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Genetic Variation and Population Structure of the Carpet Shell Clam Ruditapes Decussatus Along the Tunisian Coast Inferred from Mtdna and ITS1 Sequence Analysis

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Genetic Variation and Population Structure of the Carpet Shell Clam Ruditapes Decussatus Along the Tunisian Coast Inferred from Mtdna and ITS1 Sequence Analysis Biologia 65/4: 688—696, 2010 Section Zoology DOI: 10.2478/s11756-010-0069-8 Genetic variation and population structure of the carpet shell clam Ruditapes decussatus along the Tunisian coast inferred from mtDNA and ITS1 sequence analysis Aicha Gharbi1,2, Noureddine Chatti2,KhaledSaid2 & Alain Van Wormhoudt1 1Station de Biologie Marine du Muséum National d’Histoire Naturelle, BP225, 29900 Concarneau, France; e-mail: [email protected] 2Unité de Recherche: Génétique, Biodiversité et Valorisation des Bioressources, UR03ES09, Institut Supérieur de Biotech- nologie de Monastir, Tunisie 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 dis- tributed 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. Key words: Ruditapes decussates; COI; ITS1; Tunisia Introduction netic variation within and among populations. In the Mediterranean Sea, the shared stocks of the clam R. The carpet shell clam (Ruditapes decussatus L., 1758), decussatus represent important marine fishery resource is a commercially valuable bivalve mollusk and among exploited by all coastal countries. An increasing number the most common clam species found on the market for of studies on marine bivalve genetic structure are avail- human consumption, widely distributed in the Mediter- able, especially concerning exploited species. Knowl- ranean and its adjacent Atlantic waters from the North edge about population structure is among the most im- Sea to the coast of Senegal (Breber 1985). In Tunisia, portant questions to investigate. The resulting informa- this species is distributed along the coastline except the tion can be critical both for the understanding of the Cap Bon and Gulf of Hammamet (Medhioub 1993). Ac- biology of the species and for better management of cording to fishery statistics (capture production) pub- their stocks. The development of molecular techniques lished by the Food and Agriculture Organisation of that identify nucleotide-level DNA sequence polymor- the United Nations (FAO 2006a) the world’s nomi- phisms among species has created a large source of ge- nal catches of “clams, cockles and arkshells” in 2006 netic markers which can be used in phylogenetic and was 738,845 tons. Moreover, World aquaculture pro- population studies. Compared to protein analysis tech- duction of this species group in 2006 was 4,310,488 niques, analysis of DNA variation is rapidly becom- tons (FAO 2006b). Bivalve species have also important ing the method of choice because DNA is more ther- roles in ecosystems. As filter feeders, they form a signif- mostable than proteins and the higher probability of icant link with primary producers (mainly phytoplank- variation being neutral. DNA-based methods such as ton and bacteria), and also act as calcium and carbon nucleotide sequence analysis, RAPD (random ampli- accumulators, which they use in their shell construc- fication of polymorphic DNA) and RFLP (restriction tion. fragment length polymorphism) analysis are useful ge- Studies on the genetic structure of wild pop- netic techniques for population’s studies. RAPD is a ulations aim at identifying the evolutionary events very fast method that can identify a large number of that have shaped the contemporary distribution of ge- polymorphism, but its major drawback is the poor re- c 2010 Institute of Zoology, Slovak Academy of Sciences Genetic variation of Ruditapes decussates 689 producibility of the results obtained. PCR-RFLP analy- sisissimplerandlessexpensive than conventional DNA nucleotide sequence analysis and better suited for large- scale genetic surveys requiring a large number of spec- imens. However, this technique detects differences in DNA sequences only when they are present at the spe- cific recognition site of the corresponding endonuclease. In this work, we have chosen conventional sequencing of PCR products, a relatively costly approach but allowed us a detailed comparison of individual sequences. It has been proposed that benthic marine species with pelagic larvae have population genetic variation reflecting the dispersal capacity of larvae. Most of them are thought to have little genetic structure. Consider- able work has been conducted to test this hypothesis on many species, including scallops, oysters, mussels, gastropods, abalones, pearl oysters, ophiuroids, anos- tracans and many other invertebrates with planktonic larvae (Yuan et al. 2009 and references therein). Mitochondrial DNA sequences (including 16S rDNA and COI) were used for many of these studies. In the bivalve R. decussatus, this hypothesis has not been tested. Since the 1980s, many papers have been published on the population genetic of the carpet shell clam R. Fig. 1. Location of the twelve Ruditapes decussatus populations decussatus. In all papers, allozyme variation was used sampled from Tunisia. to characterize genetic variation among natural popu- lations covering its distribution area (Jarne et al. 1988; (S-T) Strait in phylogeographical structuring of marine Borsa et al. 1994; Worms & Pasteur 1982; Borsa & species. To explain the concordance of patterns of ge- Thiriot-Quiévreux 1990; Passamonti et al. 1997; Jor- netic differentiation observed in these marine species, daens et al. 2000).We believed that no studies which a hypothesis has been proposed wherein eastern and analysed DNA sequence information for comparing in- western Mediterranean populations have been isolated traspecific phylogeography have been conducted on bi- due to sea level changes during glacial maxima and valve R. decussatus. Most of PCR-based methods for R. subsequently reconnected, possibly several times, in the decussatus have focused on phylogenetic studies of the past. Ruditapes genus (Fernandez et al. 2000, 2001, 2002a, We recently revealed a certain genetic differenti- b; Passamonti et al. 1998; Canapa et al. 1996, 2003; ation among R. decussatus populations collected from Kappner & Bieler 2006; Cordero et al. 2008). eleven localities in the eastern and western Mediter- DNA-level markers could validate and better elu- ranean coasts of Tunisia, using allozyme electrophoresis cidate gene flow patterns based on allozyme data. The as genetic markers (A. Gharbi et al., in litt.). The aim variations at the DNA level come from base alterations of the present study was to establish the extend of gene that may be found in both coding and non-coding re- flow and to approximate the detailed levels of genetic gions of the genome. These variations are more encom- structure of R. decussatus populations, using nucleotide passing than the changes covered by allozyme analysis, sequence analysis of the first subunit of the cytochrome which are confined to coding regions of the genome. c oxidase (COI) region of mitochondrial DNA (mtDNA) The marine environment holds many peculiarities, and the internal transcribed spacer region (ITS-1) be- which, in conjunction with other life history character- tween 5.8S and 18S ribosomal DNA genes. We believe istics of marine organisms, hints at genetic differenti- this study represents the first survey of sequence vari- ation within apparent panmictic populations. In fact, ation at COI and ITS-1 among geographically distant the marine environment shows much more heterogene- populations of bivalve R. decussatus, at least in Tunisia ity owing to the influence of climate, hydrodynamics scale. and topography on natural barriers, which affects dis- persal (Cowen et al. 2000). Genetic structuring is en- Material and methods hanced furthermore by certain biological traits, such Samples and DNA extraction as sex-dependent migration, which can counteract dis- Ruditapes decussatus samples were collected from eleven lo- persal and gene flow. Hence, numerous marine species cations originating from coastal lagoon and marine sites maintain a genetic structure despite a great potential in Tunisia (Fig. 1). Samples from Concarneau (Brittany) for dispersal (Shaw et al. 1999; Maes & Volckaert 2002). and from Thau (French south) were included in this study Studies on several fishes, molluscs and crustaceans to make comparisons between Mediterranean and Atlantic have suggested the importance of the Siculo-Tunisian samples. Live specimens were shipped to the laboratory
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