Meaning of biodistance statistics: a test case using adult monozygotic twins

Anthropometry, historically one of the primary research techniques in physical anthropology, has been widely utilized in biodistance studies. The complex genetic and environmental interaction that governs the expression of anthropometric dimensions, together with concerns over measurement error, have sometimes clouded the interpretation of biodistances based upon anthropometry. In this study, 51 pairs of adult monozygotic twins were analysed using discriminant analysis and Mahalanobis' generalized distance. Both male and female twins, grouped by first- versus second-born, displayed very small, statistically insignificant distances between groups. When literature estimates of intra-observer measurement errors were used as a frame of reference, the average absolute differences between the twin pairs were approximately twice the size of the measurement error estimates. The results of this study suggest that, first, the environmental effect upon the genetically influenced traits measured by anthropometry is not large enough to bring about significant multivariate differences between identical twin pairs; and, second, biodistance studies based upon anthropometry can be reliable so long as measurement error is minimized.     

The rise of coastal Middle Bronze Age Levant – A multidisciplinary approach for investigating in Sidon,Lebanon

Objectives

The Levantine Middle Bronze Age (MBA, circa 2000–1500 BCE) marks a period of increased trade and regional interaction, spurred on by technological developments. In light of previous research exhibiting limited mobility in Sidon, further investigation was conducted using biodistance analysis to understand local population history and site development.

Materials and Methods

Dental nonmetric traits, a proxy for genetic information, were explored using ASUDAS on a sub-sample of primary inhumations (n = 35). The biodistance matrix was generated using Gower distance measures, and further tested using PERMDISP, PERMANOVA, Mantel test and hierarchical cluster analysis. The data was also contrasted to ⁸⁷Sr/⁸⁶Sr and δ¹⁸O as well as δ¹³C and δ¹⁵N values.

Results

There were no significant diachronic differences in isotopes values, and there was biological continuity (n = 35, Mantel test r = 0.11, p = 0.02, comparing local phases and biodistance). The analysis also suggested of a sub-group of individuals with biological proximity shared a more limited range of mobility and dietary habits.

Conclusions

The isotopes (⁸⁷Sr/⁸⁶Sr, δ¹⁸O, δ¹³C, δ¹⁵N) and biodistance analysis conducted on the Sidon College site skeletal assemblage exhibits stability and continuity of the people, despite the site's increasing role in the maritime network. This continuity may have been a key factor in Sidon's success, allowing it to accumulate wealth and resources for centuries to come.

     

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.     

Quantitative genetics of cranial nonmetric traits in randombred mice: heritability and etiology

Cheverud and Buikstra (1981) demonstrated a tendency for nonmetric traits representing the number of foramina to have lower heritabilities than those representing hyperstotic or hypostotic traits in a sample of rhesus macaques. Based on this observation, Cheverud and Buikstra hypothesize that differences in the heritability of the two sets of traits may be due to differences in trait etiology. This study addresses the proposed relationship between trait heritability and etiology. Heritability values are calculated for 35 cranial nonmetric traits in a sample of 320 randombred mice using analysis of variance. The results are minimally consistent with the etiological hypothesis, but only 4 of the 35 traits showed statistically significant heritability values. These results are discussed with reference to the assumption that nonmetric traits have a strong genetic component. It is concluded that the developmental pathways that genetic variation traverses before being expressed in the form of nonmetric traits must be understood before variation in nonmetric traits can be used to its fullest potential.     

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.     

An examination of Nubian and Egyptian biological distances: Support for biological diffusion or in situ development?

Many authors have speculated on Nubian biological evolution. Because of the contact Nubians had with other peoples, migration and/or invasion (biological diffusion) were originally thought to be the biological mechanism for skeletal changes in Nubians. Later, a new hypothesis was put forth, the in situ hypothesis. The new hypothesis postulated that Nubians evolved in situ, without much genetic influence from foreign populations. This study examined 12 Egyptian and Nubian groups in an effort to explore the relationship between the two populations and to test the in situ hypothesis. Data from nine cranial nonmetric traits were assessed for an estimate of biological distance, using Mahalanobis D² with a tetrachoric matrix. The distance scores were then input into principal coordinates analysis (PCO) to depict the relationships between the two populations. PCO detected 60% of the variation in the first two principal coordinates. A plot of the distance scores revealed only one cluster; the Nubian and Egyptian groups clustered together. The grouping of the Nubians and Egyptians indicates there may have been some sort of gene flow between these groups of Nubians and Egyptians. However, common adaptation to similar environments may also be responsible for this pattern. Although the predominant results in this study appear to support the biological diffusion hypothesis, the in situ hypothesis was not completely negated.     

Genetic correlations between sides and heritability of asymmetry for nonmetric traits in rhesus macaques on Cayo Santiago

The use of nonmetric traits for estimation of biological distance is a long-standing practice in biological anthropology. Nonmetric traits can be scored using either the individual or the side of the individual as the unit of measure. If sides of the individual are genetically correlated the use of sides would produce redundant genetic information. For this reason, Korey (Am. J. Phys. Anthropol. 53:19-23, 1980) argues for the use of individuals as the unit of measure for nonmetric traits. Ossenberg (Am. J. Phys, Anthropol. 54:471-479, 1981), however, argues that bilateral occurrence of nonmetric traits indicates greater genetic liability for the trait and that therefore the sides are the more biologically correct unit of measure. Genetic correlations for 13 cranial nonmetric traits are estimated for a sample of rhesus macaque skeletons from Cayo Santiago. In addition, heritability of asymmetry is estimated for these 13 traits as a test of Ossenberg's contention that asymmetry is genetically influenced. Significant genetic correlations between sides support Korey's contention that nonmetric traits should be scored by individual. Only two asymmetry heritabilities were significantly different from zero, providing no significant support for Ossenberg's contention that asymmetry is genetically determined. Our results support the theory that asymmetry represents a measure of the ability of an organism to buffer stresses. Therefore, a measure of the heritability of asymmetry is a measure of the heritability of the ability to buffer stresses. This ability does not appear to be heritable in this sample.     

Sahara: Barrier or corridor? Nonmetric cranial traits and biological affinities of North African late holocene populations

The Garamantes flourished in southwestern Libya, in the core of the Sahara Desert ~3,000 years ago and largely controlled trans-Saharan trade. Their biological affinities to other North African populations, including the Egyptian, Algerian, Tunisian and Sudanese, roughly contemporary to them, are examined by means of cranial nonmetric traits using the Mean Measure of Divergence and Mahalanobis D(2) distance. The aim is to shed light on the extent to which the Sahara Desert inhibited extensive population movements and gene flow. Our results show that the Garamantes possess distant affinities to their neighbors. This relationship may be due to the Central Sahara forming a barrier among groups, despite the archaeological evidence for extended networks of contact. The role of the Sahara as a barrier is further corroborated by the significant correlation between the Mahalanobis D(2) distance and geographic distance between the Garamantes and the other populations under study. In contrast, no clear pattern was observed when all North African populations were examined, indicating that there was no uniform gene flow in the region.     

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. 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.     

Comparison between morphological and genetic data to estimate biological relationship: the case of the Egyin Gol necropolis (Mongolia)

Osseous and dental nonmetric (discrete) traits have long been used to assess population variability and affinity in anthropological and archaeological contexts. However, the full extent to which nonmetric traits can reliably be used as a proxy for genetic data when assessing close or familial relationships is currently poorly understood. This study represents the unique opportunity to directly compare genetic and nonmetric data for the same individuals excavated from the Egyin Gol necropolis, Mongolia. These data were analyzed to consider the general efficacy of nonmetric traits for detecting familial groupings in the absence of available genetic data. The results showed that the Egyin Gol population is quite homogenous both metrically and genetically confirming a previous suggestion that the same people occupied the necropolis throughout the five centuries of its existence. Kinship analysis detected the presence of potential family burials in the necropolis. Moreover, individuals buried in one sector of the necropolis were differentiated from other sectors on the basis of nonmetric data. This separation is likely due to an outside Turkish influence in the paternal line, as indicated by the results of Y-chromosome analysis. Affinity matrices based on nonmetric and genetic data were correlated demonstrating the potential of nonmetric traits for detecting relationships in the absence of genetic data. However, the strengths of the correlations were relatively low, cautioning against the use of nonmetric traits when the resolution of the familial relationships is low.     

The value of infracranial nonmetric variation in studies of modern Homo sapiens: an Australian focus

The value of quantitative infracranial nonmetric variation is examined in the study of population relationships by using samples from populations originating from five major geographic regions: Australia (two populations), Africa, East Asia, Europe, and Polynesia. According to the nonspecificity hypothesis, there are no distinct large classes of genes affecting one group of attributes exclusively; thus infracranial nonmetric traits should compare with other osteologic data sets in addressing questions of population relationships. By using the mean measure of divergence, infracranial nonmetric traits are shown to be useful in separating populations, particularly when using female and pooled-sex samples. The two Australian female samples (New South Wales coastal Australian and South Australian Aboriginals) are shown to be closer than any other two samples. The picture of intrapopulation and interpopulation variation in infracranial nonmetric traits is extended and clarified. Distance studies with infracranial nonmetric traits are possible but more illuminating if the sexes are first separated. Infracranial nonmetric variation does extend the knowledge of human population studies in yielding biologically meaningful results relating to development and ontogeny.     

The relationship between cranial metric and nonmetric traits in the rhesus macaques from Cayo Santiago

This study addresses the relationship between cranial metric variables and nonmetric traits using the skeletal sample of rhesus macaques from Cayo Santiago. Discriminant function analysis is used to study the metric differences between macaque crania grouped according to the presence or absence of nine nonmetric traits. The computation of total structure coefficients from the discriminant function analyses provides information regarding how closely each metric variable is related to the discriminant functions derived. Total structure coefficients have not been used previously in the study of the relationship between metric and nonmetric traits. The results of the analysis are interpreted using an explicit approach to cranial morphogenesis-functional cranial analysis. It is concluded that the relationship between cranial metric and nonmetric traits is explicable in terms of a common developmental pathway shared by the two types of traits. Identification of the specific etiology of nonmetric traits depends on future anatomical studies or organisms throughout the period of nonmetric trait development.     

Evidence for long‐term migration on the Balkan Peninsula using dental and cranial nonmetric data: Early interaction between Corinth (Greece) and its colony at Apollonia (Albania)

This article seeks to identify “Greeks” and “non‐Greeks” in “mixed” mortuary contexts in a Greek colony. Specifically, we test the hypothesis that Illyrian and Greek individuals lived and were buried together at the Corinthian colony of Apollonia, Albania (established ca. 600 BC). The pattern of human biological interaction at Apollonia is tested by identifying variation in genetic relatedness using biodistance analysis of dental and cranial nonmetric traits for three sites: Apollonia (n = 116), its founder‐city Corinth (n = 69), and Lofkënd (n = 108), an inland site near Apollonia pre‐dating colonization. Logistic regression analysis estimates that individuals from colonial Apollonia are most closely related to prehistoric Illyrian populations (from Lofkënd and prehistoric Apollonia), rather than Greeks (from Corinth). The phenotypic similarity between colonial Apollonia and prehistoric Illyria suggests that there was a large Illyrian contribution to the gene pool at the colony of Apollonia. However, some trait combinations show low biological distances among all groups, suggesting homogeneity among Illyrian and Greek populations (assessed through pseudo‐Mahalanobis' D²). The degree of phenotypic similarity suggests shared ancestry and long‐term migration throughout these regions. The impacts of missing data and small sample sizes are also considered. Am J Phys Anthropol 153:236–248, 2014. © 2013 Wiley Periodicals, Inc.     

The settlement of Patagonia: a matrix correlation study.

Matrix correlation represents an innovative methodology to evaluate the explanatory power of several hypotheses by measuring their correspondence with observed morphological variation. In this paper, we view the origins of Patagonians from a matrix correlation approach. Personal and published data on nonmetric cranial traits were used to estimate a biological distance matrix involving five major groups from Patagonia and two from the northwest and northeast regions of Argentina. To evaluate correspondence with other important factors, we used a geographic distance matrix and four design matrices, representing several patterns of settlement and differentiation. Biological distance was found to be strongly associated with spatial separation; the correlation between geography and nonmetric cranial distances was highly significant. When geographic distance is held constant, correlation between a model representing high levels of heterogeneity between the samples and morphological (nonmetric) variation becomes highly significant.     

POPULATION STRUCTURE OF MORPHOLOGICAL TRAITS IN CLARKIA DUDLEYANA. II. CONSTANCY OF WITHIN-POPULATION GENETIC VARIANCE

Recent quantitative genetic studies have attempted to infer long-term selection responsible for differences in observed phenotypes. These analyses are greatly simplified by the assumption that the within-population genetic variance remains constant through time and over space, or for the multivariate case, that the matrix of additive genetic variances and covariances (G matrix) is constant. We examined differences in G matrices and the association of these differences with differences in multivariate means (Mahalanobis D²) among 11 populations of the California endemic annual plant, Clarkia dudleyana. Based on nine continuous morphological traits, the relationship between Mahalanobis D² and a distance measure summarizing differences in G matrices reflected no concomitant change in (co)variances with changes in means. Based on both broad- and narrow-sense analyses, we found little evidence that G matrices differed between populations. These results suggest that both the additive and nonadditive (co)variances for traits have remained relatively constant despite changes in means.     

Morphologic variation in the cranium and mandible of the white-tailed deer (Odocoileus virginianus): A comparative study of geographical and four biological distances

Several biological distances based on cranial and mandibular variation among breeding groups of white-tailed deer were calculated and compared with geographic distances among the groups. Distances based on epigenetic variation among ten groups were calculated using 16 non-metric variants of the cranium and mandible. Penrose's size and shape distances and Mahalanobis' D² distance were calculated for 11 groups; the calculations were based on seven skeletal and seven dental metric variables of the mandible. The biological distances were correlated with geographic distance as follows: the epigenetic distance, 0.74; Penrose's shape distance, 0.71; Penrose's size distance, 0.45; and Mahalanobis' distance, 0.37. All correlations were significant at the 0.01 level. The epigenetic and Penrose shape correlations were significantly higher than the Mahalanobis correlation. Because of the conditions under which the breeding groups were selected, it was assumed that genetic affinites among the groups would be a function of geographic distance. The results suggest that the epigenetic distance and Penrose's shape distance reflect genetic affinities among groups better than do the Penrose size and Mahalanobis distances.     

A strategy on constructing core collections by least distance stepwise sampling

A strategy was proposed for constructing core collections by least distance stepwise sampling (LDSS) based on genotypic values. In each procedure of cluster, the sampling is performed in the subgroup with the least distance in the dendrogram during constructing a core collection. Mean difference percentage (MD), variance difference percentage (VD), coincidence rate of range (CR) and variable rate of coefficient of variation (VR) were used to evaluate the representativeness of core collections constructed by this strategy. A cotton germplasm collection of 1,547 accessions with 18 quantitative traits was used to construct core collections. Genotypic values of all quantitative traits of the cotton collection were unbiasedly predicted based on mixed linear model approach. By three sampling percentages (10, 20 and 30%), four genetic distances (city block distance, Euclidean distance, standardized Euclidean distance and Mahalanobis distance) combining four hierarchical cluster methods (nearest distance method, furthest distance method, unweighted pair-group average method and Ward’s method) were adopted to evaluate the property of this strategy. Simulations were conducted in order to draw consistent, stable and reproducible results. The principal components analysis was performed to validate this strategy. The results showed that core collections constructed by LDSS strategy had a good representativeness of the initial collection. As compared to the control strategy (stepwise clusters with random sampling strategy), LDSS strategy could construct more representative core collections. For LDSS strategy, cluster methods did not need to be considered because all hierarchical cluster methods could give same results completely. The results also suggested that standardized Euclidean distance was an appropriate genetic distance for constructing core collections in this strategy.     

Methods of constructing core collections by stepwise clustering with three sampling strategies based on the genotypic values of crops

A genetic model with genotype×environment (GE) interactions for controlling systematical errors in the field can be used for predicting genotypic values by an adjusted unbiased prediction (AUP) method. Mahalanobis distance, calculated based on the genotypic values, is then applied to measure the genetic distance among accessions. The unweighted pair-group average, Ward’s and the complete linkage methods of hierarchical clustering combined with three sampling strategies are proposed to construct core collections in a procedure of stepwise clustering. A homogeneous test and t-tests are suggested for use in testing variances and means, respectively. The coincidence rate (CR%) for range and the variable rate (VR%) for the coefficient of variation are designed to evaluate the property of core collections. A worked example of constructing core collections in cotton with 21 traits was conducted. Random sampling can represent the genetic diversity structure of the initial collection. Preferred sampling can keep the accessions with special or valuable characteristics in the initial collection. Deviation sampling can retain the larger genetic variability of the initial collection. For better representation of the core collection, cluster methods should be combined with different sampling strategies. The core collections based on genotypic values retained larger genetic variability and had superior representatives than those based on phenotypic values. Received: 15 October 1999 / Accepted: 24 November 1999     

Investigation of Combining Plant Genotypic Values and Molecular Marker Information for Constructing Core Subsets

In the present study, a strategy was proposed for constructing plant core subsets by clusters based on the combination of continuous data for genotypic values and discrete data for molecular marker InformaUon. A mixed linear model approach was used to predict genotyplc values for eliminating the environment effect. The ＂mixed genetic distance＂ was designed to solve the difficult problem of combining continuous and discrete data to construct a core subset by cluster. Four commonly used genetic distances for continuous data （Euclidean distance, standardized Euclidean distance, city block distance, and Mahalanobls distance） were used to assess the validity of the conUnuous data part of the mixed genetic distance; three commonly used genetic distances for discrete data （cosine distance, correlaUon distance, and Jaccard distance） were used to assess the validity of the discrete data part of the mixed genetic distance, A rice germplasm group with eight quantitative traits and information for 60 molecular markers was used to evaluate the validity of the new strategy. The results suggest that the validity of both parts of the mixed geneUc distance are equal to or higher than the common geneUc distance. The core subset constructed on the basis of a combination of data for genotyplc values and molecular marker information was more representative than that constructed on the basis of data from genotypic values or molecular marker informaUon alone. Moreover, the strategy of using combined data was able to treat dominant marker informaUon and could combine any other continuous data and discrete data together to perform cluster to construct a plant core subset.