Welcome
About me
Credit: Magnus Bergström.
I am a Wallenberg Academy Fellow at Stockholm University, 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.
News
2023/12/19
Three chapters published in a new comprehensive book on sedimentary ancient DNA!
Published today in Tracking Environmental Change Using Lake Sediments, Developments in Paleoenvironmental Research 21 (eds. Capo, E., Barouillet, C. & Smol, J. P.).
Ch. 3: Heintzman, P. D., et al. The sedimentary ancient DNA workflow.
Ch. 8: Revéret, A., et al. Aquatic vegetation DNA from lake sediments.
Ch. 11: Murchie, T. J., et al. Terrestrial Fauna and Hominin DNA from Sedimentary Archives.
2023/10/06
The Potential of Deep-Time (sedimentary) Palaeogenomics
Published today in Science!
Abstract: Although 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.
2023/09/24
Recruiting a PhD student (deadline: 2023/11/10)
I am currently recruiting a fully-funded 4-yr PhD position on using ancient DNA from bones and sediments to understand the impacts of human dispersal on faunal biodiversity.
Background: The PhD project is part of the First Contact research program funded by the Knut and Alice Wallenberg Foundation, with the goal of understanding the impacts of human dispersal on faunal biodiversity. The PhD project will use state-of-the-art ancient DNA techniques from both bones and sediments to reconstruct the evolutionary and ecological histories of animal communities across time intervals that include the first arrival of humans in multiple regions. You can read more about the project here.
You can apply here.
2023/05/02
and 2023/08/01
and 2023/08/01
Two new PhD students start in the Heintzman Group
Welcome to Flore Wijnands and Stephanie Dolenz, who are starting their PhD projects on deep-time ancient DNA from terrestrial and marine sedimentary systems!
2022/12/15
Recruiting two PhD students (deadline: 2023/01/15)
I am currently recruiting two fully-funded 4-yr PhD positions on deep-time ancient DNA from terrestrial and marine sedimentary systems.
Background: The PhD projects are part of the DeepTime sedimentary ancient DNA (sedaDNA) research program funded by a Knut and Alice Wallenberg Foundation Academy Fellowship, with the goal of investigating biodiversity turnovers at glacial-interglacial transitions throughout the last 800,000 years. You can read more about the projects here.
Terrestrial ecosystems PhD project: The project will aim to reconstruct plant and animal communities of terrestrial ecosystems from permafrost of northwestern North America, using state-of-the-art sedaDNA techniques. The project will initially focus on Late Pleistocene sediments with the goal of targeting sediments up to 800,000 years old. The project will take advantage of samples already in storage at CPG, with additional fieldwork planned in 2023 and 2024.
Marine ecosystems PhD project: The project aims to reconstruct planktonic and benthic communities of marine ecosystems from the Arctic Ocean, using state-of-the-art sedaDNA techniques. The project will initially focus on recent sediments to provide bench-marking data with the goal of targeting sediments up to half a million years old. The project will take advantage of an extensive archive of marine sediment cores housed at the Department of Geological Sciences, with the possibility of additional fieldwork in 2024.
2022/11/24
Funding awarded from the BNP Parabis Foundation!
For the research project: FLO-CHAR - Fluxes from Land to Ocean: How Coastal Habitats in the Arctic Respond
PI: Bennet Juhls, with myself as a Work Package leader (€702,990).
2022/10/14
Funding awarded from the Knut and Alice Wallenberg Foundation!
For the research program: First Contact - a multidisciplinary assessment of the impact of human arrival on faunal biodiversity
PI: Anders Götherström, with myself, Maja Krzewińska, and Love Dalén as co-Is (26,700,000 SEK).
See the Stockholm University announcement here.
2022/10/05
Pete joins the Department of Geological Sciences and Centre for Palaeogenetics at Stockholm University
2022/07/06
Pete will be joining the Department of Geological Sciences and Centre for Palaeogenetics at Stockholm University as a Wallenberg Academy Fellow in October!
Two PhD positions will be announced after the summer.
See the Knut and Alice Wallenberg Foundation announcement here.
2021/12/03
New Exhibition opened at The Arctic University Museum of Norway on: "A mammoth discovery of the world’s oldest DNA"
Open from 3rd Dec. 2021 to 31 May 2022.
2021/08/25
How can we merging information from tissue-based palaeogenomes and sedimentary ancient DNA?
We describe potential approaches for integrating palaeogenomics information from multiple taxonomic groups with ecosystem state information derived from sedimentary ancient DNA.
2021/08/24
Rhinoceros family tree resolved
We used genomes from all five living and three extinct ice age rhinos to resolve rhinoceros phylogeny and understand each of their population histories.
The Siberian unicorn, with a pair of Merck's rhinoceros in the background and a woolly rhinoceros in the distance.
Credit: Beth Zaiken.
2021/07/30
It took millennia for plant diversity to reach current levels in northern Scandinavia after the last ice age
We report a new regional-scale sedimentary ancient DNA data set from 10 lake cores that span the past 11,700 years.
Collecting a surface core from Lake Nesservatnet (Northern Norway)
Credit: Inger Alsos.
2021/05/18
Beringian horse genomes reveal their cross-continental connnections
We report new nuclear and mitochondrial palaeogenomes that reveal the movements and mixing of horses between the northern continents over the past million years.
Credit: Julius Csotonyi.
2021/04/19
Sedimentary ancient DNA moves into genome-wide population genomics
We report nuclear genome-wide data from black and short-faced bears recovered directly from cave sediment... and three whole genomes of the extinct short-faced bear (Arctodus simus)!
2021/02/17
Million-year barrier broken!
We report the oldest ancient DNA from a 1.2 million-year-old Siberian mammoth.
We report the oldest ancient DNA from a 1.2 million-year-old Siberian mammoth.
Read a popular summary of this work by Patrícia Pečnerová here.
Million-year-old Steppe mammoths roaming the Siberian tundra.
Credit: Beth Zaiken/Centre for Palaeogenetics.
2021/02/16
Reconstructing population genomic variation directly from lake sediment!
New paper out in Communications Biology
Read a popular summary of this work by Youri Lammers here.
2021/02/15
New review paper on the state of the art of ancient DNA from lake sediments
2021/01/26
New metadata resource for ancient metagenomic data sets
2020/11/30
Recruiting a PhD fellow (deadline: 2020/12/20, extended to 2021/01/04)
I am currently recruiting a 4-yr PhD fellow to develop sedimentary ancient DNA bioinformatic methods.
Background: Ancient DNA extracted from sediments and other environmental sources is an emerging and fast-moving field that has the potential to revolutionize our ability to reconstruct past communities at unprecedented temporal resolution. However, computational methods for processing, identifying, and analyzing total ancient DNA from sediments are still rudimentary. The goal of the position is to therefore develop novel bioinformatic methods for the optimal processing of metagenomic sequence data generated from complex and degraded biological remains. The project will use a combination of published and recently generated data sets from lake, cave, permafrost, and archaeological sites across the Pleistocene and Holocene of Europe, Asia, and North America, as well as simulated data sets to test and verify the developed methods. You will gain expertise in bioinformatics, metagenomics, ancient DNA/palaeogenomics, molecular biology, palaeoecology, and analysis of large genomic data sets.
2020/10/14
The episode of the BBC Radio 4 programme "Costing the Earth" that I was featured in last year (see below) won the "Under the Microscope" award for the entry that provides most insight into the process and personalities of science, by the Association of British Science Writers (ABSW).
2020/10/12
The life and death of Bison Bob
2020/08/13
Woolly rhino genome sequenced
The baby woolly rhino, Sasha, recovered from Siberian permafrost.
Credit: Albert Protopopov.
2020/03/09
A new sedimentary ancient DNA record from Svalbard
2019/12/03
Interview with Science Magazine
Today I talked about the perils and pitfalls of recovering sedimentary ancient DNA, especially from lake sediments, with Paul Voosen.
Update: 2019/12/10: Quotes from this interview are now published in Science: DNA recovered from Arctic lakes holds clues for our future world.
2019/10/01
Now an Associate Professor
I have now started a new position at the Tromsø University Museum as an Associate Professor, focusing on ancient DNA, paleontology, and sediments.
Watch this space for future hiring announcements!
2019/09/11
A new source of ancient proteins: tooth enamel!
To fully appreciate past biodiversity, we need to know how extinct species are related to those that are still alive. Was the woolly mammoth more closely related to the African or Asian elephant, for example?
There are several way we can do this. We can examine how they looked, but this approach is often misleading. Alternatively, we can look at their DNA or protein signatures, which give us a much clearer idea. DNA gives us the clearest answer, but it only preserves for up to 1 million years in the best circumstances. This means we cannot use it for older extinct species. Proteins preserve longer - up to 4-5 million years - but do not give as clear an answer as DNA (which showed that mammoths are more closely related to Asian elephants).
In our new paper, we use a new source of proteins - the hard, outer part of teeth called enamel - which gives a much clearer answer than the proteins that had been used previously.
We use this to confirm that the extinct rhinoceros Stephanorhinus, which used to roam Europe and Asia, was more closely related to the extinct woolly rhinoceros than to any of the five living rhinoceros species.
As a bonus, teeth are one of the most abundant types of fossil and many extinct species are only known from teeth. This new approach provides the means to robustly place them in the tree of life.
Artistic reconstruction of Stephanorhinus in its natural environment.
Credit: Mauricio Anton.
2019/09/05
Interview with the BBC
Today I discussed ancient environmental DNA with Jheni Osman and Anne-Marie Bullock, which appeared on the 8th episode of the BBC Radio 4 programme "Costing the Earth", called "The e-DNA Revolution" (aired on Oct. 1, 15.30 BST and Oct. 2, 21.00 BST)
