Chapter 3 PHYLOGEOGRAPHY OF SOUTHERN HEMISPHERE BLUE MUSSELS OF THE GENUS MYTILUS: EVOLUTION, BIOSECURITY, AQUACULTURE AND FOOD LABELLING

oceanography, climate change, reefs, marine science, marine conservation, marine researc

Molecular genetic differentiation of native populations of Mediterranean blue mussels, Mytilus galloprovincialis Lamarck, 1819, and the relationship with environmental variables

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Genetic diversity and connectivity within Mytilus spp. in the subarctic and Arctic

Climate changes in the Arctic are predicted to alter distributions of marine species. However, such changes are difficult to quantify because information on present species distribution and the genetic variation within species is lacking or poorly examined. Blue mussels,Mytilusspp. are ecosystem engineers in the coastal zone globally. In order to improve knowledge of distribution and genetic structure of theMytilus eduliscomplex in the Arctic, we analyzed 81 SNPs in 534Mytilusspp. individuals sampled at 13 sites to provide baseline data for distribution and genetic variation ofMytilusmussels in the European Arctic.Mytilus eduliswas the most abundant species found with a clear genetic split between populations in Greenland and the Eastern Atlantic. Surprisingly, analyses revealed the presence ofM. trossulusin high Arctic NW Greenland (77°N) andM. galloprovincialisor their hybrids in SW Greenland, Svalbard and the Pechora Sea. Furthermore, a high degree of hybridization and introgression between species was observed. Our study highlights the importance of distinguishing between congener species, which can display local adaptation and suggests that information on dispersal routes and barriers are essential for accurate predictions of regional susceptibility to range expansions or invasions of boreal species in the Arctic

A marine biodiversity observation network for genetic monitoring of hard-bottom communities (ARMS-MBON)

Marine hard-bottom communities are undergoing severe change under the influence of multiple drivers, notably climate change, extraction of natural resources, pollution and eutrophication, habitat degradation, and invasive species. Monitoring marine biodiversity in such habitats is, however, challenging as it typically involves expensive, non-standardized, and often destructive sampling methods that limit its scalability. Differences in monitoring approaches furthermore hinders inter-comparison among monitoring programs. Here, we announce a Marine Biodiversity Observation Network (MBON) consisting of Autonomous Reef Monitoring Structures (ARMS) with the aim to assess the status and changes in benthic fauna with genomic-based methods, notably DNA metabarcoding, in combination with image-based identifications. This article presents the results of a 30-month pilot phase in which we established an operational and geographically expansive ARMS-MBON. The network currently consists of 20 observatories distributed across European coastal waters and the polar regions, in which 134 ARMS have been deployed to date. Sampling takes place annually, either as short-term deployments during the summer or as long-term deployments starting in spring. The pilot phase was used to establish a common set of standards for field sampling, genetic analysis, data management, and legal compliance, which are presented here. We also tested the potential of ARMS for combining genetic and image-based identification methods in comparative studies of benthic diversity, as well as for detecting non-indigenous species. Results show that ARMS are suitable for monitoring hard-bottom environments as they provide genetic data that can be continuously enriched, re-analyzed, and integrated with conventional data to document benthic community composition and detect non-indigenous species. Finally, we provide guidelines to expand the network and present a sustainability plan as part of the European Marine Biological Resource Centre (www.embrc.eu).Peer reviewe

Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past.

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this record.Marine mollusc shells enclose a wealth of information on coastal organisms and their environment. Their life history traits as well as (palaeo-) environmental conditions, including temperature, food availability, salinity and pollution, can be traced through the analysis of their shell (micro-) structure and biogeochemical composition. Adding to this list, the DNA entrapped in shell carbonate biominerals potentially offers a novel and complementary proxy both for reconstructing palaeoenvironments and tracking mollusc evolutionary trajectories. Here, we assess this potential by applying DNA extraction, high-throughput shotgun DNA sequencing and metagenomic analyses to marine mollusc shells spanning the last ~7,000 years. We report successful DNA extraction from shells, including a variety of ancient specimens, and find that DNA recovery is highly dependent on their biomineral structure, carbonate layer preservation and disease state. We demonstrate positive taxonomic identification of mollusc species using a combination of mitochondrial DNA genomes, barcodes, genome-scale data and metagenomic approaches. We also find shell biominerals to contain a diversity of microbial DNA from the marine environment. Finally, we reconstruct genomic sequences of organisms closely related to the Vibrio tapetis bacteria from Manila clam shells previously diagnosed with Brown Ring Disease. Our results reveal marine mollusc shells as novel genetic archives of the past, which opens new perspectives in ancient DNA research, with the potential to reconstruct the evolutionary history of molluscs, microbial communities and pathogens in the face of environmental changes. Other future applications include conservation of endangered mollusc species and aquaculture management.We thank Tom Schiøtte and Martin Vinther Sørensen at the Zoological Museum of Copenhagen for providing historical shell samples from the Invertebrate Collection. We thank Adeline Bidault for Vibrio DNA extraction, Kristian Hanghøj for technical assistance, Mikkel Schubert and Gabriel Renaud for fruitful discussions, the PALEOMIX group and the staff of the Danish National High-Throughput DNA Sequencing Centre for support. This work was supported by the Danish Council for Independent Research, Natural Sciences (FNU, 4002-00152B); the Danish National Research Foundation (DNRF94); the EPT PROXACHEOBIO from Université Européenne de Bretagne (2010–2012); the APEGE initiative PaleoCOO of the Centre National de la Recherche Scientifique; the cluster of excellence LabexMER (ANR-10-LABX-19; METHOMOL) under the program “Investissements d'Avenir”; the UK Natural Environment Research Council (NE/H023356/1); the EU Marie Curie ARAMACC Initial Training Network (FP7-PEOPLE-2013-ITN 604802); the “Chaires d'Attractivité 2014” IDEX, University of Toulouse, France (OURASI)

Evidence for a Fourteenth mtDNA-Encoded Protein in the Female-Transmitted mtDNA of Marine Mussels (Bivalvia: Mytilidae)

BACKGROUND: A novel feature for animal mitochondrial genomes has been recently established: i.e., the presence of additional, lineage-specific, mtDNA-encoded proteins with functional significance. This feature has been observed in freshwater mussels with doubly uniparental inheritance of mtDNA (DUI). The latter unique system of mtDNA transmission, which also exists in some marine mussels and marine clams, is characterized by one mt genome inherited from the female parent (F mtDNA) and one mt genome inherited from the male parent (M mtDNA). In freshwater mussels, the novel mtDNA-encoded proteins have been shown to be mt genome-specific (i.e., one novel protein for F genomes and one novel protein for M genomes). It has been hypothesized that these novel, F- and M-specific, mtDNA-encoded proteins (and/or other F- and/or M-specific mtDNA sequences) could be responsible for the different modes of mtDNA transmission in bivalves but this remains to be demonstrated. METHODOLOGY/PRINCIPAL FINDINGS: We investigated all complete (or nearly complete) female- and male-transmitted marine mussel mtDNAs previously sequenced for the presence of ORFs that could have functional importance in these bivalves. Our results confirm the presence of a novel F genome-specific mt ORF, of significant length (>100aa) and located in the control region, that most likely has functional significance in marine mussels. The identification of this ORF in five Mytilus species suggests that it has been maintained in the mytilid lineage (subfamily Mytilinae) for ∼13 million years. Furthermore, this ORF likely has a homologue in the F mt genome of Musculista senhousia, a DUI-containing mytilid species in the subfamily Crenellinae. We present evidence supporting the functionality of this F-specific ORF at the transcriptional, amino acid and nucleotide levels. CONCLUSIONS/SIGNIFICANCE: Our results offer support for the hypothesis that "novel F genome-specific mitochondrial genes" are involved in key biological functions in bivalve species with DUI

Influence of selected additives and admixtures on underwater concrete and the environment

The intensive civilization development implies searching for new possibilities connected with extension of city agglomerations, both the areas of flat building and the industrial areas. One of the most interesting solution is to use water reservoirs, rivers and sea areas. The extension of buildings affects the building materials, especially hydrotechnical concrete. Water structures are usually the objects of huge dimensions exposed to extreme conditions. In most cases these buildings are specific and complicated. They require an individual approach to concrete mix design and should be monitored by measurement technologies supported by automated numerical examinations. Nowadays health monitoring systems are applied to large variety of engineering structures. In order to get the required quality of hydrotechnical concrete, additives and admixtures are necessary. The material properties of underwater concrete can be also improved using polymer and steel fibers of various content and length. The majority of areas are built of concrete, that is the reason to be aware of admixture influence on the environment and living organisms. The attempt to evaluate the description of different kinds of hydrotechnical concrete as potential habitat of water organisms, was indicated in the paper