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- Assessing genetic diversity in clonal organisms: low diversity or low resolution? Combining power and cost efficiency in selecting markersPublication . ARNAUD-HAOND, Sophie; Alberto, F.; Teixeira, Sara; Procaccini, G.; Serrão, Ester; Duarte, C. M.The increasing use of molecular tools to study populations of clonal organisms leads us to question whether the low polymorphism found in many studies reflects limited genetic diversity in populations or the limitations of the markers used. Here we used microsatellite datasets for two sea grass species to provide a combinatory statistic, combined with a likelihood approach to estimate the probability of identical multilocus genotypes (MLGs) to be shared by distinct individuals, in order to ascertain the efficiency of the markers used and to optimize cost-efficiently the choice of markers to use for deriving unbiased estimates of genetic diversity. These results strongly indicate that conclusions from studies on clonal organisms derived using markers showing low polymorphism, including microsatellites, should be reassessed using appropriate polymorphic markers.
- Genetic structure at range edge: Low diversity and high inbreeding in Southeast Asian mangrove (Avicennia marina) populationsPublication . ARNAUD-HAOND, Sophie; Teixeira, Sara; Massa, S. I.; Billot, C.; Saenger, P.; Coupland, G.; Duarte, C. M.; Serrão, EsterUnderstanding the genetic composition and mating systems of edge populations provides important insights into the environmental and demographic factors shaping species’ distribution ranges. We analysed samples of the mangrove Avicennia marina from Vietnam, northern Philippines and Australia, with microsatellite markers. We compared genetic diversity and structure in edge (Southeast Asia, and Southern Australia) and core (North and Eastern Australia) populations, and also compared our results with previously published data from core and southern edge populations. Comparisons highlighted significantly reduced gene diversity and higher genetic structure in both margins compared to core populations, which can be attributed to very low effective population size, pollinator scarcity and high environmental pressure at distribution margins. The estimated level of inbreeding was significantly higher in northeastern populations compared to core and southern populations. This suggests that despite the high genetic load usually associated with inbreeding, inbreeding or even selfing may be advantageous in margin habitats due to the possible advantages of reproductive assurance, or local adaptation. The very high level of genetic structure and inbreeding show that populations of A. marina are functioning as independent evolutionary units more than as components of a metapopulation system connected by gene flow. The combinations of those characteristics make these peripheral populations likely to develop local adaptations and therefore to be of particular interest for conservation strategies as well as for adaptation to possible future environmental changes.
- Polymorphic microsatellite markers in the brown seaweed Fucus vesiculosusPublication . Candeias, Rui; Casado-Amezúa, Pilar; Pearson, G. A.; Serrão, Ester; Teixeira, SaraBackground: Fucus vesiculosus is a brown seaweed dominant on temperate rocky shores of the northern hemisphere and, is typically distributed in the mid-upper intertidal zone. It is an external fertilizer that reproduces sexually, providing an excellent model to address conflicting theories related to mating systems and sexual selection. Microsatellite markers have been reported for several Fucus species, however the genomic libraries from where these markers have been isolated, have originated from two or more species pooled together (F. vesiculosus and F. serratus in one library; F. vesiculosus, F. serratus and Ascophyllum nodosum in a second library), or when the genomic DNA originated from only one species it was from Fucus spiralis. Although these markers cross-amplify F. vesiculosus individuals, the level of polymorphism has been low for relatedness studies. Findings: The microsatellite markers described here were obtained from an enriched genomic library, followed by 454 pyrosequencing. A total of 9 microsatellite markers were tested across 44 individuals from the North of Portugal. The mean number of alleles across loci was 8.7 and the gene diversity 0.67. Conclusions: The high variability displayed by these microsatellite loci should be useful for paternity analysis, assessing variance of reproductive success and in estimations of genetic variation within and between populations.
- Characterization of polymorphic microsatellite loci in the Antarctic krill Euphausia superbaPublication . Candeias, Rui; Teixeira, Sara; Duarte, C. M.; Pearson, G. A.Background: The Antarctic krill, Euphausia superba is a pelagic crustacean, abundant in high-density swarms (10 000 – 30 000 ind/m2) with a circumpolar distribution and a key role in the food web of the Southern Ocean. Only three EST derived microsatellite markers have been used in previous genetic studies, hence we developed additional highly polymorphic microsatellite markers to allow robust studies of the genetic variability and population differentiation within this species. Findings: The microsatellite markers described here were obtained through an enriched genomic library, followed by 454 pyrosequencing. A total of 10 microsatellite markers were tested in 32 individuals from the Antarctic Peninsula. One of the tested loci was fixed for one allele while the other was variable. Of the remaining nine markers, seven showed no departure from Hardy-Weinberg equilibrium. The mean number of alleles was 14.9. Conclusions: These markers open perspectives for population genetic studies of this species to unravel genetic structure, dispersal and population biology, vital information for future conservation.
- High connectivity across the fragmented chemosynthetic ecosystems of the deep Atlantic Equatorial Belt: efficient dispersal mechanisms or questionable endemism?Publication . Teixeira, Sara; Olu, Karine; Decker, C.; Cunha, R. L.; Fuchs, S.; Hourdez, S.; Serrão, Ester; ARNAUD-HAOND, SophieChemosynthetic ecosystems are distributed worldwide in fragmented habitats harbouring seemingly highly specialized communities. Yet, shared taxa have been reported from highly distant chemosynthetic communities. These habitats are distributed in distinct biogeographical regions, one of these being the so-called Atlantic Equatorial Belt (AEB). Here, we combined genetic data (COI) from several taxa to assess the possible existence of cryptic or synonymous species and to detect the possible occurrence of contemporary gene flow among populations of chemosynthetic species located on both sides of the Atlantic. Several Evolutionary Significant Units (ESUs) of Alvinocarididae shrimp and Vesicomyidae bivalves were found to be shared across seeps of the AEB. Some were also common to hydrothermal vent communities of the Mid-Atlantic Ridge (MAR), encompassing taxa morphologically described as distinct species or even genera. The hypothesis of current or very recent large-scale gene flow among seeps and vents was supported by microsatellite analysis of the shrimp species Alvinocaris muricola/ Alvinocaris markensis across the AEB and MAR. Two nonmutually exclusive hypotheses may explain these findings. The dispersion of larvae or adults following strong deep-sea currents, possibly combined with biochemical cues influencing the duration of larval development and timing of metamorphosis, may result in large-scale effective migration among distant spots scattered on the oceanic seafloor. Alternatively, these results may arise from the prevailing lack of knowledge on the ocean seabed, apart from emblematic ecosystems (chemosynthetic ecosystems, coral reefs or seamounts), where the widespread classification of endemism associated with many chemosynthetic taxa might hide wider distributions in overlooked parts of the deep sea.
- Recent population expansion and connectivity in the hydrothermal shrimp Rimicaris exoculata along the Mid-Atlantic RidgePublication . Teixeira, Sara; Cambon-Bonavita, M.- A.; Serrão, Ester; Desbruyéres, D.; ARNAUD-HAOND, SophieAim: Deep-sea hydrothermal vents are unstable habitats that are both spatially and temporally fragmented. In vent species, a ‘short-term insurance’ hypothesis would lead us to expect mostly self-recruitment, limiting the loss of larvae in the deep ocean or water column and increasing genetic differentiation over the time elapsed since colonization. Alternatively, a ‘long-term insurance’ hypothesis would support the prediction of selection for large-scale dispersal, to ensure longterm persistence in these ephemeral habitats. The main goal of this study was to infer the spatial and temporal distribution of genetic diversity of the shrimp Rimicaris exoculata, which forms high-density local populations on hydrothermal vents along the Mid-Atlantic ridge. Location: Deep-sea hydrothermal vents along the Mid-Atlantic Ridge. Methods: We used sequences of mitochondrial cytochrome c oxidase subunit I (COI, 710 bp) to assess the spatio-temporal distribution of genetic diversity across five hydrothermal fields from 36 N to 4 S. Results: In contrast to previous results from pioneer studies, very high haplotype diversity was observed in vents across the entire region (i.e. 0.69–0.82), indicating current large effective population size and low drift. The star-like shape of the network of haplotypes, the lack of spatial genetic structure and the significance of tests reflecting demographic effects, together with the fitting of a population expansion model, all support a recent population expansion. Main conclusions: Our results suggest a very recent common history of R. exoculata populations/demes along the Mid-Atlantic Ridge, derived after a common bottleneck or founder event and followed by a concomitant demographic expansion. This study therefore suggests a large effective population size and/or high dispersal capacity, as well as a possible recent (re)colonization of Mid-Atlantic hydrothermal vents by R. exoculata.
- High connectivity among Vesicomyid bivalves from cold seeps and deep-sea fans of CongoPublication . Hassan, Mohamad; Teixeira, Sara; Decker, Carole; Fuchs, Sandra; Mouchel, Olivier; Olu, Karine; Arnaud-Haond, SophieChemosynthetic ecosystems are scattered in the deep ocean, harbouring highly specialized communities, among which the degree of connectivity and dispersal is scarcely studied. This gap is largely due to limited range distribution, either real or due to highly partial exploration, preventing the availability of a sufficient number of samples for population genetic analysis. For the few species that escaped this gap, large-scale panmixia was often reported, raising wonders as to the evolutionary mechanisms involved in the first steps of speciation. Vesicomyid bivalves are one of the most abundant groups of chemosynthetic fauna, for which depth was proposed as an essential driver of differentiation. Early stages of speciation are thus expected to involve genetic differentiation along depth gradients. The vesicomyid bivalve Christineconcha regab was studied across widely separated localities along the Western African margin, from the cold-seeps of Regab pockmarks located at 3150 m depth on the Congo margin to the turbiditic lobes of the Congo deep-sea fan located at 5000 m depth, using mitochondrial (COI) sequences and eight microsatellite loci. Despite rather high density in relation to high organic matter availability, results obtained showed rather low levels of genetic diversity at both mtDNA and microsatellites. The main consistent pattern of differentiation was observed across depths from Regab pockmark (South-Western part) and lobe areas (Lobe B and C). This is likely due to the largest sample sizes characterizing Regab_SW and Lobe C allowing the detection of faint genetic differentiation, and possibly to a stronger signature in the demographically declining (thus acknowledgedly under sampled) Lobe B. Other significant results were not congruent among markers, suggesting low statistical power due to limited sample size or the occurrence of chaotic genetic patchiness. Altogether, the results suggest the occurrence of effective gene flow at regional scale, and departure from equilibrium in the recently discovered lobes of the Congo River, possibly resulting from unstable environmental conditions and recurrent events of extinction recolonization.