The genomic study of specimens dating to the Early and Middle Pleistocene (EP and MP), a period spanning from 2.6 million years ago (Ma) to 126 thousand years ago (ka), has the potential to elucidate the evolutionary processes that shaped present-day biodiversity. Obtaining genomic data from this period is challenging, but mitochondrial DNA, given its higher abundance compared to nuclear DNA, could play an important role to understand evolutionary processes at this time scale. In this study, we report 34 new mitogenomes, including two EP and nine MP mammoth (Mammuthus spp.) specimens from Siberia and North America and analyze them jointly with >200 publicly available mitogenomes to reconstruct a transect of mammoth mitogenome diversity throughout the last million years. We find that our EP mitogenomes fall outside the diversity of all Late Pleistocene (LP) mammoths, while those derived from MP mammoths are basal to LP mammoth Clades 2 and 3, supporting an ancient Siberian origin of these lineages. In contrast, the geographical origin of Clade 1 remains unresolved. With these new deep-Time mitogenomes, we observe diversification events across all clades that appear consistent with previously hypothesized MP and LP demographic changes. Furthermore, we improve upon an existing methodology for molecular clock dating of specimens >50 ka, demonstrating that specimens need to be individually dated to avoid biases in their age estimates. Both the molecular and analytical improvements presented here highlight the importance of deep-Time genomic data to discover long-lost genetic diversity, enabling better assessments of evolutionary histories.

Ancient genomic studies have extensively explored human-microbial interactions, yet research on non-human animals remains limited. In this study, we analyzed ancient microbial DNA from 483 mammoth remains spanning over 1 million years, including 440 newly sequenced and unpublished samples from a 1.1-million-year-old steppe mammoth. Using metagenomic screening, contaminant filtering, damage pattern analysis, and phylogenetic inference, we identified 310 microbes associated with different mammoth tissues. While most microbes were environmental or post-mortem colonizers, we recovered genomic evidence of six host-associated microbial clades spanning Actinobacillus, Pasteurella, Streptococcus, and Erysipelothrix. Some of these clades contained putative virulence factors, including a Pasteurella-related bacterium that had previously been linked to the deaths of African elephants. Notably, we reconstructed partial genomes of Erysipelothrix from the oldest mammoth sample, representing the oldest authenticated host-associated microbial DNA to date. This work demonstrates the potential of obtaining ancient animal microbiomes, which can inform further paleoecological and evolutionary research.

The assessment of sex is fundamental in osteoarcheological analysis, yet traditional morphological methods are less reliable for children due to the incomplete development of sexually dimorphic traits. This study applies a multi-method approach—integrating morphological, metric, and genetic data—to assess sex and, through analysis of burial assemblages, explore gender expression as an interpretative complement. While analytically distinct, gender and sex are deeply intertwined, and considering both can offer a fuller understanding of identity.

The study focuses on the Viking Age (c. 750–1050 ce) burial site of Ihre, Gotland, with particular attention to individuals under 20. Results reveal strong alignment between metric and genetic sex. Mandibular odontometric analysis proved more consistent than traditional morphological traits when compared to genetic sex, offering an accessible and effective supplement for sex estimation in children. In adolescents, pelvic traits were most informative, while cranial traits showed limited reliability. Genetic sexing provided a critical reference, highlighting misclassifications in morphological assessments, particularly among genetic males.

Burial assemblage analysis indicates that gender expression often corresponded with biological sex but varied with age. Female graves typically included dress items such as brooches and pendants, especially after adolescence, while male graves more frequently featured tools and weapons. These patterns suggest that gendered roles and identities were materially expressed and changed over the life course.

The findings underscore the importance of a multi-method approach in sex estimation, particularly for children, and demonstrate the value of contextual archeological analysis in interpreting past identities. At Ihre, the interplay between sex, gender, and social identity in mortuary practices suggests a framework that, while broadly organized around binary distinctions, was shaped by age and culturally specific factors—highlighting identity as dynamic, layered, and context-dependent.

INTRODUCTION: Çatalhöyük is a Neolithic settlement in Anatolia and a United Nations Educational, Scientific and Cultural Organization (UNESCO) World Heritage Site. Occupied for 1000 years (7000 to 6000 BCE), it is renowned for its size, apparent egalitarian social structure, and subfloor burials, where children and adults were buried within houses during their use. It is also known for its large corpus of female figurines, which were long debated as possible representatives of a “Mother Goddess” cult and signs of a matriarchal society.

RATIONALE: In this work, we studied social organization at Çatalhöyük, fusing rich archaeological data with a paleogenomic dataset of 131 individuals buried in 35 houses. We focused on identifying genetic ties between individuals buried together inside the same buildings.

RESULTS: Comparing genetic ties within and between buildings, we found that the maternal lineage had a key role in connecting Çatalhöyük household members, as represented by burials within each building. We estimated that 70 to 100% of the time, female offspring remained connected to buildings, whereas adult male offspring may have moved away. We also discovered preferential treatment of female infant and child burials, with five times more grave goods offered to females than to males.

Our data further show how social organization patterns changed over time in Çatalhöyük. In the early phases of the settlement, individuals buried together within houses frequently represented extended family members. Through time, the genetic composition of house burials became less homogeneous. In later periods, we found groups of neonates who were genetically unrelated but buried in the same house. Meanwhile, their mothers appear to have had similar diets. This implies that genetic relatedness became less central to social organization over time, which could be explained by fostering and adoption-like mechanisms becoming widespread, which is also observed today in various societies. Despite this shift, female-centered practices continued at Çatalhöyük through the occupation.

CONCLUSION: Our results reveal the malleable nature of social organization in Neolithic villages, with the composition of households possibly changing within a few dozen generations. We also found the first direct indication of female-centered practices in Neolithic Southwest Asia, a question of frequent debate. This female focus identified in Çatalhöyük is in sharp contrast to patterns observed in later European Neolithic sites, which have their origins in Anatolia. Many of these European societies show evidence of patrilocality—where males stay within their natal community upon attaining adulthood and females move out—and elaborate burial treatments that are frequently associated with males. The Çatalhöyük evidence now shows that such male-centered practices were not an inherent characteristic of early agricultural societies.

Many known and unknown historical events have remained below detection thresholds of genetic studies because subtle ancestry changes are challenging to reconstruct. Methods based on shared haplotypes1,2 and rare variants3,4 improve power but are not explicitly temporal and have not been possible to adopt in unbiased ancestry models. Here we develop Twigstats, an approach of time-stratified ancestry analysis that can improve statistical power by an order of magnitude by focusing on coalescences in recent times, while remaining unbiased by population-specific drift. We apply this framework to 1,556 available ancient whole genomes from Europe in the historical period. We are able to model individual-level ancestry using preceding genomes to provide high resolution. During the first half of the first millennium ce, we observe at least two different streams of Scandinavian-related ancestry expanding across western, central and eastern Europe. By contrast, during the second half of the first millennium ce, ancestry patterns suggest the regional disappearance or substantial admixture of these ancestries. In Scandinavia, we document a major ancestry influx by approximately 800 ce, when a large proportion of Viking Age individuals carried ancestry from groups related to central Europe not seen in individuals from the early Iron Age. Our findings suggest that time-stratified ancestry analysis can provide a higher-resolution lens for genetic history.

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.

Rapid and minimally destructive methods for estimating the endogenous organic content of subfossil bone save time, lab consumables, and valuable ancient materials. Fourier transform infrared (FTIR) spectroscopy is an established method to estimate bone protein content, and portable spectroscopes enable field applications. We review the ability of benchtop and portable FTIR indices to predict %N and %collagen from 137 bone specimens drawn from eight taxa. We also explore associations of these indices with the endogenous DNA content estimated for 105 specimens. Bulk bone elemental abundance and crystallinity index data reflect diagenetic alteration of these specimens, which come from a variety of depositional environments in four countries (Madagascar, Greece, Monaco, and Germany). Infrared (IR) indices from benchtop and portable units perform similarly well in predicting observed sample N content and collagen yields. Samples that include little collagen (0–5 wt%) tend to have similar IR index values, and we present a Bayesian approach for the prediction of collagen yields. Bone type best explains variation in target species DNA content (endogenous DNA being particularly abundant in petrosals), but low IR index values were consistently associated with minimal DNA content. We conclude that, although portable FTIR fails to distinguish collagen preservation among poorly preserved samples, a simple approach with minimal sample preparation can effectively screen bone from a variety of taxa, elements, and environments for the extraction of organics.

Between the 8th and 11th centuries CE, the Iberian Peninsula underwent profound upheaval due to the Umayyad invasion against the Visigoths, resulting in population shifts and lasting demographic impacts. Our understanding of this period is hindered by limited written sources and few archaeogenetic studies. We analyzed 33 individuals from Las Gobas, a necropolis in northern Spain, spanning the 7th to 11th centuries. By combining archaeological and osteological data with kinship, metagenomics, and ancestry analyses, we investigate conflicts, health, and demography of these individuals. We reveal intricate family relationships and genetic continuity within a consanguineous population while also identifying several zoonoses indicative of close interactions with animals. Notably, one individual was infected with a variola virus phylogenetically clustering with the northern European variola complex between ~885 and 1000 CE. Last, we did not detect a significant increase of North African or Middle East ancestries over time since the Islamic conquest of Iberia, possibly because this community remained relatively isolated.

With the Neolithic transition, human lifestyle shifted from hunting and gathering to farming. This change altered subsistence patterns, cultural expression, and population structures as shown by the archaeological/zooarchaeological record, as well as by stable isotope and ancient DNA data. Here, we used metagenomic data to analyse if the transitions also impacted the microbiome composition in 25 Mesolithic and Neolithic hunter-gatherers and 13 Neolithic farmers from several Scandinavian Stone Age cultural contexts. Salmonella enterica, a bacterium that may have been the cause of death for the infected individuals, was found in two Neolithic samples from Battle Axe culture contexts. Several species of the bacterial genus Yersinia were found in Neolithic individuals from Funnel Beaker culture contexts as well as from later Neolithic context. Transmission of e.g. Y. enterocolitica may have been facilitated by the denser populations in agricultural contexts.

Prehistoric chewed pitch has proven to be a useful source of ancient DNA, both from humans and their microbiomes. Here we present the metagenomic analysis of three pieces of chewed pitch from Huseby Klev, Sweden, that were dated to 9,890–9,540 before present. The metagenomic profile exposes a Mesolithic oral microbiome that includes opportunistic oral pathogens. We compared the data with healthy and dysbiotic microbiome datasets and we identified increased abundance of periodontitis-associated microbes. In addition, trained machine learning models predicted dysbiosis with 70–80% probability. Moreover, we identified DNA sequences from eukaryotic species such as red fox, hazelnut, red deer and apple. Our results indicate a case of poor oral health during the Scandinavian Mesolithic, and show that pitch pieces have the potential to provide information on material use, diet and oral health.