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

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

Geographic distribution of <i>Rumina</i> haplotypes.

<p>Geographic distribution of <i>Rumina</i> haplotypes.</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