Updating splits, lumps, and shuffles: Reconciling GenBank names with standardized avian taxonomies

Abstract
Biodiversity research has advanced by testing expectations of ecological and evolutionary hypotheses through the linking of large-scale genetic, distributional, and trait datasets. The rise of molecular systematics over the past 30 years has resulted in a wealth of DNA sequences from around the globe. Yet, advances in molecular systematics also have created taxonomic instability, as new estimates of evolutionary relationships and interpretations of species limits have required widespread scientific name changes. Taxonomic instability, colloquially “splits, lumps, and shuffles,” presents logistical challenges to large-scale biodiversity research because (1) the same species or sets of populations may be listed under different names in different data sources, or (2) the same name may apply to different sets of populations representing different taxonomic concepts. Consequently, distributional and trait data are often difficult to link directly to primary DNA sequen..., Taxonomic reconciliationWe downloaded all names from the NCBI Taxonomy database (Schoch et al., 2020) that descended from “Aves” (TaxID: 8782) on 3 May 2020 (Data Repository D2). From this list, we extracted all species and subspecies names as well as their NCBI Taxonomy ID (TaxID) numbers. We then ran a custom Perl script (Data Repository D3) to exactly match binomial (genus, species) and trinomial (genus, species, subspecies) names from NCBI Taxonomy to the names recognized by eBird/Clements v2019 Integrated Checklist (August 2019; Data Repository D4). For each mismatch with the NCBI Taxonomy name, we then identified the corresponding equivalent eBird/Clements species or subspecies. We first searched for names in Avibase (Lepage et al., 2014). However, Avibase’s search function currently facilitates only exact matches to taxonomies it implements. For names that were not an exact match to an Avibase taxonomic concept, we implemented web searches (Google) which often identified minor sp..., D1:\"PetersVsClements2Final.txt\" - This file tells which species from the Peters taxonomy match the 2019 Clements/ebird taxonomy. The first column has a species name from the Peters taxonomy. In the second column, \"Clements\" indicates that the species name matches the Clements/ebird taxonomy, \"No\" means it does match, and \"Close\" means that the names match when you disregard the last two letters.\"SibleyMonroeVsClements_Final.txt\" - This file tells which species from the Sibley Monroe taxonomy match the 2019 Clements/ebird taxonomy. The first column has a species ID number from the Sibley Monroe taxonomy. The second column has the species scientific name from the Sibley Monroe taxonomy. The third column has the common name from the Sibley Monroe taxonomy. In the fourth column, \"Clements\" indicates that the species name matches the Clements/ebird taxonomy, \"No\" means it does match, and \"Close\" means that the names match when you disregard the last two letters.D2:\"taxonomy_result.unix.xml\" ...