Pangenomes and Structural Variants in Molecular Ecology
Beyond the small, single-letter changes in DNA that scientists usually study, larger genomic rearrangements—insertions, deletions, and inversions—may play an underappreciated role in evolution. This project asks: do these “structural variants“ evolve differently than the mutations we know best, and can studying them reveal new insights into how wild populations adapt?
This project explores the evolutionary dynamics of a relatively understudied type of genomic variant—structural variants (SVs)—in natural populations of animals. SVs are genomic changes that span multiple nucleotides, including insertions, deletions, inversions, and other genomic rearrangements, ranging in size from just a few base pairs (bp) to several million bp. This makes them fundamentally different from the more commonly studied single-nucleotide polymorphisms (SNPs), which involve a change at just one DNA base pair. Recent advances in genomic technology now allow researchers to examine this class of mutations in wild animals and ask how their evolutionary dynamics differ from those of SNPs.
The project investigates the population genetics of structural variants in a common North American bird species with rich life-history and ecological data and readily available biological samples: the Song Sparrow (Melospiza melodia). It involves conducting long-read DNA sequencing—a more expensive method, but one far better able to detect large structural rearrangements than conventional sequencing—on a small number of individuals (approximately five to eight). The structural variants discovered this way will then be screened for cheaply in additional individuals using traditional short-read DNA sequencing, which is well suited to detecting known variants at scale but cannot reliably identify large rearrangements on its own. This approach will make it possible to determine whether structural variants are subject to natural selection, and whether they can distinguish between different populations more effectively than SNPs.
Understanding the evolutionary genetics of populations is fundamental to understanding both basic questions about how evolution works, as well as helping understand how genetic variation is useful as populations adapt to changing environments, including climate change. Although the Song Sparrow is not an endangered species, by studying it researchers can understand what types of SVs are expected to arise and persist in large, healthy populations. Then, when SV diversity is studied in endangered, geographically restricted species, if the diversity and abundance of SVs looks markedly different, this may mean that unhealthy—or "deleterious"—variation is accumulating.