Conservation Genomics of the Declining North American Bumblebee Bombus terricola Reveals Inbreeding and Selection on Immune Genes

Kent, C. F., Dey, A., Patel, H., Tsvetkov, N., Tiwari, T., MacPhail, V. J., Gobeil, Y., Harpur, B. A., Gurtowski, J., Schatz, M. C., Colla, S. R., Zayed, A. (August 2018) Conservation Genomics of the Declining North American Bumblebee Bombus terricola Reveals Inbreeding and Selection on Immune Genes. Front Genet, 9. p. 316. ISSN 1664-8021 (Print)1664-8021

URL: https://www.ncbi.nlm.nih.gov/pubmed/30147708
DOI: 10.3389/fgene.2018.00316

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 35x. Second, we sequenced the individual genomes of 22 bumblebee gynes from Ontario and Quebec using Illumina HiSeq 2500, each at an average depth of 20x, 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.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > population genetics
Investigative techniques and equipment > assays > whole genome sequencing
CSHL Authors:
Communities: CSHL labs > Schatz lab
Depositing User: Matthew Dunn
Date: 10 August 2018
Date Deposited: 28 Aug 2018 19:30
Last Modified: 28 Aug 2018 19:30
PMCID: PMC6095975
Related URLs:
URI: http://repository.cshl.edu/id/eprint/37160

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