Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 07/09/2026This work was led by @martaciuc.bsky.social, with contributions from the group and collaborators. We thank everyone involved in making this study possible. 🐗🧬 010
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 07/09/2026🧵5/5 The GFH is currently listed as “Least Concern,” but these findings highlight the deep evolutionary structure within the giant forest hog and have important implications for its conservation. Further research and reassessment of the GFH status is needed. 110
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 07/09/2026🧵4/5 Our results support the western and eastern GFH populations (H.m. ivoriensis and H.m. meinertzhageni) as distinct evolutionary significant units (ESUs). #Genomics #Conservation #Evolution 100
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 07/09/2026🧵3/5 The Guinean population has exceptionally low #genetic diversity 🧬. This appears to reflect a long history of low effective population size rather than recent inbreeding. Ongoing habitat loss, degradation, fragmentation & hunting may further increase genetic erosion. #Genomics #Conservation 100
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 07/09/2026🧵2/5 One of our most striking findings is the extreme genetic differentiation between GFHs from Guinea and Uganda, which is comparable to, and in some cases exceeds, that seen between recognized African #suid species. 🐗🐗🐗 #Genomics #Conservation #Evolution 100
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 07/09/2026🧵1/5 🧬 New paper from our group! We present the first whole-genome data for the giant forest hog, #Hylochoerus #meinertzhageni (GFH), filling a major gap in our understanding of African #suid #evolution 🐗🧬 📖 Read the full paper in iScience: doi.org/10.1016/j.is... #Genomics #Conservation 112
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 07/05/2026🧵2/2 New features in #AdapterRemoval v3 include QC reports, automatic adapter selection, improved demultiplexing, new trimming/filtering algorithms, automatic poly-G trimming, flexible output merging, SAM/BAM output, Windows support and more:github.comGitHub - MikkelSchubert/adapterremoval: AdapterRemoval v2 - rapid adapter trimming, identification, and read merging · GitHubAdapterRemoval v2 - rapid adapter trimming, identification, and read merging - MikkelSchubert/adapterremoval 010
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 07/05/2026🧵1/2 AdapterRemoval v3, a dang fast(Q) processor, is here! 🚀 AdapterRemoval v3 filters and trims high-throughput sequencing data, merges overlapping reads, performs demultiplexing, & generates detailed QC reports (HTML & JSON), and does so much faster than #AdapterRemoval v2. 143
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 07/01/2026🧵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! 010
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 07/01/2026🧵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. 110
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 07/01/2026🧵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... 100
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 07/01/2026🧵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 100
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 07/01/2026🧵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... 133
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 25/11/2025Big 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! 👏 021
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 22/10/2025Our 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! 031
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 29/09/2025🧵 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. 000
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 29/09/2025🧵 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. 110
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 29/09/2025🧵 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. 100
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 29/09/2025🧵 This recent introgression was thought to be the cause of their high genetic diversity (Figure 4d). 100
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 29/09/2025🧵 🧬 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). 100
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 29/09/2025🧵 🧬 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) 100
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 29/09/2025🧵 🧬 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) 100
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 29/09/2025🧵 🧬 We sequenced 126 WGS from 7 breeds 🐂 (Fig 1), revealing a unique evolutionary history and its promise for sustainable cattle #farming. 100
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 29/09/2025Our 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 #agriculturenature.comThe genetic diversity of Indonesian cattle has been shaped by multiple introductions and adaptive introgression - Nature CommunicationsIndonesian 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. 153
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 29/09/2025🚀 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 #EvolutionaryBiologycandidate.hr-manager.netPostdoctoral Fellowship in Water Buffalo Population GenomicsThe 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 074
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 29/08/2025What 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! 🙌✨ 011
Reposted by Population and Statistical Genetics Group at UCPHSabhrina Aninta @sagitaninta.bsky.social · 20/08/2025Had 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! 1151
Reposted by Population and Statistical Genetics Group at UCPHEPICconference @epicconference.bsky.social · 12/08/2025Day 1 of #EPIC25 @sagitaninta.bsky.social (KU) presented her work on Indonesian cattle and the evolutionary forces shaping their genomic landscape. 121
Reposted by Population and Statistical Genetics Group at UCPHEPICconference @epicconference.bsky.social · 12/08/2025Day 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. 111
Reposted by Population and Statistical Genetics Group at UCPHEPICconference @epicconference.bsky.social · 12/08/2025Day 1 of #EPIC25 Nuno Martins (KU) presented his preliminary analyses on the Greenlandic #reindeers 111
Reposted by Population and Statistical Genetics Group at UCPHEPICconference @epicconference.bsky.social · 13/08/2025We then continued with Emil Jørsboe (SSI) and explored the genetics of permanent tooth eruption. 101
Reposted by Population and Statistical Genetics Group at UCPHEPICconference @epicconference.bsky.social · 13/08/2025Shixu 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!? 101
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 06/08/2025Another 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 152
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 06/08/2025Wrapped 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 031
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 05/08/2025On 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! 021
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 30/05/2025Alex 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! 031
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 28/05/2025Just 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 022
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 06/05/2025This 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 064
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 06/05/2025Congratulations and thanks to all co-authors, especially to the two co-first authors @erillgenis.bsky.social and Shanlin Liu for starting and leading this project and the seniors @aalbrechtsen.bsky.social, Tom Gilbert and Rasmus Heller. 000
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 06/05/2025We also found that the gradual decline caused extremely low genetic diversity and strong purging of genetic load. Combining these two populations could reduce the otherwise high realized genetic load and increase species viability 100
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 06/05/2025We generate a de novo genome sequence for a male saola and sequenced 26 recently discovered and near-extinct saola samples. We found two highly differentiated populations that diverged and gradually declined over >5,000 years ago. 100
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 06/05/2025We sequenced and analyzed the world's rarest large mammal, the #saola 🦄. That turned into a cool paper substantially increasing what we know about this elusive animal, its evolutionary history, population structure, and long-term decline. Check it out here 👇 www.cell.com/cell/fulltex...cell.comGenomes of critically endangered saola are shaped by population structure and purgingThe generation of whole-genome sequencing data from 26 saolas provides insights into the phylogenetic placement, population structure, historical decline, and genetic diversity in one of the world’s m... 23213
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 24/04/2025Are you an evolutionary/population geneticist in Denmark? The EPIC conference is back and it will take place on 11-12 August 2025 in Aarhus. Come along for two days of great talks and networking! #EPICdk25 Hosts: @molbiolau.bsky.social & @popgendk.bsky.social Register now at: popgen.dk/epic/ 043
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 24/04/2025Featuring lectures & talks by Martin Sikora, Shyam Gopalakrishnan @shyamsg.bsky.social , Katia Bougiouri @katiabou.bsky.social , Fernando Racimo, Ida Moltke @idamoltke.bsky.social and Anders Albrechtsen @aalbrechtsen.bsky.social 000
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 24/04/2025Our population genetics PhD summer course 2025 @popgendk.bsky.social, Globe_UCPH is open for registration! We'll cover multiple topics and tools commonly used in PopGen analyses. For more info: 🔗 website.popgen.dk/summer/ 133
Reposted by Population and Statistical Genetics Group at UCPHAnna Brüniche-Olsen @annabruniche.bsky.social · 16/04/2025🦒🧬 New preprint🦒🧬 We investigated the degree of admixture, genetic diversity and inbreeding in ex situ giraffes using WGS data from the famous Marius, 12 zoo giraffes, and a data set from 71 wild giraffes. #ConsGen #PopGen #Genomics #Giraffes #Marius www.biorxiv.org/content/10.1... 24316
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 16/04/2025Welcome back to our monthly #EPIC seminars! We started yesterday with two speakers, Evelyn Todd and Marta Ciucani, talking about their research on #Scandinavian #wolves 🐺 and #African forest #hogs 🐗 Next seminar 🔜 May 21st Join us for some interesting talks and pizza 🍕 000
Reposted by Population and Statistical Genetics Group at UCPHRuth Mottram @ruthmottram.eurosky.social · 17/03/2025Really fascinating bit of work on #genetics of #Greenland - it really demonstrates why it's important to include people from diverse origins in genetic databases, but more importantly, it's also about HOW to include indigenous people in research + data sovreignty. : www.nature.com/articles/s41...nature.comGenetic architecture in Greenland is shaped by demography, structure and selection - NatureWe illustrate that including data from Greenlandic Inuit can greatly reduce inequity in genomic-based healthcare in Greenland and other indigenous Arctic populations. 13713
Reposted by Population and Statistical Genetics Group at UCPHNature @nature.com · 13/02/2025Nature research paper: Genetic architecture in Greenland is shaped by demography, structure and selection go.nature.com/42Sc7pNgo.nature.comGenetic architecture in Greenland is shaped by demography, structure and selection - NatureWe illustrate that including data from Greenlandic Inuit can greatly reduce inequity in genomic-based healthcare in Greenland and other indigenous Arctic populations. 0305
Population and Statistical Genetics Group at UCPH @popgendk.bsky.social · 20/03/2025The study is the result of a long and close collaboration with Steno Diabetes Center Greenland, Centre for Public Health in Greenland, and the University of Copenhagen. Also read the @NatureNV news and views: nature.com/articles/d41586-025-00091-6 and News www.nature.com/articles/d41... 🧵6/6nature.comGenetic data from Indigenous Greenlanders could help to narrow health-care gapPopulation genetics for the Greenlandic Inuit. 010