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’

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

Are well-studied marine biodiversity hotspots still blackspots for animal barcoding?

Marine biodiversity underpins ecosystem health and societal well-being. Preservation of biodiversity hotspots is a global challenge. Molecular tools, like DNA barcoding and metabarcoding, hold great potential for biodiversity monitoring, possibly outperforming more traditional taxonomic methods. However, metabarcoding-based biodiversity assessments are limited by the availability of sequences in barcoding reference databases; a lack thereof results in high percentages of unassigned sequences. In this study we (i) present the current status of known vs. barcoded marine species at a global scale based on online taxonomic and genetic databases; and (ii) compare the current status with data from ten years ago. Then we analyzed occurrence data of marine animal species from five Large Marine Ecosystems (LMEs) classified as biodiversity hotspots, to identify any consistent disparities in COI barcoding coverage between geographic regions and at phylum level. Barcoding coverage varied among LMEs (from 36.8% to 62.4% COI-barcoded species) and phyla (from 4.8% to 74.7% COI-barcoded species), with Porifera, Bryozoa and Platyhelminthes being highly underrepresented, compared to Chordata, Arthropoda and Mollusca. We demonstrate that although barcoded marine species increased from 9.5% to 14.2% since the last assessment in 2011, about 15,000 (corresponding to 7.8% increase) new species were described from 2011 to 2021. The next ten years will thus be crucial to enroll concrete collaborative measures and long term initiatives (e.g., Horizon 2030, Ocean Decade) to populate barcoding libraries for the marine realm.the Department of Biological, Geological and Environmental Sciences (BiGeA) of the University of Bologna (UniBo). The CoMBoMed initiative was supported by the European Marine Research Network (EUROMARINE Network), the Inter-Departmental Research Centre for Environmental Sciences (CIRSA – UniBo), the Cultural Heritage Department (DBC - UniBo, https://beniculturali.unibo.it/it), the Fondazione Flaminia and the ERANet Mar-Tera Project SEAMoBB (Solutions for sEmi-Automated Monitoring of Benthic Biodiversity).Peer reviewe

Autosomal differences between males and females in hybrid zones: a first report from Barbus barbus and Barbus meridionalis (Cyprinidae)

International audienceNarrow hybrid zones are generally subjected to the action of two forces: dispersal, which tends to homogenise the hybridising taxa, and selection against hybrids, which, in contrast, produces steep clines of introgression for diagnostic markers. Although differences between sexes in dispersal abilities or in susceptibility to hybrid counterselection are common in hybrid zones, autosomal genetic differences between males and females have never been reported to our knowledge. Barbus barbus and Barbus meridionalis (Cyprinidae) form a hybrid zone along the Lergue river. By carrying out a genetic analysis of males and females in six samples from two central stations of the hybrid zone using codominant markers (six allozymes and four microsatellite loci), we revealed significant multilocus and monolocus differences between the sexes. This could reflect a genetic difference among sexes within a same cohort, caused either by a survival (or fertility) differential among sexes or by a sex-specific pattern of dispersal. Alternatively, this may be due to genetic differentiation between cohorts, since male and female barbel exhibit different maturation, growth and survival patterns leading to different age distributions among sexes, and particularly among reproducers