Archaeological and palaeogenomic data show that dogs were the only domestic animals introduced during the early peopling of the Americas. Hunter-gatherer groups spread quickly towards the south of the continent, but it is unclear when dogs reached Central and South America. To address this issue, we generated and analysed 70 complete mitochondrial genomes from archaeological and modern dogs ranging from Central Mexico to Central Chile and Argentina, revealing the dynamics of dog populations. Our results demonstrate that pre-contact Central and South American dogs are all assigned to a specific clade that diverged after dogs entered North America. Specifically, the divergence time between North, Central and South American dog clades is consistent with the spread of agriculture and the adoption of maize in South America between 7000 and 5000 years ago. An isolation-by-distance best characterizes how dogs expanded into South America. We identify the arrival of new lineages of dogs in post-contact South America, likely of European origin, and their legacy in modern village dogs. Interestingly, the pre-contact Mesoamerican maternal origin of the Chihuahua has persisted in some modern individuals.

As the first domestic species, dogs likely dispersed with different cultural groups during the Late Pleistocene and Holocene. To test this hypothesis, we analyzed 73 ancient dog genomes, including 17 newly sequenced individuals sampled from East Asia to the West Eurasian Steppe spanning nearly 10,000 years. Our results indicate correlations between the ancestry of dogs and specific ancient human populations from eastern Europe to Eastern Siberia, including Ancient Paleo-Siberians, Eastern hunter-gatherers, East Asians, and Steppe pastoralists. We also identify multiple shifts in the ancestry of dogs that coincide with specific dispersals of hunter-gatherers, farmers, and pastoralists. Combined, our results reveal the long-term and integral role that dogs played in a multitude of human societies.

Distinguishing early domesticates from their wild progenitors presents a significant obstacle for understanding human-mediated effects in the past. The origin of dogs is particularly controversial because potential early dog remains often lack corroborating evidence that can provide secure links between proposed dog remains and human activity. The Tumat Puppies, two permafrost-preserved Late Pleistocene canids, have been hypothesized to have been littermates and early domesticates due to a physical association with putatively butchered mammoth bones. Through a combination of osteometry, stable isotope analysis, plant macrofossil analysis, and genomic and metagenomic analyses, this study exploits the unique properties of the naturally mummified Tumat Puppies to examine their familial relationship and to determine whether dietary information links them to human activities. The multifaceted analysis reveals that the 14,965–14,046 cal yr BP Tumat Puppies were littermates who inhabited a dry and relatively mild environment with heterogeneous vegetation and consumed a diverse diet, including woolly rhinoceros in their final days. However, because there is no evidence of mammoth consumption, these data do not establish a link between the canids and ancient humans.

Dogs exhibit an exceptional range of morphological diversity as a result of their long-term association with humans. Attempts to identify when dog morphological variation began to expand have been constrained by the limited number of Pleistocene specimens, the fragmentary nature of remains, and difficulties in distinguishing early dogs from wolves on the basis of skeletal morphology. In this study, we used three-dimensional geometric morphometrics to analyze the size and shape of 643 canid crania spanning the past 50,000 years. our analyses show that a distinctive dog morphology first appeared at about 11,000 calibrated years before present, and substantial phenotypic diversity already existed in early Holocene dogs. Thus, this variation emerged many millennia before the intense human-mediated selection shaping modern dog breeds beginning in the 19th century.

Thermospores, the dormant resting stages of thermophilic bacteria, have been shown to be frequent but enigmatic components of cold marine sediments around the world. Multiple hypotheses have been proposed to explain their distribution, emphasizing their potential as model organisms for studying microbial dispersal via ocean currents. In the Arctic Ocean, the abundance and diversity of thermospores have previously been assumed to be low. However, this assessment has been based on data mainly from the western fjords of Svalbard, thus leaving most of the Arctic unexplored. Here, we expand the knowledge about the distribution of thermospores in the Arctic Ocean by investigating the abundance and diversity of thermospores in heated shelf sediments from three sites in the outer Laptev Sea. Two of the sites are located in an area with methane-emitting cold seeps with a thermogenic source signature suggestive of an origin in a deep hydrocarbon reservoir, while the third site is a reference site not known to be impacted by seepage. We found that activity of viable thermospore populations was more prominent at one of the investigated seep sites. This finding is supported by both radiotracer growth experiments showing thermophilic, sulfate-reducing activity triggered by heating, as well as 16S gene sequence analyses showing significantly enriched ASVs affiliated to the phylum Firmicutes following high-temperature incubations. An enrichment of the sulfate-reducing, endospore-forming class Desulfotomaculia in heated samples compared to unheated samples was also observed. Furthermore, several ASVs identified at the seep site are closely related to thermospore-producing bacteria associated with the deep biosphere, including hydrocarbon and hydrothermal systems. Based on the combined information from induced activity, estimated abundance, and phylogenetic composition using 16S rRNA gene sequencing, we propose likely source environments and dispersal vectors for thermospores in the Arctic Ocean.

Ancient DNA (aDNA) obtained from human remains is typically fragmented and present in relatively low amounts. Here we investigate a set of optimal methods for producing aDNA data by comparing silica-based DNA extraction and aDNA library preparation protocols. We also test the efficiency of whole-genome enrichment (WGC) on ancient human samples by modifying a number of parameter combinations. We find that the Dabney extraction protocol performs significantly better than alternatives. We further observed a positive trend with the BEST library protocol indicating lower clonality. Notably, our results suggest that WGC is effective at retrieving endogenous DNA, particularly from poorly-preserved human samples, by increasing human endogenous proportions by 5x. Thus, aDNA studies will be most likely to benefit from our results.

The analysis of coprolites provides direct evidence of resources consumed and may be paired with ethnographic data to elucidate the dietary and medicinal use of plants in archaeological communities. This article combines and contrasts the macroscopic analysis and DNA metabarcoding of 10 coprolites from Bonneville Estates Rockshelter, Nevada, USA. While the results from both methods confirm previous understandings of subsistence practices at the site, minimal overlap in identified taxa suggests that each accesses different components of the consumed material. The two methods should therefore be seen as complementary and employed together, where possible.

How can we better understand the human agency in prehistory? A recent study explores a novel way of using sedimentary DNA extracted from sediments of a rock shelter to investigate the human impact on the landscape.

The postglacial recolonization of Fennoscandian flora and fauna was initiated when the land became accessible as the last ice sheet retreated. In northern Sweden, plants are represented in pollen and macrofossil records, but there is no genetic evidence from the first plants, animals or humans in the region, mainly owing to an absence of osteological finds. The questions of who the first postglacial peoples, or pioneers, were and where they came from therefore remain unanswered. Previous palaeogenomic analyses from remains from adjacent regions have suggested that two main routes into Sweden could have been taken by the pioneers, one from the SW through modern-day Denmark and Norway, and one from the east via Finland. However, no direct genetic evidence from the pioneers of northern Sweden exists. Modern technology has provided the ancient DNA field with an updated toolbox that could allow for novel approaches for revealing the origin and genetic profiles of the first Scandinavians, of which sedimentary ancient DNA (sedaDNA) is well placed. Lake sediments are now a routine source of sedaDNA that have been used to record environmental changes and detect species that lived in the surrounding lake catchment. This review will provide context and background, a summary of the ground-breaking studies within the field of lacustrine sedaDNA, and relevant methodology to address the scientific questions at hand. We conclude that the field is mature enough to provide insight into the origins and arrival times of the first postglacial humans that migrated into northern Sweden.

This article discusses ethical frameworks for planning and implementing composite research in the United States. Composites, defined here as archaeological materials with multiple genetic sources, include materials such as sediment, coprolites, birch pitch, and dental calculus. Although composites are increasingly used in genetic research, the ethical considerations of their use in ancient DNA studies have not been widely discussed. Here, we consider how composites' compositions, contexts, and potential to act as proxies can affect research plans and offer an overview of the primary ethical concerns of ancient DNA research. It is our view that ethical principles established for analyses of Ancestral remains and related materials can be used to inform research plans when working with composite evidence. This work also provides a guide to archaeologists unfamiliar with genetics analyses in planning research when using composite evidence from the United States with a focus on collaboration, having a clear research plan, and using lab methods that provide the desired data with minimal destruction. Following the principles discussed in this article and others allows for engaging in composite research while creating and maintaining positive relationships with stakeholders. El presente trabajo analiza las preocupaciones eticas para la planificacion e implementacion de investigaciones compuestas en los Estados Unidos. Los compuestos, definidos aqui como muestras arqueologicas con multiples fuentes geneticas, incluyen materiales como sedimentos, paleofecas, brea de abedul y calculo dental. Sin embargo, si bien los compuestos se han utilizado cada vez mas en la investigacion genetica arqueologica, las consideraciones eticas de su uso en estudios de aADN no se han discutido ampliamente. Aqui consideramos como las composiciones, los contextos y el potencial de los compuestos para actuar como sustitutos pueden afectar los planes de investigacion y ofrecer una vision general de las principales preocupaciones eticas de la investigacion del ADN antiguo. Es la opinion de los autores que los principios eticos establecidos para los analisis de restos humanos y materiales relacionados se pueden utilizar para informar los planes de investigacion cuando se trabaja con evidencia compuesta. Este trabajo ofrece tambien una guia para planificar la investigacion cuando se utiliza evidencia compuesta con un enfoque en la colaboracion, en planes de investigacion claros y uso de metodos de laboratorio que proporcionen los datos deseados con una destruccion minima de la muestra. Seguir los principios descritos en este documento permite participar en la investigacion compuesta sin dejar de lado la creacion y mantencion de relaciones positivas con las partes interesadas.