Peter D Heintzman

Stockholm University | SU · Department of Geological Sciences

Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale¹, the oldest genomic...

Ancient genomes provide a tool to investigate the genetic basis of adaptations in extinct organisms. However, the identification of species-specific fixed genetic variants requires the analysis of genomes from multiple individuals. Moreover, the long-term scale of adaptive evolution coupled with the short-term nature of traditional time series data...

Ancient 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 in...

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, disc...

Palaeogenomics has greatly increased our knowledge of past evolutionary and ecological change, but has been restricted to the study of species that preserve either as or within fossils. Here we show the potential of shotgun metagenomics to reveal population genomic information for a taxon that does not preserve in the body fossil record, the algae...

The importance of small wetlands and springs to Mesolithic cultures is well established. However, few studies have focused on their significance and use by Early Neolithic agro-pastoralists. Here we present a multiproxy palaeoenvironmental analysis, including sedaDNA, of the site of Seven Springs, Martlesham, UK, demonstrating that springs provided...

Environmental 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, target...

Environmental DNA is increasingly being used to reconstruct past and present biodiversity including from freshwater ecosystems. 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 di...

Disentangling 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 (sedaDN...

The European Alps are highly rich in species, but their future may be threatened by ongoing changes in human land use and climate. Here, we reconstructed vegetation, temperature, human impact and livestock over the past ~12,000 years from Lake Sulsseewli, based on sedimentary ancient plant and mammal DNA, pollen, spores, chironomids, and microcharc...

Population size has increasingly been taken as the driver of past human environmental impact worldwide, and particularly in the Arctic. However, sedimentary ancient DNA (sedaDNA), pollen and archaeological data show that over the last 12,000 years, paleoeconomy and culture determined human impacts on the terrestrial ecology of Arctic Norway. The la...

What drives ecosystem buildup, diversity, and stability? We assess species arrival and ecosystem changes across 16 millennia by combining regional-scale plant sedimentary ancient DNA from Fennoscandia with near-complete DNA and trait databases. We show that postglacial arrival time varies within and between plant growth forms. Further, arrival time...

Woolly mammoths had a set of adaptations that enabled them to thrive in the Arctic environment. Many mammoth-specific single nucleotide polymorphisms (SNPs) responsible for unique mammoth traits have been previously identified from ancient genomes. However, a multitude of other genetic variants likely contributed to woolly mammoth evolution. In thi...

Locations of sampling sites from sedimentary ancient environmental DNA (aeDNA) studies. aeDNA is DNA that has degraded into short fragments, exhibits post-mortem damage signatures, and is recovered from a non-living tissue, organism, or environmental sample. Here we focus on sedimentary archives with contiguous records such as lake and marine sedim...

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics,...

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics,...

Ancient DNA (aDNA) has played a major role in our understanding of the past. Important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understanding of processes such as past demography, introgression, domestication, adaptation and speciation. However, to date and with the notable exception of micro...

Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identif...

The effects of climate change on species richness are debated but can be informed by the past. Here, we generated a sedimentary ancient DNA dataset covering 10 lakes and applied novel methods for data harmonization. We assessed the impact of Holocene climate changes and nutrients on terrestrial plant richness in northern Fennoscandia. We find that...

The Bering Land Bridge (BLB) last connected Eurasia and North America during the Late Pleistocene. Although the BLB would have enabled transfers of terrestrial biota in both directions, it also acted as an ecological filter whose permeability varied considerably over time. Here we explore the possible impacts of this ecological corridor on genetic...

Since the seminal paper in 1998 (Coolen and Overmann), sedimentary ancient DNA (sedaDNA) has become a powerful tool in paleoecology to reconstruct past changes in terrestrial and aquatic biodiversity. Still, sedaDNA is an emerging tool and there is a need for calibrations and validations to ensure the reliability of sedaDNA as a proxy to reconstruc...

About 14,000 years ago, on the cusp of major environmental changes that affected the distribution of animals, vegetation cover and hydrology, humans entered interior Alaska for the first time. A sedimentary ancient DNA (sedaDNA) record from a lake in the Tanana valley, which lies close to several of the oldest dated archaeological sites, documents...

Analysis of ancient environmentalDNA(eDNA) has revolutionized our ability to describe biological communities in space and time, by allowing for parallel sequencing of DNA from all trophic levels. However, because environmental samples contain sparse and fragmented data from multiple individuals, and often contain closely related species, the field...

The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building...

Ancient DNA and RNA are valuable data sources for a wide range of disciplines. Within the field of ancient metagenomics, the number of published genetic datasets has risen dramatically in recent years, and tracking this data for reuse is particularly important for large-scale ecological and evolutionary studies of individual taxa and communities of...

The effects of climate change on species richness is debated but can be informed by the past. Here, we assess the impact of Holocene climate changes and nutrients on terrestrial plant richness across multiple sites from northern Fennoscandia using new sedimentary ancient DNA (sedaDNA) data quality control methods. We find that richness increased st...

Detailed paleoecological evidence from Arctic Alaska’s past megafauna can help reconstruct paleoenvironmental conditions and can illustrate ecological adaptation to varying environments. We examined a rare, largely articulated and almost complete skeleton of a steppe bison (Bison priscus) recently unearthed in Northern Alaska. We used a multi-proxy...

Ancient DNA and RNA are valuable data sources for a wide range of disciplines. Within the field of ancient metagenomics, the number of published genetic datasets has risen dramatically in recent years, and tracking this data for reuse is particularly important for large-scale ecological and evolutionary studies of individual microbial taxa, microbi...

Ancient DNA has significantly improved our understanding of the evolution and population history of extinct megafauna. However, few studies have used complete ancient genomes to examine species responses to climate change prior to extinction. The woolly rhinoceros (Coelodonta antiquitatis) was a cold-adapted megaherbivore widely distributed across...

Palaeogenomics has greatly increased our knowledge of past evolutionary and ecological change, but has been restricted to the study of species that preserve as fossils. Here we show the potential of shotgun metagenomics to reveal population genomic information for a taxon that does not preserve in the body fossil record, the algae Nannochloropsis....

Arctic hotspots, local areas of high biodiversity, are potential key sites for conservation of Arctic biodiversity. However, there is a need for improved understanding of their long-term resilience. The Arctic hotspot of Ringhorndalen has the highest registered diversity of vascular plants in the Svalbard archipelago, including several remarkable a...

The sequencing of ancient DNA has enabled the reconstruction of speciation, migration and admixture events for extinct taxa¹. However, the irreversible post-mortem degradation² of ancient DNA has so far limited its recovery—outside permafrost areas—to specimens that are not older than approximately 0.5 million years (Myr)³. By contrast, tandem mass...

The remains of a Holocene extinct steppe bison, Bison priscus Bojanus 1827, that died 9.5 thousand years ago, were discovered on the Rauchua River (Chukotka, Russia) in 2012. Sample F-3246 yielded ancient DNA and, when compared to other extant and extinct Bison lineages, clustered outside the known bison genetic diversity, suggesting that this biso...

All organisms release their DNA into the environment through processes such as excretion and the senescence of tissues and limbs. This DNA, often referred to as environmental DNA (eDNA) or sedimentary ancient DNA (sedaDNA), can be recovered from both present-day and ancient soils, fecal samples, bodies of water and lake cores, and even air. While e...

This fully updated second edition explores protocols that address the most challenging aspects of experimental work in ancient DNA, such as preparing ancient samples for DNA extraction, the DNA extraction itself, and transforming extracted ancient DNA molecules for sequencing library preparation. The volume also examines the analysis of high-throug...

Were these extinct animals related to horses, donkeys, or zebras, or were they something else entirely? Using ancient DNA, we have finally solved this mystery.

We present a Holocene record of floristic diversity and environmental change for the central Varanger Peninsula, Finnmark, based on ancient DNA extracted from the sediments of a small lake (sedaDNA). The record covers the period c. 10 700 to 3300 cal. a BP and is complemented by pollen data. Measures of species richness, sample evenness, and beta-d...

Ancient DNA (aDNA) sequencing has enabled unprecedented reconstruction of speciation, migration, and admixture events for extinct taxa. Outside the permafrost, however, irreversible aDNA post-mortem degradation has so far limited aDNA recovery within the ~0.5 million years (Ma) time range. Tandem mass spectrometry (MS)-based collagen type I (COL1)...

DNA metabarcoding is an increasingly popular method to characterize and quantify biodiversity in environmental samples. Metabarcoding approaches simultaneously amplify a short, variable genomic region, or “barcode,” from a broad taxonomic group via the polymerase chain reaction (PCR), using universal primers that anneal to flanking conserved region...

Recent genomic analyses have provided substantial evidence for past periods of gene flow from polar bears (Ursus maritimus) into Alaskan brown bears (Ursus arctos), with some analyses suggesting a link between climate change and genomic introgression. However, because it has mainly been possible to sample bears from the present day, the timing, fre...

The extinct ‘New World stilt-legged’, or NWSL, equids constitute a perplexing group of Pleistocene horses endemic to North America. Their slender distal limb bones resemble those of Asiatic asses, such as the Persian onager. Previous palaeogenetic studies, however, have suggested a closer relationship to caballine horses than to Asiatic asses. Here...

Statistics from the phylogenetic inference analyses of nuclear genomes using all four approaches. (A) Read mapping statistics. (B) Relative transversion frequencies for approaches 1–3. (C) Relative private transversion frequencies for approach 4. DNA extraction 1: (Rohland et al., 2010); DNA extraction 2: (Dabney et al., 2013b); library preparation...

Bayesian time tree analysis results, with support and estimated divergence times for major nodes, and the tMRCAs for Haringtonhippus, E. asinus, and E. quagga summarized. All analyses supported topology one in Appendix 2—figure 3. HPD: highest posterior density.

Measurement data for (A) equid third metatarsals, which were used in the morphometrics analysis, and (B) other NWSL equid elements.

A compilation of all 634 putative synapomorphic sites in the mitochondrial genome for Hippidion, Haringtonhippus, and Equus (A), with a comparison to the published MS272 mitochondrial genome sequence at the 140 sites with a base state that matches one of the three genera (B). The horse reference mtDNA has Genbank accession NC_001640.1.

Summary of nuclear genome data from all 17 NWSL equids pooled together and analyzed using approach four. Minimum and maximum NWSL:Equus ratios between relative frequencies are in bold, and are used for the divergence estimates in Figure 1—figure supplement 3. Total and mean values are for the four longest bins only (90–99 to 120–129 bp). Mean value...

Metadata for all samples used in the mitochondrial and nuclear genomic analyses, with the francisci holotype included for reference. *mtDNA coverage is based on the iterative assembler or as previously published. **New mtDNA genome sequence, coverage, and radiocarbon data are reported for MS272.

Data from the sex determination analyses of 17 NWSL equids, based on alignment to the horse genome (EquCab2).

Genetics of the passenger pigeon The now-extinct passenger pigeon used to be one of the most numerous vertebrates on Earth. Murray et al. examined the genomes of four passenger pigeon samples from different locales within its range. They describe the interplay between passenger pigeon population size, genome structure and recombination, and natural...

Discovery of the skull of Stephanorhinus kirchbergensis (Jäger, 1839) above the Arctic Circle – CORRIGENDUM - Irina V. Kirillova, Olga F. Chernova, Jan van der Made, Vladimir V. Kukarskih, Beth Shapiro, Johannes van der Plicht, Fedor K. Shidlovskiy, Peter D. Heintzman, Thijs van Kolfschoten, Oksana G. Zanina

The skull of the extinct rhinoceros Stephanorhinus kirchbergensis (Jäger, 1839) was discovered in the Chondon River valley (Arctic Yakutia, Russia) during the summer of 2014. This is the first find of Stephanorhinus above the Arctic Circle, expanding significantly the known geographic range of the genus. ¹⁴ C dating and geologic evidence indicate t...

A partial skeleton of a bison was recovered during residential house construction in Whitehorse, Yukon, Canada. The specimen represents a young (estimated 6 year old) bison individual that died, was partially scavenged by carnivores, and subsequently buried by calcareous silt sediment in a pond or small lake during the middle Holocene, ~5400 years...

Recent genomic analyses have provided substantial evidence for past periods of gene flow from polar bears ( Ursus maritimus ) into Alaskan brown bears ( Ursus arctos ), with some analyses suggesting a link between climate change and genomic introgression. However, because it has only been possible to sample bears from the present day, the timing, f...

The extinct “New World stilt-legged”, or NWSL, equids constitute a perplexing group of Pleistocene horses endemic to North America. Their slender distal limb bones resemble those of Asiatic asses, such as the Persian onager. Previous palaeogenetic studies, however, have suggested a closer relationship to caballine horses than to Asiatic asses. Here...

The extinct passenger pigeon was once the most abundant bird in North America, and possibly the world. While theory predicts that large populations will be more genetically diverse and respond more efficiently to selection, passenger pigeon genetic diversity was surprisingly low. To investigate this we analysed 41 mitochondrial and 4 nuclear genome...

Aim The Bering Land Bridge ( BLB ) connected Asia and North America during glacial periods, supported a diverse ecosystem of now‐vanished megafauna, and is a proposed glacial refugium. This study tests whether southern coastal Beringia was a refugium for woody taxa during the Last Glacial Maximum ( LGM ) and hypotheses about habitats available on t...

Significance The appearance of bison in North America is both ecologically and paleontologically significant. We analyzed mitochondrial DNA from the oldest known North American bison fossils to reveal that bison were present in northern North America by 195–135 thousand y ago, having entered from Asia via the Bering Land Bridge. After their arrival...

Retracing complex population processes that precede extreme bottlenecks may be impossible using data from living individuals. The wisent (Bison bonasus), Europe's largest terrestrial mammal, exemplifies such a population history, having gone extinct in the wild but subsequently restored by captive breeding efforts. Using low coverage genomic data f...

The Megin Mammoth specimen represents the first and almost complete skeleton of a mammoth discovered in Eastern Siberia. It was found in 2015 in the Suola River bank (Lena River Basin) deposits, in the vicinity of Nizhniy Bestyakh, Yakutian Republic. The site deposits were accumulated during Sartanian (~29,000 – 14,000 calBP) glacial. Here, we char...

Significance St. Paul Island, Alaska, is famous for its late-surviving population of woolly mammoth. The puzzle of mid-Holocene extinction is solved via multiple independent paleoenvironmental proxies that tightly constrain the timing of extinction to 5,600 ± 100 y ago and strongly point to the effects of sea-level rise and drier climates on freshw...

Retracing complex population processes that precede extreme bottlenecks may be impossible using data from living individuals. The wisent (Bison bonasus), Europetextquoterights largest terrestrial mammal, exemplifies such a population history, having gone extinct in the wild but subsequently restored by captive breeding efforts. Using low coverage g...

The Ice Free Corridor has been invoked as a route for Pleistocene human and animal dispersals between eastern Beringia and more southerly areas of North America. Despite the significance of the corridor, there are limited data for when and how this corridor was used. Hypothetical uses of the corridor include: the first expansion of humans from Beri...

Paleogenomics is the science of reconstructing and analyzing the genomes of organisms that are not alive in the present day. Paleogenomic analyses can provide insights as to when and by what means traits evolved, and how extinct organisms are related to living species and populations. Paleogenomics is a relatively new field that has been made possi...