Incipient resistance to an effective pesticide results from genetic adaptation and the canalization of gene expression

Abstract

1The resistance of bacteria, disease vectors, and pests to chemical controls has vast ecological, 2 economic, and human-health costs. In most cases, resistance is only detected after non-3 susceptible phenotypes have spread throughout the entire population. Detecting resistance in its 4 incipient stages, by comparison, provides time to implement preventative strategies. Incipient 5 resistance (IR) can be detected by coupling standard toxicology assays with large-scale gene 6 expression experiments. We apply this approach to a system where an invasive parasite, sea 7 lamprey (Petromyzon marinus), has been treated with the highly-effective pesticide 3-8 trifluoromethyl-4-nitrophenol (TFM) for 60 years. Toxicological experiments revealed that 9 lamprey from treated populations did not have higher survival to TFM exposure than lamprey 10 from their native range, demonstrating that full-fledged resistance has not yet evolved. In stark 11 contrast, we find hundreds of genes differentially expressed in response to TFM in the 12 population with the longest history of exposure, many of which relate to TFM's primary mode of 13 action, the uncoupling of oxidative phosphorylation. One gene critical to oxidative 14 phosphorylation, ATP5PB, which encodes subunit b of ATP synthase, was nearly fixed for 15 alternative alleles in comparisons between native and treated populations (FST > 9 SD from the 16 mean). A gene encoding an additional subunit of ATP synthase, ATP5F1B, was canalized for 17 high expression in treated populations, but remained plastic in response to treatment in sea 18 lamprey from the native range. These combined genomic and transcriptomic results illustrate that 19 an adaptive, genetic response to TFM is driving incipient resistance in a damaging pest species. 20 S3). Remarkably, when comparing samples treated with 0.3 mg/L TFM to control samples, we 113 found 336 genes that were differentially expressed (275 upregulated, 61 downregulated in 114 comparison to control individuals) in muscle tissue in the Lake Michigan population, dwarfing 115 the number of differentially expressed genes (DEGs) found in both the Lake Champlain (n = 21) 116 and the Connecticut River (n = 68) populations (Fig. 3A-C; Table S4). No DEGs were shared 117 among all three populations and different population responses were observed when lower 118 concentrations (i.e., 0.2 mg/L) of TFM were applied and when different tissues were examined 119 (Figures S2-S5). 120The primary mode of action for TFM is to uncouple oxidative phosphorylation in the 121 mitochondria resulting in severe ATP depletion and eventual death (25, 26, 32). Of the 336 122 DEGs identified in Lake Michigan, several genes were directly related to this mode of action 123 including CRCM1 (LogFC = 2.60), a calcium release-activated channel protein that controls the 124 influx of calcium into cells when depleted, and PLCD4 (LogFC = 2.41), an enzyme responsible 125 for hydrolyzing phosphatidylinositol 4,5-bisphosphate into two secondary messenger molecules, 126 one of which (...

Rapid genetic adaptation to recently colonized environments is driven by genes underlying life history traits

“…Thus, adaptive differentiation at SLC25A15 may be a reflection of changes in sea lamprey’s prey and their capacity of adjusting nitrogen metabolism depending on which host fishes are available. Additionally, SLC25A15 could also be potentially related to osmoregulation, ammonia detoxification, or even as a response to TFM treatment since the protein is located within mitochondria [ 30 ].…”

“…We collected 565 larval sea lamprey from the Manistee River in Lake Michigan, 517 larval sea lamprey from Corbeau Creek and the LaPlatte River in Lake Champlain, and 404 larval sea lamprey from the Connecticut River in 2016 (Fig. 1 a), among which 283 individuals from each population were used to test the sensitivity of sea lamprey to TFM (see [ 30 ] for details). We sampled a total of 43 individuals (Lake Michigan: n = 16, Lake Champlain: n = 13, Connecticut River: n = 14) for RNA-seq after a four-month acclimation period in a common environment at the Aquaculture Research Lab at Purdue University (see Methods of Supplementary Information for details).…”

“…All samples were collected on the same day and immediately frozen with liquid nitrogen in cryovials, which were later transferred to a −80 °C freezer. These individuals were previously used to determine whether invasive sea lamprey are evolving resistance to the pesticide TFM (see [ 30 ] for details).…”

“…Sea lamprey have 99 chromosomes, among which the first 90 are assembled. The map in ( a ) is modified with permission from Yin et al [ 30 ] …”