Discrepancy between Cranial and DNA Data of Early Americans: Implications for American Peopling

Currently, one of the major debates about the American peopling focuses on the number of populations that originated the biological diversity found in the continent during the Holocene. The studies of craniometric variation in American human remains dating from that period have shown morphological differences between the earliest settlers of the continent and some of the later Amerindian populations. This led some investigators to suggest that these groups—known as Paleomericans and Amerindians respectively—may have arisen from two biologically different populations. On the other hand, most DNA studies performed over extant and ancient populations suggest a single migration of a population from Northeast Asia. Comparing craniometric and mtDNA data of diachronic samples from East Central Argentina dated from 8,000 to 400 years BP, we show here that even when the oldest individuals display traits attributable to Paleoamerican crania, they present the same mtDNA haplogroups as later populations with Amerindian morphology. A possible explanation for these results could be that the craniofacial differentiation was a local phenomenon resulting from random (i.e. genetic drift) and non-random factors (e.g. selection and plasticity). Local processes of morphological differentiation in America are a probable scenario if we take into consideration the rapid peopling and the great ecological diversity of this continent; nevertheless we will discuss alternative explanations as well.     

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.     

Craniometric Relationships of Plains Populations: Historical and Evolutionary Implications

Abstract

Large skeletal samples from cemeteries in the Northern Plains near Mobridge, South Dakota have made possible the accurate determination of craniometric relationships between populations ancestoral to the historic Arikara. There is considerable change throughout the approximately 200 years represented, due primarily to gene flow from adjacent Siouan speaking groups. Arikara crania from the Northern Plains are seen to be morphologically similar to earlier crania further south, in particular St. Helena materials in northeastern Nebraska. This offers Support for the archaeological hypothesis that Coalescent Tradition cultures grew out of the Central Plains Tradition. Early crania from the Northern Plains are markedly different from those in the Central Plains and more similar to historic Mandan. The craniometric evidence argues for biological continuity rather than replacement in the Plains area.     

Missing data in craniometrics: a simulation study

Craniometric measurements represent a useful tool for studying the differentiation of mammal populations. However, the fragility of skulls often leads to incomplete data matrices. Damaged specimens or incomplete sets of measurements are usually discarded prior to statistical analysis. We assessed the performance of two strategies that avoid elimination of observations: (1) pairwise deletion of missing cells, and (2) estimation of missing data using available measurements. The effect of these distinct approaches on the computation of inter-individual distances and population differentiation analyses were evaluated using craniometric measurements obtained from insular populations of deer micePeromyscus maniculatus (Wagner, 1845). In our simulations, Euclidean distances were greatly altered by pairwise deletion, whereas Gower’s distance coefficient corrected for missing data provided accurate results. Among the different estimation methods compared in this paper, the regression-based approximations weighted by coefficients of determination (r ²) outperformed the competing approaches. We further show that incomplete sets of craniometric measurements can be used to compute distance matrices, provided that an appropriate coefficient is selected. However, the application of estimation procedures provides a flexible approach that allows researchers to analyse incomplete data sets.     

What constitutes a population for the plant parasitic nematode Globodera pallida in its native area (Peru)?

Although numerous species are distributed in discrete populations easily recognised by geographical barriers, continuous populations are a common feature of plants or marine organisms. This is particularly true for soil organisms as their habitat is continuous and their range cannot easily be assessed as they are buried below ground. In the case of organisms for which standard methods such as Capture/Mark/Recapture cannot be used, population genetics provide a straightforward approach to delimitate populations. In this study, we have pursued this topic with a soil-dwelling nematode (Globodera pallida), which parasitises potato roots and is indigenous to South America. Potential barriers to gene flow were identified using the analysis of the F(ST)/(1-F(ST)) ratio against geographical distance and spatial autocorrelation combined with model-based clustering algorithm. Inside regions, neither genetic differentiation nor isolation by distance (IBD) occur among fields less than 50 km distant. We hypothesise that the large amount of gene flow revealed by the absence of genetic structure of this organism could be due to large passive dispersion inside an agronomic area where G. pallida has a continuous distribution and is found at high density. The first evidence of genetic differentiation appeared when a field was separated from others by an area free of farms (where G. pallida is absent or rare). Among regions, a high genetic structure coupled with an IBD pattern occurs as the consequences of the limitations of passive dispersal across deep valleys or high mountains. To our knowledge, this is the first study identifying the spatial limit of a population for a plant nematode parasite.     

Genetic differentiation in South Amerindians is related to environmental and cultural diversity: evidence from the Y chromosome

The geographic structure of Y-chromosome variability has been analyzed in native populations of South America, through use of the high-frequency Native American haplogroup defined by the DYS199-T allele and six Y-chromosome-linked microsatellites (DYS19, DYS389A, DYS389B, DYS390, DYS391, and DYS393), analyzed in 236 individuals. The following pattern of within- and among-population variability emerges from the analysis of microsatellite data: (1) the Andean populations exhibit significantly higher levels of within-population variability than do the eastern populations of South America; (2) the spatial-autocorrelation analysis suggests a significant geographic structure of Y-chromosome genetic variability in South America, although a typical evolutionary pattern could not be categorically identified; and (3) genetic-distance analyses and the analysis of molecular variance suggest greater homogeneity between Andean populations than between non-Andean ones. On the basis of these results, we propose a model for the evolution of the male lineages of South Amerindians that involves differential patterns of genetic drift and gene flow. In the western part of the continent, which is associated with the Andean area, populations have relatively large effective sizes and gene-flow levels among them, which has created a trend toward homogenization of the gene pool. On the other hand, eastern populations-settled in the Amazonian region, the central Brazilian plateau, and the Chaco region-have exhibited higher rates of genetic drift and lower levels of gene flow, with a resulting trend toward genetic differentiation. This model is consistent with the linguistic and cultural diversity of South Amerindians, the environmental heterogeneity of the continent, and the available paleoecological data.     

East-West cranial differentiation in pre-Columbian populations from Central and North America

In a recent study we found that crania from South Amerindian populations on each side of the Andes differ significantly in terms of craniofacial shape. Western populations formed one morphological group, distributed continuously over 14,000km from the Fuegian archipelago (southern Chile) to the Zulia region (northwestern Venezuela). Easterners formed another group, distributed from the Atlantic Coast up to the eastern foothills of the Andes. This differentiation is further supported by several genetic studies, and indirectly by ecological and archaeological studies. Some authors suggest that this dual biological pattern is consistent with differential rates of gene flow and genetic drift operating on both sides of the Cordillera due to historical reasons. Here we show that such East-West patterning is also observable in North America. We suggest that the "ecological zones model" proposed by Dixon, explaining the spread of the early Americans along a Pacific dispersal corridor, combined with the evolution of different population dynamics in both regions, is the most parsimonious mechanism to explain the observed patterns of within- and between-group craniofacial variability.     

Global Genetic Differentiation in a Cosmopolitan Pest of Stored Beans: Effects of Geography,Host-Plant Usage and Anthropogenic Factors

Genetic differentiation can be promoted allopatrically by geographic isolation of populations due to limited dispersal ability and diversification over time or sympatrically through, for example, host-race formation. In crop pests, the trading of crops across the world can lead to intermixing of genetically distinct pest populations. However, our understanding of the importance of allopatric and sympatric genetic differentiation in the face of anthropogenic genetic intermixing is limited. Here, we examined global sequence variation in two mitochondrial and one nuclear genes in the seed beetle Callosobruchus maculatus that uses different legumes as hosts. We analyzed 180 samples from 42 populations of this stored bean pest from tropical and subtropical continents and archipelagos: Africa, the Middle East, South and Southeast Asia, Oceania and South America. For the mitochondrial genes, there was weak but significant genetic differentiation across continents/archipelagos. Further, we found pronounced differentiation among subregions within continents/archipelagos both globally and within Africa but not within Asia. We suggest that multiple introductions into Asia and subsequent intermixing within Asia have generated this pattern. The isolation by distance hypothesis was supported globally (with or without continents controlled) but not when host species was restricted to cowpeas Vigna unguiculata, the ancestral host of C. maculatus. We also document significant among-host differentiation both globally and within Asia, but not within Africa. We failed to reject a scenario of a constant population size in the recent past combined with selective neutrality for the mitochondrial genes. We conclude that mitochondrial DNA differentiation is primarily due to geographic isolation within Africa and to multiple invasions by different alleles, followed by host shifts, within Asia. The weak inter-continental differentiation is most likely due to frequent inter-continental gene flow mediated by human crop trade.     

South Amerindian craniofacial morphology: diversity and implications for Amerindian evolution

The most compelling models concerning the peopling of the Americas consider that modern Amerindians share a common biological pattern, showing affinities with populations of the Asian Northeast. The aim of the present study was to assess the degree of variation of craniofacial morphology of South American Amerindians in a worldwide context. Forty-three linear variables were analyzed on crania derived from American, Asian, Australo-Melanesian, European, South-Saharan African, and Polynesian regions. South America was represented by seven Amerindian samples. In order to understand morphologic diversity among Amerindians of South America, variation was estimated using regions and local populations as units of analysis. Variances and F(ST) values were calculated for each unit, respectively. Both analyses indicated that morphologic variation in Southern Amerindians is extremely high: an F(ST) of 0.01531 was obtained for Southern Amerindians, and values from 0.0371-0.1205 for other world regions. Some aspects linked to the time and mode of the peopling of the Americas and various microevolutionary processes undergone by Amerindians are discussed. Some of the alternatives proposed to explain this high variation include: a greater antiquity of the peopling than what is mostly accepted, a peopling by several highly differentiated waves, an important effect of genetic drift, and gene flow with Paleoamericans. A combination of some of these alternatives explains at least some of the variation.     

Biogeochemical and craniometric investigation of dietary ecology, niche separation, and taxonomy of Plio-Pleistocene cercopithecoids from the Makapansgat Limeworks

Three sympatric fossil cercopithecoid genera (Cercopithecoides, Parapapio, and Theropithecus) occur in Members 3 and 4 at the Makapansgat Limeworks hominin locality, South Africa, and their presence in a single ecosystem suggest a certain degree of ecological and/or dietary differentiation between taxa. Here, we explore the extent of dietary niche separation amongst these taxa using stable isotope (13C/12C, 18O/16O) and trace-element (Sr, Ba, Ca) analyses of fossil tooth enamel. In particular we searched for evidence of subtle niche separation between the more closely related, morphologically similar taxa of the genus Parapapio, as uncertainties exist around their taxonomy and taxonomic identification. Given these uncertainties, craniometric analyses were also performed to ground the dietary interpretations in a morphological context. The results found no clear taxonomic signal in the craniometric data for the Parapapio sample, and further indicate that this sample was no more variable morphologically than a single, geographically circumscribed, extant chacma baboon sample. In contrast, two overlapping dietary ecologies were found within this same Makapansgat Parapapio sample. Additionally, two widely differing dietary ecologies were found within the Cercopithecoides williamsi sample, while results for Theropithecus darti indicate a predominantly C4 diet. Hence, although biogeochemical dietary indicators point towards distinct dietary ecologies within and between fossil genera at Makapansgat, within the genus Parapapio disjunctions exist between the dietary categories and the taxonomic assignment of specimens.     

Amerindians show no association of PC-1 gene Gln121 allele and obesity: a thrifty gene population genetics

PC-1 Gln121 gene is a risk factor for type 2 diabetes, obesity and insulin resistance in European/American Caucasoids and Orientals. We have aimed to correlate for the first time this gene in Amerindians with obesity and their corresponding individuals genotypes with obesity in order to establish preventive medicine programs for this population and also studying the evolution of gene frequencies in world populations. Central obesity was diagnosed by waist circumference perimeter and food intake independent HDL-cholesterol plasma levels were measured. HLA genes were determined in order to more objectively ascertain participants Amerindians origin. 321 Amerindian blood donors who were healthy according to the blood doning parameters were studied. No association was found between PC-1 Gln121 variant and obesity. Significant HDL-cholesterol lower values were found in the PC-1 Lys121 bearing gene individuals versus PC-1 Gln121 bearing gene ones (45.1 ± 12.7 vs. 48.7 ± 15.2 mg/dl, p < 0.05). Population analyses showed a world geographical gradient in the PC-1 Gln121 allele frequency: around 9% in Orientals, 15% in European Caucasoids and 76% in Negroids. The conclusions are: (1) No association of PC-1 Gln121 gene is found with obesity in Amerindians when association is well established in Europeans. (2) PC-1 Gln121 gene is associated to higher levels of HDL-cholesterol than the alternative PC-1 Lys121 allele. This may be specific for Amerindians. (3) Amerindians have an intermediate frequency of this possible PC-1 Gln121 thrifty gene when compared with Negroid African Americans (78.5%) or Han Chinese (7.5%, p < 0.0001). Historical details of African and other groups may support the hypothesis that PC-1 Gln121 is indeed a thrifty gene.     

Rivers influence the population genetic structure of bonobos (Pan paniscus)

Bonobos are large, highly mobile primates living in the relatively undisturbed, contiguous forest south of the Congo River. Accordingly, gene flow among populations is assumed to be extensive, but may be impeded by large, impassable rivers. We examined mitochondrial DNA control region sequence variation in individuals from five distinct localities separated by rivers in order to estimate relative levels of genetic diversity and assess the extent and pattern of population genetic structure in the bonobo. Diversity estimates for the bonobo exceed those for humans, but are less than those found for the chimpanzee. All regions sampled are significantly differentiated from one another, according to genetic distances estimated as pairwise FSTs, with the greatest differentiation existing between region East and each of the two Northern populations (N and NE) and the least differentiation between regions Central and South. The distribution of nucleotide diversity shows a clear signal of population structure, with some 30% of the variance occurring among geographical regions. However, a geographical patterning of the population structure is not obvious. Namely, mitochondrial haplotypes were shared among all regions excepting the most eastern locality and the phylogenetic analysis revealed a tree in which haplotypes were intermixed with little regard to geographical origin, with the notable exception of the close relationships among the haplotypes found in the east. Nonetheless, genetic distances correlated with geographical distances when the intervening distances were measured around rivers presenting effective current-day barriers, but not when straight-line distances were used, suggesting that rivers are indeed a hindrance to gene flow in this species.     

Population structure and genetic diversity of Ammodytes personatus in the Northwestern Pacific revealed by microsatellites markers

Genetic diversity and population structure of Ammodytes personatus in the Northwestern Pacific were investigated for 16 collections using eight highly variable microsatellite loci. Microsatellite analyses gave strong support for the presence of two distinct groups of genotypes. Pleistocene glaciations can cause significant geographical differentiation in A. personatus populations. However, microsatellite data cannot confirm completely reproductive isolation between north group and south group. About half of comparison values within the first and second cluster were significant after sequential Bonferroni corrections. Routine oceanic currents associated with strong wind condition may provide an excellent chance for connectivity of among populations within clusters. However, gene flow can be restricted by marine gyres due to complex geographical characteristic.     

Population structure in the South American tern Sterna hirundinacea in the South Atlantic: two populations with distinct breeding phenologies

The South American tern Sterna hirundinacea is a migratory species for which dispersal, site fidelity and migratory routes are largely unknown. Here, we used five microsatellite loci and 799 bp partial mitochondrial DNA sequences (Cytochrome b and ND2) to investigate the genetic structure of South American terns from the South Atlantic Ocean (Brazilian and Patagonian colonies). Brazilian and Patagonian colonies have two distinct breeding phenologies (austral winter and austral summer, respectively) and are under the influence of different oceanographic features (e.g. Brazil and Falklands/Malvinas ocean currents, respectively), that may promote genetic isolation between populations. Results show that the Atlantic populations are not completely panmictic, nevertheless, contrary to our expectations, low levels of genetic structure were detected between Brazilian and Patagonian colonies. Such low differentiation (despite temporal isolation of the colonies) could be explained by demographic history of these populations coupled with ongoing levels of gene flow. Interestingly, estimations of gene flow through Maximum likelihood and Bayesian approaches has indicated asymmetrical long term and contemporary gene flow from Brazilian to Patagonian colonies, approaching a source–sink metapopulation dynamic. Genetic analysis of other South American tern populations (especially those from the Pacific coast and Falklands–Malvinas Islands) and other seabird species showing similar geographical distribution (e.g. royal tern Thalasseus maximus), are fundamental in gaining a better understanding of the main processes involved in the diversification of seabirds in the southern hemisphere.     

Gene flow and population subdivision in a pantropical plant with sea-drifted seeds Hibiscus tiliaceus and its allied species: evidence from microsatellite analyses

The genetic differentiation and structure of Hibiscus tiliaceus , a pantropical plant with sea-drifted seeds, and four allied species were studied using six microsatellite markers. A low level of genetic differentiation was observed among H. tiliaceus populations in the Pacific and Indian Ocean regions, similar to the results of a previous chloroplast DNA (cpDNA) study. Frequent gene flow by long-distance seed dispersal is responsible for species integration of H. tiliaceus in the wide distribution range. On the other hand, highly differentiated populations of H. tiliaceus were detected in West Africa, as well as of Hibiscus pernambucensis in southern Brazil. In the former populations, the African continent may be a geographical barrier that prevents gene flow by sea-drifted seeds. In the latter populations, although there are no known land barriers, the bifurcating South Equatorial Current at the north-eastern horn of Brazil can be a potential barrier to gene flow and may promote the genetic differentiation of these populations. Our results also suggest clear species segregation between H. tiliaceus and H. pernambucensis , which confirms the introgression scenario between these two species that was suggested by a previous cpDNA study. Our results also provide good evidence for recent transatlantic long-distance seed dispersal by sea current. Despite the distinct geographical structure observed in the cpDNA haplotypes, a low level of genetic differentiation was found between Pacific and Atlantic populations of H. pernambucensis , which could be caused by transisthmian gene flow.     

Genetic variation of cassava (Manihot esculenta Crantz) cultivated by Chibchan Amerindians of Costa Rica

This study focuses on the genetic diversity of the cassava (Manihot esculenta Crantz) grown by the Chibchan Amerindians of Costa Rica. The authors collected cassava in various locations within two Amerindian Reserves: Talamanca, inhabited by Cabecares and Bribris, and Coto Brus, inhabited by Guaymi. Through the use of isozyme electrophoretic techniques we found variation for six out of nine systems analyzed, namely DIA, EST, IDH, MDH, PGI, and SKD. No variation was found in ADH, PGD, and PGM systems. We analyzed the distribution of variation within and between the reserves, and found most of the variation occurred within reserves (Gst = 0.1084). Only low levels of genetic differentiation were found between reserves (Nei’s genetic distance = 0.0088). The high levels of genetic variation within reserves that we found concur with results of previous studies on cassava grown by South American Amerindians and farmers. The role of the breeding system of cassava and the agricultural practices of Amerindians in the maintenance of high levels of genetic diversity are discussed.     

The neural basis of cultural differences in delay discounting

People generally prefer to receive rewarding outcomes sooner rather than later. Such preferences result from delay discounting, or the process by which outcomes are devalued for the expected delay until their receipt. We investigated cultural differences in delay discounting by contrasting behaviour and brain activity in separate cohorts of Western (American) and Eastern (Korean) subjects. Consistent with previous reports, we find a dramatic difference in discounting behaviour, with Americans displaying much greater present bias and elevated discount rates. Recent neuroimaging findings suggest that differences in discounting may arise from differential involvement of either brain reward areas or regions in the prefrontal and parietal cortices associated with cognitive control. We find that the ventral striatum is more greatly recruited in Americans relative to Koreans when discounting future rewards, but there is no difference in prefrontal or parietal activity. This suggests that a cultural difference in emotional responsivity underlies the observed behavioural effect. We discuss the implications of this research for strategic interrelations between Easterners and Westerners.     

Phylogeography of a high‐dispersal New Zealand sea‐star: does upwelling block gene‐flow?

New Zealand's (NZ) geographical isolation, extensive coastline and well-characterized oceanography offer a valuable system for marine biogeographical research. Here we use mtDNA control region sequences in the abundant endemic sea-star Patiriella regularis to test the following literature-based predictions: that coastal upwelling disrupts north-south gene flow and promotes population differentiation (hypothesis 1); and that an invasive Tasmanian population of the species was introduced anthropogenically from southern New Zealand (hypothesis 2). We sequenced 114 samples from 22 geographical locations, including nine sites from North Island, nine from South Island, one from Stewart Island and three from Tasmania. Our analysis of these sequences revealed an abundance of shallow phylogenetic lineages within P. regularis (68 haplotypes, mean divergence 0.9%). We detected significant genetic heterogeneity between pooled samples from northern vs. southern New Zealand (FST = 0.072; P = 0.0002), consistent with the hypothesis that upwelling disrupts gene flow between these regions (hypothesis 1). However, we are currently unable to rule out the alternative hypothesis that Cook Strait represents a barrier to dispersal (North Island vs. South Island; FST = 0.031; P = 0.0467). The detection of significant spatial structure in NZ samples is consistent with restricted gene flow, and the strong structure evident in northern NZ may be facilitated by distinct ocean current systems. Four shared haplotypes and nonsignificant differentiation (FST = 0.025; P = 0.2525) between southern New Zealand and Tasmanian samples is consistent with an anthropogenic origin for the latter population (hypothesis 2).     

Brief communication: human cranial variation fits iterative founder effect model with African origin

Recent studies comparing craniometric and neutral genetic affinity matrices have concluded that, on average, human cranial variation fits a model of neutral expectation. While human craniometric and genetic data fit a model of isolation by geographic distance, it is not yet clear whether this is due to geographically mediated gene flow or human dispersal events. Recently, human genetic data have been shown to fit an iterative founder effect model of dispersal with an African origin, in line with the out-of-Africa replacement model for modern human origins, and Manica et al. (Nature 448 (2007) 346-349) have demonstrated that human craniometric data also fit this model. However, in contrast with the neutral model of cranial evolution suggested by previous studies, Manica et al. (2007) made the a priori assumption that cranial form has been subject to climatically driven natural selection and therefore correct for climate prior to conducting their analyses. Here we employ a modified theoretical and methodological approach to test whether human cranial variability fits the iterative founder effect model. In contrast with Manica et al. (2007) we employ size-adjusted craniometric variables, since climatic factors such as temperature have been shown to correlate with aspects of cranial size. Despite these differences, we obtain similar results to those of Manica et al. (2007), with up to 26% of global within-population craniometric variation being explained by geographic distance from sub-Saharan Africa. Comparative analyses using non-African origins do not yield significant results. The implications of these results are discussed in the light of the modern human origins debate.