High-throughput monitoring of wild bee diversity and abundance via mitogenomics

1. Bee populations and other pollinators face multiple, synergistically acting threats, which have led to population declines, loss of local species richness and pollination services, and extinctions. However, our understanding of the degree, distribution and causes of declines is patchy, in part due to inadequate monitoring systems, with the challenge of taxonomic identification posing a major logistical barrier. Pollinator conservation would benefit from a high-throughput identification pipeline. 2. We show that the metagenomic mining and resequencing of mitochondrial genomes (mitogenomics) can be applied successfully to bulk samples of wild bees. We assembled the mitogenomes of 48 UK bee species and then shotgun-sequenced total DNA extracted from 204 whole bees that had been collected in 10 pan-trap samples from farms in England and been identified morphologically to 33 species. Each sample data set was mapped against the 48 reference mitogenomes. 3. The morphological and mitogenomic data sets were highly congruent. Out of 63 total species detections in the morphological data set, the mitogenomic data set made 59 correct detections (93�7% detection rate) and detected six more species (putative false positives). Direct inspection and an analysis with species-specific primers suggested that these putative false positives were most likely due to incorrect morphological IDs. Read frequency significantly predicted species biomass frequency (R2 = 24�9%). Species lists, biomass frequencies, extrapolated species richness and community structure were recovered with less error than in a metabarcoding pipeline. 4. Mitogenomics automates the onerous task of taxonomic identification, even for cryptic species, allowing the tracking of changes in species richness and istributions. A mitogenomic pipeline should thus be able to contain costs, maintain consistently high-quality data over long time series, incorporate retrospective taxonomic revisions and provide an auditable evidence trail. Mitogenomic data sets also provide estimates of species counts within samples and thus have potential for tracking population trajectories.

Explaining patterns of avian diversity and endemicity: climate and biomes of southern Africa over the last 140,000 years

Aim Test hypotheses that present biodiversity and endemic species richness are related to climatic stability and/or biome persistence.Location Africa south of 15° S. Methods Seventy eight HadCM3 general circulation model palaeoclimate experiments spanning the last 140,000 years, plus a pre-industrial experiment,were used to calculate measures of climatic variability for 0.5° grid cells. Models were fitted relating distributions of the nine biomes of South Africa,Lesotho and Swaziland to present climate. These models were used to simulate potential past biome distribution and extent for the 78 palaeoclimate experiments, and three measures of biome persistence. Climatic response surfaces were fitted for 690 bird species regularly breeding in the region and used to simulate present species richness for cells of the 0.5° grid. Species richness was evaluated for residents, mobile species (nomadic or partially/altitudinally migrant within the region), and intra-African migrants, and also separately for endemic/near-endemic (hereafter ‘endemic’) species as a whole and those associated with each biome. Our hypotheses were tested by analysing correlations between species richness and climatic variability or biome persistence. Results The magnitude of climatic variability showed clear spatial patterns. Marked changes in biome distributions and extents were projected, although limited areas of persistence were projected for some biomes. Overall species richness was not correlated with climatic variability, although richness of mobile species showed a weak negative correlation. Endemic species richness was significantly negatively correlated with climatic variability. Strongest correlations, however, were positive correlations between biome persistence and richness of endemics associated with individual biomes. Main conclusions Low climatic variability, and especially a degree of stability enabling biome persistence, is strongly correlated with species richness of birds endemic to southern Africa. This probably principally reflects reduced extinction risk for these species where the biome to which they are adapted persisted

Spatial patterns and environmental constraints on ecosystem services at a catchment scale

Improved understanding and prediction of the fundamental environmental controls on ecosystem service supply across the landscape will help to inform decisions made by policy makers and land-water managers. To evaluate this issue for a local catchment case study, we explored metrics and spatial patterns of service supply for water quality regulation, agriculture production, carbon storage, and biodiversity for the Macronutrient Conwy catchment. Methods included using ecosystem models such as LUCI and JULES, integration of national scale field survey datasets, earth observation products and plant trait databases, to produce finely resolved maps of species richness and primary production. Analyses were done with both 1x1 km gridded and subcatchment data. A common single gradient characterised catchment scale ecosystem services supply with agricultural production and carbon storage at opposing ends of the gradient as reported for a national-scale assessment. Species diversity was positively related to production due to the below national average productivity levels in the Conwy combined with the unimodal relationship between biodiversity and productivity at the national scale. In contrast to the national scale assessment, a strong reduction in water quality as production increased was observed in these low productive systems. Various soil variables were tested for their predictive power of ecosystem service supply. Soil carbon, nitrogen, their ratio and soil pH all had double the power of rainfall and altitude, each explaining around 45% of variation but soil pH is proposed as a potential metric for ecosystem service supply potential as it is a simple and practical metric which can be carried out in the field with crowd-sourcing technologies now available. The study emphasises the importance of considering multiple ecosystem services together due to the complexity of covariation at local and national scales, and the benefits of exploiting a wide range of metrics for each service to enhance data robustness.