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

Abstract

Summary 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 (R 2 = 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.

The complete mitochondrial genome of Florida gar (Lepisosteus platyrhincus)

“…GZ2014122012). Then we sequenced the complete mitochondrial genome using Illumine Hiseq 4000 platform (Illumina, San Diego, CA) at BGI-Shenzhen, China and assembled it with the SOAPdenovo-Trans (Kmer-71) (Tang et al 2015). All experiments followed the guidelines of the Animal Ethics and were approved by the Institutional Review Board on Bioethics and Biosafety of BGI.…”

Protecting an Ecosystem Service

“…Moreover, taxonomic experts are needed regularly but this may not be possible if 659 experts are few and in high demand. Researchers are therefore exploring the developments of 660 novel molecular tools to aid the efforts in both identification and quantification (Kuhlmann, 661 2015), with the aim of providing greater taxonomic precision, a robust method of monitoring 662 aspects of pollinator populations and to quantify pollinator community structure under 663 different environmental conditions (Tang et al, 2015). The overall objective is to monitor 664 reliably across multiple sites to gain spatial aspects of pollinator community structure 665 repeatedly over time to assess trends and react adaptively to protecting insect pollinator 666 services.…”

“…from 708 multiple pan traps), keeping costs low. However, this methodology is associated with various 709 problems such as biases in amplification success across different taxa, which may create false 710 negatives (Clarke et al, 2014;Tang et al, 2015), contamination risk and potential co-711 amplification of mitochondrial pseudogenes (Song et al, 2008), and the comparatively short 712 sequence achievable with the current NGS technology, which limits the analysis of the COI 713 gene to roughly a half-length 'minibarcode' and hence reduces discriminatory power (Tang et 714 al., 2015). 715 for each sample; these indexed primers can be used to sort the samples out bioinformatically 727 after sequencing.…”

“…was recently applied to bee communities and provides powerful 'super-barcodes' used as a 745 reference library (Tang et al, 2015). These reference mitochondrial genomes are used to 746 profile any number and mixture of specimens that may be collected (for example in field pan 747 traps that attract and collect flying insect pollinators).…”

The complete mitochondrial genome of Eastern paradise fish (Polynemus dubius)

“…GZ2014122001). Although its genome is not available, we sequenced its mitochondrial genome using Illumina Hiseq 4000 sequencing platform (Illumina Inc., San Diego, CA) (Tang et al 2015). Finally, we assembled the complete mitochondrial genome.…”