Population Affinities Research Articles

A comprehensive portrait of Y-STR diversity of Indian populations and comparison with 129 worldwide populations

India, known for its rich cultural, linguistic and ethnic diversity, has attracted the attention of population geneticists to understand its genetic diversity employing autosomal, Y-chromosomal and mitochondrial DNA markers. Y-chromosomal short tandem repeats (Y-STRs) are useful in understanding population substructures and reveal the patrilineal affinities among populations. Previous studies on Indian populations based on Y-STR markers were either limited to restricted number of markers or focused on few selected populations. In this study we genotyped 407 unrelated male individuals from 12 states in India employing the suite of Y-STRs present in PowerPlex Y23 (Promega, Madison, WI, USA). These populations clustered genetically close to each other irrespective of their geographic co-ordinates and were characterized primarily by R1a, H and L haplogroups. Interestingly, comparison with 129 worldwide populations showed genetic affinity of the Indian populations with few populations from Europe and Levantine. This study presents the first pan-Indian landscape of 23 Y-STRs and serves as a useful resource for construction of an Indian Y-STR database.

Investigating the genetic diversity and affinities of historical populations of Tibet

This study elucidates Y chromosome distribution patterns in the three general provincial populations of historical Tibet, Amdo (n = 88), Dotoe (n = 109) and U-Tsang (n = 153) against the backdrop of 37 Asian reference populations. The central aim of this study is to investigate the genetic affinities of the three historical Tibetan populations among themselves and to neighboring populations. Y-SNP and Y-STR profiles were assessed in these historical populations. Correspondence analyses (CA) were generated with Y-SNP haplogroup data. Y-STR haplotypes were determined and employed to generate multidimensional scaling (MDS) plots based on Rst distances. Frequency contour maps of informative Y haplogroups were constructed to visualize the distributions of specific chromosome types. Network analyses based on Y-STR profiles of individuals under specific Y haplogroups were generated to examine the genetic heterogeneity among populations. Average gene diversity values and other parameters of population genetics interest were estimated to characterize the populations. The Y chromosomal results generated in this study indicate that using two sets of markers (Y-SNP, and Y-STR) the three Tibetan populations are genetically distinct. In addition, U-Tsang displays the highest gene diversity, followed by Amdo and Dotoe. The results of this transcontinental biogeographical investigation also indicate various degrees of paternal genetic affinities among these three Tibetan populations depending on the type of loci (Y-SNP or Y-STR) analyzed. The CA generated with Y-SNP haplogroup data demonstrates that Amdo and U-Tsang are closer to each other than to any neighboring non-Tibetan group. In contrast, the MDS plot based on Y-STR haplotypes displays Rst distances that are much shorter between U-Tsang and its geographic nearby populations of Ladakh, Punjab, Kathmandu and Newar than between it and Amdo. Moreover, although Dotoe is isolated from all other groups using both types of marker systems, it lies nearer to the other Tibetan collections in the Y-SNP CA than in the Y-STR MDS plot. High resolution and shallow evolutionary time frames engendered by Y-STR based analyses may reflect a more recent demographic history than that delineated by the more conserved Y-SNP markers.

DECIDUOUS HUMAN TEETH FROM THE UPPER PALEOLITHIC SITE OF YUDINOVO, WESTERN RUSSIA

Population affinities of the Timonovka-Yudinovo Upper Paleolithic people are reconstructed on the basis of three isolated deciduous teeth––a lower lateral incisor, lower and upper second molars, likely representing three individuals––from Yudinovo in the middle Desna basin (15–12 ka BP), found in 1987–1996. Based on measurements and descriptive traits and computed microtomography, the teeth were compared with those from other Upper Paleolithic sites in northern Eurasia. The principal component analyses of metric and nonmetric traits revealed similar patterns. To minimize random variation, results of both analyses were integrated. Results indicate affi nity with Pavlov people in Central Europe. The diagnostic trait combination includes weak expression of the Carabelli cusp on the upper second molar, accessory sixth cusp on the lower second molar, large bucco-lingual diameter of both molars, and moderate mesio-distal diameter of the lower second molar. These results support the view that the Timonovka-Yudinovo tradition is related to eastern Gravette.

Making the Ethical Transition in South Africa: Acquiring Human Bodies for Training in Anatomy.

While dissection remains the method of choice for teaching human anatomy, ethical requirements for obtaining cadavers has made the process of acquiring human bodies more strenuous for institutions. In Africa and at the School of Anatomical Sciences in South Africa, dependence on unclaimed bodies has been prevalent. The aim of the present study was to determine whether more rigorous application of ethical consent has altered the provenance of the cadavers in the School of Anatomical Sciences, University of the Witwatersrand. The numbers of bequeathed/donated/unclaimed cadavers received over the period 2013-2017, as well as their sex and population affinity were analyzed. The majority (96.8%) of the cadavers dissected over the period were from bequests/donations. Marginally more females than males were available. In addition, the population affinity of the cadavers had changed from a majority of South African African (unclaimed) bodies to a majority of South African White (bequest/donated) bodies. The study shows that even with ethical constraints it is possible to transition from the use of mainly unclaimed bodies to the acquisition of bequeathed/donor bodies. However, there may be challenges in relation to anatomical collections in the School as few of the bequest/donated cadavers remain in the School to be added to the collections. These changes also affect the demographics of the Schools' collections.

Understanding (Mis)classification Trends of Latin Americans in Fordisc 3.1: Incorporating Cranial Morphology, Microgeographic Origin, and Admixture Proportions for Interpretation

Assigning correct population affinity to a skeleton can contribute important information to an investigation-yet recent work highlights high error rates when classifying Latinos with a traditional tool, Fordisc 3.1 (FD3). Our study examines whether misclassification trends exist, and whether these can be used to infer population affinity. We examine the relationships among ancestry, geography, and FD3 misclassifications of Latinos using canonical variate analysis and unsupervised model-based clustering of craniometrics. Northern Mexicans appear more strongly associated with FD3 references samples with elevated amounts of European ancestry (e.g., American Blacks and Whites), while Southern Mexicans are more strongly associated with FD3 reference samples with reduced amounts of European ancestry (e.g., Guatemalans and Native Americans). FD3 classifications revealed that Latinos exhibited lower posterior probabilities when compared to other common case demographics (Whites and African Americas), even when the classification was "correct." We make recommendations for practitioner interpretation of FD3 reports for casework.

The influence of latitude, geographic distance, and habitat discontinuities on genetic variation in a high latitude montane species

Examining the factors that influence contemporary genetic patterns is important given the alarming rate at which natural environments are changing. In particular habitat fragmentation and climate change are expected to influence the distribution and diversity of natural populations. In this study we used both mitochondrial control region (mtDNA) and microsatellite data to answer the following questions about genetic diversity and divergence in mountain chickadees (Poecile gambeli) a resident bird species in western North America: (1) Do populations exhibit similar levels of genetic diversity across the range? (2) What is the genetic affinity of western populations in Oregon and Washington? (3) Do genetic patterns exhibit isolation by distance, or are genetic patterns more heavily influenced by habitat discontinuity? We tested the effects of isolation by distance and habitat distribution on genetic structure by analyzing 266 samples from 17 sites across western Canada and the United States. We found a near significant relationship between genetic diversity and latitude, however, our results indicate that overall, latitude is not a strong predictor of genetic diversity. Our analyses of populations in Oregon and Washington revealed a mismatch between patterns detected with mtDNA and microsatellite data. In particular, Washington clustered with the Coast Range/Cascades/Rocky Mountain mtDNA group, but with populations in southern Oregon/California based on microsatellite data. These results suggest the presence of a contact zone in Washington between the two mtDNA clades Coast Range/Cascades/Rocky Mountain and southern Oregon/California clades. Finally, our study revealed a greater effect of isolation by distance than isolation by habitat for both mtDNA and microsatellite data. Overall the isolation by distance signal was greater for mtDNA than microsatellite patterns. The greater signal of isolation by distance on mtDNA patterns likely reflects the strong effects of Pleistocene glaciations in shaping genetic patterns in western North America.

An extinct hummingbird species that never was: a cautionary tale about sampling issues in molecular phylogenetics.

The selection of species and individuals for molecular analyses critically affects inferences in various fields of systematic biology including phylogenetics, phylogeography, and species delimitation. Especially in areas like the Neotropical region where molecular analyses have recovered substantial within-species divergence and unexpected affinities of populations (Turchetto-Zolet et al. 2013), biases resulting from incomplete taxonomic or geographic sampling may compromise the understanding of phylogenetic relationships (Avendaño et al. 2017). Here we describe a case in which assessments of the validity of a potentially extinct species of Neotropical bird were likely compromised because within-species variation was not accounted for in phylogenetic analyses evaluating the alternative hypothesis that the only known specimen may represent a hybrid.

CD4 T Cell Affinity Diversity Is Equally Maintained during Acute and Chronic Infection.

TCR affinity for peptide MHC dictates the functional efficiency of T cells and their propensity to differentiate into effectors and form memory. However, in the context of chronic infections, it is unclear what the overall profile of TCR affinity for Ag is and if it differs from acute infections. Using the comprehensive affinity analysis provided by the two-dimensional micropipette adhesion frequency assay and the common indirect affinity evaluation methods of MHC class II tetramer and functional avidity, we tracked IAb GP61-80-specific cells in the mouse model of acute (Armstrong) and chronic (clone 13) lymphocytic choriomeningitis virus infection. In each response, we show CD4 T cell population affinity peaks at the effector phase and declines with memory. Of interest, the range and average relative two-dimensional affinity was equivalent between acute and chronic infection, indicating chronic Ag exposure did not skew TCR affinity. In contrast, functional and tetramer avidity measurements revealed divergent results and lacked a consistent correlation with TCR affinity. Our findings highlight that the immune system maintains a diverse range in TCR affinity even under the pressures of chronic Ag stimulation.

Measurements of the talus in the assessment of population affinity

As part of their routine work, forensic anthropologists are expected to report population affinity as part of the biological profile of an individual. The skull is the most widely used bone for the estimation of population affinity but it is not always present in a forensic case. Thus, other bones that preserve well have been shown to give a good indication of either the sex or population affinity of an individual. In this study, the potential of measurements of the talus was investigated for the purpose of estimating population affinity in South Africans. Nine measurements from two hundred and twenty tali of South African Africans (SAA) and South African Whites (SAW) from the Raymond A. Dart Collection of Human Skeletons were used. Direct and step-wise discriminant function and logistic regression analyses were carried out using SPSS and SAS. Talar length was the best single variable for discriminating between these two groups for males while in females the head height was the best single predictor. Average accuracies for correct population affinity classification using logistic regression analysis were higher than those obtained from discriminant function analysis. This study was the first of its type to employ discriminant function analyses and logistic regression analyses to estimate the population affinity of an individual from the talus. Thus these equations can now be used by South African anthropologists when estimating the population affinity of dismembered or damaged or incomplete skeletal remains of SAA and SAW.

Composition of the Kirsten Skeletal Collection at Stellenbosch University

The Kirsten Skeletal Collection is curated in the Division of Anatomy and Histology, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa. It comprises the largest documented cadaver-derived South African coloured skeletal collection in the world. Our aim in this paper is to present an inventory and characterise the identified skeletons in the Kirsten Skeletal Collection as well as provide a descriptive indication of what researchers can expect to encounter at the anthropology unit at Stellenbosch University. The skeletal material was derived mainly from the cadaver donation programme of the Division of Anatomy and Histology over a 58-year period (1957–2015). All pertinent information for each individual skeleton is entered into a database and a full skeletal inventory is established. The skeletal database registry was analysed to demonstrate the distribution of age, sex and population affinity of individuals in the collection. Currently, this collection consists of 1161 skeletons with known records. Despite differences in the age and sex composition, the skeletal profile in general reflects mainly the profile of the Western Cape population. Most individuals were born between 1920 and 1950, placing the Kirsten Skeletal Collection in the early to mid-20th century. The age at death for the greatest proportion (41.8%) of individuals was between 40 and 60 years. Current biological profile techniques in age, ancestry and sex estimation can be improved and, among others, new regional and ancestral specific standards for the biologically unique and diverse South African coloured population can be developed.
 Significance:
 
 We present the largest documented skeletal collection of the South African coloured population in the world.
 This work contributes to the skeletal reference database for use by physical anthropologists and others.

Результаты изучения молочных зубов с верхнепалеолитической стоянки Юдиново (Среднее Подесенье)

Population affinities of the Timonovka-Yudinovo Upper Paleolithic people are reconstructed on the basis of three isolated deciduous teeth––a lower lateral incisor, lower and upper second molars, likely representing three individuals––from Yudinovo in the middle Desna basin (15–12 ka BP), found in 1987–1996. Based on measurements and descriptive traits and computed microtomography, the teeth were compared with those from other Upper Paleolithic sites in northern Eurasia. The principal component analyses of metric and nonmetric traits revealed similar patterns. To minimize random variation, results of both analyses were integrated. Results indicate affi nity with Pavlov people in Central Europe. The diagnostic trait combination includes weak expression of the Carabelli cusp on the upper second molar, accessory sixth cusp on the lower second molar, large bucco-lingual diameter of both molars, and moderate mesio-distal diameter of the lower second molar. These results support the view that the Timonovka-Yudinovo tradition is related to eastern Gravette.

Finding what is missing: Three-dimensional coordinates estimation for ancestry assessment through geometric morphometrics

Accurate and effective data collection from human remains in a forensic examination is often hindered by unpredictable factors such as taphonomy, pathology and recovery. The main purpose of this preliminary work is to illustrate the value of statistical reconstruction of missing cranial landmark three-dimensional coordinates in the context of ancestry estimation through 3D-ID software. Twenty-eight to thirty-one Cartesian coordinates were collected from 60 individuals from the 21st c. Identified Skeletal Collection housed at the University of Coimbra (Portugal) using the arm digitizer MicroScribe® G2X and missing Cartesian coordinates were calculated using R functions. When assessing ancestry using 3D-ID, the obtained results before and after missing points estimation showed differences in 25 individuals (41.7 %) from the total sample. Albeit more studies will be required, this method is becoming valuable for forensic anthropologists evaluating population affinities of skeletonized individuals.

Direct observation of conformational population shifts in crystalline human hemoglobin

Although X-ray crystallography is the most commonly used technique for studying the molecular structure of proteins, it is not generally able to monitor the dynamic changes or global domain motions that often underlie allostery. These motions often prevent crystal growth or reduce crystal order. We have recently discovered a crystal form of human hemoglobin that contains three protein molecules allowed to express a full range of quaternary structures, whereas maintaining strong X-ray diffraction. Here we use this crystal form to investigate the effects of two allosteric effectors, phosphate and bezafibrate, by tracking the structures and functions of the three hemoglobin molecules following the addition of each effector. The X-ray analysis shows that the addition of either phosphate or bezafibrate not only induces conformational changes in a direction from a relaxed-state to a tense-state, but also within relaxed-state populations. The microspectrophotometric O2 equilibrium measurements on the crystals demonstrate that the binding of each effector energetically stabilizes the lowest affinity conformer more strongly than the intermediate affinity one, thereby reducing the O2 affinity of tense-state populations, and that the addition of bezafibrate causes an ∼5-fold decrease in the O2 affinity of relaxed-state populations. These results show that the allosteric pathway of hemoglobin involves shifts of populations rather than a unidirectional conversion of one quaternary structure to another, and that minor conformers of hemoglobin may have a disproportionate effect on the overall O2 affinity.

Reconstructing human population history from dental phenotypes

Dental phenotypic data are often used to reconstruct biological relatedness among past human groups. Teeth are an important data source because they are generally well preserved in the archaeological and fossil record, even when associated skeletal and DNA preservation is poor. Furthermore, tooth form is considered to be highly heritable and selectively neutral; thus, teeth are assumed to be an excellent proxy for neutral genetic data when none are available. However, to our knowledge, no study to date has systematically tested the assumption of genetic neutrality of dental morphological features on a global scale. Therefore, for the first time, this study quantifies the correlation of biological affinities between worldwide modern human populations, derived independently from dental phenotypes and neutral genetic markers. We show that population relationship measures based on dental morphology are significantly correlated with those based on neutral genetic data (on average r = 0.574, p < 0.001). This relatively strong correlation validates tooth form as a proxy for neutral genomic markers. Nonetheless, we suggest caution in reconstructions of population affinities based on dental data alone because only part of the dental morphological variation among populations can be explained in terms of neutral genetic differences.

Sex estimation using dimensions around the nutrient foramen of the long bones of the arm and forearm in South Africans

South Africa has had an increase in rates of crime, interpersonal violence and homicide since the introduction of democracy in 1994. Forensic osteological standards was lacking for South Africans of different population groups necessitating the generation of new standards for forensic identification of individuals from skeletal remains. For these reasons, there is a concerted demand for methods of identifying skeletal remains with sex being amongst the most important of the biological characteristics required. The nutrient foramen has been used to estimate sex in lower limb long bones with much accuracy but this has not been demonstrated in the upper limb long bones. The aim of this study was to develop osteometric standards for sex estimation from measurements around the nutrient foramen of the arm and forearm bones of South Africans of different population affinities. A total of 660 bones consisting of humeri, radii and ulnae of black South Africans and white South Africans were assessed for sex estimation using dimensions related to the nutrient foramen. Sex was correctly classified with a range of 84–85% for the humerus and 83–88% for the arm bones. The study showed that length measurements were more sexually dimorphic than width dimensions in South Africans, as length was consistently selected as the best predictor of sex in all bones. However, the average accuracy increased when length was used in combination with measurements related to the nutrient foramen. In conclusion, the dimensions of upper limb long bones that are directly related to the nutrient foramen are sexually dimorphic and are useful in the estimation of sex in South Africans, with the highest accuracy shown in the white South African population group.

Stability of upper face sexual dimorphism in central European populations (Czech Republic) during the modern age.

One of the most fundamental issues in forensic anthropology is the determination of sex and population affinity based on various skeletal elements. Therefore, we compared the sexual dimorphism of the upper facial skeleton from a recent Czech population (twenty-first century) with that of a population from Early Modern Age Bohemia (sixteenth to eighteenth centuries). Methods of geometric morphometrics were applied. According to the results, sexual dimorphism in terms of size, shape, and form was statistically significant in both populations. The best results of sex estimation originated from analyses of form. Thus, both size and shape differences should be taken into account for determination of the sex. The accuracy of prediction achieved 91.1% for individuals in the recent population and 87.5% for individuals from the early modern population. Only minor differences were found between sexual dimorphism in the studied populations. We conclude that sexual dimorphism of the upper facial skeleton is stable during the relatively short time period.

Frequency-Dependent Mate Selection in the Guppy (Poeciliidae: Poecilia reticulata)

Heterogeneity within a population enhances its long-term survival. A fundamental method of maintaining population heterogeneity is the retention of rare or uncommon phenotypes by selective mating strategies. Employing two color morphs, red tuxedo and red, of the guppy (Poecilia reticulata, Poeciliidae), this study was designed to investigate whether P. reticulata females would preferentially seek out heterogeneous groupings of males exhibiting two color morphs. Adult female guppies were exposed simultaneously to two groups of males (n=10); one comprised of only the tuxedo color morph (n=5) and the other of both color morphs (n=5). For the latter group, the ratio of males exhibiting the two colorations was changed incrementally over multiple trials, beginning and ending with homogeneous groupings (5:0, 4:1, 3:2, 2:3, 1:4, 0:5). Experiments were conducted employing a 76 L aquarium partitioned at both ends to house the male groups. Individual females were placed into an acclimation, holding column located in the center compartment of the experimental aquarium. Subsequent to a five minute acclimation period in the holding column, each female was released. Courting behaviors and population affinities (i.e. female location relative to the male compartments) were recorded every five seconds over a five minute observation period. Females did not show a preference for male groupings exhibiting either the 4:1 or 1:4 color ratios. However, females clearly showed affinity for the male groupings of 3:2 and 2:3 (p &lt;0.05). This investigation on female mate choice in P. reticulata clearly reveals that a mating strategy is occurring in this species and that it is frequency-dependent.

Speciation in Indo-Pacific swiftlets (Aves: Apodidae): integrating molecular and phenotypic data for a new provisional taxonomy of the Collocalia esculenta complex.

White-bellied swiftlets of the Collocalia esculenta complex constitute a radiation of colony-breeding swifts distributed throughout the tropical Indo-Pacific region. Resolution of their taxonomy is challenging due to their morphological uniformity. To analyze the evolutionary history of this complex, we combine new biometric measurements and results from plumage assessment of museum specimens with novel as well as previously published molecular data. Together, this body of information constitutes the largest systematic dataset for white-bellied swiftlets yet compiled, drawn from 809 individuals belonging to 32 taxa for which new molecular, biometric, and/or plumage data are presented. We propose changing the classification of white-bellied swiftlets, for which two species are currently recognized, to elevate eight regional forms to species level, and we also describe two new subspecies. The ten taxa we recommend recognizing at the species level are: Collocalia linchi (Java to Lombok, Sumatran hills), C. dodgei (montane Borneo), C. natalis (Christmas Island), C. affinis (Greater Sundas, including the Thai-Malay Peninsula and Andaman-Nicobar Islands), C. marginata (Philippines), C. isonota (Philippines), C. sumbawae (west Lesser Sundas), C. neglecta (east Lesser Sundas), C. esculenta (Sulawesi, Moluccas, New Guinea, Bismarck Archipelago, Solomon Islands), and C. uropygialis (Vanuatu, New Caledonia). Future molecular and morphological work is needed to resolve questions of speciation and population affinities in the Philippines, Christmas Island, Wallacea and central Melanesia, and to shed light on historic diversification and patterns of gene flow in the complex.

Determining the population affinity of an unprovenienced human skull for repatriation

An archaeological assessment was carried out on an unprovenienced human skull recovered in eastern Idaho, exhibiting cranial deformation and peri-mortem application of a red pigment. A combination of scanning electron microscopy (SEM), X-ray fluorescence (XRF), and energy-dispersive X-ray spectroscopy (EDS) identified the major and trace elements present in the red pigment as natural cinnabar. Carbon and oxygen stable isotopes from teeth and bone suggest a mostly C3 plant-based diet with subsidiary consumption of salmon or marine resources, and a regional geographic transition between early life and late adulthood. Radiocarbon dating determined the approximate age of the skull to be between 600 and 700years old, and ancient mitochondrial DNA assessment identified characteristics of haplogroup B, one of four major Native American mitochondrial DNA lineages, which is consistent with the osteological analyses.

Genetic structure of Tibetan populations in Gansu revealed by forensic STR loci

The origin and diversification of Sino-Tibetan speaking populations have been long-standing hot debates. However, the limited genetic information of Tibetan populations keeps this topic far from clear. In the present study, we genotyped 15 forensic autosomal short tandem repeats (STRs) from 803 unrelated Tibetan individuals from Gansu Province (635 from Gannan and 168 from Tianzhu) in northwest China. We combined these data with published dataset to infer a detailed population affinities and genetic substructure of Sino-Tibetan populations. Our results revealed Tibetan populations in Gannan and Tianzhu are genetically very similar with Tibetans from other regions. The Tibetans in Tianzhu have received more genetic influence from surrounding lowland populations. The genetic structure of Sino-Tibetan populations was strongly correlated with linguistic affiliations. Although the among-population variances are relatively small, the genetic components for Tibetan, Lolo-Burmese, and Han Chinese were quite distinctive, especially for the Deng, Nu, and Derung of Lolo-Burmese. Han Chinese but not Tibetans are suggested to share substantial genetic component with southern natives, such as Tai-Kadai and Hmong-Mien speaking populations, and with other lowland East Asian populations, which implies there might be extensive gene flow between those lowland groups and Han Chinese after Han Chinese were separated from Tibetans. The dataset generated in present study is also valuable for forensic identification and paternity tests in China.