Research

First Contact (funded by the Knut & Alice Wallenberg Foundation)

First Contact will generate large-scale multi-species population genomic and sedimentary DNA datasets from several localities across the Northern Hemisphere and combine these with archaeological data and chronometric dating to: (1) Establish a refined chronology of regional human arrival across the Northern Hemisphere. (2) Test the hypothesis that wildlife demography was affected by human arrival and subsequent demographic expansions. (3) Explore the timing, rate, and faunal biodiversity consequences of human-induced landscape modifications. (4) Investigate how the arrival of domesticated animals affected resident wildlife populations. (5) Assess the extent of pathogen transmission from humans and domestics into wildlife populations.

Lauren Clark (PhD), Jamie Alumbaugh (postdoc)

Dan Hammarlund, Anna Linderholm, Carl Régnell, Gabriel Ángel Servera Vives, Sandra Garcés Pastor

Outputs:

• The potential of lacustrine sedimentary ancient DNA for revealing human postglacial recolonisation patterns in northern Sweden.

FLO CHAR (funded by the BNP Paribas Foundation)

FLO CHAR aims to resolve our understanding of climate induced land-ocean matter fluxes, permafrost thaw, and associated impacts on the most rapidly changing ecosystem on Earth, the Arctic coastal environment. FLO CHAR will deliver key datasets on the magnitude and impacts of land-ocean fluxes to coastal waters in the rapidly changing Arctic. By identifying the biogeochemical and physical characteristics of the water column and surface sediments as well as the properties of coastal subsea permafrost, the results will improve our understanding of climate change impact on near-shore and coastal ecosystems, including their biodiversity. Communities in the ISR of northern Canada rely upon traditional food harvesting, including marine mammals, fish, and invertebrates as key sources of nutrition, and to support local economies. FLO CHAR will provide unique knowledge that will contribute to the sustainable management of these important resources. In order to carry out this project, we bring together a diverse team of experienced and early-career scientists from Europe and North America with exceptional working experience in the Arctic.

Inda Brinkmann (postdoc)

Matt O'Regan, Blanda Matzenbacher, Julie Lattaud, Bennet Jules, Paul Overduin The whole team can be found here.

Smaller projects from Iberia and Alaska

Outputs:

• Neolithic pastoralism and plant community interactions at high altitudes of the Pyrenees, southern Europe.

• Steppe-tundra composition and deglacial floristic turnover in interior Alaska revealed by sedimentary ancient DNA (sedaDNA).

Stephanie Dolenz (PhD), Georgios Xenikoudakis (lab tech), Jamie Alumbaugh (postdoc)

Tom van der Valk, Chenyu Jin, Youri Lammers, Jack Williams, SPAAM and sedaDNA cyberinfrastructure communities.

Methods (metagenomic/paleogenomic):

• Improving taxonomic inference from ancient environmental metagenomes by masking microbial-like regions in reference genomes.

• Unravelling reference bias in ancient DNA datasets.

• Environmental Genomics of Late Pleistocene Black Bears and Giant Short-Faced Bears.

• Environmental palaeogenomic reconstruction of an Ice Age algal population.

• The southern coastal Beringian land bridge: cryptic refugium or pseudorefugium for woody plants during the Last Glacial Maximum?

• Timing and causes of mid-Holocene mammoth extinction on St. Paul Island, Alaska.

Methods (metabarcoding):

• Sedimentary ancient DNA shows terrestrial plant richness continuously increased over the Holocene in northern Fennoscandia.

• Targeted Amplification and Sequencing of Ancient Environmental and Sedimentary DNA.

• Minimizing polymerase biases in metabarcoding.

Methods (general):

• A high-throughput ancient DNA extraction method for large-scale sample screening.

• The sedimentary ancient DNA workflow.

• Ancient DNA: Methods and Protocols.

Databases and reviews:

• Strengthening global-change science by integrating aeDNA with paleoecoinformatics.

• Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics.

• Lake sedimentary DNA research on past terrestrial and aquatic biodiversity: Overview and recommendations.

• Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir.

Rose Power (postdoc)

Beth Shapiro, Grant Zazula, Duane Froese, Mat Wooller, Love Dalén, Andre Soares, Alisa Vershinina.

Bison:

• Palaeogenomics reveals a loss of bovine lineages in mid-latitude Asia over the last 200,000 years.

• A detailed life history of a Pleistocene steppe bison (Bison priscus) skeleton unearthed in Arctic Alaska.

• Ancient DNA analysis of a Holocene bison from the Rauchua River, northwestern Chukotka, and the existence of a deeply divergent mitochondrial clade.

• A middle Holocene steppe bison and paleoenvironments from the Versleuce Meadows, Whitehorse, Yukon, Canada.

• Fossil and genomic evidence constrains the timing of bison arrival in North America.

• Complex admixture preceded and followed the extinction of wisent in the wild.

• Bison phylogeography constrains dispersal and viability of the Ice Free Corridor in western Canada.

Horses: 

• Ancient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge.

• A new genus of horse from Pleistocene North America.

Mammoths:

• Ancient RNA expression profiles from the extinct woolly mammoth.

• Genomic and morphological analysis reveals long-term mammoth hybridization in British Columbia, Canada.

• A million years of mammoth mitogenome evolution.

• Temporal dynamics of woolly mammoth genome erosion prior to extinction.

• Genomics of adaptive evolution in the woolly mammoth.

• Evolutionary consequences of genomic deletions and insertions in the woolly mammoth genome.

• Morphology, Individual Age and Sex of the Yuka Mammoth (Mammuthus primigenius) from Northern Yakutia, Russia.

• Million-year-old DNA sheds light on the genomic history of mammoths.

• Timing and causes of mid-Holocene mammoth extinction on St. Paul Island, Alaska.

Camels:

• Genomic data from extinct North American Camelops revise camel evolutionary history.

Rhinos: 

• Ancient and modern genomes unravel the evolutionary history of the rhinoceros family.

• Pre-extinction demographic stability and genomic signatures of adaptation in the Woolly Rhinoceros.

• Early Pleistocene enamel proteome from Dmanisi resolve Stephanorhinus phylogeny.

• Discovery of the skull of Stephanorhinus kirchbergensis (Jäger, 1839) above the Arctic Circle.

Bears:

• Ancient environmental genome reveals a migratory brown bear individual in Early Holocene Scandinavia.

• Genomic data from the extinct California brown bear suggests a potential source population for reintroduction to California.

• Environmental Genomics of Late Pleistocene Black Bears and Giant Short-Faced Bears.

• Genomic evidence of widespread admixture from polar bears into brown bears during the last ice age.

Birds:

• Natural selection shaped the rise and fall of passenger pigeon genomic diversity.

Beetles:

• Characterizing DNA preservation in degraded specimens of Amara alpina (Carabidae: Coleoptera).