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 2: AM Talks
Hernán Morales, Temporal genomics, extinction risk and recovery potential
Hernán works as part of the Evolutionary and Conservation Genomics Group at the Globe Institute of the University of Copenhagen. His work involves sequencing genomes from historic and contemporary species (mainly birds) to determine the genetic costs of severe population declines.
- Some species, such as the paradise flycatcher, have lost up to 98% of their
genetic diversity. Runs of homozygosity (ROH) within the genome are useful metrics to determine the genetic load of population declines, as ROHs build up with genetic diversity declines but are broken up by recombination when a population recovers (unless there is a lot of inbreeding). Turns out ‘cheating’ in these birds may contribute to reduced ROHs! - Whooping cranes have recovered from severe population decline (and several bottlenecks) but lack really long ROHs in captive populations. However, they have a high realized genetic load, which may impact wild populations in the future.
- Orange-bellied parrots have only 13 breeding males left in the breeding population, and a huge reduction in genetic diversity. This has resulted in the loss of many alleles in the toll-like receptor immune genes, which has left them extremely susceptible to Psittacine beak and feather disease (PBFD), a devastating disease.
- Regent honeyeaters have gone extinct through most of their native range, but have only lost a moderate amount of genetic diversity, and do not have high inbreeding as measured by ROHs. This may sound like good news, but habitat niche models predict an even more severe loss of habitat in the future. Simulations suggest that the honeyeater is experiencing a time lag in genetic diversity loss, which will drastically accelerate and likely reach close to 100% in the next 100 years.
- Large ancestral populations have a higher extinction risk once they encounter a genetic bottleneck due to a higher genetic load because small populations have lower variance in fitness effects due to their already reduced genetic diversity. However, this same reduction in diversity means they lack the standing genetic variation to adapt to environmental changes.
- However, the last surviving population of Wooly Mammoths on Wrangler Island encountered these same genetic challenges and persisted for an additional 4,000 years before extinction, so the ‘real’ likelihood of extinction remains unclear (caveat: the Wooly mammoths had much less severe environmental change compared to these contemporary populations!)
Carlos Garza, Novel approaches to anadromous fish conservation informed by genomic methods
Carlos works at both the Southwest Fisheries Science Center and UC Santa Cruz. His work investigates genetic diversity in salmonids.
- Variation in salmonid species comes down largely to ecotypes, such as whether or not they spend part of their life cycle in the ocean or the time they return to natal rivers to spawn.
- Whether or not a salmonid migrates to the ocean for a few years prior to returning for spawning has a huge phenotypic effect on size.
- The time of year a Chinook salmon returns to spawn is largely explained by variance in a single region of the genome containing the genes GREB1L and ROCK1.
- Recent dam removals on the Klamath River have allowed for salmon to reach habitat they were once extirpated from and leads to an opportunity to reintroduce this iconic species (we will see how this works out!)
- Chinook from the Central Valley of California have an additional run time as well as a duplicated genomic region. Whether or not an individual has a duplication has an additive effect on the GREB1L/ROCK1 region of +/- 15 or so days
- Coho salmon are close to extirpation in some of their range. Hatchery salmon were HIGHLY related to one another and under extreme inbreeding. Outcrossing of salmon from other streams helped reduce this and bolstered reintroduction efforts.
Caren Helbing, Revolutionizing conservation efforts by seeing the unseen with environmental DNA
Caren is part of the iTrackDNA team at the Universtiy of Victoria. Her work largely uses environmental DNA to observe biodiversity that may be cryptic/rare or hard to observe via traditional methods. eDNA is genetic material sloughed off organisms into their environments (water, soil, air, etc) and allows us to infer the presence/absence of taxa.
- There are different methods of detecting eDNA, including metabarcoding based on regions with high differentiation between target species or amplifying targeted DNA from a single species to confirm presence/absence.
- eDNA sampling as especially great for testing for multiple taxa per sample and is less invansive to both taxa of interest and their ecosystems.
- eDNA has been used to confirm traditional ecological knowledge of species (Arctic Grayling) presence and implemented into management decisions.
- Another example is in recording the distribution of the Tailed Frog in British Columbia in much fewer sites over much smaller timescales and with a much higher detection rate. This information expanded the recorded distribution of the species!
- The Sharp-Tailed snake is a tiny (pencil-sized) organism that traditionally relied on placing an artificial cover object in a site and then returning to physically record the presence of the snakes. eDNA from swabs of the covers allowed for much higher detection of the species.
- eDNA can also be used in surveys for indicator (such as the presence of polychaetes associated with water pollution) or invasive (such as zebra/quagga mussels) organisms. Early identification allows for faster mitigation and better conservation outcomes overall.
- Non-aquatic uses of eDNA include determining the presence of a species from historical sediment samples and again confirming Indigenous knowledge of the historic presence of a species that is now extinct in that habitat.
- eDNA is also useful in confirming the efficacy of phytosanitation efforts to prevent the spread of an invasive nematode from North American wood products.
- However, there are still knowledge gaps in both assay/study design and genomic resources. The iTrackDNA project seeks to address these to increase the utility of eDNA methods in conservation and other management efforts! This includes the generations of assay kits and analytical methods to promote robust experimental design and standardization of eDNA methods.