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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281 to 290 of 295 Results

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)
jmodeltest.sh Sep 4, 2020 - Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum Shell Script - 826 B - MD5: 083b0144bee47b1ffbc55d8aa77b23e6 Code Bash script used to run JmodelTest2 to infer the best substitution model. The results generated by JmodelTest2 were subsequently used in the phylogenetic reconstruction, the skyline plot and the inference of the chronogram. More information is provided in Ben Chehida et al. (2020...
Mitobim.sh Sep 4, 2020 - Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum Shell Script - 1.4 KB - MD5: db521dc52342ba5bb7328c4d44aaf39b Code Bash script used to assemble mitogenomes from MiSeq 100PE reads using MITOBIM. It generates a fasta file for each individual assembled. More information is provided in Text S2 in Ben Chehida et al. (2020, Scientific Reports, DOI: 10.1038/s41598-020-71603-9)
Pi_rarefaction.sh Sep 4, 2020 - Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum Shell Script - 2.2 KB - MD5: f2c8d5171b65ec11dfa709337923b1b1 Code Shell wrapper that calculates the nucleotide diversity using a rarefaction method and the infoseq_diversity function from libDiversity (provided in this data archive as a courtesy of the author, Guillaume Achaz (guillaume.achaz[at]mnhn.fr). See details in Ben Chehida et al. (2020...
porpoise_mitogenome_final_alignment.fasta Sep 4, 2020 - Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum Unknown - 1.0 MB - MD5: e8d15f7d21d09a589396bbd2fe8d4e9a Data Final multiple sequences alignment (fasta format) of 16,302 base pairs (bps) for 71 cetacean mitogenomes. It includes 63 porpoises and 7 outgroup sequences. The porpoise mitogenomes were assembled from short read MiSeq 100PE with MITOBIM and Geneious. The assembled fasta sequence...
random_number.py Sep 4, 2020 - Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum Python Source Code - 1.2 KB - MD5: acfd75a55d7296be44e476b842408231 Code Python script used to select randomly sequences from a fasta file. This script is used to conduct the rarefaction analysis. See details in Ben Chehida et al. (2020, Scientific Reports, DOI: 10.1038/s41598-020-71603-9).

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)

jmodeltest.sh

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

Shell Script - 826 B -

Code

Bash script used to run JmodelTest2 to infer the best substitution model. The results generated by JmodelTest2 were subsequently used in the phylogenetic reconstruction, the skyline plot and the inference of the chronogram. More information is provided in Ben Chehida et al. (2020...

Mitobim.sh

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

Shell Script - 1.4 KB -

Code

Bash script used to assemble mitogenomes from MiSeq 100PE reads using MITOBIM. It generates a fasta file for each individual assembled. More information is provided in Text S2 in Ben Chehida et al. (2020, Scientific Reports, DOI: 10.1038/s41598-020-71603-9)

Pi_rarefaction.sh

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

Shell Script - 2.2 KB -

Code

Shell wrapper that calculates the nucleotide diversity using a rarefaction method and the infoseq_diversity function from libDiversity (provided in this data archive as a courtesy of the author, Guillaume Achaz (guillaume.achaz[at]mnhn.fr). See details in Ben Chehida et al. (2020...

porpoise_mitogenome_final_alignment.fasta

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

Unknown - 1.0 MB -

Data

Final multiple sequences alignment (fasta format) of 16,302 base pairs (bps) for 71 cetacean mitogenomes. It includes 63 porpoises and 7 outgroup sequences. The porpoise mitogenomes were assembled from short read MiSeq 100PE with MITOBIM and Geneious. The assembled fasta sequence...

random_number.py

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

Python Source Code - 1.2 KB -

Code

Python script used to select randomly sequences from a fasta file. This script is used to conduct the rarefaction analysis. See details in Ben Chehida et al. (2020, Scientific Reports, DOI: 10.1038/s41598-020-71603-9).

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