Biology subjects

Yeap, H. L.

Publications and source records attributed to Yeap, H. L..

4 recordsLinked to original sources

bioRxiv2026

Rapid thermal adaptation in coral photosymbionts draws on standing variation and recombination

Bleaching tolerance in corals depends in part on the thermal tolerance of their microalgal symbionts. Laboratory evolution has increased the thermal tolerance of the symbiont Cladocopium proliferum in ~120 generations, but the genetic basis of that response was unknown. We compared single nucleotide polymorphisms in transcriptomes of three heat-evolved C. proliferum strains and one wild-type (unselected) strain from the same progenitor. We found 15,640 polymorphic loci, but no variant was both private to a strain and consistent across its replicates, which indicates that new mutations contributed little to the response in expressed sequences. Instead, allele frequencies at 350 loci differed significantly between strains, and linkage patterns indicated recombination had occurred within scaffolds both before and after the strains were separated. Selection and recombination of variation already present in the progenitor therefore underpinned the rapid thermal adaptation. Experimental evolution for reef restoration should start from genetically diverse cultures rather than single cell isolates.

evolutionary biology↗

bioRxiv2026

Evaluating the cross-species transferability and scaling of sequence-to-function predictions in AlphaGenome

Deep learning models that predict molecular phenotypes directly from DNA sequence offer a powerful framework for interpreting genomic variation. Recently, AlphaGenome was introduced as a deep sequence-to-function architecture capable of predicting observations that historically required experiments. While the model has shown high accuracy, it was primarily evaluated on human variants scored against a reference genome. Here, we test performance on mouse data, the other species AlphaGenome was trained on although with fivefold fewer features than human (1,128 versus 5,930). We demonstrate that AlphaGenomes predictive performance varies considerably depending on the functional task. Specifically, predicted quantitative expression effects are directionally weak and compressed roughly 100-fold relative to empirical benchmarks across both reconstructed-haplotype and single-variant regimes. In contrast, canonical splice-site disruptions are recognized with near-identical accuracy in mouse and human (AUC 0.96 versus 0.98), displaying no cross-species divergence in predicted effect magnitude. We developed a scoring-approach for AI-agents to autonomously assess AlphaGenome prediction confidence and accurately differentiate between AlphaGenomes robust sequence-level recognition across species and its current limitations when interpreting un-fine-mapped regulatory variants. This demonstrates how GenAI innovations that are still under development can safely be harnessed by wrapping a responsible AI layer around the call to intercept flawed results, thereby adhering to international standards, such as the Australian Voluntary AI Safety Standard (VAISS).

bioinformatics↗

bioRxiv2022

Flow cytometry-based biomarker assay for in vitro identification of heat tolerance conferring coral symbionts

Corals tolerance to high temperature stress largely depends on their symbiotic microalgae (Symbiodiniaceae). However, the contributing microalgal traits are largely unclear. Here we compare the in vitro cellular profiles of seven Cladocopium C1acro microalgal strains (derived from the same ancestral strain) during a four-week exposure to 27{degrees}C or 31{degrees}C. One was an unselected wild-type strain (WT), three were selected at 31{degrees}C for nine years and shown to confer thermal tolerance on the coral host (SS+) and three others were similarly selected but did not confer tolerance (SS-). Flow cytometry was used to measure the intracellular stress indicators reactive oxygen species (ROS), reduced glutathione (rGSH) and mitochondrial-membrane potential ({Delta}{Psi}m), as well as cell size/shape and photosynthetic pigments. Cell densities and photosynthetic efficiency ({Phi}PSII, Fv/Fm) were also measured. WT showed the highest levels of intracellular ROS and {Delta}{Psi}m, lowest rGSH and largest cell sizes at both temperatures. SS+ strains had the lowest ROS and highest rGSH values and a unique pattern of correlations among parameters at 31{degrees}C. Our results support previous reports implicating the role of microalgal ROS, {Delta}{Psi}m and rGSH in holobiont thermal tolerance and suggest flow cytometry is a useful pre-screening tool for identifying microalgal strains with enhanced thermal tolerance.

microbiology↗

bioRxiv2021

A wAlbB Wolbachia transinfection displays stable phenotypic effects across divergent Aedes aegypti mosquito backgrounds

Aedes mosquitoes harboring intracellular Wolbachia bacteria are being released in arbovirus and mosquito control programs. With releases taking place around the world, understanding the contribution of host variation to Wolbachia phenotype is crucial. We generated a Wolbachia transinfection (wAlbBQ) in Aedes aegypti and performed backcrossing to introduce the infection into Australian or Malaysian nuclear backgrounds. Whole Wolbachia genome sequencing shows that the wAlbBQ transinfection is near-identical to the reference wAlbB genome, suggesting few changes since the infection was first introduced to Ae. aegypti over 15 years ago. However, these sequences were distinct from other available wAlbB genome sequences, highlighting the potential diversity of wAlbB in natural Ae. albopictus populations. Phenotypic comparisons demonstrate effects of wAlbB infection on egg hatch and nuclear background on fecundity and body size, but no interactions between wAlbB infection and nuclear background for any trait. The wAlbB infection was stable at high temperatures and showed perfect maternal transmission and cytoplasmic incompatibility regardless of host background. Our results demonstrate the stability of wAlbB across host backgrounds and point to its long-term effectiveness for controlling arbovirus transmission and mosquito populations.

evolutionary biology↗