Ferran Palero

Phylogeography of the European spiny lobster (Palinurus elephas): Influence of current oceanographical features and historical processes

The European spiny lobster (Palinurus elephas) is a suitable model organism to study the effects of past history and current oceanographic processes on the genetic diversity and population structure of marine species with a long-lived larval phase. A portion of the COI gene was sequenced in 227 individuals from 11 localities, covering most of the present distribution of the species. Divergence was found between Atlantic and Mediterranean regions, which could be explained by restricted gene flow between populations. Moreover, a principal component analysis detected differences within basins. The existence of genetic differentiation between Brittany and Ireland-Scotland populations could be accounted for by the large effect of the Gulf Stream, while mesoscale processes suffered by the incoming Atlantic waters could be responsible of genetic differentiation within the Mediterranean. Furthermore, historical processes could be responsible for a reduction on the overall genetic variability of P. elephas. The haplotypic distribution found in P. elephas, with the presence of one abundant haplotype and a large number of closely related haplotypes, is typical of species experiencing reduction in variability and subsequent expansions. Climatic fluctuations related to glacial cycles could explain the present level of variability and nucleotide diversity found. Interestingly, these glacial events do not seem to have the same impact in other species of the same genus. Our results indicate that recent glacial events could have had a lower impact on Palinurus mauritanicus, a congeneric species that presents an overlapping distribution area but is found in cooler waters than P. elephas.

Phylogenetic relationships between spiny, slipper and coral lobsters (Crustacea, Decapoda, Achelata)

Molecular data can aid in the resolution of conflicting hypotheses generated through difficulties in the interpretation of morphological data and/or an incomplete fossil record. Moreover, the reconstruction of phylogenetic relationships using molecular data may help to trace back the origin of morphological innovations which had a major impact on the radiation of a taxonomical group. In this work, different nuclear (18S, 28S, and H3) and mitochondrial (16S and COI) gene regions were sequenced in a total of 35 Achelatan species to test conflicting hypotheses of evolutionary relationships within the Achelata infraorder and solve the taxonomic disagreements in the group. The combined molecular dataset strongly supports the hypothesis that Achelata is a monophyletic group composed of two main families: Palinuridae and Scyllaridae. Synaxidae is found to be a polyphyletic group, which should be included within Palinuridae. Consequently, our results indicate that the origin of the stridulating organ occurred only once during Achelata evolution. Finally, the two main clades found within the Scyllaridae are in agreement with previous inferences based on adult morphological data. The dating of divergence of Achelata obtained with a relaxed-clock model is compatible with previous hypotheses of a Triassic origin of the Achelata.

Rapid radiation in spiny lobsters (Palinurus spp) as revealed by classic and ABC methods using mtDNA and microsatellite data

BackgroundMolecular tools may help to uncover closely related and still diverging species from a wide variety of taxa and provide insight into the mechanisms, pace and geography of marine speciation. There is a certain controversy on the phylogeography and speciation modes of species-groups with an Eastern Atlantic-Western Indian Ocean distribution, with previous studies suggesting that older events (Miocene) and/or more recent (Pleistocene) oceanographic processes could have influenced the phylogeny of marine taxa. The spiny lobster genus Palinurus allows for testing among speciation hypotheses, since it has a particular distribution with two groups of three species each in the Northeastern Atlantic (P. elephas, P. mauritanicus and P. charlestoni) and Southeastern Atlantic and Southwestern Indian Oceans (P. gilchristi, P. delagoae and P. barbarae). In the present study, we obtain a more complete understanding of the phylogenetic relationships among these species through a combined dataset with both nuclear and mitochondrial markers, by testing alternative hypotheses on both the mutation rate and tree topology under the recently developed approximate Bayesian computation (ABC) methods.ResultsOur analyses support a North-to-South speciation pattern in Palinurus with all the South-African species forming a monophyletic clade nested within the Northern Hemisphere species. Coalescent-based ABC methods allowed us to reject the previously proposed hypothesis of a Middle Miocene speciation event related with the closure of the Tethyan Seaway. Instead, divergence times obtained for Palinurus species using the combined mtDNA-microsatellite dataset and standard mutation rates for mtDNA agree with known glaciation-related processes occurring during the last 2 my.ConclusionThe Palinurus speciation pattern is a typical example of a series of rapid speciation events occurring within a group, with very short branches separating different species. Our results support the hypothesis that recent climate change-related oceanographic processes have influenced the phylogeny of marine taxa, with most Palinurus species originating during the last two million years. The present study highlights the value of new coalescent-based statistical methods such as ABC for testing different speciation hypotheses using molecular data.

Temporal and spatial genetic differentiation in the crab Liocarcinus depurator across the Atlantic-Mediterranean transition

Spatial genetic studies often require sampling broadly separated areas, difficult to access simultaneously. Although comparing localities surveyed at different time periods might result in spurious genetic differentiation, there is a general believe on the stability of genetic structure through time, particularly if sampled localities are isolated or very distant. By analysing spatial and temporal genetic differentiation of the portunid crab Liocarcinus depurator we assessed the contribution of historical and contemporary processes on population connectivity patterns across three main oceanographic discontinuities along the Atlantic-Mediterranean transition: Gibraltar Strait, Almeria-Oran Front and Ibiza Channel. A partial fragment of the cytochrome oxidase I gene was sequenced in 366 individuals collected from localities at both sides of each discontinuity during three time periods. Although localities showed genetic fluctuations through time, a significant gradient was detected along the coast for all sampling periods. Significant inter-annual differences identified within the Alicante area, north of the Almeria-Oran Front, were associated with shifts in the relative contribution of Atlantic and Mediterranean water masses. The persistence of a clinal pattern in the Atlantic-Mediterranean transition area together with local fluctuations suggests a complex balance of dispersal and selection.

Genetic Diversity Levels in Fishery-Exploited Spiny Lobsters of the Genus Palinurus (Decapoda: Achelata)

Abstract Most fisheries involving spiny lobsters of the genus Palinurus have been overexploited during the last decades, so there is a raising concern about management decisions for these valuable resources. A total of 13 microsatellite DNA loci recently developed in Palinurus elephas were assayed in order to assess genetic diversity levels in every known species of the genus. Microsatellite markers gave amplifications and showed polymorphism in all species, with gene diversity values varying from 0.650 ± 0.077 SD (Palinurus barbarae) to 0.792 ± 0.051 SD (Palinurus elephas). Most importantly, when depth distribution was taken into account, shallower water species consistently showed larger historical effective population sizes than their deeper-water counterparts. This could explain why deeper-water species are more sensitive to overfishing, and would indicate that overexploitation may have a larger impact on their long-term genetic diversity.

Isolation and characterization of microsatellite loci in Palinurus elephas.

The European spiny lobster (Palinurus elephas) mean annual catches have decreased alarmingly during recent decades along its entire distribution area due to stock over‐exploitation, which makes it a primary target for conservation plans. A total of 164 microsatellite loci were isolated from a genomic library of P. elephas enriched for CA, GA, CAA and GATA repeats. A total of 15 polymorphic loci have been screened in 48 individuals. High numbers of alleles per locus (averaging 20 ± 10.5) and observed heterozygosity (averaging 0.789 ± 0.197) have been detected. None of the pairs of loci showed significant linkage disequilibrium. Two of the loci (Pael1 and Pael2) showed significant departure from Hardy–Weinberg equilibrium in Sagres, while Pael38 showed significant departure in Tunis. These highly polymorphic markers will be useful in determining the spatial patterns of genetic diversity between and within populations of Palinurus elephas.

Mealybug species from Chilean agricultural landscapes and main factors influencing the genetic structure of Pseudococcus viburni

The present study aimed to characterize the distribution of mealybug species along Chilean agro-ecosystems and to determine the relative impact of host plant, management strategy, geography and micro-environment on shaping the distribution and genetic structure of the obscure mealybug Pseudococcus viburni. An extensive survey was completed using DNA barcoding methods to identify Chilean mealybugs to the species level. Moreover, a fine-scale study of Ps. viburni genetic diversity and population structure was carried out, genotyping 529 Ps. viburni individuals with 21 microsatellite markers. Samples from 16 localities were analyzed using Bayesian and spatially-explicit methods and the genetic dataset was confronted to host-plant, management and environmental data. Chilean crops were found to be infested by Ps. viburni, Pseudococcus meridionalis, Pseudococcus longispinus and Planococcus citri, with Ps. viburni and Ps. meridionalis showing contrasting distribution and host-plant preference patterns. Ps. viburni samples presented low genetic diversity levels but high genetic differentiation. While no significant genetic variance could be assigned to host-plant or management strategy, climate and geography were found to correlate significantly with genetic differentiation levels. The genetic characterization of Ps. viburni within Chile will contribute to future studies tracing back the origin and improving the management of this worldwide invader.

MICROSATELIGHT—Pipeline to Expedite Microsatellite Analysis

MICROSATELIGHT is a Perl/Tk pipeline with a graphical user interface that facilitates several tasks when scoring microsatellites. It implements new subroutines in R and PERL and takes advantage of features provided by previously developed freeware. MICROSATELIGHT takes raw genotype data and automates the peak identification through PeakScanner. The PeakSelect subroutine assigns peaks to different microsatellite markers according to their multiplex group, fluorochrome type, and size range. After peak selection, binning of alleles can be carried out 1) automatically through AlleloBin or 2) by manual bin definition through Binator. In both cases, several features for quality checking and further binning improvement are provided. The genotype table can then be converted into input files for several population genetics programs through CREATE. Finally, Hardy-Weinberg equilibrium tests and confidence intervals for null allele frequency can be obtained through GENEPOP. MICROSATELIGHT is the only freely available public-domain software that facilitates full multiplex microsatellite scoring, from electropherogram files to user-defined text files to be used with population genetics software. MICROSATELIGHT has been created for the Windows XP operating system and has been successfully tested under Windows 7. It is available at http://sourceforge.net/projects/microsatelight/.

Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description

Advanced stages of Scyllarus phyllosoma larvae were collected by demersal trawling during fishery research surveys in the western Mediterranean Sea in 2003―2005. Nucleotide sequence analysis of the mitochondrial 16S rDNA gene allowed the final-stage phyllosoma of Scyllarus arctus to be identified among these larvae. Its morphology is described and illustrated. This constitutes the second complete description of a Scyllaridae phyllosoma with its specific identity being validated by molecular techniques (the first was S. pygmaeus). These results also solved a long lasting taxonomic anomaly of several species assigned to the ancient genus Phyllosoma Leach, 1 8 14 . Detailed examination indicated that the final-stage phyllosoma of S. arctus shows closer affinities with the American scyllarid Scyllarus depressus or with the Australian Scyllarus sp. b (sensu Phillips et al., 1981) than to its sympatric species S. pygmaeus.