Every semester, EES organise a seminar series, which takes place on Mondays at 16:00 at Biozentrum, Lecture Hall B 01.027
Winter Semester 2026/27
Scott Edwards
Harvard University, USA
Pangenomes from passerine birds: evolutionary processes and bioinformatic implications
Abstract: Population-scale long-read sequencing and pangenome methods are growing in applications to natural populations. Birds are a good test case for these approaches because their genomes have been characterized as conservative in mode of evolution and depauperate in repeat content. Here I present a synthesis of findings of structural variation derived from five multi-haplotype, long read pangenomes from both oscine and suboscine birds, 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 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.
Host: Maude Baldwin, Jochen Wolf
Previous and future talks in the EES seminar series