Present-day Populations Research Articles

Maternal genetic diversity of ancient goats in Finland and Estonia and comparison with extant northern European goat breeds.

Countries in the northern Baltic Sea region have been historically linked for thousands of years, and animal husbandry is one of the many information sources that enables the study of historical connections. Although goat husbandry in this part of Europe has been evidenced by scant archaeological materials, zooarchaeological and historical evidence has revealed its continuity, at least since the Late Iron Age. To explore the historical relationship between goat lineages and investigate affinities between the past and present-day populations in the Baltic Sea region, we analysed a 476-bp fragment of the mitochondrial DNA control region in 14 ancient goats from Finland and Estonia and 10 extant goats from Finland. The results revealed high mitochondrial diversity among the ancient goats. Two maternal lineages were shared between the Late Iron Age and medieval individuals from Finland and Estonia. Moreover, ancient Finnish and Estonian goats showed maternal affinity to extant Finngoat and Swedish Landrace breeds. Overall, the analysis of maternal goat lineages confirmed tight historical connections in the region.

Spatiotemporal fluctuations of population structure in the Americas revealed by a meta-analysis of the first decade of archaeogenomes.

Since 2010, genome-wide data from hundreds of ancient Native Americans have contributed to the understanding of Americas' prehistory. However, these samples have never been studied as a single dataset, and distinct relationships among themselves and with present-day populations may have never come to light. Here, we reassess genomic diversity and population structure of 223 ancient Native Americans published between 2010 and 2019. The genomic data from ancient Americas was merged with a worldwide reference panel of 278 present-day genomes from the Simons Genome Diversity Project and then analyzed through ADMIXTURE, D-statistics, PCA, t-SNE, and UMAP. We find largely similar population structures in ancient and present-day Americas. However, the population structure of contemporary Native Americans, traced here to at least 10,000 years before present, is noticeably less diverse than their ancient counterparts, a possible outcome of the European contact. Additionally, in the past there were greater levels of population structure in North than in South America, except for ancient Brazil, which harbors comparatively high degrees of structure. Moreover, we find a component of genetic ancestry in the ancient dataset that is closely related to that of present-day Oceanic populations but does not correspond to the previously reported Australasian signal. Lastly, we report an expansion of the Ancient Beringian ancestry, previously reported for only one sample. Overall, our findings support a complex scenario for the settlement of the Americas, accommodating the occurrence of founder effects and the emergence of ancestral mixing events at the regional level.

Evaluation of respiratory function among homemakers exposed to indoor air pollution.

Indoor air contamination is a condition that can increase cardiovascular and respiratory mortality in the present-day population. Utilizing cooking exhaust in working environments, pollutants such as Polycyclic aromatic hydrocarbons (PAHs), incense sticks, cooking in fuel and kindling oven in the kitchen, and tobacco smoke are the significant reasons for indoor air contamination. The point of this study is to make mindfulness among homemakers presented to indoor air contamination. A spellbinding cross-sectional review including 100 homemaker female subjects in the age of 40-50 know about indoor air contamination. An overview was directed among 100 home creators in regard to indoor air contamination to make mindfulness. The strategy for testing done is basic arbitrary inspecting. The aftereffects of the current review showed that respondents were greatly presented to the indoor air contamination and created side effects connected with it and generally respondents in the age gathering of 40-50 years had encountered more exhaustion, dry bothersome skin, copying and aggravation of the eyes and stodgy nose, and affiliation was measurably huge. This finding revealed the indoor air toxins that can be considered to assume a part underway to infections like asthma, and so forth.

He-star donor AM CVn stars and their progenitors as LISA sources

Context. Ultracompact cataclysmic variables (CVs) of the AM CVn type are deemed to be important verification sources for the future space gravitational wave detectors such as the Laser Interferometer Space Antenna (LISA). Aims. We model the present-day Galactic population of AM CVn stars with He-star donors. Such a population has long expected to exist, though only a couple of candidates are known. Methods. We applied the hybrid method of binary population synthesis (BPS) which combines a simulation of the population of immediate precursors of AM CVn stars by a fast BPS code with subsequent tracking of their evolution by a full evolutionary code. Results. The model predicts that the present birthrate of He-donor AM CVn stars in the Galaxy is 4.6 × 10−4 yr−1 and the Galaxy may harbour ≃112 000 objects of this class which have orbital periods P ≲ 42 − 43 min. The foreground confusion limit and instrumental noise of LISA prevent the discovery of longer periods systems in gravitational waves. We find that about 500 He-star AM CVns may be detected by LISA with signal-to-noise ratio (S/N) > 5 during a 4 yr mission. Within 1 Kpc from the Sun, there may exist up to 130 He-star AM CVns with the periods in the same range, which may serve as verification binaries, if detected in the electromagnetic spectrum. In the Milky Way, there are also ≃14 800 immediate precursors of AM CVn stars. They are detached systems with a stripped low-mass He-star and a white dwarf companion, out of which about 75 may potentially be observed by LISA during its mission.

Mitogenomic diversity and stable isotopes provide insights into the maternal genetic history, mobility patterns, and diet of early medieval individuals from the Eastern Italian Alps

The Eastern Italian Alps (South Tyrol) is a connection area between continental Italy and the northern Alps. Various local factors, such as the heterogeneous environment, complex historical events, and different mobility patterns, may have influenced the genetic makeup of early medieval alpine groups. However, no ancient genetic data from these groups are currently available. This study provides a first picture of the ancient mitochondrial DNA (mtDNA) diversity of alpine groups from four locations in South Tyrol (Adige, Isarco, Venosta, and Merano). In total, 94 ancient mitogenomes of individuals (dated from 400 to 1100AD) were reconstructed by shotgun sequencing and a mtDNA capture approach. Moreover, stable isotope ratios (δ13C, δ15N, δ34S) were analyzed in a subset of 32 individuals. The results indicate different mtDNA haplogroup distributions among the alpine locations and the presence of rare lineages besides a possible maternal relatedness between individuals buried in the same and in diverse archaeological contexts. The study also shows differences in the genetic and mobility patterns (δ34S) between individuals from the central and north-eastern parts (Adige, Merano, Isarco) and those from the north-western part of South Tyrol (Venosta). These results suggest genetic exchanges with allochthonous people in the first group probably linked to high mobility and to geomorphological, historical, and socio-cultural factors. Comparisons extended to present-day alpine populations also suggested maternal genetic continuity in this alpine area. Finally, stable isotope (δ13C, δ15N, δ34S) data provided further support for regional differences in the diet of past alpine groups possibly linked to altitude and/or social status.

SPYGLASS. II. The Multigenerational and Multiorigin Star Formation History of Cepheus Far North

Young stellar populations provide a record of past star formation, and by establishing their members’ dynamics and ages, it is possible to reconstruct the full history of star formation events. Gaia has greatly expanded the number of accessible stellar populations, with one of the most notable recently discovered associations being Cepheus Far North (CFN), a population containing hundreds of members spanning over 100 pc. With its proximity (d ≲ 200 pc), apparent substructure, and relatively small population, CFN represents a manageable population to study in depth, with enough evidence of internal complexity to produce a compelling star formation story. Using Gaia astrometry and photometry combined with additional spectroscopic observations, we identify over 500 candidate CFN members spread across seven subgroups. Combining ages from isochrones, asteroseismology, dynamics, and lithium depletion, we produce well-constrained ages for all seven subgroups, revealing a largely continuous 10 Myr star formation history in the association. By tracing back the present-day populations to the time of their formation, we identify two spatially and dynamically distinct nodes in which stars form, one associated with β Cephei, which shows mostly co-spatial formation, and one associated with EE Draconis with a more dispersed star formation history. This detailed view of star formation demonstrates the complexity of the star formation process, even in the smallest of regions.

A longitudinal study of how disability has affected survival in Swedish populations across 150 years

Abstract Background Studies from across the world report that disability jeopardizes people's health and increases the risk of premature death. The trend has been demonstrated in present-day populations but there has been little research about whether disability affected survival in historical populations. Our objective was to identify long-term developments in the relationship between disability and survival. Methods We focused on all causes of mortality in ages 25-42 among groups with any type of disability in Swedish populations in the 1800s, 1900s and 2000s. We used Cox proportional regression and longitudinal micro-level data, measuring both relative differences (HRs) and absolute differences (excess LYL) in premature mortality, across time by disability status and sex. Results Although the overall mortality declined profoundly in Sweden during the centuries studied, the strong association between disability and premature mortality persisted, generating a significant disability-survival gap that has held since the 1800s. The absolute difference in this gap narrowed only slightly during the 1900s, from excess LYL due to disability for men of 1.67 (CI 0.17-3.44) in the 1800s, to 0.69 (CI 0.54-0.85) in the 2000s, while for women the change was even smaller, from 1.24 (CI -0.46-3.12) to 0.59 (CI 0.43-0.69). However, the relative difference widened, particularly for women, from HR of 2.46 (CI 0.91-6.70) in the 1800s to HR 12.00 (CI 9.88-14.60) in the 2000s. For men we found a change in HR from 2.30 (CI 1.31-4.06) to 8.48 (CI 7.26-9.92). Conclusions Our study is unique in providing comprehensive results about how disability has limited survival for more than 150 years. In Sweden, fundamental societal changes and extensive welfare provisions promoting equality in health and social wellbeing of all citizens have not been enough to improve the survival of younger generations with disabilities. Key messages • The strong association between disability and premature mortality persisted from the 1800s to the 2000s. • In Sweden, fundamental societal changes and extensive welfare provisions promoting equality in health have not improved survival of young adults with disabilities.

The matrilineal ancestry of Nepali populations.

The Tibetan plateau and high mountain ranges of Nepal are one of the challenging geographical regions inhabited by modern humans. While much of the ethnographic and population-based genetic studies were carried out to investigate the Tibetan and Sherpa highlanders, little is known about the demographic processes that enabled the colonization of the hilly areas of Nepal. Thus, the present study aimed to investigate the past demographic events that shaped the extant Nepalese genetic diversity using mitochondrial DNA (mtDNA) variations from ethnic Nepalese groups. We have analyzed mtDNA sequences of 999 Nepalese and compared data with 38,622 published mtDNA sequences from rest of the world. Our analysis revealed that the genomic landscapes of prehistoric Himalayan settlers of Nepal were similar to that of the low-altitude extant Nepalese (LAN), especially Newar and Magar population groups, but differ from contemporary high-altitude Sherpas. LAN might have derived their East Eurasian ancestry mainly from low-altitude Tibeto-Burmans, who likely have migrated from East Asia and assimilated across the Eastern Himalayas extended from the Eastern Nepal to the North-East of India, Bhutan, Tibet and Northern Myanmar. We also identified a clear genetic sub-structure across different ethnic groups of Nepal based on mtDNA haplogroups and ectodysplasin-A receptor (EDAR) gene polymorphism. Our comprehensive high-resolution mtDNA-based genetic study of Tibeto-Burman communities reconstructs the maternal origins of prehistoric Himalayan populations and sheds light on migration events that have brought most of the East Eurasian ancestry to the present-day Nepalese population.

Dental Paleobiology in a Juvenile Neanderthal (Combe-Grenal, Southwestern France).

Simple SummaryNumerous prehistoric sites in Europe and the Near East provided bones and dental remains of the populations of the past. One of them is the Combe-Grenal Cave (SW France), where fossils of children and adults represent the Neanderthals who lived there more than 60 ky ago, during a harsh period of the last glaciation. In this paper, we analyze a sample of the tartar of a juvenile individual. The numerous bacteria forming the plaque are compared to those of one adult from Israel, Kebara 2, revealing the differences between the most common bacteria in a young and an older individual, probably because of their immunological systems, and the different living conditions of the human groups they represented.Combe-Grenal site (Southwest France) was excavated by F. Bordes between 1953 and 1965. He found several human remains in Mousterian levels 60, 39, 35 and especially 25, corresponding to MIS 4 (~75–70/60 ky BP) and with Quina Mousterian lithics. One of the fossils found in level 25 is Combe-Grenal IV, consisting of a fragment of the left corpus of a juvenile mandible. This fragment displays initial juvenile periodontitis, and the two preserved teeth (LLP4 and LLM1) show moderate attrition and dental calculus. The SEM tartar analysis demonstrates the presence of cocci and filamentous types of bacteria, the former being more prevalent. This result is quite different from those obtained for the two adult Neanderthals Kebara 2 and Subalyuk 1, where more filamentous bacteria appear, especially in the Subalyuk 1 sample from Central Europe. These findings agree with the available biomedical data on periodontitis and tartar development in extant individuals, despite the different environmental conditions and diets documented by numerous archeological, taphonomical and geological data available on Neanderthals and present-day populations. New metagenomic analyses are extending this information, and despite the inherent difficulties, they will open important perspectives in studying this ancient human pathology.

Linkage of historical GB Census data to present day population registers.

ObjectivesThis research links, for the first time, individual level entire GB population census data for 1851-1911 to present day individual level population registers. Precise georeferencing of individual records using AddressBase Premium and further linkage to Indices of Multiple Deprivation (IMDs) enables family group analysis of inter-generational social mobility outcomes. ApproachPresent-day individual names and addresses taken from Electoral Registers and consumer data are georeferenced and linked to IMD data using AddressBase. This enables calculation of average IMD scores for every family group (surname). Individual level names and addresses from 1851-1911 censuses are assigned to harmonised historical parishes. The present day surname IMD scores are attributed to every resident in the historical censuses. Parish average ‘future IMD’ scores are calculated to show which areas have bequeathed the highest and lowest IMD scores on their residents’ descendants. This is a measure of how ‘north – south divides’ shape inter-generational social mobility. ResultsA linked data website, apps.cdrc.ac.uk/gbnames, profiles social mobility outcomes for 13,000+ family names, according to average neighbourhood quality experienced by family name bearers. There are clear and enduring regional divides in “future deprivation” inherited from ancestors by the present-day GB population. The research traces the origins of a north-south divide in England. Family roots in northern industrial cities are associated with unfavourable outcomes today. In Scotland, an east-west divide identifies eastern areas sharing similarly high levels of hardship to nineteenth-century industrial cities such as Liverpool and Manchester. Migration partially mitigates these inequalities, but most family groups remain concentrated in their ancestral heartlands, and continue to experience the long-term disadvantages bestowed by geographical location. ConclusionSurnames provide an under-exploited way of linking precisely georeferenced geographies of entire historical populations to their descendants today. Additional linkage to areal deprivation measures makes it possible to evaluate how social and spatial inequalities both endure and are promulgated through the generations. Geography is destiny for much of the population.

The Genetic Echo of the Tarim Mummies in Modern Central Asians.

The diversity of Central Asians has been shaped by multiple migrations and cultural diffusion. Although ancient DNA studies have revealed the demographic changes of the Central Asian since the Bronze Age, the contribution of the ancient populations to the modern Central Asian remains opaque. Herein, we performed high-coverage sequencing of 131 whole genomes of Indo-European-speaking Tajik and Turkic-speaking Kyrgyz populations to explore their genomic diversity and admixture history. By integrating the ancient DNA data, we revealed more details of the origins and admixture history of Central Asians. We found that the major ancestry of present-day Tajik populations can be traced back to the admixture of the Bronze Age Bactria–Margiana Archaeological Complex and Andronovo-related populations. Highland Tajik populations further received additional gene flow from the Tarim mummies, an isolated ancient North Eurasian–related population. The West Eurasian ancestry of Kyrgyz is mainly derived from Historical Era populations in Xinjiang of China. Furthermore, the recent admixture signals detected in both Tajik and Kyrgyz are ascribed to the expansions of Eastern Steppe nomadic pastoralists during the Historical Era.

A class of identifiable phylogenetic birth–death models

In a striking result, Louca and Pennell [S. Louca, M. W. Pennell, Nature 580, 502-505 (2020)] recently proved that a large class of phylogenetic birth-death models is statistically unidentifiable from lineage-through-time (LTT) data: Any pair of sufficiently smooth birth and death rate functions is "congruent" to an infinite collection of other rate functions, all of which have the same likelihood for any LTT vector of any dimension. As Louca and Pennell argue, this fact has distressing implications for the thousands of studies that have utilized birth-death models to study evolution. In this paper, we qualify their finding by proving that an alternative and widely used class of birth-death models is indeed identifiable. Specifically, we show that piecewise constant birth-death models can, in principle, be consistently estimated and distinguished from one another, given a sufficiently large extant timetree and some knowledge of the present-day population. Subject to mild regularity conditions, we further show that any unidentifiable birth-death model class can be arbitrarily closely approximated by a class of identifiable models. The sampling requirements needed for our results to hold are explicit and are expected to be satisfied in many contexts such as the phylodynamic analysis of a global pandemic.

Insights into evolutionary dynamics of East Asians through Ancient DNA

<p indent="0mm">Human origins and evolution are a principal focus of the Earth and Life Sciences. To address these important scientific subjects, the extraction, sequencing, and analysis of ancient DNA from subfossil materials and sediments has emerged as a powerful tool, forming a cutting-edge research field for the country’s innovation competitions. Ancient DNA provides unique advantages by allowing the direct observation of the changing genetic composition of ancient populations to unveil an expanding picture of the origin and evolution of humans in rich detail. Since 2010, the genomic data of ancient humans have grown exponentially, which has dramatically increased our knowledge of important questions such as the interaction between archaic humans and early modern humans, and the genetic components of past modern human lineages. However, compared to other regions worldwide, China had lagged far behind in the ancient DNA research field, and the genetic history of humans in East Asia, especially China, remained poorly understood. Before 2017, while hundreds of genomes of past Europeans and North Asians had been generated, those of East Asians were extremely limited (only four ancient human genomes had been generated from Japan), highlighting large gaps in our knowledge of past population histories between eastern and western Eurasia. In 2017, Qiaomei Fu’s research team had published the oldest East Asian genome sequenced to date, from the approximately 40000-year-old Tianyuan individual near Beijing, which opened up new prospects for the genetic study of past East Asians. Since then, they have continued to extensively sequence large numbers of ancient human genomes across different times and regions of China, including genomes from approximately 33000-to-300-year-old humans from Heilongjiang, Inner Mongolia, Shandong, Fujian, Guangxi, Xinjiang and the Taiwan Strait. This data has been used to identify the genetic characteristics of different ancient populations in East Asia, such as Basal East Asians (represented by the Tianyuan individual) and the Ancient Guangxi population (represented by the Longlin individual) which did not contribute to present-day Eurasians, as well as explore the primary ancestries of Ancient Northern East Asians and Ancient Southern East Asians, which compose the genetic makeup of East Asians today. These studies revealed the previously unknown genetic connections among past East Asians and other ancient and present-day populations in different regions of the world, elucidated the migration and interaction models of related populations, and characterized the genetic variation associated with environmental adaptations. These pioneering works have untangled the evolutionary dynamics of East Asians over a large timescale, challenged, supported, or revised several existing hypotheses, and played a significant role in a more comprehensive reconstruction of human history. The results of these studies have additionally provided important scientific value and practical significance for human microevolution and medical genetics research.

Range expansion and contraction of Tillandsia landbeckii lomas in the hyperarid Chilean Atacama Desert indicates ancient introgression and geneflow

Among the fascinating and highly specialized vascular plants in the hyperarid core of the Chilean and Peruvian Atacama Desert there are few Tillandsia species from the bromeliad family (Bromeliaceae). These grow epiarenically on bare sand without a functional root system, and in some rare cases they build up a monospecific and often the only landscape characterizing vegetation type, which is called Tillandsiales or Tillandsia loma. Tillandsia landbeckii is the dominating epiarenic species in Chile totally dependent on fog serving as the only water resource. Herein we elaborate on the hypothesis that migration and multiple colonization in concert with putative introgression from other Tillandsia species build up the present day phylogeographic distribution pattern and may contribute to the evolutionary dynamics and long-term success in hyperarid desert systems. Genomic analyses using GBS (genotyping-by-sequencing) data from the nuclear and plastid genome were conducted at the population level. A genome skimming approach was used to generate reference plastome data. The results indicate that both, multiple colonization and secondary contact of old gene pools and interspecies geneflow, contribute to present-day population genetic structure. Local-scale analysis also indicates that these past footprints of evolutionary history do contribute to present-day local adaptive potential of the species.

Estimating the timing of multiple admixture events using 3-locus linkage disequilibrium.

Estimating admixture histories is crucial for understanding the genetic diversity we see in present-day populations. Allele frequency or phylogeny-based methods are excellent for inferring the existence of admixture or its proportions. However, to estimate admixture times, spatial information from admixed chromosomes of local ancestry or the decay of admixture linkage disequilibrium (ALD) is used. One popular method, implemented in the programs ALDER and ROLLOFF, uses two-locus ALD to infer the time of a single admixture event, but is only able to estimate the time of the most recent admixture event based on this summary statistic. To address this limitation, we derive analytical expressions for the expected ALD in a three-locus system and provide a new statistical method based on these results that is able to resolve more complicated admixture histories. Using simulations, we evaluate the performance of this method on a range of different admixture histories. As an example, we apply the method to the Colombian and Mexican samples from the 1000 Genomes project. The implementation of our method is available at https://github.com/Genomics-HSE/LaNeta.

Larval Growth to Metamorphosis in the Northern Green Frog (Lithobates clamitans melanota) in a South Central Pennsylvania Pond during 2009–2016

Abstract A measure of predictability exists in geographic variation in some of the life history traits of the green frog, Lithobates clamitans. A long breeding and larval transformation season and a small transformation body size of this species in the southern United States give way to opposite patterns farther north. Overwintering of tadpoles occurs northward in its range and eventually typifies many northern populations. Our examination of larval growth and transformation in the northern green frog, L. clamitans melanota, corroborated findings of intermediacy in duration of transformation season (May–August) and mean transformation body size (30 mm) of mid-Atlantic populations. The latter finding may be obscured by metamorphoslings (32 mm) during May–June, presumed to have overwintered and therefore larger than those that transformed in August (29 mm) of the same year they hatched. It remains unknown how often two cohorts emerge within or between years in Pennsylvania. The potential for a warming climate to predispose this species to more frequent within-year transformation of smaller individuals akin to present-day southerly populations should be investigated.

Lineage-specific positive selection on ACE2 contributes to the genetic susceptibility of COVID-19.

The Angiotensin-Converting Enzyme-2 (ACE2) gene, located on Xp22.2, attracts a great deal of attention because the protein it encodes is believed to be the functional cellular receptor for the new coronavirus (SARS-CoV-2). However, recent studies are controversial, especially concerning the intrinsic link between ACE2 diversity and COVID-19 susceptibility. Here, we conduct a population genetic study on ACE2 in 6354 individuals representing 210 present-day populations and 5329 individuals of ancient or archaic groups. We dissected the genetic architecture of ACE2 and identified two major haplogroups (hg) in East Asians, i.e. ACE2-hg1 (43%) and ACE2-hg2 (53%), while other populations harbor more diverse ACE2-hgs. Accordingly, there was a significant loss of ACE2 common variations in East Asians in contrast to the X-chromosome-wide and genome-wide patterns. Notably, association analysis between ACE2-hgs and COVID-19 severity in 1229 Han Chinese individuals with various levels of COVID-19 severity showed a higher risk of ACE2-hg1 (odds ratio = 1.56, P < 0.01) and a lower risk of ACE2-hg2 (odds ratio = 0.65, P < 0.01). Interestingly, ACE2-hg1 is in strong linkage disequilibrium with rs1849863-C, which is an assumed risk factor of elevated plasma ACE2 level and is related to a higher risk of COVID-19 severity, hospitalization and infection. Strikingly, remarkable signatures of positive selection were detected, especially on ACE2-hg2, and were traced back to 100 000 years ago (but rose to a strong level during the Bronze Age, 5000∼3000 years ago, in East Asians). The selection pressures could have stemmed from multiple sources, but pre-COVID-19 viral epidemics and pandemics might have been potential driving forces, which consequently contributed to the genetic susceptibility to COVID-19 within and between populations.

Mathematical modelling of the progression of active tuberculosis: Insights from fluorography data.

Little is known about the dynamics of the early stages of untreated active pulmonary tuberculosis: unknown are both the rates of progression and the model “scheme”. The “parallel” scheme assumes that infectiousness of tuberculosis cases is effectively predefined at the onset of the disease, and the “serial” scheme considers all cases to be non-infectious at the onset, with some of them later becoming infectious.Our aim was to estimate the progression of the early stages of pulmonary tuberculosis using data from a present-day population. We used the routine notification data from Moscow, Russia, 2013–2018 that contained the results and time of the last fluorographic screening preceding the detection of tuberculosis cases. This provided time limits on the duration of untreated tuberculosis.Parameters of TB progression under both models were estimated. By the goodness of fit to the data, we could prefer neither the “parallel”, nor the “serial” model, although the latter had a bit worse fit. On the other hand, the observed rise in the fraction of infectious tuberculosis cases with the time since the last screening was explained by the “serial” model in a more plausible way – as gradual progression of some cases to infectiousness. The “parallel” model explained it through less realistic quick removal of non-infectious cases and accumulation of the infectious ones.The results demonstrate the potential of using such detection data enriched with reassessments of the previous screenings.

Genomic Insights Into the Demographic History of the Southern Chinese

Southern China is the birthplace of rice-cultivating agriculture and different language families and has also witnessed various human migrations that facilitated cultural diffusions. The fine-scale demographic history in situ that forms present-day local populations, however, remains unclear. To comprehensively cover the genetic diversity in East and Southeast Asia, we generated genome-wide SNP data from 211 present-day Southern Chinese and co-analyzed them with ∼1,200 ancient and modern genomes. In Southern China, language classification is significantly associated with genetic variation but with a different extent of predictability, and there is strong evidence for recent shared genetic history particularly in Hmong–Mien and Austronesian speakers. A geography-related genetic sub-structure that represents the major genetic variation in Southern East Asians is established pre-Holocene and its extremes are represented by Neolithic Fujianese and First Farmers in Mainland Southeast Asia. This sub-structure is largely reduced by admixture in ancient Southern Chinese since &amp;gt; ∼2,000 BP, which forms a “Southern Chinese Cluster” with a high level of genetic homogeneity. Further admixture characterizes the demographic history of the majority of Hmong–Mien speakers and some Kra-Dai speakers in Southwest China happened ∼1,500–1,000 BP, coeval to the reigns of local chiefdoms. In Yellow River Basin, we identify a connection of local populations to genetic sub-structure in Southern China with geographical correspondence appearing &amp;gt; ∼9,000 BP, while the gene flow likely closely related to “Southern Chinese Cluster” since the Longshan period (∼5,000–4,000 BP) forms ancestry profile of Han Chinese Cline.

Ancient Mitogenomes Reveal the Origins and Genetic Structure of the Neolithic Shimao Population in Northern China.

Shimao City is considered an important political and religious center during the Late Neolithic Longshan period of the Middle Yellow River basin. The genetic history and population dynamics among the Shimao and other ancient populations, especially the Taosi-related populations, remain unknown. Here, we sequenced 172 complete mitochondrial genomes, ranging from the Yangshao to Longshan period, from individuals related to the Shimao culture in northern Shaanxi Province and Taosi culture in southern Shanxi Province, Middle Yellow River basin. Our results show that the populations inhabiting Shimao City had close genetic connections with an earlier population in the Middle Neolithic Yangshao period of northern Shaanxi Province, revealing a mostly local origin for the Shimao Society. In addition, among the populations in other regions of the Yellow River basin, the Shimao-related populations had the closest maternal affinity with the contemporaneous Taosi populations from the Longshan period. The Shimao-related populations also shared more affinity with present-day northern Han populations than with the minorities and southern Han in China. Our study provides a new perspective on the genetic origins and structure of the Shimao people and the population dynamics in the Middle Yellow River basin during the Neolithic period.