From Long Ago

Kevin Lewis

October 09, 2021

The origin and legacy of the Etruscans through a 2000-year archeogenomic time transect
Cosimo Posth et al.
Science Advances, September 2021

The origin, development, and legacy of the enigmatic Etruscan civilization from the central region of the Italian peninsula known as Etruria have been debated for centuries. Here we report a genomic time transect of 82 individuals spanning almost two millennia (800 BCE to 1000 CE) across Etruria and southern Italy. During the Iron Age, we detect a component of Indo-European–associated steppe ancestry and the lack of recent Anatolian-related admixture among the putative non–Indo-European–speaking Etruscans. Despite comprising diverse individuals of central European, northern African, and Near Eastern ancestry, the local gene pool is largely maintained across the first millennium BCE. This drastically changes during the Roman Imperial period where we report an abrupt population-wide shift to ~50% admixture with eastern Mediterranean ancestry. Last, we identify northern European components appearing in central Italy during the Early Middle Ages, which thus formed the genetic landscape of present-day Italian populations.

A signature of Neanderthal introgression on molecular mechanisms of environmental responses
Anthony Findley et al.
PLoS ONE, September 2021

Ancient human migrations led to the settlement of population groups in varied environmental contexts worldwide. The extent to which adaptation to local environments has shaped human genetic diversity is a longstanding question in human evolution. Recent studies have suggested that introgression of archaic alleles in the genome of modern humans may have contributed to adaptation to environmental pressures such as pathogen exposure. Functional genomic studies have demonstrated that variation in gene expression across individuals and in response to environmental perturbations is a main mechanism underlying complex trait variation. We considered gene expression response to in vitro treatments as a molecular phenotype to identify genes and regulatory variants that may have played an important role in adaptations to local environments. We investigated if Neanderthal introgression in the human genome may contribute to the transcriptional response to environmental perturbations. To this end we used eQTLs for genes differentially expressed in a panel of 52 cellular environments, resulting from 5 cell types and 26 treatments, including hormones, vitamins, drugs, and environmental contaminants. We found that SNPs with introgressed Neanderthal alleles (N-SNPs) disrupt binding of transcription factors important for environmental responses, including ionizing radiation and hypoxia, and for glucose metabolism. We identified an enrichment for N-SNPs among eQTLs for genes differentially expressed in response to 8 treatments, including glucocorticoids, caffeine, and vitamin D. Using Massively Parallel Reporter Assays (MPRA) data, we validated the regulatory function of 21 introgressed Neanderthal variants in the human genome, corresponding to 8 eQTLs regulating 15 genes that respond to environmental perturbations. These findings expand the set of environments where archaic introgression may have contributed to adaptations to local environments in modern humans and provide experimental validation for the regulatory function of introgressed variants. 

Hemispheric black carbon increase after the 13th-century Māori arrival in New Zealand
Joseph McConnell et al.
Nature, 7 October 2021, Pages 82–85

New Zealand was among the last habitable places on earth to be colonized by humans. Charcoal records indicate that wildfires were rare prior to colonization and widespread following the 13th- to 14th-century Māori settlement, but the precise timing and magnitude of associated biomass-burning emissions are unknown, as are effects on light-absorbing black carbon aerosol concentrations over the pristine Southern Ocean and Antarctica. Here we used an array of well-dated Antarctic ice-core records to show that while black carbon deposition rates were stable over continental Antarctica during the past two millennia, they were approximately threefold higher over the northern Antarctic Peninsula during the past 700 years. Aerosol modelling demonstrates that the observed deposition could result only from increased emissions poleward of 40° S — implicating fires in Tasmania, New Zealand and Patagonia — but only New Zealand palaeofire records indicate coincident increases. Rapid deposition increases started in 1297 (±30 s.d.) in the northern Antarctic Peninsula, consistent with the late 13th-century Māori settlement and New Zealand black carbon emissions of 36 (±21 2 s.d.) Gg y−1 during peak deposition in the 16th century. While charcoal and pollen records suggest earlier, climate-modulated burning in Tasmania and southern Patagonia, deposition in Antarctica shows that black carbon emissions from burning in New Zealand dwarfed other preindustrial emissions in these regions during the past 2,000 years, providing clear evidence of large-scale environmental effects associated with early human activities across the remote Southern Hemisphere. 

Pre-Columbian fire management and control of climate-driven floodwaters over 3,500 years in southwestern Amazonia
Neil Duncan et al.
Proceedings of the National Academy of Sciences, 5 October 2021

In landscapes that support economic and cultural activities, human communities actively manage environments and environmental change at a variety of spatial scales that complicate the effects of continental-scale climate. Here, we demonstrate how hydrological conditions were modified by humans against the backdrop of Holocene climate change in southwestern Amazonia. Paleoecological investigations (phytoliths, charcoal, pollen, diatoms) of two sediment cores extracted from within the same permanent wetland, ∼22 km apart, show a 1,500-y difference in when the intensification of land use and management occurred, including raised field agriculture, fire regime, and agroforestry. Although rising precipitation is well known during the mid to late Holocene, human actions manipulated climate-driven hydrological changes on the landscape, revealing differing histories of human landscape domestication. Environmental factors are unable to account for local differences without the mediation of human communities that transformed the region to its current savanna/forest/wetland mosaic beginning at least 3,500 y ago. Regional environmental variables did not drive the choices made by farmers and fishers, who shaped these local contexts to better manage resource extraction. The savannas we observe today were created in the post-European period, where their fire regime and structural diversity were shaped by cattle ranching. 

Ten millennia of hepatitis B virus evolution
Arthur Kocher et al.
Science, 8 October 2021, Pages 182-188

Hepatitis B virus (HBV) has been infecting humans for millennia and remains a global health problem, but its past diversity and dispersal routes are largely unknown. We generated HBV genomic data from 137 Eurasians and Native Americans dated between ~10,500 and ~400 years ago. We date the most recent common ancestor of all HBV lineages to between ~20,000 and 12,000 years ago, with the virus present in European and South American hunter-gatherers during the early Holocene. After the European Neolithic transition, Mesolithic HBV strains were replaced by a lineage likely disseminated by early farmers that prevailed throughout western Eurasia for ~4000 years, declining around the end of the 2nd millennium BCE. The only remnant of this prehistoric HBV diversity is the rare genotype G, which appears to have reemerged during the HIV pandemic. 

Constraining the chronology and ecology of Late Acheulean and Middle Palaeolithic occupations at the margins of the monsoon
James Blinkhorn et al.
Scientific Reports, October 2021

South Asia hosts the world’s youngest Acheulean sites, with dated records typically restricted to sub-humid landscapes. The Thar Desert marks a major adaptive boundary between monsoonal Asia to the east and the Saharo-Arabian desert belt to the west, making it a key threshold to examine patterns of hominin ecological adaptation and its impacts on patterns of behaviour, demography and dispersal. Here, we investigate Palaeolithic occupations at the western margin of the South Asian monsoon at Singi Talav, undertaking new chronometric, sedimentological and palaeoecological studies of Acheulean and Middle Palaeolithic occupation horizons. We constrain occupations of the site between 248 and 65 thousand years ago. This presents the first direct palaeoecological evidence for landscapes occupied by South Asian Acheulean-producing populations, most notably in the main occupation horizon dating to 177 thousand years ago. Our results illustrate the potential role of the Thar Desert as an ecological, and demographic, frontier to Palaeolithic populations. 

Late Pleistocene/Early Holocene sites in the montane forests of New Guinea yield early record of cassowary hunting and egg harvesting
Kristina Douglass et al.
Proceedings of the National Academy of Sciences, 5 October 2021

How early human foragers impacted insular forests is a topic with implications across multiple disciplines, including resource management. Paradoxically, terminal Pleistocene and Early Holocene impacts of foraging communities have been characterized as both extreme—as in debates over human-driven faunal extinctions—and minimal compared to later landscape transformations by farmers and herders. We investigated how rainforest hunter-gatherers managed resources in montane New Guinea and present some of the earliest documentation of Late Pleistocene through mid-Holocene exploitation of cassowaries (Aves: Casuariidae). Worldwide, most insular ratites were extirpated by the Late Holocene, following human arrivals, including elephant birds of Madagascar (Aepyornithidae) and moa of Aotearoa/New Zealand (Dinornithiformes)—icons of anthropogenic island devastation. Cassowaries are exceptional, however, with populations persisting in New Guinea and Australia. Little is known of past human exploitation and what factors contributed to their survival. We present a method for inferring past human interaction with mega-avifauna via analysis of microstructural features of archaeological eggshell. We then contextualize cassowary hunting and egg harvesting by montane foragers and discuss the implications of human exploitation. Our data suggest cassowary egg harvesting may have been more common than the harvesting of adults. Furthermore, our analysis of cassowary eggshell microstructural variation reveals a distinct pattern of harvesting eggs in late ontogenetic stages. Harvesting eggs in later stages of embryonic growth may reflect human dietary preferences and foraging seasonality, but the observed pattern also supports the possibility that—as early as the Late Pleistocene—people were collecting eggs in order to hatch and rear cassowary chicks.


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