Biology subjects

Hateley, S.

Publications and source records attributed to Hateley, S..

4 recordsLinked to original sources

bioRxiv2025

Population and adaptation history of 739 Thlaspi arvense natural accessions

Pennycress (Thlaspi arvense) is a promising intermediate oilseed crop, producing oil suitable for conversion to biofuels--including aviation fuels. While domestication efforts are ongoing, a deeper understanding of the genetic architecture of traits is crucial for informing future breeding efforts. Here, we conducted the largest genomic and phenotypic survey of pennycress to date, analyzing 739 accessions collected across four continents. Leveraging whole-genome sequencing and field-collected phenotypes, we characterized the standing genetic variation underlying key agronomic traits and climate resilience. Our findings revealed multiple independent migration events to North America, with substantial genetic admixture. We identified homologs of Arabidopsis thaliana flowering-time genes that contribute to adaptation and demonstrated the agronomic benefits of winter-type pennycress. Furthermore, through multi-season field trials, we identified a genomic region containing a cluster of mTERF genes strongly associated with green canopy coverage, a critical trait for biomass retention and yield stability. These insights provide a genomic roadmap for accelerating pennycress domestication and improving its resilience to climate variability.

genomics↗

bioRxiv2023

Conflicts in natural selection constrain adaptation to climate change in Arabidopsis thaliana

Climate change has already caused noticeable changes in species-wide traits, such as the well-documented acceleration of spring flowering. Because the evolutionary past has favored certain combinations of traits, some strategies like fast growth with early flowering that are adaptive today are at odds with other plant resilience strategies such as elevated water use efficiency. We know that the evolution of trait combinations is shaped by genomic constraints, but it is unclear whether and how this is affected by natural selection from climate change. Growing hundreds of Arabidopsis thaliana natural populations under different rainfall regimes revealed opposing natural selection on flowering time and water use efficiency, with strong antagonistic genetic correlations and contrasting causal alleles identified by Genome-Wide Association analyses. Inactivation of the central flowering regulator FLC in multiple, diverse accessions relaxed trait correlations in a genetic background-dependent manner and allowed for the emergence of a novel adaptive trait combination--early flowering and intermediate water use efficiency. Future climates are predicted to escalate conflicts in natural selection among adaptive traits, but our work shows that surprisingly simple genetic changes can help solve these conflicts.

evolutionary biology↗

bioRxiv2021

Quantifying the scale of genetic diversity extinction in the Anthropocene

More species than ever before are at risk of extinction due to anthropogenic habitat loss and climate change. But even species that are not threatened have seen reductions in their populations and geographic ranges, likely impacting their genetic diversity. Although preserving genetic diversity is key to maintaining adaptability of species, we lack predictive tools and global estimates of genetic diversity loss across ecosystems. By bridging theories of biodiversity and population genetics, we introduce a mathematical framework to understand the loss of naturally occurring DNA mutations within decreasing habitat within a species. Analysing genome-wide variation data of 10,095 geo-referenced individuals from 20 plant and animal species, we show that genome-wide diversity follows a power law with geographic area (the mutations-area relationship), which can predict genetic diversity loss in spatial computer simulations of local population extinctions. Given pre-21st century values of ecosystem transformations, we estimate that over 10% of genetic diversity may already be lost, surpassing the United Nations targets for genetic preservation. These estimated losses could rapidly accelerate with advancing climate change and habitat destruction, highlighting the need for forecasting tools that facilitate implementation of policies to protect genetic resources globally.

ecology↗

bioRxiv2017

Fusion detection and quantification by pseudoalignment

RNA sequencing in cancer cells is a powerful technique to detect chromosomal rearrangements, allowing for de novo discovery of actively expressed fusion genes. Here we focus on the problem of detecting gene fusions from raw sequencing data, assembling the reads to define fusion transcripts and their associated breakpoints, and quantifying their abundances. Building on the pseudoalignment idea that simplifies and accelerates transcript quantification, we introduce a novel approach to fusion detection based on inspecting paired reads that cannot be pseudoaligned due to conflicting matches. The method and software, called pizzly, filters false positives, assembles new transcripts from the fusion reads, and reports candidate fusions. With pizzly, fusion detection from raw RNA-Seq reads can be performed in a matter of minutes, making the program suitable for the analysis of large cancer gene expression databases and for clinical use. pizzly is available at https://github.com/pmelsted/pizzly

bioinformatics↗