Pangenomics transforms evolutionary biology

08 - 09 June 2026 09:00 - 17:00 Apex Grassmarket Hotel, Edinburgh Free
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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

  • Joana Meier

    Dr Joana Meier

    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.

  • Henry North

    Dr Henry North

    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.

  • Charlotte Wright

    Dr Charlotte Wright

    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.

Schedule

Chair

Henry North

Dr Henry North

University of Cambridge, UK

09:00-09:05 Welcome
Dr Joana Meier

Dr Joana Meier

Wellcome Sanger Institute, UK

09:05-09:30 Talk title TBC
Dr Erik Garrison

Dr Erik Garrison

University of Tennessee Health Science Center, US

09:30-09:45 Discussion
09:45-10:15 Talk title TBC
Professor Peter Sudmant

Professor Peter Sudmant

University of California, Berkeley, US

10:15-10:30 Discussion
10:30-11:00 Break
11:00-11:30 Talk title TBC
Dr Éloi Durant

Dr Éloi Durant

Luxembourg Institute of Science and Technology, Luxembourg

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 Ebler

Dr Jana Ebler

Heinrich Heine University Düsseldorf, Germany

12:15-12:30 Discussion

Chair

Charlotte Wright

Dr Charlotte Wright

Wellcome Sanger Institute, UK

13:30-14:00 Talk title TBC
Dr Mona Schreiber

Dr Mona Schreiber

Philipps University Marburg, Germany

14:00-14:15 Discussion
14:15-14:45 Talk title TBC
Dr Laura Kelly

Dr Laura Kelly

Royal Botanic Gardens, Kew, UK

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 Curran

Dr Emma Curran

University of Sheffield, UK

16:00-16:15 Discussion
16:15-16:45 Talk title TBC
Dr Andreas Bachler

Dr Andreas Bachler

Commonwealth Scientific and Industrial Research Organisation, Australia

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 FRS

Professor Richard Durbin FRS

University of Cambridge, UK

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 Miga

Professor Karen Miga

University of California, Santa Cruz, US

10:15-10:30 Discussion
10:30-11:00 Break
11:00-11:30 Talk title TBC
Dr Lewis Stevens

Dr Lewis Stevens

Wellcome Sanger Institute, UK

11:30-11:45 Discussion
11:45-12:15 Talk title TBC
Professor Scott Edwards

Professor Scott Edwards

Harvard University, US

12:15-12:30 Discussion

Chair

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Dr Mara Lawniczak

Wellcome Sanger Institute, UK

13:30-14:00 Talk title TBC
Professor Paolo Franchini

Professor Paolo Franchini

Tuscia University, Italy

14:00-14:15 Discussion
14:15-14:45 Talk title TBC
Dr Katharine Jenike

Dr Katharine Jenike

University of Cambridge, UK

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 Meier

Dr Joana Meier

Wellcome Sanger Institute, UK