BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology.

BACKGROUND: Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as "Web services") and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust "in silico" science. However, use of this approach in biodiversity science and ecology has thus far been quite limited. RESULTS: BioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on-line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorporating R programs. Deploying these tools into an easy-to-use and accessible 'virtual laboratory', free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services and contribute to the activity. CONCLUSIONS: Our work shows we can deliver an operational, scalable and flexible Internet-based virtual laboratory to meet new demands for data processing and analysis in biodiversity science and ecology. In particular, we have successfully integrated existing and popular tools and practices from different scientific disciplines to be used in biodiversity and ecological research.

Ecological comparison of native (Apis mellifera mellifera) and hybrid (Buckfast) honeybee drones in southwestern Sweden indicates local adaptation.

Honeybee drones' only known task is to mate with a virgin queen. Apart from their mating behaviour, their ecology has been little studied, especially in comparison to honeybee females. Previous knowledge is primarily based on short-term direct observations at single experimental hives, rarely, if ever, addressing the effect of drones' genetic origin. Here, Radio Frequency Identification Technology was utilised to gather drone and worker bee lifetime data of Apis mellifera mellifera and Apis mellifera x (hybrid Buckfast) colonies over one mating season (spring and summer) with the ultimate goal to investigate differences at subspecies level. This technique enabled continuous monitoring of tagged bees at the hive entrance and recording of individuals' movement directions. The results confirmed that spring-born drones survive longer than summer-born drones and that they generally live longer than worker bees. Drones' peak activity occurred in the afternoon while worker bees showed more even activity levels throughout the day. Earlier orientation flights than usually reported for drones were observed. In summer, mating flights were practiced before reaching sexual maturity (at 12 days of age). Differences were found between Apis m. mellifera and Buckfast drones, where Apis m. mellifera showed later drone production in spring, but significantly earlier first activities outside the hive in summer and a later peak in diurnal activity. Additionally, Apis m. mellifera flew more in higher light intensities and windy conditions and performed significantly longer flights than Buckfast drones. The observed differences in drone ecology indicate the existence of a local adaptation of the native subspecies Apis m. mellifera to environmental conditions in southwestern Sweden.

Loss of species and genetic diversity during colonization: Insights from acanthocephalan parasites in northern European seals.

Studies on host-parasite systems that have experienced distributional shifts, range fragmentation, and population declines in the past can provide information regarding how parasite community richness and genetic diversity will change as a result of anthropogenic environmental changes in the future. Here, we studied how sequential postglacial colonization, shifts in habitat, and reduced host population sizes have influenced species richness and genetic diversity of Corynosoma (Acanthocephala: Polymorphidae) parasites in northern European marine, brackish, and freshwater seal populations. We collected Corynosoma population samples from Arctic, Baltic, Ladoga, and Saimaa ringed seal subspecies and Baltic gray seals, and then applied COI barcoding and triple-enzyme restriction-site associated DNA (3RAD) sequencing to delimit species, clarify their distributions and community structures, and elucidate patterns of intraspecific gene flow and genetic diversity. Our results showed that Corynosoma species diversity reflected host colonization histories and population sizes, with four species being present in the Arctic, three in the Baltic Sea, two in Lake Ladoga, and only one in Lake Saimaa. We found statistically significant population-genetic differentiation within all three Corynosoma species that occur in more than one seal (sub)species. Genetic diversity tended to be high in Corynosoma populations originating from Arctic ringed seals and low in the landlocked populations. Our results indicate that acanthocephalan communities in landlocked seal populations are impoverished with respect to both species and intraspecific genetic diversity. Interestingly, the loss of genetic diversity within Corynosoma species seems to have been less drastic than in their seal hosts, possibly due to their large local effective population sizes resulting from high infection intensities and effective intra-host population mixing. Our study highlights the utility of genomic methods in investigations of community composition and genetic diversity of understudied parasites.

Winter weight loss of different subspecies of honey bee Apis mellifera colonies (Linnaeus, 1758) in southwestern Sweden.

Honey bees are currently facing mounting pressures that have resulted in population declines in many parts of the world. In northern climates winter is a bottleneck for honey bees and a thorough understanding of the colonies' ability to withstand the winter is needed in order to protect the bees from further decline. In this study the influence of weather variables on colony weight loss was studied over one winter (2019-2020) in two apiaries (32 colonies in total) in southwestern Sweden with weather stations recording wind and temperature at 5-min intervals. Three subspecies of honey bees and one hybrid were studied: the native Apis mellifera mellifera, the Italian A. m. ligustica, the Carniolan A. m. carnica and the hybrid Buckfast. Additionally, we recorded Varroa mite infestation. To analyze factors involved in resource consumption, three modelling approaches using weather and weight data were developed: the first links daily consumption rates with environmental variables, the second modelled the cumulative weight change over time, and the third estimated weight change over time taking light intensity and temperature into account. Weight losses were in general low (0.039 ± 0.013kg/day and colony) and comparable to southern locations, likely due to an exceptionally warm winter (average temperature 3.5°C). Weight losses differed only marginally between subspecies with indications that A. m. mellifera was having a more conservative resource consumption, but more studies are needed to confirm this. We did not find any effect of Varroa mite numbers on weight loss. Increased light intensity and temperature both triggered the resource consumption in honey bees. The temperature effect on resource consumption is in accordance with the metabolic theory of ecology. The consequences of these findings on honey bee survival under predicted climate changes, is still an open question that needs further analysis.

Host records and geographical distribution of Corynosoma magdaleni, C. semerme and C. strumosum (Acanthocephala: Polymorphidae).

A literature survey was conducted to investigate the host and geographical distribution patterns of three Corynosoma species (Acanthocephala: Polymorphidae), viz. C. magdaleni, C. semerme and C. strumosum. All three species appear to be restricted to the Northern Hemisphere. Occurrence records of C. magdaleni are limited to the Northern Atlantic coasts, while C. semerme has a circumpolar distribution. The geographical range of Corynosoma strumosum encompasses the distributions of the other two species, but also extends into warmer southern regions. Some Corynosoma populations are living with their definitive hosts in very isolated locations, such as in the brackish Baltic Sea or different freshwater lakes (e.g. Lake Saimaa). All three species have a heteroxenous life cycle, comprising a peracaridan intermediate host, a fish paratenic host and a mammalian definitive host. Occasionally, an acanthocephalan may enter an accidental host, from which it is unable to complete its life cycle. The host records reported here are categorised by type, i.e. intermediate, paratenic, definitive or accidental. While most of the definitive hosts are shared amongst the three Corynosoma species, C. strumosum showed the broadest range of paratenic hosts, which reflects its more extensive geographical distribution. One aim of this study and extensive literature summary is to guide future sampling efforts and therewith contribute to throw more light on the on-going species and morphotype discussion for this interesting parasite species.

Integrating experimental and distribution data to predict future species patterns.

Predictive species distribution models are mostly based on statistical dependence between environmental and distributional data and therefore may fail to account for physiological limits and biological interactions that are fundamental when modelling species distributions under future climate conditions. Here, we developed a state-of-the-art method integrating biological theory with survey and experimental data in a way that allows us to explicitly model both physical tolerance limits of species and inherent natural variability in regional conditions and thereby improve the reliability of species distribution predictions under future climate conditions. By using a macroalga-herbivore association (Fucus vesiculosus - Idotea balthica) as a case study, we illustrated how salinity reduction and temperature increase under future climate conditions may significantly reduce the occurrence and biomass of these important coastal species. Moreover, we showed that the reduction of herbivore occurrence is linked to reduction of their host macroalgae. Spatial predictive modelling and experimental biology have been traditionally seen as separate fields but stronger interlinkages between these disciplines can improve species distribution projections under climate change. Experiments enable qualitative prior knowledge to be defined and identify cause-effect relationships, and thereby better foresee alterations in ecosystem structure and functioning under future climate conditions that are not necessarily seen in projections based on non-causal statistical relationships alone.

Phocid seals, seal lice and heartworms: a terrestrial host-parasite system conveyed to the marine environment.

Adaptation of pinnipeds to the marine habitat imposed parallel evolutions in their parasites. Ancestral pinnipeds must have harboured sucking lice, which were ancestors of the seal louse Echinophthirius horridus. The seal louse is one of the few insects that successfully adjusted to the marine environment. Adaptations such as keeping an air reservoir and the ability to hold on to and move on the host were necessary, as well as an adjustment of their life cycle to fit the diving habits of their host. E. horridus are confined to the Northern Hemisphere and have been reported from 9 species of northern phocids belonging to 4 genera, including land-locked seal species. The transmission from seal to seal is only possible when animals are hauled-out on land or ice. Lice are rarely found on healthy adult seals, but frequently on weak and young animals. The seal louse is suggested to play an important role as an intermediate host transmitting the heartworm Acanthocheilonema spirocauda among seals. However, the evidence is restricted to a single study where the first 3 larval stages of the heartworm were shown to develop in the louse. The fourth-stage larvae develop in the blood system of seals and eventually transform into the adult stage that matures in the heart. Since all other studies failed to confirm the presence of heartworm larvae in seal lice, other unknown intermediate hosts could be involved in the transmission of the heartworm. Transplacental transmission of microfilariae in seals has been suggested as an additional possibility, but is not likely to be important since the occurrence of heartworms in adult seals is very rare compared with juveniles. Furthermore, there are no findings of the first 3 larval stages in seals. This review shows that the heartworm infects nearly the same species of seals as the seal louse, except for the grey seal Halichoerus grypus, where the heartworm is absent. Prevalence and intensity of infection differ among regions in the Northern Hemisphere. As for seal lice, heartworms mainly infect immature seals, and after infection the prevalence seems to decrease with increasing age of the host.

The Analysis Portal and the Swedish LifeWatch e-infrastructure for biodiversity research.

BACKGROUND: During the last years, more and more online portals were generated and are now available for ecologists to run advanced models with extensive data sets. Some examples are the Biodiversity Virtual e-Laboratory (BioVel) Portal (https://portal.biovel.eu) for ecological niche modelling and the Mobyle SNAP Workbench (https://snap.hpc.ncsu.edu) for evolutionary and population genetics analysis. Such portals have the main goal to facilitate the run of advanced models, through access to large-capacity computers or servers. In this study, we present the Analysis Portal (www.analysisportal.se), which is a part of the Swedish LifeWatch e-infrastructure for biodiversity research that combines a variety of Swedish web services to perform different kinds of dataprocessing. NEW INFORMATION: For the first time, the Swedish Analysis Portal for integrated analysis of species occurrence data is described in detail. It was launched in 2013 and today, over 60 Million Swedish species observation records can be assessed, visualized and analyzed via the portal. Datasets can be assembled using sophisticated filtering tools, and combined with environmental and climatic data from a wide range of providers. Different validation tools, for example the official Swedish taxon concept database Dyntaxa, ensure high data quality. Results can be downloaded in different formats as maps, tables, diagrams and reports.

Evaluating the potential of ecological niche modelling as a component in marine non-indigenous species risk assessments.

Marine biological invasions have increased with the development of global trading, causing the homogenization of communities and the decline of biodiversity. A main vector is ballast water exchange from shipping. This study evaluates the use of ecological niche modelling (ENM) to predict the spread of 18 non-indigenous species (NIS) along shipping routes and their potential habitat suitability (hot/cold spots) in the Baltic Sea and Northeast Atlantic. Results show that, contrary to current risk assessment methods, temperature and sea ice concentration determine habitat suitability for 61% of species, rather than salinity (11%). We show high habitat suitability for NIS in the Skagerrak and Kattegat, a transitional area for NIS entering or leaving the Baltic Sea. As many cases of NIS introduction in the marine environment are associated with shipping pathways, we explore how ENM can be used to provide valuable information on the potential spread of NIS for ballast water risk assessment.

Mapping present and future potential distribution patterns for a meso-grazer guild in the Baltic Sea.

AIM: The Baltic Sea is one of the world's largest semi-enclosed brackish water bodies characterized by many special features, including endemic species that may be particularly threatened by climate change. We mapped potential distribution patterns under present and future conditions for a community with three trophic levels. We analysed climate-induced changes in the species' distribution patterns and examined possible consequences for the chosen food web. LOCATION: Baltic Sea and northern Europe. METHODS: We developed two open-source workflow-based analytical tools: one for ecological niche modelling and another for raster layer comparison to compute the extent and intensity of change in species' potential distributions. Individual ecological niche models were generated under present conditions and then projected into a future climate change scenario (2050) for a food web consisting of a guild of meso-grazers (Idotea spp.), their host algae (Fucus vesiculosus and Fucus radicans) and their fish predator (Gasterosteus aculeatus). We used occurrence data from the Global Biodiversity Information Facility (GBIF), literature and museum collections, together with five environmental layers at a resolution of 5 and 30 arc-minutes. RESULTS: Habitat suitability for Idotea balthica and Idotea chelipes in the Baltic Sea seems to be mostly determined by temperature and ice cover rather than by salinity. 2050 predictions for all modelled species show a northern/north-eastern shift in the Baltic Sea. The distribution ranges for Idotea granulosa and G. aculeatus are predicted to become patchier in the Baltic than in the rest of northern Europe, where the species will gain more suitable habitats. MAIN CONCLUSIONS: For the Baltic Sea, climate-induced changes resulted in a gain of suitable habitats for F. vesiculosus,I. chelipes and I. balthica, whereas lower habitat suitability was predicted for I. granulosa,F. radicans and G. aculeatus. The predicted north-eastern shift of I. balthica and I. chelipes into the distribution area of F. radicans in the Baltic Sea may result in increased grazing pressure. Such additional threats to isolated Baltic populations can lead to a higher extinction risk for the species, especially as climate changes are likely to be very rapid.

Characterization of the heartworm Acanthocheilonema spirocauda (Leidy, 1858) Anderson, 1992 (Nematoda: Onchocercidae) in Scandinavia.

The heartworm Acanthocheilonema spirocauda (Leidy, Proc Acad Nat Sci Philadelphia 10:110-112, 1858) Anderson, 1992 is described from material collected from harbour seals in Scandinavia and compared with types and other specimens described by Anderson (Can J Zool 37:481-493, 1959) from harbour seals in eastern USA. Most morphometric characters of the material from USA fall within the ranges established for the Scandinavian one. Some intraspecific variability in the organisation of papillae on the male tail was detected among the Scandinavian specimens. Differences between the specimens from Scandinavia and Eastern USA are also found in the organisation of papillae on the tail of males and females. An excretory pore was not discernible, but a clearly hemizonid-like structure is described. For the first time, scanning electron micrographs present external morphological structures of the species.