Biology subjects

Cohen, Z. P.

Publications and source records attributed to Cohen, Z. P..

4 recordsLinked to original sources

bioRxiv2026

Bacterial DNA invasion triggers transposable element proliferation and genome expansion

Genome size variation in eukaryotes is driven largely by transposable elements (TEs), yet the biological mechanisms that initiate their proliferation remain understudied. Here, we identify a recurrent association between bacterial horizontal gene transfer (HGT) and bursts of TE activity that contribute to genome expansion. By leveraging comparative genomics and genus-level pangenome analyses across three species of the nut weevil, Curculio, we detect extensive bacterially derived DNA sequences embedded within structurally dynamic genomic regions. These HGT-associated regions are dominated by a small number of young, proliferating TE families, particularly DNA type II Mavericks, which encapsulate transferred bacterial sequences and comprise a substantial fraction of recent genomic DNA in derived lineages. Analyses of codon usage bias, intron length, and functional enrichment suggest that most transferred genes undergo progressive pseudogenization over evolutionary time, whereas a subset of selectively advantageous HGTs persist. Together, our findings support a model linking foreign DNA invasion with TE proliferation, genome size variation, and molecular innovation.

genomics↗

bioRxiv2022

Evidence of hard-selective sweeps suggest independent adaptation to insecticides in Colorado potato beetle (Coleoptera: Chrysomelidae) populations

Pesticide resistance provides one of the best examples of rapid evolution to environmental change. The Colorado potato beetle has a long and noteworthy history as a super-pest due to its ability to repeatedly develop resistance to novel insecticides and rapidly expand its geographic and host plant range. Here, we investigate regional differences in demography, recombination and selection using whole genome resequencing data from two highly resistant CPB populations in the United States (Hancock, Wisconsin and Long Island, New York). Demographic reconstruction corroborates historical records for a single pest origin during the colonization of the Midwestern and Eastern United States in the mid-to late-19th century and suggests that the effective population size might be higher in Long Island, NY than Hancock, WI despite contemporary potato acreage of Wisconsin being far greater. Population-based recombination maps show similar background recombination rates between these populations, as well as overlapping regions of low recombination that intersect with important metabolic detoxification genes. In both populations, we find compelling evidence for hard selective sweeps linked to insecticide resistance with multiple sweeps involving genes associated with xenobiotic metabolism, stress response, and defensive chemistry. Notably, only two candidate insecticide resistance genes are shared among both populations, but both appear to be independent hard selective sweep events. This suggests that repeated, rapid, and independent evolution of genes may underlie CPBs pest status among geographically distinct populations.

evolutionary biology↗

bioRxiv2021

Genome resequencing reveals rapid, repeated evolution in the Colorado potato beetle, Leptinotarsa decemlineata

BackgroundInsecticide resistance and rapid pest evolution threatens food security and the development of sustainable agricultural practices. An improved understanding of the evolutionary mechanisms that allow pests to rapidly adapt to novel control tactics will help prevent economically damaging outbreaks. The Colorado potato beetle (CPB), Leptinotarsa decemlineata, is a global super-pest that rapidly evolves resistance to insecticides. Using whole genome resequencing and transcriptomic data focused on its ancestral and pest range in North America, we assess evidence for three, non-mutually exclusive models of rapid evolution: pervasive selection on novel mutations, rapid regulatory evolution, and repeated selection on standing genetic variation. ResultsPopulation genomic analysis demonstrates that CPB is geographically structured, even among recently established pest populations. Pest populations exhibit only modest reductions in nucleotide diversity, relative to non-pest ancestral populations, and show evidence of recent demographic expansion. Genome scans of selection provide clear signatures of repeated adaptation across different CPB populations, with especially strong evidence that insecticide resistance involves selection of different genes in different populations. Similarly, analyses of gene expression show that constitutive upregulation of candidate insecticide resistance genes drives distinctive population patterns. ConclusionCPB evolves insecticide resistance repeatedly across agricultural regions, and oftentimes at the same loci, supporting a prominent role of polygenic evolution from standing genetic variation. Despite expectations, we do not find support for strong selection on novel mutations, or rapid evolution from selection on regulatory genes. An important future goal will be to understand how polygenic resistance phenotypes spread among local pest populations, in order to refine integrated pest management practices to maintain the efficacy and sustainability of novel control techniques.

evolutionary biology↗

bioRxiv2019

Elevated rates of positive selection drive the evolution of pestiferousness in the Colorado potato beetle (Leptinotarsa decemlineata, Say)

Insect pests are characterized by expansion, preference and performance on agricultural crops, high fecundity and rapid adaptation to control methods, which we collectively refer to as pestiferousness. Which organismal traits and evolutionary processes facilitate certain taxa becoming pests remains an outstanding question for evolutionary biologists. In order to understand these features, we set out to test the relative importance of genomic properties that underlie the rapid evolution of pestiferousness in the emerging pest model: the Colorado potato beetle (CPB), Leptinotarsa decemlineata Say. Within the Leptinotarsa genus, only CPB has risen to pest status on cultivated Solanum. Using whole genomes from ten closely related Leptinotarsa species, we reconstructed a high-quality species tree of this genus. Within this phylogenetic framework, we tested the relative importance of four drivers of rapid adaptation: standing genetic variation, gene family expansion and contraction, transposable element variation, and protein evolution. Throughout approximately 20 million years of divergence, Leptinotarsa show little evidence of gene family turnover or transposable element variation contributing to pest evolution. However, there is a clear pattern of pest lineages experiencing greater rates of positive selection on protein coding genes, as well as retaining higher levels of standing genetic variation. We also identify a suite of positively selected genes unique to the Colorado potato beetle that are directly associated with pestiferousness. These genes are involved in xenobiotic detoxification, chemosensation, and hormones linked with pest behavior and physiology.

evolutionary biology↗