Biology subjects

Woolley, S.

Publications and source records attributed to Woolley, S..

3 recordsLinked to original sources

bioRxiv2026

A dual-clam species 63K SNP array for sustainable production and conservation of wild resources

Bivalves play an essential role in coastal ecosystems and their aquaculture represents an important economic sector in Europe playing a pivotal role within the EU Blue Growth Strategy. Among clam species, the Manila clam, Ruditapes philippinarum, and the grooved carpet shell, R. decussatus, are within the top five species in terms of production volume and economic value. In this study we designed and validated the first medium-density 63K single nucleotide polymorphism (SNP) array for these two commercially important species. By leveraging a new chromosome-level genome assembly for R. philippinarum and that of R. decussatus, we identified over 300 million SNPs through whole-genome resequencing and genotyping-by-sequencing strategies. After stringent filtering, we selected 49,392 high-quality SNPs for R. philippinarum and 14,193 for R. decussatus to construct a dual-species array. Array validation was carried out by genotyping 384 individuals across multiple wild populations and hatchery samples, demonstrating excellent performance, with 67.7% and 67.5% of SNPs classified as high-quality polymorphic markers for R. philippinarum and R. decussatus, respectively. Minor allele frequency, missing data rate, and inter-marker distance met stringent quality thresholds, confirming the array robustness for clam population genetics. Parentage analysis in R. philippinarum families highlighted significant power for pedigree reconstruction in breeding programs. This publicly available genomic resource provides a reliable, cost-effective genotyping platform to enable population genomics and advanced selective breeding, genome-wide association studies, and genetic monitoring, ultimately strengthening management of genetic diversity and sustainable farming for two key clam species.

genomics↗

bioRxiv2025

Climate Change, Fisheries Management, and Increases in Demersal Fish Distribution in a Southern Ocean Biodiversity Hotspot

The worlds oceans and their biodiversity are undergoing going change driven by climate change and anthropogenic impacts such as fishing. The Kerguelen Plateau is a biodiversity hotspot with many endemic fish species, furthermore the region has economic importance in supporting valuable fisheries. This region is also a climate change hotspot with known notable changes in the location of the polar front, ocean currents, and primary productivity. In this study we use data from long-term scientific trawl surveys and contemporary joint species distribution models to understand how the demersal fish assemblage of the Kerguelen Plateau has changed through time and space. The modelling indicates that most demersal species have had notable changes in their occurrence and CPUE from 2003 to 2016. This included a significant increase in species richness throughout the study period. The modelling also provides novel insights into the depth, climatic and environmental preferences for all species, including many species that were previously data limited. It is unclear whether these changes reflect shifts in the fishery, management, or the effects of climate change, but most likely a combination of all. We also found evidence of several species distributions responding to temperature variability, with species being exposed to the ongoing impacts of climate change. This new information can be used by managers and policy makers to ensure continuation of sustainable fisheries and the protection of biodiversity into the future.

ecology↗

bioRxiv2017

A Statistical Model of Shared Variability in the Songbird Auditory System

Vocal communication evokes robust responses in primary auditory cortex (A1) of songbirds, and single neurons from superficial and deep regions of A1 have been shown to respond selectively to songs over complex, synthetic sounds. However, little is known about how this song selectivity arises and manifests itself on the level of networks of neurons in songbird A1. Here, we examined the network-level coding of song and synthetic sounds in A1 by simultaneously recording the responses of multiple neurons in unanesthetized zebra finches. We developed a latent factor model of the joint simultaneous activity of these neural populations, and found that the shared variability in the activity has a surprisingly simple structure; it is dominated by an unobserved latent source with one degree-of-freedom. This simple model captures the structure of the correlated activity in these populations in both spontaneous and stimulus-driven conditions, and given both song and synthetic stimuli. The inferred latent variability is strongly suppressed under stimulation, consistent with similar observations in a range of mammalian cortical regions.

neuroscience↗