Late Quaternary dynamics of Arctic biota from ancient environmental genomics.

During the last glacial-interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood1-8. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key findings include: (1) a relatively homogeneous steppe-tundra flora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistently co-occurred in space and time; (3) humans appear to have been a minor factor in driving animal distributions; (4) higher effective precipitation, as well as an increase in the proportion of wetland plants, show negative effects on animal diversity; (5) the persistence of the steppe-tundra vegetation in northern Siberia enabled the late survival of several now-extinct megafauna species, including the woolly mammoth until 3.9 ± 0.2 thousand years ago (ka) and the woolly rhinoceros until 9.8 ± 0.2 ka; and (6) phylogenetic analysis of mammoth environmental DNA reveals a previously unsampled mitochondrial lineage. Our findings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics.

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

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 diversity within, and connectivity among, populations of a once wide-ranging group, the caballine horses (Equus spp.). Using a panel of 187 mitochondrial and eight nuclear genomes recovered from present-day and extinct caballine horses sampled across the Holarctic, we found that Eurasian horse populations initially diverged from those in North America, their ancestral continent, around 1.0-0.8 million years ago. Subsequent to this split our mitochondrial DNA analysis identified two bidirectional long-range dispersals across the BLB ~875-625 and ~200-50 thousand years ago, during the Middle and Late Pleistocene. Whole genome analysis indicated low levels of gene flow between North American and Eurasian horse populations, which probably occurred as a result of these inferred dispersals. Nonetheless, mitochondrial and nuclear diversity of caballine horse populations retained strong phylogeographical structuring. Our results suggest that barriers to gene flow, currently unidentified but possibly related to habitat distribution across Beringia or ongoing evolutionary divergence, played an important role in shaping the early genetic history of caballine horses, including the ancestors of living horses within Equus ferus.

Recent summer warming in northwestern Canada exceeds the Holocene thermal maximum.

Eastern Beringia is one of the few Western Arctic regions where full Holocene climate reconstructions are possible. However, most full Holocene reconstructions in Eastern Beringia are based either on pollen or midges, which show conflicting early Holocene summer temperature histories. This discrepancy precludes understanding the factors that drove past (and potentially future) climate change and calls for independent proxies to advance the debate. We present a ~13.6 ka summer temperature reconstruction in central Yukon, part of Eastern Beringia, using precipitation isotopes in syngenetic permafrost. The reconstruction shows that early Holocene summers were consistently warmer than the Holocene mean, as supported by midges, and a thermal maximum at ~7.6-6.6 ka BP. This maximum was followed by a ~6 ka cooling, and later abruptly reversed by industrial-era warming leading to a modern climate that is unprecedented in the Holocene context and exceeds the Holocene thermal maximum by +1.7 ± 0.7 °C.

A new genus of horse from Pleistocene North America.

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, we report complete mitochondrial and partial nuclear genomes from NWSL equids from across their geographic range. Although multiple NWSL equid species have been named, our palaeogenomic and morphometric analyses support the idea that there was only a single species of middle to late Pleistocene NWSL equid, and demonstrate that it falls outside of crown group Equus. We therefore propose a new genus, Haringtonhippus, for the sole species H. francisci. Our combined genomic and phenomic approach to resolving the systematics of extinct megafauna will allow for an improved understanding of the full extent of the terminal Pleistocene extinction event.

Airborne Petcoke Dust is a Major Source of Polycyclic Aromatic Hydrocarbons in the Athabasca Oil Sands Region.

Oil sands mining has been linked to increasing atmospheric deposition of polycyclic aromatic hydrocarbons (PAHs) in the Athabasca oil sands region (AOSR), but known sources cannot explain the quantity of PAHs in environmental samples. PAHs were measured in living Sphagnum moss (24 sites, n = 68), in sectioned peat cores (4 sites, n = 161), and snow (7 sites, n = 19) from ombrotrophic bogs in the AOSR. Prospective source samples were also analyzed, including petroleum coke (petcoke, from both delayed and fluid coking), fine tailings, oil sands ore, and naturally exposed bitumen. Average PAH concentrations in near-field moss (199 ng/g, n = 11) were significantly higher (p = 0.035) than in far-field moss (118 ng/g, n = 13), and increasing temporal trends were detected in three peat cores collected closest to industrial activity. A chemical mass-balance model estimated that delayed petcoke was the major source of PAHs to living moss, and among three peat core the contribution to PAHs from delayed petcoke increased over time, accounting for 45-95% of PAHs in contemporary layers. Petcoke was also estimated to be a major source of vanadium, nickel, and molybdenum. Scanning electron microscopy with energy-dispersive X-ray spectroscopy confirmed large petcoke particles (>10 µm) in snow at near-field sites. Petcoke dust has not previously been considered in environmental impact assessments of oil sands upgrading, and improved dust control from growing stockpiles may mitigate future risks.

Tephra from ice- A simple method to routinely mount, polish, and quantitatively analyze sparse fine particles.

A method involving a graphite substrate has been developed for the mounting and analysis of sparse, fine particles from a liquid suspension to enable improved study of volcanic ash (tephra) and atmospheric dust preserved in glacial ice. Unpolished grains may be studied by scanning electron microscope-energy dispersive spectrometry (SEM-EDS) at full vacuum without the need for a conductive coating due to the close proximity of the underlying graphite. The same grains in the same relative positions may be subsequently examined in polished mounts by a variety of methods including SEM-EDS, electron probe microanalysis, laser ablation-inductively coupled plasma-mass spectroscopy, secondary ion mass spectrometry, and optical microscopy. Particles as small as 3-5 microm may be routinely and easily prepared for analysis as polished grains, and particles of significantly different sizes may be exposed simultaneously. The general approach also offers significant flexibility, including both single- and multiple-sample mounts, and may be adjusted to suit a variety of samples and analytical methods.

Ancient DNA reveals late survival of mammoth and horse in interior Alaska.

Causes of late Quaternary extinctions of large mammals ("megafauna") continue to be debated, especially for continental losses, because spatial and temporal patterns of extinction are poorly known. Accurate latest appearance dates (LADs) for such taxa are critical for interpreting the process of extinction. The extinction of woolly mammoth and horse in northwestern North America is currently placed at 15,000-13,000 calendar years before present (yr BP), based on LADs from dating surveys of macrofossils (bones and teeth). Advantages of using macrofossils to estimate when a species became extinct are offset, however, by the improbability of finding and dating the remains of the last-surviving members of populations that were restricted in numbers or confined to refugia. Here we report an alternative approach to detect 'ghost ranges' of dwindling populations, based on recovery of ancient DNA from perennially frozen and securely dated sediments (sedaDNA). In such contexts, sedaDNA can reveal the molecular presence of species that appear absent in the macrofossil record. We show that woolly mammoth and horse persisted in interior Alaska until at least 10,500 yr BP, several thousands of years later than indicated from macrofossil surveys. These results contradict claims that Holocene survival of mammoths in Beringia was restricted to ecologically isolated high-latitude islands. More importantly, our finding that mammoth and horse overlapped with humans for several millennia in the region where people initially entered the Americas challenges theories that megafaunal extinction occurred within centuries of human arrival or were due to an extraterrestrial impact in the late Pleistocene.

Non-destructive sampling of ancient insect DNA.

BACKGROUND: A major challenge for ancient DNA (aDNA) studies on insect remains is that sampling procedures involve at least partial destruction of the specimens. A recent extraction protocol reveals the possibility of obtaining DNA from past insect remains without causing visual morphological damage. We test the applicability of this protocol on historic museum beetle specimens dating back to AD 1820 and on ancient beetle chitin remains from permafrost (permanently frozen soil) dating back more than 47,000 years. Finally, we test the possibility of obtaining ancient insect DNA directly from non-frozen sediments deposited 3280-1800 years ago -- an alternative approach that also does not involve destruction of valuable material. METHODOLOGY/PRINCIPAL FINDINGS: The success of the methodological approaches are tested by PCR and sequencing of COI and 16S mitochondrial DNA (mtDNA) fragments of 77-204 base pairs (-bp) in size using species-specific and general insect primers. CONCLUSION/SIGNIFICANCE: The applied non-destructive DNA extraction method shows promising potential on insect museum specimens of historical age as far back as AD 1820, but less so on the ancient permafrost-preserved insect fossil remains tested, where DNA was obtained from samples up to ca. 26,000 years old. The non-frozen sediment DNA approach appears to have great potential for recording the former presence of insect taxa not normally preserved as macrofossils and opens new frontiers in research on ancient biodiversity.

Ancient permafrost and a future, warmer Arctic.

Climate models predict extensive and severe degradation of permafrost in response to global warming, with a potential for release of large volumes of stored carbon. However, the accuracy of these models is difficult to evaluate because little is known of the history of permafrost and its response to past warm intervals of climate. We report the presence of relict ground ice in subarctic Canada that is greater than 700,000 years old, with the implication that ground ice in this area has survived past interglaciations that were warmer and of longer duration than the present interglaciation.

Rise and fall of the Beringian steppe bison.

The widespread extinctions of large mammals at the end of the Pleistocene epoch have often been attributed to the depredations of humans; here we present genetic evidence that questions this assumption. We used ancient DNA and Bayesian techniques to reconstruct a detailed genetic history of bison throughout the late Pleistocene and Holocene epochs. Our analyses depict a large diverse population living throughout Beringia until around 37,000 years before the present, when the population's genetic diversity began to decline dramatically. The timing of this decline correlates with environmental changes associated with the onset of the last glacial cycle, whereas archaeological evidence does not support the presence of large populations of humans in Eastern Beringia until more than 15,000 years later.