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.

Featured Dataverses

In order to use this feature you must have at least one published or linked dataverse.

Publish Dataverse

Are you sure you want to publish your dataverse? Once you do so it must remain published.

Publish Dataverse

This dataverse cannot be published because the dataverse it is in has not been published.

Delete Dataverse

Are you sure you want to delete your dataverse? You cannot undelete this dataverse.

31 to 40 of 45 Results

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 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)
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...

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

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)

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...

Add Data

Share Dataverse

Link Dataverse

Reset Modifications