Background Islands harbour exceptional concentrations of endemic biodiversity, yet their biotas have been profoundly reshaped by human colonisation. In the Azores, deforestation and the introduction of invasive mammals drove major ecological transformations, and the fossil record reveals that the archipelago once supported avian communities far more diverse than those of today. During palaeontological expeditions conducted between 2011 and 2018, we recovered cranial and postcranial remains from several islands that were unambiguously assigned to the genus Fringilla , but exhibited substantially enlarged cranial morphology relative to the extant Azorean common chaffinch ( F. moreletti ). Remarkably, skull and beak proportions closely resembled those of the Canary Islands blue chaffinches ( F. teydea and F. polatzeki ), raising the possibility of a shared evolutionary origin. Results Using endogenous DNA extracted from fossil remains, we reconstructed complete or near-complete mitochondrial genomes from seven individuals. Combined with dense taxonomic sampling and whole-genome resequencing across Fringilla , these data enabled reconstruction of the evolutionary history of the Azorean forms. Contrary to expectations based on morphology, phylogenetic analyses unequivocally placed the extinct giant morphotypes within the clade of extant Azorean common chaffinches. Conclusions These findings reveal an extraordinary degree of ecological plasticity in passerines and demonstrate that pronounced morphological divergence can evolve without substantial genome-wide divergence. More broadly, our results highlight the importance of integrating genomic and morphological evidence when reconstructing the evolutionary history of extinct island taxa.

A surge of genetic data from the skeletal remains of Neanderthals disproves some assumptions and generates fresh questions about these ancient hominins. A surge of genetic data from the skeletal remains of Neanderthals disproves some assumptions and generates fresh questions about these ancient hominins.

ABSTRACT The introduction of agriculture in Western Eurasia during the Mesolithic-Neolithic transition reshaped human lifestyle, demography and pathogen exposure. Yet, the associated selective pressures remain incompletely resolved because previous ancient DNA studies relied on targeted SNP panels and yielded non-overlapping results. Here, using high-coverage whole-genome data from 152 ancient individuals, including 12 newly sequenced genomes from the Iron Gates, we show that adaptation during this transition was geographically structured and involved selection of both Early Farmer and Hunter-Gatherer alleles. By combining scans of population differentiation, extended haplotype homozygosity, and adaptive admixture, we identify candidate loci under selection in ancestral and admixed populations. Extending the analysis beyond SNPs, we also detect differential copy-number variants, ancestry-associated shifts in transposable-element abundance, and an early Neolithic hepatitis B infection. Functional analyses including effects on gene expression suggested selection on immune, metabolic, reproductive, sensory, and behavioural processes. Taken together, our results reveal a broader and more regionally variable adaptive landscape than previously appreciated.

The infection of humans by the causal agent of Plague, Yersinia pestis , has been attested as far back as 5,500 BP. Although the specific patho-mechanism and ultimate origin of the disease caused by these prehistoric genomes remains unclear, the bacterium spread through Europe, likely during the Late Neolithic to Bronze Age (LNBA). In this study, we analysed 9 genomic samples originating from 8 different human individuals dating to around 4950 cal BP from the site of Grotta della Spinosa, Tuscany, Italy. Metagenomic screening of these samples reveals one individual (GSP013) to be co-infected by Yersinia pestis, Erysipelothrix rhusiopathiae, and Hepatitis B virus (HBV). At least three further individuals from the site were infected with HBV, indicating its wider presence within the community. The phylogenetic placement of Y. pestis in GSP013 shows that this strain is closely related to the earliest LNBA Caucasus genomes of the bacterium, basal to later European diversity. This represents the earliest evidence of Y. pestis in the Italian peninsula (and Southern Europe more widely) to date, predating previously discovered genomes by at least 200 years. Furthermore, we retrieved 60 newly reported ancient genomes of Erysipelothrix rhusiopathiae and Erysipelothrix tonsillarum from animals and humans, dating back from 8,300 BP to 100 BP. Of these new genomes, 15 of which stem from individuals known to be infected by Y. pestis . This contributes to our understanding of Y. pestis transmission in prehistoric Europe and possible reservoirs, and offers insights into disease dynamics in communities during the 3rd millennium BCE.

The maritime Phoenician civilization from the Levant transformed the entire Mediterranean during the first millennium BCE1-3. However, the extent of human movement between the Levantine Phoenician homeland and Phoenician-Punic settlements in the central and western Mediterranean has been unclear in the absence of comprehensive ancient DNA studies. Here, we generated genome-wide data for 210 individuals, including 196 from 14 sites traditionally identified as Phoenician and Punic in the Levant, North Africa, Iberia, Sicily, Sardinia and Ibiza, and an early Iron Age individual from Algeria. Levantine Phoenicians made little genetic contribution to Punic settlements in the central and western Mediterranean between the sixth and second centuries BCE, despite abundant archaeological evidence of cultural, historical, linguistic and religious links4. Instead, these inheritors of Levantine Phoenician culture derived most of their ancestry from a genetic profile similar to that of Sicily and the Aegean. Much of the remaining ancestry originated from North Africa, reflecting the growing influence of Carthage5. However, this was a minority contributor of ancestry in all of the sampled sites, including in Carthage itself. Different Punic sites across the central and western Mediterranean show similar patterns of high genetic diversity. We also detect genetic relationships across the Mediterranean, reflecting shared demographic processes that shaped the Punic world.

The oral pathobiont Streptococcus mutans can contribute to dental caries development through metabolism of dietary carbohydrates. Adoption of carbohydrate-rich agricultural diets is associated with increased prevalence of dental caries in archaeological populations; however, the evolutionary impact of changing subsistence strategies on cariogenic microbes like S. mutans remains to be explored. Here, we use a novel hybridization capture reagent to generate genome-wide ancient DNA data from a global set of 75 S. mutans strains spanning the last 8,000 years. Most virulence-associated genes predate the origins of agriculture; however, we highlight loci regulating genetic competence, bacteriocin production, and biofilm formation which are absent in 5 strains from pre-agricultural ancient hunter-gatherers, suggesting that their acquisition may have been associated with adaptation to carbohydrate-rich agricultural diets. Together, our study highlights ancient DNA as a promising tool for exploring the dynamic interplay between subsistence strategy, microbes, and dental pathology in human populations through time. ### Competing Interest Statement The authors have declared no competing interest.

Analyses of 45,000-year-old bones from Europe allow scientists to pin down when modern humans interbred with Neanderthals, shedding light on the histories of populations with no present-day descendants. Oldest Homo sapiens genomes point to dates of mixture with Neanderthals.

It has been unclear how the periods of Roman and later Germanic political control shaped the demography of the Iberian Peninsula and how Iberia differs in these respects from other parts of the Roman Empire. We report genome-wide data from 248 ancient individuals from the largely unsampled period 100-800 CE and co-analyze them with previously reported data. In the Roman era, we document profound demographic transformation, with an influx of people with ancestry from the Central and Eastern Mediterranean in all the areas under study and of North Africans, especially in central and southern Iberia. Germanic (Buri, Suebi, Vandals & Visigoths) and Sarmatian (Alans) took over political control beginning in the 5th century, and although we identify individuals with Germanic-associated ancestry at sites with Germanic-style ornaments and observe that such individuals were closely related across large distances as in the case of two siblings separated by 700 km, for Iberia as a whole, we observe high continuity with the previous Hispano-Roman population. The demographic patterns in Iberia contrast sharply with those in Britain, which showed the opposite pattern of little change in the Roman period followed by great change in the Migration period, and also from demographic patterns in the central Mediterranean where both periods were associated with profound transformation, raising broader questions about the forces that precipitated change over this time. ### Competing Interest Statement The authors have declared no competing interest.

The Xerces Blue (Glaucopsyche xerces) is considered to be the first butterfly to become extinct in historical times. It was notable for its chalky lavender wings with conspicuous white spots on the ventral wings. The last individuals were collected in their restricted habitat, in the dunes near the Presidio military base in San Francisco, in 1941. We sequenced the genomes of four 80- to 100-year-old Xerces Blue, and seven historical and one modern specimens of its closest relative, the Silvery Blue (Glaucopsyche lygdamus). We compared these to a novel annotated genome of the Green-Underside Blue (Glaucopsyche alexis). Phylogenetic relationships inferred from complete mitochondrial genomes indicate that Xerces Blue was a distinct species that diverged from the Silvery Blue lineage at least 850,000 years ago. Using nuclear genomes, both species experienced population growth during the Eemian interglacial period, but the Xerces Blue decreased to a very low effective population size subsequently, a trend opposite to that observed in the Silvery Blue. Runs of homozygosity and deleterious load in the former were significantly greater than in the later, suggesting a higher incidence of inbreeding. These signals of population decline observed in Xerces Blue could be used to identify and monitor other insects threatened by human activities, whose extinction patterns are still not well known.

Western Eurasia witnessed several large-scale human migrations during the Holocene 1 – 5 . Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes—mainly from the Mesolithic and Neolithic periods—from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a ‘great divide’ genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 bp , consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 bp , resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a ‘Neolithic steppe’ cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.

The rise and fall of the Roman Empire was a socio-political process with enormous ramifications for human history. The Middle Danube was a crucial frontier and a crossroads for population and cultural movement. Here, we present genome-wide data from 136 Balkan individuals dated to the 1st millennium CE. Despite extensive militarization and cultural influence, we find little ancestry contribution from peoples of Italic descent. However, we trace a large-scale influx of people of Anatolian ancestry during the Imperial period. Between-250 and 550 CE, we detect migrants with ancestry from Central/Northern Europe and the Steppe, confirming that "barbarian"migrations were propelled by ethnically diverse confederations. Following the end of Roman control, we detect the large-scale arrival of individuals who were genetically similar to modern Eastern European Slavic-speaking populations, who contributed 30%-60% of the ancestry of Balkan people, representing one of the largest permanent demographic changes anywhere in Europe during the Migration Period.

This study presents an exceptional collection of 54 Late Pleistocene human remains that correspond to at least three Neanderthal individuals from Simanya Gran, the main gallery of Cova Simanya, located in the northeastern Iberian Peninsula. The collection comprised 53 unpublished remains that were unearthed during the 1970s and an additional tooth discovered during 2021 excavations. The specimens represent an adult with a small stature, a periadolescent aged approximately 11.5 years, and an immature individual aged approximately 7.7 years, thus offering a more complete demographic perspective. The collection encompasses diverse anatomical parts including upper and lower dentition, mandible, vertebrae, and limb bones from both the upper and lower extremities. Attempts to extract aDNA were unsuccessful. Renewed archaeological investigations at Cova Simanya have facilitated the reevaluation of the original stratigraphic context of these remains, leading to the discovery of the additional tooth, aligning with the periadolescent individual. This assemblage is currently the most extensive Neanderthal collection from the northeastern Mediterranean Iberia, offering invaluable insights into the morphology and evolutionary trajectory of Late Pleistocene hominins. Hence, Simanya Neanderthals will enhance our understanding of Neanderthal demographics and evolution, paving the way for an in-depth examination of the morphological diversity and evolutionary context of Iberian Neanderthals.

Human populations underwent range contractions during the Last Glacial Maximum (LGM) which had lasting and dramatic effects on their genetic variation. The genetic ancestry of individuals associated with the post-LGM Magdalenian technocomplex has been interpreted as being derived from groups associated with the pre-LGM Aurignacian. However, both these ancestries differ from that of central European individuals associated with the chronologically intermediate Gravettian. Thus, the genomic transition from pre- to post-LGM remains unclear also in western Europe, where we lack genomic data associated with the intermediate Solutrean, which spans the height of the LGM. Here we present genome-wide data from sites in Andalusia in southern Spain, including from a Solutrean-associated individual from Cueva del Malalmuerzo, directly dated to ~23,000 cal yr BP. The Malalmuerzo individual carried genetic ancestry that directly connects earlier Aurignacian-associated individuals with post-LGM Magdalenian-associated ancestry in western Europe. This scenario differs from Italy, where individuals associated with the transition from pre- and post-LGM carry different genetic ancestries. This suggests different dynamics in the proposed southern refugia of Ice Age Europe and posits Iberia as a potential refugium for western European pre-LGM ancestry. More, individuals from Cueva Ardales, which were thought to be of Palaeolithic origin, date younger than expected and, together with individuals from the Andalusian sites Caserones and Aguilillas, fall within the genetic variation of the Neolithic, Chalcolithic and Bronze Age individuals from southern Iberia.

In recent years, the increased availability of genomic data generated from ancient human remains has revolutionized the study of the past, and enabled researchers to tackle a range of questions that previously were targeted almost exclusively by disciplines in the Humanities such as History and Archaeology. Importantly, results obtained through characterizing the genetics of archaic hominins including evidence for adaptation, admixture, past demography, sex determination, or social structure, can be correlated with morphological and archaeological observations drawn from the fossil record. Admixture, defined as the exchange of genes between previously isolated species or populations, is now considered to be an important source of variation among ancient human lineages. The palaeogenomic studies are unravelling the complex evolutionary patterns of the human lineages, showing multiple admixture events in different moments and regions, as well as providing information on adaptations to environmental conditions, past migrations, demographic trends, and social structures.

The first studies to retrieve genome-wide data from two Medieval European Jewish communities from England and Germany illustrate the complex interplay of ancestry, disease, religion, culture and ethics.

Human populations have been shaped by catastrophes that may have left long-lasting signatures in their ge-nomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeat-edly returned for over 300 years, with typical village and town mortality estimated at 10%-40%.1 It is assumed that this high mortality affected the gene pools of these populations. First, local population crashes reduced genetic diversity. Second, a change in frequency is expected for sequence variants that may have affected survival or susceptibility to the etiologic agent (Yersinia pestis).2 Third, mass mortality might alter the local gene pools through its impact on subsequent migration patterns. We explored these factors using the Nor-wegian city of Trondheim as a model, by sequencing 54 genomes spanning three time periods: (1) prior to the plague striking Trondheim in 1,349 CE, (2) the 17th-19th century, and (3) the present. We find that the pandemic period shaped the gene pool by reducing long distance immigration, in particular from the British Isles, and inducing a bottleneck that reduced genetic diversity. Although we also observe an excess of large FST values at multiple loci in the genome, these are shaped by reference biases introduced by mapping our relatively low genome coverage degraded DNA to the reference genome. This implies that attempts to detect selection using ancient DNA (aDNA) datasets that vary by read length and depth of sequencing coverage may be particularly challenging until methods have been developed to account for the impact of differential refer-ence bias on test statistics.

Museo-what? Museomics! Museomics is emerging as a distinct discipline from ancient DNA research and involves natural history museums and herbaria across the world. Museomics can be defined as the application of -omics techniques (genomics, paleogenomics and even paleoproteomics) to previously intractable historical and archival specimens that allow the retrieval of genomic data from extinct or currently declining species. This information has the potential to document genetic erosion in endangered species, to obtain genomes from extinct species, to establish molecular phylogenies, to understand species invasions in the last few centuries, to resolve taxonomic doubts with holotypes, and to explore past diversity of extant species, prior to the current climate crisis. In addition, it can provide information on epigenetic modifications or even past pathogens, which can be of biomedical interest.