bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.64898/2026.10.15.759414

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

Venkitachalam, S.·Heath, N. A.·Albright, A.·York, M.·Kuehnel, M.·Robinson, K.·Vazquez, S.·Middleton, K. M.·King, E. G.
View original source ↗Export metadata ↓

Abstract

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.

Explore related subjects

evolutionary biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Venkitachalam, S., Heath, N. A., Albright, A., York, M., Kuehnel, M., Robinson, K., Vazquez, S., Middleton, K. M., King, E. G.. 2026-10-16. Complex-trait dissection with Evolve-and-Resequence: Selection for improved flight performance in laboratory fruit fly populations. https://doi.org/10.64898/2026.10.15.759414

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

An unconstrained Euclidean parametrisation of phylogenetic tree space

Phylogenetic trees combine a discrete topology with continuous branch lengths, which makes them difficult to work with. We introduce a recursive contour-grafting construction that encodes both components using unconstrained real-valued coordinates. After fixing an order of the leaves, each new leaf is attached at a point selected by a contour traversal of the tree constructed so far. Moving a graft coordinate continuously along the contour enables changes of topology when internal branches contract to zero. For trees with n labelled leaves, we apply the construction to rooted ultrametric trees, rooted trees with unrestricted branch lengths, and unrooted trees, obtaining parametrisations of dimensions n-1, 2n-2, and 2n-3, respectively. We show that the resulting construction functions are surjective and continuous onto the corresponding spaces of phylogenetic trees. We also determine the number of representations of a generic tree and calculate the Jacobian of each parametrisation. These results provide explicit change-of-variables formulae between Euclidean coordinates and the phylogenetic tree spaces, and we show how probability distributions on tree space can be sampled using generic algorithms that target unconstrained Euclidean coordinates. This approach paves the way for the development and application of new methodology in Bayesian phylogenetic inference.

evolutionary biology↗
bioRxiv2026

Triangulating evidence to detect signatures of stabilizing selection acting on protein levels in humans

Stabilizing selection is thought to maintain quantitative traits near evolutionary optima, yet the extent to which it constrains human molecular phenotypes remains largely unknown. Here, we investigate signatures of stabilizing selection on the circulating levels of 2'923 plasma proteins in up to 50'000 UK Biobank participants by integrating complementary evidence across evolutionary timescales. We combine genetic signatures of selection accumulated over generations with associations between protein abundance and contemporary fitness-related outcomes. Genetic evidence was assessed using the frequency-dependent architecture of common variants with LDpred2 and a newly developed likelihood-based framework leveraging rare loss-of-function variant burdens. Contemporary evidence was obtained through quadratic associations between protein abundance and three fitness proxies: reproductive success, somatic health, and parental longevity. Across all approaches, negative selection coefficients predominated. Among significant estimates, 100% of common-variant and 92.4% of rare-variant estimates were consistent with stabilizing selection, compared with 99.8% for somatic health, 97.7% for parental longevity, and 89.3% for reproductive success. Despite capturing distinct aspects of selection, the approaches showed partial convergence. Rare-variant-based estimates correlated with health-score-derived coefficients (rho = 0.36, p = 5.2 x 10^-6) and independent measures of evolutionary constraint, including protein heritability, loss-of-function intolerance, and cross-species transcript evolutionary rates. Together, our findings suggest that stabilizing selection is widespread across the human plasma proteome and highlight the value of integrating genetic architecture with fitness-related phenotypes to understand evolutionary constraints on molecular variation.

evolutionary biology↗
bioRxiv2026

Strain-specific higher-order interactions break phylogenetic conservatism in microbial communities

Whether strains of the same species sharing the same ecological role are truly interchangeable has not been directly tested experimentally in communities, where higher-order interactions govern outcomes. Using 79 co-occurring Bacillaceae isolates from the Cuatrocienegas Basin, we combined whole-genome analyses with systematic strain substitutions in BARS, a three-species community in which a resistant strain protects a sensitive strain from an antagonist. Trait conservatism strongly predicted pairwise antagonistic outcomes. Yet across 34 assembled triads, 13 showed rescue beyond pairwise expectations and five showed suppression; single-strain substitutions rarely restored protection, although protection was recovered in one fully reconfigured triad. These outcomes could not be inferred from taxonomic relatedness, pangenomic content or pairwise assays; phylogenetic conservatism thus reaches its limit at the transition from pairwise to higher-order interactions. To explain this limit, we propose that strains behave as non-equivalent biological tiles whose interaction edges must align, a dynamic biological tessellation.

evolutionary biology↗