Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum

Version 2.0
Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum
Ben Chehida, Yacine; Thumloup, Julie; Schumacher, Cassie; Harkins, Timothy; Aguilar, Alex; Borrell, Asunción; Ferreira, Marisa; Rojas-Bracho, Lorenzo; Robertson, Kelly M.; Taylor, Barbara L.; Víkingsson, Gísli A.; Weyna, Arthur; Romiguier, Jonathan; Morin, Philip A.; Fontaine, M. C., 2020, "Data and scripts for: Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum", https://doi.org/10.23708/QBIUMI, DataSuds, V2
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Description
These data and scripts are accompanying the manuscript "Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum" by Ben Chehida Y., Thumloup J., Schumacher C., Harkins T., Aguilar A., Borrell A., Ferreira M., Rojas-Bracho L., Robertson K.M., Taylor B.L., Vikingsson G.A., Weyna A., Romiguier J., Morin P.A., & Fontaine M.C.

The archive here includes the final alignment of complete mitogenome sequences (16,302 bp) from 71 cetaceans (63 from the different porpoise species and 7 outgroup sequences) and various scripts used for the bioinformatics and data analyses. (2020-08-27)
Subject Medicine, Health and Life Sciences
Keyword Biodiversity and Ecology, Evolution, Genetics and genomics, Cetacea, Phylogeny and phylogeography
Related Publication Ben Chehida Y., Thumloup J., Schumacher C., Harkins T., Aguilar A., Borrell A., Ferreira M., Rojas-Bracho L., Robertson K.M., Taylor B.L., Vikingsson G.A., Weyna A., Romiguier J., Morin P.A., & Fontaine M.C. (2020) Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum. Scientific Reports, 10. doi: 10.1038/s41598-020-71603-9
Notes Data Type: dataset (text) - Fasta multiple sequence alignment (.fasta); XML data files as input for the program BEAST; Shell and python scripts
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Divergence_time_beast.sh
PorpoisesGG/Shell Script - 852 B
Published Sep 4, 2020
13 Downloads
MD5: 3da14ba7c072d5b354c04f98edba3cc8
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)
Code
Divergence_time_beast.xml
PorpoisesGG/XML - 1.1 MB
Published Sep 4, 2020
12 Downloads
MD5: 123ff8c0bc59283a8a6364798a24e81c
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)
Data
jmodeltest.sh
PorpoisesGG/Shell Script - 826 B
Published Sep 4, 2020
9 Downloads
MD5: 083b0144bee47b1ffbc55d8aa77b23e6
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, Scientific Reports, DOI: 10.1038/s41598-020-71603-9)
Code
Mitobim.sh
PorpoisesGG/Shell Script - 1.4 KB
Published Sep 4, 2020
11 Downloads
MD5: db521dc52342ba5bb7328c4d44aaf39b
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)
Code
Pi_rarefaction.sh
PorpoisesGG/Shell Script - 2.2 KB
Published Sep 4, 2020
11 Downloads
MD5: f2c8d5171b65ec11dfa709337923b1b1
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, Scientific Reports, DOI: 10.1038/s41598-020-71603-9).
Code
porpoise_mitogenome_final_alignment.fasta
PorpoisesGG/Unknown - 1.0 MB
Published Sep 4, 2020
11 Downloads
MD5: e8d15f7d21d09a589396bbd2fe8d4e9a
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 sequences were aligned with MUSCLE. A poorly resolved region of 226 bps in the D-loop was cropped from the final alignment (from position 15,508 to 15,734). Additional information is provided in Table S1 and S2 in Ben Chehida et al. (2020, Scientific Reports, DOI: 10.1038/s41598-020-71603-9).
Data
random_number.py
PorpoisesGG/Python Source Code - 1.2 KB
Published Sep 4, 2020
10 Downloads
MD5: acfd75a55d7296be44e476b842408231
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).
Code
skyline_beast.sh
PorpoisesGG/Shell Script - 872 B
Published Sep 4, 2020
9 Downloads
MD5: 55a14528fb89152ed013e14964f94266
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)
Code
skyline_file.xml
PorpoisesGG/XML - 198.1 KB
Published Sep 4, 2020
9 Downloads
MD5: 820c82a0bb4b3688607eaa051a8a6375
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: 10.1038/s41598-020-71603-9).
Data
Trimmomatics.sh
PorpoisesGG/Shell Script - 1.3 KB
Published Sep 4, 2020
9 Downloads
MD5: a2cc3c42e514b85eb265f66c33f2a88c
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)
Code
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