Biology subjects

Ip, J. C.-H.

Publications and source records attributed to Ip, J. C.-H..

3 recordsLinked to original sources

bioRxiv2026

Tracing the 'Panda of the Sea': Species-Specific qPCR Assays for eDNA Monitoring of Critically Endangered Bahaba taipingensis in the Pearl River Estuary

Chinese Bahaba (Bahaba taipingensis, Sciaenidae) is a Critically Endangered, Grade I state-protected marine fish in China. Reliable, non-invasive monitoring tools are urgently needed to inform conservation and restocking efforts. We developed and validated three TaqMan probe-based qPCR assays targeting mitochondrial 12S rRNA, ND5, and control region (D-loop) loci for species-specific detection of B. taipingensis. Primer-probe sets were designed from complete mitochondrial genomes and evaluated in silico against GenBank and in vitro against tissue DNA from B. taipingensis and closely related sciaenids, plus positive eDNA samples; sensitivity was quantified using serial dilutions of synthetic target DNA. All three assays showed high specificity and consistent amplification; 12S rRNA assay (Bhb_12S) was selected for field screening based on superior low-copy sensitivity and minimal by-products. We applied the Bhb_12S assay to 414 seawater samples collected from 23 sites in western Hong Kong during 2025 surveys, detecting B. taipingensis eDNA in the September samples (0.71-2.85 copies per L; mean 2.05), with positive detections confirmed by Sanger sequencing. Overall, these validated qPCR assays provide a robust molecular toolkit for non-invasive monitoring of B. taipingensis and will aid conservation planning, restocking evaluation, and long-term biodiversity assessments in the Pearl River Estuary and adjacent coastal waters.

ecology↗

bioRxiv2025

Two routes to land: Genomic underpinnings of parallel aerial egg deposition in aquatic Old-World Pila and New-World Pomacea (Ampullariidae)

The parallel evolution of aerial oviposition in Old-World Pila and New-World Pomacea apple snails--diverged since the Gondwanan breakup yet convergently transitioning from aquatic to terrestrial egg deposition--offers a powerful model for probing genomic adaptations underpinning key evolutionary innovations. We generated chromosomal-level genomes of Pila celebensis and Pila pesmei, revealing a genus-specific doubling in genome size driven by transposable element expansions. Parallel chromosomal rearrangements linked to environmental sensing, stress responses, and metabolism were identified in both lineages. Gene family analyses uncovered parallel expansions in cellulases, immune genes, and environmental sensors, alongside convergent positive selection in aquaporins critical for aerial osmoregulation. Strikingly, proteomics of egg perivitelline fluid (PVF) highlighted parallel adaptations in the PV1 protein family, where increased hydrophobicity enhances desiccation resistance in aerially deposited eggs. Phylogenetic and structural evidence traced PV1s likely origin to horizontal gene transfer (HGT) from a virus in the Ampullariidae ancestor, with subsequent duplications enabling lineage-specific aerial adaptations. Despite distinct genomic trajectories, Pila and Pomacea demonstrate that parallel molecular evolution and HGT-driven innovation facilitated their convergent transition to terrestrial reproduction, providing unprecedented insights into the genomic architecture of adaptive convergence.

evolutionary biology↗

bioRxiv2025

Multiple-omics analyses of the Alviniconcha holobiont reveal multi-faceted adaptations to deep-sea hydrothermal vents

Deep-sea hydrothermal vents are extreme environments with constantly fluctuating physicochemical conditions - but dense animal aggregations thrive primarily through symbiosis with chemoautotrophic bacteria to exploit the unusual chemistry. Alviniconcha snails, which harbor symbionts in their enlarged gill at an intracellular-extracellular intermediate state, are a prime example. Here, we present chromosome-level genomes of two Alviniconcha species (A. adamantis and A. marisindica) to investigate the adaptations of this holobiont. Significant expansion of solute carrier families enhances nutrient transport between the two parties. Alviniconcha lacks complete methionine biosynthesis pathways, compensated by symbiont provisioning, highlighting host-symbiont metabolic complementarity. High myoglobin expression in gills, contradicting prior reports of hemoglobin, suggests myoglobin-mediated oxygen storage to mitigate fluctuating environmental oxygen. Spatial transcriptomics further delineated gills functional zones on the gill filament responsible for symbiont digestion via phagocytosis in bacteriocytes, oxygen transport in secretory zones, and ciliary water flow regulation. Our findings elucidate molecular and physiological adaptations underpinning the Alviniconcha holobionts success in dynamic and treacherous vent ecosystems.

microbiology↗