Data for: Marine and freshwater fishes of Alabama: a revised checklist and discussion of taxonomic issues
OVERVIEW In support of the manuscript by Bagley et al. (2023), this repository provides (1) the final combined database of cleaned FishNet2 collections and SEAMAP records used in our study, (2) the final database subsetted to checklist species, (3) additional supplementary data, and (4) additional discussion in Appendix S1. Supplementary data are provided under separate tabs in a single Excel spreadsheet file named "Bagley_et_al_Supplementary_Data.xlsx." Sites in Figs. 2 and 3 of the manuscript correspond to coordinates in Table S2. Due to space limitations, the contents of this accession are more fully described in the enclosed PDF file, "Bagley_et_al_Data_Description.pdf." REFERENCES Bagley JC, Johnson CC, McGregor SW, Breitman MF, Armbruster JW, Harris PM, O'Neil PE (2023) Marine and freshwater fishes of Alabama: a revised checklist and discussion of taxonomic issues. Zootaxa.
Steps to reproduce
Procedures for obtaining and editing the data in this accession from FishNet2 (http://www.fishnet2.net), as well as other sources including SEAMAP, are described below and in the main text of our article (Bagley et al. 2023). Steps to reproduce data analysis: - Download regional fish collections records from FishNet2 database (http://www.fishnet2.net/). Here, our region was Alabama and the Mobile River Basin, which drains much of the area of the state and also extends into outlying areas of Mississippi and Georgia as well as a very small portion of southeastern Tennessee. Our study area also included coastal marine waters of Alabama in Mobile Bay and the northern Gulf of Mexico. The FishNet2 data have the advantage of backing collection localities/records with specimens accessioned in natural history museums. - Clean and edit records to (1) remove nonsense names, hybrid specimens, pet shop specimens, and collections with erroneous locality information; (2) fix taxonomic names of species and families to currently accepted names wherever possible; (3) keep only taxa meeting criteria for inclusion; and (4) fix incorrect or improperly formatted geographical coordinates (latitude/longitude, with conversion to decimal degrees format if possible) or set as missing/null ("–") for record. o Recommended: clean dataset using spreadsheet operations, as well as accurate and customized search and replace steps based on regular expressions (computer language of choice; we used BBEdit and UNIX command line software for this purpose). - Score each record by the (presumed) ecological habitat preferences ("Habitat") of the corresponding fish species/taxon; records scored with categorical variable labels 'F' (freshwater), 'M' (marine), or 'F, M' (freshwater and marine) for taxa that are diadromous or are known to occur in both habitat types during their lifetimes. - Download fisheries-independent SEAMAP data from https://seamap.gsmfc.org/. Link STAREC table with station location information and sort to stations off Alabama's coast. Subset to stations within ~3 nautical miles of AL shore using various methods/mapping checks. Clean SEAMAP species names and geographical coordinates, score marine taxa as 'M' or 'F, M'. - Combined FishNet2 and SEAMAP datasets into final combined database and identify unique coordinates and species obtained from the SEAMAP data. - Map collection localities, both overall and after subsetting locality (site) data by habitat type, using GIS software (here, QGIS). - Use reasonable criteria (e.g., species, distribution, distance/area, provenance) to develop/expanded checklist of marine and freshwater fishes occurring in the study region based on the collections data. - Save working datasets and final datasets in Microsoft Excel and place in short-term and long-term storage according to data management plan.