Very particular!

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)!

On the NZ mainland, there are <150 breeding pairs, and many chicks die from respiratory distress syndrome (RDS) caused by a 🦠gyrovirus (YPGV). Subantarctic hoiho carry the virus too, but don’t show disease. Why the difference?
www.sciencedirect.com/science/arti...

Population genomics reveal three divergent subspecies with urgent #conservation implications. #popgen

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!