The advent of genome-wide ancient DNA analysis has revolutionized our understanding of prehistoric societies. However, studying biological relatedness in these groups requires tailored approaches due to the challenges of analyzing ancient DNA. READv2, an optimized Python3 implementation of the most widely used tool for this purpose, addresses these challenges while surpassing its predecessor in speed and accuracy. For sufficient amounts of data, it can classify up to third-degree relatedness and differentiate between the two types of first-degree relatedness, full siblings and parent-offspring. READv2 enables user-friendly, efficient, and nuanced analysis of biological relatedness, facilitating a deeper understanding of past social structures.

Barley is one of the founder crops of the Neolithic transition in West Asia. While recent advances in genomics have provided a rather detailed picture of barley domestication, there are contradictory views on how the domestication process affected genetic diversity. We set out to revisit this question by integrating public DNA sequencing data from ancient barley and wide collections of extant wild and domesticated accessions. Using two previously overlooked approaches - analyses of chloroplast genomes and genome-wide proportions of private variants - we found that the barley cultivated six millennia ago was genetically unique and more diverse when compared to extant landraces and cultivars. Moreover, the chloroplast genomes revealed a link between the ancient barley, an obscure wild genotype from north-eastern Libya, and a distinct population of barley cultivated in Ethiopia/Eritrea. Based on these results, we hypothesize past existence of a wider North African population that included both wild and cultivated types and suffered from genetic erosion in the past six millennia, likely due to a rapid desertification that ended the Holocene African humid period. Besides providing clues about the origin of Ethiopian landraces, the hypothesis explains the post-domestication loss of diversity observed in barley. Analyses of additional samples will be necessary to resolve the history of African barley and its contribution to the extant cultivated gene pool.

Sirenia, an iconic marine taxon with a tropical and subtropical worldwide distribution, face an uncertain future. All species are designated \'Vulnerable\' to extinction by the IUCN. Nonetheless, a comprehensive understanding of geographic structuring across the global range is lacking, impeding our ability to highlight particularly vulnerable populations for conservation priority. Here, we use ancient DNA to investigate dugong (Dugong dugon) population structure, analysing 56 mitogenomes from specimens comprising the known historical range. Our results reveal geographically structured and distinct monophyletic clades characterized by contrasting evolutionary histories. We observe deep-rooted and divergent lineages in the East (Indo-Pacific) and obtain new evidence for the relatively recent dispersal of dugongs into the western Indian Ocean. All populations are significantly differentiated from each other with western populations having approximately 10-fold lower levels of genetic variation than eastern Indo-Pacific populations. Additionally, we find a significant temporal loss of genetic diversity in western Indian Ocean dugongs since the mid-twentieth century, as well as a decline in population size beginning approximately 1000 years ago. Our results add to the growing body of evidence that dugong populations are becoming ever more susceptible to ongoing human action and global climate change.

Connaraceae is a pantropical family of about 200 species containing lianas and small trees with remarkably diverse floral polymorphisms, including distyly, tristyly, homostyly, and dioecy. To date, relationships within the family have not been investigated using a targeted molecular phylogenetic treatment, severely limiting systematic understanding and reconstruction of trait evolution. Accordingly, their last infrafamilial classification was based only on morphological data. Here, we used phylogenomic data obtained using the Angiosperms353 nuclear target sequence capture probes, sampling all tribes and almost all genera, entirely from herbarium specimens, to revise infrafamilial classification and investigate the evolution of heterostyly. The backbone of the resulting molecular phylogenetic tree is almost entirely resolved. Connaraceae consists of two clades, one containing only the African genus Manotes (4 or 5 species), which we newly recognize at the subfamily level. Vegetative and reproductive synapomorphies are proposed for Manotoideae. Within Connaroideae, Connareae is expanded to include the former Jollydoreae. The backbone of Cnestideae, which contains more than half of the Connaraceae species, remains incompletely resolved. Reconstructions of reproductive system evolution are presented that tentatively support tristyly as the ancestral state for the family, with multiple parallel losses, in agreement with previous hypotheses, plus possible re-gains. However, the great diversity of stylar polymorphisms and their phylogenetic lability preclude a definitive answer. Overall, this study reinforces the usefulness of herbarium phylogenomics, and unlocks the reproductive diversity of Connaraceae as a model system for the evolution of complex biological phenomena.
UNASSIGNED: The online version contains supplementary material available at 10.1007/s00606-024-01909-y.

We here present CLUES2, a full-likelihood method to infer natural selection from sequence data that is an extension of the method CLUES. We make several substantial improvements to the CLUES method that greatly increases both its applicability and its speed. We add the ability to use ancestral recombination graphs on ancient data as emissions to the underlying hidden Markov model, which enables CLUES2 to use both temporal and linkage information to make estimates of selection coefficients. We also fully implement the ability to estimate distinct selection coefficients in different epochs, which allows for the analysis of changes in selective pressures through time, as well as selection with dominance. In addition, we greatly increase the computational efficiency of CLUES2 over CLUES using several approximations to the forward-backward algorithms and develop a new way to reconstruct historic allele frequencies by integrating over the uncertainty in the estimation of the selection coefficients. We illustrate the accuracy of CLUES2 through extensive simulations and validate the importance sampling framework for integrating over the uncertainty in the inference of gene trees. We also show that CLUES2 is well-calibrated by showing that under the null hypothesis, the distribution of log-likelihood ratios follows a χ2 distribution with the appropriate degrees of freedom. We run CLUES2 on a set of recently published ancient human data from Western Eurasia and test for evidence of changing selection coefficients through time. We find significant evidence of changing selective pressures in several genes correlated with the introduction of agriculture to Europe and the ensuing dietary and demographic shifts of that time. In particular, our analysis supports previous hypotheses of strong selection on lactase persistence during periods of ancient famines and attenuated selection in more modern periods.

The medieval period in Sicily was turbulent, involving successive regime changes, from Byzantine (Greek Christian), Aghlabid (Sunni Muslim), Fatimid (Shī\'a Muslim), to Normans and Swabians (Latin Christian). To shed new light on the local implications of regime changes, we conducted a multidisciplinary analysis of 27 individuals buried in adjacent Muslim and Christian cemeteries at the site of Segesta, western Sicily. By combining radiocarbon dating, genome-wide sequencing, stable and radiogenic isotopic data, and archaeological records, we uncover genetic differences between the two communities but find evidence of continuity in other aspects of life. Historical and archaeological evidence shows a Muslim community was present by the 12th century during Norman governance, with the Christian settlement appearing in the 13th century under Swabian governance. A Bayesian analysis of radiocarbon dates from the burials finds the abandonment of the Muslim cemetery likely occurred after the establishment of the Christian cemetery, indicating that individuals of both faiths were present in the area in the first half of the 13th century. The biomolecular results suggest the Christians remained genetically distinct from the Muslim community at Segesta while following a substantially similar diet. This study demonstrates that medieval regime changes had major impacts beyond the political core, leading to demographic changes while economic systems persisted and new social relationships emerged.

Dingoes are culturally and ecologically important free-living canids whose ancestors arrived in Australia over 3,000 B.P., likely transported by seafaring people. However, the early history of dingoes in Australia-including the number of founding populations and their routes of introduction-remains uncertain. This uncertainty arises partly from the complex and poorly understood relationship between modern dingoes and New Guinea singing dogs, and suspicions that post-Colonial hybridization has introduced recent domestic dog ancestry into the genomes of many wild dingo populations. In this study, we analyzed genome-wide data from nine ancient dingo specimens ranging in age from 400 to 2,746 y old, predating the introduction of domestic dogs to Australia by European colonists. We uncovered evidence that the continent-wide population structure observed in modern dingo populations had already emerged several thousand years ago. We also detected excess allele sharing between New Guinea singing dogs and ancient dingoes from coastal New South Wales (NSW) compared to ancient dingoes from southern Australia, irrespective of any post-Colonial hybrid ancestry in the genomes of modern individuals. Our results are consistent with several demographic scenarios, including a scenario where the ancestry of dingoes from the east coast of Australia results from at least two waves of migration from source populations with varying affinities to New Guinea singing dogs. We also contribute to the growing body of evidence that modern dingoes derive little genomic ancestry from post-Colonial hybridization with other domestic dog lineages, instead descending primarily from ancient canids introduced to Sahul thousands of years ago.

The Neolithic transition introduced major diet and lifestyle changes to human populations across continents. Beyond well-documented bioarcheological and genetic effects, whether these changes also had molecular-level epigenetic repercussions in past human populations has been an open question. In fact, methylation signatures can be inferred from UDG-treated ancient DNA through postmortem damage patterns, but with low signal-to-noise ratios; it is thus unclear whether published paleogenomes would provide the necessary resolution to discover systematic effects of lifestyle and diet shifts. To address this we compiled UDG-treated shotgun genomes of 13 pre-Neolithic hunter-gatherers (HGs) and 21 Neolithic farmers (NFs) individuals from West and North Eurasia, published by six different laboratories and with coverage c.1×-58× (median = 9×). We used epiPALEOMIX and a Monte Carlo normalization scheme to estimate methylation levels per genome. Our paleomethylome dataset showed expected genome-wide methylation patterns such as CpG island hypomethylation. However, analyzing the data using various approaches did not yield any systematic signals for subsistence type, genetic sex, or tissue effects. Comparing the HG-NF methylation differences in our dataset with methylation differences between hunter-gatherers versus farmers in modern-day Central Africa also did not yield consistent results. Meanwhile, paleomethylome profiles did cluster strongly by their laboratories of origin. Using larger data volumes, minimizing technical noise and/or using alternative protocols may be necessary for capturing subtle environment-related biological signals from paleomethylomes.

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.

This study analyzed ancient DNA from the remains of horses unearthed from the Shihuyao tombs. These were found to date from the Han and Tang Dynasties in Xinjiang (approximately 2200 to 1100 years ago). Two high-quality mitochondrial genomes were acquired and analyzed using next-generation sequencing. The genomes were split into two maternal haplogroups, B and D, according to a study that included ancient and contemporary samples from Eurasia. A close genetic affinity was observed between the horse of the Tang Dynasty and Akhal-Teke horses according to the primitive horse haplotype G1. Historical evidence suggests that the ancient Silk Road had a vital role in their dissemination. Additionally, the matrilineal history of the Akhal-Teke horse was accessed and suggested that the early domestication of the breed was for military purposes.