Biological and Physical Anthropology 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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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.”

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 …

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 …

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 …

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 …

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 …

Concluding Remarks: What's In A Name? "Negritos" In The Context Of The Human Prehistory Of Southeast Asia, Stanley J. Ulijaszek

Human Biology

The "negrito" hypothesis posits that various indigenous groups throughout Island and Mainland Southeast Asia have a shared phenotype due to common descent from a putative ancestral population, representing a preagricultural substrate of humanity in the region. This has been examined and tested many times in the past, with no clear resolution. With many new resources to hand, the articles in this volume reexamine this hypothesis in a range of different ways. The evidence presented in this double issue of Human Biology speaks more against the category of "negrito" than for it. While populations with the negrito phenotype form a small …

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 …

Making Friends In The Rainforest: "Negrito" Adaptation To Risk And Uncertainty, Lye Tuck-Po

Human Biology

The so-called negritos adapt not just to a tropical forest environment but also to an environment characterized by perturbations and fluctuations. As with other hunter-gatherers in the region and, indeed, throughout the world, they use both social and ecological methods to enhance their chances of survival in this changing environment: socially, they have developed networks of trading and marriage partners; ecologically, they maintain patches of key resources that are available for future harvesting. As evidenced in the case of the Batek (Orang Asli), patterns of forest structure and composition are sometimes direct outcomes of intentional resource concentration and enrichment strategies. …

Why Have The Peninsular "Negritos" Remained Distinct?, Geoffrey Benjamin

Human Biology

The primary focus of this article is on the so-called negritos of Peninsular Malaysia and southern Thailand, but attention is also paid to other parts of Southeast Asia. I present a survey of current views on the "negrito" phenotype—is it single or many? If the phenotype is many (as now seems likely), it must have resulted from parallel evolution in the several different regions where it has been claimed to exist. This would suggest (contrary to certain views that have been expressed on the basis of very partial genetic data) that the phenotype originated recently and by biologically well-authenticated processes …

Terror From The Sky: Unconventional Linguistic Clues To The Negrito Past, Robert Blust

Human Biology

Within recorded history. most Southeast Asian peoples have been of "southern Mongoloid" physical type, whether they speak Austroasiatic, Tibeto-Burman, Austronesian, Tai-Kadai, or Hmong-Mien languages. However, population distributions suggest that this is a post-Pleistocene phenomenon and that for tens of millennia before the last glaciation ended Greater Mainland Southeast Asia, which included the currently insular world that rests on the Sunda Shelf, was peopled by short, dark-skinned, frizzy-haired foragers whose descendants in the Philippines came to be labeled by the sixteenth-century Spanish colonizers as "negritos," a term that has since been extended to similar groups throughout the region. There are three …

Time And Place In The Prehistory Of The Aslian Languages, Michael Dunn, Nicole Kruspe, Niclas Burenhult

Human Biology

The Aslian language family, located in the Malay Peninsula and southern Thai Isthmus, consists of four distinct branches comprising some 18 languages. These languages predate the now dominant Malay and Thai. The speakers of Aslian languages exhibit some of the highest degree of phylogenetic and societal diversity present in Mainland Southeast Asia today, among them a foraging tradition particularly associated with locally ancient, Pleistocene genetic lineages. Little advance has been made in our understanding of the linguistic prehistory of this region or how such complexity arose. In this article we present a Bayesian phylogeographic analysis of a large sample of …

Kinship Matters: Structures Of Alliance, Indigenous Foragers, And The Austronesian Diaspora, James West Turner

Human Biology

The study of kinship systems has direct relevance for the field of human genetics and the study of microevolution in human populations. Some types of postmarital residence rules—rules requiring a married couple to live with or near relatives of the husband or wife—will have consequences for the distribution of mitochondrial DNA and Y chromosome lineages. Rules that proscribe or encourage marriage with close kin will also have consequences for allele frequency. A preference for marrying at a distance, both socially and geographically, creates alliances that can have survival value for individuals and groups in an environment of periodic or unpredictable …

Who Are The Philippine Negritos? Evidence From Language, Lawrence A. Reid

Human Biology

This article addresses the linguistic evidence from which details about Philippine "negritos" can be inferred. This evidence comes from the naming practices of both negrito and non-negrito peoples, from which it can be inferred that many negrito groups have maintained a unique identity distinct from other groups since the dispersal of Malayo-Polynesian languages. Other names, such as Dupaningan and Dumagat, reference locations, from which it is assumed the negritos left after contact with Malayo-Polynesian people. Evidence also comes from the relative positions of negrito groups vis-à-vis other groups within the subfamily with which their current language can be grouped. Many …

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 …

Anthropology And Gis: Temporal And Spatial Distribution Of The Philippine Negrito Groups, Sabino G. Padilla Jr

Human Biology

The Philippine "negrito" groups comprise a diverse group of populations speaking over 30 different languages, who are spread all over the archipelago, mostly in marginal areas of Luzon Island in the north, the central Visayas islands, and Mindanao in the south. They exhibit physical characteristics that are different from more than 100 Philippine ethnolinguistic groups that are categorized as non-negritos. Given their numbers, it is not surprising that Philippine negritos make up a major category in a number of general ethnographic maps produced since the nineteenth century. Reports from various ethnological surveys during this period, however, have further enriched our …

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 …