🧵5/5
The paper is first-authored jointly by @zilongli21 and @ffstaeger.bsky.social and recently published in Bioinformatics. This method is designed for single sample SV genotyping. Stay tuned for population-level joint SV genotyping!

🧵4/5
Limitation: all SV genotype callers perform poorly for SVs with neighbors (>20% error), which make up ~40% of SVs. Our results apply to the remaining 60%. If SVs with neighbors are important to your analysis, HiFi data + kanpig is currently the least-bad option.

🧵3/5
SVUPP reduces genotyping error by at least 23%. The improvement of SVUPP was consistent across
• Read depths
• Read lengths
• Sequencing technology
Make sure to look into the supplementary figures academic.oup.com/bio...

🧵2/5
SVUPP works by
1. Pre-phasing long reads only using SNPs
2. Assigning each read to reference or alternative SV
3. Combining this information to compute genotype likelihoods
We used QUILT2 for pre-phasing and cuteSV2 for SV assignment

🧵1/5
Thought long-read sequencing had “solved” structural variant genotyping? We did. Turns out many SVs still have high genotype error rates with current tools. Our new method SVUPP uses long-read pre-phasing to reduce errors and improve genotype quality
doi.org/10.1093/bioi...

Big science highlights this month at our #EPIC seminar! Kees uncovered new insights into isolation by distance and shorebird diversity🐧, and Anna showed how ancient chewing gums provide a remarkable snapshot into #microbiome 🦠evolution and health. Fascinating work from both! 👏

Our monthly #EPIC seminars are back! 🎉
This month, Thomas Bøggild kicked things off with a fascinating talk on stopped recombination in new sex chromosomes, and @audald.bsky.social followed with great insights into recombination maps and imputation in #PopGen studies.
See you next month!

🧵 This project is co-lead by Casia Nursyifa as her PhD project, and Xi Wang as her postdoc project. Congratulations to all 31 authors, including the senior authors Rasmus Heller, Bambang Purwantara, & Mohammad Agil.

🧵 The potential of new unique variants that can improve cattle productivity via genomic selection, making them high yield while being adaptive to hot climate, and potentially breed environmentally friendly cattle with low carbon footprint.

🧵 This study reveal ~3.5mio novel genetic variants previously unknown to cattle genomics, where the ones coming from high proportion of banteng ancestry coincides with traits related to coat coloring (Figure 5a & b) and productivity traits, among other things.

🧵 This recent introgression was thought to be the cause of their high genetic diversity (Figure 4d).

🧵 🧬 Genomics also shown that Indonesian cattle came to islands of Indonesia via mainland Southeast Asia as opposed to India where they have been thought to originate. They came in two pulses, Sumatra and Java (Figure 4a).

🧵 🧬 Genomic analyses found that from 7 breeds, 5 were hosting a recent introgression from local wild cattle, banteng, which is listed as Critically Endangered by the IUCN. One breed, Madura cattle, has 36% of its genome from the banteng (Fig 3)

🧵 🧬 Compared to other domestic cattle where genomic data were available, Indonesian cattle hosted more genetic variation and lower level of inbreeding relative to other cattle, especially Madura, Jabres, and Pasundan (Fig 2)

🧵 🧬 We sequenced 126 WGS from 7 breeds 🐂 (Fig 1), revealing a unique evolutionary history and its promise for sustainable cattle #farming.

The genetic diversity of Indonesian cattle has been shaped by multiple introductions and adaptive introgression - Nature Communications Indonesian cattle are unique due to their history of admixture involving both zebu and banteng. Here, Wang et al. identify ~3.5 million novel introgressed SNP variants and provide a genomic map of banteng introgression within and across many cattle breeds, each with unique introgression histories.

Our new paper on Indonesian cattle #genomics is out on @natcomms.nature.com 🎉
Did you know Indonesian #cattle 🐂 were a mix of two species?
🧵
Great work by Xi, @sagitaninta.bsky.social, Casia, Rasmus & co-authors
Read 👉 www.nature.com/articles/s41...
#popgen #evolution #agriculture

Postdoctoral Fellowship in Water Buffalo Population Genomics The Department of Biology, Faculty of Science at University of Copenhagen is offering a post doc position to work on population genomic analyses in water buffal

🚀 We’re hiring a #Postdoc!
🔬 Join our group in Copenhagen to study Water Buffalo 🐃 #Population #Genomics
Highly motivated & enthusiastic candidates are welcome!

👉 **Apply:** candidate.hr-manager...

⏰Deadline Oct 15th 2025
#WaterBuffalo #Conservation #EvolutionaryBiology

What a busy August it’s been for our group! 🌍✈️
From our Summer Course in Copenhagen to #EPIC25 in Aarhus and #ESEB25 in Barcelona. So great to see so many of our researchers sharing their work through talks and posters!
An inspiring month full of science, learning, and collaboration! 🙌✨

Me and my selection at introgressed genomes poster

Me presenting my selection introgression poster to a very cool audience with a lot of great questions

Me with my topi poster

Had a blast presenting my postdoc projects from @popgendk.bsky.social at #ESEB2025: figuring out the conservation units of topis from Africa & the selection pressure on the introgression landscape of Indonesian admixed cattles. Thanks for those who came by & gave really useful comments!

Day 1 of #EPIC25
@sagitaninta.bsky.social (KU) presented her work on Indonesian cattle and the evolutionary forces shaping their genomic landscape.

Day 1 of #EPIC25
Cool talk by Marta Ciucani (KU) on the giant forest hog and what its #genome reveals about the evolutionary history of its subspecies.

Day 1 of #EPIC25
Nuno Martins (KU) presented his preliminary analyses on the Greenlandic #reindeers

We then continued with Emil Jørsboe (SSI) and explored the genetics of permanent tooth eruption.

Shixu He (KU) gave a brilliant talk about the #metagenome of the Greenland population, revealing unique microbial signatures. Seems like ice-cream can improve your health!?

Another great research talk today (online version this time!) from Martin Sikora on #ancient human #pathogens - from #plague to #pandemics and #zoonosis. Did lifestyle shifts shape #disease #burden over time? Seems like it!
Thanks for joining us! #AncientDNA

Wrapped up yesterday's lectures with a canal tour in #Copenhagen — sunshine (mostly), good vibes (lots), and... as we entered #Nyhavn, a beautiful rainbow appeared. 🌈🚤🇩🇰 #CanalTour #Summercourse25 #popgendk

On our second day of this year summer course we had Victor Moreno-Mayar talking about the #ancient population of #Rapa #Nui. Was the data consistent with the population #collapse proposed so far? The biological data seems to disagree!
Thanks for joining us and thanks Victor for the incredible talk!

Alex Brown @blackochreomics.bsky.social from the @thekidsau.bsky.social gave a great talk on #indigenous #genomics and how to address health #inequality in these communities!
Thanks for joining us!

Just a few more days left to sign up for the EPIC conference 2025! Join us in Aarhus this August 🥳
✍️Registration deadline for talk/poster: 1st June 2025
✍️Registration deadline for attendance : 31st July 2025
#EPICdk25

This is a physical course but an online version will be available for those who can’t attend. We especially encourage students from African institutions to join online as this is offered as part of the African BioGenome Project Open Institute East&Central Africa Regional Workshop