Periodic Reporting for period 1 - MethylRIDE (MethylRIDE: Charting DNA methylation reprogramming of Ice Age horses in the face of global climate change and extinction)
Periodo di rendicontazione: 2021-01-01 al 2022-12-31
The DNA libraries of 73 specimens were subjected to shotgun sequencing, while the remaining were subjected to DNA capture, together with 25 additional ones that provided experimental controls and validation. Direct processing of the underlying sequencing data through DamMet, as originally planned, failed detecting hyper-methylated regions, which required new statistical methodologies (Liu et al. 2023). Preliminary data analyses did not reveal the presence of genomic regions showing differential DNA methylation levels, neither between ancient and modern horses, or various categorizations of ancient American horses (e.g. temporal and geographic binning). This may indicate limited statistical power in our analyses, potentially due to the limited set of genomic regions targeted.
Due to the cross-cultural emphasis of MethylRIDE and our attempt to develop a truly collaborative project with our Indigenous partners, the communication, dissemination and reporting schedule has required adjustment. YC serves as a co-author for the following papers: Early dispersal of domestic horses into the Great Plains and Northern Rockies (published and providing the basis for the cover page of Science on March 31, 2023), and DNA methylation-based profiling of archaeological horse remains for age-at-death and castration (published in iScience on February 1, 2023).
Much has been gained from this revolutionary cross-cultural collaboration, including a global call for integrating Indigenous knowledge and sciences as a response to the ongoing climate shift. The MSCA support in this initiative was truly essential and the additional articles are aimed at sharing our successful collaborative experience to empower similar research initiatives and help others to be able to successfully navigate both scientific systems and reach authentic collaboration.
MethylRIDE was also able to create an opportunity that could potentially revolutionize the future of the field of ancient genomics. Applying Lakota scientific protocols regarding the extraction and screening of ancient DNA helped isolate high-quality DNA. This is worth further exploration, as it may extend the sensitivity of the techniques currently available. Finally, the project results can be potentially useful to those interested in conservation efforts, scientific collaboration, wild horse management, ecology, sustainability and rewilding efforts, as well as preservation of Indigenous culture as it relates to particular keystone species.