Pleistocene separation of mitochondrial lineages of Mytilus spp. mussels from Northern and Southern Hemispheres and strong genetic differentiation among southern populations

International audienceSmooth-shelled mussels, Mytilus spp., have an antitropical distribution. In the Northern Hemisphere, the M. edulis complex of species is composed of three genetically well delineated taxa: M. edulis, M. galloprovincialis and M. trossulus. In the Southern Hemisphere, morphological characters, allozymes and intron length polymorphisms suggest that Mytilus spp. populations from South America and Kerguelen Islands are related to M. edulis and those from Australasia to M. galloprovincialis. On the other hand, a phylogeny of the 16S rDNA mitochondrial locus demonstrates a clear distinctiveness of southern mussels and suggests that they are related to Mediterranean M. galloprovincialis. Here, we analysed the faster-evolving cytochrome oxidase subunit I locus. The divergence between haplotypes of populations from the two hemispheres was confirmed and was found to predate the divergence between haplotypes of northern M. edulis and M. galloprovincialis. In addition, strong genetic structure was detected among the southern samples, revealing three genetic entities that correspond to (1) South America and Kerguelen Island, (2) Tasmania, (3) New Zealand. Using the trans-Arctic interchange as a molecular clock calibration, we estimated the time since divergence of populations from the two hemispheres to be between 0.5 million years (MY) and 1.3 MY (average 0.84 MY). The contrasting patterns observed for the nuclear and the organelle genomes suggested two alternative, complex scenarios: two trans-equatorial migrations and the existence of differential barriers to mitochondrial and nuclear gene flow, or a single trans-equatorial migration and a view of the composition of the nuclear genome biased by taxonomic preconception

Translational machinery of the chaetognath Spadella cephaloptera: a transcriptomic approach to the analysis of cytosolic ribosomal protein genes and their expression

<p>Abstract</p> <p>Background</p> <p>Chaetognaths, or arrow worms, are small marine, bilaterally symmetrical metazoans. The objective of this study was to analyse ribosomal protein (RP) coding sequences from a published collection of expressed sequence tags (ESTs) from a chaetognath (<it>Spadella cephaloptera</it>) and to use them in phylogenetic studies.</p> <p>Results</p> <p>This analysis has allowed us to determine the complete primary structures of 23 out of 32 RPs from the small ribosomal subunit (SSU) and 32 out of 47 RPs from the large ribosomal subunit (LSU). Ten proteins are partially determined and 14 proteins are missing. Phylogenetic analyses of concatenated RPs from six animals (chaetognath, echinoderm, mammalian, insect, mollusc and sponge) and one fungal taxa do not resolve the chaetognath phylogenetic position, although each mega-sequence comprises approximately 5,000 amino acid residues. This is probably due to the extremely biased base composition and to the high evolutionary rates in chaetognaths. However, the analysis of chaetognath RP genes revealed three unique features in the animal Kingdom. First, whereas generally in animals one RP appeared to have a single type of mRNA, two or more genes are generally transcribed for one RP type in chaetognath. Second, cDNAs with complete 5'-ends encoding a given protein sequence can be divided in two sub-groups according to a short region in their 5'-ends: two novel and highly conserved elements have been identified (5'-TAATTGAGTAGTTT-3' and 5'-TATTAAGTACTAC-3') which could correspond to different transcription factor binding sites on paralog RP genes. And, third, the overall number of deduced paralogous RPs is very high compared to those published for other animals.</p> <p>Conclusion</p> <p>These results suggest that in chaetognaths the deleterious effects of the presence of paralogous RPs, such as apoptosis or cancer are avoided, and also that in each protein family, some of the members could have tissue-specific and extra-ribosomal functions. These results are congruent with the hypotheses of an allopolyploid origin of this phylum and of a ribosome heterogeneity.</p

Comparative phylogeography of two sister (congeneric) species of cardiid bivalve: Strong influence of habitat, life history and post-glacial history

International audienceSister (congeneric) species may exhibit disparate patterns of biogeographic genetic structures due to different life histories and habitat preferences. The common cockle Cerastoderma edule and the lagoon cockle Cerastoderma glaucum probably diverged from their common ancestor in the present territory of Sahara around 5 million years ago. Although it is difficult to separate both species morphologically, various genetic markers, both mitochondrial and nuclear, clearly distinguish them. Furthermore, their lifestyles are different, as C. edule has a much less fragmented coastal habitat and a longer duration of pelagic larval stage than C. glaucum. A comparative genetic analysis was conducted on 17 populations of C. edule and 13 populations of C. glaucum using a 506 bp fragment of mitochondrial DNA (COI).We tested the hypothesis that differences in habitat types and life history are reflected in the genetic structure patterns of these two cockles. Indeed substantial differences in population genetic structures between them are revealed. Genetic diversity within C. glaucum populations decreases northwards as a consequence of post-glacial (re)colonization from southern refugia, while C. edule displays an opposite pattern indicating survival in glacial refuges in the northern Atlantic. Among populations within geographic groups, genetic differentiation is low in C. edule, probably as a result of larval dispersal with coastal currents, while it is extremely high in C. glaucum, best explained by the fragmented habitats. Interestingly, long distance divergence is less expressed in C. glaucum than in C. edule, which supports the speculation that migrating birds (frequently observed in lagoons) may occasionally transport the former more often or more efficiently than the latter. The approach applied in this study (e.g., rarefaction procedure, selection of samples of both species from the same regions) enabled a new and reliable comparative analysis of the existing raw datasets

Quantitative criteria for choosing targets and indicators for sustainable use of ecosystems

The authors thank Simon Greenstreet, Cristina Herbon, Simon Jennings, Tiziana Luisetti, Lucille Paltriguera, and Christian Wilson for comments on previous versions of this paper. This work has resulted from the DEVOTES (DEVelopment Of innovative Tools for understanding marine biodiversity and assessing Good Environmental Status) project funded by the EU under the 7th Framework Programme, ‘The Ocean of Tomorrow’ Theme (No. 308392), www.devotes-project.eu. Further, A.G.R. was partially funded by the Natural Environment Research Council and the UK Department for Food, Environment and Rural Affairs (Defra) within the Marine Ecosystems Research Program (MERP), C.P.L. by Defra (M1228), A.Z. by BIOsingle bondC3 within the joint Baltic Sea Research and Development Programme (EU 7th and Research Council of Lithuania, BONUS-1/2014), and M.C.U. by the Spanish Programme for talent and employability in I + D + i ‘Torres Quevedo’

An efficient method to find potentially universal population genetic markers, applied to metazoans

<p>Abstract</p> <p>Background</p> <p>Despite the impressive growth of sequence databases, the limited availability of nuclear markers that are sufficiently polymorphic for population genetics and phylogeography and applicable across various phyla restricts many potential studies, particularly in non-model organisms. Numerous introns have invariant positions among kingdoms, providing a potential source for such markers. Unfortunately, most of the few known EPIC (Exon Primed Intron Crossing) loci are restricted to vertebrates or belong to multigenic families.</p> <p>Results</p> <p>In order to develop markers with broad applicability, we designed a bioinformatic approach aimed at avoiding multigenic families while identifying intron positions conserved across metazoan phyla. We developed a program facilitating the identification of EPIC loci which allowed slight variation in intron position. From the <it>Homolens </it>databases we selected 29 gene families which contained 52 promising introns for which we designed 93 primer pairs. PCR tests were performed on several ascidians, echinoderms, bivalves and cnidarians. On average, 24 different introns per genus were amplified in bilaterians. Remarkably, five of the introns successfully amplified in all of the metazoan genera tested (a dozen genera, including cnidarians). The influence of several factors on amplification success was investigated. Success rate was not related to the phylogenetic relatedness of a taxon to the groups that most influenced primer design, showing that these EPIC markers are extremely conserved in animals.</p> <p>Conclusions</p> <p>Our new method now makes it possible to (i) rapidly isolate a set of EPIC markers for any phylum, even outside the animal kingdom, and thus, (ii) compare genetic diversity at potentially homologous polymorphic loci between divergent taxa.</p

Does natural selection explain the fine scale genetic structure at the nuclear exon Glu-5 0 in blue mussels from Kerguelen?

Abstract The Kerguelen archipelago, isolated in the Southern Ocean, shelters a blue mussel Mytilus metapopulation far from any influence of continental populations or any known hybrid zone. The finely carved coast leads to a highly heterogeneous habitat. We investigated the impact of the environment on the genetic structure in those Kerguelen blue mussels by relating allele frequencies to habitat descriptors. A total sample comprising up to 2248 individuals from 35 locations was characterized using two nuclear markers, mac-1 and Glu-5 0 , and a mitochondrial marker (COI). The frequency data from 9 allozyme loci in 9 of these locations were also reanalyzed. Two other nuclear markers (EFbis and EFprem&apos;s) were monomorphic. Compared to Northern Hemisphere populations, polymorphism in Kerguelen blue mussels was lower for all markers except for the exon Glu-5 0 . At Glu-5 0 , genetic differences were observed between samples from distinct regions (F CT = 0.077), as well as within two regions, including between samples separated by &lt;500 m. No significant differentiation was observed in the AMOVA analyses at the two other markers (mac-1 and COI). Like mac-1, all allozyme loci genotyped in a previous publication, displayed lower differentiation (Jost&apos;s D) and F ST values than Glu-5 0 . Power simulations and confidence intervals support that Glu-5 0 displays significantly higher differentiation than the other loci (except a single allozyme for which confidence intervals overlap). AMOVA analyses revealed significant effects of the giant kelp Macrocystis and wave exposure on this marker. We discuss the influence of hydrological conditions on the genetic differentiation among regions. In marine organisms with high fecundity and high dispersal potential, gene flow tends to erase differentiation, but this study showed significant differentiation at very small distance. This may be explained by the particular hydrology and the carved coastline of the Kerguelen archipelago, together with spatially variable selection at Glu-5 0

Dispersal similarly shapes both population genetics and community patterns in the marine realm.

Dispersal plays a key role to connect populations and, if limited, is one of the main processes to maintain and generate regional biodiversity. According to neutral theories of molecular evolution and biodiversity, dispersal limitation of propagules and population stochasticity are integral to shaping both genetic and community structure. We conducted a parallel analysis of biological connectivity at genetic and community levels in marine groups with different dispersal traits. We compiled large data sets of population genetic structure (98 benthic macroinvertebrate and 35 planktonic species) and biogeographic data (2193 benthic macroinvertebrate and 734 planktonic species). We estimated dispersal distances from population genetic data (i.e., FST vs. geographic distance) and from β-diversity at the community level. Dispersal distances ranked the biological groups in the same order at both genetic and community levels, as predicted by organism dispersal ability and seascape connectivity: macrozoobenthic species without dispersing larvae, followed by macrozoobenthic species with dispersing larvae and plankton (phyto- and zooplankton). This ranking order is associated with constraints to the movement of macrozoobenthos within the seabed compared with the pelagic habitat. We showed that dispersal limitation similarly determines the connectivity degree of communities and populations, supporting the predictions of neutral theories in marine biodiversity patterns.RADIALES (IEO)Versión del edito

Report on identification of keystone species and processes across regional seas. DEVOTES FP7 Project

WP6, Deliverable 6.1, DEVOTES ProjectIn managing for marine biodiversity, it is worth recognising that, whilst every species contributes to biodiversity, each contribution is not of equal importance. Some have important effects and interactions, both primary and secondary, on other components in the community and therefore by their presence or absence directly affect the biodiversity of the community as a whole. Keystone species have been defined as species that have a disproportionate effect on their environment relative to their abundance. As such, keystone species might be of particular relevance for the marine biodiversity characterisation within the assessment of Good Environmental Status (GEnS), for the Marine Strategy Framework Directive (MSFD).The DEVOTES Keystone Catalogue and associated deliverable document is a review of potential keystone species of the different European marine habitats. The catalogue has 844 individual entries, which includes 210 distinct species and 19 groups classified by major habitat in the Baltic Sea, North East Atlantic, Mediterranean, Black Sea (EU Regional Seas) and Norwegian Sea (Non-­‐EU Sea). The catalogue and the report make use/cite 164 and 204 sources respectively. The keystones in the catalogue are indicated by models, by use as indicators, by published work (e.g. on traits and interactions with other species), and by expert opinion based on understanding of systems and roles of species/groups. A total of 74 species were considered to act as keystone predators, 79 as keystone engineers, 66 as keystone habitat forming species, while a few were thought of having multiple roles in their marine ecosystems. Benthic invertebrates accounted for 50% of the reported keystone species/groups, while macroalgae contributed 17% and fish12%. Angiosperms were consistently put forward as keystone habitat forming and engineering species in all areas. A significant number of keystones were invasive alien species.Only one keystone, the bivalve Mya arenaria, was common to all four EU regional seas. The Mediterranean Sea had the largest number of potential keystones (56% of the entries) with the least in the Norwegian Sea. There were very few keystones in deep waters (Bathyal-­‐Abyssal, 200+ m), with most reported in sublittoral shallow and shelf seabeds or for pelagic species in marine waters with few in reduced/variable salinity waters. The gaps in coverage and expertise in the catalogue are analysed at the habitat and sea level, within the MSFD biodiversity component groups and in light of knowledge and outputs from ecosystem models (Ecopath with Ecosim).The understanding of keystones is discussed as to when a species may be a dominant or keystone with respect to the definition term concerning ‘disproportionate abundance’, how important are the ‘disproportionate effects’ in relation to habitat formers and engineers, what separates a key predator and key prey for mid-­‐trophic range species and how context dependency makes a species a keystone. Keystone alien invasive species are reviewed and the use of keystone species model outputs investigated. In the penultimate sections of the review the current level of protection on keystone species and the possibilities for a keystone operational metric and their use in management and in GEnS assessments for the MSFD are discussed. The final section highlights the one keystone species and its interactions not covered in the catalogue but with the greatest impact on almost all marine ecosystems, Homo sapiens

A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses

<p>Abstract</p> <p>Background</p> <p>Polyploidy is important from a phylogenetic perspective because of its immense past impact on evolution and its potential future impact on diversification, survival and adaptation, especially in plants. Molecular population genetics studies of polyploid organisms have been difficult because of problems in sequencing multiple-copy nuclear genes using Sanger sequencing. This paper describes a method for sequencing a barcoded mixture of targeted gene regions using next-generation sequencing methods to overcome these problems.</p> <p>Results</p> <p>Using 64 3-bp barcodes, we successfully sequenced three chloroplast and two nuclear gene regions (each of which contained two gene copies with up to two alleles per individual) in a total of 60 individuals across 11 species of Australian <it>Poa </it>grasses. This method had high replicability, a low sequencing error rate (after appropriate quality control) and a low rate of missing data. Eighty-eight percent of the 320 gene/individual combinations produced sequence reads, and >80% of individuals produced sufficient reads to detect all four possible nuclear alleles of the homeologous nuclear loci with 95% probability.</p> <p>We applied this method to a group of sympatric Australian alpine <it>Poa </it>species, which we discovered to share an allopolyploid ancestor with a group of American <it>Poa </it>species. All markers revealed extensive allele sharing among the Australian species and so we recommend that the current taxonomy be re-examined. We also detected hypermutation in the <it>trn</it>H-<it>psb</it>A marker, suggesting it should not be used as a land plant barcode region. Some markers indicated differentiation between Tasmanian and mainland samples. Significant positive spatial genetic structure was detected at <100 km with chloroplast but not nuclear markers, which may be a result of restricted seed flow and long-distance pollen flow in this wind-pollinated group.</p> <p>Conclusions</p> <p>Our results demonstrate that 454 sequencing of barcoded amplicon mixtures can be used to reliably sample all alleles of homeologous loci in polyploid species and successfully investigate phylogenetic relationships among species, as well as to investigate phylogeographic hypotheses. This next-generation sequencing method is more affordable than and at least as reliable as bacterial cloning. It could be applied to any experiment involving sequencing of amplicon mixtures.</p