Ka rawe, such a wonderful acknowledgement of your engaging, passionate engagement and for sparking curiosity!

Amazing group of people to work with! @jemmageoghegan.bsky.social @peterkdearden.bsky.social @annasanture.bsky.social @cegrueber.bsky.social And everyone else not on bsky! Double thanks to Janelle for the amazing pictures!

Preprint out now: “Population genomics of yellow‑eyed penguins uncovers subspecies divergence and candidate genes linked to respiratory distress syndrome.”
www.biorxiv.org/content/10.1...

Full press release: www.otago.ac.nz/news/newsroo...

This was a partnership across the Universities of Otago and Auckland, Department of Conservation, Ngāi Tahu, Dunedin Wildlife Hospital, and Genomics Aotearoa, building on national genomics infrastructure (incl. tools first honed with #kākāpō).

#Conservation implications: treating hoiho as three subspecies changes the playbook. Mainland M. a. murihiku needs urgent, tailored action, and genetic rescue from subantarctic birds could risk outbreeding depression by introducing local adaptations younger than the species divergence.

Take‑home on disease: it’s likely host genetics + virus + environment, not a single mutation “on/off” switch. That’s why species‑wide genomics + ARG‑aware GWAS are so powerful here.

Selection scans also show the Southern subspecies have younger TMRCAs (signals of recent selection) in cilia‑related pathways; hair‑like structures lining airways that trap and clear pathogens. This could help explain why Southern chicks resist RDS.

Re: RDS on the mainland. A GWAS within the Northern subspecies and all subspecies flags candidate genes tied to immunity and respiration.

Using ARGs, we can trace population divergence across the genome. This “excess coalescence” plot shows when genomes begin to diverge. The timing aligns with the BEAST-inferred divergence windows, but using separate methodology.
(Not in the preprint, BTS!)

Methodologically cool bit: we also used ancestral recombination graphs (ARGs) to time coalescent events & control relatedness in analyses. Hundreds of thousands of local trees support the divergence times based only on mutation rate (generations rather than years ago). #tsinfer #tskit #tsdate.

When did they split? Molecular dating points to ~5–16k years for the Northern vs Southern split and ~3–11k years between the two Southern groups, dating to before human arrival in Aotearoa NZ. (Fig. 3)

With Ngāi Tahu kaitiakitanga, three subspecies are proposed:
• M. a. murihiku — mainland “Northern” hoiho
• M. a. motu maha — Enderby (Auckland Is)
• M. a. motu ihupuku — Campbell Is
These lineages are evolutionarily independent.

We sequenced ~249 whole genomes 🧬 spanning the mainland and subantarctic Enderby & Campbell Islands. Result: three distinct genetic lineages, with negligible gene flow among them (See PCA/tree in Fig. 2, and migration rates in supplement)!