Species delimitation in sharpnose sharks (genus Rhizoprionodon) in the western Atlantic Ocean using mitochondrial DNA

Despite Springer’s (1964) revision of the sharpnose sharks (genus Rhizoprionodon), the taxonomic definition and ranges of Rhizoprionodon in the western Atlantic Ocean remains problematic. In particular, the distinction between Rhizoprionodon terraenovae and R. porosus, and the occurrence of R. terraenovae in South American waters are unresolved issues involving common and ecologically important species in need of fishery management in Caribbean and southwest Atlantic waters. In recent years, molecular markers have been used as efficient tools for the detection of cryptic species and to address controversial taxonomic issues. In this study 415 samples of the genus Rhizoprionodon captured in the western Atlantic Ocean from Florida to southern Brazil were examined for sequences of the COI gene and the D-loop and evaluated for nucleotide differences. The results on nucleotide composition, AMOVA tests, and relationship distances using Bayesian-likelihood method and haplotypes network, corroborates Springer’s (1964) morphometric and meristic finding and provide strong evidence that supports consideration of R. terraenovae and R. porosus as distinct species.

Salamandra salamandra (Amphibia: Caudata: Salamandridae) in Portugal: not all black and yellow

The fire salamander complex is quite diverse in the Iberian Peninsula where nine subspecies of Salamandra salamandra are currently recognized. Here, we analysed the geographical distribution of the subspecies S. s. gallaica and S. s. crespoi using partial sequences of the mitochondrial cytochrome b gene of 168 individuals from 12 locations in Portugal. Our results support the existence of a deep lineage divergence between the two subspecies, with non-overlapping geographical distributions except in two contact zones: one in Sesimbra on the western coast, and another in Alcoutim on the southeastern border with Spain. Moreover, S. s. crespoi displays signs of gene flow among the sampled locations whereas S. s. gallaica shows evidence of some restriction to gene flow. Present-day genetic make-up of S. s. gallaica and S. s. crespoi is a result of past historical events, fine-tuned by contemporary Iberian geoclimate. Humid mountain areas were found to harbour increased genetic diversity possibly acting as past refugia during drier interglacial periods. To analyse wider geographical patterns and lineage splitting events within S. salamandra we performed a Bayesian dating analysis completing our data set with previously published sequences. The observed divergences were associated to successive biogeographic scenarios, and to other Iberian species showing similar trends.

Genetic diversity and connectivity remain high in Holothuria polii (Delle Chiaje 1823) across a coastal lagoon-open sea environmental gradient

Coastal lagoons represent habitats with widely heterogeneous environmental conditions, particularly as regards salinity and temperature,which fluctuate in both space and time. These characteristics suggest that physical and ecological factors could contribute to the genetic divergence among populations occurring in coastal lagoon and opencoast environments. This study investigates the genetic structure of Holothuria polii at a micro-geographic scale across theMar Menor coastal lagoon and nearbymarine areas, estimating the mitochondrial DNA variation in two gene fragments, cytochrome oxidase I (COI) and 16S rRNA (16S). Dataset of mitochondrial sequences was also used to test the influence of environmental differences between coastal lagoon andmarine waters on population genetic structure. All sampled locations exhibited high levels of haplotype diversity and low values of nucleotide diversity. Both genes showed contrasting signals of genetic differentiation (non-significant differences using COI and slight differences using 16S, which could due to different mutation rates or to differential number of exclusive haplotypes. We detected an excess of recent mutations and exclusive haplotypes, which can be generated as a result of population growth. However, selective processes can be also acting on the gene markers used; highly significant generalized additive models have been obtained considering genetic data from16S gene and independent variables such as temperature and salinity.

Genetic differentiation among Parastichopus regalis populations in the Western Mediterranean Sea: potential effects from its fishery and current connectivity

Parastichopus regalis (Cuvier, 1817) is the most expensive seafood product on the Catalonian market (NE Spain), with prices at approximately 130 €/Kg (fresh weight). Despite its ecological and economic importance, biological and genetic information on this sea cucumber species is scarce. Here, we provide both the first insight on the genetic structure of P. regalis using sequences of cytochrome oxidase I (COI) and 16S genes and a morphological description of its population. Individual sea cucumbers were collected in six locations along the Spanish Mediterranean coast, including an area under fishery pressure (Catalonia). We found high haplotype diversity and low nucleotide diversity for both genes, with higher levels of genetic diversity observed in the COI gene. The population pairwise fixation index (FST), AMOVA and correspondence analysis (CA) based on the COI gene revealed significant genetic differentiation among some locations. However, further analysis using nuclear markers (e.g., microsatellites) is necessary to corroborate these results. Moreover, the genetic and morphological data may indicate fishery effects on the Catalonian population with a decrease in the size and weight averages and lower genetic diversity compared with locations that lack fishery pressure. For the appropriate management of this species, we suggest the following: 1) accurately assessing the stock status along the Spanish coasts; 2) studying the reproductive cycle of this target species and the establishment of a closed fishery season according to the reproductive cycle; and 3) establishing protected areas (i.e., not take zones) to conserve healthy populations and favour recruitment in the nearby areas.

In two waters: contemporary evolution of lagoonal and marine white seabream (Diplodus sargus) populations

Brackish water ecosystems are often exposed to wide variations in environmental variables, including temperature and salinity, which may cause strong selective pressures on organisms modifying the genetic patterns of species. The aim of this work was to test whether there is a ‘divergence-with-gene flow’ in coastal lagoon populations of white seabream (Diplodus sargus) (Ria Formosa, S Portugal and Mar Menor, SE Spain) respect to four marine populations, by using partial sequences of cyt b mitochondrial gene and information from nine microsatellite loci. Genetic diversity was highest in both coastal lagoons (Mar Menor and Ria Formosa) considering mitochondrial and nuclear markers. Although some of FST population pairwise comparisons were not significant, analyses of molecular variance (AMOVAs) detected differences between groups (coastal lagoon and marine) close to significance. Also, only two haplotypes (Cytb-17 and Cytb-18) were detected in both coastal lagoon sampling sites and these localities (Mar Menor and Ria Formosa) showed the highest number of singletons, some of them with a high number of mutations, as has been already described for other Mar Menor populations (Pomatochistus marmoratus and Holothuria polii). Also, several tests detected significant positive and balancing selection considering mtDNA and microsatellite data. These data support the hypothesis of selection as one of the drivers of the genetic differences found between coastal lagoon and marine populations. The life strategy adopted by Diplodus sargus in coastal lagoons allows it to decrease its mortality rate and improve the heritability of its genes. Also, the increase time spent in coastal lagoons with different temperatures and salinities favours the fitness selection and the maintenance of exclusive haplotypes and genotypes in coastal lagoon inhabitants favouring the ‘divergence-with-gene-flow’.

Biogeography of the fire salamander (Salamandra salamandra, L.) in Portugal

Dissertação de mest., Biologia Marinha, Faculdade de Ciências do Mar e do Ambiente, Universidade do Algarve, 2008