Joseph Guhlin
@josephguhlin.bsky.social
(he/him) Computer nerd doing conservation genetics. The Kākāpō Genomics Guy. #Conservation #Bioinformatics #Rust #CompBio 🦀 #genomics #CompBio #popgen #Stats #MachineLearning 🏳️🌈
Finally posted an ad for the postdoc position on my new NSF-funded project—come help build a new method to study plants' responses to environmental variation in space and over time, and figure out interesting ways to use it! Apply by 23 August to ensure consideration. Details: buff.ly/qTvaqvD
July 2025: “Conservation-related tourism is worth around $3.4 billion a year,” says Mr Potaka. www.doc.govt.nz/news/media-r...
2025 media releases
View DOC media releases from 2025.
doc.govt.nz
This article and the government's response appears to focus on the $2 billion poultry industry without considering that native birds are a major driver of our $46.6 billion tourist industry.
Newsroom NZ@newsroom.co.nz · 3w agoComment: It’s fall or fly time for safeguarding NZ’s $2b poultry industry as avian flu lands on our shores. Chicken farmers won't live with an elimination strategy.
Want to see what genes change their copy number with your favourite complex trait while controlling for phylogeny? Try this. www.biorxiv.org/content/10.6...
OrthoGLMM: Phylogenetic Association Testing for Gene Content and Trait Evolution
Motivation Comparative genome projects can now assemble and annotate hundreds of species, creating an opportunity to test whether species-level traits are associated with repeated changes in gene cont...
biorxiv.org
Here in Brisbane at the Genetics Society of Australia conference - off to a cracking start with an inspiring presentation from our MJD White prize winner Peter Dearden, reminding us to step back from data and seek functional evidence #GSA2026 @geneticsaus.bsky.social
EDTA v2: enabling scalable TE annotation in animal genomes https://www.biorxiv.org/content/10.64898/2026.07.01.735963v1
OrthoGLMM: Phylogenetic Association Testing for Gene Content and Trait Evolution https://www.biorxiv.org/content/10.64898/2026.07.03.736217v1
The work we did with kākāpō is now not possible because the govt has said that our funding should go to science that makes money. Members of our current govt have said that if an endangered species is in the way of a mine or a new road then it’s goodbye #nzpol peterkdearden.substack.com/p/on-kakapo
on Kākāpō
and extinction
peterkdearden.substack.com
on the destruction of New Zealand Science open.substack.com/pub/peterkde...
on the destruction of New Zealand Science
and earthquakes
open.substack.com
Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357
salmon 2.0 (the rust re-write) is now live! It's also the version you get if you install via bioconda. This is a from-scratch rewrite in rust, and the base for future development. I'll post a more detailed thread tomorrow, but you can read the docs here combine-lab.github.io/salmon/
salmon
Fast, accurate transcript quantification from RNA-seq reads.
combine-lab.github.io
Gene duplication and retrotransposition diversify the antiviral repertoire of macaque IFITM proteins https://www.biorxiv.org/content/10.64898/2026.06.11.731520v1
The new OrthoFinder paper is out now! In this new work, we introduce major advances in accuracy and scalability, allowing analysis on much larger datasets www.nature.com/articles/s41... github.com/OrthoFinder/...
OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability - Nature Methods
The updated OrthoFinder v3 software boosts accuracy and scalability in phylogenetic orthology inference with massive and diverse datasets.
nature.com
New study 🧬 Inbreeding depression is a concern in small populations, and evaluating its genomic proxies is important for #ConservationGenomics. In hihi, genome-wide homozygosity best predicts lifetime reproductive success, compared to genetic load and FROH. Publication: doi.org/10.1111/eva.... 1/3
Genome‐Wide Homozygosity Predicts Inbreeding Depression in the Hihi/Stitchbird (Notiomystis cincta) Better Than Realised Load
Population declines result in increasingly small populations, which often experience an increase in inbreeding. Inbreeding may be negatively associated with fitness traits like survival and reproduct...
doi.org
Excessive paperwork and inefficient systems are sabotaging scientific progress. Really proud to be part of this global manifesto spearheaded by @kentimmis.bsky.social. We need action at all levels to tackle the root causes. Our analysis & proposals @microbiotech.bsky.social: doi.org/10.1111/1751...
Scientists' Warning to Humanity: Unnecessary Bureaucracy Is a Global Impediment to Productivity, Advancement of Human and Planetary Wellbeing, Science and Sustainability
Unnecessary bureaucracy is a global impediment to progress and productivity that increases stress and lowers workplace morale and motivation. In research it smothers creativity and innovation that ar....
doi.org
We’re celebrating Professor Louise Bicknell - a DNA detective whose work is bringing answers and hope to families affected by rare genetic diseases. Read more about Louise's research journey as told at her recent Inaugural Professorial Lecture www.otago.ac.nz/news/newsroo...
Celebrating Professor Louise Bicknell, DNA detective and source of hope for families with rare genetic diseases
The Department of Biochemistry celebrated Louise Bicknell’s promotion to professor at her Inaugural Professorial Lecture earlier this month, marking a stellar academic career defined by a deep love of...
otago.ac.nz
#penguins #popgen #genomics #aotearoa #nz
Genetic drivers of disease susceptibility in endangered penguin populations - Nature Ecology & Evolution
A population genetic study of endangered penguins combined with genome-wide associations in the context of infectious disease outbreaks highlights the need for tailored management and conservation pla...
nature.com
OPINION: The hoiho, also known as takaraka or yellow-eyed penguin, holds a special place in Aotearoa New Zealand’s natural identity. Read more ⬇️
Why the race to save these cherished penguins just became more urgent
Researchers found the endangered yellow-eyed penguin is made up of three distinct subspecies, with the mainland lineage at greatest risk.
theconversation.com
And our piece in The Conversation about the story theconversation.com/why-the-race...
Why the race to save these cherished penguins just became more urgent
Researchers found the endangered yellow-eyed penguin is made up of three distinct subspecies, with the mainland lineage at greatest risk.
theconversation.com
New paper out today with @josephguhlin.bsky.social where we did penguin GWAS to better understand disease risk and found that these penguins represent three deep evolutionary lineages www.nature.com/articles/s41...
Population genomics of yellow-eyed penguins uncovers subspecies divergence and candidate genes linked to respiratory distress syndrome - Nature Ecology & Evolution
Whole-genome data from 249 yellow-eyed penguins (hoiho) identify three lineages with high geographical and genomic divergence, and candidate gene variants associated with differential susceptibility t...
nature.com
New paper! 🐧 We sequenced 249 hoiho / yellow-eyed penguins across mainland Aotearoa New Zealand and the sub-Antarctic to understand their history and why a deadly chick disease is hitting the mainland population so hard. #Science #Conservation #Genomics #NZWildlife www.nature.com/articles/s41...
Check out our new letter in Conservation Biology where we argue that (re-)introduced large herbivores are often wrongly framed as harmful because herbivory is automatically equated with ecological damage - overlooking their potential to restore biodiversity and ecosystem functioning.
Matt Kerr@mattkerr.bsky.social · 3mo agoHerbivory is a fundamental ecological process; treating it as harm (like recent work has suggested) misinforms conservation decisions about introduced herbivores. conbio.onlinelibrary.wiley.com/doi/10.1111/...
Thank you illumina for the opening slide of my lab meeting presentation today.
Might be of interest! makingsciencepublic.com/2026/04/03/v...
Vibe-coding spaghetti: Unpacking an AI metaphor for biology
I recently saw a post on Bluesky just saying “Coconuts”. Intriguing! Underneath was a screenshot of a tweet which was even more intriguing. The tweet said: “A techbro told me that biolo…
makingsciencepublic.com
New preprint! We sequenced 175 'Alalā (Hawaiian crow) genomes to understand why >50% of eggs fail to hatch in a species recovered from just 9 individuals. What we found was a both exciting and surprising. www.biorxiv.org/content/10.6...
