Practical issues affecting the utility of field survey data for biodiversity monitoring

There is growing emphasis on monitoring biodiversity in European waters not least due to the EC’s recent Marine Strategy Framework Directive (MSFD) listing biodiversity as one descriptor of ‘Good Environmental Status’ (GES). Member States already have various monitoring surveys in place, in particular groundfish and other fisheries surveys, which may provide a cost-effective way of assessing some elements of biodiversity. The MSFD recognises the “need to ensure, as far as possible, compatibility with existing programmes”. Although existing field surveys are a potential source of quantitative data for examining spatial and temporal biodiversity patterns, it must be acknowledged that such surveys were often not originally designed to monitor ‘biodiversity’, and long-term surveys may have had changes in survey design at some point, and/or subtle changes in survey protocols over time. Field surveys for infauna and plankton typically collect and preserve samples at sea, and subsequent laboratory work includes the use of reference collections, quality assurance and longer-term sample storage. Surveys with towed gears can collect large amounts of complex biological material which is typically processed at sea, and so different forms of quality assurance are required. The taxonomic knowledge, experience and enthusiasm of sea-going staff can also influence the biodiversity information collected (e.g. time spent sorting complex catches, species identification). Hence, matrices of species-station data can contain ‘artefacts’ that need to be understood and addressed before deriving biodiversity metrics, and may even necessitate some degree of data filtering. This paper uses field data from selected surveys to illustrate how various factors can affect ‘biodiversity information’

Circadian clock mechanism driving mammalian photoperiodism.

The annual photoperiod cycle provides the critical environmental cue synchronizing rhythms of life in seasonal habitats. In 1936, Bünning proposed a circadian-basis for photoperiodic synchronization. Here, light-dark cycles entrain a circadian rhythm of photosensitivity, and the expression of summer or winter biology depends on whether light coincides with the phase of high photosensitivity. Formal studies support the universality of this so-called coincidence timer, but we lack understanding of the mechanisms involved. Here we show in mammals that coincidence timing takes place in the pars tuberalis of the pituitary, through a melatonin-dependent flip-flop switch between circadian transcriptional activation and repression. Long photoperiods produce short night-time melatonin signals, leading to induction of the circadian transcription factor BMAL2, in turn triggering summer biology through the eyes absent / thyrotrophin (EYA3 / TSH) pathway. Conversely, short photoperiods produce long melatonin signals, inducing circadian repressors including DEC1, in turn suppressing BMAL2 and the EYA3/TSH pathway, triggering winter biology. These actions are associated with progressive genome-wide changes in chromatin state, elaborating the effect of the circadian coincidence timer. Hence, circadian clock interactions with pituitary epigenetic pathways form the basis of the mammalian coincidence timer mechanism. Our results constitute a blueprint for circadian-based seasonal timekeeping in vertebrates

Targeted reprogramming of H3K27me3 resets epigenetic memory in plant paternal chromatin

Epigenetic marks are reprogrammed in the gametes to reset genomic potential in the next generation. In mammals, paternal chromatin is extensively reprogrammed through the global erasure of DNA methylation and the exchange of histones with protamines(1,2). Precisely how the paternal epigenome is reprogrammed in flowering plants has remained unclear since DNA is not demethylated and histones are retained in sperm(3,4). Here, we describe a multi-layered mechanism by which H3K27me3 is globally lost from histone-based sperm chromatin in Arabidopsis. This mechanism involves the silencing of H3K27me3 writers, activity of H3K27me3 erasers and deposition of a sperm-specific histone, H3.10 (ref. (5)), which we show is immune to lysine 27 methylation. The loss of H3K27me3 facilitates the transcription of genes essential for spermatogenesis and pre-configures sperm with a chromatin state that forecasts gene expression in the next generation. Thus, plants have evolved a specific mechanism to simultaneously differentiate male gametes and reprogram the paternal epigenome

Cross-basin and cross-taxa patterns of marine community tropicalization and deborealization in warming European seas

Ocean warming and acidification, decreases in dissolved oxygen concentrations, and changes in primary production are causing an unprecedented global redistribution of marine life. The identification of underlying ecological processes underpinning marine species turnover, particularly the prevalence of increases of warm-water species or declines of cold-water species, has been recently debated in the context of ocean warming. Here, we track changes in the mean thermal affinity of marine communities across European seas by calculating the Community Temperature Index for 65 biodiversity time series collected over four decades and containing 1,817 species from different communities (zooplankton, coastal benthos, pelagic and demersal inverte�brates and fish). We show that most communities and sites have clearly responded to ongoing ocean warming via abundance increases of warm-water species (tropicalization, 54%) and decreases of cold-water species (debor�ealization, 18%). Tropicalization dominated Atlantic sites compared to semi�enclosed basins such as the Mediterranean and Baltic Seas, probably due to physical barrier constraints to connectivity and species colonization. Semi�enclosed basins appeared to be particularly vulnerable to ocean warming, experiencing the fastest rates of warming and biodiversity loss through deborealization

A generic approach to develop a trait-based indicator of trawling-induced disturbance

Biological trait analysis has become a popular tool to infer the vulnerability of benthic species to trawling-induced disturbance. Approaches using multiple traits are being developed, but their generic relevance across faunal components and geographic locations remains poorly tested, and the importance of confounding effects are poorly recognised. This study integrates biological traits of benthic species that are responsive to instantaneous effects of trawling (i.e. sensitivity) and traits expressing recoverability over the longer term (i.e. years). We highlight the functional independence between these 2 components in response to trawling, test the behaviours of single and combined traits and account for potential confounding effects of environment and trawling intensity on benthic communities through variation partitioning. Two case studies are considered: epibenthos from the Bay of Biscay and endobenthos of the Dutch sector of the North Sea. The response to trawling is most pronounced when multiple traits covering different aspects that determine population dynamics (i.e. sensitivity and recoverability) are combined, despite confounding effects between gradients of benthic production and trawling intensity, especially for endobenthos. The integration of traits reflecting both sensitivity and recoverability provides complementary information on the faunal response to trawling, bridging the gap between fishing impact assessments and benthic community status assessment

Stability of the relationships among demersal fish assemblages and environmental-trawling drivers at large spatio-temporal scales in the northern Mediterranean Sea

Trawling pressure and environmental changes may affect the composition of fish assemblages. Our knowledge on large spatio-temporal patterns of demersal fish composition remains incomplete for the Mediterranean Sea. We investigated (1) the spatio-temporal stability of demersal assemblages, (2) the relationships between these assemblages and potential structuring factors (trawling pressure and environmental conditions) in order to assess the dynamic of the assemblage structure at the scale of the northern Mediterranean Sea. We analysed a dataset of 18062 hauls from 10 to 800 m depth performed annually during the last two decades across 17 Geographical Sub-Areas (GSAs) (MEDITS program). A multi-table analysis (STATICO-CoA) evidenced a strong inter-GSAs stability in the organization of assemblages, with specificities for some GSAs. The most stable structuring factors were linked to combined gradients of chlorophyll a, phytoplancton carbon biomass and temperature, inversely correlated with depth, salinity and nutrient gradients (axis 1 of the STATICO-CoA compromise, 93.74% of the total variability). A common pattern linking the distribution of species to these environmental gradients was evidenced for most of the 17 GSAs. Estimate of trawling pressure showed a minor role in the organization of the assemblages for the spatial scale and years investigated (axis 2, 4.67%)