Redefining the treponemal history through pre-Columbian genomes from Brazil.

The origins of treponemal diseases have long remained unknown, especially considering the sudden onset of the first syphilis epidemic in the late 15th century in Europe and its hypothesized arrival from the Americas with Columbus' expeditions1,2. Recently, ancient DNA evidence has revealed various treponemal infections circulating in early modern Europe and colonial-era Mexico3-6. However, there has been to our knowledge no genomic evidence of treponematosis recovered from either the Americas or the Old World that can be reliably dated to the time before the first trans-Atlantic contacts. Here, we present treponemal genomes from nearly 2,000-year-old human remains from Brazil. We reconstruct four ancient genomes of a prehistoric treponemal pathogen, most closely related to the bejel-causing agent Treponema pallidum endemicum. Contradicting the modern day geographical niche of bejel in the arid regions of the world, the results call into question the previous palaeopathological characterization of treponeme subspecies and showcase their adaptive potential. A high-coverage genome is used to improve molecular clock date estimations, placing the divergence of modern T. pallidum subspecies firmly in pre-Columbian times. Overall, our study demonstrates the opportunities within archaeogenetics to uncover key events in pathogen evolution and emergence, paving the way to new hypotheses on the origin and spread of treponematoses.

Elevated genetic risk for multiple sclerosis emerged in steppe pastoralist populations.

Multiple sclerosis (MS) is a neuro-inflammatory and neurodegenerative disease that is most prevalent in Northern Europe. Although it is known that inherited risk for MS is located within or in close proximity to immune-related genes, it is unknown when, where and how this genetic risk originated1. Here, by using a large ancient genome dataset from the Mesolithic period to the Bronze Age2, along with new Medieval and post-Medieval genomes, we show that the genetic risk for MS rose among pastoralists from the Pontic steppe and was brought into Europe by the Yamnaya-related migration approximately 5,000 years ago. We further show that these MS-associated immunogenetic variants underwent positive selection both within the steppe population and later in Europe, probably driven by pathogenic challenges coinciding with changes in diet, lifestyle and population density. This study highlights the critical importance of the Neolithic period and Bronze Age as determinants of modern immune responses and their subsequent effect on the risk of developing MS in a changing environment.

Entwined African and Asian genetic roots of medieval peoples of the Swahili coast.

The urban peoples of the Swahili coast traded across eastern Africa and the Indian Ocean and were among the first practitioners of Islam among sub-Saharan people1,2. The extent to which these early interactions between Africans and non-Africans were accompanied by genetic exchange remains unknown. Here we report ancient DNA data for 80 individuals from 6 medieval and early modern (AD 1250-1800) coastal towns and an inland town after AD 1650. More than half of the DNA of many of the individuals from coastal towns originates from primarily female ancestors from Africa, with a large proportion-and occasionally more than half-of the DNA coming from Asian ancestors. The Asian ancestry includes components associated with Persia and India, with 80-90% of the Asian DNA originating from Persian men. Peoples of African and Asian origins began to mix by about AD 1000, coinciding with the large-scale adoption of Islam. Before about AD 1500, the Southwest Asian ancestry was mainly Persian-related, consistent with the narrative of the Kilwa Chronicle, the oldest history told by people of the Swahili coast3. After this time, the sources of DNA became increasingly Arabian, consistent with evidence of growing interactions with southern Arabia4. Subsequent interactions with Asian and African people further changed the ancestry of present-day people of the Swahili coast in relation to the medieval individuals whose DNA we sequenced.

Genetic continuity and change among the Indigenous peoples of California.

Before the colonial period, California harboured more language variation than all of Europe, and linguistic and archaeological analyses have led to many hypotheses to explain this diversity1. We report genome-wide data from 79 ancient individuals from California and 40 ancient individuals from Northern Mexico dating to 7,400-200 years before present (BP). Our analyses document long-term genetic continuity between people living on the Northern Channel Islands of California and the adjacent Santa Barbara mainland coast from 7,400 years BP to modern Chumash groups represented by individuals who lived around 200 years BP. The distinctive genetic lineages that characterize present-day and ancient people from Northwest Mexico increased in frequency in Southern and Central California by 5,200 years BP, providing evidence for northward migrations that are candidates for spreading Uto-Aztecan languages before the dispersal of maize agriculture from Mexico2-4. Individuals from Baja California share more alleles with the earliest individual from Central California in the dataset than with later individuals from Central California, potentially reflecting an earlier linguistic substrate, whose impact on local ancestry was diluted by later migrations from inland regions1,5. After 1,600 years BP, ancient individuals from the Channel Islands lived in communities with effective sizes similar to those in pre-agricultural Caribbean and Patagonia, and smaller than those on the California mainland and in sampled regions of Mexico.

Hemispheric black carbon increase after the 13th-century Maori arrival in New Zealand.

New Zealand was among the last habitable places on earth to be colonized by humans1. Charcoal records indicate that wildfires were rare prior to colonization and widespread following the 13th- to 14th-century Maori settlement2, but the precise timing and magnitude of associated biomass-burning emissions are unknown1,3, as are effects on light-absorbing black carbon aerosol concentrations over the pristine Southern Ocean and Antarctica4. 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 modelling5 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 Maori 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 Patagonia6,7, 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.

Towards a rigorous understanding of societal responses to climate change.

A large scholarship currently holds that before the onset of anthropogenic global warming, natural climatic changes long provoked subsistence crises and, occasionally, civilizational collapses among human societies. This scholarship, which we term the 'history of climate and society' (HCS), is pursued by researchers from a wide range of disciplines, including archaeologists, economists, geneticists, geographers, historians, linguists and palaeoclimatologists. We argue that, despite the wide interest in HCS, the field suffers from numerous biases, and often does not account for the local effects and spatiotemporal heterogeneity of past climate changes or the challenges of interpreting historical sources. Here we propose an interdisciplinary framework for uncovering climate-society interactions that emphasizes the mechanics by which climate change has influenced human history, and the uncertainties inherent in discerning that influence across different spatiotemporal scales. Although we acknowledge that climate change has sometimes had destructive effects on past societies, the application of our framework to numerous case studies uncovers five pathways by which populations survived-and often thrived-in the face of climatic pressures.

Coupling of Indo-Pacific climate variability over the last millennium.

The Indian Ocean Dipole (IOD) affects climate and rainfall across the world, and most severely in nations surrounding the Indian Ocean1-4. The frequency and intensity of positive IOD events increased during the twentieth century5 and may continue to intensify in a warming world6. However, confidence in predictions of future IOD change is limited by known biases in IOD models7 and the lack of information on natural IOD variability before anthropogenic climate change. Here we use precisely dated and highly resolved coral records from the eastern equatorial Indian Ocean, where the signature of IOD variability is strong and unambiguous, to produce a semi-continuous reconstruction of IOD variability that covers five centuries of the last millennium. Our reconstruction demonstrates that extreme positive IOD events were rare before 1960. However, the most extreme event on record (1997) is not unprecedented, because at least one event that was approximately 27 to 42 per cent larger occurred naturally during the seventeenth century. We further show that a persistent, tight coupling existed between the variability of the IOD and the El Niño/Southern Oscillation during the last millennium. Indo-Pacific coupling was characterized by weak interannual variability before approximately 1590, which probably altered teleconnection patterns, and by anomalously strong variability during the seventeenth century, which was associated with societal upheaval in tropical Asia. A tendency towards clustering of positive IOD events is evident in our reconstruction, which-together with the identification of extreme IOD variability and persistent tropical Indo-Pacific climate coupling-may have implications for improving seasonal and decadal predictions and managing the climate risks of future IOD variability.

The population history of northeastern Siberia since the Pleistocene.

Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of 'Ancient North Siberians' who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to 'Ancient Palaeo-Siberians' who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name 'Neo-Siberians', and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.

No evidence for globally coherent warm and cold periods over the preindustrial Common Era.

Earth's climate history is often understood by breaking it down into constituent climatic epochs1. Over the Common Era (the past 2,000 years) these epochs, such as the Little Ice Age2-4, have been characterized as having occurred at the same time across extensive spatial scales5. Although the rapid global warming seen in observations over the past 150 years does show nearly global coherence6, the spatiotemporal coherence of climate epochs earlier in the Common Era has yet to be robustly tested. Here we use global palaeoclimate reconstructions for the past 2,000 years, and find no evidence for preindustrial globally coherent cold and warm epochs. In particular, we find that the coldest epoch of the last millennium-the putative Little Ice Age-is most likely to have experienced the coldest temperatures during the fifteenth century in the central and eastern Pacific Ocean, during the seventeenth century in northwestern Europe and southeastern North America, and during the mid-nineteenth century over most of the remaining regions. Furthermore, the spatial coherence that does exist over the preindustrial Common Era is consistent with the spatial coherence of stochastic climatic variability. This lack of spatiotemporal coherence indicates that preindustrial forcing was not sufficient to produce globally synchronous extreme temperatures at multidecadal and centennial timescales. By contrast, we find that the warmest period of the past two millennia occurred during the twentieth century for more than 98 per cent of the globe. This provides strong evidence that anthropogenic global warming is not only unparalleled in terms of absolute temperatures5, but also unprecedented in spatial consistency within the context of the past 2,000 years.

Reconciling divergent trends and millennial variations in Holocene temperatures.

Cooling during most of the past two millennia has been widely recognized and has been inferred to be the dominant global temperature trend of the past 11,700 years (the Holocene epoch). However, long-term cooling has been difficult to reconcile with global forcing, and climate models consistently simulate long-term warming. The divergence between simulations and reconstructions emerges primarily for northern mid-latitudes, for which pronounced cooling has been inferred from marine and coastal records using multiple approaches. Here we show that temperatures reconstructed from sub-fossil pollen from 642 sites across North America and Europe closely match simulations, and that long-term warming, not cooling, defined the Holocene until around 2,000 years ago. The reconstructions indicate that evidence of long-term cooling was limited to North Atlantic records. Early Holocene temperatures on the continents were more than two degrees Celsius below those of the past two millennia, consistent with the simulated effects of remnant ice sheets in the climate model Community Climate System Model 3 (CCSM3). CCSM3 simulates increases in 'growing degree days'-a measure of the accumulated warmth above five degrees Celsius per year-of more than 300 kelvin days over the Holocene, consistent with inferences from the pollen data. It also simulates a decrease in mean summer temperatures of more than two degrees Celsius, which correlates with reconstructed marine trends and highlights the potential importance of the different subseasonal sensitivities of the records. Despite the differing trends, pollen- and marine-based reconstructions are correlated at millennial-to-centennial scales, probably in response to ice-sheet and meltwater dynamics, and to stochastic dynamics similar to the temperature variations produced by CCSM3. Although our results depend on a single source of palaeoclimatic data (pollen) and a single climate-model simulation, they reinforce the notion that climate models can adequately simulate climates for periods other than the present-day. They also demonstrate that amplified warming in recent decades increased temperatures above the mean of any century during the past 11,000 years.

Anomalously weak Labrador Sea convection and Atlantic overturning during the past 150 years.

The Atlantic meridional overturning circulation (AMOC) is a system of ocean currents that has an essential role in Earth's climate, redistributing heat and influencing the carbon cycle1, 2. The AMOC has been shown to be weakening in recent years 1 ; this decline may reflect decadal-scale variability in convection in the Labrador Sea, but short observational datasets preclude a longer-term perspective on the modern state and variability of Labrador Sea convection and the AMOC1, 3-5. Here we provide several lines of palaeo-oceanographic evidence that Labrador Sea deep convection and the AMOC have been anomalously weak over the past 150 years or so (since the end of the Little Ice Age, LIA, approximately AD 1850) compared with the preceding 1,500 years. Our palaeoclimate reconstructions indicate that the transition occurred either as a predominantly abrupt shift towards the end of the LIA, or as a more gradual, continued decline over the past 150 years; this ambiguity probably arises from non-AMOC influences on the various proxies or from the different sensitivities of these proxies to individual components of the AMOC. We suggest that enhanced freshwater fluxes from the Arctic and Nordic seas towards the end of the LIA-sourced from melting glaciers and thickened sea ice that developed earlier in the LIA-weakened Labrador Sea convection and the AMOC. The lack of a subsequent recovery may have resulted from hysteresis or from twentieth-century melting of the Greenland Ice Sheet 6 . Our results suggest that recent decadal variability in Labrador Sea convection and the AMOC has occurred during an atypical, weak background state. Future work should aim to constrain the roles of internal climate variability and early anthropogenic forcing in the AMOC weakening described here.

Proto-Endocrinological Theories of Masculinity/Femininity (1490-1904).

From the mid-seventeenth century, resorption of a testicular "ferment" and resorption of some part of the semen constituted reputable accounts of secondary sexual characteristics. Only in the early twentieth century was the latter, "recrementitious secretion" theory, explicitly considered superseded by one of internal secretion, an advance ushering in the hormone era. A reconstruction of these proto-endocrinological concepts is offered onward from the first, 1490 print edition of Galen's On Semen. Early modern physicians picking up from Galen deliberated widely on the medium and pathway of male and female testicular influences on "the entire body," including the mind, causing "femininity" and "masculinity" in physical, mental-temperamental, and behavioral terms. A switch is discernible from "heat and strength" (Galen) to blood-borne "virility" or testicular vapor (such as proposed in 1564 by Tomás Rodrigues da Veiga), to iatrochemical postulations of a "seminal ferment" (suggested in the late 1650s, perhaps independently, by Thomas Willis at Oxford and Lambert van Velthuysen in Utrecht), finally to a "seminal recrement" or "reabsorbed semen" concept soon after (emergent in the posthumous work of Giovanni Alfonso Borelli, among others). During the late eighteenth century, mounting controversy surrounded both the very idea of that concept and the involved anatomical pathways, informed by multiple experiments.

Agricultural intensification and climate change are rapidly decreasing insect biodiversity.

Major declines in insect biomass and diversity, reviewed here, have become obvious and well documented since the end of World War II. Here, we conclude that the spread and intensification of agriculture during the past half century is directly related to these losses. In addition, many areas, including tropical mountains, are suffering serious losses because of climate change as well. Crops currently occupy about 11% of the world's land surface, with active grazing taking place over an additional 30%. The industrialization of agriculture during the second half of the 20th century involved farming on greatly expanded scales, monoculturing, the application of increasing amounts of pesticides and fertilizers, and the elimination of interspersed hedgerows and other wildlife habitat fragments, all practices that are destructive to insect and other biodiversity in and near the fields. Some of the insects that we are destroying, including pollinators and predators of crop pests, are directly beneficial to the crops. In the tropics generally, natural vegetation is being destroyed rapidly and often replaced with export crops such as oil palm and soybeans. To mitigate the effects of the Sixth Mass Extinction event that we have caused and are experiencing now, the following will be necessary: a stable (and almost certainly lower) human population, sustainable levels of consumption, and social justice that empowers the less wealthy people and nations of the world, where the vast majority of us live, will be necessary.

People have shaped most of terrestrial nature for at least 12,000 years.

Archaeological and paleoecological evidence shows that by 10,000 BCE, all human societies employed varying degrees of ecologically transformative land use practices, including burning, hunting, species propagation, domestication, cultivation, and others that have left long-term legacies across the terrestrial biosphere. Yet, a lingering paradigm among natural scientists, conservationists, and policymakers is that human transformation of terrestrial nature is mostly recent and inherently destructive. Here, we use the most up-to-date, spatially explicit global reconstruction of historical human populations and land use to show that this paradigm is likely wrong. Even 12,000 y ago, nearly three quarters of Earth's land was inhabited and therefore shaped by human societies, including more than 95% of temperate and 90% of tropical woodlands. Lands now characterized as "natural," "intact," and "wild" generally exhibit long histories of use, as do protected areas and Indigenous lands, and current global patterns of vertebrate species richness and key biodiversity areas are more strongly associated with past patterns of land use than with present ones in regional landscapes now characterized as natural. The current biodiversity crisis can seldom be explained by the loss of uninhabited wildlands, resulting instead from the appropriation, colonization, and intensifying use of the biodiverse cultural landscapes long shaped and sustained by prior societies. Recognizing this deep cultural connection with biodiversity will therefore be essential to resolve the crisis.

History of biological, mechanistic, and clinical understanding of concussion.

The history behind the biological, mechanistic, and clinical insights into concussion provides awareness of the current understanding and future areas for study. Although the initial description of concussion appeared in the 10th century, the potential long-term structural consequences were first defined by Harrison Martland, M.D., who performed a postmortem study of former boxers in 1928. He found evidence of perivascular microhemorrhage that he believed eventually evolved into a "replacement gliosis" underlying a clinical syndrome that he named "punch drunk," which was characterized by acute confusion with chronic cognitive and physical symptoms developing in those with prolonged exposure. Further research into the potential long-term consequences of repetitive concussions, particularly in athletics and the military, led to an understanding of chronic traumatic encephalopathy. To ameliorate possible long-term risks, research has been focused on preventative and therapeutic measures for concussion. In this review article, the authors present the history of concussion and the long-term sequelae of repeated head injury. Specifically, they consider how the understanding of concussion has evolved from antiquity into the modern era, and how this change in understanding of head injury has led to an appreciation of the fact that its long-term implications sometimes manifest as the clinical and histopathological entity of chronic traumatic encephalopathy.

Anthropological genetics perspectives on the transatlantic slave trade.

During the Trans-Atlantic Slave Trade (TAST), around twelve million Africans were enslaved and forcibly moved from Africa to the Americas and Europe, durably influencing the genetic and cultural landscape of a large part of humanity since the 15th century. Following historians, archaeologists, and anthropologists, population geneticists have, since the 1950's mainly, extensively investigated the genetic diversity of populations on both sides of the Atlantic. These studies shed new lights into the largely unknown genetic origins of numerous enslaved-African descendant communities in the Americas, by inferring their genetic relationships with extant African, European, and Native American populations. Furthermore, exploring genome-wide data with novel statistical and bioinformatics methods, population geneticists have been increasingly able to infer the last 500 years of admixture histories of these populations. These inferences have highlighted the diversity of histories experienced by enslaved-African descendants, and the complex influences of socioeconomic, political, and historical contexts on human genetic diversity patterns during and after the slave trade. Finally, the recent advances of paleogenomics unveiled crucial aspects of the life and health of the first generation of enslaved-Africans in the Americas. Altogether, human population genetics approaches in the genomic and paleogenomic era need to be coupled with history, archaeology, anthropology, and demography in interdisciplinary research, to reconstruct the multifaceted and largely unknown history of the TAST and its influence on human biological and cultural diversities today. Here, we review anthropological genomics studies published over the past 15 years and focusing on the history of enslaved-African descendant populations in the Americas.

Detecting evolutionary forces in language change.

Both language and genes evolve by transmission over generations with opportunity for differential replication of forms. The understanding that gene frequencies change at random by genetic drift, even in the absence of natural selection, was a seminal advance in evolutionary biology. Stochastic drift must also occur in language as a result of randomness in how linguistic forms are copied between speakers. Here we quantify the strength of selection relative to stochastic drift in language evolution. We use time series derived from large corpora of annotated texts dating from the 12th to 21st centuries to analyse three well-known grammatical changes in English: the regularization of past-tense verbs, the introduction of the periphrastic 'do', and variation in verbal negation. We reject stochastic drift in favour of selection in some cases but not in others. In particular, we infer selection towards the irregular forms of some past-tense verbs, which is likely driven by changing frequencies of rhyming patterns over time. We show that stochastic drift is stronger for rare words, which may explain why rare forms are more prone to replacement than common ones. This work provides a method for testing selective theories of language change against a null model and reveals an underappreciated role for stochasticity in language evolution.

Artificial intelligence's interpretation of the neuroanatomical aspect of Peter Paul Rubens's copy of "The Battle of Anghiari" by Leonardo da Vinci.

We tested to see how Ruben's copy of "The Battle of Anghiari" by Leonardo da Vinci would be interpreted by AI in a neuroanatomical aspect. We used WOMBO Dream, an artificial intelligence (AI)-based algorithm that creates images based on words and figures. The keyword we provided for the algorithm was "brain" and the reference image was Ruben's drawing. AI interpreted the whole drawing as a representation of the brain. The image generated by the algorithm was similar to our interpretation of the same painting.

Acceleration of plague outbreaks in the second pandemic.

Historical records reveal the temporal patterns of a sequence of plague epidemics in London, United Kingdom, from the 14th to 17th centuries. Analysis of these records shows that later epidemics spread significantly faster ("accelerated"). Between the Black Death of 1348 and the later epidemics that culminated with the Great Plague of 1665, we estimate that the epidemic growth rate increased fourfold. Currently available data do not provide enough information to infer the mode of plague transmission in any given epidemic; nevertheless, order-of-magnitude estimates of epidemic parameters suggest that the observed slow growth rates in the 14th century are inconsistent with direct (pneumonic) transmission. We discuss the potential roles of demographic and ecological factors, such as climate change or human or rat population density, in driving the observed acceleration.

Systemic racism, systemic sexism, and the embryological enterprise.

The core of systemic racism and sexism is not merely an emphasis about human differences and thinking that another group of people is inferior to one's own. Rather, the institutional nature of racism or sexism establishes a permanent group hierarchy that is believed to reflect the laws of nature or the decrees of God. It thus becomes the norm of a culture to think and behave according to these rules. Notions of hierarchy became solidified into the Great Chain of Being during the Middle Ages, as did views concerning hereditary racial and gender superiority. During the Enlightenment, such classifications became established by philosophy and science. Starting in the 1800s, embryology and anthropology were used to provide evidence for the unilinear progression of species and races. The first evolutionary schemes were not "branching trees." In these schemes, women and non-white races were seen as embryonic or juvenile forms of the adult white male, and they were often depicted as intermediaries between the fully human and the animals. Such linear schemes of evolution remain part of popular culture and even some science, promoting the racism and sexism associated with them.