Days in Sri Lanka for SI

Sharks International 2026 held in Colombo, Sri Lanka, concluded with immense excitement, leaving us with a clear mandate for increasing evidence-based conservation and high expectations for the future.

The conference scope encompasses the entire class of Chondrichthyes (cartilaginous fishes). This includes elasmobranchs—a term I suspect many experienced participants often wanted to correct for its pronunciation: (ih-LAS-muh-brangk: /ɪˈlæs məˌbræŋk/ or ih-LAZ-muh-brangk: /ɪˈlæz-/)—comprising sharks and batoids (rays, skates, and sawfish), as well as chimaerids (ghost sharks, ratfish, or rabbitfish). 

One of my personal takeaways from this conference: we must clarify the often-conflated "DNA-based approaches". While frequently grouped under the broad term 'genetics,' its application are diverse, spanning multiple distinct disciplines. To adequately select and combine these tools for tackling intricate problems, I believe it is first essential to recognize them as distinct pillars:

​1. Population genetics: requiring abundant individuals (between which genetics variations are to be detected by microsatellites or single nucleotide polymorphisms) to track connectivity

​2. Evolutionary/comparative genomics: requiring as few as one individual to decode the entire blueprint of the species—or at least aiming for a genome-wide scope even when it ends up reporting non-genome-wide findings.

​3. Gene-level analysis: focusing on certain biological processes through genes responsible for them to address 'why' and 'how' questions

4.​ Barcoding for species identification: focusing on specific markers like COI (cytochrome oxidase I), which now encompasses environmental DNA (eDNA)

​At our consortium Squalomix, we work on these applications with a strong emphasis on Pillar 2 and 3. It is worth noting that our unique efforts in whole genome assembly mainly for Pillar 2 contribute to high-resolution population genetics (Pillar 1). We aim to promote this overarching view to help solve the intriguing enigma of animal diversity and evolution. Crucially, this integrated perspective is vital because each pillar demands different sampling and storage protocols. For instance, while some applications are flexible, whole genome sequencing necessitates fresh or flash-frozen tissue to ensure the integrity of long DNA molecules required for chromosomal-scale assembly.

​It was a tremendously valuable opportunity to introduce our recent achievements regarding sex chromosome organization in sharks and rays (Yamaguchi et al., 2023; Niwa et al., PNAS, 2025). Our studies usually take time as we tackle profound "genomic grammar"—deciphering how tens of thousands of genes in the genome make sense—and do not always provide immediate, ready-to-use solutions. However, the applications of this emerging knowledge on sex determination mechanisms lead to the sex identification of fins, meat, gill plates, early embryos, and museum samples. These are all cases where morphological and anatomical keys are lacking, yet high-fidelity population or archival sample tracing is essential. Our trials are reported in this preprint - Oishi et al., bioRxiv 2026)

​Below is a listing of how traditional and emerging DNA-based solutions potentially enrich field surveys:

a) Species identification: targeting mtDNA (e.g., COI)

b) Sex identification: targeting sex chromosomes

c) Age estimation: targeting DNA methylation

d) Diet profiling: targeting mtDNA or nuclear rDNA of stomach contents

​I hope this categorization of techniques is useful to those navigating these diverse methodologies.

​Particularly memorable among the countless exchanges were reunions with fellows affiliated with Centro Studi Squali based in Italy, represented this time by Francesca Romana Reinero, as well as the encounter with dedicated crews from Thailand devoted to ReShark—an inspiring rewilding program for the zebra shark (or leopard shark, Stegostoma tigrinum) in Southeast Asia. Finally, a special "monument" of this conference attendance was our "shark genome-ish" dinner. It was a privilege to gather with such brilliant minds to exchange these very ideas over Sri Lanka's casual food and drinks. Thank you all for joining and for the invaluable conversations!

​Looking forward to turning these discussions into deeper biological understanding and impactful actions.