Species Delimitation Analyses
The genetic distance between individuals was calculated using two
matrices: one containing the COI barcode sequences and the other with
the SNPs obtained in the GBS analysis. They were estimated in Mega X
(Kumar et al., 2018) using the substitution model Kimura-2-Parameters
(K2P; Kimura, 1980) with the pairwise deletion option, which removes
sites containing missing data or alignment gaps from the analysis as the
need arises. We compared the results obtained with the different
molecular markers to evaluate the efficiency of SNPs markers with the
commonly used markers in molecular taxonomy studies (COI barcode
region). Three methods for molecular species delimitation were employed
to test the sensitivity between them, checking if the proposed taxonomic
delimitation would be found. The Automatic Barcode Gap Discovery (ABGD)
(Puillandre et al., 2012), based on the COI alignment, was applied using
the mean genetic distances calculated under the K2P substitution model,
with default options, through the online graphic version
(https://bioinfo.mnhn.fr/abi/public/abgd/abgdweb.html). The PTP and bPTP
methods (Zhang et al., 2013) were carried out using the tree
reconstructed with the COI sequences and executed for
105 generations with a thinning of 100 and “burn-in”
of 0.1. These analyses were performed using the online server of
Exelixis Labs
(http://species.h-its.org/).