Are genetic databases sufficiently populated to detect non-indigenous species?

Abstract

Correct species identifications are of tremendous importance for invasion ecology, as mistakes could lead to misdirecting limited resources against harmless species or inaction against problematic ones. DNA barcoding is becoming a promising and reliable tool for species identifications, however the efficacy of such molecular taxonomy depends on gene region(s) that provide a unique sequence to differentiate among species and on availability of reference sequences in existing genetic databases. Here, we assembled a list of aquatic and terrestrial non-indigenous species (NIS) and checked two leading genetic databases for corresponding sequences of six genome regions used for DNA barcoding. The genetic databases were checked in 2010, 2012, and 2016. All four aquatic kingdoms (Animalia, Chromista, Plantae and Protozoa) were initially equally represented in the genetic databases, with 64, 65, 69, and 61 % of NIS included, respectively. Sequences for terrestrial NIS were present at rates of 58 and 78 % for Animalia and Plantae, respectively. Six years later, the number of sequences for aquatic NIS increased to 75, 75, 74, and 63 % respectively, while those for terrestrial NIS increased to 74 and 88 % respectively. Genetic databases are marginally better populated with sequences of terrestrial NIS of plants compared to aquatic NIS and terrestrial NIS of animals. The rate at which sequences are added to databases is not equal among taxa. Though some groups of NIS are not detectable at all based on available data-mostly aquatic ones-encouragingly, current availability of sequences of taxa with environmental and/or economic impact is relatively good and continues to increase with time.

Population attenuation in zooplankton communities during transoceanic transfer in ballast water

“…Results from BLAST may not be fully accurate in part due to a lack of online sequence references for particular taxonomic groups (Briski et al 2016). Moreover, studies have shown that some groups of zooplankton-such as copepods and rotifers-form species complexes that are poorly defined taxonomically (e.g., Lee 2000;Gomez et al 2002).…”

Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding

“…PR2 database for the 18S, BOLD database for COI) (von Ammon et al 2018b, Rey et al 2019. GenBank may contain reference sequences from many different genetic markers and includes all domains of life (Briski et al 2016, Ardura 2019, but it is more prone to errors, since it contains a high number of non-curated data entries (López-Escardó et al 2018). For example, von Ammon et al (2018b) were able to detect the invasive species Sabella spallanzanii in a New Zealand's marina by using 2 approaches: 18S with taxonomic assignment to PR2 and COI with taxonomic assignment to BOLD, but the taxonomic assignment in GenBank delivered matches only at the genus level.…”

Recommendations for developing and applying genetic tools to assess and manage biological invasions in marine ecosystems

“…a specific molecular reference). DNA sequence data is therefore often only as good as the reference database used to interpret it, and those databases in turn are only as good as the taxonomic expertise behind deposited reference sequences and associated meta-data [ 23 , 24 ]. Unfortunately, such expertise has been in decline for decades [ 25 , 26 ].…”

“…While the growth of dedicated bar-coding databases maintaining stringent quality control standards (e.g. the Barcode of Life Database, http://www.boldsystems.org/ ) has proceeded rapidly, such repositories still barely scratch the surface of estimated extant eukaryotic diversity, particularly in marine systems [ 39 ], and are heavily biased toward taxa and regions that have been well sampled and receive generous support for molecular data collection [ 23 , 40 , 41 ]. With a few exceptions (e.g [ 42 ].…”