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

Frontiers in Genetics
Clement F KentAmro Zayed

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. t...Continue Reading

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Citations

Feb 27, 2020·Nature Reviews. Genetics·Christina M Grozinger, Amro Zayed
Mar 14, 2019·Scientific Reports·Kleber de Sousa PereiraGuy Smagghe
Jul 6, 2019·Scientific Reports·Kevin MaebeGuy Smagghe
Oct 15, 2019·Annual Review of Entomology·Sydney A Cameron, Ben M Sadd
Dec 29, 2020·Journal of Invertebrate Pathology·Lewis J BartlettLena Wilfert
Jul 15, 2021·Ecology and Evolution·Fang ZhaoZuhao Huang

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Datasets Mentioned

BETA
PRJNA399520

Methods Mentioned

BETA
electrophoresis
Illumina sequencing
genotyping

Software Mentioned

Celera Assembler
GenotypeGVCF
NeEstimator
Admixture
VMP
Plink
Pilon
BUSCO
GATK Haplotype Caller
NextGenMap ( NGM

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