Genetic variation and population structure of the carpet shell clam Ruditapes decussatus along the Tunisian coast inferred from mtDNA and ITS1 sequence analysis

Abstract

Surveys of allozyme polymorphisms in the carpet shell clam Ruditapes decussatus have revealed sharp genetic differentiation of populations. Analysis of population structure in this species has now been extended to include nuclear and mitochondrial genes. A partial sequence of a mitochondrial COI gene and of the internal transcribed spacer region (ITS-1) were used to study haplotype distribution, the pattern of gene flow, and population genetic structure of R. decussatus. The samples were collected from twelve populations from the eastern and western Mediterranean coasts of Tunisia, one from Concarneau and one from Thau. A total of twenty and twenty-one haplotypes were detected in the examined COI and ITS1 regions respectively. The study revealed higher levels of genetic diversity for ITS1 compared to COI. The analysis of haplotype frequency distribution and molecular variation indicated that the majority of the genetic variation was distributed within populations (93% and 86% for COI and ITS1 respectively). No significant differentiation was found among eastern and western groups on either side of the Siculo-Tunisian strait. However, distinct and significant clinal changes in haplotypes frequencies between eastern and western samples were found at the most frequent COI haplotype and at three out of five major ITS1 haplotypes. These results suggest the relative importance of historical processes and contemporary hydrodynamic features on the observed patterns of genetic structure.

Impacts of supplementation aquaculture on the genetic diversity of wild Ruditapes decussatus from northern Spain

“…Al - though there are no previous mtDNA data from Asturian estuaries to compare levels of genetic diversity before and after the enhancement program, the sampled populations exhibited low nucleotide (π) and haplotype diversity (h). Diversity indices, particularly nucleotide diversity, of the studied population were lower than those found for most R. decussatus populations along the eastern Atlantic and Mediterranean coasts (Gharbi et al 2010, Cordero et al 2014. Moreover, the lowest levels of genetic diversity were found in the population of Ría de Villaviciosa, which is a recurrent receptor of hatchery seeds.…”

“…4). Hap_6 (GenBank ID: KJ560310) was the most common haplotype (65.18%) and was shared by all 3 populations under study as well as a Tunisian sample analyzed by Gharbi et al (2010). Haplotype Hap_21 (GenBank ID: KJ560316), which accounted for 3.24% of the total population, was represented only in the wild populations of Eo and Villaviciosa, and the remaining 11 haplotypes were population-specific (private haplotypes; Fig.…”

“…Additional haplotypes from Ruditapes sp. with different geographic origins from Gharbi et al (2010) (KC 149953, KC149954, KC149956−KC149959), Mao et al (2011) (AB244374, AB244375, AB244379, AB244380, AB244392, AB244393), Cordero et al (2014) (JX 051518, JX051520, JX051522−JX051538, JX051541− JX051546), and BOLD systems (GBMBV 1220_13, GBMBV1225_13, GBMBV694_13− GBMBV 697_13, GBMBV 997_13, GBMIN1961_12) were used to locate Asturian samples in the worldwide species distribution. Six other R. philippinarum haplotypes from Ría de Villaviciosa and Ría del Eo (GenBank accession numbers KJ560352−KJ560357) were also used.…”

Genetic structure of the Peruvian scallop Argopecten purpuratus inferred from mitochondrial and nuclear DNA variation

“…Developing larvae spend a variable 395 period of time (averagely two weeks in A. purpuratus) as part of plankton, which can be 396 passively drifted by water currents, often over considerable distances (Gharbi et al, 2010). Further studies with larger sample sizes in each 456 population using more microsatellite markers are required.…”

Population genetics ofCerastoderma edulein Ria Formosa (southern Portugal): the challenge of understanding an intraspecific hotspot of genetic diversity

“…It is also important to stress that although the work of Krakau et al (2012) was carried out in several localities at a large spatial scale showing high values of genetic diversity in the northern populations, comparisons among different lagoons and several localities inside each lagoon were not included; the authors did not consider the analysis of microgeographic genetic variation in C. edule, assuming genetic homogeneity inside each sampled coastal bay, estuary or lagoon Sequences of a particular fragment of the mitochondrial COI have been employed in a number of studies to investigate genetic structuring and demographic history in populations of marine bivalve species, in which the observed values of haplotype diversity (h) and nucleotide diversity (p) were lower than those recorded for C. edule in the present study. For example, lower diversity values were recorded in other bivalve species: Amusium pleuronectes with h ¼ 0.237, p ¼ 0.0006 (Mahidol et al, 2007), Ruditapes decussatus at h ¼ 0.486 and p ¼ 0.011 (Gharbi et al, 2010), Scrobicularia plana with h ¼ 0.52, p ¼ 0.0016 (Santos et al, 2012), Donax serra with h ¼ 0.30, p ¼ 0.001 (Bezuidenhout et al, 2014), Crassostrea iredalei with h ¼ 0.565, p ¼ 0.0018 (Zainal Abidin et al, 2014) and Gemma gemma with values of h ¼ 0.314, p ¼ 0.0012 (Zhang et al, 2014). In our study of C. edule, estimates of haplotype and nucleotide diversity were higher than those recorded in these studies using marine samples.…”