Biology subjects

Erickson, K.

Publications and source records attributed to Erickson, K..

3 recordsLinked to original sources

bioRxiv2025

Parallel polygenic urban adaptation despite high gene flow in a coastal marine invertebrate

Urbanization results in novel environments, offering a unique opportunity to investigate natural selection on small spatiotemporal scales. Although each city is different, geographically distinct cities can in some ways represent evolutionary replicates, allowing for the investigation of parallel and predictable evolutionary responses to urban environments. Additionally, there are few examples of urban adaptation in high gene flow marine systems, whose patterns might differ markedly from aquatic and terrestrial systems. Using whole genomes from Pacific purple sea urchins (Strongylocentrotus purpuratus) across three coastal cities spanning >2000km, we investigated genomic signals for adaptation to urban environments. We found genetic variants differentiating urban and nonurban sites within each city region, despite high gene flow and little evidence for differentiation across latitudinal gradients. While these SNP-level candidates for selection were largely non-overlapping, polygenic approaches uncover a distinct parallel signal of urban adaptation across the sampled range. Our results suggest that adaptation over small scale urbanization gradients is possible even in high gene flow systems and the polygenic architecture of adaptation is, at least in part, parallel. More broadly, our work highlights the importance of polygenic methods in ecological genomics in expanding our understanding of how evolutionary forces operate in natural systems.

genomics↗

bioRxiv2021

Seascape genomics reveals metapopulation connectivity network of Paramuricea biscaya in the northern Gulf of Mexico

The degree of connectivity among populations influences their ability to respond to natural and anthropogenic stressors. In marine systems, determining the scale, rate, and directionality of larval dispersal is therefore central to understanding how coral metapopulations are interconnected and the degree of resiliency in the event of a localized disturbance. Understanding these source-sink dynamics is essential to guide restoration efforts and for the study of ecology and evolution in the ocean. The patterns and mechanisms of connectivity in the deep-sea (> 200 meters deep) are largely understudied. In this study, we investigated the spatial diversity patterns and metapopulation connectivity of the octocoral Paramuricea biscaya throughout the northern Gulf of Mexico (GoM). Paramuricea biscaya is one of the most abundant corals on the lower continental slope (between 1200 and 2500 m) in the GoM. The 2010 Deepwater Horizon oil spill (DWH) directly impacted populations of this species and thus are considered primary targets for restoration. We used a combination of seascape genomic analyses, high-resolution ocean circulation modeling, and larval dispersal simulations to quantify the degree of population structuring and connectivity among P. biscaya populations. Evidence supports the hypotheses that the genetic diversity of P. biscaya is predominantly structured by depth, and that larval dispersal among connected populations is asymmetric due to dominant ocean circulation patterns. Our results suggest that there are intermediate unsampled populations in the central GoM that serve as stepping stones for dispersal. The data suggest that the DeSoto Canyon area, and possibly the West Florida Escarpment, critically act as sources of larvae for areas impacted by the DWH oil spill in the Mississippi Canyon. This work illustrates that the management of deep-sea marine protected areas should incorporate knowledge of connectivity networks and depth-dependent processes throughout the water column.

ecology↗

bioRxiv2019

Transcriptome-based design of antisense inhibitors re-sensitizes CRE E. coli to carbapenems

Carbapenems are a powerful class of antibiotics, often used as a last-resort treatment to eradicate multidrug-resistant infections. In recent years, however, the incidence of carbapenem-resistant Enterobacteriaceae (CRE) has risen substantially, and the study of bacterial resistance mechanisms has become increasingly important for antibiotic development. Although much research has focused on genomic contributors to carbapenem resistance, relatively few studies have examined CRE pathogens through changes in gene expression. In this research, we used transcriptomics to study a CRE Escherichia coli clinical isolate that is sensitive to meropenem but resistant to ertapenem, to both explore carbapenem resistance and identify novel gene knockdown targets for carbapenem re-sensitization. We sequenced total and small RNA to analyze gene expression changes in response to treatment with ertapenem or meropenem, as compared to an untreated control. Significant expression changes were found in genes related to motility, maltodextrin metabolism, the formate hydrogenlyase complex, and the general stress response. To validate these transcriptomic findings, we used our labs Facile Accelerated Specific Therapeutic (FAST) platform to create antisense peptide nucleic acids (PNA), gene-specific molecules designed to inhibit protein translation. FAST PNA were designed to inhibit the pathways identified in our transcriptomic analysis, and each PNA was then tested in combination with each carbapenem to assess its effect on the antibiotics minimum inhibitory concentrations. We observed significant treatment interaction with five different PNAs across six PNA-antibiotic combinations. Inhibition of the genes hycA, dsrB, and bolA were found to re-sensitize CRE E. coli to carbapenems, whereas inhibition of the genes flhC and ygaC was found to confer added resistance. Our results identify new resistance factors that are regulated at the level of gene expression, and demonstrate for the first time that transcriptomic analysis is a potent tool for designing antibiotic PNA.

microbiology↗