Investigating mammalian evolution using million-year genomic transects

Project Information

PrimiGenomes

Grant agreement ID: 101054984

DOI

10.3030/101054984

EC signature date 21 October 2022

Start date 1 January 2023

End date 31 December 2027

Funded under

• European Research Council (ERC)

Total cost

€ 2 500 000,00

EU contribution

€ 2 500 000,00

Coordinated by

STOCKHOLMS UNIVERSITET
Sweden

Periodic Reporting for period 1 - PrimiGenomes (Investigating mammalian evolution using million-year genomic transects)

Reporting period: 2023-01-01 to 2025-06-30

Summary of the context and overall objectives of the project

In recent years, ancient DNA has emerged as a highly useful tool to understand prehistory. The application of genomic methods on ancient remains has resulted several significant discoveries in evolutionary biology, archaeology and palaeontology. These findings have led to a better understanding the impact of climate change on biodiversity at the end of the last Ice Age, the discovery of gene flow from Neanderthals to modern humans, and revisions of the relationship between extinct and extant taxa. In the PrimiGenomes project, we aim to address an important gap in our knowledge on such evolutionary genomic changes, through studies over longer temporal scales than previously done. We do this by extending ancient DNA recovery and analysis beyond the current focus on the last 50,000 years to one million years and beyond. To accomplish this, we are sequencing a large number of genomes from the Early to Middle Pleistocene to trace macroevolutionary processes through genomic deep-time. More specifically, the project seeks to investigate fundamental questions about speciation rates, the role of genetic introgression, lineage-specific adaptations, and the impacts of environmental change on mammalian demography and evolution. The research will have a broad focus, aiming to study the evolution of both small and large mammals, and will target samples collected across Eurasia as well as northernmost North America. Furthermore, the project will develop and utilize cutting-edge laboratory and computational methods specialized for the field of palaeogenomics. We expect the PrimiGenomes project to result in a paradigm shift in palaeogenomics by offering detailed insights into long-term species evolution during key climatic transitions, deepening our understanding of the forces that shape biodiversity. The project anticipates several outputs, including open-access genomic datasets and high-impact publications, and aims to promote cross-disciplinary collaboration as well as fostering a new generation of early-career researchers in the field of palaeogenomics.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Over the last two years, field expeditions and museum collections have been crucial in gathering Pleistocene remains for ancient DNA analysis. Field work northern Yukon, Atapuerca in Spain, and northern Greenland yielded significant finds, ranging from small mammals to megafauna, with ages spanning thousands to over a million years. These efforts have substantially expanded our collection for research.

All members of the PrimiGenomes research team have been hired, and research is progressing as planned. On the theoretical side, we have refined the framework for deep-time genomics and proposed key hypotheses on evolutionary genomic changes during Pleistocene environmental shifts. Published contributions include a foundational review in Science, and an assessment of mammoth evolution across the last two million years. Additional work, currently under review, explores genetic variation, biodiversity, climate impacts, as well as speciation in cold-adapted species.

We have also developed novel methodologies. A bioinformatics pipeline supports ultrashort DNA fragment recovery and addresses reference bias issues, with initial results published. We have also created a high-throughput DNA extraction method for ancient samples and have refined a computational approach to estimate specimen ages beyond radiocarbon dating limits, and both these studies are set to be published in early 2025. These advancements provide a foundation for future deep-time genomic studies.

Large-scale data-driven projects on Pleistocene mammalian evolution are ongoing. In our work on woolly mammoths, we have published two studies on genetic variation and genome structure in the journal Cell. We are also completing a paper on adaptive evolution over the last million years. Three additional papers in review detail a high-quality woolly mammoth genome assembly, ancient RNA recovery, and microbial analyses from approximately 500 mammoth samples spanning over a million years.

Beyond mammoths, we are writing up a 350,000-year genomic analysis of collared lemmings, redefining their speciation timeline. A study on cave lion evolution, submitted for publication, identifies it as a distinct species with limited hybridization with modern lions. Research on water vole evolution, based on 500 samples with morphometric data, is underway. We have also collected samples of extinct stag moose and helmeted muskox that will provide the foundation for additional research projects.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

One key achievement has been uncovering issues in some of the sequence read alignment tools widely used in the field of ancient DNA, including reference bias and spurious mapping of ultrashort DNA fragments. In response, we have developed a computational approach to identify and address these biases, improving data analysis accuracy. This work provides a framework for refining ancient DNA methodologies across the field. The computational advances have culminated in a beta version of a bioinformatics pipeline, now in internal testing. A cornerstone of the pipeline has already been published, and includes an effective approach for evaluating biases and spurious mapping in ultrashort fragments. Additional features under development include a refined approach to estimate the ages of Middle and Early Pleistocene samples by identifying missing mutations in mitochondrial genomes. Support from the ERC grant and the National Bioinformatics Infrastructure Sweden, with expert bioinformaticians, has been invaluable in building this pipeline.

We have also created an in-house ancient DNA extraction method using 96-well silica plates, enabling the simultaneous processing of large sample numbers. This method rapidly identifies specimens with sufficient DNA preservation for down-stream genome sequencing.

Two breakthroughs have emerged from pilot projects where we have uncovered previously undescribed aspects of the woolly mammoth genome. This has resulted in two manuscripts that currently are under review. We expect that these discoveries will yield a better understanding of biomolecular preservation in permafrost remains, enable us to assess which genes are important in different tissue typers, and help reducing biases in aligning deep-time DNA sequences during upcoming studies.