Modern Populations Research Articles

Genetic species concept as applied to multilocus nuclear data

Using the example of multiple species groups and species complexes, it is empirically shown that the resolving power of a set of 10–20 nuclear loci is insufficient for the study of their genetic differentiation. For the adequate analysis of phylogenetic relationships (including reticulation events) and assessment of divergence levels within such groups of closely related species, it is necessary to multiply the number of nuclear loci and transit to high-throughput next-generation deep sequencing. However, the question of the genomic coverage required for the purposes of such study remains open. In other words, exactly how many genes in a set are needed to measure the genetic distance resolving the relationships between branches on the phylogenetic tree reconstruction of a complex of closely related species? We chose protein-coding sequences as a standard set of markers. Distances for 160–180 genes with a combined length of 270 000–300 000 bp were used to estimate the divergence levels of closely related mammalian species. In most cases, the interspecific distances are within the 0.15–0.75% range (median of 0.33%). The range of distances between semi-species is 0.12–0.28% (median of 0.14%). Intraspecific distances are always lower than 0.11%. Rodents show higher values of interspecific distances, 0.25–2.3% (median of 0.72%); distances between half-species range from 0.1 to 0.35%. To determine the number of nuclear loci and their combined length sufficient for the calculation of a genetic distance, we use simulations based on a model that included the following parameters: the average rate of gene evolution, its dispersion, and the level of polymorphism in the modern and ancestral populations. We performed a preliminary analysis of the distribution of loci evolution rates among mammalian taxa based on the data on ~50 thousand nuclear markers. It is shown that a relative error of 10–15%, comparable to the same value for mitochondrial distances between close species based on individual genes (approximately 1000 bp in length), is achieved using approximately 100 loci of 300 bp in length. Based on these data, we propose the following working hypothesis: the threshold of interspecific/intraspecific genetic distance calculated on the basis of the exons most frequently used in mammalian molecular phylogenetics is approximately 0.15%. This hypothesis assumes a species rank for the forms in statu nascendi. It should be noted that not all “good” species have significant genetic distances, since in some cases reproductive barriers form faster than substitutions accumulate in the genome.

Frailty or resilience? Hazard-based and cumulative phenotype approaches to discerning signals of health inequality in medieval London.

Bioarchaeology uses human skeletal remains to reconstruct varied experiences of individuals and populations in the past, including patterns of health across time periods and cultural contexts. In the past three decades, bioarchaeological studies have highlighted the concept of "frailty," operationalizing it as increased risk of mortality or cumulative phenotypes. Using data from medieval London cemeteries, we integrate these two approaches to frailty in past populations. First, we estimate the risks of mortality and survivorship (hazard and survival analyses) associated with 10 biomarkers and use these results to construct population-specific frailty and resilience indices. Then, we apply the indices to adult individuals to explore frailty and resilience differentials between males and females in medieval London. Findings suggest that the male-female morbidity-mortality paradox observed in modern populations may not have existed in this context, which may be explained by preferential cultural buffering of men in this patriarchal, urban setting.

Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe.

Genomic resources are important for evaluating genetic diversity and supporting conservation efforts. The garden dormouse (Eliomys quercinus) is a small rodent that has experienced one of the most severe modern population declines in Europe. We present a high-quality haplotype-resolved reference genome for the garden dormouse, and combine comprehensive short and long-read transcriptomics data sets with homology-based methods to generate a highly complete gene annotation. Demographic history analysis of the genome reveal a sharp population decline since the last interglacial, indicating an association between colder climates and population declines before anthropogenic influence. Using our genome and genetic data from 100 individuals, largely sampled in a citizen-science project across the contemporary range, we conduct the first population genomic analysis for this species. We find clear evidence for population structure across the species' core Central European range. Notably, our data show that the Alpine population, characterized by strong differentiation and reduced genetic diversity, is reproductively isolated from other regions and likely represents a differentiated evolutionary significant unit (ESU). The predominantly declining Eastern European populations also show signs of recent isolation, a pattern consistent with a range expansion from Western to Eastern Europe during the Holocene, leaving relict populations now facing local extinction. Overall, our findings suggest that garden dormouse conservation may be enhanced in Europe through the designation of ESUs.

Diachronic Height Changes in Europe From the Mesolithic to the Present: Exploring Possible Causes and Regional Specificities.

A meta-analysis of diachronic changes in average height across Europe from the Mesolithic to the present, based on a broad range of literature sources. The analysis of chronological height variability was based on skeletal remains (from the Mesolithic to the 19th century), from which height was reconstructed, and on data from living individuals measured from the late 19th to the early 21st century. In total, data from 73 skeletal series and 342 groups of modern populations, primarily from Eastern Europe, were analyzed. A regression analysis was performed using R to describe the patterns of variability. The findings indicate that height decreases during the Neolithic and remains relatively stable until the Medieval period. A decline in average height is observed during the High Medieval period. The Early Modern period marks a transition to the 20th century, during which there is a consistent increase in average height, most pronounced until the 1980s, after which the rate of increase slows slightly into the early 21st century. Temporal height variability in the European part of Russia shows regional differences. The results suggest a wave-like pattern of trans-epochal changes in the somatic status of populations over an extended period, likely driven by various socioeconomic factors that dominated in different historical periods: the transition to agriculture, urbanization, political systems, industrial revolutions, and significant improvements in quality of life. Diachronic changes in height exhibit regional specificities, reflected in the variability of rates and magnitudes of secular gains across different regions and time periods.

Genetic Diversity in the Orenburg Goat Breed Revealed by Single-Nucleotide Polymorphism (SNP) Analysis: Initial Steps in Saving a Threatened Population

Background/Objectives: Orenburg goats are renowned for their soft down that acts as a substrate for warm clothing, particularly shawls that have an international reputation. As with many local livestock breeds, however, the Orenburg is presently at risk of extinction, an issue that can be addressed by assessing population genetic diversity and, thereafter, encouraging as much outbreeding as possible. Using single-nucleotide polymorphism (SNP)-based data, therefore, we analyzed the genetic diversity and population structure of modern Orenburg goats using samples collected from an expedition to Orenburg Oblast in 2024. Methods: We applied the Goat SNP50 BeadChip (Illumina, San Diego, CA, USA) for the genotyping of Orenburg goats from modern and archived populations. SNP genotypes of three Orenburg populations sampled in 2017 and 2019, Altai Mountain, Altai White, and Soviet Mohair breeds, were added to the dataset. Results: Principal component analysis and network and admixture analyses demonstrated that the genetic background inherent to the archived group of Orenburg goats was maintained in all modern populations. Values of genetic diversity indicators in modern populations were compatible with those obtained in comparison groups. Runs of homozygosity (ROH) were found in all the Orenburg goat populations (with a mean ROH length of 72.6–108.9 Mb and mean ROH number of 28–36). Genomic inbreeding based on ROH was low in all the Orenburg populations (FROH = 0.03–0.045). Conclusions: We showed that the ancestral background is retained in present-day Orenburg goats sampled in 2024. We provide the genetic basis through which certain breeder animals may be selected and bred traditionally or ex situ through a conservation program of gamete preservation.

Genetic analysis of a Yayoi individual from the Doigahama site provides insights into the origins of immigrants to the Japanese Archipelago.

Mainland Japanese have been recognized as having dual ancestry, originating from indigenous Jomon people and immigrants from continental East Eurasia. Although migration from the continent to the Japanese Archipelago continued from the Yayoi to the Kofun period, our understanding of these immigrants, particularly their origins, remains insufficient due to the lack of high-quality genome samples from the Yayoi period, complicating predictions about the admixture process. To address this, we sequenced the whole nuclear genome of a Yayoi individual from the Doigahama site in Yamaguchi prefecture, Japan. A comprehensive population genetic analysis of the Doigahama Yayoi individual, along with ancient and modern populations in East Asia and Northeastern Eurasia, revealed that the Doigahama Yayoi individual, similar to Kofun individuals and modern Mainland Japanese, had three distinct genetic ancestries: Jomon-related, East Asian-related, and Northeastern Siberian-related. Among non-Japanese populations, the Korean population, possessing both East Asian-related and Northeastern Siberian-related ancestries, exhibited the highest degree of genetic similarity to the Doigahama Yayoi individual. The analysis of admixture modeling for Yayoi individuals, Kofun individuals, and modern Japanese respectively supported a two-way admixture model assuming Jomon-related and Korean-related ancestries. These results suggest that between the Yayoi and Kofun periods, the majority of immigrants to the Japanese Archipelago originated primarily from the Korean Peninsula.

From Local Farms to Supermarket Foods: The Story of the Homogenization of the Argentine Diet Told by the IsotopeRatios of Modern Teeth.

Nutritional changes over the last century, driven by globalization, hypermarketization, and malnutrition, are global in scale. Large countries in the Global South might be resilient to dietary homogenization due to their natural diversity of regions and ecosystems, which might have prevented the adoption of supermarket diets. Argentina has a wide array of ecosystems and historically different subsistence diets dependent on regional characteristics. We analyzed the spatiotemporal variation of stable isotope values in Argentina using modern teeth to test for regional dietary patterns and its consistence over time. We collected teeth from voluntary donors born between 1940 and 2010, from 72 locations across Argentina. A total of 119 teeth were analyzed for the markers δ13Cdentine, δ13Cenamel, δ15N, and δ34S. A reconstruction of isotopic niches was performed to estimate dietary patterns across different regions and time periods. This study is the first to analyze changes in modern dietary patterns in Argentina using isotopic data measured in contemporary teeth. We showed latitudinal, longitudinal, and temporal differences in isotopic values, reflecting the variation in available resources within the country. Changes in the diet were observed over time, including declining δ15N values, a reduction in δ34S range, and a trend toward homogenization of δ13Cenamel values. Conversely, δ13Cdentine values remained constant over time, maintaining latitudinal patterns and regional differences across regions. This study increases our understanding of modern population dietary patterns both spatially and over the last 70 years. Our findings suggest that the Argentine population has shifted toward a supermarket diet in recent years.

How Does Social Inequality Alter Relationships Between Porous Cranial Lesions and Mortality? Examining the Relationship Between Skeletal Indicators of Stress, Socioeconomic Status, and Survivorship in a Pediatric Autopsy Sample.

In prior exploration of modern and archeological populations, lower SES has been associated with an increased risk of mortality. However, SES is often difficult to ascertain in archeological populations. Thus, explorations of skeletal lesions and their association with mortality may be subject to confounding factors that alter the strength and/or direction of this association. The present study uses data from a modern, documented coronial pediatric dataset to examine the association between porous cranial lesions (PCLs) (cribra orbitalia [CO] and porotic hyperostosis [PH]) and age at death while controlling for SES, as inferred through housing type, with manufactured or apartment housing identified as reflecting individuals from lower SES backgrounds in this context. We include 887 (535 males, 352 females) individuals aged 0.5-20.9 years from New Mexico who died between 2011 and 2022. Kaplan-Meier survival analysis was used to assess survivorship as related to PCLs and SES. Low SES is associated with lower survivorship. CO does not have a significant association with age at death when not controlling for SES; PH alone is associated with older age at death. Disadvantaged individuals with PCLs have significantly reduced survivorship than those with higher SES. The findings of this study demonstrate that low SES results in reduced survivorship, and those with low SES and PCLs have worse survivorship than less disadvantaged individuals with PCLs. Thus, the strong contribution of SES to mortality necessitates the consideration of the sociocultural context as a confounding factor when examining associations between variables of interest (such as lesions) and mortality in both past and present populations.

Ancient mitochondrial DNA extraction from Bison bison long bones from Head-Smashed-In Buffalo Jump, UNESCO World Heritage site

Head-Smashed-In Buffalo Jump (HSIBJ) is a UNESCO World Heritage Site located on the southern end of the Porcupine Hills, near Fort Macleod, Alberta, Canada. Using a system of drive lanes, Indigenous groups drove herds of bison over the cliff edge for thousands of years. The well-stratified deposits at the base of the cliff offer a unique opportunity to investigate the genetic diversity of the American bison before European contact and their genetic bottleneck in the 19th century. We extracted ancient DNA from twenty-one bison long bones, amplified and sequenced the mitochondrial DNA control region. Comparisons between ancient and modern bison populations revealed novel haplotypes in the HSIBJ population, suggesting a loss of genetic diversity due to the bottleneck. Furthermore, we discovered a shared haplotype between the bison hunted at the site and modern populations, which may help elucidate the complex history of living herds.

Advancements and prospects in reconstructing the genetic genealogies of ancient and modern human populations using ancestral recombination graphs.

With the release of large-scale genomic resources from ancient and modern populations, advancements in computational biology tools, and the enhancement of data mining capabilities, the field of genomics is undergoing a revolutionary transformation. These advancements and changes have not only significantly deepened our understanding of the complex evolutionary processes of human origins, migration, and admixture but have also unveiled the impact of these processes on human health and disease. They have accelerated research into the genetic basis of human health and disease and provided new avenues for uncovering the evolutionary trajectories recorded in the human genome related to population history and disease genetics. The ancestral recombination graph (ARG) reconstructs the evolutionary relationships between genomic segments by analyzing recombination events and coalescence patterns across different regions of the genome. An ARG provides a record of all coalescence and recombination events since the divergence of the sequences under study and specifies a complete genealogy at each genomic position, which is the ideal data structure for genomic analysis. Here, we review the theoretical foundations and research advancements of the ARG, and explore its translational applications and future prospects across various disciplines, including forensic genomics, population genetics, evolutionary medicine, and medical genomics. Our goal is to promote the application of this technique in genomic research, thereby deepening our understanding of the human genome.

Freshwater Mussel (Unio pictorum) Shells Reveal Hydrological and Environmental Change From 1300 BC to the Present Day.

Preserved biological communities can provide baseline data about the historical ecosystems and environmental conditions that preceded recent anthropogenic alteration. Freshwater mussel shells show particularly good preservation, and the shell assemblages commonly found during archaeological excavations can offer insights into past ecosystems. We studied assemblages of Unio pictorum mussel shells from palaeochannel silts associated with the Late Bronze Age site of Must Farm in eastern England (c. 850 BC), on an ancient tributary of the modern-day River Nene. We compared archaeological shells from two sediment horizons (broadly 1300-700 BC) to live individuals collected from two analogous sites on the present-day Nene. Size and growth rate, interannual growth variability and stable isotope (δ18O and δ13C) composition were compared between the populations. Size and the von Bertalanffy growth parameter L∞ differed among all four populations. Mean lengths and L∞ were higher in the two modern populations (mean lengths 77.3 ± SE 0.8 and 73.8 ± SE 1.1 mm, L∞ 91.8 ± 5.4 and 79.0 ± 8.1 mm) than the ancient populations (mean lengths 58.1 ± SE 1.6 mm and 68.4 ± SE 0.9 mm; L∞ 71.5 ± 16.9 and 76.8 ± 6.2 mm). Modern individuals also showed greater variation in age-corrected year-to-year growth. δ13C was lower in modern shells (-11.8‰ for modern shells, -9.03‰ and -9.02‰ for ancient shell populations), potentially reflecting altered hydrological and nutrient regimes. δ18O and δ13C were positively correlated for all but one sampled ancient shell, but not modern shells. These results reflect changes in local environmental conditions, particularly the transition from a shallow, slow-flowing tributary to a deeper, canalised river with faster flow, as well as effects of anthropogenic nutrient enrichment. The findings demonstrate the importance of long-term data in studying anthropogenic ecosystem alteration and avoiding shifting baseline syndrome in conservation planning.

Knowledge, Behavior, and Influencing Factors of Coarse Grain Consumption among Chinese Adults: A Focus Group Study in Xi’an

BackgroundCoarse grains are rich in fiber, minerals, and other beneficial nutrients but are consumed at low levels in modern populations. The factors that influence coarse grain consumption in current living and dietary environments are not fully understood. ObjectiveThis study aimed to explore the knowledge and behavior related to coarse grain consumption and identify the influencing factors among Chinese citizens. MethodSix focus group discussions were conducted with 39 participants aged 18–65 years from diverse social backgrounds in Xi'an, China. All discussions were transcribed verbatim and analyzed using inductive thematic analysis. ResultsThe majority of participants demonstrated insufficient knowledge about coarse grains, including their definitions, health benefits, and recommended intake. A small number of the participants reported regular consumption. The barriers to coarse grain consumption were poor sensory properties, insufficient cooking skills and time, limited availability of ready-to-eat foods, established dietary habits, and high price. Additionally, the new barriers included psychological burden, concerns about food safety, the impact of processing methods on health benefits, and special health conditions. Health benefits and family influence emerged as the two primary factors motivating coarse grain consumption. Most participants expressed a positive attitude toward partially replacing staple foods with coarse grains. Enhancing health education, innovating food processing methods, improving labeling systems, and strengthening safety supervision have been recommended for increasing coarse grain consumption. ConclusionA gap exists between health awareness and healthy behaviors regarding in coarse grain consumption, thus, collaborative efforts among government agencies, educational institutions, nutrition societies, the food industry, policymakers, and health professionals are essential to overcome these challenges.

Synthesis of Thioglycolic Acid-Modified Molybdenum Disulfide Nanosheets for Electrochemical Sensing and Its Application in Molnupiravir Detection

In the modern world, population growth, industrialization, and lifestyle changes have led to a rise in existing and new diseases, increasing global drug consumption. Proper pharmaceutical dosage is vital since drugs are only effective within specific concentration ranges. Therefore, developing reliable analytical methods for drug analysis in pharmaceuticals and biological samples is essential. Electroanalytical methods are particularly advantageous due to their low cost, ease of use, and rapid response. This study introduces a highly sensitive electrochemical sensor based on thioglycolic acid (TA)-decorated metallic phase molybdenum disulfide (MP-MoS2) nanosheets for the selective detection of molnupiravir (MOL), an antiviral drug used in Covid-19 treatment. The TA@MP-MoS2 nanomaterial was characterized using FTIR, TEM, and EIS. Screen-printed carbon electrodes (SPCE) were modified with TA@MP-MoS2 nanosheets to evaluate their electro-chemical and catalytic behaviours towards MOL by cyclic voltammetry (CV) and square wave voltammetry (SWV). The sensor displayed a well-defined electro-oxidation signal for MOL at 0.534 V, with the linear responses in two concentration ranges: 0.50–3.40 μM and 3.40–9.55 μM, and a low detection limit of 22.6 nM. The proposed design that has promising results could be an alternative strategy to fabricate the sensitive sensor for the detection of antiviral agents in real samples.

Contrasting Patterns of Genetic Diversity in European Mammals in the Context of Glacial Refugia

Phylogeographic studies have been conducted on many different mammal species in order to track their recent demographic histories. The climatic fluctuations associated with the Last Glacial Maximum (LGM) appear to have had a profound influence on the geographic patterning of genetic diversity in mammals. However, most phylogenetic studies have focused on single species. Few have used a holistic approach covering multiple taxa to explore common patterns. Here, we conducted meta-analyses of mitochondrial DNA control region sequences, identifying haplotype diversity and private allelic richness patterns in a geographic context. Four general patterns emerged among European mammals: an east–west decline in variation, a Western-Central belt of the highest diversity, southern richness, and homogeneity with no geographic pattern. These patterns likely reflect the refugial origins of modern populations. The east–west variation decline suggests species with eastern LGM refugia; the Western-Central belt of the highest diversity may harbor taxa with cryptic northern refugia, while southern richness may correspond to traditional southern refugia. Species with homogeneity and no geographic pattern may have been panmictic without a specific refugium or may reflect the occurrence of both southern and cryptic northern refugia. Surprisingly, the “no pattern” phenomenon is seldom discussed and may frequently have been discounted. Our study emphasizes the importance of considering multiple taxa, providing valuable insights into the responses of European mammals to past climatic changes.

Breeding work with kazakh horses Zhabe type

Background and Aim. Kazakh horses of Zhabе type differ from local horses in their higher live weight and larger body measurements. Breeding work with Kazakh horses of the Zhabе type is carried out at Tailak farm in Zharminsky district of East Kazakhstan through targeted reproduction, cultivation, and widespread use of the best individuals based on their origin, exterior, productivity, adaptation to year-round grazing, and quality of offspring from stallions and mares. Individuals that are not up to these standards are strictly culled. The aim of the research is to determine meat productivity and study genetic characteristics of a sample of modern population of Kazakh horses of Zhabe type using DNA markers.Materials and Methods. The material for the study was DNA genotyping data from 20 horses of the Kazakh breed type Zhabe. The horses were genotyped according to 17 STR lоci rеcommended by the Internаtional Sоciety for Animаl Gеnetics (ISАG). The international alphabetical code was used to identify alleles. Genetic and population analyses were performed using the GenAIEx software 6.5. The follоwing indicаtors wеre calculаted: the averаge numbеr of allеles per lоcus (Na), the effеctive numbеr of allеles (Ne), levеls of expеcted (He) and obsеrved heterozygоsity (Ho), and inbreеding cоefficient (FIS) .Results. A study on 17 STR loci of DNA in Kazakh horses Zhabе type has shown that they have a unique allele pool with a significant number of identified alleles and high genetic variability. The average inbreeding coefficient (FIS) is negative (-0.059), indicating that the genetic diversity of this breed is preserved within this group.Conclusion. The improvement of these horses is achieved through breeding and cultivation of animals with high genetic potential for productivity, which is passed down through generations of descendants. This is done by carefully selecting horses with desirable traits for breeding.

Picturing the Multiple Sclerosis Patient Journey: A Symptomatic Overview.

Background: Multiple sclerosis (MS) presents a wide range of clinical symptoms, historically understood through long-term studies of earlier patient cohorts. However, due to improved diagnostic criteria, modern patients are diagnosed earlier and benefit from effective treatments, altering the disease's natural history. This study aimed to assess the clinical symptoms of MS patients in a modern population at various stages: before diagnosis, at diagnosis, during the disease course, and at the time of the survey. Methods: This was an observational study with retrospective and cross-sectional components; patients that fulfilled the 2017 revised McDonald criteria for MS completed a survey evaluating demographic and clinical data. Results: We included 163 patients, 69.9% female, with a mean age of 48.21 years; 87.1% had relapsing-remitting MS (RRMS), with a median EDSS of 2.0. Before diagnosis, 74.2% of patients experienced symptoms, mainly sensory issues (39.3%), fatigue (29.4%), and imbalance (27%). Motor and coordination symptoms were more common in progressive forms. At diagnosis, sensory (46.6%) and motor complaints (36.8%) were most prevalent. In RRMS and secondary progressive MS (SPMS), sensory and motor complaints predominated alongside imbalance, while primary progressive MS (PPMS) was characterized by motor, imbalance, and genitourinary symptoms. Throughout the disease, sensory symptoms were most common (76.1%), with fatigue (73%) and motor issues (62.6%) more prevalent in progressive forms. At the time of the survey, 50.7% of RRMS patients were asymptomatic, while progressive patients continued to experience motor symptoms, imbalance, and fatigue. Conclusions: The study reflects the modern spectrum of MS symptoms, consistent with previous research.

Ensuring social standards as a principle of functioning of state authorities in accordance with the Association Agreement (theoretical and legal aspect)

The article discloses the content of social standards that state authorities are obliged to observe in the process of exercising their competence after the Association Agreement enters into force. Attention is focused on the fact that EU requirements regarding the activities of all branches of the state apparatus of Ukraine in terms of ensuring social standards are of primary importance in the context of the introduction of European approaches to good governance. It is substantiated that the timely and optimal implementation of EU social standards in Ukraine is possible only if a special legal mechanism is developed and applied. The heart of such a mechanism is the Association Agreement. Based on the analysis of the provisions of the specified document, the essence of the most significant social standards, which Ukraine undertakes to implement in practice, has been identified and disclosed. In particular, it is ensuring justice and improving the quality of life of citizens on the basis of equality and non-discrimination, increasing the level of social orientation of state policy towards migrants, introducing innovative approaches in the sphere of activity of authorities to combat the illegal circulation of narcotic drugs, precursors and psychotropic substances in order to overcome negative consequences for health and the negative social consequences of drug addiction, taking into account the social interests of the modern population while simultaneously caring for future generations, developing measures aimed at minimizing the risks to the population’s health from the nuclear industry, the social orientation of the organization of the fiscal and economic policy of the state. It has been proven that against the background of the deepening of the European integration processes of Ukraine, the modernization of the domestic social policy of the state is inevitable. First of all, this process requires the creation of an innovative legal basis for diversifying the mechanisms of its implementation, leveling the level of socio-economic development of Ukraine in order to avoid regional socio-economic asymmetry. In practice, this takes the form of changes in the legal regulation of a significant number of institutions of social security law of Ukraine, revision of organizational and legal approaches of state administration in the direction of implementing social standards.

Investigating population continuity and ghost admixture among ancient genomes

Ancient DNA (aDNA) can prove a valuable resource when investigating the evolutionary relationships between ancient and modern populations. Performing demographic inference using datasets that include aDNA samples however, requires statistical methods that explicitly account for the differences in drift expected among a temporally distributed sample. Such drift due to temporal structure can be challenging to discriminate from admixture from an unsampled, or “ghost", population, which can give rise to very similar summary statistics and confound methods commonly used in population genetics. Sequence data from ancient individuals also have unique characteristics, including short fragments, increased sequencing-error rates, and often limited genome-coverage that poses further challenges. Here we present a novel and conceptually simple approach for assessing questions of population continuity among a temporally distributed sample. We note that conditional on heterozygote sites in an individual genome at a particular point in time, the mean proportion of derived variants at those sites in other individuals has different expectations forwards in time and backwards in time. The difference in these processes enables us to construct a statistic that can detect population continuity in a temporal sample of genomes. We show that the statistic is sensitive to historical admixture events from unsampled populations. Simulations are used to evaluate the power of this approach. We investigate a set of ancient genomes from Early Neolithic Scandinavia to assess levels of population continuity to an earlier Mesolithic individual.

Population Genomic Scans for Natural Selection and Demography.

Uncovering the fundamental processes that shape genomic variation in natural populations is a primary objective of population genetics. These processes include demographic effects such as past changes in effective population size or gene flow between structured populations. Furthermore, genomic variation is affected by selection on nonneutral genetic variants, for example, through the adaptation of beneficial alleles or balancing selection that maintains genetic variation. In this article, we discuss the characterization of these processes using population genetic models, and we review methods developed on the basis of these models to unravel the underlying processes from modern population genomic data sets. We briefly discuss the conditions in which these approaches can be used to infer demography or identify specific nonneutral genetic variants and cases in which caution is warranted. Moreover, we summarize the challenges of jointly inferring demography and selective processes that affect neutral variation genome-wide.

Estimating osteological sex using predictive geometric morphometric analyses of the greater sciatic notch

Accurately estimating the biological sex of human skeletal remains is crucial in both forensic and archaeological contexts for constructing biological profiles. Presently, one of the most commonly used methods involves an ordinal scale describing the shape of the greater sciatic notch (GSN). However, this approach is limited by variations influenced by temporal, geographic, and ancestral factors affecting pelvic morphology. Consequently, its reliable applicability is restricted to populations resembling the original reference group. Recent advancements in quantitative analyses offer a promising alternative by enabling detailed measurement of subtle morphological changes, thus enhancing the accuracy of sex estimation using skeletal pelvic remains. In this study, we employ 2D landmark-based geometric morphometrics (GMM) to develop a protocol for pelvic sex estimation by quantifying the curve and angle of the GSN. These techniques are applied to both a contemporary population of adult European-Americans of known biological sexes (33 females, 38 males) and an archaeological population (n = 73) from south-west England. Our analysis reveals that our GMM approach achieves a 90 % accuracy rate in modern populations. Results indicate that both GSN morphology and angle are highly indicative of biological sex, allowing confidence in sex estimations of archaeological remains using these features.