Periodic Reporting for period 2 - ApeGenomeDiversity (Great ape genome variation now and then: current diversity and genomic relics of extinct primates)
Reporting period: 2021-12-01 to 2023-05-31
In our quest to fully understand the processes that shape the genomic variation of species, describing variation of the past is a fundamental objective. However, the origins and the extent of great ape variation remain unknown. Even today, and in contraposition to human evolutionary biology, the minimal presence of great ape samples (both from present and the past) has precluded a comprehensive exploration of such diversity.
In this project, we are generating genome sequencing from diferent primates both from present day and from museum collections. The goal is to generate the most complete catalog of variation now and in the past, to then estimate the proportion of lost diversity and infer past events, that only the genome can uncover, such as the presence of lost genome species with whom current species did hybridize.
With so doing, we hope to contribute to evolutionary biology and conservation efforts by providing the current status of genomic health in those species and providing new views and tools that can help to better understand our closest relatives.
In this project, we are generating genome sequencing from diferent primates both from present day and from museum collections. The goal is to generate the most complete catalog of variation now and in the past, to then estimate the proportion of lost diversity and infer past events, that only the genome can uncover, such as the presence of lost genome species with whom current species did hybridize.
With so doing, we hope to contribute to evolutionary biology and conservation efforts by providing the current status of genomic health in those species and providing new views and tools that can help to better understand our closest relatives.
In this first report, and despite of the COVID situation, we have managed to generate genome data for hundreds of samples (mainly non invasive (fecal samples) and museum samples) including all apes (chimpanzees, bonobos, gorilla and orangutans) as well as for other primates.
Specifically:
- The generation of genomic data from non-invasive samples for chimpanzees is finished. the work was analyzed and published last year (2022), Fontsere et al. Cell Genomics 2022 a work that was the cover of the journal.
- For the rest of the apes, we are generating or analyzing the data. I expect that some species will finish in 2023 and other in 2024. We have collected the necesary samples and endogenous estimations and capture experiments are being carried out.
- We also finalized our first approximation to uncover extinct species in the current dataset. We have chosen gorillas as a case study and the paper is currently under review and has been uploaded to Bioarxiv.
- Also, as an expansion of the current project of this ERC grant, we did publish several manuscripts related to primate genomics (a new species genome assembly for a outgroup (Lemurs), Ebola impact on a group of gorillas, among others)
Specifically:
- The generation of genomic data from non-invasive samples for chimpanzees is finished. the work was analyzed and published last year (2022), Fontsere et al. Cell Genomics 2022 a work that was the cover of the journal.
- For the rest of the apes, we are generating or analyzing the data. I expect that some species will finish in 2023 and other in 2024. We have collected the necesary samples and endogenous estimations and capture experiments are being carried out.
- We also finalized our first approximation to uncover extinct species in the current dataset. We have chosen gorillas as a case study and the paper is currently under review and has been uploaded to Bioarxiv.
- Also, as an expansion of the current project of this ERC grant, we did publish several manuscripts related to primate genomics (a new species genome assembly for a outgroup (Lemurs), Ebola impact on a group of gorillas, among others)
The current orientation of the grant is well positioned to achieve the goals of the project within the time planned. However, and given the opportunity, we are also expanding the species of primates to be studied beyond the great apes. I hope that during the duration of the grant, we should be able to provide a better genomic characterization of global diversity in all primates with repercussion to human variation and disease.