Present-day Populations Research Articles

Detecting Detached Black Hole Binaries through Photometric Variability

Understanding the connection between the properties of black holes (BHs) and their progenitors is interesting in many branches of astrophysics. Discovering BHs in detached orbits with luminous companions (LCs) promises to help establish this connection since the LC and BH progenitor are expected to have the same metallicity and formation time. We explore the possibility of detecting BH–LC binaries in detached orbits using photometric variations of the LC flux, induced by tidal ellipsoidal variation, relativistic beaming, and self-lensing. We create realistic present-day populations of detached BH–LC binaries in the Milky Way (MW) using binary population synthesis where we adopt observationally motivated initial stellar and binary properties, star formation history, and the present-day distribution of these sources in the MW based on detailed cosmological simulations. We test detectability of these sources via photometric variability by Gaia and TESS missions by incorporating their respective detailed detection biases as well as interstellar extinction. We find that Gaia is expected to resolve ∼300–1000 (∼700–1500) detached BH–LC binaries with signal-to-noise ratio (SNR) ≥ 10 (1) depending on the photometric precision and details of supernova physics. Similarly, the number of resolved BH–LC binaries with TESS is ∼50–200 (∼140–350). We find that 136−15+15 BH–LC binaries would be common between Gaia and TESS. Moreover, ∼60–70 (∼50–200) BH–LC binaries identifiable using photometry with SNR ≥ 10 may also be resolved using Gaia’s radial velocity (astrometry).

Population connectivity and size reductions in the Anthropocene: the consequence of landscapes and historical bottlenecks in white forsythia fragmented habitats

BackgroundWhite forsythia (Abeliophyllum distichum) is an endangered Korean Peninsula endemic that has been subjected to recent population genomics studies using SNPs via RAD sequencing. Here, we primarily employed the often underutilized haplotype information from RAD loci to further describe the species’ previously uninvestigated haplotype-based genomic variation and structure, and genetic-geographic characteristics and gene flow patterns among its five earlier identified genetic groups. We also inferred the time of past events that may have impacted the effective population size of these groups, as well as the species’ potential future distribution amidst the warming climate and anthropogenic threats.ResultsOur findings emphasized the recognition of the species’ regional patterns of genetic structure, and the role of topography and its associated gene flow patterns as some of the possible factors that may have influenced the species’ present-day fragmented population distribution. The inferred bottleneck events during the Anthropocene, some of which aligned with the time of historical catastrophic events on the Peninsula (e.g., the Korean War), were revealed to have contributed to the generally low effective population size of its five lineages, particularly those with marginal distributional range. Future distribution under both optimistic and pessimistic climatic scenarios suggests unlikely suitable habitats for these populations to expand from their current range limits, at least in the next 80 years.ConclusionsThe small effective population size and landscape-driven limited gene flow among white forsythia populations will remain a big challenge for the conservation management of the species’ already fragmented population distribution. To help mitigate these impacts, the merging of various research approaches and the use of genomic data to their full potential is recommended to provide the optimized knowledge-based tools for the conservation of this endangered species, and other similar plants under pressure.

Phylogeography of Y-chromosome haplogroup I-P37.2 in Serbian population groups originating from distinct parts of the Balkan Peninsula

Genetic structure of the contemporary Serbian population was shaped by a long history of turbulent historical and demographical events. The most important migrations of Serbs towards present day Serbia, in the recent history, occurred between the 15th to the 18th century from the regions of Old Herzegovina and Kosovo and Metohija. Previous haplogroup analysis revealed wide spectrum of main haplogroups, among which haplogroup I-P37.2 was the most frequent one in Serbian population groups originating from the Balkan Peninsula. Within this study 464 Serbian males samples from three geographical regions in the Balkan Peninsula inhabited by Serbs: present-day Serbia, regions of Old Herzegovina and Kosovo and Metohija, previously classified as haplogroup I-P37.2, were genotyped using the 22 Y-single nucleotide polymorphisms (Y-SNPs) in order to determine deeper phylogenetic and phylogeographic analysis of haplogroup I-P37.2. Based on SNP typing all samples in the Old Herzegovina and present-day Serbia dataset and 122 out of 128 samples from Kosovo and Metohija were assigned to haplogroup I-L621. Further SNP typing revealed very similar haplogroup distribution in all datasets, with the predominant haplogroup being I-PH908, followed by haplogroup I-Z17855. Analysis within haplogroup I-PH908 distinguished haplogroup I-FT14506 as the most frequent in the Kosovo and Metohija dataset, while haplogroup I-FT16449 was the most frequent in the Old Herzegovina dataset. In the present-day Serbia dataset, occurrence of haplogroups I-FT14506 and I-FT16449 was almost equal, comprising 40.2 % and 34.4 %, respectively. Low level of differentiation, within haplogroup I-PH908, was detected between all datasets, with the lowest one detected between present-day Serbia and Old Herzegovina datasets and highest one between Kosovo and Metohija and Old Herzegovina datasets. Furthermore, median-joining network analysis and shared haplotypes statistics revealed closer genetic relationship between Old Herzegovina and present-day Serbia haplotypes. Results obtained within this study support the thesis that migrations from historical region of Old Herzegovina and geographical region of Kosovo and Metohija, had great contribution on the present-day Serbian population genetic structure. Furthermore, here presented results, gave insight into geographic distribution of detected haplogroups I-Z17855, I-Y4460, I-PH908, I-Y5596, I-Y4882, I-FT14506, I-FT16449 and I-A5913 and analyzed SNPs, enabling further improvement of the geographic resolution of paternal ancestry inference.

Archaeogenomic analysis of Chesapeake Atlantic sturgeon illustrates shaping of its populations in recovery from severe overexploitation.

Atlantic sturgeon (Acipenser oxyrinchus ssp. oxyrinchus) has been a food resource in North America for millennia. However, industrial-scale fishing activities following the establishment of European colonies led to multiple collapses of sturgeon stocks, driving populations such as those in the Chesapeake area close to extinction. While recent conservation efforts have been successful in restoring census numbers, little is known regarding genomic consequences of the population bottleneck. Here, we characterize its effect on present-day population structuring and genomic diversity in James River populations. To establish a pre-collapse baseline, we collected genomic data from archaeological remains from Middle Woodland Maycock's Point (c. 200-900 CE), as well as Jamestown and Williamsburg colonial sites. Demographic analysis of recovered mitogenomes reveals a historical collapse in effective population size, also reflected in diminished present-day mitogenomic diversity and structure. We infer that James River fall- and spring-spawning populations likely took shape in recent years of population recovery, where genetic drift enhanced the degree of population structure. The mismatch of mitogenomic lineages to geographical-seasonal groupings implies that despite their homing instinct and differential adaptation manifested as season-specific behaviour, colonization of new rivers has been a key ecological strategy for Atlantic sturgeon over evolutionary timescales.

The genetic consequences of historic climate change on the contemporary population structure of a widespread temperate North American songbird

Studies of widely distributed species can inform our understanding of how past demographic events tied to historic glaciation and ongoing population genetic processes interact to shape contemporaneous patterns of biodiversity at a continental scale. In this study, we used whole-genome resequencing to investigate the current population structure and genetic signatures of past demographic events in the widespread migratory American goldfinch (Spinus tristis). Phylogenetic relationships inferred from whole mitochondrial genomes were poorly resolved. In contrast, a genome-wide panel of > 4.5 million single nucleotide polymorphisms (SNPs) strongly supported the existence of eastern and western populations separated by western mountain ranges and additional population structuring within the western clade. Demographic modeling estimated that the eastern and western populations diverged approximately one million years ago, and both populations experienced subsequent population bottlenecks during the last glacial period. Species distribution models showed a severe contraction of suitable habitat for the American goldfinch during this period, with predicted discontinuities that are consistent with multiple, isolated glacial refugia that coincide with present-day population structure. Low overall genetic differentiation between the eastern and western populations (FST ∼ 0.01) suggests ongoing gene flow accompanied divergence, and individuals with admixed genomic signatures were sampled along a potential contact zone. Nevertheless, outlier SNPs were identified near genes associated with feather color, song, and migratory behavior and provide strong candidates for further study of the mechanisms underlying reproductive isolation and speciation in birds.

Predicted short-term mesoscavenger release gives way to apex-scavenger dominance.

Vultures play a crucial role in scavenging communities as apex scavengers. Scavenging communities in turn are a key component of terrestrial ecosystems, ensuring that dead biomass is removed quickly and efficiently. Anthropogenic disturbances, particularly mass poisonings, have caused crashes in vulture populations in Africa and Asia. We ask if vultures can re-establish themselves in a scavenging community from a point of near extirpation. To allow for maximum knowledge transfer across ecosystems, we focus on an ecosystem that is otherwise considered pristine. We chose Kruger National Park (KNP), a well-documented African scavenging community, as our focal ecosystem and parameterised a mathematical model of scavenging-community dynamics using field data from the park. We predicted the upper limit of vulture population size in an ecosystem like KNP. We then analysed vultures' path to recovery, using this empirically parameterised scavenging-community model. We used perturbation methods to determine how parameter values that may be specific to KNP influence our predictions. Comparisons of predicted vulture carrying capacity with recent population estimates suggest that the cumulative effect of human activities on vulture abundance is larger than previously believed. Our analysis shows that vulture populations can reach their carrying capacity approximately five decades after a poisoning event that would almost extirpate the population. Over shorter time scales, we predict a decade of enhanced mammal abundance (i.e. mesoscavenger release) before the mammals are excluded from the scavenging community. In our study system, jackals and hyenas are the mammalian groups predicted to benefit from the absence of vultures. However, neither group removes biomass as efficiently as vultures and animal carcasses are predicted to accumulate in the ecosystem while the vulture population recovers. In our framework, the carrying capacity for vulture populations is determined by carcass availability. As evidence for an alternative regulating factor is lacking, we conclude that present-day vulture population densities are orders of magnitude below their upper limits. Our results therefore suggest that with a recovery plan in place, the long-term prospects for vulture species and the associated ecosystems are positive.

The Genomic and Cultural Diversity of the Inka Qhapaq Hucha Ceremony in Chile and Argentina.

The South American archaeological record has ample evidence of the socio-cultural dynamism of human populations in the past. This has also been supported through the analysis of ancient genomes, by showing evidence of gene flow across the region. While the extent of these signals is yet to be tested, the growing number of ancient genomes allows for more fine-scaled hypotheses to be evaluated. In this study, we assessed the genetic diversity of individuals associated with the Inka ritual, Qhapaq hucha. As part of this ceremony, one or more individuals were buried with Inka and local-style offerings on mountain summits along the Andes, leaving a very distinctive record. Using paleogenomic tools, we analyzed three individuals: two newly generated genomes from El Plomo Mountain (Chile) and El Toro Mountain (Argentina), and a previously published genome from Argentina (Aconcagua Mountain). Our results reveal a complex demographic scenario with each of the individuals showing different genetic affinities. Furthermore, while two individuals showed genetic similarities with present-day and ancient populations from the southern region of the Inka empire, the third individual may have undertaken long-distance movement. The genetic diversity we observed between individuals from similar cultural contexts supports the highly diverse strategies Inka implemented while incorporating new territories. More broadly, this research contributes to our growing understanding of the population dynamics in the Andes by discussing the implications and temporality of population movements in the region.

Neolithic to Bronze Age human maternal genetic history in Yunnan, China

Yunnan in southwest China is a geographically and ethnically complex region at the intersection of southern China and Southeast Asia, and a focal point for human migrations. To clarify its maternal genetic history, we generated 152 complete mitogenomes from 17 Yunnan archaeological sites. Our results reveal distinct genetic histories segregated by geographical regions. Maternal lineages of ancient populations from northwestern and northern Yunnan exhibit closer affinities with past and present-day populations from northern East Asia and Tibet, providing important genetic evidence for the migration and interaction of populations along the Tibetan-Yi corridor since the Neolithic. Between 5500 and 1800 years ago, central Yunnan populations maintained their internal genetic relationships, including a 7000-year-old basal lineage of the rare and widely dispersed haplogroup M61. At the Xingyi site, changes in mitochondrial DNA haplogroup occurred between the Late Neolithic and Bronze Age, with haplogroup shifting from those predominant in the Yellow River region to those predominant in coastal southern China. These results highlight the high diversity of Yunnan populations during the Neolithic to Bronze Age.

Science-based exit from stringent countermeasures against COVID-19: Mortality prediction using immune landscape between 2021 and 2022 in Japan

BackgroundStringent public health and social measures against COVID-19 infection were implemented to avoid an overwhelming hospital caseload and excessive number of deaths, especially among elderly people. We analyzed population-level immunity and predicted mortality, calculated as the potential number of deaths on a given calendar date in Japan, to develop a science-based exit strategy from stringent control measures. MethodsImmune proportions were inferred by age group using vaccination coverage data and the estimated number of naturally infected individuals. Immunity against symptomatic illness and death were estimated separately, allowing for inference of the immune fraction that was protected against either COVID-19-related symptomatic infection or death. By multiplying the infection fatality risk by age group for the immune fraction, the potential number of deaths was obtained. ResultsAccounting for a second and third dose of messenger RNA vaccine in the present-day population, approximately 155,000 potential deaths would be expected among people aged ≥ 60 years if all individuals were infected at the very end of 2022. A fourth dose (i.e., second booster) with a coverage identical to that of the third dose could reduce mortality by 60%. In all examined settings, the largest number of deaths occurred among people aged 80 years and older. ConclusionsOur estimates can help policymakers understand the mortality impact of the COVID-19 epidemic in a quantitative manner and the critical importance of timely immunization so as to assist in decision making.

Milky Way-est: Cosmological Zoom-in Simulations with Large Magellanic Cloud and Gaia–Sausage–Enceladus Analogs

We present Milky Way-est, a suite of 20 cosmological cold-dark-matter-only zoom-in simulations of Milky Way (MW)-like host halos. Milky Way-est hosts are selected such that they (i) are consistent with the MW’s measured halo mass and concentration, (ii) accrete a Large Magellanic Cloud (LMC)-like (≈1011 M ⊙) subhalo within the last 2 Gyr on a realistic orbit, placing them near 50 kpc from the host center at z ≈ 0, and (iii) undergo a >1:5 sub-to-host halo mass ratio merger with a Gaia–Sausage–Enceladus (GSE)-like system at early times (0.67 < z < 3). Hosts satisfying these LMC and GSE constraints constitute <1% of all halos in the MW’s mass range, and their total masses grow rapidly at late times due to LMC analog accretion. Compared to hosts of a similar final halo mass that are not selected to include LMC and GSE analogs, Milky Way-est hosts contain 22% more subhalos with present-day virial masses above 108 M ⊙ throughout the virial radius, on average. This enhancement reaches ≈80% in the inner 100 kpc and is largely, if not entirely, due to LMC-associated subhalos. These systems also induce spatial anisotropy in Milky Way-est subhalo populations, with ≈60% of the total subhalo population within 100 kpc found in the current direction of the LMC. Meanwhile, we find that GSE-associated subhalos do not significantly contribute to present-day Milky Way-est subhalo populations. These results provide context for our Galaxy’s dark matter structure and subhalo population and will help interpret a range of measurements that are currently only possible in the MW.

AGE ESTIMATION USING DIAPHYSEAL LONG BONE LENGTHS IN A NON-ADULT SKELETAL SAMPLE FROM GONUR DEPE, TURKMENISTAN

Introduction. The aim of this study is to provide group-specific regression equations for age estimation of immature human skeletal remains younger than 12 years of age from the diaphyseal length of the six long bones. Further, to compare inverse and classical calibration models for age estimation and the suitability of previously published regression methods for archaeological and present-day populations in relation to the analyzed sample. Materials and methods. The studied sample consists of 128 non-adult individuals from Gonur Depe – the major BMAC site in Turkmenistan (2300–1500 BCE). Regression formulae were obtained for each of the six long bones, separately for entire sample (0–12 years of age) and for two subsamples below and above 2 years of age. For each equation the coefficient of determination (R2) and F-statistics were calculated. Residuals were tested for normality of distribution, autocorrelation, homoscedasticity, and the equality of mean to zero (one-sample t-test). Comparison between inverse and classical calibration was provided using paired samples t-test. To assess the applicability of other regression formulae to the studied sample both the mean residuals (MR) and mean of the absolute value of the residuals (MAR) were calculated, as an estimate of bias and accuracy respectively. Results. All regression models showed a strong statistical significance and high R2 value. The slope coefficients of the regression lines of diaphyseal length upon age are greater for the upper limb bones both in the entire sample and two subsamples separately. The lower limb bones are characterized by lower growth rates. In contrast to the inverse calibration, for the classical model the mean standard errors (MSE) were smaller for the upper limb bones rather than for the lower limb bones. For the lower limb bones the standard error of the estimate (SE) was generally smaller in inverse formulae. Comparison of both models for the femur however shows their equal performance. For the exception of proposed and classical calibration formulae all inverse models for femur diaphyseal length show consistent differences from zero in relation to the studied sample. Discussion. The inverse and classical calibration models as a technique for age estimation using diaphyseal long bone lengths are both equally applicable in the studied sample. It is recommended to use the equations for the lower limb bones in the inverse model and for the upper limb bones in the classical model. The Gonur Depe population is characterized by relatively higher growth rates of the upper limb bones and distal limb segments relative to the proximal ones. Most of the previously published inverse calibration models are not recommended for uncritically use due to the high risk of obtaining biased estimates on samples that are different chronologically and/or territorially.

Denisovan admixture facilitated environmental adaptation in Papua New Guinean populations

Neandertals and Denisovans, having inhabited distinct regions in Eurasia and possibly Oceania for over 200,000 y, experienced ample time to adapt to diverse environmental challenges these regions presented. Among present-day human populations, Papua New Guineans (PNG) stand out as one of the few carrying substantial amounts of both Neandertal and Denisovan DNA, a result of past admixture events with these archaic human groups. This study investigates the distribution of introgressed Denisovan and Neandertal DNA within two distinct PNG populations, residing in the highlands of Mt Wilhelm and the lowlands of Daru Island. These locations exhibit unique environmental features, some of which may parallel the challenges that archaic humans once confronted and adapted to. Our results show that PNG highlanders carry higher levels of Denisovan DNA compared to PNG lowlanders. Among the Denisovan-like haplotypes with higher frequencies in highlander populations, those exhibiting the greatest frequency difference compared to lowlander populations also demonstrate more pronounced differences in population frequencies than frequency-matched nonarchaic variants. Two of the five most highly differentiated of those haplotypes reside in genomic areas linked to brain development genes. Conversely, Denisovan-like haplotypes more frequent in lowlanders overlap with genes associated with immune response processes. Our findings suggest that Denisovan DNA has provided genetic variation associated with brain biology and immune response to PNG genomes, some of which might have facilitated adaptive processes to environmental challenges.

Distinct positions of genetic and oral histories: Perspectives from India

Over the past decade, genomic data has contributed to several insights on global human population histories. These studies have been met both with interest and critically, particularly by populations with oral histories that are records of their past and often reference their origins. While several studies have reported concordance between oral and genetic histories, there is potential for tension that may stem from genetic histories being prioritized or used to confirm community-based knowledge and ethnography, especially if they differ. To investigate the interplay between oral and genetic histories, we focused on the southwestern region of India and analyzed whole-genome sequence data from 156 individuals identifying as Bunt, Kodava, Nair, and Kapla. We supplemented limited anthropological records on these populations with oral history accounts from community members and historical literature, focusing on references to non-local origins such as the ancient Scythians in the case of Bunt, Kodava, and Nair, members of Alexander the Great’s army for the Kodava, and an African-related source for Kapla. We found these populations to be genetically most similar to other Indian populations, with the Kapla more similar to South Indian tribal populations that maximize a genetic ancestry related to Ancient Ancestral South Indians. We did not find evidence of additional genetic sources in the study populations than those known to have contributed to many other present-day South Asian populations. Our results demonstrate that oral and genetic histories may not always provide consistent accounts of population origins and motivate further community-engaged, multi-disciplinary investigations of non-local origin stories in these communities.

Growing in Scarcity: Pre-Hispanic Rain-Fed Agriculture in the Semi-Arid and Frost-Prone Andean Altiplano (Bolivia)

Ancient Andean agricultural landscapes have been the subject of a large number of archaeological and agro-ecological studies, which generally refer to regions with favourable environmental conditions or, in the case of arid and semi-arid environments, those with irrigation facilities. The aim of this article is to present and analyse the pre-Hispanic rain-fed farming systems widely represented in two adjacent regions of Bolivia’s arid and cold southern Altiplano. The search for archaeological agricultural areas combined aerial analysis and field surveys. Agro-ecological characterisation was based on historical and ethnographic studies of the region’s present-day populations. Despite their geographical proximity, similar environmental conditions, and same agropastoral way of life, the typology of cultivated areas developed in the southern altiplano differs significantly. Within this same framework of adaptation and resilience, the sectorisation of agricultural systems observed in these two regions reveals a regional productive specialisation that favoured internal exchanges and exchanges with other regions. These differences are related to two models of non-centralised, low-inequality societies—one strongly based on cohesion and the other characterised by greater fragmentation and social conflict—underlining the limits of strict environmental determinism in shaping agricultural landscapes. These results provide new food for thought in the debate on the use and value of rain-fed agricultural practices and more broadly on the diversity of adaptations by human societies in extreme and unstable environmental contexts.

Genetic diversity among the present Japanese population: evidence from genotyping of human cell lines established in Japan

Japan is often assumed to have a highly homogeneous ethnic population, because it is an island country. This is evident in human cell lines collected from cell banks; however, these genotypes have not been thoroughly characterized. To examine the population genotypes of human cell lines established in Japan, we conducted SNP genotyping on 57 noncancerous cell lines and 43 lung cancer cell lines. Analysis of biogeographic ancestry revealed that 58 cell lines had non-admixed Japanese genotypes, 21 cell lines had an admixture of Japanese and East Asian genotypes, and the remaining 21 cell lines had East Asian genotypes. The proportion of non-admixed Japanese genotypes was similar between lung cancer and noncancerous cell lines, suggesting that patients in Japan may not exclusively have Japanese genotypes. This could influence the incidence of inherited diseases and should be taken into account in personalized medicine tailored to genetic background. The genetic makeup of the present-day Japanese population cannot be fully explained by the ancestral Jomon and Yayoi lineages. Instead, it is necessary to consider a certain level of genetic admixture between Japanese and neighboring Asian populations. Our study revealed genetic variation among human cell lines derived from Japanese individuals, reflecting the diversity present within the Japanese population.

Gene pool preservation across time and space In Mongolian-speaking Oirats

The Oirats are a group of Mongolian-speaking peoples residing in Russia, China, and Mongolia, who speak Oirat dialects of the Mongolian language. Migrations of nomadic ethnopolitical formations of the Oirats across the Eurasian Steppe during the Late Middle Ages/early Modern times resulted in a wide geographic spread of Oirat ethnic groups from present-day northwestern China in East Asia to the Lower Volga region in Eastern Europe. In this study, we generate new genome-wide and mitochondrial DNA data for present-day Oirat-speaking populations from Kalmykia in Eastern Europe, Western Mongolia, and the Xinjiang region of China, as well as Issyk-Kul Sart-Kalmaks from Central Asia, and historically related ethnic groups from Altai, Tuva, and Northern Mongolia to study the genetic structure and history of the Oirats. Despite their spatial and temporal separation, small current population census, both the Kalmyks of Eastern Europe and the Oirats of Western Mongolia in East Asia are characterized by strong genetic similarity, high effective population size, and low levels of interpopulation structure. This contrasts the fine genetic structure observed today at a smaller geographic scale in traditionally sedentary populations, and is conditioned by high mobility and marriage practices (traditional strict exogamy) in nomadic groups. Conversely, the genetic profile of the Issyk-Kul Sart-Kalmaks suggests a distinct source(s) of genetic ancestry, along with indications of isolation and genetic drift compared to other Oirats. Our results also show that there was limited gene flow between the ancestors of the Oirats and the Altaians during the late Middle Ages.Source of the yurt image: https://www.vecteezy.com/free-vector/yurt.

Reconstructing the Genetic Relationship between Ancient and Present-Day Siberian Populations.

Human populations across a vast area in northern Eurasia, from Fennoscandia to Chukotka, share a distinct genetic component often referred to as the Siberian ancestry. Most enriched in present-day Samoyedic-speaking populations such as Nganasans, its origins and history still remain elusive despite the growing list of ancient and present-day genomes from Siberia. Here, we reanalyze published ancient and present-day Siberian genomes focusing on the Baikal and Yakutia, resolving key questions regarding their genetic history. First, we show a long-term presence of a unique genetic profile in southern Siberia, up to 6,000 yr ago, which distinctly shares a deep ancestral connection with Native Americans. Second, we provide plausible historical models tracing genetic changes in West Baikal and Yakutia in fine resolution. Third, the Middle Neolithic individual from Yakutia, belonging to the Belkachi culture, serves as the best source so far available for the spread of the Siberian ancestry into Fennoscandia and Greenland. These findings shed light on the genetic legacy of the Siberian ancestry and provide insights into the complex interplay between different populations in northern Eurasia throughout history.

The Early Iron Age elite grave from the Kapiteljska njiva barrow cemetery (Novo mesto, Slovenia): an approach to dental profiling through non-invasive and minimally-invasive techniques.

Kapiteljska njiva is a prehistoric cemetery located in the town of Novo mesto in southern Slovenia. There is a long history of archaeological research at this site, as the first investigations date back to the end of the 19th century. In 2004, an Early Iron Age barrow XVI was investigated. The oldest surviving grave in the barrow is the central grave, numbered XVI/34, which according to its position and the richness of the grave goods, belongs to a woman of higher status. Most likely, she was the first member or initiator of a family that continued to bury its dead in the barrow for the next 300 years. There were no preserved skeletal elements; however, in the head part of the grave, remains of human teeth, mostly the tooth crowns and the shells of enamel from the tooth crowns, were found among the scattered amber beads of a necklace. Moreover, these tooth remains are one of the few human biological materials (mostly fragments of skull and long limb bones) unearthed in this cemetery, reflecting the influence of acidic soil from the burial site. This study aimed to create a dental profile of the deceased in a similar way as during a forensic investigation. The remains were examined macroscopically and stereo-microscopically. The morphological traits were scored following the ASUDAS protocol. Ancestry was estimated by entering these scores into a beta version of the web-based application rASUDAS. Brothwell's system was used for age at death estimation from occlusal attrition. Identification of sex was based on the analysis of sex-specific amelogenin isoforms in dental enamel by nanoflow liquid chromatography tandem mass spectrometry (nanoLC-MS/MS). The present study reveals that the dental remains from Kapiteljska njiva belong to the permanent dentition of a single individual and that only the right upper central incisor and third molar are completely absent. The remains of teeth exhibit a simple external morphology, characterised by the absence of morphological dental traits, with a notable exception of the two-rooted left lower canine. The probability of assigning this individual to the Western Eurasian ancestry group is 98%. According to the degree of dentine exposure on the occlusal surfaces of molars, the estimated age range is 17-25 years. Another line of evidence comes from the observation that the first signs of approximal attrition are present in lower third molars but absent in the only preserved upper counterpart, indicating that the age at which the lower third molars entered into occlusion represents a proxy of the individual's age at death. Data on the chronology of the lower third molar development and eruption in present-day European populations from forensic literature (Brkić et al. 2011; Olze et al. 2008; Selmanagić et al. 2013) and The London Atlas confirm the above age-range estimate. Caution is, however, needed in the interpretation of results, because reference data are not based on the population of the individual's origin. Proteomic analysis classified the individual as a female, which is in line with the archaeological evidence. No pathological lesions or indicators of systemic stress were identified; however, the absence of approximal attrition facets in upper anterior teeth indicates interdental spacing. The results of dental profiling are discussed in the context of historical background, today's clinical knowledge, and epidemiological data.

Simulation-based benchmarking of ancient haplotype inference for detecting population structure

Paleogenomic data has informed us about the movements, growth, and relationships of ancient populations. It has also given us context for medically relevant adaptations that appear in present-day humans due to introgression from other hominids, and it continues to help us characterize the evolutionary history of humans. However, ancient DNA (aDNA) presents several practical challenges as various factors such as deamination, high fragmentation, environmental contamination of aDNA, and low amounts of recoverable endogenous DNA, make aDNA recovery and analysis more difficult than modern DNA. Most studies with aDNA leverage only SNP data, and only a few studies have made inferences on human demographic history based on haplotype data, possibly because haplotype estimation (or phasing) has not yet been systematically evaluated in the context of aDNA. Here, we evaluate how the unique challenges of aDNA can impact phasing and imputation quality, we also present an aDNA simulation pipeline that integrates multiple existing tools, allowing users to specify features of simulated aDNA and the evolutionary history of the simulated populations. We measured phasing error as a function of aDNA quality and demographic history, and found that low phasing error is achievable even for very ancient individuals (∼ 400 generations in the past) as long as contamination and average coverage are adequate. Our results show that population splits or bottleneck events occurring between the reference and phased populations affect phasing quality, with bottlenecks resultingin the highest average error rates. Finally, we found that using estimated haplotypes, even if not completely accurate, is superior to using the simulated genotype data when reconstructing changes in population structure after population splits between present-day and ancient populations. We also find that the imputation of ancient data before phasing can lead to better phasing quality, even in cases where the reference individuals used for imputation are not representative of the ancient individuals.

Simulation-based benchmarking of ancient haplotype inference for detecting population structure

Paleogenomic data has informed us about the movements, growth, and relationships of ancient populations. It has also given us context for medically relevant adaptations that appear in present-day humans due to introgression from other hominids, and it continues to help us characterize the evolutionary history of humans. However, ancient DNA (aDNA) presents several practical challenges as various factors such as deamination, high fragmentation, environmental contamination of aDNA, and low amounts of recoverable endogenous DNA, make aDNA recovery and analysis more difficult than modern DNA. Most studies with aDNA leverage only SNP data, and only a few studies have made inferences on human demographic history based on haplotype data, possibly because haplotype estimation (or phasing) has not yet been systematically evaluated in the context of aDNA. Here, we evaluate how the unique challenges of aDNA can impact phasing and imputation quality, we also present an aDNA simulation pipeline that integrates multiple existing tools, allowing users to specify features of simulated aDNA and the evolutionary history of the simulated populations. We measured phasing error as a function of aDNA quality and demographic history, and found that low phasing error is achievable even for very ancient individuals (∼ 400 generations in the past) as long as contamination and average coverage are adequate. Our results show that population splits or bottleneck events occurring between the reference and phased populations affect phasing quality, with bottlenecks resulting in the highest average error rates. Finally, we found that using estimated haplotypes, even if not completely accurate, is superior to using the simulated genotype data when reconstructing changes in population structure after population splits between present-day and ancient populations. We also find that the imputation of ancient data before phasing can lead to better phasing quality, even in cases where the reference individuals used for imputation are not representative of the ancient individuals.