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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201 to 210 of 220 Results

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
Replication data for: No leading-edge effect in North Atlantic harbor porpoises: Evolutionary and conservation implications Mar 11, 2021 - Porpoises genetics and genomics Ben Chehida, Yacine; Loughnane, Roisin; Thumloup, Julie; Kaschner, Kristin; Garilao, Cristina; Rosel, Patricia E.; Fontaine, Michael C., 2021, "Replication data for: No leading-edge effect in North Atlantic harbor porpoises: Evolutionary and conservation implications", https://doi.org/10.23708/LMH8Y8, DataSuds, V1, UNF:6:j1jcc4A1Rs+FEedPbYzYIQ== [fileUNF] These data are accompanying the manuscript "No leading-edge effect in North Atlantic harbor porpoises: Evolutionary and conservation implications" by Ben Chehida Y., Loughnane R., Thumloup J., Kaschner K., Garilao C., Rosel P.E., & Fontaine M.C. The manuscript has been posted as...
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)
Divergence_time_beast.xml Sep 4, 2020 - Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum XML - 1.1 MB - MD5: 123ff8c0bc59283a8a6364798a24e81c Data Input file used in the script Divergence_time_beast.sh which uses BEAST software to infer the chronogram (divergence time estimates). This file was created with BEAUti program of BEAST. See details in Ben Chehida et al. (2020, Scientific Reports, DOI: 10.1038/s41598-020-71603-9)

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 -

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 -

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 -

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 -

Data

Names of the samples and their order, after excluding sample 7Tt182. See materials and methods and supplementary material for details on data generation

Replication data for: No leading-edge effect in North Atlantic harbor porpoises: Evolutionary and conservation implications

Mar 11, 2021 - Porpoises genetics and genomics

Ben Chehida, Yacine; Loughnane, Roisin; Thumloup, Julie; Kaschner, Kristin; Garilao, Cristina; Rosel, Patricia E.; Fontaine, Michael C., 2021, "Replication data for: No leading-edge effect in North Atlantic harbor porpoises: Evolutionary and conservation implications", https://doi.org/10.23708/LMH8Y8, DataSuds, V1, UNF:6:j1jcc4A1Rs+FEedPbYzYIQ== [fileUNF]

These data are accompanying the manuscript "No leading-edge effect in North Atlantic harbor porpoises: Evolutionary and conservation implications" by Ben Chehida Y., Loughnane R., Thumloup J., Kaschner K., Garilao C., Rosel P.E., & Fontaine M.C. The manuscript has been posted as...

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 -

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 -

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 -

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 -

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)

Divergence_time_beast.xml

Sep 4, 2020 - Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum

XML - 1.1 MB -

Data

Input file used in the script Divergence_time_beast.sh which uses BEAST software to infer the chronogram (divergence time estimates). This file was created with BEAUti program of BEAST. See details in Ben Chehida et al. (2020, Scientific Reports, DOI: 10.1038/s41598-020-71603-9)

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