Joseph Guhlin

Under the Lens Podcast | Bioprotection Aotearoa

We made a podcast for @bioprotection.bsky.social Have a look if you are interested in all things that start with b, Nick singing 80's songs or, perhaps more importantly, why and how to save the planet. bioprotection.org.nz/under-the-le...

Nest Survival Models and Genomics Illuminate Hybridisation Attempts, Guiding Culturally Informed Management to Recover a Critically Endangered Seabird Long-term monitoring has revealed hybridisation attempts between the Critically Endangered Kuaka Whenua Hou (KWH, Pelecanoides whenuahouensis) and the abundant Kuaka (P. urinatrix). Here we use model...

I'm delighted to share that our publication 'Nest survival models and genomics illuminate hybridisation attempts, guiding culturally informed management to recover a critically endangered seabird' is out now in Animal Conservation @animalconserv.bsky.social! doi.org/10.1111/acv.... 🧵 1/9

D-BLUP: a differentiable genomic BLUP model with learnable variance and marker weights https://www.biorxiv.org/content/10.1101/2025.11.25.690542v1

Big bluestem has been a lovely and complex system to work with for the majority of my PhD and will always have a piece of my heart! Very excited to share this work with the community.

Help. Can anyone in my network (or outside) endorse me for arXiv q-bio? #breeding #breeding

It’s Tuesday folks, and you know what that means:

Hoiho DNA key to combating disease Attempts to conserve the hoiho/yellow-eyed penguin may have just reached a turning point, after landmark genomic research found the species is...

www.odt.co.nz/news/dunedin...

More Hoiho coverage! #Conservation #animals #birds #genomics

Young'uns, looking adorably fluffy

Reposting for other time zones! Check this out and please give us a boost! :)

Good quesiton! Most likely a bad idea. We find genomic regions within each subspecies show signs of local adaptations that happened after the divergence. So bringing in genetics optimal for the subantarctic islands to the mainland would most likely be detrimental.

YouTube video by The Graham Norton Show Benedict Mispronouncing Penguin Has Us Weak😭 #Shorts

www.youtube.com/shorts/GflW9...

I love typst. I just convert to pdf to submit, but submitting the source would be nicer

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!

Population genomics of yellow-eyed penguins uncovers subspecies divergence and candidate genes linked to respiratory distress syndrome Yellow-eyed penguins (hoiho/takaraka, Megadyptes antipodes ) are among the world’s rarest penguins and are regarded as a taonga (treasured) species in Aotearoa New Zealand. Since 2019, chicks on the N...

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).

Hoiho chicks

#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.

Manhattan Plot for RDS Association and YPGV Status GWAS

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

Not in publication: Excess coalescence over generations

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.

BEAST Divergence Times estimation, using multiple other penguins for divergence dating (not shown, see preprint!)

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.

Map of Aotearoa New Zealand indicating the geographic distribution of yellow-eyed penguins and proposed new subspecies designations

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)!

A novel gyrovirus is abundant in yellow-eyed penguin (Megadyptes antipodes) chicks with a fatal respiratory disease Yellow-eyed penguins (Megadyptes antipodes), or hoiho in te reo Māori, are predicted to become extinct on mainland Aotearoa New Zealand in the next fe…

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 of yellow-eyed penguins uncovers subspecies divergence and candidate genes linked to respiratory distress syndrome Yellow-eyed penguins (hoiho/takaraka, Megadyptes antipodes ) are among the world’s rarest penguins and are regarded as a taonga (treasured) species in Aotearoa New Zealand. Since 2019, chicks on the N...

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

Hoiho - the world’s rarest penguin, fewer than 150 mainland pairs left

🐧We researched one of the world’s rarest #penguins. The yellow‑eyed penguin (aka hoiho/takaraka) isn’t one homogeneous species after all!

www.biorxiv.org/content/10.1...

#hoiho #conservation #genomics #birds #nzwildlife #endangered #wildlife #nature

Study reveals genetic secrets of one of world’s rarest penguins Landmark genomic research has found the endangered hoiho is made up of three distinct subspecies, a discovery that may help guard against a fatal disease.

A landmark Ōtākou Whakaihu Waka-led study has found the endangered hoiho 🐧 is made up of 3 subspecies, a finding that may help protect the species against fatal disease.

“This is a turning point for hoiho conservation," says senior author Professor Jemma Geoghegan.

Read more here ⬇️

A pangenome of maize provides genetic insights into drought resistance - Nature Genetics This study presents 25 new maize genome assemblies and integrates them with 31 publicly available maize genomes to conduct a pangenome analysis that provides genetic insights into drought resistance.

www.nature.com/articles/s41...

Spatio‐Temporal Variation in Aerial Arthropod Abundance Revealed by Weather Radars Alarming arthropod decline has been reported from around the world, but we lack conensus on the generality, severity, and potential causes of these declines. We use weather radars for large-scale aer...

This is very cool. Global Change Biology | Environmental Change Journal | Wiley Online Library onlinelibrary.wiley.com/doi/10.1111/...