Phylogeography on the rocks: The contribution of current and historical factors in shaping the genetic structure of <i>Chthamalus montagui</i> (Crustacea, Cirripedia) - Fig 2

<p>A. Median-joining network of <i>COI</i> haplotypes obtained in <i>Chthamalus montagui</i> from the 13 sampled locations. Each line in the network represents one mutational step; each small bar on the branches represents an additional mutational step. The area of each circle is proportional to the number of individuals showing that haplotype. B. Bayesian assignment analysis of <i>COI</i> sequences. Each vertical bar represents an individual and its associated probability of belonging to one of the five genetic clusters detected. Asterisks on the bar graph indicate individuals with uncertain assignment (<i>P</i> < 0.05). Pie charts indicate the percentage of genetic clusters contributing to each location. Pie charts were constructed with individual net assignments and after removing individuals with uncertain assignment.</p

Frequency distribution of the number of pairwise nucleotide differences (mismatch) between <i>COI</i> haplotypes in the three populations of <i>Chthamalus montagui</i>.

<p>The solid line is the theoretical distribution under the model of demographic expansion.</p

Location of <i>Chthamalus montagui</i> sampling sites.

<p>Location abbreviations are as reported in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178287#pone.0178287.t001" target="_blank">Table 1</a>.</p

<i>Chthamalus montagui</i>.

<p>Sum of squared deviations (SSD) between the expected and observed mismatch distributions of pairwise differences, Harpending’s [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178287#pone.0178287.ref038" target="_blank">38</a>] raggedness index (<i>r</i>) of the observed mismatch distribution and Fu’s [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178287#pone.0178287.ref039" target="_blank">39</a>] <i>F</i>_S neutrality test on <i>COI</i> sequences pooled according to the three biogeographical areas; <i>P</i> values were obtained by coalescent simulations with 10000 replicates.</p

Bayesian skyline plots of effective population size through time in <i>Chthamalus montagui</i> from the three biogeographical areas, based on the 537bp sequences of <i>COI</i> and a nucleotide substitution rate of 3.1%/my.

<p>The bold black curve is the median of the parameter <i>N</i>_e<i>T</i>, which is proportional to the effective population size; the dotted lines delimit the 95% highest posterior density. For comparison, all <i>x</i>-axes have the same scale. The plots are truncated to the median estimate of each area’s TMRCA.</p

Genetic diversity of the <i>Tetraclita</i> species in the West Indian Ocean based on the mitochondrial COI gene.

<p>Number of sequences (N), number of haplotypes (Na), haplotype diversity (h), nucleotide diversity (π), Tajima’s <i>D</i>, Fu’s <i>F</i>_S, are shown. p values:</p>*<p> = p<0.05,</p>**<p> = p<0.01,</p>***<p> = p<0.001.</p

Distribution pattern of <i>Tetraclita</i> spp. in relation to physical factors in the West Indian Ocean.

<p>A. Sampling localities and biogeography of <i>Tetraclita</i> spp. (red – <i>T. ehsani</i>, blue – <i>T. rufotincta</i>, pink – <i>T. achituvi</i>, yellow – <i>T</i>. sp. nov., purple – <i>T. reni</i>, green – <i>T. serrata</i>) in the present study. Closed circles indicate samples with DNA sequences for molecular analysis and open circles indicate museum samples which were used for morphological identifications. NEMC – North East Monsoon Current, IMC – Indian Monsoon Current, ECC – Equatorial Counter Current, EACC – East Africa Coastal Current, SEC – South Equatorial Current, SC – Somali Current, SCC – Somali Counter Current, MC - Mozambique Current, AC –Agulhas Current, EMC – East Madagascar Current. Sea surface temperature map in 2009 of West Indian Ocean produced with the Giovanni online data system (developed and maintained by the NASA GES DISC) showing (B) January-February, (C) March-April, (D) July-August, (E) October-November. (F) Annual average salinity map in 2009 produced with the Marine Ocean Atlas Figures 2009 (NOAA) showing the variation in salinity profiles in the West Indian Ocean.</p

Pairwise genetic divergence among the <i>Tetraclita</i> species in the West Indian Ocean and the two outgroups based on H3.

<p>The intraspecific divergence is shown on the diagonal. Tach: <i>Tetraclita achituvi</i>; Truf: <i>Tetraclita rufotincta</i>; Tren: <i>Tetraclita reni</i>; Tsp: <i>Tetraclita</i> sp. nov.; Tehs: <i>Tetraclita ehsani</i>; Tser1 and 2: <i>Tetraclita serrata</i> clade 1 and 2; Tkuo: <i>Tetraclita kuroshioensis</i>; and Tros: <i>Tesseropora rosea</i>. The intraspecific divergence for Tkuo and Tros is not available as only one specimen was analyzed for each of them.</p

Sampling locations, abbreviations and numbers of samples sequenced and morphologically examined for each location.

<p>Abbreviations designate those locations with molecular data. Site names with barnacles under morphological examination only are not abbreviated.</p

Genetic diversity of the <i>Tetraclita</i> species in the West Indian Ocean based on the mitochondrial 12S gene.

<p>Number of sequences (N), number of haplotypes (Na), haplotype diversity (h), nucleotide diversity (π), Tajima’s <i>D</i>, Fu’s <i>F</i>_S, are shown. p values:</p>*<p> = p<0.05,</p>**<p> = p<0.01,</p>***<p> = p<0.001.</p