Peter HeintzmanWallenberg Academy Fellow, Paleogenetics
About me
I am a Wallenberg Academy Fellow at the Department of Geological Sciences and the Centre for Palaeogenetics, where I use ancient DNA to understand the natural world over the past one million years.
I am particularly interested in molecular and computational approaches, and how best to leverage these to understand the ecology and evolutionary history of past species and populations of animals and plants.
My recent research focuses on using ancient DNA directly from environmental sources (soils, mud, etc) to reconstruct past ecological communities and their responses to past drivers of change.
I am also interested in general ancient DNA methods development and understanding past (mega)fauna based on tissue-derived paleogenomic information.
Teaching
BL7069: BSc course in Evolutionary Biology (15 ECTS), 1 lecture
BL7052: MSc course in Palaeogenetics (15 ECTS), 6 lectures
GG7023: MSc course in Palaeontology (7.5 ECTS), 2 lectures
Publications
A selection from Stockholm University publication database
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Deep-time paleogenomics and the limits of DNA survival
2023. Love Dalén (et al.). Science 382 (6666), 48-53
ArticleRead more about Deep-time paleogenomics and the limits of DNA survivalAlthough most ancient DNA studies have focused on the last 50,000 years, paleogenomic approaches can now reach into the early Pleistocene, an epoch of repeated environmental changes that shaped present-day biodiversity. Emerging deep-time genomic transects, including from DNA preserved in sediments, will enable inference of adaptive evolution, discovery of unrecognized species, and exploration of how glaciations, volcanism, and paleomagnetic reversals shaped demography and community composition. In this Review, we explore the state-of-the-art in paleogenomics and discuss key challenges, including technical limitations, evolutionary divergence and associated biases, and the need for more precise dating of remains and sediments. We conclude that with improvements in laboratory and computational methods, the emerging field of deep-time paleogenomics will expand the range of questions addressable using ancient DNA.
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Strengthening global-change science by integrating aeDNA with paleoecoinformatics
2023. John W. Williams (et al.). Trends in Ecology & Evolution 38 (10), 946-960
ArticleRead more about Strengthening global-change science by integrating aeDNA with paleoecoinformaticsAncient environmental DNA (aeDNA) data are close to enabling insights into past global-scale biodiversity dynamics at unprecedented taxonomic extent and resolution. However, achieving this potential requires solutions that bridge bioinformatics and paleoecoinformatics. Essential needs include support for dynamic taxonomic inferences, dynamic age inferences, and precise stratigraphic depth. Moreover, aeDNA data are complex and heterogeneous, generated by dispersed researcher networks, with methods advancing rapidly. Hence, expert community governance and curation are essential to building high-value data resources. Immediate recommendations include uploading metabarcoding-based taxonomic inventories into paleoecoinformatic resources, building linkages among open bioinformatic and paleoecoinformatic data resources, harmonizing aeDNA processing workflows, and expanding community data governance. These advances will enable transformative insights into global-scale biodiversity dynamics during large environmental and anthropogenic changes.
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Environmental DNA of aquatic macrophytes: The potential for reconstructing past and present vegetation and environments
2023. Alois Reveret (et al.). Freshwater Biology
ArticleRead more about Environmental DNA of aquatic macrophytesEnvironmental DNA is increasingly being used to reconstruct past and present biodiversity including from freshwater ecosystems. Macrophytes are especially good environmental indicators, thus their environmental DNA palaeorecord might shed light on past postglacial environments. Here, we first review and compare studies that use metagenomics, targeted capture, and various barcoding and metabarcoding markers, in order to explore how each of these methods can be used to capture aquatic vegetation diversity and change. We then investigate the extent to which such a record can be leveraged for reconstructing local environmental conditions, using a case study based on macrophyte ecological niches. We find that, with state-of-the-art DNA barcode reference libraries, using metabarcoding to target the P6 loop region of the chloroplast trnL (UAA) intron is optimal to maximise taxonomic resolution and the diversity of past macrophyte communities. Shotgun sequencing also retrieves a high proportion of aquatic macrophyte diversity, but has the lowest taxonomic resolution, and targeted capture needs to be more widely applied before comparisons can be made. From our case study, we infer past aquatic habitats from sedimentary ancient DNA records of macrophyte taxa. We reconstructed Holocene thermal range, continentality, water pH, trophic status, and light conditions in northern Fennoscandia. We show an overall stability since 9,000 years ago, even though individual lakes display different trends and variation in local climatic and physico-chemical conditions. Combined with the availability of near-exhaustive barcode and traits databases, metabarcoding data can support wider ecological reconstructions that are not limited to aquatic plant taxonomic inventories but can also be used to infer past changes in water conditions and their environmental drivers. Sedimentary DNA is also a powerful tool to measure present diversity, as well as to reconstruct past lacustrine and fluvial communities of aquatic macrophytes.
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Sedimentary Ancient DNA Reveals Local Vegetation Changes Driven by Glacial Activity and Climate
2023. Lucas D. Elliott (et al.). Quaternary 6 (1)
ArticleRead more about Sedimentary Ancient DNA Reveals Local Vegetation Changes Driven by Glacial Activity and ClimateDisentangling the effects of glaciers and climate on vegetation is complicated by the confounding role that climate plays in both systems. We reconstructed changes in vegetation occurring over the Holocene at Jøkelvatnet, a lake located directly downstream from the Langfjordjøkel glacier in northern Norway. We used a sedimentary ancient DNA (sedaDNA) metabarcoding dataset of 38 samples from a lake sediment core spanning 10,400 years using primers targeting the P6 loop of the trnL (UAA) intron. A total of 193 plant taxa were identified revealing a pattern of continually increasing richness over the time period. Vegetation surveys conducted around Jøkelvatnet show a high concordance with the taxa identified through sedaDNA metabarcoding. We identified four distinct vegetation assemblage zones with transitions at ca. 9.7, 8.4 and 4.3 ka with the first and last mirroring climatic shifts recorded by the Langfjordjøkel glacier. Soil disturbance trait values of the vegetation increased with glacial activity, suggesting that the glacier had a direct impact on plants growing in the catchment. Temperature optimum and moisture trait values correlated with both glacial activity and reconstructed climatic variables showing direct and indirect effects of climate change on the vegetation. In contrast to other catchments without an active glacier, the vegetation at Jøkelvatnet has displayed an increased sensitivity to climate change throughout the Middle and Late Holocene. Beyond the direct impact of climate change on arctic and alpine vegetation, our results suggest the ongoing disappearance of glaciers will have an additional effect on plant communities.
Show all publications by Peter Heintzman at Stockholm University