Shells of <i>Rumina</i> spp.

<p>A) <i>R. saharica,</i> B) <i>R. decollata,</i> C) <i>R. paivae,</i> D) dark phenotype of <i>R. decollata</i> (MOTU A), and E) light phenotype of <i>R. decollata</i> (MOTU Eb). Scale = 1 cm.</p

Frequency distributions of pairwise K2P distances for COI.

<p>Grey: intragroup divergences; Black: divergences between the focal group and all other groups together. Δ corresponds to the gap range. a) <i>R. decollata</i> vs <i>R. saharica,</i> b) to o) respectively MOTU A, B, C, D, Da, Db, E, Ea, Eb, Ea3-4, Eb1-4, Eb5-8, F, F+Ea1-2, vs the remaining MOTUs, p) <i>R. saharica</i> vs <i>R. decollata</i>, q) MOTU Sa vs the remaining MOTUs and r) MOTU Sb vs the remaining MOTUs.</p

Number of putative species delimited by the different species delimitation methods applied to the COI dataset: overall barcoding gap analysis (OGA), pairwise gap analysis (PGA), 3% threshold, stylommatophoran 4% threshold, 10× rule, 3.2–4.1× rule, ABGD method, SDP (<i>Rosenberg’s P_AB</i> and <i>Rodrigo’s P(RD)</i>), GSI with both BI and ML trees and GMYC method.

<p>+: MOTU supported as a putative species;</p><p>−: no support as a putative species; empty cases: group is not suggested or cannot be analyzed by the method; parentheses: MOTU responsible for the absence of barcoding gap;</p>*<p>: additional MOTU defined by the COI data.</p

Phylogenetic trees of <i>Rumina</i> based on concatenated ITS1 and ITS2 sequences.

<p>ML bootstrap/BI posterior probabilities/NJ bootstrap/MP bootstrap values are indicated near the nodes. Posterior probabilities of the species tree are shown under the line. Meaningful support (≥70% for bootstrapping <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060736#pone.0060736-Barrett1" target="_blank">[48]</a> or p≥0.95 for posterior probabilities <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060736#pone.0060736-Hebert2" target="_blank">[49]</a>) is shown on dark within the circle (upper right pie: ML; lower right pie: BI; lower left pie NJ; upper left pie: MP); white circles: no support; +: meaningful support for the species tree; *: <i>R. paivae</i> specimens; °: haplotypes that are placed in other groups than with mtDNA; <u>underlined</u>: copies from heterozygous specimens are.</p

Summary statistics reported by the Species Delimitation plugin for COI in each putative species A) BI tree (Clade support is PP) and B) ML (Clade support is BS).

<p><i>Intra / Inter</i> – ratio of <i>Intra</i> (genetic differentiation among members of a putative species) to <i>Inter</i> (genetic differentiation between the members of a putative species and the members of the closest putative species), <i>P ID(Strict)</i> - mean (95% confidence interval) probability of correctly identifying an unknown member of a given clade using the criterion that it must fall within, but not sister to, the species clade in a tree, <i>Rosenberg’s P_AB</i> - probability of reciprocal monophyly under a random coalescent model and <i>Rodrigo’s P(RD)</i> – probability that a clade has the observed degree of distinctiveness due to random coalescent processes.</p>*<p>Significant values (values remained significant after Bonferroni correction).</p

Bootstrap support for NJ, MP and ML, and posterior probabilities for BI of the different MOTUs obtained with individual gene fragments and concatenated data (cmtDNA and cITS).

<p>ns - not-supported (i.e. if PP<0.95 or BS<70).</p><p><i>poly</i> - polyphyletic group.</p><p><i>para</i> - paraphyletic group.</p

Phylogenetic trees of <i>Rumina</i> based on concatenated mtDNA sequences (12S, 16S, COI, CytB).

<p>A) BI tree with ML bootstrap values (left), BI posterior probabilities (right) and posterior probabilities of the species tree (under the line). B) NJ tree with NJ bootstrap values (left) and MP bootstrap values (right). Meaningful support (≥70% for bootstrapping <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060736#pone.0060736-Barrett1" target="_blank">[48]</a> or p≥0.95 for posterior probabilities <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060736#pone.0060736-Hebert2" target="_blank">[49]</a>); circles with left half black: meaningful support only for ML or NJ; circles with right half black: meaningful support only for BI or MP; white circles: no support; +: meaningful support for the species tree; *: <i>R. paivae</i> specimens. Haplotypes are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060736#pone.0060736.s003" target="_blank">Table S1</a>.</p

Positions of indels that are specific to the MOTUs in the cmtDNA (A) and cITS (B) data.

<p>Positions of indels that are specific to the MOTUs in the cmtDNA (A) and cITS (B) data.</p

Sequence information for the different gene fragments without the outgroup (values with the outgroup in parentheses).

<p>Fragment length in bp, number of variable sites (PS), number of parsimony informative sites (PI), and number of gap positions or missing data (G/M; see text). On the right side: models selected by the Akaike Information Criterion <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060736#pone.0060736-Akaike1" target="_blank">[44]</a> in the programs jModelTest v. 0.1.1 and MrModeltest v. 2.2 for Bayesian analysis, and alpha value for the substitution models.</p

Illustrative selection of p- and K2P distance values for <i>Rumina</i> sp. and other Stylommatophora.

<p>Interspecific (A) and intraspecific (B) sequence divergences.</p