Life Sciences Commons^™

Probability, Populations, Phylogenetics And Hominin Speciation, Niccolo Caldararo

Human Biology Open Access Pre-Prints

A number of recent articles have appeared on the hominin Denisova fossil remains. Many of them focus on attempts to produce DNA sequences from the extracted samples. Often these project mtDNA sequences from the fossil remains of a number of Neandertal fossils and the Denisovans in an attempt to understand the evolution of Mid Pleistocene human ancestors. These papers, introduce a number of problems in the interpretation of speciation in hominins. One concerns the degradation of the ancient DNA and its interpretation as authentic genetic information. Another concerns the idea of “species” versus that of “population” and the use of …

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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Open-Source Tools For Dense Facial Tissue Depth Mapping (Ftdm) Of Computed Tomography Models, Terrie Simmons-Ehrhardt, Catyana Falsetti, Anthony B. Falsetti, Christopher J. Ehrhardt

Human Biology Open Access Pre-Prints

Computed tomography (CT) scans provide anthropologists with a resource to generate three- dimensional (3D) digital skeletal material to expand quantification methods and build more standardized reference collections. The ability to visualize and manipulate the bone and skin of the face simultaneously in a 3D digital environment introduces a new way for forensic facial approximation practitioners to access and study the face. Craniofacial relationships can be quantified with landmarks or with surface processing software that can quantify the geometric properties of the entire 3D facial surface. This paper describes tools for the generation of dense facial tissue depth maps (FTDMs) using …

Of Typicality And Predictive Distributions In Discriminant Function Analysis, Lyle W. Konigsberg, Susan R. Frankenberg

Human Biology Open Access Pre-Prints

While discriminant function analysis is an inherently Bayesian method, researchers attempting to estimate ancestry in human skeletal samples often follow discriminant function analysis with the calculation of frequentist-based typicalities for assigning group membership. Such an approach is problematic in that it fails to account for admixture and for variation in why individuals may be classified as outliers, or non-members of particular groups. This paper presents an argument and methodology for employing a fully Bayesian approach in discriminant function analysis applied to cases of ancestry estimation. The approach requires adding the calculation, or estimation, of predictive distributions as the final step …

Mitochondrial Dna Analysis Of Mazahua And Otomi Indigenous Populations From Estado De Mexico Suggests A Distant Common Ancestry, Angelica GonzáLez-Oliver, Ernesto Garfias-Morales, D G. Smith, Mirsha Quinto-Sánchez

Human Biology Open Access Pre-Prints

The indigenous Mazahua and Otomi have inhabited the same localities in Estado de Mexico since pre-Columbian times. Their languages, Mazahua and Otomi, belong to the Otomanguean linguistic family, and, while they share cultural traditions and a regional history that suggest close genetic relationships and common ancestry, the historical records concerning their origin are confusing. To understand the biological relationships between Mazahua and Otomi we analyzed the mitochondrial DNA (mtDNA) genetic variation. We identified the mtDNA haplogroups by restriction fragment length polymorphism typing and sequenced the hypervariable region I of the mtDNA control region in 141 Mazahua and 100 Otomi. These …

Evaluating Nubian Population Structure From Cranial Nonmetric Traits: Gene Flow, Genetic Drift, And Population History Of The Nubian Nile Valle, Kanya Godde, Richard L. Jantz

Human Biology Open Access Pre-Prints

Paleolithic archaeological and skeletal remains from the Nile Valley have yielded a complex picture of life along the river. Sociocultural and sociopolitical events during this timeframe shaped population structure, while gene flow and genetic drift further developed it. In this paper, we take a population genetics approach to modeling Nubian biological relationships in an effort to describe how an accumulation of events formed Nubian population structure. A variety of Nubian samples were utilized, spanning the Mesolithic-Christian time periods, and geographically, from just above the first through the third cataracts. Population genetics statistics were employed to estimate and depict biological affinities …

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 …

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 …

Identification Of Whole Mitochondrial Genomes From Venezuela And Implications On Regional Phylogenies In South America, Esther J. Lee, D. Andrew Merriwether

Human Biology Open Access Pre-Prints

Recent studies have expanded and refined the founding haplogroups of the Americas using whole mitochondrial (mtDNA) genome analysis. In addition to pan-American lineages, a number of studies have identified specific variants that show higher frequencies in restricted geographical areas. In order to further characterize Native American maternal lineages and specifically examine local patterns within South America, we analyzed twelve maternally unrelated Yekuana whole mtDNA genomes from one village (Sharamaña) that include the four major Native American haplogroups A2, B2, C1, and D1. Our study proposes a reconfiguration of one subhaplogroup A2 (A2aa) that is specific to South America and identifies …

Mitochondrial Dna Suggests A Western Eurasian Origin For Ancient (Proto-) Bulgarians, D V. Nesheva, S Karachanak-Yankova, M Lari, Y Yordanov, A Galabov, David Caramelli, Draga Toncheva

Human Biology Open Access Pre-Prints

Ancient (proto-) Bulgarians have long been thought to as a Turkic population. However, evidence found in the past three decades show that this is not the case. Until now, this evidence does not include ancient mitochondrial DNA (mtDNA) analysis. In order to fill this void, we have collected human remains from the VIII-X century AD located in three necropolises in Bulgaria: Nojarevo (Silistra region) and Monastery of Mostich (Shumen region), both in Northeast Bulgaria and Tuhovishte (Satovcha region) in Southwest Bulgaria. The phylogenetic analysis of 13 ancient DNA samples (extracted from teeth) identified 12 independent haplotypes, which we further classified …

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 …

Population Genetic Structure Of Traditional Populations In The Peruvian Central Andes And Implications For South American Population History, Graciela S. Cabana, Cecil M. Lewis, Jr., Raúl Y. Tito, R. Alan Covey, Angela M. Cáceres, C. Leslie Castillo Pampas, Augusto F. De La Cruz, Diana Durand, Genevieve Housman, Brannon I. Hulsey, Gian Carlo Iannacone, Paul W. Lopez, Rolando Martínez, Ángel Medina, Olimpio Ortega Dávila, Karla Paloma Osorio Pinto, Susan I. Polo Santillán, Percy Rojas Domínguez, Meagan Rubel, Heather F. Smith, Silvia E. Smith, Verónica Rubín De Celis, Beatriz Lizárraga, Anne C. Stone

Human Biology Open Access Pre-Prints

Molecular-based characterizations of Andean peoples are traditionally conducted in the service of elucidating continental-level evolutionary processes in South America. Consequently, “western” Andean population genetic variation is often represented in relation to “eastern” variation among Amazon and Orinoco River Basin populations. This west-east contrast in patterns of population genetic variation is typically attributed to large-scale phenomena, such as dual founder colonization events and/or differing long-term microevolutionary histories. However, alternative explanations that consider the nature and causes of population genetic diversity within the Andean region remain underexplored.

Here we examine population genetic diversity in the Peruvian Central Andes using mtDNA HVI and …

The Australian Barrineans And Their Relationship To Southeast Asian Negritos: An Investigation Using Mitochondrial Genomics, Peter Mcallister, Nano Nagle, Robert John Mitchell

Human Biology

The existence of a short-statured Aboriginal population in the Far North Queensland (FNQ) rainforest zone of Australia’s northeast coast and Tasmania has long been an enigma in Australian anthropology. Based on their reduced stature and associated morphological traits such as tightly curled hair, Birdsell and Tindale proposed that these "Barrinean" peoples were closely related to "negrito" peoples of Southeast Asia and that their ancestors had been the original Pleistocene settlers of Sahul, eventually displaced by taller invaders. Subsequent craniometric and blood protein studies, however, have suggested an overall homogeneity of indigenous Australians, including Barrineans. To confirm this finding and determine …

Evolution Of The Pygmy Phenotype: Evidence Of Positive Selection From Genome-Wide Scans In African, Asian, And Melanesian Pygmies, Andrea Bamberg Migliano, Irene Gallego Romero, Mait Metspalu, Matthew Leavesley, Luca Pagani, Tiago Antao, Da-Wei Huang, Brad T. Sherman, Katharine Siddle, Clarissa Scholes, Georgi Hudjashov, Elton Kaitokai, Avis Babalu, Maggie Belatti, Alex Cagan, Bryony Hopkinshaw, Colin Shaw, Mari Nelis, Ene Metspalu, Reedik Mägi, Richard A. Lempicki, Richard Villems, Marta Mirazon Lahr, Toomis Kivisild

Human Biology

Human pygmy populations inhabit different regions of the world, from Africa to Melanesia. In Asia, short-statured populations are often referred to as "negritos." Their short stature has been interpreted as a consequence of thermoregulatory, nutritional, and/or locomotory adaptations to life in tropical forests. A more recent hypothesis proposes that their stature is the outcome of a life history trade-off in high-mortality environments, where early reproduction is favored and, consequently, early sexual maturation and early growth cessation have coevolved. Some serological evidence of deficiencies in the growth hormone/insulin-like growth factor axis have been previously associated with pygmies’ short stature. Using genome-wide …

Mount Pinatubo, Inflammatory Cytokines, And The Immunological Ecology Of Aeta Hunter-Gatherers, Robin M. Bernstein, Nathaniel J. Dominy

Human Biology

Early growth cessation and reproduction are predicted to maximize fitness under conditions of high adult mortality, factors that could explain the pygmy phenotype of many rainforest hunter-gatherers. This life-history hypothesis is elegant but contentious in part because it lacks a clear biological mechanism. One mechanism stems from the field of human immunological ecology and the concept of inflammation "memory" across the life cycle and into subsequent generations. Maternal exposures to disease can infl uence immunological cues present in breast milk; because maternal provisioning via lactation occurs during critical periods of development, it is plausible that these cues can also mediate …

Genetic Diversity Of Four Filipino Negrito Populations From Luzon: Comparison Of Male And Female Effective Population Sizes And Differential Integration Of Immigrants Into Aeta And Agta Communities, E Heyer, M Georges, M Pachner, P Endicott

Human Biology

Genetic data corresponding to four negrito populations (two Aeta and two Agta; n = 120) from the Luzon region of the Philippines have been analyzed. These data comprise mitochondrial DNA (mtDNA) hypervariable segment 1 haplotypes and haplogroups, Y-chromosome haplogroups and short tandem repeats (STRs), autosomal STRs, and X-chromosome STRs. The genetic diversity and structure of the populations were investigated at a local, regional, and interregional level. We found a high level of autosomal differentiation, combined with no significant reduction in diversity, consistent with long-term settlement of the Luzon region by the ancestors of the Agta and Aeta followed by reduced …

Admixture Patterns And Genetic Differentiation In Negrito Groups From West Malaysia Estimated From Genome-Wide Snp Data, Timothy A. Jinam, Maude E. Phipps, Naruya Saitou, The Hugo Pan-Asian Snp Consortium

Human Biology

Southeast Asia houses various culturally and linguistically diverse ethnic groups. In Malaysia, where the Malay, Chinese, and Indian ethnic groups form the majority, there exist minority groups such as the "negritos" who are believed to be descendants of the earliest settlers of Southeast Asia. Here we report patterns of genetic substructure and admixture in two Malaysian negrito populations (Jehai and Kensiu), using ~50,000 genome-wide single-nucleotide polymorphism (SNP) data. We found traces of recent admixture in both the negrito populations, particularly in the Jehai, with the Malay through principal component analysis and STRUCTURE analysis software, which suggested that the admixture was …

The Andaman Islanders In A Regional Genetic Context: Reexamining The Evidence For An Early Peopling Of The Archipelago From South Asia, Gyaneshwer Chaubey, Phillip Endicott

Human Biology

The indigenous inhabitants of the Andaman Islands were considered by many early anthropologists to be pristine examples of a "negrito" substrate of humanity that existed throughout Southeast Asia. Despite over 150 years of research and study, questions over the extent of shared ancestry between Andaman Islanders and other small-bodied, gracile, dark-skinned populations throughout the region are still unresolved. This shared phenotype could be a product of shared history, evolutionary convergence, or a mixture of both. Recent population genetic studies have tended to emphasize long-term physical isolation of the Andaman Islanders and an affinity to ancestral populations of South Asia. We …

Craniodental Affinities Of Southeast Asia's "Negritos" And The Concordance With Their Genetic Affinities, David Bulbeck

Human Biology

Genetic research into Southeast Asia's "negritos" has revealed their deep-rooted ancestry, with time depth comparable to that of Southwest Pacific populations. This finding is often interpreted as evidence that negritos, in contrast to other Southeast Asians, can trace much of their ancestry directly back to the early dispersal of Homo sapiens in the order of 70 kya from Africa to Pleistocene New Guinea and Australia. One view on negritos is to lump them and Southwest Pacific peoples into an "Australoid" race whose geographic distribution had included Southeast Asia prior to the Neolithic incursion of "Mongoloid" farmers. Studies into Semang osteology …

Genetic Variation Of X-Strs In The Wichí Population From Chaco Province, Argentina, Laura Angela Glesmann, Pablo Francisco Martina, Cecilia Inés Catanesi

Human Biology Open Access Pre-Prints

The Wichí people from Chaco province inhabit the region called Impenetrable Chaqueño, where the climatic conditions are extreme. Besides the scarce communication with the main urban centers, the cultural patterns of the Wichí cause these communities to live in certain degree of isolation. The effect of this situation is an increased genetic differentiation from other populations, as it was observed through autosomal and Y chromosome markers. However, the genetic variation of X chromosome has not been fully analyzed yet. The patterns of allele distribution of different markers of X chromosome can be highly informative in comparative studies, because its special …

Analysis Of Uniparental Lineages In Two Villages Of Santiago Del Estero, Argentina, Seat Of “Pueblos De Indios” In Colonial Times, Maia Pauro, Angelina García, Rodrigo Nores, Darío A. Demarchi

Human Biology Open Access Pre-Prints

Based on the analysis of the mitochondrial control region and seven biallelic markers of the Y Chromosome, we investigated the genetic composition of two rural populations of southern Santiago del Estero, Argentina, that were seats in colonial times of “pueblos de indios”, a colonial practice that consisted of concentrating the indigenous populations in organized and accessible settlements, to facilitate Christianizing and policing. We found the Native American Y chromosome haplogroup Q1a3a in only 11% (3/27) of the males. Haplogroup R, common in European populations, is the most frequent haplogroup in Santiago del Estero (55%). In contrast, the persistence of Native …