bottlenose dolphin reference genome (see subfolder mapped_Ttruncatus) (Figures 1c, S5 and S6). To uncompress, type "tar xzvf 3.1.2.smartpca_fromhaplo...

Louis_et_al2023_3.2.single_read_PCA.tar.gz

Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Gzip Archive - 16.2 KB -

CodeData

Scripts and input files to run and plot a single-read PCA (Figure S8). To uncompress, type "tar xzvf 3.2.single_read_PCA.tar.gz"

Louis_et_al2023_3.3.tfa.tar.gz

Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Gzip Archive - 1.1 MB -

CodeData

Scripts and input file to run and plot the tfa - factor analysis (Figures 1d and S7). To uncompress, type "tar xzvf 3.3.tfa.tar.gz"

Louis_et_al2023_3.4.PCA_downsampling_modern.tar.gz

Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Gzip Archive - 13.1 MB -

CodeData

Scripts and input files to run smartpca (subfolder 3.4.1.smartpca) and the single read PCA (subfolder 3.4.2.single_read) on the modern data including one individual downsampled to 0.03x (Figure S3). To uncompress, type "tar xzvf 3.4.PCA_downsampling_modern.tar.gz"

Louis_et_al2023_4.1.D_statistics.tar.gz

Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Gzip Archive - 12.8 KB -

CodeData

Scripts and input files to run D-statistics (Figures S9 and S10). To uncompress, type "tar xzvf 4.1.D_statistics.tar.gz"

Louis_et_al2023_4.2.qpbrute.tar.gz

Jun 9, 2023 - Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Gzip Archive - 21.9 MB -

CodeData

Scripts and input file to format the files and run qprbute from an haplo file (subfolder 4.2.1.pseudohaploid_withSP1060) or a vcf file (subfolder 4.2.2.genotypes_modern) (Figure 2 and S11). To uncompress, type "tar xzvf 4.2.qpbrute.tar.gz"

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