Ancient Paths
Simulating 500 million years of evolution with a language model
Thomas Hayes et al.
Science, forthcoming
Abstract:
More than three billion years of evolution have produced an image of biology encoded into the space of natural proteins. Here we show that language models trained at scale on evolutionary data can generate functional proteins that are far away from known proteins. We present ESM3, a frontier multimodal generative language model that reasons over the sequence, structure, and function of proteins. ESM3 can follow complex prompts combining its modalities and is highly responsive to alignment to improve its fidelity. We have prompted ESM3 to generate fluorescent proteins. Among the generations that we synthesized, we found a bright fluorescent protein at a far distance (58% sequence identity) from known fluorescent proteins, which we estimate is equivalent to simulating five hundred million years of evolution.
Ancient DNA reveals reproductive barrier despite shared Avar-period culture
Ke Wang et al.
Nature, forthcoming
Abstract:
After a long-distance migration, Avars with Eastern Asian ancestry arrived in Eastern Central Europe in 567 to 568 CE and encountered groups with very different European ancestry. We used ancient genome-wide data of 722 individuals and fine-grained interdisciplinary analysis of large seventh- to eighth-century CE neighbouring cemeteries south of Vienna (Austria) to address the centuries-long impact of this encounter. We found that even 200 years after immigration, the ancestry at one site (Leobersdorf) remained dominantly East Asian-like, whereas the other site (Mödling) shows local, European-like ancestry. These two nearby sites show little biological relatedness, despite sharing a distinctive late-Avar culture. We reconstructed six-generation pedigrees at both sites including up to 450 closely related individuals, allowing per-generation demographic profiling of the communities. Despite different ancestry, these pedigrees together with large networks of distant relatedness show absence of consanguinity, patrilineal pattern with female exogamy, multiple reproductive partnerships (for example, levirate) and direct correlation of biological connectivity with archaeological markers of social status. The generation-long genetic barrier was maintained by systematically choosing partners with similar ancestry from other sites in the Avar realm. Leobersdorf had more biological connections with the Avar heartlands than with Mödling, which is instead linked to another site from the Vienna Basin with European-like ancestry. Mobility between sites was mostly due to female exogamy pointing to different marriage networks as the main driver of the maintenance of the genetic barrier.
Continental influx and pervasive matrilocality in Iron Age Britain
Lara Cassidy et al.
Nature, forthcoming
Abstract:
Roman writers found the relative empowerment of Celtic women remarkable. In southern Britain, the Late Iron Age Durotriges tribe often buried women with substantial grave goods. Here we analyse 57 ancient genomes from Durotrigian burial sites and find an extended kin group centred around a single maternal lineage, with unrelated (presumably inward migrating) burials being predominantly male. Such a matrilocal pattern is undescribed in European prehistory, but when we compare mitochondrial haplotype variation among European archaeological sites spanning six millennia, British Iron Age cemeteries stand out as having marked reductions in diversity driven by the presence of dominant matrilines. Patterns of haplotype sharing reveal that British Iron Age populations form fine-grained geographical clusters with southern links extending across the channel to the continent. Indeed, whereas most of Britain shows majority genomic continuity from the Early Bronze Age to the Iron Age, this is markedly reduced in a southern coastal core region with persistent cross-channel cultural exchange. This southern core has evidence of population influx in the Middle Bronze Age but also during the Iron Age. This is asynchronous with the rest of the island and points towards a staged, geographically granular absorption of continental influence, possibly including the acquisition of Celtic languages.
Family relations of Moche elite burials on the North Coast of Peru (~500 CE): Analyses of the Señora de Cao and relatives
Jeffrey Quilter et al.
Proceedings of the National Academy of Sciences, 7 January 2025
Abstract:
The Moche archaeological culture flourished along Peru’s North Coast between the 4th and 10th centuries CE and was characterized by a complex social hierarchy dominated by political and religious elites. Previous archaeological evidence suggests kinship was a key factor in maintaining political authority within Moche society. To test this hypothesis, we applied archaeological, genetic, and isotopic methods to examine familial relationships between six individuals, including the prominent Señora de Cao (~500 CE), buried together in a pyramid-like, painted temple, Huaca Cao Viejo, in the Chicama Valley, Peru. Our findings reveal that all six individuals were biologically related, with varying degrees of kinship. The Señora de Cao was interred with a sacrificed juvenile, identified as a possible niece, and at least one, and potentially two siblings and a grandparent in separate tombs nearby. One of the male siblings was accompanied in death by his sacrificed son. Isotopic analysis indicates that while most individuals had diets rich in maize and animal protein and spent their childhoods in or near the Chicama Valley, the sacrificed juvenile accompanying the Señora had a distinct diet and geographic origin. These results demonstrate that Moche elites were interred with family members, including some raised far from their parental homes. This supports the hypothesis that kinship was central to transmitting status and authority. Moreover, sacrificing family members to accompany deceased elites underscores the significance of ritual sacrifice in reinforcing familial ties and linking the deceased to both ancestors and the divine.
Earliest evidence of sedentism in the Antilles: Multiple isotope data from Canímar Abajo, Cuba
Yadira Chinique de Armas et al.
Proceedings of the National Academy of Sciences, 7 January 2025
Abstract:
The early populations that inhabited the Antilles were traditionally understood as highly mobile groups of hunters/fishers and gatherers. Although more recent data have demonstrated that some populations engaged in the production of domestic plants and cultivars, questions remain about other aspects of their lifeways, including whether the adoption of domesticates was accompanied by a decrease in residential mobility. The level of sedentism in a population is an instrumental variable to understand community social relations and complexity, adaptations, and lifeways. Here, we combined enamel strontium (87Sr/86Sr), oxygen (δ18Oen), and carbon (δ13Cen) isotopes of 44 human teeth from the site of Canímar Abajo -- where the oldest human remains from the insular Caribbean have been reported -- to examine the mobility patterns of early Antillean groups. In contrast with traditional narratives, the homogeneous strontium isotope values observed in most individuals from the older funerary area of the site (cal. BC 2237–790) were consistent with the pattern expected for a sedentary population subsisting primarily on local resources obtained close to the coast. The isotopic evidence reveals that between cal. AD 403–1282, the mound was reused for funerary practices by both local communities and nonlocal individuals. The evidence suggests that this period saw higher population mobility, with influxes of individuals from more distant locations and diverse dietary and burial traditions. The isotope results from Canímar Abajo provide the earliest isotopic evidence of populations with low-level residential mobility in the Antilles.