Figure Legends
FIGURE 1(a) Primer binding position, taxa amplified, and PCR reaction conditions for each primer set relative to published Mnemiopsis leidyi sequence, including the ‘Folmer’ region (b) primer sequences and position used to amplify and sequence all groups of ctenophores including LCO1490/HCO2198 (Folmer et al. 1994) and meta-COI-F2/meta-COI-R2 (Pett et al. 2011). Differences fromM. leidyi are indicated in bold and colored according to base. Primers marked with * are more universal.
FIGURE 2 Bayesian unrooted phylogeny for 765 bp COI fragment for all ctenophores sequenced with successful primer pairs indicated by colored triangles. Closed triangles indicate forward and open indicate reverse direction primers. Multiple triangles indicate multiple successful primer pairs. Branches colored by group including; Lobates (pink), Beroids (blue), and Platyctenes (green).
FIGURE 3(a) Transitions and transversions versus GTR sequence divergence and (b) Pairwise percent sequence distance (GTR) within and amongst all ctenophore species sequenced for the COI fragment.
FIGURE 4 Bayesian and maximum likelihood estimated phylogenies for fragments of (a) 18S (1780 bp, TrN+i+Γ) and (b) COI (765 bp, GTR+i+Γ) limited to Lobate ctenophores. Bolinopsis species are bolded, showing the scattered distribution with 18S . Colored backgrounds indicate the species of Lampocteis which are identical with 18S but form distinct clades with COI . Both likelihood and Bayesian support values are indicated by triangles on the nodes, with unlabeled nodes having low support. Locations (Table S1) are indicated in the blue labels including: (AU) Australia, (BA) Bahamas, (CA) California, (FL) Florida, (GC) Gulf of California, (HI) Hawaii, US, (JP) Japan, (NO) Norway, (TA) Tahiti, (WA) Washington, (WH) Woods Hole
FIGURE 5 Images and known depths in meters of specimens of (a)Lampocteis cruentiventer (~250–1500 m) (b)Lampocteis sp. ‘V’ (~1500–3000 m), (c)Lampocteis sp. ‘A’, (~500–2800 m), (d)Bathocyroe aff. fosteri ‘A’ (560–3572 m, small red gut), (e) Bathocyroe aff. fosteri ‘B’ (> 3000 m, peach gut), (f) Bathocyroe aff. longigula (1900–2858 m, big gut)
FIGURE 6 Presence and absence matrix of assigned ctenophore species for a 311 bp fragment of COI from 100 meter-depth net tows collected in 2012 along a transect that spanned from Central California, USA, to Southern Baja California, Mexico from Pitz et al. (2020).
SUPPLEMENTARY FIGURE S1 Transitions and transversions versus GTR sequence divergence for Beroe cucumis (MK361035), Beroe forskalii (MG655623), Coeloplana loyai (LN898113),Coeloplana yulianicorum (LN898115), Hormiphora californensis (MN544300), and Mnemiopsis leidyi (JF760210) forCOI (1311 bp), COII (536 bp), COIII (601), CytB (570 bp), ND4 (429 bp), and ND5 (506 bp)