Cross-realm assessment of climate change impacts on species' abundance trends

Climate change, land-use change, pollution and exploitation are among the main drivers of species' population trends; however, their relative importance is much debated. We used a unique collection of over 1,000 local population time series in 22 communities across terrestrial, freshwater and marine realms within central Europe to compare the impacts of long-term temperature change and other environmental drivers from 1980 onwards. To disentangle different drivers, we related species' population trends to species- and driver-specific attributes, such as temperature and habitat preference or pollution tolerance. We found a consistent impact of temperature change on the local abundances of terrestrial species. Populations of warm-dwelling species increased more than those of cold-dwelling species. In contrast, impacts of temperature change on aquatic species' abundances were variable. Effects of temperature preference were more consistent in terrestrial communities than effects of habitat preference, suggesting that the impacts of temperature change have become widespread for recent changes in abundance within many terrestrial communities of central Europe.Additionally, we appreciate the open access marine data provided by the International Council for the Exploration of the Sea. We thank the following scientists for taxonomic or technical advice: C. Brendel, T. Caprano, R. Claus, K. Desender, A. Flakus, P. R. Flakus, S. Fritz, E.-M. Gerstner, J.-P. Maelfait, E.-L. Neuschulz, S. Pauls, C. Printzen, I. Schmitt and H. Turin, and I. Bartomeus for comments on a previous version of the manuscript. R.A. was supported by the EUproject LIMNOTIP funded under the seventh European Commission Framework Programme (FP7) ERA-Net Scheme (Biodiversa, 01LC1207A) and the long-term ecological research program at the Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB). R.W.B. was supported by the Scottish Government Rural and Environment Science and Analytical Services Division (RESAS) through Theme 3 of their Strategic Research Programme. S.D. acknowledges support of the German Research Foundation DFG (grant DO 1880/1-1). S.S. acknowledges the support from the FP7 project EU BON (grant no. 308454). S.K., I.Kü. and O.S. acknowledge funding thorough the Helmholtz Association’s Programme Oriented Funding, Topic ‘Land use, biodiversity, and ecosystem services: Sustaining human livelihoods’. O.S. also acknowledges the support from FP7 via the Integrated Project STEP (grant no. 244090). D.E.B. was funded by a Landes–Offensive zur Entwicklung Wissenschaftlich–ökonomischer Exzellenz (LOEWE) excellence initiative of the Hessian Ministry for Science and the Arts and the German Research Foundation (DFG: Grant no. BO 1221/23-1).Peer Reviewe

Master track of HEINCKE cruise HE580 in 1 sec resolution (zipped, 6.0 MB)

Raw data acquired by position sensors on board RV Heincke during expedition HE580 were processed to receive a validated master track which can be used as reference of further expedition data. During HE580 the inertial navigation system IXSEA PHINS III and the GPS receivers Trimble Marine SPS461 and SAAB R5 SUPREME NAV were used as navigation sensors. Data were downloaded from DAVIS SHIP data base (https://dship.awi.de) with a resolution of 1 sec. Processing and evaluation of the data is outlined in the data processing report found at EPIC repository https://hdl.handle.net/10013/epic.4be95b14-aded-41c2-b1eb-a78be8dc2b00. Processed data are provided as a master track with 1 sec resolution derived from the position sensors' data selected by priority and a generalized track with a reduced set of the most significant positions of the master track

Master tracks in different resolutions of HEINCKE cruise HE580, Bremerhaven - Bremerhaven, 2021-07-17 - 2021-07-30

Raw data acquired by position sensors on board RV Heincke during expedition HE580 were processed to receive a validated master track which can be used as reference of further expedition data. During HE580 the inertial navigation system IXSEA PHINS III and the GPS receivers Trimble Marine SPS461 and SAAB R5 SUPREME NAV were used as navigation sensors. Data were downloaded from DAVIS SHIP data base (https://dship.awi.de) with a resolution of 1 sec. Processing and evaluation of the data is outlined in the data processing report found at EPIC repository https://hdl.handle.net/10013/epic.4be95b14-aded-41c2-b1eb-a78be8dc2b00. Processed data are provided as a master track with 1 sec resolution derived from the position sensors' data selected by priority and a generalized track with a reduced set of the most significant positions of the master track

Raw data of physical oceanography during RV HEINCKE cruise HE580

Raw physical oceanography data was acquired by a ship-based Seabird SBE911plus CTD-Rosette system onboard RV HEINCKE . The CTD was equipped with duplicate sensors for temperature (SBE3plus) and conductivity (SBE4) as well as one sensor for oxygen (SBE43). Additional sensors such as a WET Labs C-Star transmissometer, a WET Labs ECO-AFL fluorometer (FLRTD) and an altimeter (Teledyne Benthos PSA-916) were mounted to the CTD. The data was recorded using pre-cruise calibration coefficients. No correction, post-cruise calibration or quality control was applied. Processed profile data are available via the link below

Physical oceanography during RV HEINCKE cruise HE580

Conductivity-temperature-depth profiles were measured using a Seabird SBE 911plus CTD during RV HEINCKE cruise HE580 between 2021-07-17 and 2021-07-30. Additional sensors included a WET Labs C-Star transmissometer and a WET Labs ECO-AFL fluorometer. Data were connected to the station book of the specific cruise as available in the DSHIP database. Processing of the data including removal of obvious outliers followed the procedures described in CTD Processing Logbook of RV HEINCKE (hdl:10013/epic.47427). A detailed report on the CTD data of HE580 is available at https://hdl.handle.net/10013/epic.794e4bc7-5cb4-4f51-8f42-97745b90204a

Continuous thermosalinograph oceanography along RV HEINCKE cruise track HE580

Raw data acquired by an SBE21 thermosalinograph and an auxiliary SBE38 temperature sensor (Sea-Bird Scientific, USA) installed in an underway seawater flow-through system on board RV Heincke were processed to yield a calibrated and validated data set of seawater temperature and salinity along the cruise track. The seawater inlet is located at a depth of 2 m. The raw hexadecimal data were downloaded from the DAVIS SHIP data base (https://dship.awi.de) at a resolution of 1 s, and converted to temperature and conductivity using the pre-deployment factory calibration coefficients. The converted data were averaged to 1 min values, outliers were removed, and sensor drift was corrected using coefficients obtained from a post-season calibration performed at Sea-Bird at the end of the measurement season. Salinity was calculated from internal temperature, conductivity and pressure according to the PSS-78 Practical Salinity Scale. Processed data are provided as 1 min means of seawater temperature, conductivity and salinity, aligned with position data taken from the master track. Quality flags are appended according to the SeaDataNet Data Quality Control Procedures (version from May 2010). More details are described in the attached processing report

Annotated checklist and biodiversity analysis of benthic fauna at Sylt Outer Reef and Borkum Reef Ground (North Sea)

Benthic fauna caught by ring dredge and 2 m beam trawl at the NATURA 2000 Sylt Outer Reef (SAR) and Borkum Reef Ground (BRG) sites in the North Sea are examined in relation to the intensity of mobile bottom-trawling fisheries. Samples were taken from 33 stations in the two areas, and the collected benthic fauna, consisting of infauna, epifauna, and demersal fish was determined. A total of 123 species were found, consisting of the phyla Chordata, Mollusca, Arthropoda, Echinodermata, Annelida, Cnidaria, and Bryozoa, with Chordata and Mollusca being the most species-rich phyla. The species compositions of BRG and SAR are relatively clearly separated. There was greater species diversity at BRG, likely due to lower fishing pressure from mobile bottom trawling than at SAR. Long-term data acquisition and analysis will be needed to visualize past and future changes in biodiversit

Baseline Inventory of Benthic Macrofauna in German Marine Protected Areas (2020–2022) before Closure for Bottom-Contact Fishing

The response of benthic habitats and organisms to bottom-contact fishing intensity is investigated in marine protected areas (MPAs) of the German EEZ in the North and Baltic Seas. We examined the current state of macrofauna biodiversity in 2020–2022. Comparative analysis for macrofauna (in- and epifauna) inhabiting nine Natura 2000 MPAs constitutes a baseline to assess the effects of bottom-contact fishing exclusion in the future. Aspects of spatial and temporal variability are briefly summarized and discussed. We provide a species list for each region, including 481 taxa, of which 79 were found in both regions, 183 only in the North Sea, and 219 only in the Baltic Sea. The Baltic Sea dataset surprisingly included higher numbers of taxa and revealed more Red List species. The share of major taxonomic groups (polychaetes, bivalves and amphipods) in species richness showed peculiar commonalities between the two regions. In the North Sea, multivariate analysis of community structure revealed significantly higher within-similarity and stronger separation between the considered MPAs compared to the Baltic MPAs. Salinity, temperature and sediment fractions of sand were responsible for over 60% of the variation in the North Sea macrofauna occurrence data. Salinity, mud fraction and bottom-contact fishing were the most important drivers in the Baltic Sea and, together with other considered environmental drivers, were responsible for 53% of the variation. This study identifies aspects of macrofauna occurrence that may be used to assess (causes of) future changes

Cross-taxa generalities in the relationship between population abundance and ambient temperatures

Identifying patterns in the effects of temperature on species' population abundances could help develop a general framework for predicting the consequences of climate change across different communities and realms. We used long-term population time series data from terrestrial, freshwater, and marine species communities within central Europe to compare the effects of temperature on abundance across a broad range of taxonomic groups. We asked whether there was an average relationship between temperatures in different seasons and annual abundances of species in a community, and whether species attributes (temperature range of distribution, range size, habitat breadth, dispersal ability, body size, and lifespan) explained interspecific variation in the relationship between temperature and abundance. We found that, on average, warmer winter temperatures were associated with greater abundances in terrestrial communities (ground beetles, spiders, and birds) but not always in aquatic communities (freshwater and marine invertebrates and fish). The abundances of species with large geographical ranges, larger body sizes, and longer lifespans tended to be less related to temperature. Our results suggest that climate change may have, in general, positive effects on species’ abundances within many terrestrial communities in central Europe while the effects are less predictable in aquatic communities

Chromosome-level genome assembly of a benthic associated Syngnathiformes species: the common dragonet, Callionymus lyra.

BACKGROUND: The common dragonet, Callionymus lyra, is one of three Callionymus species inhabiting the North Sea. All three species show strong sexual dimorphism. The males show strong morphological differentiation, e.g., species-specific colouration and size relations, while the females of different species have few distinguishing characters. Callionymus belongs to the benthic associated clade of the order Syngnathiformes. The benthic associated clade so far is not represented by genome data and serves as an important outgroup to understand the morphological transformation in long-snouted syngnatiformes such as seahorses and pipefishes. FINDINGS: Here, we present the chromosome-level genome assembly of C. lyra. We applied Oxford Nanopore Technologies long-read sequencing, short-read DNBseq, and proximity-ligation-based scaffolding to generate a high-quality genome assembly. The resulting assembly has a contig N50 of 2.2 Mbp and a scaffold N50 of 26.7 Mbp. The total assembly length is 568.7 Mbp, of which over 538 Mbp were scaffolded into 19 chromosome-length scaffolds. The identification of 94.5% complete BUSCO genes indicates high assembly completeness. Additionally, we sequenced and assembled a multi-tissue transcriptome with a total length of 255.5 Mbp that was used to aid the annotation of the genome assembly. The annotation resulted in 19,849 annotated transcripts and identified a repeat content of 27.7%. CONCLUSIONS: The chromosome-level assembly of C. lyra provides a high-quality reference genome for future population genomic, phylogenomic, and phylogeographic analyses