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

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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]
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Description
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 a preprint on biorXiv (doi: https://doi.org/10.1101/2020.11.03.366542) and is now accepted for publication in the journal Evolutionary Applications.

The archive here includes the mitochondrial DNA sequence alignments (unique haplotype and individual level), and the genotypes for the 10 microsatellite markers used in this study.

The scripts associated with this study are available via the first author GitHub repository (https://github.com/YacineBenChehidaRuG/EvolApplPorpoiseMarch2021).
Subject Medicine, Health and Life Sciences
Keyword Seascape genetics, Phylogeography, Marine glacial refugia, Migration-drift equilibrium, Cetacea, Philopatry, Conservation genetics, Marine dispersal
Related Publication Ben Chehida Y., Loughnane R., Thumloup J., Kaschner K., Garilao C., Rosel P.E., & Fontaine M.C. (2021). No leading-edge effect in North Atlantic harbor porpoises: Evolutionary and conservation implications. Evolutionary Applications, in press. BiorXiv preprint: doi: 10.1101/2020.11.03.366542
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Porpoises_NA_All_mtDNA_sequences.fasta
PorpoisesGG/Unknown - 655.4 KB
Published Mar 11, 2021
6 Downloads
MD5: da4517956b1ba25a2647dd804c0a3a3a
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 analyses requiring information on haplotypes frequencies (i.e. haplotype network, non-metric multidimentional scaling, population differentiation, isolation by distance, polymorphism, and population demographic changes based on Tajima’s D and Fu and Li’s D*). For further details, see the Materials and Methods in Ben Chehida et al. 2021 Evol. App.
Data
Porpoises_NA_Microsatellite_data_cleaned.tab
PorpoisesGG/Tabular Data - 100.6 KB
Published Mar 11, 2021
9 Downloads
25 Variables, 925 Observations UNF:6:j1jcc4A1Rs+FEedPbYzYIQ==
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 used the data without any data. Missing genotypes are encoded with the -9 character. Each microsatellite locus is encoded with two columns providing the two allelic states, with the numbers (2-3 digits) referring to the allelic size scored on a ABI capillary sequencer using GeneMapper V4.0. For further details, see the Materials and Methods in Ben Chehida et al. 2021 Evol. App. See Table S1 and S2, Figure 1 and S1 in Ben Chehida et al. (2021) for the group acronyms and geographic location of the fields "Geog. Regions" and "Local geog. sub-groups".
Data
Porpoises_NA_Unique_haplotypes.fasta
PorpoisesGG/Unknown - 469.4 KB
Published Mar 11, 2021
6 Downloads
MD5: a82b8e6724f8492893f54daf714c9543
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 details, see the Materials and Methods in Ben Chehida et al. 2021 Evol. App
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