Environmental Data: ATLFISHREF A 12S mitochondrial reference dataset f...
Description
The global biodiversity crisis driven by anthropogenic pressures significantly threatens marine ecosystems functioning. The rate of climate change and the ...
Citation
Rozanski, R., Eme, D., Richards, E., Deschez, M. e., Rufino, M., Trenkel, V., Lorance, P., Marques, V., Spitz, J., Cornette, F., Albouy-Boyer, S., Polanco, A., Ernande, B., Pellissier, L., Albouy, C. (2024). ATLFISHREF A 12S mitochondrial reference dataset for metabarcoding Atlantic Fishes frequently caught during scientific surveys in the Bay of Biscay. EnviDat. https://www.doi.org/10.16904/envidat.495.
Resources
ATL_FISHREF_12S_mitochondrial_sequences.fasta
This file contains the 12s mitochondrial sequences for the Atlantic fishes collected on a French scientific survey (Evhoe) for stock assessment.
ATL_FISHREF_12S_mitochondrial_sequences.fastaATL_FISHREF_Teleo_barcode.fasta
This file contains the Teleo Barcode for the Atlantic fishes collected during a French scientific survey (Evhoe) for stock assessment.
ATL_FISHREF_Teleo_barcode.fastaMetadata_EVHOE_2017_2018_2019.csv
This file contains the metadata associated with each scientific survey
Metadata_EVHOE_2017_2018_2019.csvSequences_Info_&_Functional_Traits_Fish_BoB.csv
This file contains the metadata associated with each 12 s mitochondrial sequence.
Sequences_Info_&_Functional_Traits_Fish_BoB.csvATL_FISHREF_chromatograms_&_pictures.zip
ATL_FISHREF_chromatograms_&_pictures.zipATL_FISHREF_12S_mitochondrial_tree_156sequences.pdf
Mitochondrial tree based on the 12s sequences obtained for altantic fish. This data represent the maximum likelihood phylogenetic tree allowing to assess 1) the clustering of the different sequences generated in this study and their closest sequences recovered through a MegaBLAST on GenBank, 2) the robustness of the clades and 3) the phylogenetic dissimilarities through the branch length of the tree among the different sequences. This tree was built with IQtree2 using the best substitution model found by modelFinder. The robustness of the node was evaluated using 1000 ultra-fast bootstrap (node information indicated on the right of the /) and SH-aLRT procedures (node information indicated on the left of the /), using a hillclimbing nearest neighbor interchange (NNI) search to reduce the risk of overestimating branch supports with ultra-fast Bootstrap caused by too severe model violations.
ATL_FISHREF_12S_mitochondrial_tree_156sequences.pdf