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Evolution, Function And Deconstructing Histories: A New Generation Of Anthropological Genetics, Omer Gokcumen

Human Biology Open Access Pre-Prints

Introduction to the Special Issue, mainly based on contributions by the speakers in the 2016 AAAG symposium, “Ancient alleles in modern populations: Ancient structure, introgression, and variation-maintaining adaptive forces.”

Genetic Differentiation In A Sample From Northern Mexico City Detected By Hla System Analysis: Impact In The Study Of Population Immunogenetics, Eva D. JuáRez CortéS, Miguel A. Contreras Sieck, AgustíN J. Arriaga Perea, Rosa M. MacíAs Medrano, Anaí Balbuena Jaime, Paola Everardo MartíNez, JoaquíN ZúÑIga, VíCtor AcuñA Alonzo, Julio Granados, Rodrigo Barquera

Human Biology Open Access Pre-Prints

The major histocompatibility complex is directly involved in the immune response and thus the genes coding for its proteins are useful markers for the study of genetic diversity, susceptibility to disease (autoimmunity and infections), transplant medicine, and pharmacogenetics, among others. The polymorphism of the system also allows researchers to use it as a proxy for population genetics analysis, such as genetic admixture and genetic structure. In order to determine the immunogenetic characteristics of a sample from the northern part of Mexico City and to use them to analyze the genetic differentiation from other admixed populations, including those from previous studies …

Chaco Canyon Dig Unearths Ethical Concerns, Katrina G. Claw, Dorothy Lippert, Jessica Bardill, Anna Cordova, Keolu Fox, Joseph M. Yracheta, Alyssa C. Bader, Deborah A. Bolnick, Ripan S. Malhi, Kimberly Tallbear, Nanibaa' A. Garrison

Human Biology Open Access Pre-Prints

The field of paleogenomics (the study of ancient genomes) is rapidly advancing with more robust methods of isolating ancient DNA and increasing access to next-generation DNA sequencing technology. As these studies progress, many important ethical issues have emerged that should be considered when ancient Native American remains, whom we refer to as ancestors, are used in research. We highlight a recent article by Kennett et al. (2017), “Archaeogenomic evidence reveals prehistoric matrilineal dynasty,” that brings several ethical issues to light that should be addressed in paleogenomics research (Kennett et al. 2017). The study helps elucidate the matrilineal relationships in ancient …

Leveraging Multiple Populations Across Time Helps Define Accurate Models Of Human Evolution: A Reanalysis Of The Lactase Persistence Adaptation, Chenling Xu Antelope, Davide Marnetto, Fergal Casey, Emilia Huerta-Sanchez

Human Biology Open Access Pre-Prints

Access to a geographically diverse set of modern human samples from the present time and from ancient remains, combined with archaic hominin samples, provides an unprecedented level of resolution to study both human history and adaptation. The amount and quality of ancient human data continues to improve, and enables tracking the trajectory of genetic variation over time. These data have the potential to help us redefine or generate new hypotheses of how human evolution occurred, and revise previous conjectures. In this review, we argue that leveraging all these data will help us better detail adaptive histories in humans. As a …

Introgression Makes Waves In Inferred Histories Of Effective Population Size, John Hawks

Human Biology Open Access Pre-Prints

Human populations have a complex history of introgression and of changing population size. Human genetic variation has been affected by both these processes, so that inference of past population size depends upon the pattern of gene flow and introgression among past populations. One remarkable aspect of human population history as inferred from genetics is a consistent “wave” of larger effective population size, found in both African and non-African populations, that appears to reflect events prior to the last 100,000 years. Here I carry out a series of simulations to investigate how introgression and gene flow from genetically divergent ancestral populations …

Infectious Disease And The Diversification Of The Human Genome, Jessica F. Brinkworth

Human Biology Open Access Pre-Prints

The human immune system is under great pathogen-mediated selective pressure. A combination of divergent infectious disease pathogenesis across human populations, and the overrepresentation of “immune genes” in genomic regions with signatures of positive selection suggests that pathogens have significantly altered the human genome. However, important features of the human immune system can confound searches for and interpretations of signatures of pathogen-mediated evolution. Immune system redundancy, immune gene pleiotropy, host ability to acquire immunity and alter the immune repertoire of their offspring through “priming”, and host microbiome complicate evolutionary interpretations of host- pathogen interactions. The overall promiscuity and sensitivity of the …

Piecewise Regression Analysis Of Secular Change In The Maximum Femoral Vertical Head Diameter Of American White Males And Females, Sandra Cridlin

Human Biology Open Access Pre-Prints

Osteometric measurements of the femur are consistently used to estimate stature, sex, and race in constructing demographic profiles. The presence of positive or negative changes in the size of the maximum vertical diameter of the femoral head could potentially affect the validity of such profiles. Additionally, changes in femoral head size may be an indicator of the socioeconomic status, health, and nutrition of a population over periods of time. Two large data sets consisting of white male and white female femoral vertical head diameter measurements with birth years spanning 1841–1990 are used in this study. A combination of both LOESS …

Secular Change In The Femur Diaphyseal Biomechanical Properties Of American Whites, Daniel J. Wescott, Lauren Rockhold Zephro

Human Biology Open Access Pre-Prints

Over the past two centuries there have been documented secular changes in stature, weight, body proportions, and skeletal maturation rates in the United States. These changes along with a more sedentary lifestyle are likely reflected in femur morphology. Here we examine secular changes in diaphyseal cross-sectional size, shape, area, robusticity, and rigidity at midshaft and subtrochanteric of the femur using 395 adult white females and males from the United States born between the 1850s and the 1970s. The effect of secular change was controlled for an age effect. We also examine the relationship between femur length (proxy for stature) and …

Craniofacial Secular Change In Recent Mexican Migrants, Katherine Spradley, Kyra E. Stull, Joseph T. Hefner

Human Biology Open Access Pre-Prints

Research by economists suggests that recent Mexican migrants are better educated and have higher socioeconomic status (SES) than previous migrants. Because factors associated with higher SES and improved education can lead to positive secular changes in overall body form, secular changes in the craniofacial complex were analyzed within a recent migrant group from Mexico. The Mexican group represents individuals in the act of migration, not yet influenced by the American environment, and thus can serve as a starting point for future studies of secular change in this population group. The excavation of a historic Hispanic cemetery in Tucson, Arizona, also …

Patterns Of Dna Methylation Across The Leptin Core Promoter In Four Diverse Asian And North American Populations, M. J. Mosher, P. E. Melton, P. Stapleton, M. S. Schanfield, M. H. Crawford

Human Biology Open Access Pre-Prints

DNA methylation is the most widely studied of epigenetic mechanisms, with environmental effects recorded through patterned attachments of methyl groups along the DNA that are capable of modifying gene expression without altering the DNA sequencing. The degree to which these patterns of DNA methylation are heritable, the expected range of normality across populations, and the phenotypic relevance of pattern variation remain unclear. Genes regulating metabolic pathways appear to be vulnerable to ongoing nutritional programming over the life course, as dietary nutrients are significant environmental determinants of DNA methylation, supplying both the methyl groups and energy to generate the methylation process. …

Genetic Structure Of First Nation Communities In The Pacific Northwest, Cris E. Hughes, Mary P. Rogers, Amanda C. Owings, Barbara Petzelt, Joycelynn Mitchell, Harold Harry, Theresa Williams, Dena Goldberg, Damian Labuda, David Glenn Smith, Jerome S. Cybulski, Ripan S. Malhi

Human Biology Open Access Pre-Prints

This study presents genetic data for nine Native American populations from northern North America. Analyses of genetic variation focus on the Pacific Northwest (PNW). Using mitochondrial, Y chromosomal and autosomal DNA variants, we aim to more closely address the relationships of geography and language with present genetic diversity among the regional PNW Native American populations. Patterns of genetic diversity exhibited by the three genetic systems were consistent with our hypotheses, in that we expected genetic variation to be more strongly explained by geographic proximity than linguistic structure. Our findings were corroborated through a variety on analytic approaches, with the unrooted …

Landscape Complexity In The Caucasus Impedes Genetic Assimilation Of Human Populations More Effectively Than Language Or Ethnicity, David Tarkhnishvili, Alexander Gavashelishvili, Marine Murtskhvaladze, Ardashel Latsuzbaia

Human Biology Open Access Pre-Prints

The analyses of 15 autosomal and 23 Y-chromosome DNA STR loci in five rural populations from the Caucasus, namely four ethnically Georgian and one ethnically Armenian populations, indicated that two populations of Georgians - one from the west and the other one from the east of the Greater Caucasus Mountains - were both patrilineally and autosomally most differentiated from each other, and the other populations of Georgians and Armenians held an intermediate position between those two. This pattern may be due to human dispersal from two distinct glacial refugia in the last glacial period and the early Holocene, followed by …

Beyond Serial Founder Effects: The Impact Of Admixture And Localized Gene Flow On Patterns Of Regional Genetic Diversity, Keith Hunley, Graciela S. Cabana

Human Biology Open Access Pre-Prints

Objectives. Geneticists have argued that the linear decay in within-population genetic diversity with increasing geographic distance from East Africa is best explained by a phylogenetic process of founder effects, growth, and isolation termed serial founder effects (SFE). However, the SFE process has not yet been adequately vetted against other evolutionary processes that may also affect geospatial patterns of diversity. Additionally, studies of SFE have been largely based on a limited 52 population sample from the HGDP-CEPH. Here, we assess the effects of SFE, admixture, and localized gene flow processes on patterns of global and regional diversity using a published dataset …

The Fortieth Anniversary Of The Founding Of The Laboratory Of Biological Anthropology, Michael H. Crawford

Human Biology Open Access Pre-Prints

The anniversary of the founding of the LBA was celebrated during the spring of 2015 by a lecture series of former members of the laboratory, plus one research collaborator, all of whom contribute an article to this special issue of Human Biology.

Isonymic Relations In The Bolivia-Argentina Border, José Edgardo Dipierri, Emma Laura Alfaro Gomez, Alvaro Rodríguez-Larralde, Virginia Ramallo

Human Biology Open Access Pre-Prints

When migrating, people carry their cultural and genetic history, changing both, the transmitting and the recipient populations. This phenomenon changes the structure of the population of a country. The question is how to analyze the impact on the border region. A demographic and geopolitical analysis of borders requires an interdisciplinary approach. An isonymic analysis can be a useful tool. Surnames are part of cultural history, socio-cultural features transmitted from ancestors to their descendants through a vertical mechanism similar to that of genetic inheritance. The analysis of surname distribution can give quantitative information about the genetic structure of populations. The isonymic …

Modelling Demic And Cultural Diffusion - An Introduction, Joaquim Fort, Enrico R. Crema, Marco Madella

Human Biology Open Access Pre-Prints

Identifying the processes by which human cultures spread across different populations is one of the most topical objectives shared amongst different fields of study. Seminal works have analysed a variety of data and attempted to determine whether empirically observed patterns are the result of demic and/or cultural diffusion. This special issue collects papers exploring several themes (from modes of cultural transmission to drivers of dispersal mechanisms) and contexts (from the Neolithic in Europe to the spread of computer programming languages), which offer new insights that will augment the theoretical and empirical basis for the study of demic and cultural diffusion. …

Secular Changes In The Postcranial Skeleton Of American Whites, Richard L. Jantz, Lee Meadows Jantz, Joanne L. Devlin

Human Biology Open Access Pre-Prints

Secular change in height has been extensively investigated, but size and shape of the postcranial skeleton much less so. The availability of large, documented collections of nineteenth- and twentieth-century skeletons makes it possible to examine changes in skeletal structure over the past 150 years. We examined secular changes in long bone lengths and proportions, their allometric relationship to stature, and cross- sectional properties of long bone shafts. Bone measurements and stature were organized into 10-year birth cohorts, ranging from 1840 to 1989. Variation among cohorts was tested by one-way ANOVA, and secular trend was examined visually by plotting mean measurements …

Population History And Mitochondrial Genetic Substructure Of The Rama Amerindians From Nicaragua, Norberto F. Baldi, Michael H. Crawford

Human Biology Open Access Pre-Prints

The Rama are a coastal population from southern Nicaragua who in large part were able to resist, at least for a time, the cultural changes and social reorganization brought on by colonial and modern influences. Historical information leaves the Rama origins and biological relationships with nearby extinct and extant groups ambiguous. The objective of this study was to examine the internal genetic microdifferentiation based on the first hypervariable region of the mitochondrial DNA (mtDNA) from a sample of approximately 20% of the population, and to expand the few available historical and anthropological data on the Rama by exploring the effects …

Finding Rare, Disease-Associated Variants In Isolated Groups: Potential Advantages Of Mennonite Populations, Fabiana L. Lopes, Liping Hou, Angelica B. W. Boldt, Layla Kassem, Veronica M. Alves, Antonio E. Nardi, Francis J. Mcmahon

Human Biology Open Access Pre-Prints

Large-scale genotyping and next-generation sequencing techniques have allowed great advances in the field of molecular genetics. Numerous common variants of low impact have been associated with many complex human traits and diseases, such as bipolar disorder and schizophrenia. Although they may exert a greater impact on risk, few rare disease variants have been found, owing to the greatly increased sample sizes that are typically necessary to demonstrate association with rarer variants. One alternative strategy is to study isolated populations, where historical bottlenecks reduce genetic diversity and some otherwise rare variants may drift to higher frequencies. Here we describe the Mennonite …

Jujuy Province (Nw Argentina): Str Markers Unveil Microgeographic Differentiation Over A Steep Mountainous Landscape, Luis Gómez-Pérez, Miguel A. Alfonso-Sánchez, José Edgardo Dipierri, Jose A. Pena

Human Biology Open Access Pre-Prints

This study explores potential signals of microdifferentiation on the gene pool of three high-altitude populations from Jujuy province (NW Argentina) using highly polymorphic markers. These human communities are characterized by extreme living conditions and very low population densities owing to considerable height above sea level and steep orography. A set of autosomal STRs located at chromosome 6 (6p21.3) was typed in samples from Quebrada Baja (~2,500 m), Quebrada Alta (~ 3,300 m), and Puna (> 3,500 m). Genetic diversity was estimated through the observed (Ho) and expected (He) heterozygosities, and the haplotype diversity. Analyses of the molecular variance (AMOVA) and …

Genetic Evidence For Modifying Oceanic Boundaries Relative To Fiji, Gerhard P. Shipley, Diana A. Taylor, Antoine D. R. N’Yeurt, Anand Tyagi, Geetanjali Tiwari, Alan J. Redd

Human Biology Open Access Pre-Prints

We present the most comprehensive genetic characterization to date of five Fijian island populations: Viti Levu, Vanua Levu, Kadavu, the Lau Islands, and Rotuma, including non-recombinant Y (NRY) chromosome and mitochondrial DNA (mtDNA) haplotypes and haplogroups. As a whole, Fijians are genetically intermediate between Melanesians and Polynesians, but the individual Fijian island populations exhibit significant genetic structure reflecting different settlement experiences in which the Rotumans and the Lau Islanders were more influenced by Polynesians, and the other Fijian island populations were more influenced by Melanesians. In particular, Rotuman and Lau Islander NRY chromosomal and mtDNA haplogroup frequencies and Rotuman mtDNA …

An Examination Of The Differential Effects Of The Modern Epidemiological Transition On Cranial Morphology In The United States And Portugal, Katherine E. Weisensee, Richard L. Jantz

Human Biology Open Access Pre-Prints

This research examines the pattern of secular change in the cranial morphology of two populations experiencing the epidemiological transition associated with decreased mortality rates in children, followed by declines in infant mortality and subsequent increases in adult longevity. The two samples examined in this study come from US and Portuguese individuals. The epidemiological transition oc- curred at different times in the United States and Portugal, with Portugal entering into the transition later than the United States. The results of the study show that the US and Portuguese samples experienced significant changes in cranial morphology during the approximately 150 years under …

Y Chromosome Haplogroups In The Bosnian-Herzegovinian Population Based On 23 Y-Str Loci, Serkan Dogan, Adna Ašić, Gulsen Dogan, Larisa Besic, Damir Marjanovic

Human Biology Open Access Pre-Prints

In a study of the Bosnian-Herzegovinian (B&H) population, Y chromosome marker frequencies for 100 individuals, generated using PowerPlex^® Y23 kit, were used to perform Y chromosome haplogroup assignment via Whit Athey’s Haplogroup Predictor. This Whit Athey’s algorithm determines Y chromosome haplogroups from Y chromosome short tandem repeat (Y-STR) data using Bayesian probability-based approach. According to the results of the present study, the most frequent haplogroup appears to be I2a, with a prevalence of 49%, followed by R1a and E1b1b, each accounting for 17% of all haplogroups within the population. Remaining haplogroups encountered in this study are J2a (5%), I1 …

An Attempt To Integrate Previous Localized Estimates Of Human Inbreeding For The Whole Of Britain, John E. Pattison

Human Biology Open Access Pre-Prints

Abstract

There have been a number of previous estimates of human inbreeding for Britons of British descent in Britain; each generally for different social classes, geographical regions, and/or time periods. In this study an attempt was made to collect all relevant published studies and to combine the results of these disparate studies into an integrated whole for all of Britain. This was achieved by combining weighted means of the percentage of consanguineous marriages (f%) reported in these earlier studies: weighted according to the number of records each author examined, the proportion of social classes or geographical regions covered …

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, Magdalena Resano, Daniela Zanetti, Esther M. Esteban, Pedro Moral

Human Biology Open Access Pre-Prints

Bahía Blanca is an urban city in a historically and geographically strategic place for the mixture of different populations in Argentina. In the present study, ten Alu elements from the X-chromosome are analysed in order to characterise 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, seven out of ten Alu insertion frequencies are polymorphic. X-chromosome Alu results in Bahía Blanca are compared with eight different populations from Africa, Europe and America. The genetic distance analysis indicates …

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, …