ACDC, a global database of amphibian cytochrome-b sequences using reproducible curation for GenBank records

Burg, Matthijs P. van den; Herrando‐Pérez, Salvador; Vieites, David R.

doi:10.1038/s41597-020-00598-9

Cited by 8 publications

(19 citation statements)

References 41 publications

(33 reference statements)

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“…Compared with Amphibia (van den Burg et al . 2020a), such errors are five‐fold more prevalent in Aves, which could result from utilizing old tissue in Aves studies, for example DNA sourced from museum voucher specimens (McCormack et al . 2015).…”

Section: Discussionmentioning

confidence: 99%

“…We followed the curation workflow for GenBank records outlined by van den Burg et al . (2020a). Specifically, on 23 April 2021 we retrieved 54 262 Aves Cytb records from GenBank using the adjusted ACDC R script (R Core Team 2019, van den Burg et al .…”

Section: Methodsmentioning

confidence: 99%

“…Before creating species‐unique fasta alignments (van den Burg et al . 2020a), the nomenclature of all Cytb sequences was assessed and curated using the IOC World Bird List v11.1 (Gill et al . 2021) when found to be outdated (see Rheindt & Ng 2021).…”

Section: Methodsmentioning

confidence: 99%

“…We visually checked all alignments for potential sequence errors and finalized the initial curation of species alignments by resolving sequence gaps (≠ 3) with ‘N’s and eliminating ambiguous terminals (van den Burg et al . 2020a).…”

Section: Methodsmentioning

confidence: 99%

“…We then created genera‐specific alignments and assessed the taxonomic assignment of sequences in flagged species alignments using an intraspecific and intrageneric Cytb divergence threshold (van den Burg et al . 2020a). Here, we used a conservative threshold of 1% for flagging potential conflicting sequences both within species (if intraspecific divergence is > 1%) or genera (if intrageneric divergence is < 1%) (Aliabadian et al .…”

Section: Methodsmentioning

confidence: 99%

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Bird genetic databases need improved curation and error reporting to NCBI

Burg

Vieites

2022

Ibis

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The ongoing biodiversity crisis is causing rapid species losses faster than taxonomists' capacity to describe new species. Integrative taxonomic approaches need robust taxonomic baseline data to correctly describe and conserve global species diversity, in which genetic data are one of the pillars. However, despite their broad use throughout the biological sciences, the quality of genetic data within public repositories is still not guaranteed. Here, we curated GenBank Cytochrome-b records of Aves, a well-known taxon undergoing continuous taxonomic changes, and provide a curated database to aid taxonomic and conservation efforts. After curation of 54 114 records, the database represents 50 280 sequences from 6867 species (63% of current bird biodiversity), with a per-genus median of two species (50% interquartile ranges of 1-4) and three sequences (1-9). Overall, 4469 bird species have ≥ 2 sequences representing 91.7% and 97.5% of currently known families and orders, respectively. We flagged 1336 erroneous records (2.5% of Aves Cytochrome-b records) in need of taxonomic curation (71%) or removal, 45% of which lack any voucher information preventing a proper taxonomic assignation. Compared with Amphibia, a group for which a similar analysis was recently published, Aves records have a five-fold higher prevalence of errors caused by contamination, sequencing errors or diverging mutation patterns. We provide a species-level taxonomic update for 839 Gen-Bank records, including changes at the genus (76), family (21) and order (16) levels. Scientific conclusions from the manuscripts that have ever used those data might be compromised. A further concern is the current availability of GenBank records previously identified as erroneous in published manuscripts, demonstrating the need for improved communication between NCBI and the community. We call for caution when utilizing GenBank records without curation of retrieved data, despite new improvements.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%