Biology subjects

Prasetyo, A. P.

Publications and source records attributed to Prasetyo, A. P..

5 recordsLinked to original sources

bioRxiv2026

A GENOMIC BASIS FOR TRANS-OCEANIC SEA TURTLE MIGRATION

Long-distance migration has evolved repeatedly across the animal kingdom, yet the underlying processes giving rise to and maintaining these complex eco-behavioral phenotypes remain poorly understood. Here, we present the first evidence of genomic determinants of migratory phenotypes in sea turtles, using whole genome resequencing to demonstrate that complex genomic architecture underlies divergent migratory destinations and reproductive timing in the critically endangered western Pacific leatherback turtle (Dermochelys coriacea). Individuals from this admixed population that navigate to foraging grounds on opposite sides of the Pacific Ocean have a putative inversion on chromosome 2 encompassing one gene, potentially conferring pleiotropic physiological effects and supporting magnetoreception. Genomic architecture underlying divergent reproductive timing is more dispersed, aligned with reduced gene flow, and is associated with genes that may influence reproductive success. Genes underlying both traits suggest a role for neurodevelopment and memory. Our study adds to the increasing evidence of at least partial genomic control of migratory traits in wild populations, with important potential implications for conservation measures such as translocation and genetic rescue. Our results align with a growing body of work describing complex genomic architecture and structural variants underlying key eco-behavioral traits, advancing the understanding of evolution of long-distance migration across taxa.

ecology↗

bioRxiv2026

Genomic indicators of risk and resilience in global leatherback turtle populations

Understanding the drivers of genomic health and their consequences for population viability is often overlooked but potentially important to effective conservation amidst the biodiversity crisis of the Anthropocene. Leatherback turtle (Dermochelys coriacea) populations have declined globally due to anthropogenic factors, with some populations losing over 90% of their abundance over the past 30-50 years. While conservation efforts have been successful in stabilizing some populations, others continue to decline, and the reasons for these differential trajectories remain unclear. To assess how recent demographic factors, such as population size and decline, influence population genomic health, we combined population monitoring information with medium depth whole-genome and reduced representation resequencing data from globally representative populations. We found that small-stable populations have lower genomic diversity and higher inbreeding than large declining populations, reflecting prolonged small population sizes and limited gene flow. Yet, small-stable populations also show evidence of deleterious allele purging, suggesting genetic resilience. This, combined with lack of detectable genomic erosion over the study period, provides hope for potential recovery of healthy leatherback populations provided that anthropogenic threats are effectively mitigated. However, potential time lags and possible recent increases in inbreeding among close relatives in recently declined populations warrant continued monitoring and assessment. Genomic and abundance-based metrics were less aligned following rapid population declines, emphasizing the different timescales of the evolutionary and demographic processes they reflect, respectively, and the strength in their complementary, integrative use for extinction risk assessments. This also supports that it is not too late to turn the tide for recently declined leatherback populations and that continued investment in conservation efforts and threat reductions are warranted. Collectively, our results highlight how recent and historical demography shapes current genomic health and recovery potential in leatherback turtles, aids understanding of current risks and informs future conservation and management strategies.

ecology↗

bioRxiv2022

Shark-dust: High-throughput DNA sequencing of processing residues unveils widespread trade in threatened sharks and rays

Illegal fishing, unregulated bycatch, and market demand for certain products (e.g. fins) are largely responsible for the rapid global decline of shark and ray populations. Controlling trade of endangered species remains difficult due to product variety, taxonomic ambiguity and trade complexity. The genetic tools traditionally used to identify traded species typically target individual tissue samples, are time-consuming and/or species-specific. Here, we performed high-throughput sequencing of trace DNA fragments retrieved from dust and scraps left behind by trade activities. We metabarcoded shark-dust samples from seven processing plants in the worlds biggest shark landing site (Java, Indonesia), and identified 54 shark and ray taxa (representing half of all chondrichthyan orders), half of which could not be recovered from tissue samples collected in parallel from the same sites. Importantly, over 80% of shark-dust sequences were found to belong to CITES-listed species. We argue that this approach is likely to become a powerful and cost-effective monitoring tool wherever wildlife is traded. One-Sentence SummaryShark-dust, the traces of biological material left behind from the processing of shark products, can now be DNA-sequenced in bulk to accurately reconstruct the biodiversity underlying trade.

genetics↗

bioRxiv2022

Universal closed-tube barcoding for monitoring the shark and ray trade in megadiverse conservation hotspots

Trade restrictions for many endangered elasmobranch species exist to disincentivise their exploitation and curb their declines. However, the variety of products and the complexity of import/export routes make trade monitoring challenging. We investigate the use of a portable, universal, DNA-based tool which would greatly facilitate in-situ monitoring. We collected shark and ray samples across the Island of Java, Indonesia, and selected 28 species (including 22 CITES-listed species) commonly encountered in landing sites and export hubs to test a recently developed real-time PCR single-assay originally developed for screening bony fish. We employed a deep learning algorithm to recognize species based on DNA melt-curve signatures. By combining visual and machine learning assignment methods, we distinguished 25 out of 28 species, 20 of which were CITES-listed. With further refinement, this method can provide a practical tool for monitoring elasmobranch trade worldwide, without the need for a lab or the bespoke design of species-specific assays. HighlightsO_LIWe applied a portable, universal, closed-tube DNA barcoding approach originally developed for bony fishes to distinguish between shark and ray species traded in Indonesia. C_LIO_LIWe built a deep machine learning model to automatically assign species from the qPCR fluorescence spectra produced by two barcodes C_LIO_LIThe model achieved 79.41% accuracy for classifying 28 elasmobranch species, despite the barcode regions being designed for teleost species C_LIO_LIThis tool can serve as a potent single-assay in-situ diagnostic tool to regulate trade operations and it will be significantly enhanced by further optimisation of the barcode regions to fit elasmobranch DNA sequence variation C_LI

genetics↗

bioRxiv2020

Disentangling the shark and ray trade in Indonesia to reconcile conservation with food security

Indonesian marine resources are among the richest on the planet, sustaining highly diverse fisheries and includes the largest elasmobranch landings in the world, making Indonesia one of the worlds largest exporters of shark and ray products. Socio-economic and food security considerations pertaining to Indonesian communities add further layers of complexity to the management and conservation of these vulnerable species. This study investigates how shark and ray trade flows in and out of Indonesia and attempts to examine patterns and drivers of the current scenario. We identify substantial discrepancies between reported landings and declared exports, and between Indonesian exports in shark fin and meat products and the corresponding figures reported by importing countries. These mismatches are estimated to amount to over $43.6M and $20.9M for fins and meat, respectively, for the period between 2012 and 2018. Although the declared exports are likely to be an underestimation because of significant unreported or illegal trading activities, we find that domestic consumption of shark and ray products plays a significant role in explaining these discrepancies due to the increasing local demand for meat. The study also unearths a general scenario of unsystematic data collection and lack of granularity of product terminology, which is inadequate to meet the challenges of over-exploitation, illegal trade and food security in Indonesia. We discuss how to improve data transparency to support trade regulations and governance actions, by improving inspection measures, and conserving elasmobranch populations without neglecting the socio-economic dimension of this complex system.

scientific communication and education↗