Porpoises genetics and genomics

The Porpoises genetics and genomics dataverse gathers together data and scripts from the porpoise ecological and evolutionary genetics & genomics project. This project aims at advancing our knowledge regarding the ecology and evolution of the seven species of porpoises (Phocoenidae) with a specific anchor on the harbour porpoise (Phocoena phocoena).

Molecular population genetics & genomics, phylogenomics, and habitat modelling are used to study the molecular ecology, phylogeography, and evolution of the populations, ecotypes, and species in order to gain knowledge on their historical demography that led to the current pattern of genetic structure, and how they will potentially evolved with the forecasted climate changes. Ultimately these genetic inferences on population structure, connectivity and demographic histories will be used to design tailored conservation and management strategies in order to design management units, identify evolutionary significant units and best preserve the evolutionary potentials of each species.

Data collected in this project includes genetic data such as microsatellite and SNPs genotypes, DNA sequences from the mitochondrial genome (fragments or complete), and whole genome resequencing data. Empirical data are collected from stranded and by-caught porpoises. Simulated genetic data are also used as part of the project for in silico data analyses.

Contact Michael C. FONTAINE (PI, UMR MIVEGEC: U. Montpellier, CNRS, IRD, Montpellier - FR) and GELIFES, U. Groningen, NL) for further information.
This project benefited from funding of the University of Groningen.

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41 to 45 of 45 Results

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).
skyline_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 - 872 B - MD5: 55a14528fb89152ed013e14964f94266 Code Bash script used to run BEAST software and reconstruct the skyline plots. See details in Ben Chehida et al. (2020, Scientific Reports, DOI: 10.1038/s41598-020-71603-9)
skyline_file.xml Sep 4, 2020 - Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum XML - 198.1 KB - MD5: 820c82a0bb4b3688607eaa051a8a6375 Data Input file used in skyline_beast.sh to run the skyline plot analysis in BEAST software which estimates the variation of the effective population size through time. This file was created with BEAUti program of BEAST See details in Ben Chehida et al. (2020, Scientific Reports, DOI:...
Trimmomatics.sh Sep 4, 2020 - Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum Shell Script - 1.3 KB - MD5: a2cc3c42e514b85eb265f66c33f2a88c Code Bash script used to clean the raw read (fastq format) with trimmomatic. Additional information is provided in Text S1 in Ben Chehida et al. (2020, Scientific Reports, DOI: 10.1038/s41598-020-71603-9)

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).

skyline_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 - 872 B -

Code

Bash script used to run BEAST software and reconstruct the skyline plots. See details in Ben Chehida et al. (2020, Scientific Reports, DOI: 10.1038/s41598-020-71603-9)

skyline_file.xml

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

XML - 198.1 KB -

Data

Input file used in skyline_beast.sh to run the skyline plot analysis in BEAST software which estimates the variation of the effective population size through time. This file was created with BEAUti program of BEAST See details in Ben Chehida et al. (2020, Scientific Reports, DOI:...

Trimmomatics.sh

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

Shell Script - 1.3 KB -

Code

Bash script used to clean the raw read (fastq format) with trimmomatic. Additional information is provided in Text S1 in Ben Chehida et al. (2020, Scientific Reports, DOI: 10.1038/s41598-020-71603-9)

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