Increased dependence on nearshore benthic resources in the Lake Simcoe ecosystem after dreissenid invasion

Changes in the lower trophic level of Lake Simcoe, Canada, coincident with the invasion of dreissenids have been well documented, but little is known regarding the effects of these changes on the pathways of energy flow to higher trophic levels. To evaluate pathways of energy flow, we analyzed stable isotopes of zooplankton, benthic invertebrates, and fish over a 26-year period. Using stable isotopes of carbon (C) and nitrogen (N), we found evidence for a dramatic increase in the importance of benthic-derived nearshore primary production in Lake Simcoe after the invasion of dreissenids; δ13C of benthos collected at 5 and 10 m depth increased by 4–5‰ on average, and benthic warmwater fishes demonstrated a similar increase. In contrast, δ13C of profundal (≥20 m) benthos and pelagic zooplankton were not significantly different during this time period, while offshore pelagic and profundal fishes changed more subtly in magnitude but in the same direction as nearshore benthos and warmwater fishes. The range of δ13C values observed across the fish community increased from 3 to 10‰, primarily due to a positive temporal shift among warmwater fishes. Our study highlights the increase in functional heterogeneity in Lake Simcoe after dreissenid invasion, likely due to an increase in nearshore benthic production. Accounting for increased contributions of benthic-derived C with time is critical in accurately modelling C and energy transfer in the lake, and for better understanding the degree of nearshore–offshore coupling in the lake

Dynamics of the invasive spiny water flea, Bythotrephes longimanus, in Lake Simcoe, Ontario, Canada

The invasion of the nonindigenous zooplankter Bythotrephes longimanus in Lake Simcoe has the potential to impact overall ecosystem functioning, yet there is currently no information regarding the status and dynamics of its population. We used a combination of uni- and multivariate analyses to examine variation in Bythotrephes interannual and seasonal abundance, and life-history characteristics in Lake Simcoe from 1999 to 2007, and we explored the biotic (predators, prey) and/or abiotic (water quality, temperature) factors that may have regulated its population over this period. The mean annual abundance of Bythotrephes varied by an order of magnitude over the period of study and was significantly associated with epilimnetic temperature and prey and predator abundance. Bythotrephes typically appeared in early summer and had 2 seasonal abundance peaks, which varied in magnitude and timing within and among years. August and September Secchi depth and total phosphorus concentration predicted groups of years with similar Bythotrephes phenologies, lending further support to the role of water clarity as a significant component of this visual predator’s habitat in its invaded range. Bythotrephes body size and reproductive patterns also varied seasonally, possibly reflecting the seasonal availability of cladoceran prey, predation pressure from planktivorous fish, or adaptations to avoid unfavourable conditions. Overall, a complex interaction of fish predation, food availability, temperature, and water clarity controlled the dynamics of Bythotrephes in Lake Simcoe. Changes to the Lake Simcoe ecosystem due to Bythotrephes invasion may have important consequences for the ecosystem services provided by the lake and merit further investigation

Symptom-based stratification of patients with primary Sjögren's syndrome: multi-dimensional characterisation of international observational cohorts and reanalyses of randomised clinical trials

Background Heterogeneity is a major obstacle to developing effective treatments for patients with primary Sjögren's syndrome. We aimed to develop a robust method for stratification, exploiting heterogeneity in patient-reported symptoms, and to relate these differences to pathobiology and therapeutic response. Methods We did hierarchical cluster analysis using five common symptoms associated with primary Sjögren's syndrome (pain, fatigue, dryness, anxiety, and depression), followed by multinomial logistic regression to identify subgroups in the UK Primary Sjögren's Syndrome Registry (UKPSSR). We assessed clinical and biological differences between these subgroups, including transcriptional differences in peripheral blood. Patients from two independent validation cohorts in Norway and France were used to confirm patient stratification. Data from two phase 3 clinical trials were similarly stratified to assess the differences between subgroups in treatment response to hydroxychloroquine and rituximab. Findings In the UKPSSR cohort (n=608), we identified four subgroups: Low symptom burden (LSB), high symptom burden (HSB), dryness dominant with fatigue (DDF), and pain dominant with fatigue (PDF). Significant differences in peripheral blood lymphocyte counts, anti-SSA and anti-SSB antibody positivity, as well as serum IgG, κ-free light chain, β2-microglobulin, and CXCL13 concentrations were observed between these subgroups, along with differentially expressed transcriptomic modules in peripheral blood. Similar findings were observed in the independent validation cohorts (n=396). Reanalysis of trial data stratifying patients into these subgroups suggested a treatment effect with hydroxychloroquine in the HSB subgroup and with rituximab in the DDF subgroup compared with placebo. Interpretation Stratification on the basis of patient-reported symptoms of patients with primary Sjögren's syndrome revealed distinct pathobiological endotypes with distinct responses to immunomodulatory treatments. Our data have important implications for clinical management, trial design, and therapeutic development. Similar stratification approaches might be useful for patients with other chronic immune-mediated diseases. Funding UK Medical Research Council, British Sjogren's Syndrome Association, French Ministry of Health, Arthritis Research UK, Foundation for Research in Rheumatology

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Temperature-dependent Allee effects in a stage-structured model for Bythotrephes establishment

Wittmann M, Lewis MA, Young JD, Yan ND. Temperature-dependent Allee effects in a stage-structured model for Bythotrephes establishment. Biological invasions. 2011;13(11):2477-2497.Whether the invasive freshwater cladoceran Bythotrephes longimanus can establish after introduction into a water body depends on several biotic and abiotic factors. Among these, water temperature is important because both development rates and mode of reproduction (parthenogenetic or sexual) in Bythotrephes are influenced by temperature. We built a stage-structured model for the population dynamics of Bythotrephes based on the temperature-dependency of events in its life cycle and used the density of resting eggs at the end of each year to track changes in population density. The model was parameterized using data from published laboratory experiments and data on the Bythotrephes population in Harp Lake, Canada, from 1994 to 2005. The parameterized model was then used to simulate the outcome of invasions with different initial resting egg densities under different temperature regimes. A strong Allee effect emerged from the model, i.e. there is a critical threshold density above which the population can establish and below which it goes extinct. We showed analytically that the existence of an Allee effect arises from the model structure and is therefore robust to the parameter values. An increase in temperature reduces the establishment threshold for introductions in the same year as well as for introductions in the previous years. We therefore hypothesize that climate warming might facilitate Bythotrephes invasions. Finally, we study how the establishment threshold is influenced by the timing of the introduction event and thus identify time periods during the year when lakes may be particularly susceptible to Bythotrephes invasions

Shifting trophic control of fishery–ecosystem dynamics following biological invasions

Increasing human population size and mobility have accelerated the translocation of nonnative species globally, which has become a major threat to conservation of biodiversity and ecosystem services. Introduced species can disrupt species interactions of the recipient ecosystem, triggering system‐wide events, and amplify or dampen effects of existing pressures. We show how two pervasive intercontinental invasive consumers in North American lakes, dreissenids (filter‐feeding mussels) and Bythotrephes (carnivorous zooplankton), nonlinearly modify consumer–resource dynamics and undermine management interventions to rebuild cold‐water predatory fish biomass. Synthesizing 30 yr (1986–2015) of lake‐wide monitoring data with a dynamic mass‐balance food‐web model (consisting of 61 species and trophic groups), we reconstructed historical food‐web dynamics of Lake Simcoe, a large, temperate lake in Ontario, Canada that has shifted from a turbid to clear‐water state. We then analyzed patterns of biomass fluctuations of three recreationally harvested, ecologically connected populations; lake trout (Salvelinus namaycush , a piscivore), lake whitefish (Coregonus clupeaformis , a benthivore), and cisco (C. artedi , a planktivore) before and after the invasions by testing hypotheses on their delayed recoveries under management interventions–predator manipulations (fishery removal and stocking) and nutrient (phosphorus) load reduction. Analyses suggest that fishery harvest primarily regulated early recovery trajectories of the piscivore and planktivore, weakening top‐down control prior to the establishment of the invasive consumers. By contrast, the benthivore biomass patterns were shaped, in part, by the invasive mussels (via diet shift), independently of management actions. Although improved water quality (with reduced hypoxia in deeper water) and, in turn, higher macrophyte production are projected to expand the predation refuge for young fish, intensified planktivory (by Bythotrephes ) and herbivory (by dreissenids) have triggered shifts in community composition (from pelagic to demersal dominance). These system‐wide shifts, in turn, have substantially diminished ecosystem productivity, thereby shrinking fishery yields. Novel consumers can rewire food webs, disrupt energy flows, and suppress predator recoveries, underscoring the need to account for altered ecological reality when sustainably managing fishery resources in invaded ecosystems

Shifting Trophic Control of Fishery–Ecosystem Dynamics Following Biological Invasions

Increasing human population size and mobility have accelerated the translocation of nonnative species globally, which has become a major threat to conservation of biodiversity and ecosystem services. Introduced species can disrupt species interactions of the recipient ecosystem, triggering system‐wide events, and amplify or dampen effects of existing pressures. We show how two pervasive intercontinental invasive consumers in North American lakes, dreissenids (filter‐feeding mussels) and Bythotrephes (carnivorous zooplankton), nonlinearly modify consumer–resource dynamics and undermine management interventions to rebuild cold‐water predatory fish biomass. Synthesizing 30 yr (1986–2015) of lake‐wide monitoring data with a dynamic mass‐balance food‐web model (consisting of 61 species and trophic groups), we reconstructed historical food‐web dynamics of Lake Simcoe, a large, temperate lake in Ontario, Canada that has shifted from a turbid to clear‐water state. We then analyzed patterns of biomass fluctuations of three recreationally harvested, ecologically connected populations; lake trout (Salvelinus namaycush , a piscivore), lake whitefish (Coregonus clupeaformis , a benthivore), and cisco (C. artedi , a planktivore) before and after the invasions by testing hypotheses on their delayed recoveries under management interventions–predator manipulations (fishery removal and stocking) and nutrient (phosphorus) load reduction. Analyses suggest that fishery harvest primarily regulated early recovery trajectories of the piscivore and planktivore, weakening top‐down control prior to the establishment of the invasive consumers. By contrast, the benthivore biomass patterns were shaped, in part, by the invasive mussels (via diet shift), independently of management actions. Although improved water quality (with reduced hypoxia in deeper water) and, in turn, higher macrophyte production are projected to expand the predation refuge for young fish, intensified planktivory (by Bythotrephes ) and herbivory (by dreissenids) have triggered shifts in community composition (from pelagic to demersal dominance). These system‐wide shifts, in turn, have substantially diminished ecosystem productivity, thereby shrinking fishery yields. Novel consumers can rewire food webs, disrupt energy flows, and suppress predator recoveries, underscoring the need to account for altered ecological reality when sustainably managing fishery resources in invaded ecosystems

Adaptation to climate through flowering phenology: a case study in Medicago truncatula

AGAP : équipe GEpopInternational audienceLocal climatic conditions likely constitute an important selective pressure on genes underlying important fitness-related traits such as flowering time and in many species flowering phenology and climatic gradients strongly covary. To test whether climate shapes genetic variation on flowering time genes and to identify candidate flowering genes involved in the adaptation to environmental heterogeneity, we used a large M. truncatula core collection to examine the association between nucleotide polymorphisms at 224 candidate genes and both climate variables and flowering phenotypes. Unlike genome-wide studies, candidate gene approaches are expected to enrich for the number of meaningful trait associations because they specifically target genes that are known to affect the trait of interest. We found that flowering time mediates adaptation to climatic conditions mainly by variation at genes located upstream in the flowering pathways, close to the environmental stimuli. Variables related to the annual precipitation regime reflected selective constraints on flowering time genes better than the other variables tested (temperature, altitude, latitude or longitude). By comparing phenotype and climate associations, we identified 12 flowering genes as the most promising candidates responsible for phenological adaptation to climate. Four of these genes were located in the known flowering time QTL region on chromosome 7. However, climate and flowering associations also highlighted largely distinct gene sets, suggesting different genetic architectures for adaptation to climate and flowering onset