Pangenomics transforms evolutionary biology

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

University of Cambridge, UK

Professor Richard Durbin FRS

University 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.

The human pangenome reference represents a fundamental shift in how human genetic variation is represented, analyzed, and shared, with broad implications for genomics research and medicine. Building on recent data releases, I will describe the transition toward a stable pangenome reference that establishes a new standard for base-level accuracy and telomere-to-telomere (T2T) representation of all chromosomes across diverse, fully phased haplotypes sampled to reflect global human genetic diversity. This resource enables more comprehensive variant discovery and interpretation by supporting analyses across multiple high-quality haplotypes and incorporating local ancestry inference (LAI) to contextualize variation within admixed genomes. The release highlights expanded international partnerships through the GA4GH Human Pangenome Project Telomere-to-Telomere (T2T) initiative, broadening both development and application of this global resource. Further, the pangenome now enables systematic analysis of satellite-rich regions of the genome, including centromeres, allowing satellite variants to be confidently and systematically reported across multiple haplotypes for the first time. Together, these advances enable more comprehensive structural variant analysis and improved functional interpretation, while driving continued pangenomics tooling and workflow innovation in support of a shared, global genomic resource.

Professor Karen Miga

University of California, Santa Cruz, US

Professor Karen Miga

University 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.

Structural variants are often thought of as simple events such as inversions, duplications, and indels, but many do not fit neatly into these categories. Hyper-divergent haplotypes (HDHs) are large stretches of sequence that differ markedly between individuals of the same species. HDHs were first described in the free-living model nematode Caenorhabditis elegans, where they span approximately 20% of the genome and are enriched for genes involved in sensory perception, pathogen defence, and xenobiotic stress. Similar haplotypes have recently been reported in other invertebrates, suggesting that this form of structural variation may be more widespread than previously realised.

We have developed new low-input long-read sequencing approaches and applied them to nematodes that parasitise humans, livestock, and wild animals. In doing so, we have discovered that HDHs are common features of parasitic nematode genomes, and often encode genes implicated in host interaction, including those previously trialled as vaccine antigens. In some cases, alternative haplotypes encode different repertoires of functionally related genes, meaning that individuals of the same species can express distinct sets of host-interacting proteins. Phylogenetic analyses suggest that these haplotypes are maintained by long-term balancing selection and may, in some cases, be generated through introgression between closely related species. We hypothesise that this “hyperdiversity” facilitates evasion of host immunity during infection.

In this talk, I will present what we currently know about hyper-divergent haplotypes in nematodes and other organisms and explain how pangenomic approaches can be used to address the many outstanding questions concerning their evolution, function, and real-world relevance.

Dr Lewis Stevens

Wellcome Sanger Institute, UK

Dr Lewis Stevens

Wellcome 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.

Birds are a good test case for the power of pangenome methods because they have been characterized as conservative in mode of evolution and depauperate in repeat content. Here we present a synthesis of findings of structural variation derived from five multi-haplotype, long read pangenomes from both oscines and suboscines, the two major lineages of passerine birds. We find that the abundance of repetitive elements, particularly satellite DNA, is vastly greater than revealed by short-read genome assemblies and that the annotation of specific repeat types depends heavily on the particular annotation tools used. The abundance of structural variants scales with population size, a pattern that extends to complex multigene families like the major histocompatibility complex (MHC), which shows evidence for extensive lineage-specific proliferation of gene duplicates, including a high incidence of MHC pseudogenes. However, accurate estimates of the frequency of multi-allelic structural variants remains challenging. Gene copy number variants reveal relationships with population size expected if gene deletions are deleterious and gene multiplications are neutral or advantageous, but discriminating between true deletions and false positives is challenging with current pipelines. We attempt to estimate the de novo mutation rate of structural variants using long read data from five family trios of the Florida Scrub-Jay (Aphelocoma coerulescens), but in our hands the incidence of false positives is prohibitively high. Early pangenomes in birds reveal broad agreement with expected rates of structural variation, yet specific types of variants, such as gene copy numbers and de novo mutations, continue to present bioinformatic challenges.

Professor Scott Edwards

Harvard University, US

Professor Scott Edwards

Harvard 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.

Cichlids are an exceptional model for dissecting the genomic basis of rapid adaptive radiation and phenotypic diversification, and ultimately the mechanisms underlying speciation. In the Neotropical Midas cichlid radiation (Amphilophus citrinellus species complex), decades of genetic and genomic research have generated substantial insight into the basis of multiple adaptive traits. However, fully resolving how these traits evolve and contribute to divergence has remained challenging, largely because of their complex, multilocus architecture and the limitations of single-reference, SNP-centric approaches. This contribution demonstrates how a pangenomic framework applied to the Midas system enables a more complete characterization of the genomic architecture underlying adaptation and phenotypic diversification in young, rapidly diversifying fishes. A high-quality pangenome built from 16 chromosome-level, haplotype-resolved genomes and integrated with extensive short-read whole-genome resequencing and transcriptomic data revealed layers of genetic variation that are inaccessible to conventional analyses. Overall, these results highlight pangenomics as a powerful tool for linking genome structure to adaptive divergence and for advancing our understanding of rapid ecological diversification.

Professor Paolo Franchini

Tuscia University, Italy

Professor Paolo Franchini

Tuscia 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.

Pangenomes provide a powerful lens into adaptation and phenotypic variation across agriculture, human health, and fundamental biology. Structurally diverse sequences revealed by pangenomes are increasingly recognized as potential contributors to phenotypic diversity, yet understanding how these sequences are organized and relate to traits remains poorly resolved. Despite rapid progress in genome sequencing, methods for analysing pangenomes are computationally demanding and have shown limited ability to resolve how complex genetic variation is organized into functional units that shape phenotypes. Addressing this need, we introduce Panagram (https://github.com/kjenike/panagram), an ultrafast reference-free platform for assembling and annotating the haplotype architecture within a pangenome consisting of evolutionarily coherent blocks of shared sequence variation. The core metric of Panagram is the pan-kmer bitmap that quantifies local sequence similarity across samples and enables rapid, on-the-fly clustering and analyses of haplotypic blocks. These capabilities provide a unified framework for association testing, introgression detection, and the flexible discovery of biologically meaningful variation across pangenomes.

Dr Katharine Jenike

University of Cambridge, UK

Dr Katharine Jenike

University 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.

A significant fraction of genetic diversity lies in structural genomic variation (SV), eg chromosomal rearrangements or copy-number variants. New high-quality reference assemblies whether taken as collection of comparable genomes or gathered as pangenome graphs provide unprecedent access into SVs, showing their prevalence and their implication in adaptation or diversification.

Here, we will reflect on the role of SVs in the evolution of diversity and adaptation, with insights from experimental and ecological studies in the seaweed flies Coelopa sp. In particular, large polymorphic chromosomal inversions are particularly important for parallel adaptation to heterogeneous environments. For instance, they underlie morphotypes with different life-history strategies. We are now building a pangenome including genomes from different geographical populations and related species to target the origin and evolution of those large balanced rearrangements.

Next, we will ask how the new genome resources may help to more systematically investigate SVs. We have developed a pipeline leveraging long-reads and genome assemblies from the Darwin Tree of Life project to address patterns of intra-specific structural variation across a broad range of taxa. We’ll discuss how such type of datasets provides opportunities to investigate the role of species’ life-history and ecology in shaping the architecture of genetic diversity and architecture.

Dr Claire Mérot

Centre National de la Recherche Scientifique - UMR 6553 - University of Rennes, France

Dr Claire Mérot

Centre National de la Recherche Scientifique - UMR 6553 - University of Rennes, France

Claire Mérot is an evolutionary biologist interested in the evolution of diversity and how genomic architecture underlies adaptation and speciation. She integrates experimental and genomic approaches, combining fieldwork and bioinformatics, mostly on insects. Her current work focuses on structural variants and chromosomal inversions. After a PhD at the National Museum of Natural History in Paris, she spent six years as a post-doc at Université Laval in Québec, and she is now a researcher (PI) at CNRS, based at the University of Rennes. She holds an ERC starting grant about the role of structural variants in eco-evolutionary processes.