Gene geography of South America: testing models of population displacement based on archeological evidence

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.

Population genetic structure of traditional populations in the Peruvian Central Andes and implications for South American population history

Molecular-based characterizations of Andean peoples are traditionally conducted in the service of elucidating continent-level evolutionary processes in South America. Consequently, genetic variation among "western" Andean populations is often represented in relation to variation among "eastern" 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 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 data from the mtDNA first hypervariable region and Y-chromosome short tandem repeats among 17 newly sampled populations and 15 published samples. Using this geographically comprehensive data set, we first reassessed the currently accepted pattern of western versus eastern population genetic structure, which our results ultimately reject: mtDNA population diversities were lower, rather than higher, within Andean versus eastern populations, and only highland Y-chromosomes exhibited significantly higher within-population diversities compared with eastern groups. Multiple populations, including several highland samples, exhibited low genetic diversities for both genetic systems. Second, we explored whether the implementation of Inca state and Spanish colonial policies starting at about ad 1400 could have substantially restructured population genetic variation and consequently constitute a primary explanation for the extant pattern of population diversity in the Peruvian Central Andes. Our results suggest that Peruvian Central Andean population structure cannot be parsimoniously explained as the sole outcome of combined Inca and Spanish policies on the region's population demography: highland populations differed from coastal and lowland populations in mtDNA genetic structure only; highland groups also showed strong evidence of female-biased gene flow and/or effective sizes relative to other Peruvian ecozones. Taken together, these findings indicate that population genetic structure in the Peruvian Central Andes is considerably more complex than previously reported and that characterizations of and explanations for genetic variation may be best pursued within more localized regions and defined time periods.

Between Andes and Amazon: the genetic profile of the Arawak-speaking Yanesha

The Yanesha are a Peruvian population who inhabit an environment transitional between the Andes and Amazonia. They present cultural traits characteristic of both regions, including in the language they speak: Yanesha belongs to the Arawak language family (which very likely originated in the Amazon/Orinoco lowlands), but has been strongly influenced by Quechua, the most widespread language family of the Andes. Given their location and cultural make-up, the Yanesha make for an ideal case study for investigating language and population dynamics across the Andes-Amazonia divide. In this study, we analyze data from high and mid-altitude Yanesha villages, both Y chromosome (17 STRs and 16 SNPs diagnostic for assigning haplogroups) and mtDNA data (control region sequences and 3 SNPs and one INDEL diagnostic for assigning haplogroups). We uncover sex-biased genetic trends that probably arose in different stages: first, a male-biased gene flow from Andean regions, genetically consistent with highland Quechua-speakers and probably dating back to Inca expansion; and second, traces of European contact consistent with Y chromosome lineages from Italy and Tyrol, in line with historically documented migrations. Most research in the history, archaeology and linguistics of South America has long been characterized by perceptions of a sharp divide between the Andes and Amazonia; our results serve as a clear case-study confirming demographic flows across that 'divide'.

Microevolutionary processes due to landscape features in the province of Jujuy (Argentina)

OBJECTIVES

We seek to evaluate the influence of a diverse and rugged physical environment on the genetic background of human populations.

METHODS

We analyzed eight polymorphic Alu insertions in 226 individuals from Jujuy province (Argentina), which is composed of several regions with well-defined geographical features and marked contrasts between them associated with differences in altitude (range: 700-3300 m). This regional division was used to assess the spatial variation of the Alu diversity.

RESULTS

Deviations from Hardy-Weinberg Equilibrium expectations resulting from heterozygous deficit were found for FXIIIB and PV92 in the highest subpopulations. Several Alu elements showed genetic heterogeneity between the highest region (La Puna) and the lowest regions (Valle and Selva). Similarly, a decreasing trend of the average heterozygosity according to altitude was found. Both the centroid method and the admixture analysis unveiled a gene flow above the average in lowland populations, indicating a higher proportion of foreign genes introduced by immigrants of European and African ancestry. Furthermore, several Alu frequency clines fitting the orientation of the altitude gradient were detected.

CONCLUSIONS

Our study reveals a spatial patterning of the Alu diversity in Jujuy, most likely determined by disparities in landscape and environmental features between the different subregions. Differences in the physical environment would have drastically reduced the homogenizing effects of the gene flow and would have promoted genetic drift episodes in the highest subpopulations. Microevolutionary processes detected in Jujuy have played an important role in the shaping of the gene pool of the populations from this sub-Andean zone from Argentina.

The late Pleistocene colonization of South America: an interdisciplinary perspective

In this article, we briefly review scenarios for the first peopling of the New World, including the Clovis First/Single Origin, Tripartite, and Dual Migration models. We then discuss bioanthropological, molecular genetic, archaeological and biogeographic evidence for the peopling of the continent. To conclude, we draw on different lines of evidence to make inferences concerning the timing, direction, and type of early human dispersion in South America.

The β-globin gene cluster distribution revisited—Patterns in Native American populations

New frequencies for the beta-globin gene cluster haplotypes are presented for the Aché (N = 82 individuals), Guarani (N = 76), and Kaingang (N = 54), three Native South American populations that live in an area between parallels 20 degrees S and 30 degrees S not covered by previous studies at this locus. The haplotype frequencies obtained for the three populations are within the interval observed for 28 other Native American populations. The Aché show much less haplotypes (five) than the other two populations (9-10), the haplotype prevalences being more similar to those of the Guarani than to the Kaingang. The Native American total heterozygosity was about half (0.41) that obtained for the African populations (0.71), but was not much different from those obtained for other continents. A geographical pattern was disclosed in South America by mapping the frequencies of the most common haplotype (haplotype 2), and by means of spatial correlation analysis. The analysis of molecular variance (AMOVA) and pairwise F(ST) data suggest three distinct sectors for the genetic landscape of Native South America: the Andes, the Center/Southeast region, and the Amazon.

Influence of cranial deformation on facial morphology among prehistoric South Central Andean populations

Calculating biodistances among South American populations using cranial measurements is often hindered, as many available skeletal collections exhibit deformation. Acknowledging vault modifications, researchers have sought measurements in other regions which are unaffected by deformation. In the 1970s, a set of 10 "relatively" unaffected facial measurements was identified in Argentinean crania that later became the basis of numerous South American biodistance studies. These measurements include: minimum frontal breadth, bizygomatic breadth, orbit height, orbit breadth, palate breath, palate length, upper facial height, basion-prosthion length, nasal height, and nasal breadth. Palate length was excluded from the present analysis due to considerable measurement error. The suitability of these measurements in populations other than Argentineans has not been rigorously tested. Using a sample of 350 prehistoric crania from the Museo Arqueológico San Miguel de Azapa (MASMA, Arica, Chile), this project tested the hypothesis that these measurements are unaffected by either annular or tabular deformation. Results obtained from MANOVA analysis indicate this hypothesis cannot be fully supported. Among males, only 3 of the 9 measurements are unaffected by either form of deformation (palate breadth, basion-prosthion length, and nasal breadth), while analysis of females indicates that 4 of the 9 measurements remain unaltered (minimum frontal breadth, orbit breadth, basion-prosthion length, and nasal breadth). Additionally, analogous to the vault, facial measurements display patterns consistent with the deformation applied. Two implications can be drawn from this research: 1) previous studies using these measurements must be interpreted cautiously, and 2) researchers using these measurements must explicitly test their suitability in each population.

Microevolution in prehistoric Andean populations: Chronologic mtDNA variation in the desert valleys of northern Chile

Archeological evidence suggests that the iconographic and technological developments that took place in the highlands around Lake Titicaca in the Central Andean region had an influence on the cultural elaborations of the human groups in the valleys and the Pacific coast of northern Chile. In a previous communication, we were able to show, by means of a distance analysis, that a craniofacial differentiation accompanied the process of cultural evolution in the valleys (Rothhammer and Santoro [2001] Lat. Am. Antiq. 12:59-66). Recently, numerous South Amerindian mtDNA studies were published, and more accurate molecular techniques to study ancient mtDNA are available. In view of these recent developments, we decided 1) to study chronological changes of ancient mtDNA haplogroup frequencies in the nearby Lluta, Azapa, and Camarones Valleys, 2) to identify microevolutionary forces responsible for such changes, and 3) to compare ancient mtDNA haplogroup frequencies with previous data in order to validate craniometrical results and to reconstruct the biological history of the prehistoric valley groups in the context of their interaction with culturally more developed highland populations. From a total of 97 samples from 83 individuals, 68 samples (61 individuals) yielded amplifications for the fragments that harbor classical mtDNA markers. The haplogroup distribution among the total sample was as follows: 26.2%, haplogroup A; 34.4%, haplogroup B; 14.8%, haplogroup C; 3.3%, haplogroup D; and 21.3%, other haplogroups. Haplogroup B tended to increase, and haplogroup A to decrease during a 3,900-year time interval. The sequence data are congruent with the haplogroup analysis. In fact, the sequencing of hypervariable region I of 30 prehistoric individuals revealed 43 polymorphic sites. Sequence alignment and subsequent phylogenetic tree construction showed two major clusters associated with the most common restriction haplogroups. Individuals belonging to haplogroups C and D tended to cluster together with nonclassical lineages.

Nonmetric cranial trait variation and prehistoric biocultural change in the Azapa Valley, Chile

Historically, interpretations of both biological and cultural change within the prehistoric Azapa Valley, northern Chile, have cited large-scale population movements, with replacement from complex societies located in the adjacent highlands to the east. Biological estimates of this change have traditionally relied upon biodistance estimates, using craniofacial measures of both deformed and nondeformed skulls. In order to evaluate whether large-scale prehistoric migrations occurred in the Azapa Valley, we examine biodistance results from nonmetric cranial traits for eight mortuary samples that represent all time periods of prehistoric occupation of the valley. None of the mean measures of divergences (MMD) among mortuary samples examined by this study were significant. These results suggest biological continuity in the Azapa Valley during 5,000 years of prehistory, with nonsignificant gene flow during the late Middle Horizon (AD 750-1100) and Late Intermediate (AD 1100-1476) periods. Biodistance results also suggest endogamy within coastal and inland populations. The broader implications of these results are discussed.

Dental relatedness corresponding to mortuary patterning at Huaca Loro, Peru

Within and between tombs at the 1,000-year-old site of Huaca Loro on north coastal Peru, interment characteristics vary to an intriguing degree. Following and elaborating upon prior intracemetery studies, biological relatedness among associated burial groupings was assessed using 23 dental characters (assuming familial allele segregation) for 29 individuals. Biological patterning was based on multivariate distance between individuals using all traits, rather than the previously widespread reliance upon univariate comparison of each trait separately within samples. This multivariate approach did seem more informative. Statistically significant variation of biological similarities and dissimilarities corresponded to spatial groupings and also to various specific archaeological indications of the cohesiveness, or lack thereof, of interment pattern. The partition of biological distances among tombs at Huaca Loro supports the archaeological evidence that the tombs represent a planned elite cemetery.

Origin and evolutionary relationships of native Andean populations

This paper represents an effort to explore the origin and the evolutionary relationships of native Andean populations using a multidisciplinary approach. Archeological and linguistic evidence is briefly reviewed. A genetic distance analysis among major linguistic groupings and among Andean and Amazonian native populations, together with information obtained from archaeological and linguistic sources was used to generate a migration model. It is suggested that in the late Pleistocene a group of nomadic hunters entered South America through the Isthmus of Panama and split afterwards into two groups, one moving southward into the central and south Andean areas and after crossing the Colombian, Equador and Peruvian highlands to people northwestern Argentina, the open park country of east Brazil and the Argentine Pampas. The second group migrated eastwards into Venezuela and Guyana and later southward, peopling the Brazilian Amazon. Following available waterways the Amazonian Indians expanded east and west arriving probably at the eastern slopes of the Andes some 3,500 years ago. It is hypothesized that present day Andean natives are descendants of the Amazonian groups that migrated eastwards.

Mitochondrial DNA polymorphisms in Chilean aboriginal populations: implications for the peopling of the southern cone of the continent

The mitochondrial DNAs (mtDNAs) from individuals belonging to three Chilean tribes, the Mapuche, the Pehuenche, and the Yaghan, were studied both by RFLP analysis and D-loop (control region) sequencing. RFLP analysis showed that 3 individuals (1.3%) belonged to haplogroup A, 19 (8%) to haplogroup B, 102 (43%) to haplogroup C, and 113 (47.7%) to haplogroup D. Among the 73 individuals analyzed by D-loop sequencing, we observed 37 different haplotypes defined by 52 polymorphic sites. Joint analysis of data obtained by RFLP and sequencing methods demonstrated that, regardless of the method of analysis, the mtDNA haplotypes of these three contemporary South American aborigine groups clustered into four main haplogroups, in a way similar to those previously described for other Amerindians. These results further revealed the absence of haplogroup A in both the Mapuche and Yaghan as well as the absence of haplogroup B in the Yaghan. These results suggest that the people of Tierra del Fuego are related to tribes from south-central South America.

Genetic structure of Quechua-speakers of the Central Andes and geographic patterns of gene frequencies in South Amerindian populations

A sample of 141 Quechua-speaking individuals of the population of Tayacaja, in the Peruvian Central Andes, was typed for the following 16 genetic systems: ABO, Rh, MNSs, P, Duffy, AcP1, EsD, GLOI, PGM1, AK, 6-PGD, Hp, Gc, Pi, C3, and Bf. The genetic structure of the population was analyzed in relation to the allele frequencies available for other South Amerindian populations, using a combination of multivariate and multivariable techniques. Spatial autocorrelation analysis was performed independently for 13 alleles to identify patterns of gene flow in South America as a whole and in more specific geographic regions. We found a longitudinal cline for the AcP1*a and EsD*1 alleles which we interpreted as the result of an ancient longitudinal expansion of a putative ancestral population of modern Amerindians. Monmonnier's algorithm, used to identify areas of sharp genetic discontinuity, suggested a clear east-west differentiation of native South American populations, which was confirmed by analysis of the distribution of genetic distances. We suggest that this pattern of genetic structures is the consequence of the independent peopling of western and eastern South America or to low levels of gene flow between these regions, related to different environmental and demographic histories.

Gradients of HLA diversity in South American Indians

Information concerning the HLA-A and -B loci was considered in relation to 3796 Amerindians living in 39 places in South America, data related to HLA-C being based on a smaller subset of 2989 persons distributed among 33 localities. Synthetic gene frequency maps were then constructed using principal-components analysis. Clearly significant longitudinal (principal component 1) and latitudinal (principal components 1, 2, and 3) clines were observed, most probably indicating ancient migration routes.

Mitochondrial DNA polymorphism in three Brazilian Indian tribes

The first 360 base pairs of the mitochondrial DNA (mtDNA) major noncoding region from 82 individuals affiliated with the Brazilian Xavante, Zoró and Gavião tribes were sequenced. A total of 14 different lineages were observed, the largest number (8) being found among the Zoró. The latter share five lineages with the Gavião (who are their neighbors and are culturally similar to them), but only one with the Xavante. The lineages can be grouped into four clusters, previously identified by other authors. The 9 base pair deletion characteristic of Asian and Pacific populations occurs in 32% of the individuals, whose mtDNA was classified in five lineages, all grouped in one of the four clusters. Nucleotide diversity, as evaluated by three indices, are not much different from those observed in Indians from Central and North America, despite the fact that the Xavante consistently show lower numbers. These results do not confirm previous generalizations about the genetic diversity of Amerindians, and the need for additional studies in this system is stressed. © 1996 Wiley-Liss, Inc.

Further blood genetic studies on Amazonian diversity--data from four Indian groups

Information related to 31 protein genetic systems was obtained for 307 individuals affiliated with the Cinta Larga, Karitiana, Surui and Kararaô Indians of northern Brazil. In terms of genetic distances the Cinta Larga showed more similarities with the Karitiana (both are Tupi-speaking tribes), while at a more distant level the Surui clustered with the Kararaô. The latter, a Cayapo subgroup, showed a completely different genetic constitution from the other subgroups of this same tribe. Both the Kararaô and Karitiana are small, remnant populations, and their gene pools have presumably been severely affected by random and founder effects. These results were incorporated with those of 25 other Amazonian Indian tribes, and analysis by two multivariate techniques confirmed a previously observed geographical dichotomy, suggesting either that the Amazon river constitutes a barrier to north-south gene flow or that latitudinally different past migrations entered the region from the west.