Beijing Institute of Mathematical Sciences and Applications

Liyan Han , Zhen Li , Qingfu Liu , Fei Long , Ke Tang

Scott Vernon Edwards

Friday, January 17, 2025 4:00 PM - 6:00 PM

A7-302

Zoom 230 432 7880 (BIMSA)

Pangenomes are collections of genomes that have been assembled and constructed in ways that faithfully capture all types of genomic variation, including single-nucleotide polymorphisms but also individual haplotypes and structural variation (SV), such as copy number variants, insertions and deletions, and complex variation in multigene families like the major histocompatibility complex (MHC). In this talk I will present an analysis of 45 genomes from three species of Scrub-Jay (Aphelocoma), each assembled with PacBio HiFi reads and the long-read genome assembler hifiasm. Heterozygosity and PSMC analysis show that the three species fall along a 60-fold gradient of effective population sizes that allow us to observe the differing dynamics of SVs and SNPs in the outbred Woodhouse’s Scrub-Jay, lower diversity Florida Scrub-Jay and the inbred Island Scrub Jay. These genomes are relatively large for birds (~1.3 Gb) and harbor an unusually high proportion of transposable elements (up to ~27%). We find compelling evidence for a rapid reduction of genome size by ~80 Mb) in the Island Scrub-Jay (A. insularis) due primarily to reductions of major satellite families. Using pangenome graphs, we found that indels (< 50 bp; ~3.1M) and SVs (> 50 bp; ~448,000), including 382 inversions, were drastically less common than SNPs (~20.3M) across the species complex and reveal that SV length correlates with the severity of estimated SV fitness effects. Telomeres can be measured fairly accurately and are shorter in Island Scrub-Jays, consistent with population genetic predictions for small populations. In Woodhouse’s Scrub Jay, we demonstrate effects of SVs on gene expression, due both to direct ablation of genes and via removal of putative noncoding enhancers. Pangenomes offer an exciting new way to monitor genetic variation and its fitness consequences in natural populations of birds.

• Member of the U.S. National Academy of Sciences
• Fellow of the American Academy of Arts and Sciences
• Fellow of the American Association for the Advancement of Science (AAAS)
• Chair and Tenured Professor of the Department of Organismic and Evolutionary Biology at Harvard University
• Curator of Ornithology and Alexander Agassiz Professor of Zoology in the Museum of Comparative Zoology

Prof. Edwards’ research spans genetics and genomics.His research primarily focuses on the evolutionary biology of birds and related species, combining field, museum and genomics approaches to understand the basis of avian diversity, evolution and behavior. To date, he has published over 200 papers in leading international journals such as Nature, Science, and Proceedings of the National Academy of Sciences (PNAS), with a total citation count of 37,855 and a single paper cited up to 6,374 times. His work is widely recognized and influential in the global academic community.Prof. Edwards has previously served as President of the American Genetic Association, President of the Society of Systematic Biologists, and Director of the Department of biological infrastructure at the U.S. National Science Foundation (NSF).He currently serves as Associate Editor of PNAS, a member of the Board of Reviewing Editors for Science, and Deputy Editor of Science Advances.