Peter D Heintzman

Peter D Heintzman
UiT The Arctic University of Norway · University Museum

Ph.D.

About

66
Publications
33,010
Reads
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1,701
Citations
Additional affiliations
October 2019 - present
UiT The Arctic University of Norway
Position
  • Professor (Associate)
February 2017 - September 2019
UiT The Arctic University of Norway
Position
  • Senior Researcher
March 2013 - December 2016
University of California, Santa Cruz
Position
  • PostDoc Position
Education
September 2009 - February 2013
Royal Holloway, University of London
Field of study
  • Ancient DNA

Publications

Publications (66)
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
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...
Data
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...
Article
Full-text available
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,...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Conference Paper
Full-text available
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...
Conference Paper
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...
Article
Full-text available
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...
Preprint
Full-text available
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...
Article
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...
Preprint
Full-text available
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...
Article
Full-text available
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...
Preprint
Full-text available
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....
Article
Full-text available
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...
Article
Full-text available
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...
Article
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...
Chapter
Full-text available
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...
Book
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...
Article
Full-text available
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.
Article
Full-text available
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...
Preprint
Full-text available
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)...
Article
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...
Article
Full-text available
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...
Article
Full-text available
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...
Data
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...
Data
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.
Data
Measurement data for (A) equid third metatarsals, which were used in the morphometrics analysis, and (B) other NWSL equid elements.
Data
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.
Data
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...
Data
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
Data from the sex determination analyses of 17 NWSL equids, based on alignment to the horse genome (EquCab2).
Article
The extinct passenger pigeon was once the most abundant bird in North America, and possibly the world. Although theory predicts that large populations will be more genetically diverse, passenger pigeon genetic diversity was surprisingly low. To investigate this disconnect, we analyzed 41 mitochondrial and 4 nuclear genomes from passenger pigeons an...
Article
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
Article
Full-text available
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...
Article
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...
Preprint
Full-text available
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...
Preprint
Full-text available
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...
Preprint
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...
Article
Full-text available
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 the BLB b...
Article
Full-text available
The arrival of bison in North America marks one of the most successful large-mammal dispersals from Asia within the last million years, yet the timing and nature of this event remain poorly determined. Here, we used a combined paleontological and paleogenomic approach to provide a robust timeline for the entry and subsequent evolution of bison with...
Article
Full-text available
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...
Conference Paper
Full-text available
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...
Article
Full-text available
Relict woolly mammoth (Mammuthus primigenius) populations survived on several small Beringian islands for thousands of years after mainland populations went extinct. Here we present multiproxy paleoenvironmental records to investigate the timing, causes, and consequences of mammoth disappearance from St. Paul Island, Alaska. Five independent indica...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
Recent advances in paleogenomic technologies have enabled an increasingly detailed understanding of the evolutionary relationships of now-extinct mammalian taxa. However, a number of enigmatic Quaternary species have never been characterized with molecular data, often because available fossils are rare or are found in environments that are not opti...
Article
Full-text available
Viruses preserved in ancient materials provide snapshots of past viral diversity and a means to trace viral evolution through time. Here, we use a metagenomics approach to identify filterable and nuclease-resistant nucleic acids preserved in 700-y-old caribou feces frozen in a permanent ice patch. We were able to recover and characterize two viruse...
Article
Full-text available
DNA preserved in degraded beetle (Coleoptera) specimens, including those derived from dry-stored museum and ancient permafrost-preserved environments, could provide a valuable resource for researchers interested in species and population histories over timescales from decades to millenia. However, the potential of these samples as genetic resources...
Article
Full-text available
Clovis, with its distinctive biface, blade and osseous technologies, is the oldest widespread archaeological complex defined in North America, dating from 11,100 to 10,700 (14)C years before present (bp) (13,000 to 12,600 calendar years bp). Nearly 50 years of archaeological research point to the Clovis complex as having developed south of the Nort...