Pangenomics transforms evolutionary biology
Theo Murphy meeting organised by Dr Joana Meier, Dr Henry North and Dr Charlotte Wright.
Genomic studies often use a reference genome from a single individual. This underestimates genetic diversity and biases against more distant relatives. Novel pangenome graphs eliminate both issues by combining the genetic variation of diverse individuals. This meeting will showcase cutting-edge pangenome tools, applied uses of pangenomes which are transforming health and agriculture, and opportunities to revolutionise biodiversity genomics.
Programme
The programme, including the speaker biographies and abstracts, will be available soon. Please note the programme may be subject to change.
Poster session
There will be a poster session on Monday 8 June. If your request to attend is approved, you will be sent further information on how to submit your poster abstract. Submissions made within one month of the meeting may not be included in the programme booklet.
Attending this event
- Free to attend and in-person only
- When requesting an invitation, please briefly state your expertise and reasons for attending
- Requests are reviewed by the meeting organisers on a rolling basis. You will receive a link to register if your request has been successful
- Catering options will be available to purchase upon registering. Participants are responsible for booking their own accommodation
- Please do not book accommodation until you have been invited to attend the meeting by the meeting organisers
Enquiries: contact the Scientific Programmes team.
Image credit: iStock.com / natrot
Organisers
Schedule
Chair
Dr Henry North
University of Cambridge, UK
Dr Henry North
University of Cambridge, UK
Henry is a research fellow at Girton College, Cambridge, broadly interested in adaptation and hybridization. He completed his undergraduate degree at the University of Queensland, Australia, working on speciation in Senecio in the Ortiz-Barrientos laboratory. He then completed his MSc through the Erasmus Mundus Programme in Evolutionary Biology, working with Carole Smadja, Robin Hopkins, and Chris Jiggins. He recently completed his PhD with Chris Jiggins, focusing on bidirectional adaptive introgression of structural variants between native and invasive species of the noctuid moth genus Helicoverpa. Henry’s current research uses this study system, as well as other instances of hybridization between native and invasive species, to investigate a range of questions in evolutionary genomics. His current interests include the mismatch of transposable elements and their suppressors in hybrid genomes, parallel evolution of structural variants, and the relationship between nucleotide diversity and gene absence-presence polymorphism.
| 09:00-09:05 |
Welcome
Dr Joana MeierWellcome Sanger Institute, UK
Dr Joana MeierWellcome Sanger Institute, UK Joana Meier studies why the species richness is so unevenly distributed across the tree of life, particularly how hybridisation and chromosomal rearrangements affect rapid species radiations. After a PhD and postdoc at the University of Bern in Switzerland on cichlid fish speciation, she held two concurrent fellowships at the University of Cambridge in the UK, working on butterfly speciation. Since 2022, she has been leading a group at the Wellcome Sanger Institute, combining her group leader position with a Royal Society URF. Her research team focuses on rapid speciation in butterflies and peacock spiders, and she also leads large collaborative sequencing projects like Project Psyche – sequencing reference genomes of all Lepidoptera found in Europe. |
|---|---|
| 09:05-09:30 |
Talk title TBC
Dr Erik GarrisonUniversity of Tennessee Health Science Center, US Dr Erik GarrisonUniversity of Tennessee Health Science Center, US Erik Garrison is an Associate Professor in the Department of Genetics, Genomics and Informatics at the University of Tennessee Health Science Center, leading research on computational methods for pangenomics and genome evolution. A core member of the Human Pangenome Reference Consortium, he led development of vg, the variation graph toolkit foundational to graph-based genomics. His open-source tools include the PanGenome Graph Builder (pggb) pipeline for constructing pangenome graphs without reference bias. His work has contributed to landmark publications including the first draft human pangenome reference, the first complete human genome assembly, and the Vertebrate Genomes Project. Previously, he was a postdoctoral fellow at UC Santa Cruz Genomics Institute. Garrison earned his PhD in Genomics from the University of Cambridge in 2019 under Richard Durbin and holds a BA in Social Studies from Harvard University. |
| 09:30-09:45 |
Discussion
|
| 09:45-10:15 |
Talk title TBC
Professor Peter SudmantUniversity of California, Berkeley, US Professor Peter SudmantUniversity of California, Berkeley, US The Sudmant Lab seeks to understand the how evolution shapes genome structure, genetic diversity, aging, and other life-history traits in humans and across the tree of life; and how aging in humans and other organisms impacts the fidelity of molecular processes such as mutation and post-transcriptional gene regulation. We use computational, statistical, and experimental approaches to explore these questions across different molecular and organismal scales. |
| 10:15-10:30 |
Discussion
|
| 10:30-11:00 |
Break
|
| 11:00-11:30 |
Talk title TBC
Dr Éloi DurantLuxembourg Institute of Science and Technology, Luxembourg
Dr Éloi DurantLuxembourg Institute of Science and Technology, Luxembourg An agronomy engineer and bioinformatician by training, Dr Éloi Durant stumbled into the worlds of pangenomics and visualization research during his PhD at the Institut de Recherche pour le Développement (IRD) in Montpellier, France. After navigating the troubled waters of "What is a pangenome?", "Why are there so many models?" and "Why would anyone want to visualize one, even?", he persevered through world-stopping events to complete his dissertation: Design of novel visual representations and tools applied to plant pangenome visualization. Drawing on his experience with pangenome graphs, he joined the Visualization & Interaction group at LIST (the Luxembourg Institute of Science and Technology), which organized EuroVis 2025. His interests have since expanded to (multilayer) network visualization while he continues exploring new ways to represent complex data. |
| 11:30-11:45 |
Discussion
|
| 11:45-12:15 |
Pangenome-based genome inference
Typical analysis workflows map reads to a reference genome in order to genotype genetic variants. Generating such alignments introduces reference biases and comes with substantial computational burden. In contrast, recent k-mer based genotypers are fast, but struggle in repetitive or duplicated genomic regions. We introduced a new algorithm, PanGenie, that leverages a haplotype-resolved pangenome reference in conjunction with k-mer counts from short-read sequencing data to genotype a wide spectrum of genetic variation – a process we refer to as genome inference. We could demonstrate that our method produces better results compared to mapping-based approaches. Improvements are especially pronounced for structural variants (SVs) and variants in repetitive regions. We studied SVs across large cohorts sequenced with short-reads, using pangenome graphs generated by the HGSVC and HPRC consortia, which enables the inclusion of these classes of variants in genome-wide association studies. Dr Jana EblerHeinrich Heine University Düsseldorf, Germany Dr Jana EblerHeinrich Heine University Düsseldorf, Germany Jana Ebler received her BSc and MSc in Bioinformatics from Saarland University in Saarbrücken, Germany. She did her PhD at the Max Planck Institute for Informatics in Saarbrücken and the Heinrich Heine University in Düsseldorf, Germany and graduated in 2023. She is currently a postdoc at the Heinrich Heine University in Düsseldorf. Her research interests include genotyping, phasing and pangenomics. She is part of the Human Pangenome Reference Consortium (HPRC) as well as the Human Genome Structural Variation Consortium (HGSVC), focusing on the construction of pangenomes from human haplotypes, as well as the analysis of structural variation in humans. |
| 12:15-12:30 |
Discussion
|
Chair
Dr Charlotte Wright
Wellcome Sanger Institute, UK
Dr Charlotte Wright
Wellcome Sanger Institute, UK
Dr Charlotte Wright is a postdoctoral fellow at the Wellcome Sanger Institute and is the Charles and Katherine Darwin research fellow at Darwin College, University of Cambridge. Charlotte’s research uses comparative and population genomic approaches to understand the evolutionary processes that shape genome evolution and how changes in genome structure impact the generation of biodiversity. Charlotte leverages large-scale sequencing datasets to investigate changes in genome evolution both within species and across the diversification of taxa. As part of this, Charlotte is particularly interested in using pangenomic approaches to understand how changes in genome structure such as chromosome rearrangements evolve. Her research focuses on butterflies and moths, and is one of the leaders of Project Psyche that aims to generate and utilise reference genomes of all butterflies and moths in Europe.
| 13:30-14:00 |
Talk title TBC
Dr Mona SchreiberPhilipps University Marburg, Germany Dr Mona SchreiberPhilipps University Marburg, Germany Mona arrived at plant science from an unexpected angle. She began in physical anthropology, drawn to the great turning points of human history, and soon found herself modelling the demographic arc of cattle domestication through ancient DNA. That evolutionary thread carried her into a PhD on cereal domestication, where genetic evidence, archaeological insight, and language braided into a deeper story of crops and people. Her postdoctoral work then reached further back in time, into the origins of land plants and the early branching of archaeplastida. In time she moved into plant ecology, where molecular evolution met her enduring affinity for trees. Alongside this scientific path, art remained a steady companion, offering a way to translate complex scientific histories into forms that feel both intuitive and alive. |
|---|---|
| 14:00-14:15 |
Discussion
|
| 14:15-14:45 |
Talk title TBC
Dr Laura KellyRoyal Botanic Gardens, Kew, UK
Dr Laura KellyRoyal Botanic Gardens, Kew, UK Laura Kelly is an evolutionary biologist whose research interests centre on using genomic and evolutionary approaches to understand current and future threats to plant health, to inform actions to mitigate these and to determine how plants adapt in the face of new environmental challenges. Her current areas of focus include using pangenomics to uncover the basis of resistance to major tree pests and pathogens, and to understand the evolutionary response of natural populations to new biotic stressors. |
| 14:45-15:00 |
Discussion
|
| 15:00-15:30 |
Break
|
| 15:30-16:00 |
The role of structural variation during adaptation to whole genome duplication
Whole genome duplication (WGD) is a dramatic mutation, hugely disrupting cellular processes. To survive and thrive, polyploids undergo rapid evolution at genes regulating fundamental processes such as meiosis. Recent studies suggest an important role for structural variants (SVs) in the adaptability of young polyploids. Do SVs play a role in adaptation to WGD? We investigate this in Arabidopsis arenosa, which has undergone WGD ~30k generations ago. Here, we build a pangenome graph of phased diploid and autotetraploid genome assemblies to detect SVs, and we leverage existing short-read datasets to look for evidence of SVs involved in adaptation to WGD. We compare this to SNP-based genome scans. We find novel candidates for genes involved in adaptation to WGD from both the SV and the SNP based analyses, with a small number of candidates indicated by overlapping SNPs and SVs. This suggests that by ignoring structural variation we are also ignoring an important component of the genetic basis of adaptation.
Dr Emma CurranUniversity of Sheffield, UK
Dr Emma CurranUniversity of Sheffield, UK Emma Curran is a postdoctoral researcher at the University of Sheffield. The aim of her research is to understand how natural populations diversify and respond to challenges in the internal and external environment, by employing population genomic, phylogenomic, and pangenomic approaches. She has investigated this in a range of systems, including divergence and convergence of colour pattern signals in stick insects and butterflies, ecotypic variation and adaptation to climate change in grasses, and the role of structural variants during adaptation to whole genome duplication in Brassicacae. |
| 16:00-16:15 |
Discussion
|
| 16:15-16:45 |
Talk title TBC
Dr Andreas BachlerCommonwealth Scientific and Industrial Research Organisation, Australia
Dr Andreas BachlerCommonwealth Scientific and Industrial Research Organisation, Australia Dr Andy Bachler is a bioinformatic Postdoctoral Fellow in the Australian government research organisation CSIRO. He completed a BSc (Adv) at the University of Sydney and an Honours degree at Monash University before undertaking his PhD at the Australian National University, where he developed the first pan-genome for a major global pest insect, Helicoverpa armigera (Cotton Bollworm). The pangenomic ‘lens’ enabled identification of a previously unrecognised group of resistance genes for the Bt toxin Vip3Aa, which had not been captured using traditional genomic approaches - advancing understanding essential to sustainable agriculture and insect resistance management. Andy’s current work focuses on improving genome annotations for eukaryotic organisms, using machine learning tools to detect and correct errors in gene models, and enhancing the characterisation of unannotated prokaryotic genes through protein structure rather than sequence. His research supports large-scale comparative and pangenomic analyses across diverse taxa, with applications in biosecurity, agricultural pest management, and the development of more robust genomic resources for applied and fundamental biology. |
| 16:45-17:00 |
Discussion
|
| 09:00-09:30 |
Pangenome sequencing reveals dramatic transposable-element induced structural variation in species radiations
Advances over the last few years in long-read reference genome assembly enable us now to obtain essentially complete genome sequences including through highly repetitive regions. Here we apply this to multiple samples from two adaptive radiations: first the cichlid fish radiation of hundreds of species in Lake Malawi in the last half million years, and second the northern European small Yponomeuta moth radiation. A large fraction of species diversity is created during adaptive radiations, in which multiple species lineages separate within a short period. It is established that the sequences of genomes in the resulting lineages are not related according to a simple bifurcating species tree. Known causes for this are incomplete lineage sorting (ILS) and hybridisation. However we also see extensive mobile element activity in both these radiations, with hundreds of active transposon families, many differentially active across the radiation, and associated with this large scale structural variation between species/lineages whose associated variable content dwarfs the single nucleotide mutation-derived variation. Professor Richard Durbin FRSUniversity of Cambridge, UK Professor Richard Durbin FRSUniversity of Cambridge, UK Richard Durbin has a BA in Mathematics and PhD from the MRC Laboratory of Molecular Biology in Cambridge. He and his group have worked in computational genomics since 1990 and more recently evolutionary genomics, initially at the Wellcome Sanger Institute and since 2017 at the Department of Genetics, University of Cambridge. They have introduced multiple bioinformatic and statistical genetics methods, and participated in large collaborative projects including the 1000 Genomes Project. Recently they have worked on pangenome and assembly sequence graph methods, in the context of reference genome sequencing across the diversity of life and evolutionary genomics in non-model vertebrate systems. Richard is a Fellow of the Royal Society, Member of EMBO and recipient of the 2023 International Prize for Biology. |
|---|---|
| 09:30-09:45 |
Discussion
|
| 09:45-10:15 |
The Human Pangenome Project: a global resource to map genomic diversity
The human reference genome is the most widely used resource in human genetics and is due for a major update. Its current structure is a linear composite of merged haplotypes from more than 20 people, with a single individual comprising most of the sequence. It contains biases and errors within a framework that does not represent global human genomic variation. A high-quality reference with global representation of common variants, including single-nucleotide variants, structural variants and functional elements, is needed. The Human Pangenome Reference Consortium aims to create a more sophisticated and complete human reference genome with a graph-based, telomere-to-telomere representation of global genomic diversity. Here we leverage innovations in technology, study design and global partnerships with the goal of constructing the highest-possible quality human pangenome reference. Our goal is to improve data representation and streamline analyses to enable routine assembly of complete diploid genomes. With attention to ethical frameworks, the human pangenome reference will contain a more accurate and diverse representation of global genomic variation, improve gene–disease association studies across populations, expand the scope of genomics research to the most repetitive and polymorphic regions of the genome, and serve as the ultimate genetic resource for future biomedical research and precision medicine. Professor Karen MigaUniversity of California, Santa Cruz, US Professor Karen MigaUniversity of California, Santa Cruz, US Karen Miga is an Associate Professor in the Biomolecular Engineering Department at UCSC, Director of the UCSC Sequencing Technology Center, and an Associate Director of the UCSC Genomics Institute. In 2019, she co-founded the Telomere-to-Telomere (T2T) Consortium, an open, community-based effort to generate the first complete assembly of a human genome. Additionally, Dr. Miga is the Director of the Genome Center for the Human Pangenome Reference Consortium (HPRC). Central to Dr. Miga’s research program is the emphasis on satellite DNA biology and the use of long-read and new genome technologies and pangenome tools to construct high-quality genetic and epigenetic maps of human centromeric regions. |
| 10:15-10:30 |
Discussion
|
| 10:30-11:00 |
Break
|
| 11:00-11:30 |
Talk title TBC
Dr Lewis StevensWellcome Sanger Institute, UK
Dr Lewis StevensWellcome Sanger Institute, UK Lewis is an evolutionary biologist working at the Wellcome Sanger Institute. He uses nematodes as a model system, and his current focus is in understanding the causes and consequences of regions of extreme genetic diversity in parasitic nematodes. |
| 11:30-11:45 |
Discussion
|
| 11:45-12:15 |
Talk title TBC
Professor Scott EdwardsHarvard University, US Professor Scott EdwardsHarvard University, US Scott Edwards is Alexander Agassiz Professor of Zoology and Curator of Ornithology in the Museum of Comparative Zoology at Harvard University. Scott is an evolutionary biologist, with diverse interests in molecular evolution, phylogenetics, comparative genomics and population genetics. His research uses birds as model systems, focusing on their evolutionary history, phylogeography, genome evolution and genetic diversity. Scott has served as President of the Society for the Study of Evolution, the Society of Systematic Biologists, and the American Genetic Association, and has served on National Geographic’s Committee for Research and Exploration and the Advisory Boards of the National Museum of Natural History (Smithsonian) and the Cornell Lab of Ornithology. He was elected to the National Academy of Sciences in 2015 and is also a member of the American Academy of Arts & Sciences, the American Philosophical Society, and the American Association for the Advancement of Science. |
| 12:15-12:30 |
Discussion
|
Chair
Dr Mara Lawniczak
Wellcome Sanger Institute, UK
Dr Mara Lawniczak
Wellcome Sanger Institute, UK
Mara Lawniczak is an evolutionary geneticist and senior group leader at the Wellcome Sanger Institute. Current research in her group spans human malaria vector population genomics to wider biodiversity genomics. She leads the multiple large projects including the Malaria Cell Atlas, BIOSCAN UK, and ANOSPP. She is also involved in multiple large consortial projects including as co-Investigator on the Darwin Tree of Life project, as a founding member of the Biodiversity Cell Atlas initiative, and through chairing the Earth BioGenome Project Sample Collection and Processing subcommittee. All areas of her research areas are aimed at studying evolutionary genomics while simultaneously creating valuable data resources for the wider community. More recently, her team has begun to explore pangenomic approaches for human malaria mosquito species across their geographic ranges to understand highly diverse and diverged regions of the genome previously inaccessible for some individuals when mapping to a single reference genome.
| 13:30-14:00 |
Talk title TBC
Professor Paolo FranchiniTuscia University, Italy Professor Paolo FranchiniTuscia University, Italy Dr Paolo Franchini is an Associate Professor of Ecology and Evolutionary Biology at the University of Tuscia, Viterbo, Italy. He earned his PhD in Animal Biology from Sapienza University of Rome in 2007 and conducted postdoctoral research at Stellenbosch University (South Africa) and the University of Konstanz (Germany), where he also managed the University’s Genomics Centre. He later held fixed-term research appointments in Rome and Viterbo before obtaining his current position. Dr Franchini’s research explores the genomic basis of adaptation, speciation, and phenotypic diversification, focusing on population and comparative genomics, as well as regulatory evolution. Cichlid fishes remain his primary research focus, but his comparative work also extends to other animal groups, such as bumblebees, marine fishes, birds, and mammals. By integrating field data, high-throughput sequencing, and computational analyses, he aims to elucidate how evolutionary and ecological processes generate and maintain biodiversity. |
|---|---|
| 14:00-14:15 |
Discussion
|
| 14:15-14:45 |
Talk title TBC
Dr Katharine JenikeUniversity of Cambridge, UK Dr Katharine JenikeUniversity of Cambridge, UK Dr Jenike is a postdoctoral fellow at the University of Cambridge where she studies plant pangenomes and develops tools to explore large pangenomic datasets. Her current work includes decoding Arabidopsis centromeres through comparative genomics and developing methods to compare multiple whole genomes of highly divergent species. Handling and comparing repetitive sequences is of particular interest, given the unique challenges of low-complexity DNA. Prior to this, she earned her PhD in Human Genetics and Genomics at Johns Hopkins School of Medicine in Baltimore Maryland. During her PhD she assembled a nightshade pangenome, focusing on non-industrialized crops and their wild relatives. In her free time she enjoys backpacking, painting bad watercolours, and hiking with her dog. |
| 14:45-15:00 |
Discussion
|
| 15:00-15:15 |
Break
|
| 15:30-16:00 |
Talk title TBC
|
| 16:00-16:15 |
Discussion
|
| 16:15-17:00 |
Panel discussion: future directions
Dr Joana MeierWellcome Sanger Institute, UK
Dr Joana MeierWellcome Sanger Institute, UK Joana Meier studies why the species richness is so unevenly distributed across the tree of life, particularly how hybridisation and chromosomal rearrangements affect rapid species radiations. After a PhD and postdoc at the University of Bern in Switzerland on cichlid fish speciation, she held two concurrent fellowships at the University of Cambridge in the UK, working on butterfly speciation. Since 2022, she has been leading a group at the Wellcome Sanger Institute, combining her group leader position with a Royal Society URF. Her research team focuses on rapid speciation in butterflies and peacock spiders, and she also leads large collaborative sequencing projects like Project Psyche – sequencing reference genomes of all Lepidoptera found in Europe. |