Abstract
The yellow-banded bumblebee Bombus terricola was common in North America but has recently declined and is now on the IUCN Red List of threatened species. The causes of B. terricola’s decline are not well understood. Our objectives were to create a partial genome and then use this to estimate population data of conservation interest, and to determine whether genes showing signs of recent selection suggest a specific cause of decline. First, we generated a draft partial genome (contig set) for B. terricola, sequenced using Pacific Biosciences RS II at an average depth of 35×. Second, we sequenced the individual genomes of 22 bumblebee gynes from Ontario and Quebec using Illumina HiSeq 2500, each at an average depth of 20×, which were used to improve the PacBio genome calls and for population genetic analyses. The latter revealed that several samples had long runs of homozygosity, and individuals had high inbreeding coefficient F, consistent with low effective population size. Our data suggest that B. terricola’s effective population size has decreased orders of magnitude from pre-Holocene levels. We carried out tests of selection to identify genes that may have played a role in ameliorating environmental stressors underlying B. terricola’s decline. Several immune-related genes have signatures of recent positive selection, which is consistent with the pathogen-spillover hypothesis for B. terricola’s decline. The new B. terricola contig set can help solve the mystery of bumblebee decline by enabling functional genomics research to directly assess the health of pollinators and identify the stressors causing declines.
Highlights
Pollinators are responsible for or augment the reproduction of 80–95% of all flowering plants (Ollerton et al, 2011), including many agricultural crops (Klein et al, 2007)
The B. terricola contig set, constructed using Pacbio and Illumina sequencing, contains 238.9 million base pairs distributed over 1,448 contigs with an N50 of 341,136 bp (Table 1)
We found a partial sweep in the vicinity of two genes involved in post-translational modification, an important regulator of insect immune systems, that are adjacent to each other on scaffold 464 (Figure 5) for genes BT3658
Summary
Pollinators are responsible for or augment the reproduction of 80–95% of all flowering plants (Ollerton et al, 2011), including many agricultural crops (Klein et al, 2007). Bumblebees (Bombus spp.) are important pollinators of many plants, in North America and Europe (Kearns et al, 1998; Berenbaum et al, 2007). In North America, members of the subgenus Bombus sensu stricto seem to be vulnerable (Grixti et al, 2009; Cameron et al, 2011; Colla et al, 2012; Hatfield et al, 2015). These species share certain ecological characteristics, including having a short tongue length and early spring emergence (Colla, 2016). The specific causes underlying the decline of any given species or population of bumblebees often remain elusive
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