Pairwise TrN distances for aligned COI haplotypes were calculated in MEGA 6.06 (Tamura et al., 2013) and analyzed by Automated Barcode Gap Discovery (ABGD; Puillandre et al., 2012) for each genus separately, using a range of priors (pmin = 0.004; pmax = 0.08), with 10 recursive steps and 20 bins. The pmax value was based on prior studies in sacoglossans in which divergent mtDNA clades were supported as CS if the minimum TrN-corrected COI distance to the sister group was 6–8% (Krug et al., 2013, 2015, 2016). A value of X = 1.5 was used as the sensitivity for gap detection, with X the minimum relative gap width required to delimit a CS; groups of sequences that differed by > 1.5 times the maximum intraspecific divergence were separated into CS. Initial ABGD analyses recovered five morphologically distinct Lobiger CS and five divergent Oxynoe CS in the Indo-West Pacific (IWP); remaining samples belonged to the O. antillarum-viridis complex, including putative O. antillarum (n = 44), O. azuropunctata-like Caribbean specimens (n = 8), IWP O. viridis (n = 30), and eastern Pacific samples (n = 10) (see Section 3). Subsequent delimitation focused on generating alternative hypotheses for complex members, as ABGD grouped IWP “O. viridis” with eastern Pacific samples but split O. azuropunctata-like samples into three CS.
Do you have any questions about this protocol?
Post your question to gather feedback from the community. We will also invite the authors of this article to respond.
Tips for asking effective questions
+ Description
Write a detailed description. Include all information that will help others answer your question including experimental processes, conditions, and relevant images.