Figure 1.
Map of the Mediterranean indicating the localisation of the sampling sites. The relative geographic coordinates are reported in Table 1. The populations are labelled as reported in Table 1.
Table 1.
Data collection.
Figure 2.
COI dataset: Bayesian cluster distribution.
Frequency distribution of the four groups of haplotypes P1, P2, P3, and P4, as evidenced by Bayesian analysis over the Mediterranean map. Due to the high number of populations, the size of the pie charts in the Sardinian-Corsican region was reduced, and the relative populations were merged in three distinct groups as reported below. North-western Sardinia group includes Baia di Porto Conte-BPC, Torre del Porticciolo-POR, Lazzaretto-LAZ, Ospedale Marino-OSM; central-eastern Sardinia group includes Molara-MOL, Capo Ceraso-CCE, Le Saline-SAL, Monte Petrosu-MPE, Porto Ottiolu-OTT; central-western Sardinia group includes Oristano-ORI, Marceddì-MAR, Isola di Mal di Ventre-IMV.
Figure 3.
COI dataset: network analysis.
Median-joining network (on the left) with haplotypes grouped according to the results of the Bayesian assignment. Small red plots on the nodes, labelled as “mv”, show median vectors representing hypothetic connecting sequences, calculated with a maximum parsimony method. The long branches leading to isolated haplotypes were shortened and indicated with “\\”. The distribution of haplogroups within populations (on the right) are displayed in the histogram. The x axis reports populations and the y axis the absolute frequency of distribution. The populations are labelled as reported in Table 1. The number of mutations on the network branches are reported in the Figure S1.
Table 2.
COI dataset: AMOVA.
Figure 4.
COI dataset: mismatch analysis.
Graphs of the mismatch distributions of (A) the entire sample, (B) Sardinia, Corsica, Elba Island, and Sicily, (C) the Venetian Lagoon, and (D) the Aegean Sea and Tunisian coasts. The x axis reports the observed distribution of pairwise nucleotide differences, and the y axis reports the frequencies. N, sample sizes; SSD, sum of squared deviations; D, Tajima’s D value; Fs, Fu’s F value. The significant values are given in bold.
Figure 5.
COI dataset: Bayesian skyline plots.
Bayesian skyline plots depicting the demographic history of Pinna nobilis. The effective population size (y-axis) is shown as a function of time (x-axis), with the units expressed as KYR (1,000 years). (A) entire dataset, (B) the regional group encompassing the Sardinian-Corsican region, Elba Island, and Sicily, (C) the Venetian lagoon and (D) the Aegean Sea and Tunisian coasts. The black lines denote the median population estimates, and the grey lines denote the 95% high posterior density (HPD) confidence limits.
Figure 6.
COI-16S dataset: Bayesian cluster distribution.
Frequency distribution of the four groups of haplotypes N1, N2, N3 and N4, as evidenced by Bayesian analysis over the Mediterranean map. Due to the high number of populations, the size of the pie charts in the Sardinian-Corsican region was reduced, and the relative populations were merged in three distinct groups as reported below. North-western Sardinia group includes Baia di Porto Conte-BPC, Torre del Porticciolo-POR, Lazzaretto-LAZ, Ospedale Marino-OSM; central-eastern Sardinia group includes Molara-MOL, Capo Ceraso-CCE, Le Saline-SAL, Monte Petrosu-MPE, Porto Ottiolu-OTT; central-western Sardinia group includes Oristano-ORI, Marceddì-MAR, Isola di Mal di Ventre-IMV.
Figure 7.
COI-16S dataset: network analysis.
Median-joining network (on the left) with haplotypes grouped according to the results of the Bayesian assignment. Small red plots on the nodes, labelled as “mv”, show median vectors, representing hypothetic connecting sequences, calculated with a maximum parsimony method. The long branches leading to isolated haplotypes were shortened and indicated with “\\”.The x axis reports populations and the y axis the absolute frequency of distribution. The populations are labelled as reported in Table 1. The number of mutations on the network branches are reported in the Figure S2.
Table 3.
COI-16S dataset: AMOVA.
Figure 8.
COI-16S dataset: mismatch analysis.
Graphs of the mismatch distributions of (A) the entire sample, (B) Sardinia, Corsica, Elba Island, and Sicily, (C) the Venetian Lagoon and (D) the Aegean Sea. The x axis reports the observed distribution of pairwise nucleotide differences, and the y axis reports the frequencies. N, sample sizes; SSD, sum of squared deviations; D, Tajima’s D value; Fs, Fu’s F value. The significant values are given in bold.