Periodic Reporting for period 1 - GENDANGERED (Measuring GENomic diversity change over time in avian enDANGERED species)
Reporting period: 2020-06-01 to 2022-05-31
The loss of global biodiversity is pushing many species to the brink of extinction. Biodiversity supports all the life processes on Earth, including the healthy ecosystems that we rely on, thus, safeguarding biodiversity is essential for all life forms, including humans. Biodiversity loss starts at the population level when populations of wild species reduce in size, often in direct response to anthropogenic pressures. When populations decline, they lose the genetic diversity needed for the long-term survival and future adaptation of the species. The main objective of GENDANGERED was to elucidate how genetic diversity is lost in response to population decline in several species of endangered birds using a combination of simulation and empirical genomic data. The project focused on two main actions: (1) Obtain empirical estimates of genomic diversity change over time by sequencing whole genomes of historical (museum-preserved, 100+ year old) and contemporary (< 10 years old) samples; (2) developing a modelling framework to perform forward-in-time simulations to capture how genomic diversity changes over time in response to habitat degradation and population decline and make predictions into future conditions.
A total of 12 species were enrolled for the project, eight species with different levels of endangered status, and four non-endangered species as control. Over 350 historical samples were obtained from 14 different natural history collections. Over 480 contemporary samples were obtained from collaborators that run important monitoring programs for these species and from natural history collections. Fresh, high-quality samples were also obtained to develop de novo reference genomes in collaboration with The Bird 10,000 Genomes (B10K) Project and The Vertebrate Genomes Project (VGP). In GENDANGERED, I show how the response of genetic diversity to population decline depends on the past demography of the species, their level of connectivity and the amount of conservation management they were subject to. I show the importance of uncovering genetic diversity loss beyond a genome-wide perspective, particularly the signature left in harmful mutations that compromise the long-term viability of the species. I capture these genetic signatures in a robust modelling framework capable of making predictions of responses to future environmental conditions and conservation actions.
The results from GENDANGERED go well beyond the current state of the art by generating an unprecedent amount of historical whole-genome sequences from critically endangered species to unravel the genomic signatures of population collapse. Together with contemporary data and high-quality reference genomes this is one of the largest genomic datasets for endangered species in the world. The development of a modelling approach capable of replicating the empirical results in-silico paves the way to predict trajectories of future genomic change in response to environmental/habitat change and conservation actions. This knowledge will bridge genomic and conservation sciences to improve ongoing biodiversity conservation efforts.