Connectivity and evolution of giant clams (Tridacnidae): a molecular genetic approach

Abstract

The Indo-West Pacific (IWP), specifically the Indo-Malay Archipelago (IMA), is known to be one of the regions exhibiting the highest marine species diversity in the world. Many hypotheses try to explain the origin of this biodiversity, mainly including the centre-of-origin, region-of-overlap, and centre-of-accumulation concepts. The IMA has a complicated geological history. Sinking sea levels during glacial periods exposed the Sunda and Sahul shelves. Therefore, the IMA provides an excellent study system for detecting the contribution of historical and ongoing processes to genetic diversity and connectivity. In addition, the Red Sea (RS) and Western Indian Ocean (WIO) are also important evolutionary centres, with many endemic species. The giant clams Tridacna crocea, T. maxima, and T. squamosa are widely distributed throughout the IWP. Their high commercial value as fishery resource and marine ornamental led to their large scale exploitation. Meanwhile, tridacnid species are listed in Appendix II of the Convention on International Trade in Endangered Species of Wild Fauna and Flora and need urgently measures for conservation. Knowledge on genetic population structure and connectivity are important baseline data for the protection of these species, especially for the design of Marine Protected Area networks. To test if concordant barriers exist that prevent gene flow among populations and to relate this to oceanography and geological history of the IWP, the genetic population structure of the three giant clam species ranging from the RS and WIO across the Eastern Indian Ocean (EIO) and IMA to the Western Pacific (WP) and the Central Pacific (CP) were compared by using the mitochondrial cytochrome c oxidase subunit I gene (COI) as a molecular marker. The three species showed restricted gene flow and highly significant genetic structures in the area studied. The Fst-values (P < 0.001) are 0.46, 0.81, and 0.68, for T. crocea (EIO to WP), T. maxima (WIO to CP), and T. squamosa (WIO to WP), respectively. The populations could be divided into three to six groups in the different species from West to East: (1) WIO (T. maxima and T. squamosa), (2) RS (T. maxima and T. squamosa), (3) EIO (and Java Sea in T. maxima), (4) central IMA, (5) WP, and (6) CP (T. maxima). The populations in the central IMA showed panmixing. To detect the reliability of the analysis based on the mitochondrial marker, ten microsatellites were selected to study the genetic population structure of T. crocea in the IMA and the results were compared with those revealed by mtDNA. Due to the symbiotic relationship between giant clams and Symbiodinium spp. (zooxanthellae), it is difficult to isolate microsatellites. By applying a recently developed method, nine novel microsatellite markers were isolated for T. crocea and the giant clam specificity was confirmed by further test in PCRs with DNA extracts from Symbiodinium. These markers were highly polymorphic. Therefore, these microsatellites potentially provide useful nuclear markers for population genetic studies on giant clams. The genetic population structure revealed by mtDNA and nDNA (nuclear DNA) markers was congruent, with only minor difference. The correlation of genetic divergence revealed by the two marker systems was positive. Three common groups were divided as follows: (1) EIO, (2) central IMA, and (3) WP. Populations in the central IMA also showed panmixing, being well connected by currents. However, the structure revealed by microsatellite was not as strong as in the mtDNA analysis, and the genetic diversity revealed by the two genetic marker systems was different in certain populations. These minor differences might be caused by the intrinsic characteristics of mtDNA and nDNA, such as the different effective population size and mutation rate. Combination of the two marker systems might provide more information of population structure and connectivity on different temporal scales. Overall, the results showed concordant barriers for gene flow in the three species and also supported that mtDNA is applicable for population genetic analysis and recovery of connectivity in giant clams. It is suggested that sea-level changes during glacial periods, as well as oceanography are important factors that shape the genetic population structure of giant clams. The observed deep evolutionary lineages in the peripheral areas of the IMA might include cryptic species, which supports the centre-of-accumulation hypothesis that aims to explain the high diversity in the IMA. As a consequence, the information will facilitate the conservation of these endangered giant clam species. The distinct groups within each species, potentially separated Evolutionary Significant Unit, are proposed to be managed separately for their adaptive diversity; small scales MPA network should be arranged to maintain the connectivity; and restoration should be performed in areas with low genetic diversity.