Postglacial viability and colonization in North America's ice-free corridor

Archaeology meets environmental genomics: implementing sedaDNA in the study of the human past

Sedimentary ancient DNA (sedaDNA) has become one of the standard applications in the field of paleogenomics in recent years. It has been used for paleoenvironmental reconstructions, detecting the presence of prehistoric species in the absence of macro remains and even investigating the evolutionary history of a few species. However, its application in archaeology has been limited and primarily focused on humans. This article argues that sedaDNA holds significant potential in addressing key archaeological questions concerning the origins, lifestyles, and environments of past human populations. Our aim is to facilitate the integration of sedaDNA into the standard workflows in archaeology as a transformative tool, thereby unleashing its full potential for studying the human past. Ultimately, we not only underscore the challenges inherent in the sedaDNA field but also provide a research agenda for essential enhancements needed for implementing sedaDNA into the archaeological workflow.

Tibetan terrestrial and aquatic ecosystems collapsed with cryosphere loss inferred from sedimentary ancient metagenomics

Glacier and permafrost shrinkage and land-use intensification threaten mountain wildlife and affect nature conservation strategies. Here, we present paleometagenomic records of terrestrial and aquatic taxa from the southeastern Tibetan Plateau covering the last 18,000 years to help understand the complex alpine ecosystem dynamics. We infer that steppe-meadow became woodland at 14 ka (cal BP) controlled by cryosphere loss, further driving a herbivore change from wild yak to deer. These findings weaken the hypothesis of top-down control by large herbivores in the terrestrial ecosystem. We find a turnover in the aquatic communities at 14 ka, transitioning from glacier-related (blue-green) algae to abundant nonglacier-preferring picocyanobacteria, macrophytes, fish, and otters. There is no evidence for substantial effects of livestock herding in either ecosystem. Using network analysis, we assess the stress-gradient hypothesis and reveal that root hemiparasitic and cushion plants are keystone taxa. With ongoing cryosphere loss, the protection of their habitats is likely to be of conservation benefit on the Tibetan Plateau.

Environmental conditions associated with initial northern expansion of anatomically modern humans

The ability of our ancestors to switch food sources and to migrate to more favourable environments enabled the rapid global expansion of anatomically modern humans beyond Africa as early as 120,000 years ago. Whether this versatility was largely the result of environmentally determined processes or was instead dominated by cultural drivers, social structures, and interactions among different groups, is unclear. We develop a statistical approach that combines both archaeological and genetic data to infer the more-likely initial expansion routes in northern Eurasia and the Americas. We then quantify the main differences in past environmental conditions between the more-likely routes and other potential (less-likely) routes of expansion. We establish that, even though cultural drivers remain plausible at finer scales, the emergent migration corridors were predominantly constrained by a combination of regional environmental conditions, including the presence of a forest-grassland ecotone, changes in temperature and precipitation, and proximity to rivers.

Exploring the complex pre-adaptations of invasive plants to anthropogenic disturbance: a call for integration of archaeobotanical approaches

Pre-adaptation to anthropogenic disturbance is broadly considered key for plant invasion success. Nevertheless, empirical evidence remains scarce and fragmentary, given the multifaceted nature of anthropogenic disturbance itself and the complexity of other evolutionary forces shaping the (epi)-genomes of recent native and invasive plant populations. Here, we review and critically revisit the existing theory and empirical evidence in the field of evolutionary ecology and highlight novel integrative research avenues that work at the interface with archaeology to solve open questions. The approaches suggested so far focus on contemporary plant populations, although their genomes have rapidly changed since their initial introduction in response to numerous selective and stochastic forces. We elaborate that a role of pre-adaptation to anthropogenic disturbance in plant invasion success should thus additionally be validated based on the analyses of archaeobotanical remains. Such materials, in the light of detailed knowledge on past human societies could highlight fine-scale differences in the type and timing of past disturbances. We propose a combination of archaeobotanical, ancient DNA and morphometric analyses of plant macro- and microremains to assess past community composition, and species' functional traits to unravel the timing of adaptation processes, their drivers and their long-term consequences for invasive species. Although such methodologies have proven to be feasible for numerous crop plants, they have not been yet applied to wild invasive species, which opens a wide array of insights into their evolution.

New age constraints for human entry into the Americas on the north Pacific coast

The timing of the initial peopling of the Americas is unresolved. Because the archaeological record necessitates discussion of human entry from Beringia into southern North America during the last glaciation, addressing this problem routinely involves evaluating environmental parameters then targeting areas suitable for human settlement. Vertebrate remains indicate landscape quality and are a key dataset for assessing coastal migration theories and the viability of coastal routes. Here, radiocarbon dates on vertebrate specimens and archaeological sites are calibrated to document species occurrences and the ages of human settlements across the western expansion and decay of the Cordilleran Ice Sheet (CIS) during the Late Wisconsin Fraser Glaciation in four subregions of the north Pacific coast of North America. The results show archaeological sites occur after glacial maxima and are generally consistent with the age of other securely dated earliest sites in southern North America. They also highlight gaps in the vertebrate chronologies around CIS maxima in each of the subregions that point to species redistributions and extirpations and signal times of low potential for human settlement and subsistence in a key portion of the proposed coastal migration route. This study, therefore, defines new age constraints for human coastal migration theories in the peopling of the Americas debate.

Exploring different methodological approaches to unlock paleobiodiversity in peat profiles using ancient DNA

Natural and human-induced environmental changes deeply affected terrestrial ecosystems throughout the Holocene. Paleoenvironmental reconstructions provide information about the past and allow us to predict/model future scenarios. Among potential records, peat bogs are widely used because they present a precise stratigraphy and act as natural archives of highly diverse organic remains. Over the decades, several techniques have been developed to identify debris occurring in peat, including their morphological description. However, this is strongly constrained by the researcher's ability to distinguish residues at the species level, which typically requires many years of experience. In addition, potential contamination hampers using these techniques to obtain information from organisms such as fungi or bacteria. Environmental DNA metabarcoding and shotgun metagenome sequencing could represent a solution to detect specific groups of organisms without any a priori knowledge of their characteristics and/or to identify organisms that have rarely been considered in previous investigations. Moreover, shotgun metagenomics may allow the identification of bacteria and fungi (including both yeast and filamentous life forms), ensuring discrimination between ancient and modern organisms through the study of deamination/damage patterns. In the present review, we aim to i) present the state-of-the-art methodologies in paleoecological and paleoclimatic studies focusing on peat core analyses, proposing alternative approaches to the classical morphological identification of plant residues, and ii) suggest biomolecular approaches that will allow the use of proxies such as invertebrates, fungi, and bacteria, which are rarely employed in paleoenvironmental reconstructions.

The MetaInvert soil invertebrate genome resource provides insights into below-ground biodiversity and evolution

Soil invertebrates are among the least understood metazoans on Earth. Thus far, the lack of taxonomically broad and dense genomic resources has made it hard to thoroughly investigate their evolution and ecology. With MetaInvert we provide draft genome assemblies for 232 soil invertebrate species, representing 14 common groups and 94 families. We show that this data substantially extends the taxonomic scope of DNA- or RNA-based taxonomic identification. Moreover, we confirm that theories of genome evolution cannot be generalised across evolutionarily distinct invertebrate groups. The soil invertebrate genomes presented here will support the management of soil biodiversity through molecular monitoring of community composition and function, and the discovery of evolutionary adaptations to the challenges of soil conditions.

Towards exhaustive community ecology via DNA metabarcoding

Exhaustive biodiversity data, covering all the taxa in an environment, would be fundamental to understand how global changes influence organisms living at different trophic levels, and to evaluate impacts on interspecific interactions. Molecular approaches such as DNA metabarcoding are boosting our ability to perform biodiversity inventories. Nevertheless, even though a few studies have recently attempted exhaustive reconstructions of communities, holistic assessments remain rare. The majority of metabarcoding studies published in the last years used just one or two markers and analysed a limited number of taxonomic groups. Here, we provide an overview of emerging approaches that can allow all-taxa biological inventories. Exhaustive biodiversity assessments can be attempted by combining a large number of specific primers, by exploiting the power of universal primers, or by combining specific and universal primers to obtain good information on key taxa while limiting the overlooked biodiversity. Multiplexes of primers, shotgun sequencing and capture enrichment may provide a better coverage of biodiversity compared to standard metabarcoding, but still require major methodological advances. Here, we identify the strengths and limitations of different approaches, and suggest new development lines that might improve broad scale biodiversity analyses in the near future. More holistic reconstructions of ecological communities can greatly increase the value of metabarcoding studies, improving understanding of the consequences of ongoing environmental changes on the multiple components of biodiversity.

The role of Beringia in human adaptation to Arctic conditions based on results of genomic studies of modern and ancient populations

The results of studies in Quaternary geology, archeology, paleoanthropology and human genetics demonstrate that the ancestors of Native Americans arrived in mid-latitude North America mainly along the Pacific Northwest Coast, but had previously inhabited the Arctic and during the last glacial maximum were in a refugium in Beringia, a land bridge connecting Eurasia and North America. The gene pool of Native Americans is represented by unique haplogroups of mitochondrial DNA and the Y chromosome, the evolutionary age of which ranges from 13 to 22 thousand years. The results of a paleogenomic analysis also show that during the last glacial maximum Beringia was populated by human groups that had arisen as a result of interaction between the most ancient Upper Paleolithic populations of Northern Eurasia and newcomer groups from East Asia. Approximately 20 thousand years ago the Beringian populations began to form, and the duration of their existence in relative isolation is estimated at about 5 thousand years. Thus, the adaptation of the Beringians to the Arctic conditions could have taken several millennia. The adaptation of Amerindian ancestors to high latitudes and cold climates is supported by genomic data showing that adaptive genetic variants in Native Americans are associated with various metabolic pathways: melanin production processes in the skin, hair and eyes, the functioning of the cardiovascular system, energy metabolism and immune response characteristics. Meanwhile, the analysis of the existing hypotheses about the selection of some genetic variants in the Beringian ancestors of the Amerindians in connection with adaptation to the Arctic conditions (for example, in the FADS, ACTN3, EDAR genes) shows the ambiguity of the testing results, which may be due to the loss of some traces of the "Beringian" adaptation in the gene pools of modern Native Americans. The most optimal strategy for further research seems to be the search for adaptive variant.

A paleogenome from a Holocene individual supports genetic continuity in Southeast Alaska

Many specifics of the population histories of the Indigenous peoples of North America remain contentious owing to a dearth of physical evidence. Only few ancient human genomes have been recovered from the Pacific Northwest Coast, a region increasingly supported as a coastal migration route for the initial peopling of the Americas. Here, we report paleogenomic data from the remains of a ∼3,000-year-old female individual from Southeast Alaska, named Tatóok yík yées sháawat (TYYS). Our results demonstrate at least 3,000 years of matrilineal genetic continuity in Southeast Alaska, and that TYYS is most closely related to ancient and present-day northern Pacific Northwest Coast Indigenous Americans. We find no evidence of Paleo-Inuit (represented by Saqqaq) ancestry in present-day or ancient Pacific Northwest peoples. Instead, our analyses suggest the Saqqaq genome harbors Northern Native American ancestry. This study sheds further light on the human population history of the northern Pacific Northwest Coast.

Mitogenome evidence shows two radiation events and dispersals of matrilineal ancestry from northern coastal China to the Americas and Japan

Although it is widely recognized that the ancestors of Native Americans (NAs) primarily came from Siberia, the link between mitochondrial DNA (mtDNA) lineage D4h3a (typical of NAs) and D4h3b (found so far only in East China and Thailand) raises the possibility that the ancestral sources for early NAs were more variegated than hypothesized. Here, we analyze 216 contemporary (including 106 newly sequenced) D4h mitogenomes and 39 previously reported ancient D4h data. The results reveal two radiation events of D4h in northern coastal China, one during the Last Glacial Maximum and the other within the last deglaciation, which facilitated the dispersals of D4h sub-branches to different areas including the Americas and the Japanese archipelago. The coastal distributions of the NA (D4h3a) and Japanese lineages (D4h1a and D4h2), in combination with the Paleolithic archaeological similarities among Northern China, the Americas, and Japan, lend support to the coastal dispersal scenario of early NAs.

Marine ecosystem shifts with deglacial sea-ice loss inferred from ancient DNA shotgun sequencing

Sea ice is a key factor for the functioning and services provided by polar marine ecosystems. However, ecosystem responses to sea-ice loss are largely unknown because time-series data are lacking. Here, we use shotgun metagenomics of marine sedimentary ancient DNA off Kamchatka (Western Bering Sea) covering the last ~20,000 years. We traced shifts from a sea ice-adapted late-glacial ecosystem, characterized by diatoms, copepods, and codfish to an ice-free Holocene characterized by cyanobacteria, salmon, and herring. By providing information about marine ecosystem dynamics across a broad taxonomic spectrum, our data show that ancient DNA will be an important new tool in identifying long-term ecosystem responses to climate transitions for improvements of ocean and cryosphere risk assessments. We conclude that continuing sea-ice decline on the northern Bering Sea shelf might impact on carbon export and disrupt benthic food supply and could allow for a northward expansion of salmon and Pacific herring.

The social lives of isolates (and small language families): the case of the Northwest Amazon

The Americas are home to patches of extraordinary linguistic (genealogical) diversity. These high-diversity areas are particularly unexpected given the recent population of the Americas. In this paper, we zoom in on one such area, the Northwest Amazon, and address the question of how the diversity in this area has persisted to the present. We contrast two hypotheses that claim opposite mechanisms for the maintenance of diversity: the isolation hypothesis suggests that isolation facilitates the preservation of diversity, while the integration hypothesis proposes that conscious identity preservation in combination with contact drives diversity maintenance. We test predictions for both hypotheses across four disciplines: biogeography, cultural anthropology, population genetics and linguistics. Our results show signs of both isolation and integration, but they mainly suggest considerable diversity in how groups of speakers have interacted with their surroundings.

Environmental DNA as an emerging tool in botanical research

Over the past quarter century, environmental DNA (eDNA) has been ascendant as a tool to detect, measure, and monitor biodiversity (species and communities), as a means of elucidating biological interaction networks, and as a window into understanding past patterns of biodiversity. However, only recently has the potential of eDNA been realized in the botanical world. Here we synthesize the state of eDNA applications in botanical systems with emphases on aquatic, ancient, contemporary sediment, and airborne systems, and focusing on both single-species approaches and multispecies community metabarcoding. Further, we describe how abiotic and biotic factors, taxonomic resolution, primer choice, spatiotemporal scales, and relative abundance influence the utilization and interpretation of airborne eDNA results. Lastly, we explore several areas and opportunities for further development of eDNA tools for plants, advancing our knowledge and understanding of the efficacy, utility, and cost-effectiveness, and ultimately facilitating increased adoption of eDNA analyses in botanical systems.

Genetic determinants and absence of breast cancer in Xavante Indians in Sangradouro Reserve, Brazil

Genetic compositions of distinct human populations are different. How genomic variants influence many common and rare genetic diseases is always of great medical and anthropological interest, and understanding of genetic architectures of population groups in relation to diseases can advance our knowledge of medicine. Here, we have studied the genomic architecture of a group of Xavante Indians, an indigenous population in Brazil, and compared them with normal populations from the 1000 Genomes Projects. Principal component analysis (PCA) indicates that the Xavante Indians are genetically distinctive when compared to other ethnic groups. No incidence of breast cancer cases has ever been reported in the population, and polygenic risk analysis indicates extremely low breast cancer risk in this population when compared with germline TCGA (The Cancer Genome Atlas) breast cancer normal control samples. Low germinal mutation burden among this population is also observed. Our findings will help to deepen the understanding of breast cancer and might also provide new approaches to study the disease.

MetaDamage tool: Examining post-mortem damage in sedaDNA on a metagenomic scale

The use of metagenomic datasets to support ancient sedimentary DNA (sedaDNA) for paleoecological reconstruction has been demonstrated to be a powerful tool to understand multi-organism responses to climatic shifts and events. Authentication remains integral to the ancient DNA discipline, and this extends to sedaDNA analysis. Furthermore, distinguishing authentic sedaDNA from contamination or modern material also allows for a better understanding of broader questions in sedaDNA research, such as formation processes, source and catchment, and post-depositional processes. Existing tools for the detection of damage signals are designed for single-taxon input, require a priori organism specification, and require a significant number of input sequences to establish a signal. It is therefore often difficult to identify an established cytosine deamination rate consistent with ancient DNA across a sediment sample. In this study, we present MetaDamage, a tool that examines cytosine deamination on a metagenomic (all organisms) scale for multiple previously undetermined taxa and can produce a damage profile based on a few hundred reads. We outline the development and testing of the MetaDamage tool using both authentic sedaDNA sequences and simulated data to demonstrate the resolution in which MetaDamage can identify deamination levels consistent with the presence of ancient DNA. The MetaDamage tool offers a method for the initial assessment of the presence of sedaDNA and a better understanding of key questions of preservation for paleoecological reconstruction.

Demography and linked selection interact to shape the genomic landscape of codistributed woodpeckers during the Ice Age

The influence of genetic drift on population dynamics during Pleistocene glacial cycles is well understood, but the role of selection in shaping patterns of genomic variation during these events is less explored. We resequenced whole genomes to investigate how demography and natural selection interact to generate the genomic landscapes of Downy and Hairy Woodpecker, species codistributed in previously glaciated North America. First, we explored the spatial and temporal patterns of genomic diversity produced by neutral evolution. Next, we tested (i) whether levels of nucleotide diversity along the genome are correlated with intrinsic genomic properties, such as recombination rate and gene density, and (ii) whether different demographic trajectories impacted the efficacy of selection. Our results revealed cycles of bottleneck and expansion, and genetic structure associated with glacial refugia. Nucleotide diversity varied widely along the genome, but this variation was highly correlated between the species, suggesting the presence of conserved genomic features. In both taxa, nucleotide diversity was positively correlated with recombination rate and negatively correlated with gene density, suggesting that linked selection played a role in reducing diversity. Despite strong fluctuations in effective population size, the maintenance of relatively large populations during glaciations may have facilitated selection. Under these conditions, we found evidence that the individual demographic trajectory of populations modulated linked selection, with purifying selection being more efficient in removing deleterious alleles in large populations. These results highlight that while genome-wide variation reflects the expected signature of demographic change during climatic perturbations, the interaction of multiple processes produces a predictable and highly heterogeneous genomic landscape.

A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA

Late Pliocene and Early Pleistocene epochs 3.6 to 0.8 million years ago1 had climates resembling those forecasted under future warming2. Palaeoclimatic records show strong polar amplification with mean annual temperatures of 11-19 °C above contemporary values3,4. The biological communities inhabiting the Arctic during this time remain poorly known because fossils are rare5. Here we report an ancient environmental DNA6 (eDNA) record describing the rich plant and animal assemblages of the Kap København Formation in North Greenland, dated to around two million years ago. The record shows an open boreal forest ecosystem with mixed vegetation of poplar, birch and thuja trees, as well as a variety of Arctic and boreal shrubs and herbs, many of which had not previously been detected at the site from macrofossil and pollen records. The DNA record confirms the presence of hare and mitochondrial DNA from animals including mastodons, reindeer, rodents and geese, all ancestral to their present-day and late Pleistocene relatives. The presence of marine species including horseshoe crab and green algae support a warmer climate than today. The reconstructed ecosystem has no modern analogue. The survival of such ancient eDNA probably relates to its binding to mineral surfaces. Our findings open new areas of genetic research, demonstrating that it is possible to track the ecology and evolution of biological communities from two million years ago using ancient eDNA.

A genomic perspective on South American human history

It has generally been accepted that the current indigenous peoples of the Americas are derived from ancestors from northeastern Asia. The latter were believed to have spread into the American continent by the end of the Last Glacial Maximum. In this sense, a joint and in-depth study of the earliest settlement of East Asia and the Americas is required to elucidate these events accurately. The first Americans underwent an adaptation process to the Americas' vast environmental diversity, mediated by biological and cultural evolution and niche construction, resulting in enormous cultural diversity, a wealth of domesticated species, and extensive landscape modifications. Afterward, in the Late Holocene, the advent of intensive agricultural food production systems, sedentism, and climate change significantly reshaped genetic and cultural diversity across the continent, particularly in the Andes and Amazonia. Furthermore, starting around the end of the 15th century, European colonization resulted in massive extermination of indigenous peoples and extensive admixture. Thus, the present review aims to create a comprehensive picture of the main events involved in the formation of contemporary South American indigenous populations and the dynamics responsible for shaping their genetic diversity by integrating current genetic data with evidence from archeology, linguistics and other disciplines.

A theoretical analysis of taxonomic binning accuracy

Many metagenomic and environmental DNA studies require the taxonomic assignment of individual reads or sequences by aligning reads to a reference database, known as taxonomic binning. When a read aligns to more than one reference sequence, it is often classified based on sequence similarity. This step can assign reads to incorrect taxa, at a rate which depends both on the assignment algorithm and on underlying population genetic and database parameters. In particular, as we move towards using environmental DNA to study eukaryotic taxa subject to regular recombination, we must take into account issues concerning gene tree discordance. Though accuracy is often compared across algorithms using a fixed data set, the relative impact of these population genetic and database parameters on accuracy has not yet been quantified. Here, we develop both a theoretical and simulation framework in the simplified case of two reference species, and compute binning accuracy over a wide range of parameters, including sequence length, species-query divergence time, divergence times of the reference species, reference database completeness, sample age and effective population size. We consider two assignment methods and contextualize our results using parameters from a recent ancient environmental DNA study, comparing them to the commonly used discriminative k-mer-based method Clark (Current Biology, 31, 2021, 2728; BMC Genomics, 16, 2015, 1). Our results quantify the degradation in assignment accuracy as the samples diverge from their closest reference sequence, and with incompleteness of reference sequences. We also provide a framework in which others can compute expected accuracy for their particular method or parameter set. Code is available at https://github.com/bdesanctis/binning-accuracy.

Demography and evolutionary history of grey wolf populations around the Bering Strait

Glacial and interglacial periods throughout the Pleistocene have been substantial drivers of change in species distributions. Earlier analyses suggested that modern grey wolves (Canis lupus) trace their origin to a single Late Pleistocene Beringian population that expanded east and westwards, starting c. 25,000 years ago (ya). Here, we examined the demographic and phylogeographic histories of extant populations around the Bering Strait with wolves from two inland regions of the Russian Far East (RFE) and one coastal and two inland regions of North‐western North America (NNA), genotyped for 91,327 single nucleotide polymorphisms. Our results indicated that RFE and NNA wolves had a common ancestry until c. 34,400 ya, suggesting that these populations started to diverge before the previously proposed expansion out of Beringia. Coastal and inland NNA populations diverged c. 16,000 ya, concordant with the minimum proposed date for the ecological viability of the migration route along the Pacific Northwest coast. Demographic reconstructions for inland RFE and NNA populations reveal spatial and temporal synchrony, with large historical effective population sizes that declined throughout the Pleistocene, possibly reflecting the influence of broadscale climatic changes across continents. In contrast, coastal NNA wolves displayed a consistently lower effective population size than the inland populations. Differences between the demographic history of inland and coastal wolves may have been driven by multiple ecological factors, including historical gene flow patterns, natural landscape fragmentation, and more recent anthropogenic disturbance.

The untapped potential of macrofossils in ancient plant DNA research

The rapid development of ancient DNA analysis in the last decades has induced a paradigm shift in ecology and evolution. Driven by a combination of breakthroughs in DNA isolation techniques, high-throughput sequencing, and bioinformatics, ancient genome-scale data for a rapidly growing variety of taxa are now available, allowing researchers to directly observe demographic and evolutionary processes over time. However, the vast majority of paleogenomic studies still focus on human or animal remains. In this article, we make the case for a vast untapped resource of ancient plant material that is ideally suited for paleogenomic analyses: plant remains, such as needles, leaves, wood, seeds, or fruits, that are deposited in natural archives, such as lake sediments, permafrost, or even ice caves. Such plant remains are commonly found in large numbers and in stratigraphic sequence through time and have so far been used primarily to reconstruct past local species presences and abundances. However, they are also unique repositories of genetic information with the potential to revolutionize the fields of ecology and evolution by directly studying microevolutionary processes over time. Here, we give an overview of the current state-of-the-art, address important challenges, and highlight new research avenues to inspire future research.

On the Use of Spores of Coprophilous Fungi Preserved in Sediments to Indicate Past Herbivore Presence

Fungal spores that grew on the faeces of herbivores in the past can be extracted from sediments and used to identify the presence of herbivores in former ecosystems. This review: (i) examines the factors that should be considered when interpreting these fungal spores, (ii) assesses the degree to which they can be used to estimate past herbivore populations and biomass density change, and (iii) identifies gaps in our current understanding that limit, or confound, the information that can be extracted from the fungal spore record. We focus on the life cycles of coprophilous fungi and highlight the importance of understanding spore dispersal mechanisms to ensure robust palaeoecological interpretation. We then discuss how variation in methodological approaches across studies and modifications can influence comparability between studies. The key recommendations that emerge relate to: (i) improving our understanding of the relationship between spores of coprophilous fungi (SCF) and herbivores through the study of the coprophilous fungi succession; (ii) refining our understanding of how climate and environment parameters effect fungal spore abundance, with particular reference to estimating past herbivore biomass density; and (iii) enhancing sedimentary DNA (SedaDNA) analysis to identify SCF that do not allow preservation in a way that allows visual identification. To further this field of study and provide more robust insights into herbivores in the past, we suggest that additional research is required to help to reduce bias during the preparation process, that concertation metrics are used for the quantification of SCF, and that multiple cores should be taken in each site and multiproxy analysis should be utilised.

Two Millennia of Complexity and Variability in a Perialpine Socioecological System (Savoie, France): The Contribution of Palynology and sedaDNA Analysis

Over the last two millennia, European Alpine ecosystems have experienced major changes in response to the important, yet fluctuating, impact of human activities. This study aims to reconstruct the environmental history of the last 1800 years on the western edge of the Alps by analyzing sediments from Lake Aiguebelette, a large lake located in the perialpine area. We have combined analyses of pollen and other palynomorphs, such as coprophilous fungal spores, together with sedimentary DNA (from plants and mammals) in order to reconstruct both vegetation and land-use histories. A sedimentological and geochemical analysis was also conducted in order to gain an understanding of changes in erosion dynamics in response to landscape modifications that were influenced by climate and human activities. This work highlights alternating phases of anthropization and agricultural abandonment allowing forest recovery. While pollen reflects the major phases of regional deforestation and afforestation related to the dynamic of farming activities, plant DNA provides precise information on the plants cultivated in fields, orchards and vegetable gardens over the past centuries. The combination of mammal DNA and coprophilous fungal spores completes this work by documenting the history of pastoral practices.

Long-term preservation of biomolecules in lake sediments: potential importance of physical shielding by recalcitrant cell walls

Even though lake sediments are globally important organic carbon (OC) sinks, the controls on long-term OC storage in these sediments are unclear. Using a multiproxy approach, we investigate changes in diatom, green algae, and vascular plant biomolecules in sedimentary records from the past centuries across five temperate lakes with different trophic histories. Despite past increases in the input and burial of OC in sediments of eutrophic lakes, biomolecule quantities in sediments of all lakes are primarily controlled by postburial microbial degradation over the time scales studied. We, moreover, observe major differences in biomolecule degradation patterns across diatoms, green algae, and vascular plants. Degradation rates of labile diatom DNA exceed those of chemically more resistant diatom lipids, suggesting that chemical reactivity mainly controls diatom biomolecule degradation rates in the lakes studied. By contrast, degradation rates of green algal and vascular plant DNA are significantly lower than those of diatom DNA, and in a similar range as corresponding, much less reactive lipid biomarkers and structural macromolecules, including lignin. We propose that physical shielding by degradation-resistant cell wall components, such as algaenan in green algae and lignin in vascular plants, contributes to the long-term preservation of labile biomolecules in both groups and significantly influences the long-term burial of OC in lake sediments.

Tropical forests in the deep human past

Since Darwin, studies of human evolution have tended to give primacy to open 'savannah' environments as the ecological cradle of our lineage, with dense tropical forests cast as hostile, unfavourable frontiers. These perceptions continue to shape both the geographical context of fieldwork as well as dominant narratives concerning hominin evolution. This paradigm persists despite new, ground-breaking research highlighting the role of tropical forests in the human story. For example, novel research in Africa's rainforests has uncovered archaeological sites dating back into the Pleistocene; genetic studies have revealed very deep human roots in Central and West Africa and in the tropics of Asia and the Pacific; an unprecedented number of coexistent hominin species have now been documented, including Homo erectus, the 'Hobbit' (Homo floresiensis), Homo luzonensis, Denisovans, and Homo sapiens. Some of the earliest members of our own species to reach South Asia, Southeast Asia, Oceania and the tropical Americas have shown an unexpected rapidity in their adaptation to even some of the more 'extreme' tropical settings. This includes the early human manipulation of species and even habitats. This volume builds on these currently disparate threads and, for the first time, draws together a group of interdisciplinary, agenda-setting papers that firmly places a broader spectrum of tropical environments at the heart of the deep human past. This article is part of the theme issue 'Tropical forests in the deep human past'.

The age of the opening of the Ice-Free Corridor and implications for the peopling of the Americas

The Ice-Free Corridor (IFC) has long played a key role in hypotheses about the peopling of the Americas. Earlier assessments of its age suggested that the IFC was available for a Clovis-first migration, but subsequent developments now suggest a pre-Clovis occupation of the Americas that occurred before the opening of the IFC, thus supporting a Pacific coastal migration route instead. However, large uncertainties in existing ages from the IFC cannot preclude its availability as a route for the first migrations. Resolving this debate over migration route is important for addressing the questions of when and how the first Americans arrived. We report cosmogenic nuclide exposure ages that show that the final opening of the IFC occurred well after pre-Clovis occupation.

The Clovis-first model for the peopling of the Americas by ∼13.4 ka has long invoked the Ice-Free Corridor (IFC) between the retreating margins of the Cordilleran and Laurentide ice sheets as the migration route from Alaska and the Yukon down to the Great Plains. Evidence from archaeology and ancient genomics, however, now suggests that pre-Clovis migrations occurred by at least ∼15.5 to 16.0 ka or earlier than most recent assessments of the age of IFC opening at ∼14 to 15 ka, lending support to the use of a Pacific coast migration route instead. Uncertainties in ages from the IFC used in these assessments, however, allow for an earlier IFC opening which would be consistent with the availability of the IFC as a migration route by ∼15.5 to 16.0 ka. Here, we use 64 cosmogenic (¹⁰Be) exposure ages to closely date the age of the full opening of the IFC at 13.8 ± 0.5 ka. Our results thus clearly establish that the IFC was not available for the first peopling of the Americas after the Last Glacial Maximum, whereas extensive geochronological data from the Pacific coast support its earlier availability as a coastal migration route.

DNA in extracellular vesicles: from evolution to its current application in health and disease

Extracellular vesicle (EV) secretion is a highly conserved evolutionary trait in all organisms in the three domains of life. The packaging and release of EVs appears to be a bulk-flow process which takes place mainly under extreme conditions. EVs participate in horizontal gene transfer, which supports the survival of prokaryotic and eukaryotic microbes. In higher eukaryotes, almost all cells secrete a heterogeneous population of EVs loaded with various biomolecules. EV secretion is typically higher in cancer microenvironments, promoting tumor progression and metastasis. EVs are now recognized as additional mediators of autocrine and paracrine communication in health and disease. In this context, proteins and RNAs have been studied the most, but extracellular vesicle DNA (EV-DNA) has started to gain in importance in the last few years. In this review, we summarize new findings related to the loading mechanism(s), localization, and post-shedding function of EV-DNA. We also discuss the feasibility of using EV-DNA as a biomarker when performing a liquid biopsy, at the same time emphasizing the lack of data from clinical trials in this regard. Finally, we outline the potential of EV-DNA uptake and its interaction with the host genome as a promising tool for understanding the mechanisms of cancer evolution.

Protecting DNA in membrane vesicles seems to be a conserved phenomenon for the horizontal genetic flux between prokaryotes and lower eukaryotes.

Capturing and analyzing this vesicular DNA enables quick and non-invasive monitoring of natural ecosystems.

Cancer-derived extracellular vesicles containing DNA open up novel directions in cell-to-cell communication and therefore disease monitoring.

Complex and fluctuating conditions of the tumor microenvironment, mimicking natural ecosystems, could favor EV-DNA release, mediating tumor multi-clonal evolution and providing survival benefits.

Environmental paleomicrobiology: using DNA preserved in aquatic sediments to its full potential

In‐depth knowledge about spatial and temporal variation in microbial diversity and function is needed for a better understanding of ecological and evolutionary responses to global change. In particular, the study of microbial ancient DNA preserved in sediment archives from lakes and oceans can help us to evaluate the responses of aquatic microbes in the past and make predictions about future biodiversity change in those ecosystems. Recent advances in molecular genetic methods applied to the analysis of historically deposited DNA in sediments have not only allowed the taxonomic identification of past aquatic microbial communities but also enabled tracing their evolution and adaptation to episodic disturbances and gradual environmental change. Nevertheless, some challenges remain for scientists to take full advantage of the rapidly developing field of paleo‐genetics, including the limited ability to detect rare taxa and reconstruct complete genomes for evolutionary studies. Here, we provide a brief review of some of the recent advances in the field of environmental paleomicrobiology and discuss remaining challenges related to the application of molecular genetic methods to study microbial diversity, ecology, and evolution in sediment archives. We anticipate that, in the near future, environmental paleomicrobiology will shed new light on the processes of microbial genome evolution and microbial ecosystem responses to quaternary environmental changes at an unprecedented level of detail. This information can, for example, aid geological reconstructions of biogeochemical cycles and predict ecosystem responses to environmental perturbations, including in the context of human‐induced global changes.

Pleistocene mitogenomes reconstructed from the environmental DNA of permafrost sediments

Traditionally, paleontologists have relied on the morphological features of bones and teeth to reconstruct the evolutionary relationships of extinct animals.¹ In recent decades, the analysis of ancient DNA recovered from macrofossils has provided a powerful means to evaluate these hypotheses and develop novel phylogenetic models.² Although a great deal of life history data can be extracted from bones, their scarcity and associated biases limit their information potential. The paleontological record of Beringia³-the unglaciated areas and former land bridge between northeast Eurasia and northwest North America-is relatively robust thanks to its perennially frozen ground favoring fossil preservation.^4,5 However, even here, the macrofossil record is significantly lacking in small-bodied fauna (e.g., rodents and birds), whereas questions related to migration and extirpation, even among well-studied taxa, remain crudely resolved. The growing sophistication of ancient environmental DNA (eDNA) methods have allowed for the identification of species within terrestrial/aquatic ecosystems,^6-12 in paleodietary reconstructions,^13-19 and facilitated genomic reconstructions from cave contexts.^8,20-22 Murchie et al.^6,23 used a capture enrichment approach to sequence a diverse range of faunal and floral DNA from permafrost silts deposited during the Pleistocene-Holocene transition.²⁴ Here, we expand on their work with the mitogenomic assembly and phylogenetic placement of Equus caballus (caballine horse), Bison priscus (steppe bison), Mammuthus primigenius (woolly mammoth), and Lagopus lagopus (willow ptarmigan) eDNA from multiple permafrost cores spanning the last 30,000 years. We identify a diverse metagenomic spectra of Pleistocene fauna and identify the eDNA co-occurrence of distinct Eurasian and American mitogenomic lineages.

Ancient human genomes and environmental DNA from the cement attaching 2,000 year-old head lice nits

Over the past few decades, there has been a growing demand for genome analysis of ancient human remains. Destructive sampling is increasingly difficult to obtain for ethical reasons, and standard methods of breaking the skull to access the petrous bone or sampling remaining teeth are often forbidden for curatorial reasons. However, most ancient humans carried head lice and their eggs abound in historical hair specimens. Here we show that host DNA is protected by the cement that glues head lice nits to the hair of ancient Argentinian mummies, 1,500–2,000 years old. The genetic affinities deciphered from genome-wide analyses of this DNA inform that this population migrated from north-west Amazonia to the Andes of central-west Argentina; a result confirmed using the mitochondria of the host lice. The cement preserves ancient environmental DNA of the skin, including the earliest recorded case of Merkel cell polyomavirus. We found that the percentage of human DNA obtained from nit cement equals human DNA obtained from the tooth, yield 2-fold compared with a petrous bone, and 4-fold to a bloodmeal of adult lice a millennium younger. In metric studies of sheaths, the length of the cement negatively correlates with the age of the specimens, whereas hair linear distance between nit and scalp informs about the environmental conditions at the time before death. Ectoparasitic lice sheaths can offer an alternative, nondestructive source of high-quality ancient DNA from a variety of host taxa where bones and teeth are not available and reveal complementary details of their history.

Ancient Metagenomic Studies: Considerations for the Wider Scientific Community

Like modern metagenomics, ancient metagenomics is a highly data-rich discipline, with the added challenge that the DNA of interest is degraded and, depending on the sample type, in low abundance. This requires the application of specialized measures during molecular experiments and computational analyses. Furthermore, researchers often work with finite sample sizes, which impedes optimal experimental design and control of confounding factors, and with ethically sensitive samples necessitating the consideration of additional guidelines. In September 2020, early career researchers in the field of ancient metagenomics met (Standards, Precautions & Advances in Ancient Metagenomics 2 [SPAAM2] community meeting) to discuss the state of the field and how to address current challenges. Here, in an effort to bridge the gap between ancient and modern metagenomics, we highlight and reflect upon some common misconceptions, provide a brief overview of the challenges in our field, and point toward useful resources for potential reviewers and newcomers to the field.

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.

Performance and automation of ancient DNA capture with RNA hyRAD probes

DNA hybridization-capture techniques allow researchers to focus their sequencing efforts on preselected genomic regions. This feature is especially useful when analysing ancient DNA (aDNA) extracts, which are often dominated by exogenous environmental sources. Here, we assessed, for the first time, the performance of hyRAD as an inexpensive and design-free alternative to commercial capture protocols to obtain authentic aDNA data from osseous remains. HyRAD relies on double enzymatic restriction of fresh DNA extracts to produce RNA probes that cover only a fraction of the genome and can serve as baits for capturing homologous fragments from aDNA libraries. We found that this approach could retrieve sequence data from horse remains coming from a range of preservation environments, including beyond radiocarbon range, yielding up to 146.5-fold on-target enrichment for aDNA extracts showing extremely low endogenous content (<1%). Performance was, however, more limited for those samples already characterized by good DNA preservation (>20%-30%), while the fraction of endogenous reads mapping on- and off-target was relatively insensitive to the original endogenous DNA content. Procedures based on two instead of a single round of capture increased on-target coverage up to 3.6-fold. Additionally, we used methylation-sensitive restriction enzymes to produce probes targeting hypomethylated regions, which improved data quality by reducing post-mortem DNA damage and mapping within multicopy regions. Finally, we developed a fully automated hyRAD protocol utilizing inexpensive robotic platforms to facilitate capture processing. Overall, our work establishes hyRAD as a cost-effective strategy to recover a set of shared orthologous variants across multiple ancient samples.

Development of droplet digital Polymerase Chain Reaction assays for the detection of long-finned (Anguilla dieffenbachii) and short-finned (Anguilla australis) eels in environmental samples

Freshwater eels are ecologically, and culturally important worldwide. The New Zealand long-finned eel (Anguilla dieffenbachii) and short-finned eel (Anguilla australis) are apex predators, playing an important role in ecosystem functioning of rivers and lakes. Recently, there has been a national decline in their populations due to habitat destruction and commercial harvest. The emergence of targeted environmental DNA detection methodologies provides an opportunity to enhance information about their past and present distributions. In this study we successfully developed species-specific droplet digital Polymerase Chain Reaction (ddPCR) assays to detect A. dieffenbachii and A. australis DNA in water and sediment samples. Assays utilized primers and probes designed for regions of the mitochondrial cytochrome b and 16S ribosomal RNA genes in A. dieffenbachii and A. australis, respectively. River water samples (n = 27) were analyzed using metabarcoding of fish taxa and were compared with the ddPCR assays. The presence of A. dieffenbachii and A. australis DNA was detected in a greater number of water samples using ddPCR in comparison to metabarcoding. There was a strong and positive correlation between gene copies (ddPCR analyses) and relative eel sequence reads (metabarcoding analyses) when compared to eel biomass. These ddPCR assays provide a new method for assessing spatial distributions of A. dieffenbachii and A. australis in a range of environments and sample types.

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

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 microbiomes and sediments, most aDNA studies have focused on single taxa or taxonomic groups, making the study of changes at the community level challenging. This is rather surprising because current sequencing and analytical approaches allow us to obtain and analyse aDNA from multiple source materials. When combined, these data can enable the simultaneous study of multiple taxa through space and time, and could thus provide a more comprehensive understanding of ecosystem-wide changes. It is therefore timely to develop an integrative approach to aDNA studies by combining data from multiple taxa and substrates. In this review, we discuss the various applications, associated challenges and future prospects of such an approach.

Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus

Archaeological dental calculus, or mineralized plaque, is a key tool to track the evolution of oral microbiota across time in response to processes that impacted our culture and biology, such as the rise of farming during the Neolithic. However, the extent to which the human oral flora changed from prehistory until present has remained elusive due to the scarcity of data on the microbiomes of prehistoric humans. Here, we present our reconstruction of oral microbiomes via shotgun metagenomics of dental calculus in 44 ancient foragers and farmers from two regions playing a pivotal role in the spread of farming across Europe-the Balkans and the Italian Peninsula. We show that the introduction of farming in Southern Europe did not alter significantly the oral microbiomes of local forager groups, and it was in particular associated with a higher abundance of the species Olsenella sp. oral taxon 807. The human oral environment in prehistory was dominated by a microbial species, Anaerolineaceae bacterium oral taxon 439, that diversified geographically. A Near Eastern lineage of this bacterial commensal dispersed with Neolithic farmers and replaced the variant present in the local foragers. Our findings also illustrate that major taxonomic shifts in human oral microbiome composition occurred after the Neolithic and that the functional profile of modern humans evolved in recent times to develop peculiar mechanisms of antibiotic resistance that were previously absent.

Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment

Cave sediments have been shown to preserve ancient DNA but so far have not yielded the genome-scale information of skeletal remains. We retrieved and analyzed human and mammalian nuclear and mitochondrial environmental "shotgun" genomes from a single 25,000-year-old Upper Paleolithic sediment sample from Satsurblia cave, western Georgia:first, a human environmental genome with substantial basal Eurasian ancestry, which was an ancestral component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe; second, a wolf environmental genome that is basal to extant Eurasian wolves and dogs and represents a previously unknown, likely extinct, Caucasian lineage; and third, a European bison environmental genome that is basal to present-day populations, suggesting that population structure has been substantially reshaped since the Last Glacial Maximum. Our results provide new insights into the Late Pleistocene genetic histories of these three species and demonstrate that direct shotgun sequencing of sediment DNA, without target enrichment methods, can yield genome-wide data informative of ancestry and phylogenetic relationships.

Environmental genomics of Late Pleistocene black bears and giant short-faced bears

Analysis of ancient environmental DNA (eDNA) has revolutionized our ability to describe biological communities in space and time,1-3 by allowing for parallel sequencing of DNA from all trophic levels.4-8 However, because environmental samples contain sparse and fragmented data from multiple individuals, and often contain closely related species,9 the field of ancient eDNA has so far been limited to organellar genomes in its contribution to population and phylogenetic studies.5,6,10,11 This is in contrast to data from fossils12,13 where full-genome studies are routine, despite these being rare and their destruction for sequencing undesirable.14-16 Here, we report the retrieval of three low-coverage (0.03×) environmental genomes from American black bear (Ursus americanus) and a 0.04× environmental genome of the extinct giant short-faced bear (Arctodus simus) from cave sediment samples from northern Mexico dated to 16-14 thousand calibrated years before present (cal kyr BP), which we contextualize with a new high-coverage (26×) and two lower-coverage giant short-faced bear genomes obtained from fossils recovered from Yukon Territory, Canada, which date to ∼22-50 cal kyr BP. We show that the Late Pleistocene black bear population in Mexico is ancestrally related to the present-day Eastern American black bear population, and that the extinct giant short-faced bears present in Mexico were deeply divergent from the earlier Beringian population. Our findings demonstrate the ability to separately analyze genomic-scale DNA sequences of closely related species co-preserved in environmental samples, which brings the use of ancient eDNA into the era of population genomics and phylogenetics.

Peopling of the Americas as inferred from ancient genomics

In less than a decade, analyses of ancient genomes have transformed our understanding of the Indigenous peopling and population history of the Americas. These studies have shown that this history, which began in the late Pleistocene epoch and continued episodically into the Holocene epoch, was far more complex than previously thought. It is now evident that the initial dispersal involved the movement from northeast Asia of distinct and previously unknown populations, including some for whom there are no currently known descendants. The first peoples, once south of the continental ice sheets, spread widely, expanded rapidly and branched into multiple populations. Their descendants-over the next fifteen millennia-experienced varying degrees of isolation, admixture, continuity and replacement, and their genomes help to illuminate the relationships among major subgroups of Native American populations. Notably, all ancient individuals in the Americas, save for later-arriving Arctic peoples, are more closely related to contemporary Indigenous American individuals than to any other population elsewhere, which challenges the claim-which is based on anatomical evidence-that there was an early, non-Native American population in the Americas. Here we review the patterns revealed by ancient genomics that help to shed light on the past peoples who created the archaeological landscape, and together lead to deeper insights into the population and cultural history of the Americas.

A Fast and Efficient Single-stranded Genomic Library Preparation Method Optimized for Ancient DNA

We present a protocol to prepare extracted DNA for sequencing on the Illumina sequencing platform that has been optimized for ancient and degraded DNA. Our approach, the Santa Cruz Reaction or SCR, uses directional splinted ligation of Illumina’s P5 and P7 adapters to convert natively single-stranded DNA and heat denatured double-stranded DNA into sequencing libraries in a single enzymatic reaction. To demonstrate its efficacy in converting degraded DNA molecules, we prepare 5 ancient DNA extracts into sequencing libraries using the SCR and 2 of the most commonly used approaches for preparing degraded DNA for sequencing: BEST, which targets and converts double-stranded DNA, and ssDNA2.0, which targets and converts single-stranded DNA. We then compare the efficiency with which each approach recovers unique molecules, or library complexity, given a standard amount of DNA input. We find that the SCR consistently outperforms the BEST protocol in recovering unique molecules and, despite its relative simplicity to perform and low cost per library, has similar performance to ssDNA2.0 across a wide range of DNA inputs. The SCR is a cost- and time-efficient approach that minimizes the loss of unique molecules and makes accessible a taxonomically, geographically, and a temporally broader sample of preserved remains for genomic analysis.

Metagenomics: A viable tool for reconstructing herbivore diet

Metagenomics can generate data on the diet of herbivores, without the need for primer selection and PCR enrichment steps as is necessary in metabarcoding. Metagenomic approaches to diet analysis have remained relatively unexplored, requiring validation of bioinformatic steps. Currently, no metagenomic herbivore diet studies have utilized both chloroplast and nuclear markers as reference sequences for plant identification, which would increase the number of reads that could be taxonomically informative. Here, we explore how in silico simulation of metagenomic data sets resembling sequences obtained from faecal samples can be used to validate taxonomic assignment. Using a known list of sequences to create simulated data sets, we derived reliable identification parameters for taxonomic assignments of sequences. We applied these parameters to characterize the diet of western capercaillies (Tetrao urogallus) located in Norway, and compared the results with metabarcoding trnL P6 loop data generated from the same samples. Both methods performed similarly in the number of plant taxa identified (metagenomics 42 taxa, metabarcoding 43 taxa), with no significant difference in species resolution (metagenomics 24%, metabarcoding 23%). We further observed that while metagenomics was strongly affected by the age of faecal samples, with fresh samples outperforming old samples, metabarcoding was not affected by sample age. On the other hand, metagenomics allowed us to simultaneously obtain the mitochondrial genome of the western capercaillies, thereby providing additional ecological information. Our study demonstrates the potential of utilizing metagenomics for diet reconstruction but also highlights key considerations as compared to metabarcoding for future utilization of this technique.

Ancient plant DNA reveals High Arctic greening during the Last Interglacial

Summer warming is driving a greening trend across the Arctic, with the potential for large-scale amplification of climate change due to vegetation-related feedbacks [Pearson et al., Nat. Clim. Chang. (3), 673-677 (2013)]. Because observational records are sparse and temporally limited, past episodes of Arctic warming can help elucidate the magnitude of vegetation response to temperature change. The Last Interglacial ([LIG], 129,000 to 116,000 y ago) was the most recent episode of Arctic warming on par with predicted 21st century temperature change [Otto-Bliesner et al., Philos. Trans. A Math. Phys. Eng. Sci. (371), 20130097 (2013) and Post et al., SciAdv (5), eaaw9883 (2019)]. However, high-latitude terrestrial records from this period are rare, so LIG vegetation distributions are incompletely known. Pollen-based vegetation reconstructions can be biased by long-distance pollen transport, further obscuring the paleoenvironmental record. Here, we present a LIG vegetation record based on ancient DNA in lake sediment and compare it with fossil pollen. Comprehensive plant community reconstructions through the last and current interglacial (the Holocene) on Baffin Island, Arctic Canada, reveal coherent climate-driven community shifts across both interglacials. Peak LIG warmth featured a ∼400-km northward range shift of dwarf birch, a key woody shrub that is again expanding northward. Greening of the High Arctic-documented here by multiple proxies-likely represented a strong positive feedback on high-latitude LIG warming. Authenticated ancient DNA from this lake sediment also extends the useful preservation window for the technique and highlights the utility of combining traditional and molecular approaches for gleaning paleoenvironmental insights to better anticipate a warmer future.

An early dog from southeast Alaska supports a coastal route for the first dog migration into the Americas

The oldest confirmed remains of domestic dogs in North America are from mid-continent archaeological sites dated approximately 9900 calibrated years before present (cal BP). Although this date suggests that dogs may not have arrived alongside the first Native Americans, the timing and routes for the entrance of New World dogs remain uncertain. Here, we present a complete mitochondrial genome of a dog from southeast Alaska, dated to 10 150 ± 260 cal BP. We compared this high-coverage genome with data from modern dog breeds, historical Arctic dogs and American precontact dogs (PCDs) from before European arrival. Our analyses demonstrate that the ancient dog belongs to the PCD lineage, which diverged from Siberian dogs around 16 700 years ago. This timing roughly coincides with the minimum suggested date for the opening of the North Pacific coastal (NPC) route along the Cordilleran Ice Sheet and genetic evidence for the initial peopling of the Americas. This ancient southeast Alaskan dog occupies an early branching position within the PCD clade, indicating it represents a close relative of the earliest PCDs that were brought alongside people migrating from eastern Beringia southward along the NPC to the rest of the Americas. The stable isotope δ¹³C value of this early dog indicates a marine diet, different from the younger mid-continent PCDs' terrestrial diet. Although PCDs were largely replaced by modern European dog breeds, our results indicate that their population decline started approximately 2000 years BP, coinciding with the expansion of Inuit peoples, who are associated with traditional sled-dog culture. Our findings suggest that dogs formed part of the initial human habitation of the New World, and provide insights into their replacement by both Arctic and European lineages.

Environmental palaeogenomic reconstruction of an Ice Age algal population

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 Nannochloropsis. We shotgun sequenced two lake sediment samples dated to the Last Glacial Maximum and reconstructed full chloroplast and mitochondrial genomes to explore within-lake population genomic variation. This revealed two major haplogroups for each organellar genome, which could be assigned to known varieties of N. limnetica, although we show that at least three haplotypes were present using our minimum haplotype diversity estimation method. These approaches demonstrate the utility of lake sedimentary ancient DNA (sedaDNA) for population genomic analysis, thereby opening the door to environmental palaeogenomics, which will unlock the full potential of sedaDNA.

Lammers et al. use sedimentary ancient DNA to reconstruct palaeogenomes of Nannochloropsis. This study demonstrates the value of sedaDNA for palaeogenomic reconstructions and population genomic analysis.

Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest

Siberian larch (Larix Mill.) forests dominate vast areas of northern Russia and contribute important ecosystem services to the world. It is important to understand the past dynamics of larches in order to predict their likely response to a changing climate in the future. Sedimentary ancient DNA extracted from lake sediment cores can serve as archives to study past vegetation. However, the traditional method of studying sedimentary ancient DNA-metabarcoding-focuses on small fragments, which cannot resolve Larix to species level nor allow a detailed study of population dynamics. Here, we use shotgun sequencing and hybridization capture with long-range PCR-generated baits covering the complete Larix chloroplast genome to study Larix populations from a sediment core reaching back to 6700 years from the Taymyr region in northern Siberia. In comparison with shotgun sequencing, hybridization capture results in an increase in taxonomically classified reads by several orders of magnitude and the recovery of complete chloroplast genomes of Larix. Variation in the chloroplast reads corroborates an invasion of Larix gmelinii into the range of Larix sibirica before 6700 years ago. Since then, both species have been present at the site, although larch populations have decreased with only a few trees remaining in what was once a forested area. This study demonstrates for the first time that hybridization capture applied directly to ancient DNA of plants extracted from lake sediments can provide genome-scale information and is a viable tool for studying past genomic changes in populations of single species, irrespective of a preservation as macrofossil.