Life Sciences Commons^™

Mitochondrial Dna Diversity And Evolutionary History Of Native Human Populations Of Northwest Patagonia (Argentina), María Bárbara Postillone, Virginia Agustina Cobos, Celmira Urrutia, Cristina Beatriz Dejean, Paula N. Gonzalez, Sergio Ivan Perez, Valeria Bernal

Human Biology Open Access Pre-Prints

The genetic composition of Amerindian descendants from Patagonia has long been a focus of interest, although the information available is still scarce for many geographic areas. Here, we report the first analysis of the variation in the mtDNA control region for an area of northwestern Patagonia, the North of Neuquén, with the aim of studying the processes and historical events that modeled the evolutionary history of these human groups. We analyzed 113 individuals from two localities of northern Neuquén, along with 6 from southern Neuquén and 223 mtDNA sequences previously published from neighboring areas from Argentina and Chile. We estimated …

How The Atacama Skeleton Might Advance Discussion Of Responsible Conduct Of Research Responsibilities, Thomas May, Mariko Nakano-Okuno

Human Biology Open Access Pre-Prints

Controversies resulting from genetic testing on skeletal remains of disputed stewardship raise important questions about obligations inherent on genetic researchers to assure ethical chain of custody. In this paper, we analyze and evaluate several proposed positions on whether such research should be published. Following jurisprudential standards for legitimate regulatory systems, we argue that responsible conduct of research requires reasonable attention to chain of custody, but cannot require guarantees, particularly in cases of ancient remains.

Genetic Overview Of The Maya Populations: Mitochondrial Dna Haplogroups, Angélica González-Oliver, Dircé Pineda-Vázquez, Ernesto Garfias-Morales, Isabel De La Cruz-Laina, Luis Medrano-González, Lourdes Márquez-Morfín, Allan Ortega-Muñoz

Human Biology Open Access Pre-Prints

We identified the mitochondrial DNA haplogroups A, B, C and D in 75 present-day Maya individuals, 24 Maya individuals of the colonial period and one pre-Columbian Maya individual from Quintana Roo, Mexico. We examined these data together with those of 21 Maya populations accounting for 647 present-day Maya individuals and 104 ancient Maya individuals. A demographic study based on the analysis of fertility and endogamy was carried out in two modern Maya populations to identify cultural factors that influence the mitochondrial haplogroup genetic diversity. Most present-day and ancient Maya populations show a distribution pattern of mitochondrial haplogroup frequencies A, C, …

Ontogenesis Of The Sella Turcica Among Egyptians: Forensic And Radiological Study, Wafaa Mohamed El-Sehly, Fatma Mohamed Magdy Badr El Dine, Mohamed Samir Shaban

Human Biology Open Access Pre-Prints

Introduction: The sella turcica has gained importance as a stable bony landmark in cephalometric studies.
Aim of the work: The aim of the work was to explore the changes that accompany postnatal ontogeny of the sella turcica until full development, and to verify its contribution in age estimation and sexual assignment among Egyptians.
Subjects and methods: Six selected measurements of the sella turcica of 215 Egyptian patients were assessed using Multidetector Computed Tomography (MDCT). The patients represented different ages and were referred to the Radiodiagnosis and Intervention Department. The gathered data were then subjected to statistical analysis including correlation and …

Genetic Variants Of Duffy And Hemoglobin S Genes In An Afrodescendent Population From Columbia, Diana C. Ortega, Heiber Cardenas, Guillermo Barreto

Human Biology Open Access Pre-Prints

Malaria is an endemic disease in a large part of Colombia, and the city of Buenaventura reports one of the highest malaria infection rates. Some genetic variants confer resistance to malaria, such as the heterozygote for hemoglobin S (HbS) and the homozygous variant FYB^ES/FYB^ES of the Duffy gene. The aim of this work was the molecular characterization of these genes in an afrodescendent population from the urban area of Buenaventura. A total of 819 individuals from a stratified random sampling in each of the 12 communities of this city were analysed. Molecular analysis was performed using PCR-RFLP, …

Complexity, Genetic Causation, And Hereditarianism, Charles Roseman

Human Biology Open Access Pre-Prints

Hereditarians have claimed that recent advances in psychological and psychiatric genetics support their contention that individual and group socially important aspects of behavior and cognition are largely insensitive to environmental context. This has been countered by anti- hereditarians who (correctly) claim that the conclusion of genetic ineluctability is false. Anti- hereditarians, however, sometimes use problematic arguments based on complexity and the ignorance that comes with complexity and a demand for mechanistic, as opposed to variational, explanations for the ways in which genes affect phenotype. I argue here, as a committed anti-hereditarian, that the complexity gambit and the demand for mechanisms …

Who Needs Data? I’Ve Got Experience!, Dawnie Wolfe Steadman

Human Biology Open Access Pre-Prints

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New Approaches To Juvenile Age Estimation In Forensics: Application Of Transition Analysis Via The Shackelford Et Al. Method To A Diverse Modern Subadult Sample, Kelly R. Kamnikar, Nicholas P. Herrmann, Amber M. Plemons

Human Biology Open Access Pre-Prints

Dental development is one of the most widely utilized and accurate methods available for estimating age in subadult skeletal remains. The timing of tooth growth and development is regulated by genetics and less affected by external factors, allowing reliable estimates of chronological age. Traditional methodology focuses on comparing tooth developmental scores to corresponding age charts. Using the Moorrees, Fanning, and Hunt (MFH) developmental scores, Shackelford and colleagues embed the dental development method in a statistical framework based on transition analysis. They generated numerical parameters underlining each “stage” and age-at-death distribution and applied them to fossil hominins and Neanderthals with limited …

Thinking Computationally About Forensics: Anthropological Perspectives On Advancements In Technologies, Data, And Algorithms, Bridget F.B. Algee-Hewitt, Jieun Kim, Cris E. Hughes

Human Biology Open Access Pre-Prints

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Mitochondrial-Dna Phylogenetic Information And The Reconstruction Of Human Population History: The South American Case, María Bárbara Postillone, S. Ivan Perez

Human Biology Open Access Pre-Prints

Objectives: Mitochondrial DNA (mtDNA) sequences are becoming increasingly important in the study of human population history. Here, we explore the differences in the amount of information of different mtDNA regions and their utility for the reconstruction of South American population history.

Material and methods: We analyzed six datasets comprising 259 mtDNA sequences from South America: Complete mtDNA, Coding, Control, hypervariable region I (HVRI), cytochrome b (cytb) plus Control, and cytb plus 12S plus 16S. The amount of information in each dataset was estimated employing several site-by-site and haplotype based statistics, distances among sequences, Neighbor-joining trees, distances among the estimated trees, …

Origins Of An Unmarked Georgia Cemetery Using Ancient Dna Analysis, Andrew T. Ozga, Raúl Y. Tito, Brian M. Kemp, Hugh Matternes, Alexandra Obregon-Tito, Leslie Neal, Cecil M. Lewis, Jr.

Human Biology Open Access Pre-Prints

Determining the origins of those buried within undocumented cemeteries is of incredible importance to historical archaeologists and in many cases, the nearby communities. In the case of Avondale Burial Place, a cemetery in Bibb County, Georgia, in use from 1820 to 1950, all written documentation of those interred within it has been lost. Osteological and archaeological evidence alone could not describe, with confidence, the ancestral origins of the 101 individuals buried there. In the present study, we utilize ancient DNA extraction methods to investigate the origins of Avondale Burial Place through the use of well-preserved skeletal fragments from 20 individuals …

Mongolians In The Genetic Landscape Of Central Asia: Exploring The Genetic Relations Among Mongolians And Other World Populations, Jane E. Brissenden, Judith R. Kidd, Baigalmaa Evsanaa, Ariunaa Togtokh, Andrew J. Pakstis, Françoise Friedlaender, Kenneth K. Kidd, Janet M. Roscoe

Human Biology Open Access Pre-Prints

Genetic data on North Central Asian populations are underrepresented in the literature, especially autosomal markers. In the present study we use 812 single nucleotide polymorphisms that are distributed across all the human autosomes and that have been extensively studied at Yale to examine the affinities of two recently collected, samples of populations: rural and cosmopolitan Mongolians from Ulaanbaatar and nomadic, Turkic-speaking Tsaatan from Mongolia near the Siberian border. We compare these two populations to one another and to a global set of populations and discuss their relationships to New World populations. Specifically, we analyze data on 521 autosomal loci (single …

Hemochromatosis: Niche Construction And The Genetic Domino Effect In The European Neolithic, John M. Mccullough, Kathleen M. Heath, Alexis M. Smith

Human Biology Open Access Pre-Prints

Hereditary hemochromatosis (HH) is caused by a potentially lethal recessive gene (HFE, C282Y allele) that increases iron absorption and reaches polymorphic levels in Northern European populations. Because persons carrying the allele absorb iron more readily than non-carriers, it has often been suggested HFE is an adaptation to anemia. We hypothesize positive selection for HFE began during or after the European Neolithic with the adoption of an iron-deficient high grain and dairying diet and consequent anemia, a finding confirmed in Neolithic and later European skeletons. HFE frequency compared with rate of lactase persistence in Eurasia yields a positive linear …

A Homogenizing Process Of Selection Has Maintained An 'Ultra-Slow' Acetylation Nat2 Variant In Humans, Blandine Patillon, Pierre Luisi, Estella S. Poloni, Sotiria Boukouvala, Pierre Darlu, E. Genin, Audrey Sabbagh

Human Biology Open Access Pre-Prints

N-acetyltransferase 2 (NAT2) is an important enzyme involved in the metabolism of a wide spectrum of naturally occurring xenobiotics, including therapeutic drugs and common environmental carcinogens. Extensive polymorphism in NAT2 gives rise to a wide interindividual variation in acetylation capacity which influences individual susceptibility to various drug-induced adverse reactions and cancers. Striking patterns of geographic differentiation have been described for the main slow acetylation variants of the NAT2 gene, suggesting the action of natural selection at this locus. In the present study, we took advantage of the whole-genome sequence data available from the 1000 Genomes project to investigate the …

Hla Class Ii Alleles In The Otomi Population Of The Mezquital Valley. A Genetic Approach To The History Of Interethnic Migrations In The Mexican Central Plateau, Ana Itzel Juárez-Martín, Blanca Zoila González-Sobrino, Ángel Eduardo Camarena Olvera, Ramcés Falfán-Valencia

Human Biology Open Access Pre-Prints

From a historic and genetic point of view, the Otomi of the Mezquital Valley are a frontier people that have played an important role in the making of the population dynamics of the Mexican Central Plateau. Due to their antiquity in the area, the Otomi may be bearers of ancient genetic variability, shared mainly today with other groups belonging to the Otomanguean linguistic family and with the Nahua.

This study analyzes the HLA class II allele frequencies reported in Mexican indigenous populations, in order to provide an intra-regional level historical perspective of the genetic relationships between the Otomi of the …

Human Diversity In Jordan: Polymorphic Alu Insertions In General Jordanian And Bedouin Groups, Daniela Zanetti, May Sadiq, Robert Carreras-Torres, Omar Khabour, Almuthanna Alkaraki, Esther Esteban, Marc Via, Pedro Moral

Human Biology Open Access Pre-Prints

Jordan, located in the Levant region, is a crucial area to investigate human migration between Africa and Eurasia. Even thought, the genetic history of Jordanians is far to be clarified including the origin of the Bedouins today resident in Jordan. Here, we provide new genetic data on autosomal independent markers in two Jordanian population samples (Bedouins and general population) in order to approach the genetic diversity inside this country and to give new information about the genetic position of these populations in the frame of the Mediterranean and Middle East area. The analyzed markers are 18 Alu polymorphic insertions characterized …

Human Paternal Lineages, Languages And Environment In The Caucasus, David Tarkhnishvili, Alexander Gavashelishvili, Marine Murtskhvaladze, Mariam Gabelaia, Gigi Tevzadze

Human Biology Open Access Pre-Prints

Publications that describe the human Y-DNA haplogroup composition in different ethnic or linguistic groups and geographic regions provide no explicit explanation of the distribution of human paternal lineages in relation to specific ecological conditions. Our research attempts to address this topic for the Caucasus – a geographic region that encompasses a relatively small area but harbors high linguistic, ethnic, and Y-DNA haplogroup diversity. 224 men that identified themselves as ethnic Georgian were genotyped for Y-chromosome 23 STR markers and assigned to their geographic places of origin. The genotyped data were supplemented with the published data on the haplogroup composition and …

Phylogeography Of E1b1b1b-M81 Haplogroup And Analysis Of Its Subclades In Morocco, Ahmed Reguig, Nourdin Harich, Abdelhamid Barakat, Hassan Rouba

Human Biology Open Access Pre-Prints

In this work, we have analyzed a total of 295 unrelated Berber-speaking men from the northern, center and southern of Morocco, in order to characterize frequency of E1b1b1b-M81 haplogroup and to refine the phylogeny of its subclades: E1b1b1b1-M107, E1b1b1b2-M183 and E1b1b1b2a-M165. For this purpose, we have typed four biallelic polymorphisms: M81, M107, M183 and M165. As results, a large majority of the Berber-speaking male lineages belong to the Y chromosomal E1b1b1b-M81 haplogroup. The frequency ranged from 79.1 to 98.5% in all localities sampled. Then, the E1b1b1b2-M183 was the most dominant subclade in our samples, which ranged from 65.1% to 83.1%. …

Mitochondrial Dna Variability Among Six South-American Amerindian Villages From The Pano Linguistic Group, Celso T. Mendes-Junior, Aguinaldo L. Simoes

Human Biology Open Access Pre-Prints

Although scattered throughout a large geographic area, the members of the Pano linguistic group present strong ethnic, linguistic and cultural homogeneity, a feature that causes them to be considered as components of a same “Pano” tribe. Nevertheless, the genetic homogeneity between Pano villages has not been examined before. To study the genetic structure of the Pano linguistic group, four major Native American mitochondrial DNA (mtDNA) founder haplogroups were analyzed in 77 Amerindians from six villages of four Pano tribes (Katukina, Kaxináwa, Marúbo, and Yaminawa) located in the Brazilian Amazon. The central position of these tribes in the continent makes them …

Questioning The “Melting Pot”: Analysis Of Alu Inserts In Three Population Samples From Uruguay, Pedro C. Hidalgo, Patricia Mut, Elizabeth Ackermann, Gonzalo Figueiro, Monica Sans

Human Biology Open Access Pre-Prints

The way that immigrants integrate to recipient societies has been discussed for decades, mainly from the perspective of the social sciences. Uruguay, as other American countries, received different waves of European immigrants, although the details of the process of assimilation, when occurred, are unclear. In this paper, we use genetic markers to understand the process experienced by the Basques, one of the major migration waves that populated Uruguay, and its relation to other immigrants as well as to Native American and African descendants. For this purpose, we analyze the allele frequencies of ten ALU loci (A25, ACE, APOA1, B65, F13B, …

Did Pre-Clovis People Inhabit The Paisley Caves (And Why Does It Matter)?, Stuart J. Fiedel

Human Biology Open Access Pre-Prints

The date and processes of initial human colonization of the Americas are crucial issues for the understanding of human biological and cultural development. For example, Soares et al. (2009) cited the American archaeological record to validate their proposed revision of the human mitochondrial molecular clock. Their suggested mutation rate puts the date of rapid expansion of Native American clades at around 13,500–15,000 cal BP. Similarly, Poznik et al. (2013) have used the “high-confidence archaeological dating” of the initial peopling of the Americas to calibrate the rates of both Y-chromosome and mtDNA mutation and thereby to reconcile the ages of the …

Comparing Partial Least Square Approaches In Gene-Or Region-Based Association Study For Multiple Quantitative Phenotypes, Zhongshang Yuan, Xiaoshuai Zhang, Fangyu Li, Jinghua Zhao, Fuzhong Xue

Human Biology Open Access Pre-Prints

On thinking quantitatively of complex diseases, there are at least three statistical strategies for association study: single SNP on single trait, gene-or region (with multiple SNPs) on single trait and on multiple traits. The third of which is the most general in dissecting the genetic mechanism underlying complex diseases underpinning multiple quantitative traits. Gene-or region association methods based on partial least square (PLS) approaches have been shown to have apparent power advantage. However, few attempts are developed for multiple quantitative phenotypes or traits underlying a condition or disease, and the performance of various PLS approaches used in association study for …

Using The Neandertal And Denisova Genetic Data To Understand The Common Mapt 17q21 Inversion In Modern Humans, Núria Setó-Salvia, Federico Sánchez-Quinto, Eudald Carbonell, Carlos Lorenzo, David Comas, Jordi Clarimón

Human Biology Open Access Pre-Prints

The polymorphic inversion on 17q21, that includes the MAPT gene, represents a unique locus in the human genome characterized by a large region with strong linkage disequilibrium. Two distinct haplotypes, H1 and H2, exist in modern humans, and H1 has been unequivocally related to several neurodegenerative disorders. Recent data indicates that recurrent inversions of this genomic region have occurred through primate evolution, with the H2 haplotype being the ancestral state. Neandertals harbored the H1 haplotype, however until now no data was available for the Denisova hominin. Neandertals and Denisovans are sister groups that share a common ancestor with modern humans. …

The Effect Of Acp1-Ada1 Genetic Interaction On Human Life Span, Nazzareno Lucarini, Valerio Napolioni, Andrea Magrini, Fulvia Gloria

Human Biology Open Access Pre-Prints

Acid phosphatase (ACP1) is a polymorphic enzyme which catalyzes the conversion of flavinmononucleotide (FMN) to riboflavin and regulates the cellular concentration of flavin-adeninedinucleotide (FAD) and, consequently, energy metabolism. Its activity is modulated by adenosine deaminase (ADA1) genotype. Aim of our work is to verify whether individuals with a high proportion of ACP1 f isozyme and carrying ADA*2 allele, displaying the highest phosphatase activity, may have a higher life expectancy. Genomic DNA was extracted from peripheral blood of 569 females and 509 males (18-106 years) randomly recruited from Central Italy. These samples were subdivided into three sexspecific age groups …

Extensive Population Structure In San, Khoe And Mixed Ancestry Populations From Southern Africa Revealed By 44 Short 5-Snp Haplotypes, Carina M. Schlebusch, Himla Soodyall

Human Biology Open Access Pre-Prints

The San and Khoe people currently represent remnant groups of a much larger and widely distributed population of hunter gatherers and pastoralists who had exclusive occupation of southern Africa before the arrival of Bantu-speaking groups in the past 1,200 years and sea-borne immigrants within the last 350 years. Genetic studies (mitochondrial DNA and Y-chromosome) conducted on San and Khoe groups revealed that they harbour some the most divergent lineages found in living peoples throughout the world. Recently, high-density autosomal SNP-array studies confirmed the early divergence of Khoe-San population groups from all other human populations. The present study made use of …

Analysis Of A Genetic Isolate: The Case Of Carloforte (Italy), R. Robledo, L. Corrias, V. Bachis, N. Puddu, A. Mameli, G. Vona, C. M. Calò

Human Biology Open Access Pre-Prints

We reviewed data collected during several studies concerning the genetic isolate of Carloforte (Sardinia, Italy) and analyzed new data on Y-chromosome markers. Carloforte is also a language island, where people still speaks Tabarchino, an archaic form of Ligurian dialect. Demographic data indicate that, in the early years of its history, Carloforte population was characterized by a high degree of endogamy and consanguinity rates that started to decrease around 1850, when marriages with Sardinian people began to occur more frequently. Cultural factors, mainly language, account for the high endogamy. Genetic data from classical markers, mtDNA and Ychromosome markers confirmed the strong …

A Tale Of Two Haplotypes: The Eda2r/Ar Intergenic Region Is The Most Divergent Genomic Segment Between Africans And East Asians In The Human Genome, Amanda M. Casto, Brenna M. Henn, Jeffery M. Kidd, Carlos D. Bustamante, Marcus W. Feldman

Human Biology Open Access Pre-Prints

Single nucleotide polymorphisms (SNPs) with large allele frequency differences between human populations are relatively rare. The longest run of SNPs with an allele frequency difference of one between the Yoruba of Nigeria and the Han Chinese is found on the long arm of the X chromosome in the intergenic region separating the EDA2R and AR genes. It has been proposed that the unusual allele frequency distributions of these SNPs are the result of a selective sweep affecting African populations that occurred after the Out-of-Africa migration. To investigate the evolutionary history of the EDA2R/AR intergenic region, we characterized the haplotype structure …

Genetic Susceptibility To Type 2 Diabetes: A Global Meta-Analysis Studying The Genetic Differences In Tunisian Populations, Rym Berhouma, S. Kouidhi, M. Ammar, H. Abid, T. Baroudi, H. Ennafaa, A. Benammar-Elgaaied

Human Biology Open Access Pre-Prints

The present study is the first meta-analysis to evaluate type 2 diabetes (T2D) - associated polymorphisms in cohorts originated from several Tunisian regions. In fact, we evaluated the effect of seven polymorphisms in the following genes; PPARg ( Pro12Ala), TNFα (-308A/G), ENPP1(K121Q), TCF7L2(rs7903146 C/T), MTHFR( C677T), ACE(I/D), CAPN10(3R/2R) on T2D risk, through a meta-analysis combining data of previous studies performed on Tunisian populations originating from the north, centre or south of the country. R statistics version 2.12.1 software was used to estimate the heterogeneity between studies. Pooled ORs were computed by the fixed-effects method of Mantel-Haenszel if no heterogeneity between …

Paternal Lineage Analysis Supports An Armenian Rather Than A Central Asian Genetic Origin Of The Hamshenis, Ashot Margaryan, Ashot Harutyunyan, Zaruhi Khachatryan, Armine Khudoyan, Levon Yepiskoposyan

Human Biology Open Access Pre-Prints

The Hamshenis are an isolated geographic group of Armenians with a strong ethnic identity who, until the early decades of the twentieth century, inhabited the Pontus area on the southern coast of the Black Sea. Scholars hold alternative views on their origin, proposing eastern Armenia, western Armenia and Central Asia, respectively, as their most likely homeland. To ascertain whether genetic data from the non-recombining portion of the Y chromosome is supportive any of these suggestions, we screened 82 Armenian males of the Hamsheni descent for 12 biallelic and 6 microsatellite Y-chromosomal markers. These data were compared with the corresponding datasets …

Resource Availability, Mortality And Fertility: A Path Analytic Approach To Global Life History Variation, Mark A. Caudell, Robert J. Quinlan

Human Biology Open Access Pre-Prints

Humans exhibit considerable diversity in timing and rate of reproduction. Life history theory suggests that ecological cues of resource richness and survival probabilities shape human phenotypes across populations. Populations experiencing high extrinsic mortality due to uncertainty in resources should exhibit faster life histories. Here we use a path analytic approach informed by life history theory to model the multiple pathways between resources, mortality rates, and reproductive behavior in 191 countries. Resources that account for the most variance in population mortality rates are predicted to explain the most variance in total fertility rates. Results indicate that resources (e.g., calories, sanitation, education, …