Welcome to #AGA2024!! Here we will share some bits, pieces, and anecdotes from this year’s presidential symposium! Our president Beth Shapiro put together a great list of speakers and we have many excellent poster presenters.
Day 3: Mid-AM Talks
Stephen Gaughran, Temporal genomics of an extreme bottleneck in the northern elephant seal
Stephen is a PostDoc in the Graham Group at Princeton University. His talk was selected from submitted abstracts. Elephant seals are generally touted as a conservation success story as the population appears to have recovered from an extreme population bottleneck. Graham’s work involved using ancient bone samples from elephant seals to sequence genomes from pre-Eurpoean contact individuals to compare samples from pre-, during, post-, and recovered bottleneck populations.
- Heterozygosity in northern elephant seals is really low
- Investigating runs of homozygosity (ROH, regions of the genome with no variation in individuals) painted a clear picture of an increase in the length of ROHs during the bottleneck period followed by a subsequent breakup of these regions following population recovery
- There appears to be a relatively low effective population size (less than 1000) in the northern elephant seals before the industrial sealing of Europeans, explaining the low heterozygosity
- Imputing genotypes revealed clear population structure pre-, during, and post-bottleneck
- Stephen also found an increase in a deleterious allele in an immune regulation gene called FOXP1 resulting from the extreme population bottleneck. The frequency of this allele has decreased with population recovery.
Faye Romero, The genetics of inbreeding depression in a pedigreed wild population of Florida Scrub-Jays
Faye is a PhD student in the Chen Lab at the University of Rochester. Her talk was also selected from submitted abstracts. Her work involves investigating the conservation implications of inbreeding depression. Traditionally, an inbreeding coefficient was calculated from pedigree data but with the advent of genomic information, we can now infer inbreeding through the presence of ROHs.
- The Florida Scrub Jay has a long history of scientific study (Archbold Biological Station has a study population beginning in the 1960s!) and we know much about their populations
- This in-depth information allows for investigations into the genomic architecture of decreased immigration, increased inbreeding, and small population size
- There is clear inbreeding depression in this population as measured by decreased hatchling weight, reduced survivability, and reduced fecundity (among others)
- Whole genome resequencing data of 3,800 individuals across ~20 years will allow for an in-depth investigation into the length and prevalence of ROHs in the Florida Scrub Jay
Bridgett vonHoldt, Ghost wolves: resurrecting an endangered canid species
Bridgett is the PI of the VonHoldt Lab at Princeton University. Her work involves unraveling genotype-phenotype evolution in both a naturally and artificially evolving species. Ghost wolves live on Galveston Island in south Texas.
- It was originally unclear if the ghost wolves were dog hybrids, coyotes, gray wolves, or red wolves (which are extinct in the wild). ~30% of the ghost wolf genome traces its ancestry to the red wolf, but the other part of the genome’s ancestry does not trace to other canids!
- But what is ‘ghost’ variation? Variation lost during a population bottleneck, or introgression of genetic variation from now-extinct lineages (such as some humans having Neanderthal DNA)
- What we now consider red wolf genetic variation is very narrow, what we consider red wolf genetics comes from a population that once consisted of only 14 individuals, so there is likely a lot of variation that has been lost that we now have no way of measuring.
- This variation may now persist within the ghost wolf population of Galveston, as there is evidence of historic gene flow between red wolves and the ghost wolves
- Future directions of this work include:
- Connecting the genetic variation of ghost wolves with behavioral, movement, morphometric, and ecological data
- Whole genome sequencing of pre-extinction and present-day canids
- Disentangling red wolf and coyote ancestry (what is a species?)
- Constructing a red wolf pangenome using a core genome to determine what is the same/different among canids to fully characterize the genetic variation of red wolves
- quantify pre-extinction and current-day red wolf genetic diversity