Biology subjects

Ellis, T. J.

Publications and source records attributed to Ellis, T. J..

7 recordsLinked to original sources

bioRxiv2026

How and why to quantify pairwise pleiotropy and genotype-by-environment interactions

Pleiotropy is when a single locus affects two or more traits. The magnitude and direction of pleiotropy can constrain or faciliate phenotypic evolution. Investigations of pleiotropy have typically relied on null-hypothesis tests to classify cases into discrete categories based on the direction of effects. This discrete approach ignores the quantitative nature of pleiotropy, and systematically underestimates pleiotropic interactions. I describe a simple method to quantify the direction and magnitude of pleiotropic effects to alleviate these issues for pairs of traits. I illustrate how genotype-by-environment interactions can be viewed as a special case of pleiotropy and described in the same way. I provide an R package, psiotropy, to apply these methods.

genetics↗

bioRxiv2025

Improving American chestnut resistance to two invasive pathogens through genome-enabled breeding

Over a century after two introduced pathogens decimated American chestnut populations, breeding programs continue to incorporate resistance from Chinese chestnut to recover self-sustaining populations. Due to complex genetics of chestnut blight resistance, it is challenging to obtain trees with sufficient resistance and competitive growth. We developed high quality reference genomes for Chinese and American chestnut and leveraged large disease phenotype and genotype datasets to develop accurate genomic selection. Inoculation and simulation results indicate that resistance may be substantially increased in trees that inherited 70% to 100% of their genome from American chestnut. To facilitate gene editing, we integrated multiple lines of evidence to discover candidate alleles for blight resistance and susceptibility. These genomic resources provide a strong foundation to accelerate restoration of this iconic tree.

genomics↗

bioRxiv2024

Bisulphite sequencing in the presence of cytosine-conversion errors

Bisulphite treatment of DNA converts unmethylated cytosines to thymine, and is a common method to infer the methylation status of cytosines when coupled with sequencing. Tagmentation approaches to bisulphite sequencing use a transposase to simultaneously make double-stranded breaks and ligate adaptors to the resulting fragments, allowing for higher throughput with less starting material. However, it has also been noted that certain tagmentation protocols have an unusually high number unmethylated cytosines that are not converted to thymine. Here we describe this phenomenon in detail, and find that results are consistent with single strand nicks by the transposase, followed by strand displacement of part or all of the DNA fragment, leading to erroneous incorporation of methylated cytosines. Nevertheless we show that these errors can be accounted for in downstream analysis and need not impede biological conclusions. We provide a Python package to allow users to implement this framework. Ultimately the additional effort of accounting for errors must be traded off against the scalability of the protocol in planning experiments.

genomics↗

bioRxiv2024

Adaptation to soil type contributes little to local adaptation in an Italian and a Swedish population of Arabidopsis thaliana growing on contrasting soils

Natural populations are subject to selection caused by a range of biotic and abiotic factors in their native habitats. Identifying these agents of selection and quantifying their effects is key to understanding how populations adapt to local conditions. We performed a fully factorial reciprocal transplant experiment using locally adapted accessions of Arabidopsis thaliana at their native sites to distinguish the contributions of adaptation to soil type and climate. Overall adaptive differentiation was strong at both sites. However, we found only very small differences in the strength of selection on local and non-local soil, and adaptation to soil type at most constituted only a few percent of overall adaptive differentiation. These results indicate that adaptation to local climatic conditions rather than soil type is the primary driver of adaptive differentiation between these ecotypes.

evolutionary biology↗

bioRxiv2024

Joint estimation of paternity, sibships and pollen dispersal in a snapdragon hybrid zone

1Inferring genealogical relationships of wild populations is useful because it gives direct estimates of mating patterns and variance in reproductive success. Inference can be improved by including information about parentage shared between siblings, or by modelling pheno-types or population data related to mating. However, we currently lack a framework to infer parent-offspring relationships, sibships, and population parameters in a single analysis. To address this we here extend a previous method Fractional Analysis of Paternity and Sibships to include population data for the case where one parent is known. We illustrate this with the example of pollen dispersal in a natural hybrid zone population of the snapdragon Antirrhinum majus. Pollen dispersal is leptokurtic, with half of mating events occurring within 30m, but with a long tail of mating events up to 859m. Using simulations we find that both sibship and population information substantially improve pedigree reconstruction, and that we can expect to resolve median dispersal distances with high accuracy.

evolutionary biology↗

bioRxiv2022

A globally distributed major virus-resistance association in Arabidopsis thaliana

Plant viruses account for enormous agricultural losses worldwide, and the most effective way to combat them is to identify genetic material conferring plant resistance to these pathogens. Aiming to identify genetic associations with responses to infection, we screened a large panel of Arabidopsis thaliana natural inbred lines for four disease-related traits caused by infection by A. thaliana-naive and -adapted isolates of the natural pathogen turnip mosaic virus (TuMV). We detected a strong, replicable association in a 1.5 Mb region on chromosome 2 with a 10-fold increase in relative risk of systemic necrosis. The region contains several plausible causal genes as well as abundant structural variation, including an insertion of a Copia transposon into a Toll/interleukin receptor (TIR-NBS-LRR) coding for a gene involved in defense, that could be either a driver or a consequence of the disease-resistance locus. When inoculated with TuMV, loss-of-function mutant plants of this gene exhibited different symptoms than wild-type plants. The direction and severity of symptom differences depended on the adaptation history of the virus. This increase in symptoms severity was specific for infections with the adapted isolate. Necrosis-associated alleles are found worldwide, and their distribution is consistent with a trade-off between resistance during viral outbreaks and a cost of resistance otherwise, leading to negative frequency-dependent selection.

genetics↗

bioRxiv2022

The genetic structure of a wild wheat population has remained associated with microhabitats over 36 years

Long-term genetic studies of wild populations are very scarce, but are essential for connecting ecological and population genetics models, and for understanding the dynamics of biodiversity. We present a study of a wild wheat population sampled over a 36-year period at high spatial resolution. We genotyped 832 individuals from regular sampling along transects during the course of the experiment. Genotypes were clustered into ecological microhabitats over scales of tens of metres, and this clustering was remarkably stable over the 36 generations of the study. Simulations show that it is difficult to explain this spatial and temporal stability using only limited dispersal, suggesting a role for fine-scale local adaptation to ecological parameters. Using a common-garden experiment, we showed that the genotypes found in distinct microhabitats differ phenotypically, further supporting the hypothesis of local adaptation. Our results provide a rare insight into the population genetics of a natural population over a long monitoring period.

evolutionary biology↗