In order to verify the accuracy of the partial coi sequences for the identification of Biomphalaria specimens using DNA barcoding methodology, BOLD Identification Criteria (thresh-ID) and Best Close Match (BCM) analyses were carried out (Meier et al., 2006 (link)) using the ape v. 5.5 (Paradis and Schliep, 2019 (link)) and spider v. 1.5.0 (Brown et al., 2012 (link)) packages of the R software v. 4.0.5 (R Foundation for Statistical Computing, 2021 ).
In order to define the barcode gap, the Kimura two-parameter (K2P) model (Tamura et al., 2004 (link)) was used to calculate the intraspecific and interspecific distances (Meyer and Paulay, 2005 (link)) between the species using the spider v. 1.5.0 (Brown et al., 2012 (link)) package in the R software v. 4.0.5 (R Foundation for Statistical Computing, 2021 ).
Additionally, the sequences were clustered/grouped into Operational Taxonomic Units (OTUs), grouping organisms by their similarity, in this case in relation to a genetic marker (Blaxter et al., 2005 (link)), using the criteria of four algorithms; Generalized Mixed Yule-Coalescent (GMYC) (Reid and Carstens, 2012 (link); Fujisawa and Barraclough, 2013 (link)), Poisson Tree Processes (bPTP) (Zhang et al., 2013 (link)), Automatic Barcode Gap Discovery (ABGD) (Puillandre et al., 2012 (link)) and Assemble Species by Automatic Partitioning (ASAP) (Puillandre et al., 2021 (link)).
de Araújo A.D., Carvalho O.D., Gava S.G, & Caldeira R.L. (2023). DNA barcoding as a valuable tool for delimiting mollusk species of the genus Biomphalaria Preston, 1910 (Gastropoda: Planorbidae). Frontiers in Cellular and Infection Microbiology, 13, 1167787.
+ Open protocol