Temim Deli. Impacts of Early Pleistocene glacial vicariance among refugial lineages and Mid-Late Pleistocene interglacial dispersal and expansion on forging population genetic structure of the giant clam Tridacna squamosa (Bivalvia: Cardiidae: Tridacninae) across the Red Sea and Indo-West Pacific Oceans[J]. Acta Oceanologica Sinica.
Citation:
Temim Deli. Impacts of Early Pleistocene glacial vicariance among refugial lineages and Mid-Late Pleistocene interglacial dispersal and expansion on forging population genetic structure of the giant clam Tridacna squamosa (Bivalvia: Cardiidae: Tridacninae) across the Red Sea and Indo-West Pacific Oceans[J]. Acta Oceanologica Sinica.
Temim Deli. Impacts of Early Pleistocene glacial vicariance among refugial lineages and Mid-Late Pleistocene interglacial dispersal and expansion on forging population genetic structure of the giant clam Tridacna squamosa (Bivalvia: Cardiidae: Tridacninae) across the Red Sea and Indo-West Pacific Oceans[J]. Acta Oceanologica Sinica.
Citation:
Temim Deli. Impacts of Early Pleistocene glacial vicariance among refugial lineages and Mid-Late Pleistocene interglacial dispersal and expansion on forging population genetic structure of the giant clam Tridacna squamosa (Bivalvia: Cardiidae: Tridacninae) across the Red Sea and Indo-West Pacific Oceans[J]. Acta Oceanologica Sinica.
Impacts of Early Pleistocene glacial vicariance among refugial lineages and Mid-Late Pleistocene interglacial dispersal and expansion on forging population genetic structure of the giant clam Tridacna squamosa (Bivalvia: Cardiidae: Tridacninae) across the Red Sea and Indo-West Pacific Oceans
This study aims at identifying the microevolutionary processes responsible for the onset of the remarkable phylogeographic structure already recorded for the endangered giant clam Tridacna squamosa across its distribution range. For this purpose, the evolutionary, biogeographic and demographic histories of the species were comprehensively reconstructed in a mitochondrial dataset comprising nearly the whole available published cytochrome c oxidase 1 gene sequences of T. squamosa. Relatively higher level of genetic diversification was unveiled within T. squamosa, in comparison to earlier macro-geographic investigations, whereby five mitochondrial clusters were delineated. The resulting divergent gene pools in the Red Sea, Western Indian Ocean, Indo-Malay Archipelago and Western Pacific were found to be driven by Early Pleistocene glacial vicariance events among refugial lineages. Accentuated genetic diversification of the species across the Indo-Malay Archipelago was successively triggered by historical dispersal event during the Mid-Pleistocene MIS19c interglacial. This latter historical event might have also enabled genetically distinct giant clams from the Indo-Malay Archipelago to subsequently colonize the Western Pacific, accounting for the genetic diversity hotspot detected within this region (comprising three divergent mitochondrial clusters). Late Pleistocene demographic expansion of T. squamosa, during the Last Interglacial period, could have contributed to forging spatial distribution of the so far delineated genetic entities across the Indo-Western Pacific. Overall, being resilient to major climate shifts during the Pleistocene through adaptation and consequent diversification, T. squamosa could be used as a model species to track the impact of climate change on genetic variability and structure of marine species. In particular, the new information, provided in this investigation, may help with understanding and/or predicting the consequences of ongoing global warming on genetic polymorphism of endangered coral reef species among which Tridacna sp. are listed as ecologically important.
Figure 1. Sampling locations of the examined Cox1 sequences of Tridacna squamosa (retrieved from previous phylogeographic investigations) along the Red Sea and Indo-West Pacific. Sampling sites are denoted with symbols specific for each population genetic study (indicated in the top right of the map). IMA: Indo-Malay Archipelago. Further details on the geographic origins and names of the giant clam sampling sites (including the exact number of sampling sites across microgeograhic spectra, i.e., in the three studies of Todd et al. (2012), Liu et al. (2020) and Lee et al. (2022)), as well as information on the number of captured specimens at each sampling site, are included in the thirteen mentioned investigations. Construction of the base map was carried out by the software DIVA-GIS 7.5.0 (http://www.diva-gis.org).
Figure 2. Identification of genetic clusters within Tridacna squamosa, based on Cox1 gene sequences, using the Bayesian genetic assignment method implemented in BAPS version 6.0. RS: Red Sea, WIO: Western Indian Ocean, IMA: Indo-Malay Archipelago, WP: Western Pacific.
Figure 3. Calibrated Bayesian phylogeny (as implemented in BEAST), exhibiting diversification patterns of the identified BAPS clusters within Tridacna squamosa through time. The retrieved divergence times between clusters as well as diversification time of each clade (mean values in black above the nodes) are expressed in million years before present. Values in grey (below the nodes) correspond to the posterior probabilities (Bayesian inference).
Figure 4. Historical biogeography of Tridacna squamosa, highlighting ancestral areas reconstruction of Cox1 BAPS clusters. Circles on each main node show the likelihood of occurrence of each ancestral haplotype at an inferred ancestral biogeographic region. Graphical results of ancestral distributions at each main node of the phylogeny were obtained by the S-DIVA (Statistical Dispersal-Vicariance Analysis) method, as implemented in RASP version 3.2. Biogeographic regions are denoted with alphabetic letters. Purple arrows indicate vicariance events at the corresponding nodes, while brown arrows highlight possible dispersal events.
Figure 5. Alternative tested evolutionary scenarios by means of the approximate Bayesian computation (ABC) method, implemented in the software DIYABC, to explain the origin of genetic divergence between BAPS clusters 1 and 2 of Tridacna squamosa, based on mtDNA data. (A) Three tested scenarios corresponding to two evolutionary processes: allopatric divergence through vicariance event (scenario 1) and historical colonization followed by founder effect (scenarios 2 and 3). NA: effective population size of the common ancestral population; N1 and N2 represent the effective population sizes of both BAPS clusters 1 and 2 respectively; t2: the historical time at which both BAPS clusters 1 and 2 are postulated to diverge. (B) Logistic regression plot for the simulated scenarios. The x-axis represents the number of simulated datasets used to calculate the posterior probability of each scenario, as expressed in the y-axis.
Figure 6. Bayesian skyline plots (BSP) for specimens of Tridacna squamosa from the Indo-Western Pacific (characterizing two kinds of datasets: BAPS cluster 1 (A) and the combined data including BAPS clusters 1 and 2 (B)), showing changes in effective population size (Ne multiplied with generation time) over time (measured in years before present). The thick solid line depicts the median estimate, and the margins of the blue area represent the highest 95 % posterior density intervals. The enclosed grey-shaded box corresponds to the Last Interglacial (LIG) period (130,000-115,000 years ago; Wilson et al., 1998).
Figure 7. A detailed and illustrative schematic diagram exhibiting the evolutionary history scenario of the giant clam Tridacna squamosa across its distribution range. RS: Red Sea, WIO: Western Indian Ocean, IMA: Indo-Malay Archipelago, WP: Western Pacific.
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