Joseph Guhlin
@josephguhlin.bsky.social
(he/him) Genomics Researcher. The Kākāpō Genomics Guy. Theoretical Genomicist. Annotation Artist. #Conservation #Bioinformatics #Rust #CompBio 🦀 #genomics #fedi22 #CompBio #popgen #Annotation #Stats #MachineLearning 🏳️🌈
Reposted by Joseph Guhlin
New review!
Theory & a practical guide to structural variants in popgen🧬
Many thanks to my co-authors: @rebekahoomen.bsky.social
@annatigano.bsky.social @marenwellenreuther.bsky.social @janawold.bsky.social @dlfield.bsky.social @clairemerot.bsky.social
onlinelibrary.wiley.com/doi/10.1111/...
Theory & a practical guide to structural variants in popgen🧬
Many thanks to my co-authors: @rebekahoomen.bsky.social
@annatigano.bsky.social @marenwellenreuther.bsky.social @janawold.bsky.social @dlfield.bsky.social @clairemerot.bsky.social
onlinelibrary.wiley.com/doi/10.1111/...
A Beginner's Guide to Structural Variants in Eco‐Evolutionary Population Genomics
Whole-genome sequencing (WGS) has greatly expanded researchers' ability to study structural variants (SVs), that is, the variation in the presence, number, orientation or position of a DNA sequence. ....
onlinelibrary.wiley.com
January 28, 2026 at 2:05 AM
New review!
Theory & a practical guide to structural variants in popgen🧬
Many thanks to my co-authors: @rebekahoomen.bsky.social
@annatigano.bsky.social @marenwellenreuther.bsky.social @janawold.bsky.social @dlfield.bsky.social @clairemerot.bsky.social
onlinelibrary.wiley.com/doi/10.1111/...
Theory & a practical guide to structural variants in popgen🧬
Many thanks to my co-authors: @rebekahoomen.bsky.social
@annatigano.bsky.social @marenwellenreuther.bsky.social @janawold.bsky.social @dlfield.bsky.social @clairemerot.bsky.social
onlinelibrary.wiley.com/doi/10.1111/...
Reposted by Joseph Guhlin
Two more #kakapo nests found on Anchor today: Waa on 3 eggs and Hauturu (pic) on 2.
Also two matings last night:
Anchor: Konini 💚 Quill
Whenua Hou: Hera 💚 Tutoko
#conservation #kakapo2026 #birds
Also two matings last night:
Anchor: Konini 💚 Quill
Whenua Hou: Hera 💚 Tutoko
#conservation #kakapo2026 #birds
January 26, 2026 at 10:34 AM
Two more #kakapo nests found on Anchor today: Waa on 3 eggs and Hauturu (pic) on 2.
Also two matings last night:
Anchor: Konini 💚 Quill
Whenua Hou: Hera 💚 Tutoko
#conservation #kakapo2026 #birds
Also two matings last night:
Anchor: Konini 💚 Quill
Whenua Hou: Hera 💚 Tutoko
#conservation #kakapo2026 #birds
Reposted by Joseph Guhlin
Very excited about this latest work led by @jermp.bsky.social! Since it's initial release, SSHash has served as the basis for several other tools (Fulgor, piscem, etc.). It was already very fast. It is now *substantially* faster!
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 22, 2026 at 9:15 PM
Very excited about this latest work led by @jermp.bsky.social! Since it's initial release, SSHash has served as the basis for several other tools (Fulgor, piscem, etc.). It was already very fast. It is now *substantially* faster!
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Joseph Guhlin
A nice opinion paper (doi.org/10.1016/j.pb... ) from @anneroulin.bsky.social that highlights the need for caution when generalizing about the importance of TEs in local plant adaptation.
#TEsky #transposon
#TEsky #transposon
doi.org
December 29, 2025 at 5:42 PM
A nice opinion paper (doi.org/10.1016/j.pb... ) from @anneroulin.bsky.social that highlights the need for caution when generalizing about the importance of TEs in local plant adaptation.
#TEsky #transposon
#TEsky #transposon
Reposted by Joseph Guhlin
Exploring #PAG33 and San Diego for the first time! If you're interested in knowing more about why bird microchromosomes are so hard to sequence, come by poster 287 this afternoon!
January 12, 2026 at 6:11 PM
Exploring #PAG33 and San Diego for the first time! If you're interested in knowing more about why bird microchromosomes are so hard to sequence, come by poster 287 this afternoon!
Reposted by Joseph Guhlin
Now published in Algorithms for Molecular Biology: link.springer.com/article/10.1.... Key message: a tiny CNN model with 7k parameters can capture main splice signals across vertebrates+insect and halves the minimap2 & miniprot junction error rate. I always use this new feature now.
Preprint on "Improving spliced alignment by modeling splice sites with deep learning". It describes minisplice for modeling splice signals. Minimap2 and miniprot now optionally use the predicted scores to improve spliced alignment.
arxiv.org/abs/2506.12986
arxiv.org/abs/2506.12986
January 6, 2026 at 11:02 PM
Now published in Algorithms for Molecular Biology: link.springer.com/article/10.1.... Key message: a tiny CNN model with 7k parameters can capture main splice signals across vertebrates+insect and halves the minimap2 & miniprot junction error rate. I always use this new feature now.
Reposted by Joseph Guhlin
#kakapo breeding seasons are always roller coasters.
☹️ Young male Tau Kuhurangi has died on Pukenui, likely from a wing injury. Population is now 236.
🙂 Second mating of the year: Esperance (pic) and Ian. #conservation #parrots #birds
☹️ Young male Tau Kuhurangi has died on Pukenui, likely from a wing injury. Population is now 236.
🙂 Second mating of the year: Esperance (pic) and Ian. #conservation #parrots #birds
January 6, 2026 at 3:36 AM
#kakapo breeding seasons are always roller coasters.
☹️ Young male Tau Kuhurangi has died on Pukenui, likely from a wing injury. Population is now 236.
🙂 Second mating of the year: Esperance (pic) and Ian. #conservation #parrots #birds
☹️ Young male Tau Kuhurangi has died on Pukenui, likely from a wing injury. Population is now 236.
🙂 Second mating of the year: Esperance (pic) and Ian. #conservation #parrots #birds
Reposted by Joseph Guhlin
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...
Under the Lens Podcast | Bioprotection Aotearoa
bioprotection.org.nz
December 6, 2025 at 9:53 PM
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...
Reposted by Joseph Guhlin
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
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...
doi.org
November 30, 2025 at 11:29 PM
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
Reposted by Joseph Guhlin
D-BLUP: a differentiable genomic BLUP model with learnable variance and marker weights https://www.biorxiv.org/content/10.1101/2025.11.25.690542v1
November 29, 2025 at 3:32 AM
D-BLUP: a differentiable genomic BLUP model with learnable variance and marker weights https://www.biorxiv.org/content/10.1101/2025.11.25.690542v1
Reposted by Joseph Guhlin
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.
Super proud of @alyssa-phillips.bsky.social 's paper, now out on biorxiv! She resolves the origin(s) of polyploid big blue-stem, a dominant species in the midwest tall-grass prairie. Her common garden analysis also informs on environmental adaptation and hints at the impacts of polyploidy.
The origins and adaptive consequences of polyploidy in a dominant prairie grass
Polyploidy is ubiquitous across North American prairies, which provide essential ecosystem services and rich soil for agriculture. Yet the mechanism driving polyploid abundance is unclear. Multiple hy...
www.biorxiv.org
November 26, 2025 at 9:11 PM
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.
November 25, 2025 at 6:47 PM
Reposted by Joseph Guhlin
It’s Tuesday folks, and you know what that means:
November 4, 2025 at 4:38 PM
It’s Tuesday folks, and you know what that means:
Reposting for other time zones! Check this out and please give us a boost! :)
🐧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
www.biorxiv.org/content/10.1...
#hoiho #conservation #genomics #birds #nzwildlife #endangered #wildlife #nature
October 29, 2025 at 8:42 AM
Reposting for other time zones! Check this out and please give us a boost! :)
🐧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
www.biorxiv.org/content/10.1...
#hoiho #conservation #genomics #birds #nzwildlife #endangered #wildlife #nature
October 28, 2025 at 8:08 PM
🐧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
www.biorxiv.org/content/10.1...
#hoiho #conservation #genomics #birds #nzwildlife #endangered #wildlife #nature
Reposted by Joseph Guhlin
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 ⬇️
“This is a turning point for hoiho conservation," says senior author Professor Jemma Geoghegan.
Read more here ⬇️
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.
www.otago.ac.nz
October 28, 2025 at 3:51 AM
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 ⬇️
“This is a turning point for hoiho conservation," says senior author Professor Jemma Geoghegan.
Read more here ⬇️
Reposted by Joseph Guhlin
Reposted by Joseph Guhlin
This is very cool. Global Change Biology | Environmental Change Journal | Wiley Online Library onlinelibrary.wiley.com/doi/10.1111/...
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...
onlinelibrary.wiley.com
October 28, 2025 at 1:48 AM
This is very cool. Global Change Biology | Environmental Change Journal | Wiley Online Library onlinelibrary.wiley.com/doi/10.1111/...
Reposted by Joseph Guhlin
At the @sydney.edu.au node of the Australian Plant Phenomics Network, we’re using drone-based LiDAR to map agroecosystems in 3D — revealing canopy structure, terrain, and floral diversity like never before.
Read more here:
🔗 plantphenomics.org.au/visualising-agricultural-landscapes-with-appn-gobi
Read more here:
🔗 plantphenomics.org.au/visualising-agricultural-landscapes-with-appn-gobi
October 27, 2025 at 9:22 AM
At the @sydney.edu.au node of the Australian Plant Phenomics Network, we’re using drone-based LiDAR to map agroecosystems in 3D — revealing canopy structure, terrain, and floral diversity like never before.
Read more here:
🔗 plantphenomics.org.au/visualising-agricultural-landscapes-with-appn-gobi
Read more here:
🔗 plantphenomics.org.au/visualising-agricultural-landscapes-with-appn-gobi
Reposted by Joseph Guhlin
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
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...
www.biorxiv.org
October 27, 2025 at 9:18 PM
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
Reposted by Joseph Guhlin
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/...
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/...
onlinelibrary.wiley.com
October 22, 2025 at 12:24 AM
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/...
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/...
Reposted by Joseph Guhlin
Population genomics of yellow-eyed penguins uncovers subspecies divergence and candidate genes linked to respiratory distress syndrome https://www.biorxiv.org/content/10.1101/2025.10.20.683354v1
October 21, 2025 at 12:49 AM
Population genomics of yellow-eyed penguins uncovers subspecies divergence and candidate genes linked to respiratory distress syndrome https://www.biorxiv.org/content/10.1101/2025.10.20.683354v1
Reposted by Joseph Guhlin
Population genomics of yellow-eyed penguins uncovers subspecies divergence and candidate genes linked to respiratory distress syndrome https://www.biorxiv.org/content/10.1101/2025.10.20.683354v1
October 20, 2025 at 7:33 PM
Population genomics of yellow-eyed penguins uncovers subspecies divergence and candidate genes linked to respiratory distress syndrome https://www.biorxiv.org/content/10.1101/2025.10.20.683354v1
Reposted by Joseph Guhlin
We wrote a thing about Penguins! www.biorxiv.org/content/10.1...
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 Ne...
www.biorxiv.org
October 20, 2025 at 8:59 PM
We wrote a thing about Penguins! www.biorxiv.org/content/10.1...