Human Population Genetics Research Articles

Mitochondrial DNA analysis of Tunisians reveals a mosaic genetic structure with recent population expansion

Tunisia is a country of great interest for human population genetics due to its strategic geographic position and rich human settlement history. These factors significantly contributed to the genetic makeup of present-day Tunisians harbouring components of diverse geographic origins. Here, we investigated the genetic structure of Tunisians by performing a mitochondrial DNA (mtDNA) comparison of 15 Tunisian population groups, in order to explore their complex genetic landscape. All Tunisian data were also analysed against 40 worldwide populations. Statistical results (Tajima's D and Fu's FS tests) suggested recent population expansion for the majority of studied populations, as well as showed (AMOVA test) that all populations were significantly different from each other, which is evidence of population structure even if it is not guided by geographic and ethnic effects. Gene flow analysis revealed the assignment of Tunisians to multiple ancestries, which agrees with their genetic heterogeneity. The resulting picture for the mtDNA pool confirms the evidence of a recent expansion of the Tunisian population and is in accordance with a mosaic structure, composed by North African, Middle Easterner, European and Sub-Saharan lineages, resulting from a complex settlement history.

A cost-efficient method for sequencing the human whole mitochondrial genome utilizing multiplex PCR-based next generation sequencing

The mitochondrial genome of human is organized as a circular loop of double-stranded DNA with 16569 bp in length. Mitochondrial DNA (mtDNA) is extensively used as a biomarker in human evolution and population genetics due to the characteristics of maternal inheritance, multiple copies in cells, high mutational rates, high heteroplasmy levels and so on. Next-generation sequencing (NGS) has become a rapid and efficient approach to sequence mtDNA recently, while library-building is complex and expensive. Multiplex PCR has the advantage of high sensitivity and saving time and effort. Therefore, this technique was used to amplify whole complete mitochondrial genomes in Chinese in the present study. The whole mitochondrial genome was covered by 73 overlapped short amplicons, which was subsequently sequenced on an Illumina HiSeq X Ten instrument. The mean per-mtDNA-base read depth was higher than 20000×. 100% mitochondrial genome coverage was obtained across all the samples with a depth of coverage threshold of 100×. The data of high throughout sequencing was qualified for mutation analysis. The present sequencing method based on multiplex PCR leaves out the process of library-building. This sequencing methodology that we have developed is efficiency, economic and has a broad application prospect in the research of complex genetic disorders.

Genetic variation of MHC Class I polymorphic Alu insertions (POALINs) in three sub-populations of the East Midlands, UK

Background: Alu elements are highly researched due to their useful nature as markers in the study of human population genetics. Recently discovered Major Histocompatibility Complex (MHC) polymorphic Alu insertions (POALINs) have not been examined extensively for genetic variation and their HLA associations.Aims: The aim of this study is to assess the genetic variation between three populations using five recently discovered POALINs.Methods and subjects: The study examined 190 healthy, unrelated subjects from three different populations in the East Midlands (UK) for the presence or absence of five Alu elements (AluHG, AluMICB, AluHJ, AluTF and AluHF) via the polymerase chain reaction followed by gel electrophoresis. Data were analysed for genetic variation and phylogenetic analyses.Results: All Alus were polymorphic in study populations. Appreciable allele frequency variation was observed at a number of loci. The British population was significantly different from both the Punjabi Jat Sikh and Gujarati Patel populations, although showing a closer genetic relationship to the Punjabi Jat Sikh population than the Gujarati Patel population (Nei’s DA = 0.0031 and 0.0064, respectively).Conclusions: MHC POALINs are useful markers in the investigation of genetic variation and the assessment of population relationships, and may have some bearing on disease associations due to their linkage disequilibrium with HLA loci; this warrants further studies.

Redemptive Ancestries: Human Population Genetics, Sex and Antiracism

Redemptive Ancestries: Human Population Genetics, Sex and Antiracism

Basics in Human Evolution. Edited by Michael P. Muehlenbein. Academic Press. Amsterdam (The Netherlands) and Boston (Massachusetts): Elsevier. $120.00. xviii + 557 p. + 32 pl.; ill.; index. ISBN: 978-0-12-802652-6. 2015.

Previous articleNext article FreeEvolutionBasics in Human Evolution. Edited by Michael P. Muehlenbein. Academic Press. Amsterdam (The Netherlands) and Boston (Massachusetts): Elsevier. $120.00. xviii + 557 p. + 32 pl.; ill.; index. ISBN: 978-0-12-802652-6. 2015.Aryeh GrossmanAryeh GrossmanAnatomy, Midwestern University, Glendale, Arizona Search for more articles by this author Anatomy, Midwestern University, Glendale, ArizonaPDFPDF PLUSFull Text Add to favoritesDownload CitationTrack CitationsPermissionsReprints Share onFacebookTwitterLinked InRedditEmailQR Code SectionsMoreThis is a laudably ambitious project. Although the title of the book indicates a focus on providing basic information about human evolution, in actuality it attempts to provide general reference to an audience interested in human evolution, modern human biology and genetics, human health and development, social organization, and human behavior—all viewed through a distinctly anthropological lens.The editor succeeded in herding 48 authors to produce 39 chapters organized into seven main parts. The first part includes only two chapters. The first chapter, introducing readers to the basic concepts of evolutionary theory and the facts of evolution, just might be the best chapter in the volume. Part II provides the primate background to human evolution, behavior, and anatomy. The introduction to the basics of primate behavior is particularly succinct and enjoyable. Part III covers the fossil record and phylogenetic hypotheses of early hominin through early to modern human evolution, and also addresses early hominin ecology, the origins of bipedal locomotion, and the evolution of tool use. Unfortunately, the chapters on hominin and human morphology and phylogeny follow a gradistic approach. For example, several authors lump Kenyathropus platyops and Australopithecus bahrelghazali with Australopithecus afarensis and prefer not to separate Paranthropus spp. from Australopithecus spp. This approach, which eliminates much of nuance of hominin evolution, is a poor choice for a book looking to provide a solid foundation into the current state of the field of human evolution. By contrast, the chapter on the origins of bipedalism provides a good review of different views about this crucial question in human evolution.From here on the volume enters its bioanthropological sections, which generally includes topics of more interest to the wider public. Part IV introduces readers to human population genetics, physiology, evolution of brain size and skin color, growth and aging, and reproductive ecology. The next part includes three chapters about modern subsistence modes. Part VI presents anthropological analyses of the relationships between changes in human environments and the rise of chronic diseases, infectious diseases, and pathogen evolution, human diet, and an introduction to paleopathology (how disease of the past are studied). This part addresses current health topics such as obesity, cardiovascular disease, and the rise of infectious disease. The final part explores the connection of biology and different human behaviors, including stress, love, war and paternal care, mating systems, cognition and language, moral systems and reciprocal behaviors, race and ethnicity, and the evolution of culture. The book ends with a good glossary and some excellent color images and figures.Although the volume is uneven, its strength is its many parts and broad spectrum of ideas. The book is a collection of idiosyncratic treatises gathered into loosely congruent sections that will allow any reader to pick and choose where and what to focus on. Thus, various chapters can form an excellent introduction to different graduate courses in bioanthropology and the volume would fit on the shelf of any anthropology or general university library. Previous articleNext article DetailsFiguresReferencesCited by The Quarterly Review of Biology Volume 92, Number 1March 2017 Published in association with Stony Brook University Article DOIhttps://doi.org/10.1086/690866 For permission to reuse, please contact [email protected]PDF download Crossref reports no articles citing this article.

Molecular diversity of 23 Y-chromosome short tandem repeat loci in the population of Tuzla Canton, Bosnia and Herzegovina

Background: Tuzla Canton is the most populated region in the ethnically mixed territory of Bosnia and Herzegovina, whose genetic analysis could provide an insight into past demographic events.Aim: Analysis of 23 Y-chromosome STR markers in the population of Tuzla Canton and investigation of the genetic relationship of the male population of the Tuzla Canton and that of the larger Bosnian and Herzegovinian population as well as neighbouring and other European populations.Subjects and methods: The study was conducted among 100 unrelated healthy adult males from Tuzla Canton that have been genotyped using 23 Y-STR loci included in the PowerPlex Y23 kit. Statistical parameters such as haplotype diversity and allele frequencies were calculated, as well as the Rst-based genetic distances between the new dataset and those from Bosnia and Herzegovina and elsewhere, which were then visualised through multi-dimensional scaling plot and neighbour-joining phylogenetic tree analyses.Results: The PowerPlex Y23 kit has shown high discrimination capacity, as all 100 individuals have unique haplotypes. The newly incorporated loci seem to be highly informative. Population comparison reveals no statistically significant differences between the study population and the general Bosnian-Herzegovinian population, and between the study population and neighbouring populations.Conclusion: These results could be used as an additional investigation of the genetic relationship between the regional populations in Bosnia and Herzegovina and neighbouring human populations, as well as for further human population and forensic genetics studies.

Medical Genetics and the First Studies of the Genetics of Populations in Mexico.

Following World War II (WWII), there was a new emphasis within genetics on studying the genetic composition of populations. This probably had a dual source in the growing strength of evolutionary biology and the new international interest in understanding the effects of radiation on human populations, following the atomic bombings in Japan. These global concerns were shared by Mexican physicians. Indeed, Mexico was one of the leading centers of this trend in human genetics. Three leading players in this story were Mario Salazar Mallén, Adolfo Karl, and Rubén Lisker. Their trajectories and the international networks in human genetics that were established after WWII, paved the way for the establishment of medical and population genetics in Mexico. Salazar Mallén's studies on the distribution and characterization of ABO blood groups in indigenous populations were the starting point while Karl's studies on the distribution of abnormal hemoglobin in Mexican indigenous populations showed the relationships observed in other laboratories at the time. It was Lisker's studies, however, that were instrumental in the development of population genetics in the context of national public policies for extending health care services to the Mexican population. In particular, he conducted studies on Mexican indigenous groups contributing to the knowledge of the biological diversity of human populations according to international trends that focused on the variability of human populations in terms of genetic frequencies. From the start, however, Lisker was as committed to the reconstruction of shared languages and practices as he was to building networks of collaboration in order to guarantee the necessary groundwork for establishing the study of the genetics of human populations in Mexico. This study also allows us to place Mexican science within a global context in which connected narratives describe the interplay between global trends and national contexts.

Genetic structure of human populations based on 5 gene loci: A preliminary report from Northern India

The genetics of human populations reveals the evolutionary causes of population structure, population history, human diversity, racial divergence, adaptation, cultural and social behaviors and understanding human adaptation to local environmental constraints. The study aimed to determine the genetic relationship among six human population of Jammu and Kashmir, Northern India. This preliminary effort involved five gene loci of genetic traits, viz. ABO and Rh blood type, phenylthiocarbamide, color blindness and sickle cell trait. A total of 3679 healthy subjects were selected from six Muslim populations viz., Gujjar and Bakarwal (n=762), Mughal (n=560), Khan (n=642), Malik (n=564), Mir (579) and Syed (n=572). The allele frequencies and heterozygosity levels show significant differences among six populations (p<0.05). The phylogentic tree revealed that Mughal and Gujjar and Bakarwal (tribal population) are close to each other and differ from other four populations (Malik, Mir, Khan and Syed). Further studies in context genomic diversity, history and origin of these populations will be undertaken in future to get more conclusive proof.

Statistical techniques in human population genetics

Statistical techniques in human population genetics

Whole-exome sequencing in an isolated population from the Dalmatian island of Vis.

We have whole-exome sequenced 176 individuals from the isolated population of the island of Vis in Croatia in order to describe exonic variation architecture. We found 290 577 single nucleotide variants (SNVs), 65% of which are singletons, low frequency or rare variants. A total of 25 430 (9%) SNVs are novel, previously not catalogued in NHLBI GO Exome Sequencing Project, UK10K-Generation Scotland, 1000Genomes Project, ExAC or NCBI Reference Assembly dbSNP. The majority of these variants (76%) are singletons. Comparable to data obtained from UK10K-Generation Scotland that were sequenced and analysed using the same protocols, we detected an enrichment of potentially damaging variants (non-synonymous and loss-of-function) in the low frequency and common variant categories. On average 115 (range 93–140) genotypes with loss-of-function variants, 23 (15–34) of which were homozygous, were identified per person. The landscape of loss-of-function variants across an exome revealed that variants mainly accumulated in genes on the xenobiotic-related pathways, of which majority coded for enzymes. The frequency of loss-of-function variants was additionally increased in Vis runs of homozygosity regions where variants mainly affected signalling pathways. This work confirms the isolate status of Vis population by means of whole-exome sequence and reveals the pattern of loss-of-function mutations, which resembles the trails of adaptive evolution that were found in other species. By cataloguing the exomic variants and describing the allelic structure of the Vis population, this study will serve as a valuable resource for future genetic studies of human diseases, population genetics and evolution in this population.

Genotypic diversity of the Killer Cell Immunoglobulin-like Receptors (KIR) and their HLA class I Ligands in a Saudi population.

Killer Cell Immunoglobulin-like Receptors (KIR) have been used as good markers for the study of genetic predisposition in many diseases and in human genetic population dynamics. In this context, we have investigated the genetic diversity of KIR genes and their main HLA class I ligands in Saudi population and compared the data with other studies of neighboring populations. One hundred and fourteen randomly selected healthy Saudi subjects were genotyped for the presence or absence of 16 KIR genes and their HLA-C1, -C2, -Bw4Thr80 and Bw4Ile80 groups, using a PCR-SSP technique. The results show the occurrence of the framework genes (3DL2, 3DL3 and 2DL4) and the pseudogenes (2DP1 and 3DP1) at highest frequencies. All inhibitory KIR (iKIR) genes appeared at higher frequencies than activating genes (aKIR), except for 2DS4 with a frequency of 90.35%. A total of 55 different genotypes were observed appearing at different frequencies, where 12 are considered novel. Two haplotypes were characterized, AA and Bx (BB and AB), which were observed in 24.5% and 75.5% respectively of the studied group. The frequencies of iKIR + HLA associations were found to be much higher than aKIR + HLA. KIR genes frequencies in the Saudi population are comparable with other Middle Eastern and North African populations.

Population inference from contemporary American craniometrics.

This analysis delivers a composite picture of population structure, admixture, ancestry variation, and personal identity in the United States, as observed through the lens of forensic anthropological casework and modern skeletal collections. It tests the applicability of the probabilistic clustering methods commonly used in human population genetics for the analysis of continuous, cranial measurement data, to improve population inference for admixed individuals without prior knowledge of sample origins. The unsupervised model-based clustering methods of finite mixture analysis are used here to reveal latent population structure and generate admixture proportions for craniofacial measurements from the Forensic Anthropology Data Bank (FDB). Craniometric estimates of ancestry are also generated under a three contributor model, sourcing parental reference populations from the Howells Craniometric Dataset. Tests of association are made among the coefficients of cluster memberships and the demographic information documented for each individual in the FDB. Clustering results are contextualized within the framework of conventional approaches to population structure analysis and individual ancestry estimation to discuss method compatibility. The findings reported here for contemporary American craniometrics are in agreement with the expected patterns of intergroup relationships, geographic origins and results from published genetic analyses. Population inference methods that allow for the model-bound estimation of admixture and ancestry proportions from craniometric data not only enable parallel-skeletal and genetic-analyses but they are also shown to be more informative than those methods that perform hard classifications using externally-imposed categories or seek to explain gross variation by low-dimensional projections. Am J Phys Anthropol 160:604-624, 2016. © 2016 Wiley Periodicals, Inc.

Biomes and human distribution during the last ice age

AbstractAimOur research attempts to provide an explicit explanation of human–biome interactions during the last glacial period and how these have influenced current human population genetics at the global scale. Publications to date have not addressed this topic.LocationWorld‐wide.MethodsUsing climate, terrain, hydrographic, fossil pollen and plant‐macrofossil data we developed a model of the distribution of biomes during climate deteriorations of the last glacial period. Subsequently, we analysed current human genetic diversity, the origins of genetic lineages and Palaeolithic human sites in relation to the inferred biomes.ResultsOur analyses indicated that: (1) current human Y‐DNA diversity, the places of origin of human Y‐DNA lineages and the distribution of Palaeolithic human settlements are best explained by distance from savanna and dry woodland during a series of glacial maxima, and (2) during periods of relatively benign climate conditions, humans dispersed through areas of high primary productivity while avoiding dense forest cover.Main conclusionsIn a metapopulation of Palaeolithic humans, the biome of savanna and dry woodland supported source populations and other biomes acted as sinks. Present‐day genetic, phenotypical and linguistic differences are largely related to discontinuity of and impeded migration between human source populations during glacial periods, rather than simply geographical distance, and in the post‐glacial period there has not been enough time for displacements and admixture of human populations to completely blur these differences.

X-Chromosome Alu Insertions in Bahía Blanca, Argentina: Assessment of Population Information from Varied Genetic Markers and Usefulness of X-Chromosome Markers to Trace Sex-Biased Parental Contributions.

Bahía Blanca is an urban city in a historically and geographically strategic location for the mixture of different populations in Argentina. In the present study, 10 Alu elements from the X chromosome are analyzed to characterize the genetic composition of the city's population, to compare it with other worldwide populations, and to explore the usefulness of X-chromosome markers for human population genetics purposes. In the Bahía Blanca sample, 7 of 10 Alu insertion frequencies are polymorphic. X-chromosome Alu results in Bahía Blanca are compared with eight different populations from Africa, Europe, and America. Genetic distance analysis indicates that the Bahía Blanca sample is closer to the European and North African samples (average distances of 0.106 and 0.113) than to the Native American (0.163) and sub-Saharan African samples (0.247). Genetic relationships shown by multidimensional scaling illustrate the intermediate position of Bahía Blanca compared with groups in other regions (European, Native American, and African). Admixture results of the Bahía Blanca sample for X-chromosome markers indicate similar proportions of Native American (0.472) and European parental contributions (0.479) and a minor sub-Saharan African contribution (0.049). These results are consistent with the past decade's genetic studies of Argentinean populations that reported higher Native American and sub-Saharan African contributions than previous data.

High level of inbreeding in final phase of 1000 Genomes Project.

The 1000 Genomes Project provides a unique source of whole genome sequencing data for studies of human population genetics and human diseases. The last release of this project includes more than 2,500 sequenced individuals from 26 populations. Although relationships among individuals have been investigated in some of the populations, inbreeding has never been studied. In this article, we estimated the genomic inbreeding coefficient of each individual and found an unexpected high level of inbreeding in 1000 Genomes data: nearly a quarter of the individuals were inbred and around 4% of them had inbreeding coefficients similar or greater than the ones expected for first-cousin offspring. Inbred individuals were found in each of the 26 populations, with some populations showing proportions of inbred individuals above 50%. We also detected 227 previously unreported pairs of close relatives (up to and including first-cousins). Thus, we propose subsets of unrelated and outbred individuals, for use by the scientific community. In addition, because admixed populations are present in the 1000 Genomes Project, we performed simulations to study the robustness of inbreeding coefficient estimates in the presence of admixture. We found that our multi-point approach (FSuite) was quite robust to admixture, unlike single-point methods (PLINK).

Population structure analysis on 2504 individuals across 26 ancestries using bioinformatics approaches

Background Characterizing genetic diversity is crucial for reconstructing human evolution and for understanding the genetic basis of complex diseases; however, human population genetics are very complicated. Previously, we proved that based on the Hardy-Weinberg equilibrium, the heterozygous vs. non-reference homozygous single nucleotide polymorphism (SNP) ratio (het/nonref-hom) is two [1]. Later, we found that this ratio is race dependent, with African being the most genetically diverse race and Asian being the most homozygous [2]. This observation prompted us to conduct further study to understand the reasoning behind this diversity.

Mitonuclear linkage disequilibrium in human populations.

There is extensive evidence from model systems that disrupting associations between co-adapted mitochondrial and nuclear genotypes can lead to deleterious and even lethal consequences. While it is tempting to extrapolate from these observations and make inferences about the human-health effects of altering mitonuclear associations, the importance of such associations may vary greatly among species, depending on population genetics, demographic history and other factors. Remarkably, despite the extensive study of human population genetics, the statistical associations between nuclear and mitochondrial alleles remain largely uninvestigated. We analysed published population genomic data to test for signatures of historical selection to maintain mitonuclear associations, particularly those involving nuclear genes that encode mitochondrial-localized proteins (N-mt genes). We found that significant mitonuclear linkage disequilibrium (LD) exists throughout the human genome, but these associations were generally weak, which is consistent with the paucity of population genetic structure in humans. Although mitonuclear LD varied among genomic regions (with especially high levels on the X chromosome), N-mt genes were statistically indistinguishable from background levels, suggesting that selection on mitonuclear epistasis has not preferentially maintained associations involving this set of loci at a species-wide level. We discuss these findings in the context of the ongoing debate over mitochondrial replacement therapy.

Mutation rate estimation for 15 autosomal STR loci in a large population from Mainland China

STR, short tandem repeats, are well known as a type of powerful genetic marker and widely used in studying human population genetics. Compared with the conventional genetic markers, the mutation rate of STR is higher. Additionally, the mutations of STR loci do not lead to genetic inconsistencies between the genotypes of parents and children; therefore, the analysis of STR mutation is more suited to assess the population mutation. In this study, we focused on 15 autosomal STR loci. DNA samples from a total of 42,416 unrelated healthy individuals (19,037 trios) from the population of Mainland China collected between Jan 2012 and May 2014 were successfully investigated. In our study, the allele frequencies, paternal mutation rates, maternal mutation rates and average mutation rates were detected. Furthermore, we also investigated the relationship between paternal ages, maternal ages, area, the time of pregnancy and average mutation rate. We found that the paternal mutation rate was higher than the maternal mutation rate and the paternal, maternal, and average mutation rates had a positive correlation with paternal age, maternal age and the time of pregnancy respectively. Additionally, the average mutation rate of coastal areas was higher than that of inland areas.

Polymorphism of M, N Allele in MN Blood Group of Chinese Population

To detect the base sequences of all exons and part of introns in the GYPA gene of the glycophorin GPA and to investigate the polymorphism of M, N alleles in Chinese population. A total of 225 blood sample were randomly colleeted from unrelated Chinese volunteers and were detected by serology techniques. The primers were designed by self, the seguencing of GYPA gene related with sample exon 1-7 full length sequences of bases and intron-1-7 partial sequence was performed, the polymorphism of M, N gene mutation in mucleotide sequence was analysed. The results of M and N genotyping were in agreement with the results of serological detection. The 23rd base of intron-2, the 55th base of intron-3, the 63rd base of intron-4, the 55th, 189th and 190th base of intron-6, the 712th base variation of exon-7 in the gene M and N were used to subdivide the gene M and N into the mutant M103, M201, M202, N101, N102, N103, N104, and N201. At the same time, it was found that 42th and 54th base were mutated, the base T was inserted between 59th and 60th base in the intron-2, the new mutations occurred in the alleles 28, 29, 65 and 102 in intron-3 in this study. The polymorphism of the the Chinese population's GYPA gene occurs in all the exons and partly in the introns. The gene polymorphism of M and N blood group in Chinese population might provide the theoretical basis for the studies of clinical blood transfusion, human population genetics and molecular biology.

Population-genetic trees, maps, and narratives of the great human diasporas

From the 1960s, mathematical and computational tools have been developed to arrive at human population trees from various kinds of serological and molecular data. Focusing on the work of the Italian-born population geneticist Luigi Luca Cavalli-Sforza, I follow the practices of tree-building and mapping from the early blood-group studies to the current genetic admixture research. I argue that the visual language of the tree is paralleled in the narrative of the human diasporas, and I show how the tree was actually mapped onto the surface of the earth. This visual and textual structure is mirrored in the liberal discourse of unity in diversity that has been criticized as running counter to the socio-political effects of human population genetics. From this perspective, one may ask how far the phylogenetic diagram in its various forms is a manifestation of the physics of power that according to Michel Foucault consists in mechanisms that analyse distributions, movements, series, combinations, and that uses instruments to render visible, to register, to differentiate and to compare. It is one among other disciplinary technologies that ensure the ordering of human diversity. In the case of intra-human phylogenetic trees, population samples and labels are one issue. Another is that the separated branches seem to show groups of people, who have in reality been interacting and converging, as isolated. Often based on so-called isolated peoples, molecular tree diagrams freeze a hierarchical kinship system that is meant to represent a state before the great historical population movements.