Biology subjects

Neto, C.

Publications and source records attributed to Neto, C..

6 recordsLinked to original sources

bioRxiv2026

Polygenic adaptation from standing variation underlies rapid evolution under anthropogenic selection in an agricultural weed

Herbicide resistance is among the clearest examples of rapid adaptation to intense anthropogenic selection. Yet, how the evolutionary origins and genetic architecture of resistance shapes its tempo and mode of evolution remain incompletely resolved. Here, we address these questions in Alopecurus myosuroides (blackgrass), Europe's most widespread and economically damaging herbicide-resistant weed. We present the first genome-wide analysis of herbicide resistance in natural blackgrass populations, uniquely combining historical and contemporary populations collected before and after the onset of intensive herbicide use. This temporal framework provides novel empirical access to pre-selection genetic variation, enabling reconstruction of the tempo and mode of both target-site (TSR) and non-target-site resistance (NTSR) evolution across space and time. TSR mutations were not found in pre-herbicide populations and evolved recently through repeated, largely independent origins across Europe. NTSR, in contrast, has a polygenic architecture and is associated with a cluster of glutathione S-transferases (GSTs) with signatures of copy number variation, and broader stress-response genes. Most NTSR-associated alleles were already segregating in historical populations, consistent with rapid adaptation from standing genetic variation. Moreover, resistance-associated loci show signatures consistent with positive selection predating herbicide use, suggesting these stress and detoxification pathways were historically maintained by prior ecological selection and subsequently recruited under herbicide pressure. Together, these findings demonstrate that herbicide resistance encompasses contrasting genetic routes, with polygenic NTSR evolving largely through selection on standing variation, offering broader insights into the evolutionary dynamics of rapid polygenic adaptation under novel anthropogenic selection.

evolutionary biology↗

bioRxiv2026

Climate-driven niche tracking and genomic resilience shape future distribution of a widespread agricultural weed

Understanding how agriculturally important species respond to environmental change is critical for maintaining productivity, mitigating agroecosystem threats, and sustaining resilience. While crops have traditionally been the focus in agroecosystems, agricultural weeds are integral components that often face even stronger selective pressures, making them powerful models for investigating ecological and evolutionary responses to climatic and human-mediated challenges. Insights from how weeds adapt rapidly under these pressures can inform strategies to improve agricultural outcomes, since both pests and crops evolve under the same multivariate selective pressures. Here, we integrate two centuries of distribution records with whole-genome sequencing from natural populations of the most damaging weed in Europe - Alopecurus myosuroides (blackgrass) - to examine its ecological and evolutionary responses in agroecosystems. Blackgrass largely maintained its historical climatic niche, expanding its range primarily by tracking environments analogous to those it historically occupied. Genome-wide analyses revealed a polygenic basis of environmental responses, with most loci linked to single environmental variables and a subset showing limited environmental pleiotropy, indicating modular adaptation to the complex selective pressures of managed agricultural landscapes. Coupling these genomic-environment relationships with projected climate change and genomic offset analyses indicated that most blackgrass populations will remain well aligned with future conditions. Our findings show that ecological niche tracking and polygenic adaptation allow agricultural weeds like blackgrass to persist under rapid environmental change, offering insights relevant not only for weed management but also for designing resilient cropping systems under future climates.

genomics↗

bioRxiv2025

Major effect mutations drive DNA methylation variation after colonization of a novel habitat

DNA methylation is important to maintain genome stability, but alterations in genome-wide methylation patterns can produce widespread genomic effects, which have the potential to facilitate rapid adaptation. We investigate DNA methylation evolution in Arabidopsis thaliana during its colonization of the drought-prone Cape Verde Islands (CVI). We identified three high impact changes in genes linking histone modification to DNA methylation that underlie variation in DNA methylation within CVI. Gene body methylation is reduced in CVI relative to the Moroccan outgroup due to a 2.7-kb deletion between two VARIANT IN METHYLATION genes (VIM2 and VIM4) that causes aberrant expression of the VIM2/4 homologs. Disruptions of CHROMOMETHYLASE 2 (CMT2) and a newly identified DNA methylation modulator, F-BOX PROTEIN 5 (FBX5), which we validated using CRISPR mutant analysis, contribute to DNA methylation of transposable elements (TEs) within CVI. Overall, our results reveal rapid methylome evolution driven largely by high impact variants in three genes.

genetics↗

bioRxiv2025

A Modular Microfluidic System to Generate Gradient Hydrogels with Simple-to-Complex Stiffness Profiles for Mechanobiology

Engineered stiffness gradient hydrogels offer exciting opportunities to probe fundamental mechanobiological processes in vitro. However, the need to spatially manipulate the properties of soft hydrogels at the micron scale poses challenges in developing fabrication platforms that can reliably modulate the gradient gel characteristics according to user needs. This study describes a modular approach leveraging thermophoresis in microfluidics to create high-fidelity stiffness gradients with linear and complex profiles, including periodic and anisotropic gradients. This study describes the platforms design and optimization, demonstrating achievable stiffness ranges and gradient slopes that correlate with many physiologic and diseased tissue types. This platform is also compatible with different hydrogel crosslinking chemistries, providing a versatile tool to engineer microenvironments with increased complexity. Directionally biased fibroblast cell proliferation and migration on fabricated stiffness gradient gelatin methacryloyl (GelMA) hydrogels indicate the effectiveness of this platform in modulating the mechanical microenvironment of cells. The results indicate that both the absolute stiffness range and the pattern of stiffness variation jointly affect cell behaviors. Considering its remarkable flexibility, the fabrication platform can significantly advance the development of biophysical gradient hydrogels that better replicate the intricacies of native tissues and help realize the next breakthroughs in mechanobiology.

bioengineering↗

bioRxiv2023

The International Weed Genomics Consortium: Community Resources for Weed Genomics Research

The International Weed Genomics Consortium is a collaborative group of researchers focused on developing genomic resources for the study of weedy plants. Weeds are attractive systems for basic and applied research due to their impacts on agricultural systems and capacity to swiftly adapt in response to anthropogenic selection pressures. Our goal is to use genomic information to develop sustainable and effective weed control methods and to provide insights about biotic and abiotic stress tolerance to assist crop breeding. Here, we outline resources under development by the consortium and highlight areas of research that will be impacted by these enabling resources.

genomics↗

bioRxiv2020

MLS3: A New Type of Multilevel Selection

In most multispecies multilevel selection (MLS) models, offspring communities are generated by random assembly of individuals in numbers reflecting sizes of parental communities releasing them (MLS1), or by differential community dispersal based on a community-level trait such as size (MLS2). In both, offspring communities colonize vacant spaces: different communities never compete for the same space. Here we propose a third MLS type (MLS3) where multispecies communities disperse (migrate) into already-occupied spaces, larger communities more frequently. Conspecific variants compete, often opposing selection for community size against fitness within species. This makes the outcome of MLS3 less apparent than MLS1 and MLS2 where such tension is absent. Our simulations show that, if community size depends strongly on reduction in the fitness of individual community members, such a reduction (comprising a sort of "inter-species altruism") will evolve. The framework we present represents a step toward conceptualizing community coalescence in the context of metacommunities.

evolutionary biology↗