Characterization of polymorphic microsatellite markers for the endangered Mediterranean bath sponge Spongia officinalis L.

Ten polymorphic microsatellite markers are described for the Mediterranean bath sponge Spongia officinalis. Loci were isolated from a genomic library enriched for AC repeats. Microsatellite markers were evaluated on a Cretan population of 28 individuals; the allelic richness ranged from 5 to 34 with an average of 17, while expected and observed heterozygosities varied from 0.505 to 0.964 and 0.444 to 0.963, respectively. In a species whose populations in the eastern Mediterranean basin have been substantially declined due to recurring mass mortality incidents and intensive harvesting, these markers are expected to assist studies of genetic structure and differentiation between populations.     

Isolation and characterization of microsatellite loci in the striped mullet,Mugil cephalus

Forty‐three microsatellites were isolated from grey mullet (Mugil cephalus) of Mediterranean origin using the standard enrichment methods followed by enhanced chemiluminescence for the rapid identification of clones containing microsatellites. Eleven microsatellites were characterized to assess genetic diversity of different populations surrounding the island of Sardinia in Italy. The versatility of these markers was also assessed using an Australian population. All 11 microsatellites were highly polymorphic with a mean heterozygosity of 0.834. The number of alleles ranged from 14 to 38 in the Sardinian populations and from 11 to 25 in the Australian samples.     

Isolation and characterization of polymorphic microsatellite markers for peacock wrasse (Symphodus tinca)

Eight polymorphic microsatellite loci were isolated and characterized for the peacock wrasse (Symphodus tinca), a labrid fish inhabiting the Mediterranean and Black seas. Characterization of 35 individuals from the western Mediterranean indicated a relatively high allelic diversity (mean = 12.4, range 9–17), and observed heterozygosity ranging from 0.65 to 0.91. We found no evidence of linkage disequilibrium between pairs of loci. Two loci showed significant departure from Hardy–Weinberg equilibrium. These polymorphic markers can be useful in most basic population genetic applications.     

A preliminary investigation of allozyme genetic variation and population structure in common pandora (<Emphasis Type="Italic">Pagellus erythrinus</Emphasis>, Sparidae) from Tunisian and Libyan coasts

The genetic characterization of natural populations of common pandora (Pagellus erythrinus, Sparidae) was studied using allozyme markers. Fish samples (n = 360) were collected from five locations along the Tunisian coasts and one from the Libyan coast. From eight enzymatic systems, 12 putative enzyme-coding loci were resolved, 8 of which were polymorphic at a level of 99%. F statistics indices revealed a significant departure from panmixia with heterozygote deficiencies and a slight genetic differentiation between samples. Neighbor-joining dendrogram constructed by Reynolds genetic distance showed that the populations sampled from the southeastern Mediterranean Sea were more differentiated from the others.     

Characterization of highly polymorphic nuclear microsatellite loci from the ascidian Ciona intestinalis

Eight nuclear polymorphic microsatellite markers were characterized from the ascidian Ciona intestinalis whole genome sequence. The behaviour of these loci was investigated against two geographically distinct populations: one from Plymouth, UK the other from the Fusaro Lagoon, Italy, both belonging to the type A Ciona cryptic species. The markers exhibited six to 29 alleles and average observed heterozygosity ranging from 0.06 to 0.73. These new microsatellite loci demonstrated to be valuable tools for both population genetic analysis at different scales and genetic identification of mutant phenotypes frequently encountered in Mediterranean populations of C. intestinalis.     

Alu insertions in the Iberian Peninsula and north west Africa--genetic boundaries or melting pot?

The Western Mediterranean Basin joins a set of ethnically different populations as Iberians and Basques in the North shore and Berbers and Arab-speakers in the South one. In spite of this differentiation, they have maintained historical contacts since ancient times. The existence of a possible common genetic background (specially for Berbers and Iberians) together with the genetic impact of the Islamic occupation of the Iberian Peninsula during 7 centuries are some of the intriguing anthropological questions that have been studied in this area using several classical and DNA markers. The aim of this work is to present the results on a survey of polymorphic Alu elements in 10 human populations of the Western Mediterranean. Recent Alu subfamilies include a significant number of polymorphic Alu insertions in humans. The polymorphic Alu elements are neutral genetic markers of identical descent with known ancestral states. This fact turns Alu insertions into useful markers for the study of human population genetics. A total number of 14 Alu insertions were analyzed in 5 Iberian populations, 3 Berber groups from North-Western Africa, an Arab-speaker population from Morocco and a sub-Saharan ethnic group from Ivory Coast. The results of this study allow the genetic characterization of Berber populations, which show a certain degree of differentiation from Arab-speaking groups of the same geographic area. Furthermore, a closer genetic distance between South Spain and Moroccan Berbers as compared with other Spanish samples supports a major genetic influx consistent with some (but not all) previous genetic studies on populations from the two shores of the Gibraltar Straits.     

The isolation of microsatellite loci in the Mediterranean fruitfly Ceratitis capitata (Diptera: Tephritidae) using a biotin/streptavidin enrichment technique

The Medfly (Ceratitis capitata) is a polyphagous dipteran pest which has spread from North Africa to the countries of the Mediterranean Basin and has also invaded tropical and subtropical regions throughout the world. Colonizing populations typically possess low levels of genetic variability. Microsatellites provide an effective means of investigating the population structure of such genetically depauperate populations, however, microsatellite markers traditionally require a long phase of development in new taxa. We used a biotin/streptavidin capture technique to isolate microsatellites directly from C. capitata genomic DNA and we describe here the identification of seven polymorphic microsatellite markers in C. capitata.     

Identification and characterization of nuclear microsatellite loci in Abies alba Mill.

Eleven polymorphic nuclear microsatellite markers for Abies alba Mill. were developed from an enriched genomic library. An average of 5.2 alleles per locus and a mean expected heterozygosity of 0.532 were found in a sample of 24 Abies alba individuals from different populations within Europe. These loci can be used in studies of genetic diversity for parentage analysis and for estimation of gene flow in silver fir populations. Moreover, successful amplifications were obtained for eight other Mediterranean Abies species, suggesting that these loci may be useful for similar applications in other fir species.     

Genetic diversity in inter‐simple sequence repeat profiles across natural populations of Indian pomegranate (Punica granatum L.)

Pomegranate (Punica granatum L.), in the monogeneric family Punicaceae, is found in Iran, Afghanistan, India and Mediterranean countries. Iran is considered to be its primary centre of origin. In India, pomegranate occurs naturally only in the Western Himalayan regions of Jammu and Kashmir, Himachal Pradesh and Uttarakhand States. However, there is no information about genetic variation in wild pomegranate at population level. In this paper, we describe genetic diversity across natural populations of Indian pomegranate based on inter‐simple sequence repeat (ISSR) markers. Forty‐nine accessions representing eight populations from two regions were analysed using ISSR. Seventeen ISSR primers resulted in 268 polymorphic bands, with 87.01% polymorphism throughout the accessions. Pair‐wise population genetic distances ranged from 0.05 to 0.45, with a mean of 0.25 between populations. amova and Nei’s genetic diversity analyses revealed higher genetic variation within populations than among populations. A higher genetic differentiation (G_ST) was observed between the spatially distant populations, indicating a low level of genetic exchange (Nm) among these populations. However, clustering of populations was not in accordance with their geographical affiliations in the tree. The results indicate that the ISSR method is sufficiently informative and powerful to assess genetic variability in pomegranate, and that patterns of genetic variability observed among populations of wild pomegranate from the Western Himalaya differ. Estimation of genetic variation reported here provides a significant insight for in situ conservation and exploitation of genetic resources for this economically important species as potential breeding material.     

Assessing the geographic scale of genetic population management with microsatellites and introns in the clam Ruditapes decussatus

The clam Ruditapes decussatus is commercially important in southwestern Europe, suffering from population decline and hybridization with exotic Manila clam (R. philippinarum). Previous studies with intronic markers showed a genetic subdivision of the species in three races (Atlantic, West Mediterranean, and Adriatic‐Aegean). However, detailed population genetic studies to help management of the main production areas in the southwest of Europe are missing. We have analyzed eight Atlantic and two Mediterranean populations from the Spanish coasts using 14 microsatellites and six intronic markers. Microsatellites confirmed the Atlantic and West Mediterranean races detected with introns and showed that genetic variability was higher in Mediterranean than in Atlantic populations. Both marker types showed that genetic differentiation of Atlantic populations was low and indicated that populations could be managed at the regional level in the case of Cantabrian and Gulf of Cadiz areas, but not in the case of Rias Baixas and the Mediterranean. This study shows the interest of including different types of markers in studies of genetic population structure of marine organisms.     

Isolation and characterization of the first polymorphic microsatellite markers for Schistosoma haematobium and their application in multiplex reactions of larval stages

The ability of microsatellite loci to reveal genetic diversity within the trematode Schistosoma haematobium is demonstrated for the first time. Nine novel polymorphic microsatellite markers were isolated and their viability assessed on 36 S. haematobium adult worm individuals from three geographical populations. Allelic diversity and gene diversity ranged from two to seven and from 0.29 to 0.76, respectively, suggesting high variability between individuals and between unrelated populations. Three primers also amplified Schistosoma mansoni and two Schistosoma japonicum. The results suggest these primers are useful for population genetic analyses of S. haematobium.     

The highly polymorphic microsatellite markers for the greater long‐tailed hamster (Tscherskia triton)

We isolated 25 dinucleotide microsatellite loci from the greater long‐tailed hamster (Tscherskia triton) populations in North China. We developed the amplification conditions of polymerase chain reaction for producing high‐resolution genetic markers for each locus. We found 10 microsatellite loci were highly polymorphic in 90 individual hamsters from three areas of North China, and the number of alleles in each locus varied from three to 11. These markers are potential tools for studying the genetic variation of the natural populations of this species.     

Isolation and characterization of polymorphic microsatellite markers from fireweed,Senecio madagascariensis Poir. (Asteraceae)

Ten polymorphic microsatellite loci were isolated and characterized from invasive fireweed (Senecio madagascariensis) populations in the Hawaiian archipelago. These loci provided markers with polymorphism of six to 24 alleles per locus within 96 individuals collected from two populations from the island of Maui. The expected and observed heterozygosities ranged from 0.31 to 0.91 and from 0.056 to 1. These markers should be useful to study the importance of genetic diversity in invasion success of this species.     

Comparative pattern of genetic structure in two Mediterranean killifishes Aphanius fasciatus and Aphanius iberus inferred from both mitochondrial and nuclear data

In this study, genetic variation was assessed in Aphanius fasciatus and Aphanius iberus characterized by similar ecological traits but with very different distribution ranges in the Mediterranean area. Five populations of A. iberus and five of A. fasciatus were analysed using five polymorphic microsatellite loci and partial mitochondrial control region (D‐loop) sequences. Congruent results were found with both nuclear and mitochondrial molecular markers. The results showed that similar levels of genetic divergence, based on mitochondrial control region sequences, are present among populations of A. iberus and among populations of A. fasciatus despite the very different geographic distance existing among the examined populations of the two species (low geographic distance in A. iberus and high in A. fasciatus). A possible explanation could be that the populations of A. iberus were isolated for a longer time than the populations of A. fasciatus supporting the hypothesis that the split in the lineage leading to A. iberus is older than the split in the lineage leading to A. fasciatus. The possibility that the wide circum‐Mediterranean distribution of A. fasciatus ensures the high connectivity of its populations, preventing, in some cases, local differentiation, however, cannot be ruled out.     

Genetic Variation and Population Structure of Oriental Migratory Locust, Locusta migratoria manilensis, in China by Allozyme, SSRP-PCR, and AFLP Markers

Allozyme analysis, microsatellite primer PCR (SSRP-PCR), and amplified fragment length polymorphism (AFLP) techniques were used to assess genetic diversity and population structure of the Chinese oriental migratory locust, Locusta migratoria manilensis. A total of 299 PCR markers (67 SSRPs and 232 AFLPs) were detected in eight populations, of which 98.7% were polymorphic markers. The proportion of polymorphic loci (95.5–98.8%) by SSRP+AFLP markers indicated no significant differences between populations, and all populations exhibited a similar level of variability; results of the allozyme analysis demonstrated that 19 loci gave rise to a lower level of polymorphism (55.6–66.7%). The genetic distances between the populations were relatively low. Shannon’s index and Nei’s gene diversity showed low differentiation among the populations. Allozyme analysis, however, reflected greater similarity and smaller differentiation between the populations than those shown by SSRP and AFLP markers. Neighbor-joining dendrograms derived from both the allozyme and SSRP+AFLP markers showed that the genetic distances among Chinese oriental migratory locust populations were not greatly influenced by geographic distance and breeding habitats.     

Development of microsatellite markers in the toxic dinoflagellate Alexandrium tamarense (Dinophyceae)

Outbreaks of paralytic shellfish poisoning caused by the toxic dinoflagellate Alexandrium tamarense (Dinophyceae) are currently a serious problem from an economic and food hygiene point of view throughout the world. We isolated 13 polymorphic microsatellite loci from this species. These loci provided microsatellite markers with high polymorphism ranging from four to 15 alleles per locus and gene diversity between 0.632 and 0.974. The markers are available for more detailed investigations of genetic structure and gene flow of A. tamarense populations.     

Detecting immigrants in a highly genetically homogeneous spiny lobster population (Palinurus elephas) in the northwest Mediterranean Sea

We investigated the genetic structure of early benthic juveniles of the spiny lobster Palinurus elephas in the northwest Mediterranean Sea by means of ten polymorphic microsatellite markers. Non‐metric Multidimensional Scaling coupled with assignment tests were used as a new approach to further delimit a reference population inside a genetically homogeneous pool of individuals and test for the presence of long distance immigrants. From this approach, we found that most early benthic juveniles collected while settling in the northwest Mediterranean Sea originated from a common larval pool. However, 4.2% of the individuals were classified as immigrants from other genetically differentiated populations, with more immigrants in the south than in the north of the sampled basin. Given currents in the northwest Mediterranean Sea and the long pelagic larval phase of P. elephas that lasts several months, this result suggest a restricted homogenized zone in the studied basin with some individuals probably coming from more differentiated populations through the Almeria‐Oran Front or the Strait of Sicily.     

Development of microsatellite markers for the Mediterranean gorgonian coral Corallium rubrum

Corallium rubrum, an endemic Mediterranean gorgonian coral, has undergone an intensive exploitation leading to the extinction of local commercial banks and changes in the structure and dynamics of coastal populations. Management and conservation of this species requires a better understanding of the genetic structuring and connectivity among populations. With this aim, seven microsatellite loci have been isolated. All loci were polymorphic with allele numbers ranging from five to 26 and observed heterozygosity ranging from 0.18 to 0.68. Significant deviations from Hardy–Weinberg expected genotype frequencies due to heterozygote deficiency were detected at all loci.     

Genetic analysis of salt-marsh sedge Carex scabrifolia Steud. populations using newly developed microsatellite markers

Nine microsatellite loci were isolated and characterized from the clonal salt-marsh sedge Carex scabrifolia, and genetic diversities within four populations were analyzed. The number of alleles per locus ranged from 2 to 7, with an average of 4.7. The observed and expected heterozygosities ranged from 0.000 to 1.000 and 0.000 to 0.679, respectively. In two populations, almost all polymorphic loci showed a significant excess of heterozygotes due to their high clonal reproduction and low number of genotypes (genets) composing the populations. Thus, the number of identical genets varied greatly among populations and ranged from 1 to 28, irrespective of population size (i.e., population area and ramet number). When attempting to conserve and restore clonal plants such as C. scabrifolia, it is important to preserve sufficient genetic diversity within a population, which can be assessed using genetic markers such as the simple sequence repeat markers described here.     

Twelve novel microsatellite loci from an endangered marine fish species golden pompano Trachinotus blochii

The golden pompano (Trachinotus blochii) is a marine fish species in tropical regions. No information about genetic variation and population structure of wild populations is available. A first set of 12 polymorphic microsatellites isolated from this species were characterized. The number of alleles ranged from 5 to 14 with an average of 8.0 alleles per locus. All 12 markers conformed to HWE and were in linkage equilibrium. These 12 microsatellite markers supply the first set of co-dominant DNA markers for studying population genetics of the species T. blochii.