Cranial metric and discrete trait variation and biological differentiation in the terminal Late Archaic of Ohio: the Duff site cemetery

Cranial metric and discrete traits were collected from adult individuals of the terminal Late Archaic Duff site cemetery (33 LO 111). Comparisons of cranial metric traits among eight terminal Late Archaic samples including the Duff site sample showed that all samples shared the same generalized variance and by inference the same pattern of shape variation. Some significant size differences were found but these were interpreted as reflecting only minor differences in the underlying polygenic system or differences in environmental interactions. The overall similarity in cranial metrics among the terminal Late Archaic samples strongly suggests that they represent populations that, at least, shared a recent common ancestor. Analysis of discrete trait variation in all the terminal Late Archaic samples showed that the biological distances between samples are associated significantly with the between-sample geographical distances. This association accounts for approximately 25% of the variation in discrete trait frequencies. These results along with the results of the analysis of cranial metrics indicate that all of the terminal Late Archaic samples considered here are related, but geographically nearer samples are more closely related than distant ones.     

Quantitative genetics of skeletal nonmetric traits in the rhesus macaques on Cayo Santiago. I. Single trait heritabilities

The use of skeletal nonmetric traits in studies of biological relationships often involves the assumption that variation in these traits is genetic. Studies of nonmetric traits in human groups and in inbred strains of mice and rabbits have indicated a genetic component to nonmetric trait variation. Skeletons of animals with known matrilineage membership were obtained from the Cayo Santiago skeletal collection in order to obtain a direct estimate of the heritabilities of several nonmetric traits in the free-ranging population of rhesus macaques on Cayo Santiago. Falconer's (1965) method was used to calculate heritability. Heritability estimates range from zero to one, and half of them are greater than 0.5. This indicates that there is a considerable amount of genetic variation for these traits among the Cayo macaques. There is a significant tendency for traits scoring the number of foramina to have lower heritabilities than those scoring hyperstotic or hypostotic traits.     

Quantitative genetics of skeletal nonmetric traits in the rhesus macaques of Cayo Santiago. III. Relative heritability of skeletal nonmetric and metric traits

This study addresses the long-standing controversy in skeletal biology concerning the relative utility of skeletal metric and nonmetric traits for studies of biological relationship. This controversy centers on the relative heritability of these two trait sets. This paper presents heritabilities for a series of skeletal metric and nonmetric traits measured with the same sample of mother-offspring pairs from the Cayo Santiago skeletal collection of rhesus macaques. Skeletal nonmetric traits display significantly greater heritability estimates than metric traits. This difference is due primarily to the high heritability estimates of hyperostotic nonmetric traits. Foraminal traits are not significantly more heritable than skeletal metric traits. The generality of this pattern of heritability values, in which hyperostotic nonmetric traits are more highly heritable than foraminal nonmetric and metric traits, depends on future empirical study of the correlation of heritability values in populations and theoretical work.     

Dermatoglyphic assessment of the genetic relationships of native American populations

Genetic distance techniques and cluster analysis were used to determine which dermatoglyphic parameters were most useful in assessing genetic relationships between native American populations. The dermatoglyphic parameters used for this analysis were those most completely reported in the papers examined in a literature survey we had carried out previously, and include digital patterns, modal types of the C-line and D-line terminations, and palmar patterns in the hypothenar, thenar/I, and interdigital areas. The populations examined were separated by sex and divided into seven major geographical groups: Eskimo; North American Indian; Maya and non-Maya (Central America); Amazonian; Quechua, and Aymara (South America). Mean frequencies of dermatoglyphic traits were computed for each group and pairwise “genetic” distances calculated using Cavalli-Sforza and Edward's D-test. Dendrograms were then generated from these D-values using Q-mode cluster analysis. Using the hypothenar, thenar/I and III and IV interdigital areas, the results of this analysis demonstrated a good fit to an expected phylogenetic tree. When digital patterns, patterns in the II interdigital area, and the modal types of the C-line were included in the analysis, the same phylogenetic relationships were observed. However, inclusion of the modal types of the D-line with the other parameters tended to introduce some distortion and a greater separation between sexes within the same populations.     

The use of nonmetric variation in estimating human population admixture: a test case with Brazilian blacks, whites, and mulattos

Measurements in populations which serve as valid indicators of biological relationship should be proportional to genetic distance. In order to test the utility of discrete cranial traits for estimating genetic distances among populations, estimates of admixture are obtained for gene frequency data and nonmetric cranial data in São Paulo mulattos (M). The gene frequency data serve as a control that the three populations are related as stated: estimates of admixture are obtained by using São Paulo whites (W) and blacks (B) as parental populations and by estimating the parameter of admixture, m, in the model p_M = (1 ? m) p_W + mp_B (Elston, 1971) where the p's are either gene frequencies or nonmetric trait frequencies. A test of goodness of fit of the model provides a means of ascertaining whether or not the data fit this linear model. While the gene frequency data indicate distances among the three populations which are highly compatible with the linear model of admixture, the nonmetric data show significant deviations from the model. This implies that the frequencies of the nonmetric traits in the populations used in this analysis are not a linear function of genetic distance. This discourages the use of nonmetric traits in making quantitative conclusions about genetic relationships. It also suggests the need for investigation of the use of other skeletal characters for estimating genetic distance, as well as approaches for such investigations through the study of hybrid individuals.     

Quantitative genetics of skeletal nonmetric traits in the rhesus macaques on Cayo Santiago. II. Phenotypic,genetic, and environmental correlations between traits

The general lack of phenotypic correlation among skeletal nonmetric traits has been interpreted as indicating a lack of genetic correlation among these traits. Nonmetric traits scored on animals in the skeletal collection of rhesus macaques from Cayo Santiago are used to calculate phenotypic, genetic, and environmental correlations between traits. The results show that even when phenotypic correlations are low, there may be large, significant genetic correlations among these traits. The genetic correlation pattern suggests that genes which affect nonmetric trait variation act primarily at a local level in the cranium, even though there are genes with pleiotropic effects on skeletal nonmetric traits throughout the cranium. Environmental and phenotypic correlations do not show this neighborhood pattern of correlation.     

The Uto‐Aztecan premolar among North and South Amerindians: Geographic variation and genetics

The Uto‐Aztecan premolar (UAP) is a dental polymorphism characterized by an exaggerated distobuccal rotation of the paracone in combination with the presence of a fossa at the intersection of the distal occlusal ridge and distal marginal ridge of upper first premolars. This trait is important because, unlike other dental variants, it has been found exclusively in Native American populations. However, the trait's temporal and geographic variation has never been fully documented. The discovery of a Uto‐Aztecan premolar in a prehistoric skeletal series from northern South America calls into question the presumed linguistic and geographic limits of this trait. We examined published and unpublished data for this rare but highly distinctive trait in samples representing over 5,000 Native Americans from North and South America. Our findings in living Southwest Amerindian populations corroborate the notion that the variable goes beyond the bounds of the Uto‐Aztecan language family. It is found in prehistoric Native Americans from South America, eastern North America, Northern and Central Mexico, and in living and prehistoric populations in the American Southwest that are not members of the Uto‐Aztecan language stock. The chronology of samples, its geographic distribution, and trait frequencies suggests a North American origin (Southwest) for UAP perhaps between 15,000 BP and 4,000 BP and a rapid and widespread dispersal into South America during the late Holocene. Family data indicate that it may represent an autosomal recessive mutation that occurred after the peopling of the Americas as its geographic range appears to be limited to North and South Amerindian populations. Am J Phys Anthropol, 2010. © 2010 Wiley‐Liss, Inc.     

Temporal aspects of biological distance: serial correlation and trend in a prehistoric skeletal lineage

A number of previous studies have examined biological variability within individual human skeletal samples, using internal chronology as an explanatory source for variation. In this paper time series and matrix comparison methods are used to examine temporal serial correlation and trend of biological characteristics within a skeletal sample. These methods follow appropriately upon the assumption that the processes of genetic drift and migration lead to temporal autocorrelation of the mean genotype within individual genetic lineages. In the current analysis, using skeletal material from the Pete Klunk Mound Group, temporal serial correlation is demonstrated between samples from different mounds. This indicates that a previous provisional archaeological ordering of the mounds is probably correct. Absence of temporal trend for any of the nonmetric traits examined here suggests a lack of directional evolutionary forces operating on these traits.     

Disentangling Signatures of Selection Before and After European Colonization in Latin Americans

Throughout human evolutionary history, large-scale migrations have led to intermixing (i.e., admixture) between previously separated human groups. Although classical and recent work have shown that studying admixture can yield novel historical insights, the extent to which this process contributed to adaptation remains underexplored. Here, we introduce a novel statistical model, specific to admixed populations, that identifies loci under selection while determining whether the selection likely occurred post-admixture or prior to admixture in one of the ancestral source populations. Through extensive simulations, we show that this method is able to detect selection, even in recently formed admixed populations, and to accurately differentiate between selection occurring in the ancestral or admixed population. We apply this method to genome-wide SNP data of ∼4,000 individuals in five admixed Latin American cohorts from Brazil, Chile, Colombia, Mexico, and Peru. Our approach replicates previous reports of selection in the human leukocyte antigen region that are consistent with selection post-admixture. We also report novel signals of selection in genomic regions spanning 47 genes, reinforcing many of these signals with an alternative, commonly used local-ancestry-inference approach. These signals include several genes involved in immunity, which may reflect responses to endemic pathogens of the Americas and to the challenge of infectious disease brought by European contact. In addition, some of the strongest signals inferred to be under selection in the Native American ancestral groups of modern Latin Americans overlap with genes implicated in energy metabolism phenotypes, plausibly reflecting adaptations to novel dietary sources available in the Americas.     

Familial segregation in the iron age community of Alfedena, Abruzzo, Italy, based on osteodental trait analysis

Numerous authors have studied human cemetery remains with an eye toward identifying different socially stratified ethnic or kinship groups within the same population. The interments of the protohistoric graveyard of Alfedena, Abruzzo, Italy, show recurrent organization in separate structures, suggesting to several involved archaeologists that these structures express family groups and/or differences in social function of the occupants. This has induced us to analyze the possible biological implications of specific models for kinship groups, lineages, or mating forms in graveyards. One hundred ninety-six metric and nonmetric skeletal and dental variables were collected. The analysis of metric features was performed by analysis of variance and by calculating divergences between each pair of individuals. The position parameters of the inter-and intragroup distance distributions were then compared by means of nonparametric tests. The nonmetric features were analyzed by contingency tables. The partition of intercircle variance is twice as frequently significant for males (20 variables) as for females (10). For metric variables in males, 20.9% displayed a probability level less than 5% for the null hypothesis of random distribution of individuals in the circles. Fewer (10.3%, but still more than expected at random) reached this level of significance for the females. In the male groups, 19% of nonmetric features showed significant frequency differences, but this was true in only 4.3% of the females.(ABSTRACT TRUNCATED AT 250 WORDS)     

The interaction between nonmetric and metric cranial variation.

Cranial discrete or 'epigenetic" traits have been analyzed for interrelationships with measurements of the skull in a sample of American Negro males. Univariate t and multivariate T2 tests are used. It has been the previous consensus view that nonmetric and metric characters are unrelated. Statistically significant associations between the total of 50 discrete and 23 metrical characters, however, are much more frequent than would be expected through random distribution. Multivariate analysis supplements simpler statistics by synthesizing patterns of variation within regions of the skull, identifying many interrelations of skull size and shape with discrete traits. A low but observable general influence is exerted upon nonmetric morphology by metrical variation of the human skull (or vice versa).     

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

Twenty-two years ago, Greenberg, Turner and Zegura (Curr. Anthropol. 27,477-495, 1986) suggested a multidisciplinary model for the human settlement of the New World. Since their synthesis, several studies based mainly on partial evidence such as skull morphology and molecular genetics have presented competing, apparently mutually exclusive, settlement hypotheses. These contradictory views are represented by the genetic-based Single Wave or Out of Beringia models and the cranial morphology-based Two Components/Stocks model. Here, we present a geometric morphometric analysis of 576 late Pleistocene/early Holocene and modern skulls suggesting that the classical Paleoamerican and Mongoloid craniofacial patterns should be viewed as extremes of a continuous morphological variation. Our results also suggest that recent contact among Asian and American circumarctic populations took place during the Holocene. These results along with data from other fields are synthesized in a model for the settlement of the New World that considers, in an integrative and parsimonious way, evidence coming from genetics and physical anthropology. This model takes into account a founder population occupying Beringia during the last glaciation characterized by high craniofacial diversity, founder mtDNA and Y-chromosome lineages and some private autosomal alleles. After a Beringian population expansion, which could have occurred concomitant with their entry into America, more recent circumarctic gene flow would have enabled the dispersion of northeast Asian-derived characters and some particular genetic lineages from East Asia to America and vice versa.     

JC virus as a marker of human migration to the Americas

JC virus is a ubiquitous human polyomavirus present in populations worldwide. Seven genotypes differing in DNA sequence by approximately 1-3% characterize three Old World population groups (African, European and Asian) as well as Oceania. It is possible to follow Old World populations into the New World by the JC virus genotypes they carried. The first population to settle in the Americas, the Native Americans, brought with them type 2A from northeast Asia. European settlers arriving after Columbus carried primarily type 1 and type 4. Africans brought by the slave trade carried type 3 and type 6.     

Environmental variation is a major predictor of global trait turnover in mammals

Aim

To evaluate how environment and evolutionary history interact to influence global patterns of mammal trait diversity (a combination of 14 morphological and life‐history traits).

Location

The global terrestrial environment.

Taxon

Terrestrial mammals.

Methods

We calculated patterns of spatial turnover for mammalian traits and phylogenetic lineages using the mean nearest taxon distance. We then used a variance partitioning approach to establish the relative contribution of trait conservatism, ecological adaptation and clade specific ecological preferences on global trait turnover.

Results

We provide a global scale analysis of trait turnover across mammalian terrestrial assemblages, which demonstrates that phylogenetic turnover by itself does not predict trait turnover better than random expectations. Conversely, trait turnover is consistently more strongly associated with environmental variation than predicted by our null models. The influence of clade‐specific ecological preferences, reflected by the shared component of phylogenetic turnover and environmental variation, was considerably higher than expectations. Although global patterns of trait turnover are dependent on the trait under consideration, there is a consistent association between trait turnover and environmental predictive variables, regardless of the trait considered.

Main conclusions

Our results suggest that changes in phylogenetic composition are not always coupled with changes in trait composition on a global scale and that environmental conditions are strongly associated with patterns of trait composition across species assemblages, both within and across phylogenetic clades.     

Mitochondrial DNA studies of Native Americans: Conceptions and misconceptions of the population prehistory of the Americas

A decade ago, the first reviews of the collective mitochondrial DNA (mtDNA) data from Native Americans concluded that the Americas were peopled through multiple migrations from different Asian populations beginning more than 30,000 years ago. 1 These reports confirmed multiple‐wave hypotheses suggested earlier by other sources and rejected the dominant Clovis‐first archeological paradigm. Consequently, it appeared that molecular biology had made a significant contribution to the study of American prehistory. As Cann 2 comments, the Americas held the greatest promise for genetics to help solve some of the mysteries of prehistoric populations. In particular, mtDNA appeared to offer real potential as a means of better understanding ancient population movements. A decade later, none of the early conclusions remain unequivocal. Nevertheless, in its maturity, the study of Native American mtDNA has produced a volume of reports that still illuminate the nature and timing of the first peopling and postcolonization population movements within the New World.     

Brief communication: Population data support the adaptive nature of HACNS1 sapiens/neandertal‐chimpanzee differences in a limb expression domain

The 546‐base pair enhancer of limb expression HACNS1, which is highly constrained in all terrestrial vertebrates, has accumulated 16 human‐specific changes after the human‐chimpanzee split. There has been discussion whether this process was driven by positive selection or biased gene conversion, without considering population data. We studied 83 South Amerindian, 11 Eskimo, 35 Europeans, 37 Bantu, and non‐Bantu Sub‐Saharan speakers, and 28 Brazilian mestizo samples and found no variation in this DNA region. Similar lack of variability in this region was found in four Africans, five Europeans or Euro‐derived, two Asians, one Paleo‐Eskimo, and one Neandertal sequence, whose whole genomes are publicly available. No difference was found. This result favors the interpretation of past positive and present conservative selection, as would expected in a region which influences Homo‐specific traits as important as opposable thumbs, manual dexterity, and bipedal walking. Am J Phys Anthropol, 2010. © 2010 Wiley‐Liss, Inc.     

β-fibrinogen allele frequencies in Peruvian Quechua,a high-altitude native population

Elevated hematocrits, which are found in many high-altitude populations, increase the oxygen-carrying capacity of blood and may represent an adaptation to hypoxic environments. However, as high hematocrit increases blood viscosity, which in turn is associated with hypertension and heart disease, it may be advantageous for high-altitude populations to limit other factors that contribute to increased blood viscosity. One such factor is the plasma concentration of the coagulation protein fibrinogen. Several common polymorphisms in the β-fibrinogen gene have been identified that affect fibrinogen concentrations. We determined the allele frequencies of three of these polymorphisms (G/A^-455(HaeIII), C/T^-148(HindIII), and G/A⁺⁴⁴⁸(MnlI)) in sample groups drawn from three populations: Quechua-speaking natives living at over 3,200 m in the Peruvian Andes, North American natives (Na-Dene) from coastal British Columbia, and Caucasian North Americans. The frequencies of the alleles previously shown to be associated with increased fibrinogen levels were so low in the Quechuas that their presence could be accounted for solely by genetic admixture with Caucasians. Frequencies in the Na-Dene, a Native American group unrelated to the Quechua, were not significantly different from those in Caucasians. Am J Phys Anthropol 109:181–186, 1999. © 1999 Wiley-Liss, Inc.     

Cranial variation in British mustelids

Nineteen measurements were made on 136 skulls belonging to seven mustelid species: Meles meles (Eurasian badger), Mustela nivalis, (weasel), Mustela erminea (stoat), Mustela putorius (polecat), Lutra lutra (otter), Mustela furo (ferret), and Mustela vison (American mink), and polecat-ferret hybrids. To investigate shape, size-related effects were eliminated by dividing all measurements by their geometric means. Canonical variate analysis was used to reveal major interspecies distinctions. Excluding the ferrets and polecat-ferrets from the analysis, only 3.2% of the skulls misclassified (one mink, one weasel, and two stoats). Three groups separated on the first canonical axis: 1) badgers, 2) polecats, mink, and otters, and 3) stoats and weasels. The important variables were width of zygomatic arch and height of sagittal crest opposed to the postorbital distance, condylobasal length, and basilar length. Otters separated out on the second canonical axis; the most important variables were postorbital breadth and width of the postorbital constriction opposed to the basioccipital width. There was reasonable separation of polecats from mink on a combination of the second and third canonical axes. On the latter the most important variables were postorbital breadth opposed to postorbital distance. Addition of the ferret data showed that they lay closest to, and overlapped with, the polecats. The stoat and weasel data alone gave complete separation, with height of sagittal crest and width of zygomatic arch opposed to basioccipital width. However, using size-in data the best separation was the relationship between postorbital breadth and either basioccipital width or postorbital distance. Sexual dimorphism was demonstrated in the skulls of badgers but was shown to be relatively insignificant when compared to the interspecific differences.     

Single nucleotide polymorphisms and haplotypes in Native American populations

Autosomal DNA polymorphisms can provide new information and understanding of both the origins of and relationships among modern Native American populations. At the same time that autosomal markers can be highly informative, they are also susceptible to ascertainment biases in the selection of the markers to use. Identifying markers that can be used for ancestry inference among Native American populations can be considered separate from identifying markers to further the quest for history. In the current study, we are using data on nine Native American populations to compare the results based on a large haplotype‐based dataset with relatively small independent sets of single nucleotide polymorphisms. We are interested in what types of limited datasets an individual laboratory might be able to collect are best for addressing two different questions of interest. First, how well can we differentiate the Native American populations and/or infer ancestry by assigning an individual to her population(s) of origin? Second, how well can we infer the historical/evolutionary relationships among Native American populations and their Eurasian origins? We conclude that only a large comprehensive dataset involving multiple autosomal markers on multiple populations will be able to answer both questions; different small sets of markers are able to answer only one or the other of these questions. Using our largest dataset, we see a general increasing distance from Old World populations from North to South in the New World except for an unexplained close relationship between our Maya and Quechua samples. Am J Phys Anthropol, 2011. © 2011 Wiley Periodicals, Inc.     

Effects of English admixture and geographic distance on anthropometric variation and genetic structure in 19th-century Ireland

The analysis of anthropometric data often allows investigation of patterns of genetic structure in historical populations. This paper focuses on interpopulational anthropometric variation in seven populations in Ireland using data collected in the 1890s. The seven populations were located within a 120-km range along the west coast of Ireland and include islands and mainland isolates. Two of the populations (the Aran Islands and Inishbofin) have a known history of English admixture in earlier centuries. Ten anthropometric measures (head length, breadth, and height; nose length and breadth; bizygomatic and bigonial breadth; stature; hand length; and forearm length) on 259 adult Irish males were analyzed following age adjustment. Discriminant and canonical variates analysis were used to determine the degree and pattern of among-group variation. Mahalanobis' distance measure, D2, was computed between each pair of populations and compared to distance measures based on geographic distance and English admixture (a binary measure indicating whether either of a pair of populations had historical indications of admixture). In addition, surname frequencies were used to construct distance measures based on random isonymy. Correlations were computed between distance measures, and their probabilities were derived using the Mantel matrix permutation method. English admixture has the greatest effect on anthropometric variation among these populations, followed by geographic distance. The correlation between anthropometric distance and geographic distance is not significant (r = -0.081, P = .590), but the correlation of admixture and anthropometric distance is significant (r = 0.829, P = .047). When the two admixed populations are removed from the analysis the correlation between geographic and anthropometric distance becomes significant (r = 0.718, P = .025). Isonymy distance shows a significant correlation with geographic distance (r = 0.425, P = .046) but not with admixture distance (r = -0.052, P = .524). The fact that anthropometrics show past patterns of gene flow and surnames do not reflects the greater impact of stochastic processes on surnames, along with the continued extinction of surnames. This study shows that 1) anthropometrics can be extremely useful in assessing population structure and history, 2) differential gene flow into populations can have a major impact on local genetic structure, and 3) microevolutionary processes can have different effects on biological characters and surnames.