title: High-throughput monitoring of wild bee diversity and abundance via mitogenomics.
abstract: 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.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.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.Mitogenomics automates the onerous task of taxonomic identification, even for cryptic species, allowing the tracking of changes in species richness and distributions. 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.
authors.affiliation: China National GeneBank BGI-Shenzhen Shenzhen Guangdong 518083 China.
authors.forename: Min
authors.initials: M
authors.lastname: Tang
authors.affiliation: Centre for Agri Environmental Research School of Agriculture Policy and Development University of Reading Reading RG66AR UK.
authors.forename: Chloe J
authors.initials: CJ
authors.lastname: Hardman
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences, Kunming Yunnan 650223 China.
authors.forename: Yinqiu
authors.initials: Y
authors.lastname: Ji
authors.affiliation: China National GeneBank BGI-Shenzhen Shenzhen Guangdong 518083 China.
authors.forename: Guanliang
authors.initials: G
authors.lastname: Meng
authors.affiliation: China National GeneBank BGI-Shenzhen Shenzhen Guangdong 518083 China.
authors.forename: Shanlin
authors.initials: S
authors.lastname: Liu
authors.affiliation: China National GeneBank BGI-Shenzhen Shenzhen Guangdong 518083 China; University of Chinese Academy of Sciences Beijing 100094 China.
authors.forename: Meihua
authors.initials: M
authors.lastname: Tan
authors.affiliation: China National GeneBank BGI-Shenzhen Shenzhen Guangdong 518083 China.
authors.forename: Shenzhou
authors.initials: S
authors.lastname: Yang
authors.affiliation: School of Biological, Biomedical and Environmental Sciences University of Hull Hull HU67RX UK.
authors.forename: Ellen D
authors.initials: ED
authors.lastname: Moss
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences, Kunming Yunnan 650223 China.
authors.forename: Jiaxin
authors.initials: J
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences, Kunming Yunnan 650223 China.
authors.forename: Chenxue
authors.initials: C
authors.lastname: Yang
authors.affiliation: School of Biological Sciences University of East Anglia Norwich Research Park Norwich Norfolk NR47TJ UK.
authors.forename: Catharine
authors.initials: C
authors.lastname: Bruce
authors.affiliation: Conservation Grade Ltd.St Neots Cambridgeshire PE196TY UK; Charles Darwin University Darwin NTNT0909 Australia.
authors.forename: Tim
authors.initials: T
authors.lastname: Nevard
authors.affiliation: Centre for Agri Environmental Research School of Agriculture Policy and Development University of Reading Reading RG66AR UK.
authors.forename: Simon G
authors.initials: SG
authors.lastname: Potts
authors.affiliation: China National GeneBank BGI-Shenzhen Shenzhen Guangdong 518083 China.
authors.forename: Xin
authors.initials: X
authors.lastname: Zhou
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences, Kunming Yunnan 650223 China; School of Biological Sciences University of East Anglia Norwich Research Park Norwich Norfolk NR47TJ UK.
authors.forename: Douglas W
authors.initials: DW
authors.lastname: Yu
keywords: Hymenoptera; agri‐environment schemes; biodiversity and ecosystem services; farmland biodiversity; genome skimming; metabarcoding; metagenomics; mitogenomes; neonicotinoids; pollination