BEAST nex files

The ZIP folder contains all nex files used for the single gene BEAST analyses according to dataset numbers in the publicatio

Distribution and molecular phylogeny of <i>Tylomelania</i>.

<p>A. Distribution area of <i>Tylomelania</i> (red) and its sister taxon <i>Pseudopotamis</i> (blue circle) on Sulawesi and the Torres Strait Islands, respectively. B. Map of Sulawesi with sample sites of <i>Tylomelania</i>. Black dot – sample sequenced for this study; white dot – museum sample. C. BI phylogram and shells of selected species of <i>Tylomelania</i>. Phylogeny based on 1,528 bp of mtDNA (COI and 16S). Numbers on branches show node support; BI posterior probability (top), ML (centre), and MP (bottom) bootstrap values. Colour code as in panel A.</p

Haplotype networks (groups) of <i>Tylomelania</i> with lineage assignment and intra-network genetic distance range (p-distance) for COI.

<p>Haplotype networks (groups) of <i>Tylomelania</i> with lineage assignment and intra-network genetic distance range (p-distance) for COI.</p

Estimated maximum mean node ages from the strict clock analysis for COI (see Figure 2).

<p>Estimated maximum mean node ages from the strict clock analysis for COI (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098917#pone-0098917-g002" target="_blank">Figure 2</a>).</p

BEAST tree files

BEAST MCC tree files of analyses [A]-[D]

Distribution of the major lineages and haplotype groups of <i>Tylomelania</i> on Sulawesi.

<p>A. Sulawesi map with assignment of sampling sites (small red dots) to haplotype groups (pie charts, haplotype group specific colour code as in panel B). Haplotype group diversity for sites in close geographic vicinity has been subsumed within a single pie chart. Numbers within pie charts are sequenced individuals. Bluish areas indicate the position of contact zones for macaque species on Sulawesi (from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098917#pone.0098917-Evans1" target="_blank">[31]</a>). Red frames show the position of the two contact zones of <i>Tylomelania</i> clades. B. BI phylogram based on tree shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098917#pone-0098917-g001" target="_blank">Figure 1</a>, all clades with a BPP of >0.90 are shown as cartoons. Colours correspond to those used in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098917#pone-0098917-g002" target="_blank">Figure 2</a> and the circles with roman numbers indicate haplotype groups within each lineage (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098917#pone.0098917.s001" target="_blank">Figure S1</a>).</p

Additional file 1: Table S1. of Origin and diversification of Lake Ohrid’s endemic acroloxid limpets: the role of geography and ecology

Specimens examined including locality information and GenBank accession numbers. (PDF 166 kb

Calibrated phylogeny of <i>Tylomelania</i> and the tectonic history of Sulawesi.

<p>A. Bayesian (BEAST) chronogram of <i>Tylomelania</i> based on 660 bp of mtDNA (COI) using a substitution rate of 1.76%/My (see Material and methods). The major lineages of <i>Tylomelania</i> are colour-coded. The pink horizontal bars link the events associated with nodes 1 (TMRCA of <i>Tylomelania</i> and <i>Pseudopotamis</i>) and 2 (first speciation event within <i>Tylomelania</i>) with the geological timescale and paleogeography of Sulawesi (panel C). B. Map of Sulawesi with major tectonic subdivisions (compare panel C) and the distribution of the major lineages of <i>Tylomelania</i> (colour-coding of areas corresponds to major lineages in panel A). C. Schematic summary of the geographic connections and the timing of separation or collision of the different parts of Sulawesi (see map in panel B). Blue tinting indicates presumably submerged areas, see legend for details. Modified from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098917#pone.0098917-Stelbrink1" target="_blank">[16]</a>. D,E. Paleogeographic reconstructions of the Asia-Australia collision zone 5 Mya and 20 Mya. Modified from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098917#pone.0098917-Hall3" target="_blank">[56]</a>.</p

Additional file 2: Figure S1. of Origin and diversification of Lake Ohrid’s endemic acroloxid limpets: the role of geography and ecology

MCC trees for the four BEAST analyses performed (outgroup removed). See Methods and Results for details. Figure S2 MCC trees for the four *BEAST analyses performed (including outgroups). See Methods and Results for details. Figure S3. Combined mitochondrial parsimony network for the two markers 16S rRNA and COI. Position of haplotypes and haplotype groups approximately refer to sampling sites across the lake (compare Fig. 3; yellow: Acroloxus macedonicus; green: non-ribbed A. macedonicus; orange: A. improvisus). Regular numbers refer to DNA voucher numbers; COI haplotype numbers are marked with a hashtag (see Additional file 1: Table S1). Figure S4. The shell of the regular (ribbed) Acroloxus macedonicus (SEM data). A–G, J–K — protoconch (C, F–G — initial plate; E, J–K — sculpture). H–I, L–M — teleoconch (L–M — fragments of ribbed surface). A–B, E, G–H — left view; C–D, I — top view; F — posterior-right view. Scale bars: A– D, F–G, J, L–M = 0.1 mm, E = 0.05 mm, H–I = 1 mm, K = 10 μm. Figure S5. The shell of non-ribbed specimens of Acroloxus macedonicus (SEM data). 1 — first specimen, 2 — second spm. 1A–C, 1E, 2A–C — teleoconch (1E — fragment of smooth surface). 1D, 2D — protoconch. 1A, 2A — left view; 1B, 2B — rear view; 1C–D, 2C–D — top view. Scale bars: 1A– D, 2A–D = 1 mm, 1E = 0.1 mm. Figure S6. The shell of Acroloxus improvisus (SEM data). A–F, I–L — protoconch (E, J, K–L — sculpture; F, I — initial plate). G–H, M — teleoconch (M — fragment of smooth surface). A — posterior-left view; B, F–G — left view; C — right view; D, H — top view; I — right and top view. Scale bars: A–F, I–K, M = 0.1 mm, G–H = 1 mm, L = 10 μm. (PDF 39654 kb

Supplementary data

Supplementary data includes the RAxML phylogram for the concatenated dataset (16S rRNA, 28S rRNA, COI and H3), the BEAST input xml file and the BEAST MCC tree file. For details see the electronic supplementary material of the article