The peopling of America: craniofacial shape variation on a continental scale and its interpretation from an interdisciplinary view

Bioclimatic and masticatory influences on human cranial diversity verified by analysis of 3D morphometric homologous models

This study analyzes the effects of bioclimate and masticatory factors on the regional variability of human cranial forms across 150 ethnic groups worldwide. Morphometric variables were generated using principal component analysis applied to 3D homologous models. Relationships between cranial form and bioclimate (temperature and precipitation) and masticatory factors (infratemporal space) were tested considering sampling bias due to past population movements during the late Pleistocene and/or early- to mid-Holocene. Cranial size correlated with thermal conditions, consistent with Bergmann's rule. The length/breadth proportion of the neurocranium aligned with Allen's rule for thermal adaptation, while no relationship with masticatory stress was found. Facial form responded to either climate or masticatory conditions, although the primary factor was unclear due to the high correlation between stresses. However, masticatory stress was identified as an equally significant factor behind facial flatness in cold regions, else than the effect of Allen's rule. High narrowness of nasal and orbital openings correlated significantly with cold temperatures and cranial size, suggesting not only functional but also allometric effect. This study demonstrated the complexity of environmental influences on cranial form diversity, nonetheless suggested reduction of selective pressure on cranial form caused by natural environmental stress due to the development of civilization.

On Roth's "human fossil" from Baradero, Buenos Aires Province, Argentina: morphological and genetic analysis

The "human fossil" from Baradero, Buenos Aires Province, Argentina, is a collection of skeleton parts first recovered by the paleontologist Santiago Roth and further studied by the anthropologist Rudolf Martin. By the end of the nineteenth century and beginning of the twentieth century it was considered one of the oldest human skeletons from South America's southern cone. Here, we present the results of an interdisciplinary approach to study and contextualize the ancient individual remains. We discuss the context of the finding by first compiling the available evidence associated with the historical information and any previous scientific publications on this individual. Then, we conducted an osteobiographical assessment, by which we evaluated the sex, age, and overall preservation of the skeleton based on morphological features. To obtain a 3D virtual reconstruction of the skull, we performed high resolution CT-scans on selected skull fragments and the mandible. This was followed by the extraction of bone tissue and tooth samples for radiocarbon and genetic analyses, which brought only limited results due to poor preservation and possible contamination. We estimate that the individual from Baradero is a middle-aged adult male. We conclude that the revision of foundational collections with current methodological tools brings new insights and clarifies long held assumptions on the significance of samples that were recovered when archaeology was not yet professionalized.

Craniovascular variation in four late Holocene human samples from southern South America

Craniovascular traits in the endocranium (traces of middle meningeal vessels and dural venous sinuses, emissary foramina) provide evidence of vascular anatomy in osteological samples. We investigate the craniovascular variation in four South American samples and the effect of artificial cranial modifications (ACM). CT scans of human adult crania from four archeological samples from southern South America (including skulls with ACM) are used for the analyses. The craniovascular features in the four samples are described, skulls with and without ACM are compared, and additionally, South Americans are compared to a previously analyzed sample of Europeans. Of the four South American samples, the Southern Patagonian differs the most, showing the most distinct cranial dimensions, no ACM, and larger diameters of the emissary foramina. Unlike previous studies, we did not find any major differences in craniovascular features between modified and non-modified skulls, except that the skulls with ACM present somewhat smaller foramina. South Americans significantly differed from Europeans, especially in the anteroposterior dominance of the middle meningeal artery, in the pattern of sinus confluence, in the occurrence of enlarged occipito-marginal sinuses, and in foramina frequencies and diameters. Craniovascular morphology is not affected by the cranial size, even in skulls with ACM, indicating a minor or null influence of structural topological factors. Concerning the samples from distinct geographic and climatic environments, it must be evaluated whether the craniovascular morphogenesis might be partially influenced by specific functions possibly associated with thermoregulation, intracranial pressure, and the maintenance of intracranial homeostasis.

Associations between 44 nonmetric permanent dental traits or anomalies with skeletal sagittal malocclusions and sex, besides correlations across the variations or abnormalities

INTRODUCTION

Nonmetric dental traits and the shape, size, or number of dental anomalies are essential to various dental fields such as orthodontics, dental anatomy, anthropology, pathology, and forensic dentistry. Nonetheless, many are not well assessed worldwide. Moreover, most studies are limited to a few nonmetric traits. Therefore, we aimed to examine several nonmetric dental traits/anomalies.

METHODS

In this cross-sectional epidemiological study, ~ 9000 permanent teeth of 331 non-syndromic orthodontic patients (radiographs and dental casts) with fully erupted permanent dentitions (except the third molars and some cases of a few teeth missing or excluded) were evaluated by two observers, each twice, in search for 62 nonmetric traits/shape-number-size anomalies. The traits/anomalies of interest were supernumerary, microdontia, peg-shaped lateral, shovelings, talon cusps, Carabelli cusps, fifth/sixth/seventh cusps on the molars, hypocone/hypoconulid absence, protostylid, deflecting wrinkle‏s, canine mesial ridge, distal trigonid crest, canine distal accessory ridge, accessory cusps in the mesial/distal marginal ridges, mesial/distal accessory ridges, and accessory cusps in the lingual of the mandibular premolars and second molars). Data, at both patient/quarter levels, were analyzed regarding the associated factors (skeletal Angle classes, crowding, sex, and sides) as well as the correlations among traits, using the chi-square test and Spearman correlation coefficient (α = 0.05).

RESULTS

Prevalence rates of 44 traits/anomalies were reported (18 out of the 62 searched traits/anomalies were not found [prevalence = 0%]). Microdontia and accessory cusps on the marginal ridge of the second mandibular molars were significantly more common in women (P < 0.05). Canine talon cusp and distal trigonid crest of the second mandibular molars were more prevalent in men (P < 0.05). Shoveling, canine talon cusp, canine distal accessory ridge, and accessory cusp in the first premolar might be more prevalent in skeletal Angle class II; whereas, accessory cusp in the mesial marginal ridge of the second premolar might be rather more prevalent in skeletal Angle class I (P < 0.05). Few dental traits were positively and moderately or strongly correlated with each other (Spearman Rho ≥ 0.4, P < 0.0005).

CONCLUSIONS

Sex dimorphism was uncommon in nonmetric dental traits/anomalies. Skeletal malocclusions may be associated with a few dental abnormalities or variations.

Global patterns of the cranial form of modern human populations described by analysis of a 3D surface homologous model

This study assessed the regional diversity of the human cranial form by using geometric homologous models based on scanned data from 148 ethnic groups worldwide. This method adopted a template-fitting technique for a nonrigid transformation via the iterative closest point algorithm to generate the homologous meshes. Through the application of principal component analysis to 342 sampled homologous models, the largest variation was detected in overall size, and small South Asian crania were clearly verified. The next greatest diversity was found in the length/breadth proportion of the neurocranium, which showed the contrast between the elongated crania of Africans and the globular crania of Northeast Asians. Notably, this component was slightly correlated with the facial profile. Well-known facial features, such as the forward projection of the cheek among Northeast Asians and compaction of the European maxilla, were reconfirmed. These facial variations were highly correlated with the calvarial outline, particularly the degree of frontal and occipital inclines. An allometric pattern was detected in facial proportions in relation to overall cranial size; in larger crania, the facial profiles tend to be longer and narrower, as demonstrated among many American natives and Northeast Asians. Although our study did not include data on environmental variables that are likely to affect cranial morphology, such as climate or dietary conditions, the large datasets of homologous cranial models will be usefully available for seeking various attributions to phenotypic skeletal characteristics.

A genomic perspective on South American human history

It has generally been accepted that the current indigenous peoples of the Americas are derived from ancestors from northeastern Asia. The latter were believed to have spread into the American continent by the end of the Last Glacial Maximum. In this sense, a joint and in-depth study of the earliest settlement of East Asia and the Americas is required to elucidate these events accurately. The first Americans underwent an adaptation process to the Americas' vast environmental diversity, mediated by biological and cultural evolution and niche construction, resulting in enormous cultural diversity, a wealth of domesticated species, and extensive landscape modifications. Afterward, in the Late Holocene, the advent of intensive agricultural food production systems, sedentism, and climate change significantly reshaped genetic and cultural diversity across the continent, particularly in the Andes and Amazonia. Furthermore, starting around the end of the 15th century, European colonization resulted in massive extermination of indigenous peoples and extensive admixture. Thus, the present review aims to create a comprehensive picture of the main events involved in the formation of contemporary South American indigenous populations and the dynamics responsible for shaping their genetic diversity by integrating current genetic data with evidence from archeology, linguistics and other disciplines.

Morphometric affinities and direct radiocarbon dating of the Toca dos Coqueiros' skull (Serra da Capivara, Brazil)

The biological variation of the earliest skeletons of South America has been intensely debated for the last two centuries. One of the major research constraints has been the limited number of available samples dating to the early Holocene. We here present the first direct radiocarbon-date for the early Holocene human skeleton from Toca dos Coqueiros (Serra da Capivara, Brazil), also known as “Zuzu” (8640 ± 30 BP; 9526–9681 cal years BP). We performed craniometric analyses using exclusively samples from Brazil, to revisit the sex of the skeleton, and to discuss the evolutionary processes involved in the occupation of the continent. The sex of the individual was estimated as a female when compared to late and early Holocene individuals, but as a male when compared only to the early Holocene series. We also found that Zuzu presents the strongest differences with the late Holocene Guajajara individuals, located nearby, and the strongest similarities with the early Holocene series from Lagoa Santa, attesting for solid biological affinities among early Holocene individuals from Brazil, as well as a moderate level of morphological variation among them. This suggests that the early individuals were part of the same heterogeneous lineage, possibly a different one from which late Holocene populations diverged.

Digital restoration of the Wilson-Leonard 2 Paleoindian skull (~10,000 BP) from central Texas with comparison to other early American and modern crania

OBJECTIVES

Craniofacial morphology (CFM) is often used to address questions about the biological affinities of the earliest Americans, or Paleoindians, but resolution is complicated in part by a lack of well-preserved crania. The Wilson-Leonard 2 (WL-2) Paleoindian skull from Texas has never been fully analyzed because it is crushed and cannot be physically reconstructed. This study employs a digital restoration for comprehensive assessment and analysis of WL-2.

MATERIALS AND METHODS

High-resolution CT data and geometric morphometrics are used to restore the WL-2 skull and analyze its morphology using 65 craniometric measurements acquired on the restoration. These data allow for a full morphological description and multivariate (Mahalanobis Distance and Principal Component) comparisons to other Paleoindians and recent populations.

RESULTS

WL-2 has a long, narrow braincase, and a short, modestly prognathic face. Compared with other Paleoindians, she is individually similar to several skulls from Brazil, but aligns most closely with pooled samples from the US and Mexico. WL-2 is most similar to recent populations from Europe, Asia, and the Americas, and markedly different to those from Africa and Australia.

DISCUSSION

The overall morphology of WL-2 and her association with Asians and Europeans align well with trends identified in other CFM analyses. Her affinity to recent Amerindians contrasts with the findings of many previous CFM studies, but is seemingly consistent with molecular analyses suggesting a close relationship between some Paleoindians and modern American Indians. This study demonstrates the potential for using digital anthropological methods to study other Paleoindian crania whose data value is limited by physical destruction and/or deformation.

Three-dimensional geometric morphometric studies of modern human occipital variation

Objectives

To investigate three-dimensional morphological variation of the occipital bone between sexes and among populations, to determine how ancestry, sex and size account for occipital shape variation and to describe the exact forms by which the differences are expressed.

Methods

CT data for 214 modern crania of Asian, African and European ancestry were compared using 3D geometric morphometrics and multivariate statistics, including principal component analysis, Hotelling’s T² test, multivariate regression, ANOVA, and MANCOVA.

Results

Sex differences in average occipital morphology are only observed in Europeans, with males exhibiting a pronounced inion. Significant ancestral differences are observed among all samples and are shared by males and females. Asian and African crania have smaller biasterionic breadths and flatter clivus angles compared to Europeans. Asian and European crania are similar in their nuchal and occipital plane proportions, nuchal and occipital angles, and lower inion positions compared to Africans. Centroid size significantly differs between sexes and among populations. The overall allometry, while significant, explains little of the shape variation. Larger occipital bones were associated with a more curved occipital plane, a pronounced inion, a narrower biasterionic breadth, a more flexed clivus, and a lower and relatively smaller foramen magnum.

Conclusions

Although significant shape differences were observed among populations, it is not recommended to use occipital morphology in sex or population estimation as both factors explained little of the observed variance. Other factors, relating to function and the environment, are suggested to be greater contributors to occipital variation. For the same reason, it is also not recommended to use the occiput in phylogenetic studies.

Adaptation and co-adaptation of skin pigmentation and vitamin D genes in native Americans

We carried out an exhaustive review regarding human skin color variation and how much it may be related to vitamin D metabolism and other photosensitive molecules. We discuss evolutionary contexts that modulate this variability and hypotheses postulated to explain them; for example, a small amount of melanin in the skin facilitates vitamin D production, making it advantageous to have fair skin in an environment with little radiation incidence. In contrast, more melanin protects folate from degradation in an environment with a high incidence of radiation. Some Native American populations have a skin color at odds with what would be expected for the amount of radiation in the environment in which they live, a finding challenging the so-called "vitamin D-folate hypothesis." Since food is also a source of vitamin D, dietary habits should also be considered. Here we argue that a gene network approach provides tools to explain this phenomenon since it indicates potential alleles co-evolving in a compensatory way. We identified alleles of the vitamin D metabolism and pigmentation pathways segregated together, but in different proportions, in agriculturalists and hunter-gatherers. Finally, we highlight how an evolutionary approach can be useful to understand current topics of medical interest.

Genetic admixture in Brazil

We review studies from our laboratories using different molecular tools to characterize the Amerindian, European and African ancestry of Brazilians. Initially we used uniparental DNA markers to investigate the contribution of distinct Y chromosome and mitochondrial DNA lineages to present-day populations. High levels of genetic admixture and strong directional mating between European males and Amerindian and African females were unraveled. We next analyzed different types of biparental autosomal polymorphisms. Especially useful was a set of 40 insertion-deletion polymorphisms (indels) that when studied worldwide proved exquisitely sensitive in discriminating between Amerindians, Europeans and Sub-Saharan Africans. When applied to the study of Brazilians these markers confirmed extensive genomic admixture. We then studied ancestry differences in different regions by statistically controlling them to eliminate color considerations. The European ancestry was predominant in all regions studied, with proportions ranging from 60.6% in the Northeast to 77.7% in the South. We propose that the immigration of 6 million Europeans to Brazil in the 19th and 20th centuries is in large part responsible for dissipating previous ancestry dissimilarities that reflected region-specific population histories. Brazilians should be assessed individually, as 210 million human beings, and not as members of specific regions or color groups.

The history behind the mosaic of the Americas

Focusing on literature published in 2018-2020, we review inferences about: (i) how ancient DNA is contributing to clarify the peopling of the Americas and the dispersal of its first inhabitants, (ii) how the interplay between environmental diversity and culture has influenced the genetic structure and adaptation of Andean and Amazon populations, (iii) how genetics has contributed to our understanding of the Pre-Columbian Tupi expansion in Eastern South America, (iv) the subcontinental origins and dynamics of Post-Columbian admixture in the Americas, and finally, (v) episodes of adaptive natural selection in the American continent, particularly in the high altitudes of the Andes.

Morphological variation of the early human remains from Quintana Roo, Yucatán Peninsula, Mexico: Contributions to the discussions about the settlement of the Americas

The human settlement of the Americas has been a topic of intense debate for centuries, and there is still no consensus on the tempo and mode of early human dispersion across the continent. When trying to explain the biological diversity of early groups across North, Central and South America, studies have defended a wide range of dispersion models that tend to oversimplify the diversity observed across the continent. In this study, we aim to contribute to this debate by exploring the cranial morphological affinities of four late Pleistocene/early Holocene specimens recovered from the caves of Quintana Roo, Mexico. The four specimens are among the earliest human remains known in the continent and permit the contextualization of biological diversity present during the initial millennia of human presence in the Americas. The specimens were compared to worldwide reference series through geometric morphometric analyses of 3D anatomical landmarks. Morphological data were analyzed through exploratory visual multivariate analyses and multivariate classification based on Mahalanobis distances. The results show very different patterns of morphological association for each Quintana Roo specimen, suggesting that the early populations of the region already shared a high degree of morphological diversity. This contrasts with previous studies of South American remains and opens the possibility that the initial populations of North America already had a high level of morphological diversity, which was reduced as populations dispersed into the southern continent. As such, the study of these rare remains illustrates that we are probably still underestimating the biological diversity of early Americans.

A geometric morphometric approach to the analysis of skull shape in Triassic dicynodonts (Therapsida, Anomodontia) from South America

Dicynodont therapsids were a major component of the Permo-Triassic terrestrial ecosystems across Pangea and have been regarded as specialized herbivores. In South America, the group was represented by several taxa of the clade Kannemeyeriiformes spanning from the Middle to the Late Triassic. In order to evaluate if cranial differences among taxa are potentially related to differences in feeding function, we performed a geometric morphometric analysis on 28 South American dicynodont crania. We digitized 19 cranial landmarks and conducted generalized Procrustes analysis, principal component analysis (PCA), principal component analysis between groups (bg-PCA), and a branch weighted squared-change parsimony approach. Phylogenetic inertia was not a significant driver of cranial shape evolution in the group, whereas PCA and bg-PCA support that major morphological shape differences are concentrated in the preorbital region (relative length of the snout and width of the caniniform process), in the position of quadrate condyle in relation to the caniniform process, and in the increase in the intertemporal surface area. In this context, tusked Dinodontosaurus, "Kannemeyeria," and Vinceria have relatively smaller adductor attachment areas and input moment arm than younger taxa lacking tusks, such as Ischigualastia, Stahleckeria, and Jachaleria. Differences in cranial morphology in later dicynodonts reflect modifications in feeding mechanics, probably due to changes in food resources (vegetation) in their habitats toward the end of the Triassic.

Y Chromosome Sequences Reveal a Short Beringian Standstill, Rapid Expansion, and early Population structure of Native American Founders

The Americas were the last inhabitable continents to be occupied by humans, with a growing multidisciplinary consensus for entry 15-25 thousand years ago (kya) from northeast Asia via the former Beringia land bridge [1-4]. Autosomal DNA analyses have dated the separation of Native American ancestors from the Asian gene pool to 23 kya or later [5, 6] and mtDNA analyses to ∼25 kya [7], followed by isolation ("Beringian Standstill" [8, 9]) for 2.4-9 ky and then a rapid expansion throughout the Americas. Here, we present a calibrated sequence-based analysis of 222 Native American and relevant Eurasian Y chromosomes (24 new) from haplogroups Q and C [10], with four major conclusions. First, we identify three to four independent lineages as autochthonous and likely founders: the major Q-M3 and rarer Q-CTS1780 present throughout the Americas, the very rare C3-MPB373 in South America, and possibly the C3-P39/Z30536 in North America. Second, from the divergence times and Eurasian/American distribution of lineages, we estimate a Beringian Standstill duration of 2.7 ky or 4.6 ky, according to alternative models, and entry south of the ice sheet after 19.5 kya. Third, we describe the star-like expansion of Q-M848 (within Q-M3) starting at 15 kya [11] in the Americas, followed by establishment of substantial spatial structure in South America by 12 kya. Fourth, the deep branches of the Q-CTS1780 lineage present at low frequencies throughout the Americas today [12] may reflect a separate out-of-Beringia dispersal after the melting of the glaciers at the end of the Pleistocene.

Early human dispersals within the Americas

Studies of the peopling of the Americas have focused on the timing and number of initial migrations. Less attention has been paid to the subsequent spread of people within the Americas. We sequenced 15 ancient human genomes spanning from Alaska to Patagonia; six are ≥10,000 years old (up to ~18× coverage). All are most closely related to Native Americans, including those from an Ancient Beringian individual and two morphologically distinct “Paleoamericans.” We found evidence of rapid dispersal and early diversification that included previously unknown groups as people moved south. This resulted in multiple independent, geographically uneven migrations, including one that provides clues of a Late Pleistocene Australasian genetic signal, as well as a later Mesoamerican-related expansion. These led to complex and dynamic population histories from North to South America.

Sex estimation from cranial morphological traits: Use of the methods across American Indians, modern North Americans, and ancient Egyptians

This paper focuses on estimating sex by visual assessment of human cranial morphology. Practitioners in the field report variation in sexual dimorphism across populations. This study evaluates again the general hypothesis that populations vary in their pattern of sexual dimorphism. Specifically, the study tests the degree of expression of four cranial morphological traits (glabella, supraorbital margins, nuchal crest, and mastoid process) across three samples from different time periods and which vary in sociocultural transitions: 1) modern Americans of rural and urban areas spanning the last 186 years; 2) Dynastic Egyptians; and 3) Averbuch American Indians, spanning approximately 1255 CE to 1425 CE, from the southeastern United States. These three populations were specifically chosen for sampling as they represent distinct temporal and groups of varied ancestral composition. Crania from these samples were scored 1-5, with 1 being consistent with expected female morphology. The estimated sex was compared to either documented sex (when available) or discriminant functions derived from craniometrics. Freeman-Fisher-Halton tests examined sample differences, within sexes, affecting the visual assessment method. Post hoc tests were applied to pinpoint where the differences lie between the samples. The findings of this study support the hypothesis that the method does not estimate the sex of crania from all populations in the same manner, indicating that populations display differing patterns of sexual dimorphism. However, understanding these patterns and adjusting for how the method is applied will lead to reliable assessments. A relative frequency table and graphs of distributions are provided for practitioners who can use the information to make successful assessments of sex.

Lagoa Santa's contribution to the origins and life of early Americans

The region of Lagoa Santa, Central-Eastern Brazil, provides an exceptional archeological record about Late Pleistocene/Early Holocene occupation of the Americas. Since the first interventions made by the Danish naturalist Peter Lund in the 19th century, hundreds of human skeletons have been exhumed in the region. These skeletons are complemented by a rich botanic, faunal, technological, and geomorphological archeological record. We explore here the contributions of Lagoa Santa material to the origins and lifestyle of early Americans, providing an historic background. Cranial morphology of Lagoa Santa skeletons allowed the proposition of a model of two biological components for the occupation of the Americas, in which early Americans are morphologically similar to people of African and Australo-Melanesian origin. Furthermore, the archeological record in the region has revealed an intense use of plant resources, a restricted spatial distribution, and the symbolic elaboration of local hunter-gatherers, unveiling a distinct lifestyle compared to early North American populations.

Remembering the past - studies on evolution done by the genetics group at Universidade Federal do Rio Grande do Sul (UFRGS)

After a brief introduction about the factors that are involved in science development, and world and Brazilian evolutionary genetics, the studies developed in Porto Alegre in this area were reviewed. Four periods in the development of this group were distinguished: (a) Origins and first expansion (1949-1961); (b) Second expansion (1962-1988); (c) Third expansion (1989-2001); and (d) The last 15 years (2002-present). The international Porto Alegre Biological Evolution Workshops (PABEWs), with five biannual events from 2007 o 2015, were also mentioned. The final message stressed the importance of the maintenance of this and other Brazilian groups of research through adequate finance and recognition.

How strong was the bottleneck associated to the peopling of the Americas? New insights from multilocus sequence data

In spite of many genetic studies that contributed for a deep knowledge about the peopling of the Americas, no consensus has emerged about important parameters such as the effective size of the Native Americans founder population. Previous estimates based on genomic datasets may have been biased by the use of admixed individuals from Latino populations, while other recent studies using samples from Native American individuals relied on approximated analytical approaches. In this study we use resequencing data for nine independent regions in a set of Native American and Siberian individuals and a full-likelihood approach based on isolation-with-migration scenarios accounting for recent flow between Asian and Native American populations. Our results suggest that, in agreement with previous studies, the effective size of the Native American population was small, most likely in the order of a few hundred individuals, with point estimates close to 250 individuals, even though credible intervals include a number as large as ~4,000 individuals. Recognizing the size of the genetic bottleneck during the peopling of the Americas is important for determining the extent of genetic markers needed to characterize Native American populations in genome-wide studies and to evaluate the adaptive potential of genetic variants in this population.

Investigating cranial morphological variation of early human skeletal remains from Chile: A 3D geometric morphometric approach

OBJECTIVES

Archaeological and genetic research has demonstrated that the Pacific Coast was a key route in the early colonization of South America. Research examining South American skeletons >8000 cal BP has revealed differences in cranial morphology between early and late Holocene populations, which may reflect distinct migration events and/or populations. However, genetic, cultural, and some skeletal data contradict this model. Given these discrepancies, this study examines ∼9000 years of prehistory to test the hypothesis that Early skeletons have a distinct cranial morphology from later skeletons.

MATERIALS AND METHODS

Using 3D digital models, craniofacial landmarks, and geometric morphometric analyses, we compared Early Holocene crania (n = 4) to later Chilean samples (n = 90) frequently absent in continental assessments of craniofacial variation. PCA, Mahalanobis distances, posterior and typicality probabilities were used to examine variation.

RESULTS

Two of the earliest skeletons from northern Chile show clear affinities to individuals from later sites in the same region. However, the hypothesis cannot be rejected as one Early individual from northern Chile and one individual from inland Patagonia did not always show clear affinities to coastal populations.

DISCUSSION

Biological affinities among northern populations and other regions of Chile align with genetic and archaeological data, supporting cultural and biological continuity along the Pacific Coast. In Patagonia, archaeological data are in accordance with skeletal differences between the Early inland steppe individual and coastal populations. This study incorporates 3D methods and skeletal datasets not widely used in assessments of biological affinity, thus contributing to a critical body of research examining the ancient population history of western South America.

Haplotype Study in SCA10 Families Provides Further Evidence for a Common Ancestral Origin of the Mutation

Spinocerebellar ataxia type 10 (SCA10) is an autosomal dominant neurodegenerative disorder characterized by progressive cerebellar ataxia and epilepsy. The disease is caused by a pentanucleotide ATTCT expansion in intron 9 of the ATXN10 gene on chromosome 22q13.3. SCA10 has shown a geographical distribution throughout America with a likely degree of Amerindian ancestry from different countries so far. Currently available data suggest that SCA10 mutation might have spread out early during the peopling of the Americas. However, the ancestral origin of SCA10 mutation remains under speculation. Samples of SCA10 patients from two Latin American countries were analysed, being 16 families from Brazil (29 patients) and 21 families from Peru (27 patients) as well as 49 healthy individuals from Indigenous Quechua population and 51 healthy Brazilian individuals. Four polymorphic markers spanning a region of 5.2 cM harbouring the ATTCT expansion were used to define the haplotypes, which were genotyped by different approaches. Our data have shown that 19-CGGC-14 shared haplotype was found in 47% of Brazilian and in 63% of Peruvian families. Frequencies from both groups are not statistically different from Quechua controls (57%), but they are statistically different from Brazilian controls (12%) (p < 0.001). The most frequent expanded haplotype in Quechuas, 19-15-CGGC-14-10, is found in 50% of Brazilian and in 65% of Peruvian patients with SCA10. These findings bring valuable evidence that ATTCT expansion may have arisen in a Native American chromosome.

Resolving relationships between several Neolithic and Mesolithic populations in Northern Eurasia using geometric morphometrics

OBJECTIVES

Remains from several Eastern European and Siberian Mesolithic and Neolithic sites are analysed to clarify their biological relationships. We assume that groups' geographical distances correlate with genetic and, therefore, morphological distances between them.

MATERIALS AND METHODS

Material includes complete male crania from several Mesolithic and Neolithic burial sites across Northern Eurasia and from several modern populations. Geometric morphometrics and multivariate statistical techniques are applied to explore morphological trends, group distances, and correlations with their geographical position, climate, and the time of origin.

RESULTS

Despite an overlap in the morphology among the modern and archeological groups, some of them show significant morphological distances. Geographical parameters account for only a small proportion of cranial variation in the sample, with larger variance explained by geography and age together. Expectations of isolation by distance are met in some but not in all cases. Climate accounts for a large proportion of autocorrelation with geography. Nearest-neighbor joining trees demonstrate group relationships predicted by the regression on geography and on climate.

DISCUSSION

The obtained results are discussed in application to relationships between particular groups. Unlike the Ukrainian Mesolithic, the Yuzhny Oleni Ostrov Mesolithic displays a high morphological affinity with several groups from Northern Eurasia of both European and Asian origin. A possibility of a common substrate for the Yuzhny Oleni Ostrov Mesolithic and Siberian Neolithic groups is reviewed. The Siberian Neolithic is shown to have morphological connection with both modern Siberian groups and the Native North Americans.

A tale of agriculturalists and hunter-gatherers: Exploring the thrifty genotype hypothesis in native South Americans

OBJECTIVES

To determine genetic differences between agriculturalist and hunter-gatherer southern Native American populations for selected metabolism-related markers and to test whether Neel's thrifty genotype hypothesis (TGH) could explain the genetic patterns observed in these populations.

MATERIALS AND METHODS

375 Native South American individuals from 17 populations were genotyped using six markers (APOE rs429358 and rs7412; APOA2 rs5082; CD36 rs3211883; TCF7L2 rs11196205; and IGF2BP2 rs11705701). Additionally, APOE genotypes from 39 individuals were obtained from the literature. AMOVA, main effects, and gene-gene interaction tests were performed.

RESULTS

We observed differences in allele distribution patterns between agriculturalists and hunter-gatherers for some markers. For instance, between-groups component of genetic variance (F_CT ) for APOE rs429358 showed strong differences in allelic distributions between hunter-gatherers and agriculturalists (p = 0.00196). Gene-gene interaction analysis indicated that the APOE E4/CD36 TT and APOE E4/IGF2BP2 A carrier combinations occur at a higher frequency in hunter-gatherers, but this combination is not replicated in archaic (Neanderthal and Denisovan) and ancient (Anzick, Saqqaq, Ust-Ishim, Mal'ta) hunter-gatherer individuals.

DISCUSSION

A complex scenario explains the observed frequencies of the tested markers in hunter-gatherers. Different factors, such as pleotropic alleles, rainforest selective pressures, and population dynamics, may be collectively shaping the observed genetic patterns. We conclude that although TGH seems a plausible hypothesis to explain part of the data, other factors may be important in our tested populations.

Genetic signature of natural selection in first Americans

When humans moved from Asia toward the Americas over 18,000 y ago and eventually peopled the New World they encountered a new environment with extreme climate conditions and distinct dietary resources. These environmental and dietary pressures may have led to instances of genetic adaptation with the potential to influence the phenotypic variation in extant Native American populations. An example of such an event is the evolution of the fatty acid desaturases (FADS) genes, which have been claimed to harbor signals of positive selection in Inuit populations due to adaptation to the cold Greenland Arctic climate and to a protein-rich diet. Because there was evidence of intercontinental variation in this genetic region, with indications of positive selection for its variants, we decided to compare the Inuit findings with other Native American data. Here, we use several lines of evidence to show that the signal of FADS-positive selection is not restricted to the Arctic but instead is broadly observed throughout the Americas. The shared signature of selection among populations living in such a diverse range of environments is likely due to a single and strong instance of local adaptation that took place in the common ancestral population before their entrance into the New World. These first Americans peopled the whole continent and spread this adaptive variant across a diverse set of environments.

Evolutionary population history of early Paleoamerican cranial morphology

The nature and timing of the peopling of the Americas is a subject of intense debate. In particular, it is unclear whether high levels of between-group craniometric diversity in South America result from multiple migrations or from local diversification processes. Previous attempts to explain this diversity have largely focused on testing alternative dispersal or gene flow models, reaching conflicting or inconclusive results. Here, a novel analytical framework is applied to three-dimensional geometric morphometric data to partition the effects of population divergence from geographically mediated gene flow to understand the ancestry of the early South Americans in the context of global human history. The results show that Paleoamericans share a last common ancestor with contemporary Native American groups outside, rather than inside, the Americas. Therefore, and in accordance with some recent genomic studies, craniometric data suggest that the New World was populated by multiple waves of dispersion from northeast Asia throughout the late Pleistocene and early Holocene.

A genomic view of the peopling of the Americas

Whole-genome studies have documented that most Native American ancestry stems from a single population that diversified within the continent more than twelve thousand years ago. However, this shared ancestry hides a more complex history whereby at least four distinct streams of Eurasian migration have contributed to present-day and prehistoric Native American populations. Whole genome studies enhanced by technological breakthroughs in ancient DNA now provide evidence of a sequence of events involving initial migrations from a structured Northeast Asian source population with differential relatedness to present-day Australasian populations, followed by a divergence into northern and southern Native American lineages. During the Holocene, new migrations from Asia introduced the Saqqaq/Dorset Paleoeskimo population to the North American Arctic ∼4500 years ago, ancestry that is potentially connected with ancestry found in Athabaskan-speakers today. This was then followed by a major new population turnover in the high Arctic involving Thule-related peoples who are the ancestors of present-day Inuit. We highlight several open questions that could be addressed through future genomic research.

A Reassessment of the Impact of European Contact on the Structure of Native American Genetic Diversity

Our current understanding of pre-Columbian history in the Americas rests in part on several trends identified in recent genetic studies. The goal of this study is to reexamine these trends in light of the impact of post-Columbian admixture and the methods used to study admixture. The previously-published data consist of 645 autosomal microsatellite genotypes from 1046 individuals in 63 populations. We used STRUCTURE to estimate ancestry proportions and tested the sensitivity of these estimates to the choice of the number of clusters, K. We used partial correlation analyses to examine the relationship between gene diversity and geographic distance from Beringia, controlling for non-Native American ancestry (from Africa, Europe and East Asia), and taking into account alternative paths of migration. Principal component analysis and multidimensional scaling were used to investigate the relationships between Andean and non-Andean populations and to explore gene-language correspondence. We found that 1) European and East Asian ancestry estimates decline as K increases, especially in Native Canadian populations, 2) a north-south decline in gene diversity is driven by low diversity in Amazonian and Paraguayan populations, not serial founder effects from Beringia, 3) controlling for non-Native American ancestry, populations in the Andes and Mesoamerica have higher gene diversity than populations in other regions, and 4) patterns of genetic and linguistic diversity are poorly correlated. We conclude that patterns of diversity previously attributed to pre-Columbian processes may in part reflect post-Columbian admixture and the choice of K in STRUCTURE analyses. Accounting for admixture, the pattern of diversity is inconsistent with a north-south founder effect process, though the genetic similarities between Mesoamerican and Andean populations are consistent with rapid dispersal along the western coast of the Americas. Further, even setting aside the disruptive effects of European contact, gene-language congruence is unlikely to have ever existed at the geographic scale analyzed here.

A three-dimensional geometric morphometrics view of the cranial shape variation and population history in the New World

OBJECTIVES

Craniofacial variation in past and present Amerindians has been attributed to the effect of multiple founder events, or to one major migration followed by in situ differentiation and possibly recurrent contacts among Circum-Arctic groups. Our study aims to: (i) detect morphological differences that may indicate several migrations; (ii) test for the presence of genetic isolation; and (iii) test the correlation between shape data and competing settlement hypotheses by taking into account geography, chronology, climate effects, the presence of genetic isolation and recurrent gene flow.

METHODS

We analyzed a large sample of three-dimensional (3D) cranial surface scans (803 specimens) including past and modern groups from America and Australasia. Shape variation was investigated using geometric morphometrics. Differential external gene flow was evaluated by applying genetic concepts to morphometric data (Relethford-Blangero approach). Settlement hypotheses were tested using a matrix correlation approach (Mantel tests).

RESULTS

Our results highlight the strong dichotomy between Circum-Arctic and continental Amerindians as well as the impact of climate adaptation, and possibly recurrent gene flow in the Circum-Arctic area. There is also evidence for the impact of genetic isolation on phenetic variation in Baja California. Several settlement hypotheses are correlated with our data.

CONCLUSIONS

The three approaches used in this study highlight the importance of local processes especially in Baja California, and caution against the use of overly simplistic models when searching for the number of migration events. The results stress the complexity of the settlement of the Americas as well as the mosaic nature of the processes involved in this process. Am. J. Hum. Biol. 28:646-661, 2016. © 2016 Wiley Periodicals, Inc.

Early South Americans Cranial Morphological Variation and the Origin of American Biological Diversity

Recent South Americans have been described as presenting high regional cranial morphological diversity when compared to other regions of the world. This high diversity is in accordance with linguistic and some of the molecular data currently available for the continent, but the origin of this diversity has not been satisfactorily explained yet. Here we explore if this high morphological variation was already present among early groups in South America, in order to refine our knowledge about the timing and origins of the modern morphological diversity. Between-group (Fst estimates) and within-group variances (trace of within-group covariance matrix) of the only two early American population samples available to date (Lagoa Santa and Sabana de Bogotá) were estimated based on linear craniometric measurements and compared to modern human cranial series representing six regions of the world, including the Americas. The results show that early Americans present moderate within-group diversity, falling well within the range of modern human groups, despite representing almost three thousand years of human occupation. The between-group variance apportionment is very low between early Americans, but is high among recent South American groups, who show values similar to the ones observed on a global scale. Although limited to only two early South American series, these results suggest that the high morphological diversity of native South Americans was not present among the first human groups arriving in the continent and must have originated during the Middle Holocene, possibly due to the arrival of new morphological diversity coming from Asia during the Holocene.

Genetic Variations in the TP53 Pathway in Native Americans Strongly Suggest Adaptation to the High Altitudes of the Andes

The diversity of the five single nucleotide polymorphisms located in genes of the TP53 pathway (TP53, rs1042522; MDM2, rs2279744; MDM4, rs1563828; USP7, rs1529916; and LIF, rs929271) were studied in a total of 282 individuals belonging to Quechua, Aymara, Chivay, Cabanaconde, Yanke, Taquile, Amantani, Anapia, Uros, Guarani Ñandeva, and Guarani Kaiowá populations, characterized as Native American or as having a high level (> 90%) of Native American ancestry. In addition, published data pertaining to 100 persons from five other Native American populations (Surui, Karitiana, Maya, Pima, and Piapoco) were analyzed. The populations were classified as living in high altitude (≥ 2,500 m) or in lowlands (< 2,500 m). Our analyses revealed that alleles USP7-G, LIF-T, and MDM2-T showed significant evidence that they were selected for in relation to harsh environmental variables related to high altitudes. Our results show for the first time that alleles of classical TP53 network genes have been evolutionary co-opted for the successful human colonization of the Andes.

POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans

How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative "Paleoamerican" relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.

Ancient remains and the first peopling of the Americas: Reassessing the Hoyo Negro skull

OBJECTIVE

A noticeably well-preserved ∼12.500 years-old skeleton from the Hoyo Negro cave, Yucatán, México, was recently reported, along with its archaeological, genetic and skeletal characteristics. Based exclusively on an anatomical description of the skull (HN5/48), Chatters and colleagues stated that this specimen can be assigned to a set of ancient remains that differ from modern Native Americans, the so called "Paleoamericans". Here, we aim to further explore the morphological affinities of this specimen with a set of comparative cranial samples covering ancient and modern periods from Asia and the Americas.

METHODS

Images published in the original article were analyzed using geometric morphometrics methods. Shape variables were used to perform Principal Component and Discriminant analysis against the reference samples.

RESULTS

Even thought the Principal Component Analysis suggests that the Hoyo Negro skull falls in a subregion of the morphospace occupied by both "Paleoamericans" and some modern Native Americans, the Discriminant analyses suggest greater affinity with a modern Native American sample.

DISCUSSION

These results reinforce the idea that the original population that first occupied the New World carried high levels of within-group variation, which we have suggested previously on a synthetic model for the settlement of the Americas. Our results also highlight the importance of developing formal classificatory test before deriving settlement hypothesis purely based on macroscopic descriptions.

The cranial morphology of the Botocudo Indians, Brazil

The Botocudo Indians were hunter-gatherer groups that occupied the East-Central regions of Brazil decimated during the colonial period in the country. During the 19th century, craniometric studies suggested that the Botocudo resembled more the Paleoamerican population of Lagoa Santa than typical Native Americans groups. These results suggest that the Botocudo Indians might represent a population that retained the biological characteristics of early groups of the continent, remaining largely isolated from groups that gave origin to the modern Native South American variation. Moreover, recently, some of the Botocudo remains have been shown to have mitochondrial and autosomal DNA lineages currently found in Polynesian populations. Here, we explore the morphological affinities of Botocudo skulls within a worldwide context. Distinct multivariate analyses based on 32 craniometric variables show that 1) the two individuals with Polynesian DNA sequences have morphological characteristics that fall within the Polynesian and Botocudo variation, making their assignation as Native American specimens problematic, and 2) there are high morphological affinities between Botocudo, Early Americans, and the Polynesian series of Easter Island, which support the early observations that the Botocudo can be seen as retaining the Paleoamerican morphology, particularly when the neurocranium is considered. Although these results do not elucidate the origin of the Polynesian DNA lineages among the Botocudo, they support the hypothesis that the Botocudo represent a case of late survival of ancient Paleoamerican populations, retaining the morphological characteristics of ancestral Late Pleistocene populations from Asia.

Geographic Variation in Zygomaxillary Suture Morphology and its Use in Ancestry Estimation

Angled/curved zygomaxillary suture coding is widely employed in cranial assessments of ancestry. However, the efficacy of this method has not been extensively evaluated across diverse populations. In this study, zygomaxillary suture morphology was assessed on a total of 411 human crania from six populations (European, Native American, African, Asian, Arctic Circle, and Aboriginal Australian) using a novel 3D coordinate landmark method. Our results indicate a predominance of angled sutures among native peoples of the Arctic and North America (85-86%), a prevalence of curved sutures among Africans and Aboriginal Australians (77-81%), and essentially equal proportions of both configurations in Asians and Europeans (50-56%). Statistically, angled/curved coding generally discriminates poorly between groups, except when populations with antithetically high frequencies of the two configurations (e.g., African vs. Native American) are compared. Moreover, comparisons across previous studies reveal conflicting frequencies for many populations, further suggesting limited utility of this trait in ancestry estimation.

Differing evolutionary histories of the ACTN3*R577X polymorphism among the major human geographic groups

It has been proposed that the functional ACTN3*R577X polymorphism might have evolved due to selection in Eurasian human populations. To test this possibility we surveyed all available population-based data for this polymorphism and performed a comprehensive evolutionary analysis of its genetic diversity, in order to assess the action of adaptive and random mechanisms on its variation across human geographical distribution. The derived 577X allele increases in frequency with distance from Africa, reaching the highest frequencies on the American continent. Positive selection, detected by an extended haplotype homozygosisty test, was consistent only with the Eurasian data, but simulations with neutral models could not fully explain the results found in the American continent. It is possible that particularities of Native American population structure could be responsible for the observed allele frequencies, which would have resulted from a complex interaction between selective and random factors.

Determination of CYP2D6 *3, *4, and *10 frequency in women with breast cancer in São Luís, Brazil, and its association with prognostic factors and disease-free survival

The CYP2D6 enzyme is crucial for the metabolism of tamoxifen. The CYP2D6 gene is highly polymorphic, and individuals can be extensive, intermediate, or poor tamoxifen metabolizers. The aim of this study was to determine the frequencies of the CYP2D6 *3, *4, and *10 alleles in women with breast cancer who were treated with tamoxifen and analyze the association of enzyme activity with prognostic factors and disease-free survival. We observed a high frequency of CYP2D6 *10, with an allelic frequency of 0.14 (14.4%). The *3 allele was not present in the studied population, and *4 had an allelic frequency of 0.13 (13.8%). We conclude that patients with reduced CYP2D6 activity did not present worse tumor characteristics or decreased disease-free survival than women with normal enzyme activity, as the difference was not statistically significant. We also observed a high frequency of CYP2D6 *10, which had not been previously described in this specific population. This study is the first in north-northeastern Brazil that aimed to contribute to the knowledge of the Brazilian regional profile for CYP2D6 polymorphisms and their phenotypes. These findings add to the knowledge of the distribution of different polymorphic CYP2D6 alleles and the potential role of CYP2D6 genotyping in clinical practice prior to choosing therapeutic protocols.

Patterns of admixture and population structure in native populations of Northwest North America

The initial contact of European populations with indigenous populations of the Americas produced diverse admixture processes across North, Central, and South America. Recent studies have examined the genetic structure of indigenous populations of Latin America and the Caribbean and their admixed descendants, reporting on the genomic impact of the history of admixture with colonizing populations of European and African ancestry. However, relatively little genomic research has been conducted on admixture in indigenous North American populations. In this study, we analyze genomic data at 475,109 single-nucleotide polymorphisms sampled in indigenous peoples of the Pacific Northwest in British Columbia and Southeast Alaska, populations with a well-documented history of contact with European and Asian traders, fishermen, and contract laborers. We find that the indigenous populations of the Pacific Northwest have higher gene diversity than Latin American indigenous populations. Among the Pacific Northwest populations, interior groups provide more evidence for East Asian admixture, whereas coastal groups have higher levels of European admixture. In contrast with many Latin American indigenous populations, the variance of admixture is high in each of the Pacific Northwest indigenous populations, as expected for recent and ongoing admixture processes. The results reveal some similarities but notable differences between admixture patterns in the Pacific Northwest and those in Latin America, contributing to a more detailed understanding of the genomic consequences of European colonization events throughout the Americas.

We collaborated with six indigenous communities in British Columbia and Southeast Alaska to generate and analyze genome-wide data for over 100 individuals. We then combined this dataset with existing data from populations worldwide, performing an investigation of the genetic structure of indigenous populations of the Pacific Northwest both locally and in relation to continental and worldwide geographic scales. On a regional scale, we identified differences between coastal and interior populations that are likely due to differences both in pre- and post-European contact histories. On a continental scale, we identified differences in genetic structure between populations in the Pacific Northwest and Central and South America, reflecting both differences prior to European contact as well as different post-contact histories of admixture. This study is among the first to analyze genome-wide diversity among indigenous North American populations, and it provides a comparative framework for understanding the effects of European colonization on indigenous communities throughout the Americas.

Technical note: Quantification of neurocranial shape variation using the shortest paths connecting pairs of anatomical landmarks

Three-dimensional geometric morphometric techniques have been widely used in quantitative comparisons of craniofacial morphology in humans and nonhuman primates. However, few anatomical landmarks can actually be defined on the neurocranium. In this study, an alternative method is proposed for defining semi-landmarks on neurocranial surfaces for use in detailed analysis of cranial shape. Specifically, midsagittal, nuchal, and temporal lines were approximated using Bezier curves and equally spaced points along each of the curves were defined as semi-landmarks. The shortest paths connecting pairs of anatomical landmarks as well as semi-landmarks were then calculated in order to represent the surface morphology between landmarks using equally spaced points along the paths. To evaluate the efficacy of this method, the previously outlined technique was used in morphological analysis of sexual dimorphism in modern Japanese crania. The study sample comprised 22 specimens that were used to generate 110 anatomical semi-landmarks, which were used in geometric morphometric analysis. Although variations due to sexual dimorphism in human crania are very small, differences could be identified using the proposed landmark placement, which demonstrated the efficacy of the proposed method.

The first peopling of South America: new evidence from Y-chromosome haplogroup Q

Recent progress in the phylogenetic resolution of the Y-chromosome phylogeny permits the male demographic dynamics and migratory events that occurred in Central and Southern America after the initial human spread into the Americas to be investigated at the regional level. To delve further into this issue, we examined more than 400 Native American Y chromosomes (collected in the region ranging from Mexico to South America) belonging to haplogroup Q – virtually the only branch of the Y phylogeny observed in modern-day Amerindians of Central and South America – together with 27 from Mongolia and Kamchatka. Two main founding lineages, Q1a3a1a-M3 and Q1a3a1-L54(xM3), were detected along with novel sub-clades of younger age and more restricted geographic distributions. The first was also observed in Far East Asia while no Q1a3a1-L54(xM3) Y chromosome was found in Asia except the southern Siberian-specific sub-clade Q1a3a1c-L330. Our data not only confirm a southern Siberian origin of ancestral populations that gave rise to Paleo-Indians and the differentiation of both Native American Q founding lineages in Beringia, but support their concomitant arrival in Mesoamerica, where Mexico acted as recipient for the first wave of migration, followed by a rapid southward migration, along the Pacific coast, into the Andean region. Although Q1a3a1a-M3 and Q1a3a1-L54(xM3) display overlapping general distributions, they show different patterns of evolution in the Mexican plateau and the Andean area, which can be explained by local differentiations due to demographic events triggered by the introduction of agriculture and associated with the flourishing of the Great Empires.

Reconciling migration models to the Americas with the variation of North American native mitogenomes

In this study we evaluated migration models to the Americas by using the information contained in native mitochondrial genomes (mitogenomes) from North America. Molecular and phylogeographic analyses of B2a mitogenomes, which are absent in Eskimo-Aleut and northern Na-Dene speakers, revealed that this haplogroup arose in North America ∼11-13 ka from one of the founder Paleo-Indian B2 mitogenomes. In contrast, haplogroup A2a, which is typical of Eskimo-Aleuts and Na-Dene, but also present in the easternmost Siberian groups, originated only 4-7 ka in Alaska, led to the first Paleo-Eskimo settlement of northern Canada and Greenland, and contributed to the formation of the Na-Dene gene pool. However, mitogenomes also show that Amerindians from northern North America, without any distinction between Na-Dene and non-Na-Dene, were heavily affected by an additional and distinctive Beringian genetic input. In conclusion, most mtDNA variation (along the double-continent) stems from the first wave from Beringia, which followed the Pacific coastal route. This was accompanied or followed by a second inland migratory event, marked by haplogroups X2a and C4c, which affected all Amerindian groups of Northern North America. Much later, the ancestral A2a carriers spread from Alaska, undertaking both a westward migration to Asia and an eastward expansion into the circumpolar regions of Canada. Thus, the first American founders left the greatest genetic mark but the original maternal makeup of North American Natives was subsequently reshaped by additional streams of gene flow and local population dynamics, making a three-wave view too simplistic.

A bayesian approach to genome/linguistic relationships in native South Americans

The relationship between the evolution of genes and languages has been studied for over three decades. These studies rely on the assumption that languages, as many other cultural traits, evolve in a gene-like manner, accumulating heritable diversity through time and being subjected to evolutionary mechanisms of change. In the present work we used genetic data to evaluate South American linguistic classifications. We compared discordant models of language classifications to the current Native American genome-wide variation using realistic demographic models analyzed under an Approximate Bayesian Computation (ABC) framework. Data on 381 STRs spread along the autosomes were gathered from the literature for populations representing the five main South Amerindian linguistic groups: Andean, Arawakan, Chibchan-Paezan, Macro-Jê, and Tupí. The results indicated a higher posterior probability for the classification proposed by J.H. Greenberg in 1987, although L. Campbell's 1997 classification cannot be ruled out. Based on Greenberg's classification, it was possible to date the time of Tupí-Arawakan divergence (2.8 kya), and the time of emergence of the structure between present day major language groups in South America (3.1 kya).

Identification of Polynesian mtDNA haplogroups in remains of Botocudo Amerindians from Brazil

There is a consensus that modern humans arrived in the Americas 15,000-20,000 y ago during the Late Pleistocene, most probably from northeast Asia through Beringia. However, there is still debate about the time of entry and number of migratory waves, including apparent inconsistencies between genetic and morphological data on Paleoamericans. Here we report the identification of mitochondrial sequences belonging to haplogroups characteristic of Polynesians in DNA extracted from ancient skulls of the now extinct Botocudo Indians from Brazil. The identification of these two Polynesian haplogroups was confirmed in independent replications in Brazil and Denmark, ensuring reliability of the data. Parallel analysis of 12 other Botocudo individuals yielded only the well-known Amerindian mtDNA haplogroup C1. Potential scenarios to try to help understand these results are presented and discussed. The findings of this study may be relevant for the understanding of the pre-Columbian and/or post-Columbian peopling of the Americas.