A high-coverage genome from a 200,000-year-old Denisovan

Denisovan ancestry in present-day humans is heterogeneously distributed and comes from genetically distinct Denisovan groups. Understanding the origin of this heterogeneity could provide insights into the early population history of modern humans in Eurasia. However, population movements and admixture after the initial dispersals of modern humans have obscured the origin of this heterogeneity. To address this, we investigated how Denisovan ancestry in early modern humans relates to that in present-day humans. We found that varying levels of Denisovan ancestry in Eurasians were shaped by admixture between diverse early modern human lineages. In particular, ancient Japanese individuals from the Jomon period have the least Denisovan ancestry among individuals from Eastern Eurasia, providing evidence for an ancient East Asian lineage with little to no Denisovan ancestry. By contrast, the earliest mainland East Asians harbor the most Denisovan ancestry in Eastern Eurasia, including ancestry from multiple divergent Denisovan groups, already before the last glacial maximum. Together with evidence of Denisovan ancestry sharing among ancient and present-day genomes, these patterns show how Denisovan ancestry in Eurasia spread through gene flow from early East Asians. Our study provides the first systematic investigation of Denisovan admixture across time and extends our understanding of human population history in Eurasia.

A previous study reported that some of the human leukocyte antigen (HLA) alleles and haplotypes in present-day humans were acquired by admixture with archaic humans; specifically, an exceptionally diverged HLA-B*73 allele was proposed to be transmitted from Denisovans, although the DNA sequence of HLA-B*73 has not been detected in the Denisovan genome. Here, we argue against the hypothesis that HLA-B*73 introgressed from Denisovans into early modern humans. A phylogenetic analysis revealed that HLA-B*73:01 formed a monophyletic group with a chimpanzee MHC-B allele, strongly suggesting that the HLA-B*73 allelic lineage has been maintained in humans as well as in chimpanzees since the divergence of humans and chimpanzees. The global distribution of HLA-B*73 allele showed that the population frequency of HLA-B*73 in west Asia (0.24 %)—a possible site of admixture with Denisovans—is lower than that in Europe (0.72 %) and in south Asia (0.69 %). Furthermore, HLA-B*73 is not observed in Melanesia even though the Melanesian genome contains the highest proportion of Denisovan ancestry in present-day human populations. Single nucleotide polymorphisms in HLA-A*11-HLA-C*12:02 or HLA-A*11-C*15 haplotypes, one of which was assumed to be transmitted together with HLA-B*73 from Denisovans by the study of Abi-Rached and colleagues, were not differentiated from those in other HLA-A-C haplotypes in modern humans. These results do not support the introgression hypothesis. Thus, we conclude that it is highly likely that HLA-B*73 allelic lineage has been maintained in the direct ancestors of modern humans.

New Light on the Earliest Hominid Occupation in East Asia

Reconstructing diet can offer an improved understanding toward the origin and evolution of modern humans. However, the diet of early modern humans in East Asia is poorly understood. Starch analysis of dental calculus is harmless to precious fossil hominins and provides the most direct evidence of plant food sources in early modern human dietary records. In this paper, we examined the starch grains in dental calculus from Fuyan Cave hominins in Daoxian (South China), which were the earliest modern humans in East Asia. Our results reveal the earliest direct evidence of a hominin diet made of acorns, roots, tubers, grass seeds, and other yet-unidentified plants in marine isotope stage 5 between 120 and 80 ka. Our study also provides the earliest evidence that acorns may have played an important role in subsistence strategies. There may have been a long-lasting tradition of using these plants during the Late Pleistocene in China. Plant foods would have been a plentiful source of carbohydrates that greatly increased energy availability to human tissues with high glucose demands. Our study provides the earliest direct consumption of carbohydrates-rich plant resources from modern humans in China for the first time. In addition, it also helps elucidate the evolutionary advantages of early modern humans in the late Middle and early Upper Pleistocene.

Aerosol emissions from human activities are extensive and changing rapidly over Asia. Model simulations and satellite observations indicate a dipole pattern in aerosol emissions and loading between South Asia and East Asia, two of the most heavily polluted regions of the world. We examine the previously unexplored diverging trends in the existing dipole pattern of aerosols between East and South Asia using the high quality, two-decade long ground-based time series of observations of aerosol properties from the Aerosol Robotic Network (AERONET), from satellites (Moderate Resolution Imaging Spectroradiometer (MODIS) and Ozone Monitoring Instrument (OMI)), and from model simulations (Modern-Era Retrospective Analysis for Research and Applications, version 2 (MERRA-2). The data cover the period since 2001 for Kanpur (South Asia) and Beijing (East Asia), two locations taken as being broadly representative of the respective regions. Since 2010 a dipole in aerosol optical depth (AOD) is maintained, but the trend is reversed—the decrease in AOD over Beijing (East Asia) is rapid since 2010, being 17% less in current decade compared to first decade of twenty-first century, while the AOD over South Asia increased by 12% during the same period. Furthermore, we find that the aerosol composition is also changing over time. The single scattering albedo (SSA), a measure of aerosol’s absorption capacity and related to aerosol composition, is slightly higher over Beijing than Kanpur, and has increased from 0.91 in 2002 to 0.93 in 2017 over Beijing and from 0.89 to 0.92 during the same period over Kanpur, confirming that aerosols in this region have on an average become more scattering in nature. These changes have led to a notable decrease in aerosol-induced atmospheric heating rate (HR) over both regions between the two decades, decreasing considerably more over East Asia (− 31%) than over South Asia (− 9%). The annual mean HR is lower now, it is still large (≥ 0.6 K per day), which has significant climate implications. The seasonal trends in AOD, SSA and HR are more pronounced than their respective annual trends over both regions. The seasonal trends are caused mainly by the increase/decrease in anthropogenic aerosol emissions (sulfate, black carbon and organic carbon) while the natural aerosols (dust and sea salt) did not change significantly over South and East Asia during the last two decades. The MERRA-2 model is able to simulate the observed trends in AODs well but not the magnitude, while it also did not simulate the SSA values or trends well. These robust findings based on observations of key aerosol parameters and previously unrecognized diverging trends over South and East Asia need to be accounted for in current state-of-the-art climate models to ensure accurate quantification of the complex and evolving impact of aerosols on the regional climate over Asia.

Simple SummaryThe intricacies of human ancestry are buried deep within our DNA. For years, scientists have been working to piece together a vast picture of our genetic lineage. The purpose of this study was to further reveal this global picture of human genetic relatedness using identical-by-descent (IBD) genomic fragments. We processed over 65 million very rare single nucleotide polymorphic (SNP) alleles and detected over 17 million shared IBD fragments, including very short IBD fragments that allowed us to trace common ancestors back to 200,000 years ago. We also determined nine geographical regions representing nine unique genetic components for mankind: East and West Africa, Northern Europe, Arctica, East Asia, Oceania, South Asia, Middle East, and South America. The levels of admixture in every studied population could be assigned to one of these regions and long-term neighboring populations are strikingly similar, despite any political, religious, and cultural differences. Additionally, we observed the topmost admixture to be in central Eurasia. The entire picture of relatedness of all the studied populations presents itself in the form of shared number/size of IBDs, providing novel insights into geographical admixtures and genetic contributions that shaped human ancestry into what it is today.We performed an exhaustive pairwise comparison of whole-genome sequences of 3120 individuals, representing 232 populations from all continents and seven prehistoric people including archaic and modern humans. In order to reveal an intricate picture of worldwide human genetic relatedness, 65 million very rare single nucleotide polymorphic (SNP) alleles have been bioinformatically processed. The number and size of shared identical-by-descent (IBD) genomic fragments for every pair of 3127 individuals have been revealed. Over 17 million shared IBD fragments have been described. Our approach allowed detection of very short IBD fragments (<20 kb) that trace common ancestors who lived up to 200,000 years ago. We detected nine distinct geographical regions within which individuals had strong genetic relatedness, but with negligible relatedness between the populations of these regions. The regions, comprising nine unique genetic components for mankind, are the following: East and West Africa, Northern Europe, Arctica, East Asia, Oceania, South Asia, Middle East, and South America. The level of admixture in every studied population has been apportioned among these nine genetic components. Genetically, long-term neighboring populations are strikingly similar to each other in spite of any political, religious, and cultural differences. The topmost admixture has been observed at the center of Eurasia. These admixed populations (including Uyghurs, Azerbaijanis, Uzbeks, and Iranians) have roughly equal genetic contributions from the Middle East, Europe, China, and India, with additional significant traces from Africa and Arctic. The entire picture of relatedness of all the studied populations unfolds and presents itself in the form of shared number/size of IBDs.

As someone who entered the United States as a foreign student in the late 1980s, my academic career was intensely shaped by the then burgeoning discourses on colonialism and postcolonialism.1 The triumvirate of Said, Spivak, and Bhabha functioned like a citation machine; and despite Said’s Orientalism, South Asia, especially India, dominated as the colonial/ postcolonial site par excellence. Much of this had to do not just with the presence of many a South Asian scholar studying, writing, and teaching in U.S. universities but also with the fact that some of the most brilliant work was being undertaken on India: Lata Mani’s work on the discourses on sati, the work of the Subaltern Studies historians, Spivak’s “Can the Subaltern Speak?” and her famous essays on the Rani of Sirmur, and of course Bhabha’s legendary essays “Sly Civility” and “Signs Taken for Wonders.” The outpouring of anglophone fiction from South Asia, topped off by the publication of Rushdie’s Midnight’s Children, made certain that there would be no dearth of work on South Asian (read Indian) postcolonial fiction, and even today, despite a fairer distribution of attention to other parts of the ex-colonial worlds, works on South Asia continue to dominate the scene. Much has been written about this privileging of South Asia (again, read India) and its incarnation as the quintessential postcolonial site, and I am not going to rehearse the debates here. But suffice it to say that while my teaching spans continents, my first book was part and parcel of the work on the discourse of gender and nationalism in colonial and postcolonial literary representations by British, Bengali, and anglophone South Asian writers. But, in another sense the book was comparative because it brought into play writers working in different languages, and I remember getting a report from Cambridge University Press asking me why there was no chapter on Rushdie.

Extinction in the Anthropocene.

Empire of Eloquence: The Classical Rhetorical Tradition in Colonial Latin America and the Iberian World

South Asia is home to a remarkable portion of the world’s population, with about 1.9 billion people, making up nearly 24% of the global total. This region, which includes countries like India, Pakistan, Bangladesh, Nepal, Bhutan, Sri Lanka, and the Maldives, plays a vital role in shaping global demographics. One of the striking characteristics of South Asia's population is its youthful nature, setting it apart from many other parts of the world. In South Asia, roughly 28-30% of the population is under the age of 14, a larger proportion than the global average of 25%. This reflects a region with a high birth rate and a significant number of young people entering the workforce and education systems. Meanwhile, about 65% of South Asians fall within the working-age group (15-64 years), aligning with global trends. However, only 5-7% of the region’s population is over 65, compared to around 10% globally. This indicates that South Asia has a smaller elderly population, in contrast to many developed countries where longer life expectancy and lower birth rates are creating aging populations. These dynamics suggest that South Asia's youthful demographic will be central to its future development and economic growth. Introduction: South Asia is one of the most populous regions globally, and its population statistics are significant when compared to the global population. As of recent estimates: Percentage of Global Population from South Asia • South Asia accounts for about 25% of the global population. The region includes countries like India, Pakistan, Bangladesh, Nepal, Bhutan, Sri Lanka, and the Maldives. • The total population of South Asia is around 1.9 to 2 billion people, with India alone contributing to a large portion (about 1.4 billion). Age Distribution South Asia has a relatively young population compared to the global average, with a higher proportion of younger age groups. Here’s a comparison of the age distribution in South Asia vs the rest of the world. South Asia • 0–14 years: About 30% of the population. • 15–24 years: Around 20% of the population. • 25–64 years: Approximately 45%. • 65 years and older: Around 5%. Global Average • 0–14 years: About 25% of the global population. • 15–24 years: Roughly 15%. • 25–64 years: Around 50%. • 65 years and older: Around 10%. Key Points • South Asia has a younger population, with a higher percentage in the 0–24 age bracket compared to the global average. • The rest of the world, particularly regions like Europe and North America, tends to have a more aging population, with higher percentages in the 65+ age group. These demographic trends have significant implications for future economic development, healthcare needs, and social policies in South Asia and globally. Obesity is increasing globally, and South Asians (SA’s) are particularly vulnerable due to a combination of genetic, environmental, and lifestyle factors. Central obesity is prevalent among South Asians, leading to metabolic issues like insulin resistance and hypertension, even at lower body mass index (BMI) levels than seen in Western populations. This has prompted organizations such as the International Diabetes Federation (IDF) to adopt ethnic-specific waist circumference cut-offs for SAs. The "thin fat" phenotype, common in this group, refers to individuals who appear lean but carry excess visceral fat, raising their cardiovascular risk. Despite identifying some obesity-related genes like FTO and MC4R, research on South Asian populations remains limited compared to studies on Europeans. Traditional BMI cut-offs often underestimate health risks in this population, highlighting the need for targeted public health interventions to address rising obesity and metabolic disorders among South Asians.

Rice is the staple food par excellence of East Asia and themost densely populated landscapes of China, Korea, Japan,Southeast Asia, and South Asia. The origins and spread ofrice and the intensification of rice farming is oftenconnected to the development of civilization and ancientstates in many parts of this region (Gorou 1984; Bray1994). While it is widely accepted that China was anindependent centre of plant domestication (Bellwood 2005;Barker 2006) and rice was one of its major domesticatedcrops, the origins of agriculture has received less problem-oriented research than in regions like the Near East orMesoamerica. Much discussion of agricultural origins hashad a Western bias, focusing on the origins of wheat, or inAmerica maize, and research by Western scholars on theorigins of these crops.In Japanese scholarship, there has long been an emphasisplaced on the divergent traditions of agriculture, environ-ment and culture in western and eastern Eurasia. Onesource of this thinking is the early twentieth centuryphilosopher Watsuji and his concept of a link betweenclimate and culture (Watsuji 1921, 1961). Watsuji devel-oped a concept of Fudo (“climatic zones”), drawing adistinction between the environment, agricultural traditionsand nature of human cultures between Western Eurasia, thezone of mugi (the cereals including wheats and barley) andthe zone of rice and monsoons in Eastern Asia. Watsuji’sinference was that at opposite ends of Eurasia there havebeen long histories of different traditions of cultural impacton the environments, understandings of the environmentand subsistence. Indeed, the accumulated evidence ofarchaeology suggests that post-Palaeolithic trajectories inEast and West Asia were quite different, with varyingemphases on grinding and bread-making in the west, wherewheat and barley were domesticated, and more technologydevoted in boiling and steaming in the east where rice andsome millets were domesticated (Fuller and Rowlands2009). It remains the case, however, that our understandingof agricultural origins and plant domestication in East Asiais far less well-documented and understood by comparisonto West Asia, and the work represented in this volumecontributes towards increasing parity.The dispersal of rice farming is often seen as pivotal inthe population history of East and Southeast Asia and islinked to the establishment of sedentism and the spread ofmajor language families (Bellwood 2005). Previous syn-theses have more often been based on cultural historicalarchaeology rather than archaeological science, pots ratherthan the evidence of plants themselves. In recent years, agreat deal of new data and new ideas on the origin of riceagriculture in China and its diffusion through East andSoutheast Asia has emerged. This is due in part to thegrowth of systematic archaeobotany in East Asia, withflotation now being practised more often in China andKorea, where such methods were rarely deployed in theregion a decade ago. New genetic data have also forcedreconsiderations of the existing models of the number oforigins and trajectories of spread of rice agriculture. Newdebates about the number of origins and where they werehave emerged from genetic inferences (e.g. Kovach et al.2007; Fuller and Sato 2008; Vaughan et al. 2008; Zhang etal 2009; Izawa et al. 2009). Genetics is also increasinglyproviding information on the particular genes that underlie

It was shown that the human Angiotensin-converting enzyme 2 (ACE2) is the receptor of recent coronavirus SARS-CoV-2, and variation in this gene may affect the susceptibility of a population. Therefore, we have analysed the sequence data of ACE2 among 393 samples worldwide, focusing on South Asia. Genetically, South Asians are more related to West Eurasian populations rather than to East Eurasians. In the present analyses of ACE2, we observed that the majority of South Asian haplotypes are closer to East Eurasians rather than to West Eurasians. The phylogenetic analysis suggested that the South Asian haplotypes shared with East Eurasians involved two unique event polymorphisms (rs4646120 and rs2285666). In contrast with the European/American populations, both of the SNPs have largely similar frequencies for East Eurasians and South Asians, Therefore, it is likely that among the South Asians, host susceptibility to the novel coronavirus SARS-CoV-2 will be more similar to that of East Eurasians rather than to that of Europeans.

It was shown that the human Angiotensin-converting enzyme 2 (ACE2) is the receptor of recent coronavirus SARS-CoV-2, and variation in this gene may affect the susceptibility of a population. Therefore, we have analysed the sequence data of ACE2 among 393 samples worldwide, focusing on South Asia. Genetically, South Asians are more related to West Eurasian populations rather than to East Eurasians. In the present analyses of ACE2, we observed that the majority of South Asian haplotypes are closer to East Eurasians rather than to West Eurasians. The phylogenetic analysis suggested that the South Asian haplotypes shared with East Eurasians involved two unique event polymorphisms (rs4646120 and rs2285666). In contrast with the European/American populations, both of the SNPs have largely similar frequencies for East Eurasians and South Asians, Therefore, it is likely that among the South Asians, host susceptibility to the novel coronavirus SARS-CoV-2 will be more similar to that of East Eurasians rather than to that of Europeans.

The archaeological record of Later Pleistocene South Asia has a crucial role to play in our understanding of the evolution of modern human behavior and the dispersal of anatomically modern humans around the Old World. Later Pleistocene records of South Asia are here summarized and placed in the context of the modernhumanorigins debate. Aspects of the South Asian record share familiar traits with other regions of the Old World, but South Asia also appears to have its own adaptive features and material culture developments. The fluctuating environment during the Later Pleistocene would have influenced the adaptations of anatomically modern and archaic humans, affecting population size, movement, and the usefulness of cultural innovations. On the basis of prevailing genetic, archaeological, and biogeographic information, it is hypothesized that Homo sapiens colonized South Asia as part of an early southern dispersal from Africa. The effect of demographic processes on the rate and direction of cultural change is proposed as an explanation for the lack of a symbolic revolution signaling the arrival of anatomically modern humans on the Indian subcontinent. Instead, the Late Paleolithic represents a diversification of adaptive behaviors that may be traced to the Middle Paleolithic.

Candida auris is an emerging multiresistant yeast against which amphotericin B (AMB) is still the first therapeutic choice in certain clinical situations (i.e., meningitis, endophthalmitis, and urinary tract infections). As data about the in vitro killing activity of AMB against C. auris clades are lacking, we determined MICs, minimum fungicidal concentrations (MFCs), and killing activity of AMB against 22 isolates representing the 4 major C. auris clades (South Asian n = 6; East Asian n = 4; South African n = 6, and South American n = 6). MIC values were ≤1 mg/L regardless of clades; MFC ranges were, 1–4 mg/L, 2–4 mg/L, 2 mg/L, and 2–8 mg/L for South Asian, East Asian, South African, and South American clades, respectively. AMB showed concentration-, clade-, and isolate-dependent killing activity. AMB was fungicidal at 1 mg/L against two of six, two of four, three of six, and one of six isolates from the South Asian, East Asian, South African, and South American clades, respectively. Widefield fluorescence microscopy showed cell number decreases at 1 mg/L AMB in cases of the South Asian, East Asian, and South African clades. These data draw attention to the weak killing activity of AMB against C. auris regardless of clades, even when MICs are low (≤1 mg/L). Thus, AMB efficacy is unpredictable in treatment of invasive C. auris infections.