Biology subjects

York, M.

Publications and source records attributed to York, M..

3 recordsLinked to original sources

bioRxiv2026

Complex-trait dissection with Evolve-and-Resequence: Selection for improved flight performance in laboratory fruit fly populations

Evolve-and-Resequence studies combine experimental evolution with molecular sequencing, enabling associations between complex trait phenotypes and evolved genomic changes. For this, a targeted complex trait is subjected to artificial laboratory selection in genetically variable populations. Using populations of fruit flies Drosophila melanogaster from the DSPR background, we have conducted a short-term selection study on a highly complex trait : flight performance. We selected for improved flight performance using a custom-built flight tunnel system, with light as a motivator and airflow as a resistive factor. As a result, flight performance significantly improved in selected populations compared to controls. We also observed signatures of evolution in flight related traits, such as activity level and wing shape, and in life-history related traits such as adult dry mass and fecundity. We used whole genome pooled sequencing on the selected and control populations, revealing significantly differentiated genomic sites. Gene ontology and enrichment analyses revealed the evolution of pathways involved in response to stimuli, growth, and development. We identified several genes of interest (e.g., Sdc, dally). The range of evolved phenotypes and associated genomic changes show that flight performance is an ideal complex trait for future Evolve-and-Resequence studies.

evolutionary biology↗

bioRxiv2025

Comparative Analysis of Tick Microbiomes in Remnant and Reconstructed Prairie Ecosystems

The ecological processes that shape tick-associated microbial communities are not fully understood. Ticks harbor diverse microbial communities that include both symbiotic and pathogenic bacteria, and these microbes can influence tick physiology, vector competence, and pathogen transmission. We evaluated bacterial microbiome diversity and composition in two medically important tick species, Amblyomma americanum and Dermacentor variabilis, collected from remnant and reconstructed tallgrass prairies in central Missouri between 2020 and 2023. Using 16S rRNA gene amplicon sequencing, we characterized microbial communities from 200 pooled tick samples and assessed patterns in alpha diversity, beta diversity, and differential abundance across tick species and prairie types. Microbiome diversity and composition differed strongly between tick species, with D. variabilis exhibiting higher alpha diversity than A. americanum and clear species-specific clustering in beta diversity analyses. In contrast, differences between remnant and reconstructed prairies were modest. Differential abundance testing revealed Rickettsia to be enriched in A. americanum and Francisella in D. variabilis, consistent across prairie types. Species-level screening further showed that A. americanum primarily harbored low virulent Rickettsia, whereas D. variabilis more frequently carried pathogenic Rickettsia species. Prairie restoration status did not significantly predict Rickettsia type, although a higher proportion of potentially pathogenic lineages was observed in reconstructed sites. These findings indicate that tick species identity is the primary determinant of microbiome structure in prairie ecosystems, with habitat context exerting secondary influences. Our results underscore the importance of incorporating microbiome ecology into medical entomology and suggest that land management practices may subtly shape vector-microbe interactions relevant to disease risk.

ecology↗

bioRxiv2024

Timing of standard chow exposure determines the variability of mouse phenotypic outcomes and gut microbiota profile

Standard chow diet contributes to reproducibility in animal model experiments since chows differ in nutrient composition, which can independently influence phenotypes. However, there is little evidence of the role of timing in the extent of variability caused by chow exposure. Here, we measured the impact of diet (5V5M, 5V0G, 2920X, and 5058) and timing of exposure (adult exposure (AE), lifetime exposure (LE), and developmental exposure (DE)) on growth & development, metabolic health indicators, and gut bacterial microbiota profiles across genetically identical C57BL6/J mice. Diet drove differences in macro-and micronutrient intake for all exposure models. AE had no effect on measured outcomes. However, LE mice exhibited significant sex-dependent diet effects on growth, body weight, and body composition. LE effects were mostly absent in the DE model, where mice were exposed to chow differences from conception to weaning. Both AE and LE models exhibited similar diet-driven beta diversity profiles for the gut bacterial microbiota, with 5058 diet driving the most distinct profile. Diet-induced beta diversity profiles were sex-dependent for LE mice. Compared to AE, LE drove 9X more diet-driven differentially abundant genera, majority of which were the result of inverse effects of 2920X and 5058. Our findings demonstrate that lifetime exposure to different chow diets has the greatest impact on reproducibility of experimental measures that are common components of preclinical mouse model studies. Importantly, weaning DE mice onto a uniform diet is likely an effective way to reduce unwanted phenotypic variability among experimental models.

developmental biology↗