2.4. Species delimitation I: ABGD analysis of pairwise COI distances

JB John S. Berriman
RE Ryan A. Ellingson
JA Jaymes D. Awbrey
DR Diane M. Rico
ÁV Ángel A. Valdés
NW Nerida G. Wilson
AA Andres Aguilar
DH David G. Herbert
YH Yayoi M. Hirano
CT Cynthia D. Trowbridge
PK Patrick J. Krug
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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.

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