New publication out, highlighting the link between genetic diversity (GD) and policy! 🧬📜 "Conserving genetic diversity in accordance with the Global Biodiversity Framework" www.annualreviews.org/content/jour... We summarize the highlights in this thread. 🧵

Evolutionary dynamics of a lethal recessive allele in reintroduced fragmented lynx populations https://www.biorxiv.org/content/10.1101/2025.11.06.686959v1

Thanks to @royalsocietynz.bsky.social for awarding me the Callaghan medal for Science Communication. Thanks to my many supporters, NZ communities for being curious, & the many people in various agencies who really do want to use evidence in decision-making. This is critical now, more than ever. 🌐🌏🧪

Siouxsie has forged a path to making science communication a little safer for the rest of us...

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

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)!

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

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 ⬇️

🐧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

We did a penguin GWAS! Turns out that yellow-eyed penguins (or hoiho) are actually three very divergent groups, which we are calling subspecies www.biorxiv.org/content/10.1... @josephguhlin.bsky.social @peterkdearden.bsky.social @annasanture.bsky.social @cegrueber.bsky.social

Over the past year we have done extensive work on re-articulating what we at @tepunahamatatini.bsky.social do, how we do it, and why we do it. The first publicly visible artifact is our new online presence: www.tepunahamatatini.ac.nz 1/n

Exciting news! The next #PopGroup meeting will take place in Lille 🍟, France, 7–9 January 2026 – just 1 hour by train from London, Brussels, and Paris. This year, PopGroup will also host ALPHY, the annual meeting of Evolutionary Genomics. More info: populationgeneticsgroup.org.uk See you there !

Our inaugural guest artist Sione Faletau launched his new artwork ‘Ongo mei he fonua – Sounds of soil (contamination)’.

Our inaugural guest artist Sione Faletau worked with Te Pūnaha Matatini Principal Investigator Emma Sharp to transform 1,000 measurements of arsenic and lead into an immersive soundscape and visual projection → www.tepunahamatatini.ac.nz/posts/ongo-m... 🧪

And a special shout-out to @pavelpipek.bsky.social, who went deep into online historical archives to uncover some incredible insights into the minds of 19th-century acclimatisation societies! 🕰️📜 See one of my favorite articles below 👇

Huge thanks to first author Bryan Thompson, and co-authors @pavelpipek.bsky.social, @huizhentan.bsky.social, @annasanture.bsky.social, @lee-rollins.bsky.social, @williampearman.bsky.social, Kamolphat Atsawawaranunt, Melissa Nehmens, E. Owen Perkins & Annabel Whibley 👏

4️⃣Using historic archives we pinpoint which translocation events were most successful and use historical accounts to interpret the shared genetic signals seen across Australia and New Zealand. Genomics 🧬 and history 🗞️ together reveal invasion dynamics that neither could fully explain alone.

We found: 1️⃣The native range was demographically stable before introductions. 2️⃣Starlings move and mix freely across NZ’s South Island and lower North Island. 3️⃣But Auckland birds stand out! Their unique genetics suggest a mysterious, unrecorded introduction. We then looked at historical articles📰...

New Zealand’s invasive starlings on the cover of Molecular Ecology! 🐦🧬 This collaborative project unpacks the invasion history of starlings in Aotearoa New Zealand, combining population genomics with historical records of human-mediated translocations. onlinelibrary.wiley.com/doi/10.1111/...

Myself and Alastair Wilson wrote an updated version of our 2016 primer to quantitative genetics in the wild: www.sciencedirect.com/science/arti.... Happy to share a copy if interested. It is also on research gate

We wrote a thing about Penguins! www.biorxiv.org/content/10.1...

Big shakeup for NZ’s research funding – Expert Reaction

Genetic load, fitness and conservation in the Seychelles warbler. A wonderful PhD opportunity - spanning important evolutionary and conservation-relevant concepts. Come work with us lnkd.in/dtGaEJV2

The notorious @thejuicemedia.com has just helped the Government of New Zealand with a new tourism ad and it's surprsingly honest and informative! Not sure how they got it past Luxon, Seymour and Peters though, OMG! www.youtube.com/watch?v=h-yj... #nzpol

Please consider signing this open letter to Winston Peters on behalf of NZ university staff, students & alumni to demand recognition of a Palestinian state. forms.gle/BPytbSHRwXE8...

What are the ‘social dimensions’ of moving species for conservation and why does engaging with them matter? This is the focus of our new paper doi.org/10.1016/j.tr... published in @cp-trendsecolevo.bsky.social olevo.bsky.social led by ever talented @aisrayne.bsky.social 📷 Kevin Parker

💡 Bonus: Open Snakemake pipelines for both simulation and imputation are provided: - github.com/vibaotram/si... - github.com/vibaotram/im... Feel free to test and optimize imputation strategies for your own datasets before committing to large-scale LCS projects.

💥 Downstream impact: - PopGen analyses (relatedness, population structure) were congruent with imputation accuracy and depend on genetic relatedness. - Inbreeding coefficient estimates were more sensitive to imputation. - Demographic analysis on imputed data showed similar results across the tools.

🔑 Choosing your imputation tool: - All tools worked well in highly related populations. - Accuracy varied in populations with low relatedness, but GLIMPSE2 & QUILT2 generally outperformed the other tools. - STITCH is useful when no reference panel exists but results in some missing data.

👩🏻‍💻 We tested 5️⃣ imputation methods (GLIMPSE2, GeneImp, QUILT2, STITCH, Beagle5.4), simulated realistic populations with different genetic structures, and applied the methods to data from 283 wild hihi (stitchbird) 🧬.

We explored that in this new study in Molecular Ecology Resources 🔎 onlinelibrary.wiley.com/doi/10.1111/... @vbtram.bsky.social @huizhentan.bsky.social @katarinastuart.bsky.social @annasanture.bsky.social

Low-coverage sequencing (LCS) + genotype imputation is a cost-effective approach to genotype hundreds of samples at a full-genome level. But how do different imputation tools perform across populations with varying relatedness and inbreeding?

🎙️ Have you discovered the Heredity Podcast? 👂 Hear about the latest genetics research straight from the authors 📚 Archive: www.nature.com/hdy/podcast @gensocuk.bsky.social

🚩Upcoming Asia-Pacific Genetics Seminar: Remember to tune in tomorrow for our ECR special symposium 🧬 - "Epigenetics in Evolution and Ecology"! Registration link on poster below

I have never in my life felt as ashamed of the settler state of New Zealand as I am today. #FreePalestineNow

‘Poverty in Aotearoa is not accidental’: How our systems deliberately keep people poor thespinoff.co.nz/books/25-09-...