Periodic Reporting for period 1 - MUSEOMIC (Establishing museomics as a tool to inform the conservation of endangered species)
Periodo di rendicontazione: 2023-09-01 al 2025-08-31
Global biodiversity is being decimated by human activities, including agriculture, deforestation and land use change. This is causing unprecedented population declines and pushing species to extinction, especially in tropical ecosystems. Genetic health is an important measure of population viability, and to help identify populations at risk, this is now
being included in conservation programs however, incorporating this level of information on genetic diversity can be challenging. Additionally, because standing levels of variation differ between species this makes assessing whether a population has “low” or “high” genetic diversity can be very difficult.
In response, MUSEOMIC, will harness new ancient genetic and museomics techniques (sequencing of museum specimens), to measure changes in genetic diversity in three extremely vulnerable mammals (anoa, babirusa and Sulawesi warty pig) in the biodiversity hotspot of Wallacea. As an isolated tropical archipelago in Indonesia, Wallacea is the perfect natural laboratory for understanding how ancient and anthropogenic disturbances have impacted the genetic erosion of the three flagship mammals and is contributing to their decline.
By tracking changes in genetic health through time and space, MUSEOMIC will gain insights into the extinction risk these unique taxa face and will directly benefit population management and long-term survival by identifying unique genetic diversity, designating conservation units, and making captive breeding recommendations. The main scientific objectives of MUSEOMIC are to:
Attribute genomic erosion to either ancient processes or recent human impacts.
Measure intraspecific population differentiation and define units for conservation.
Assess the genetic health of captive populations of anoa and babirusa to guide future management strategies
being included in conservation programs however, incorporating this level of information on genetic diversity can be challenging. Additionally, because standing levels of variation differ between species this makes assessing whether a population has “low” or “high” genetic diversity can be very difficult.
In response, MUSEOMIC, will harness new ancient genetic and museomics techniques (sequencing of museum specimens), to measure changes in genetic diversity in three extremely vulnerable mammals (anoa, babirusa and Sulawesi warty pig) in the biodiversity hotspot of Wallacea. As an isolated tropical archipelago in Indonesia, Wallacea is the perfect natural laboratory for understanding how ancient and anthropogenic disturbances have impacted the genetic erosion of the three flagship mammals and is contributing to their decline.
By tracking changes in genetic health through time and space, MUSEOMIC will gain insights into the extinction risk these unique taxa face and will directly benefit population management and long-term survival by identifying unique genetic diversity, designating conservation units, and making captive breeding recommendations. The main scientific objectives of MUSEOMIC are to:
Attribute genomic erosion to either ancient processes or recent human impacts.
Measure intraspecific population differentiation and define units for conservation.
Assess the genetic health of captive populations of anoa and babirusa to guide future management strategies
MUSEOMIC involved the collection of new samples from museum specimens held in European collections. Here, I applied novel minimally invasive techniques, for the museum sampling such as the extraction of the petrous bone through the ear canal of the skull, preserving the morphology intact. All three focal taxa have been sequenced using museomic methods, at around 4X coverage, which provides an important high-resolution historical genetic resource for these taxa. Modern anoa and babirusa genomes have also been resequenced to evaluate population structure, inbreeding levels, and mutation load. Spatial models were developed to analyse habitat suitability based on forest cover and bioclimatic data, with future projection analyses under different scenarios of climate and forest cover change currently underway. Additionally, captive Indonesian populations of anoa and babirusa to understand how the genetic diversity held in zoos, would contribute to the direct insitu conservation of babirusa and anoa as “insurance” populations. Ultimately these data will support management strategies aimed at maintaining genetic diversity and long-term population viability.
- The MUSEOMIC project has advanced the application of museomics and ancient DNA techniques in conservation biology. This project has demonstrated that DNA extracted from the petrous bone, yields superior preservation compared to other skeletal remains, irrespective of the sample's age. This finding is crucial for conservation practitioners and NGOs who might find skulls in the field of various/unknown ages. Our results would advocate the taking of the petrous bone as the genome can still be reliable recovered.
- Furthermore, the results of MUSEOMIC have revealed that populations of endangered mammals on smaller, less disturbed islands in Wallacea exhibit lower levels of harmful genetic mutations compared to those on larger islands like Sulawesi. Despite having reduced genetic diversity, these small-island populations benefit from natural selection's purging effect, offering valuable insights for conservation strategies. The results here support the long term maintenance of high quality forests and habitats for the two forest endemics and the designation of protected areas.
- Additionally, genomic analysis of free-roaming pigs in Island Southeast Asia including Sus celebensis, applying museomics, uncovered complex demographic histories shaped by multiple waves of human occupation and interactions with native pig populations. This study provides a deeper understanding of human-animal relationships and their genetic impacts over time.
- Furthermore, the results of MUSEOMIC have revealed that populations of endangered mammals on smaller, less disturbed islands in Wallacea exhibit lower levels of harmful genetic mutations compared to those on larger islands like Sulawesi. Despite having reduced genetic diversity, these small-island populations benefit from natural selection's purging effect, offering valuable insights for conservation strategies. The results here support the long term maintenance of high quality forests and habitats for the two forest endemics and the designation of protected areas.
- Additionally, genomic analysis of free-roaming pigs in Island Southeast Asia including Sus celebensis, applying museomics, uncovered complex demographic histories shaped by multiple waves of human occupation and interactions with native pig populations. This study provides a deeper understanding of human-animal relationships and their genetic impacts over time.