Size and shape in similarity coefficients based on metric characters

A variety of quantitative measures of distance and similarity have been used in physical anthropology, often without sufficient prior testing of their usefulness and understanding of their meaning. A variety of such coefficients were compared by applying them to an odontometric sample. It was found that Penrose's size-shape dichotomy extends not only to his coefficients but to all other similarity measures as well, such as the coefficient of racial likeness, generalized distance, canonical variates, and Q-mode correlation. Only size differences were detected by the C.R.L., Penrose's size distance, D², and canonical variates, and as a result these methods failed to produce an accurate classification. Penrose's shape distance and Q-mode correlation coefficients produced better results due to their determination of similarity on the basis of more important shape and morphological differences. The D² and canonical variates methods were converted to shape measures through Q-mode standardization of the raw data, whereupon they also produced more meaningful results.     

The genetic structure of a tribal population, the Yanomama indians. VII. Anthropometric differences among Yanomama villages

Anthropometric data on 12 variables in 19 villages of the Yanomama Indians demonstrate significant heterogeneity in physique among villages of this tribe. Mahalanobis' distances (D²) calculated from the data lead to the tentative conclusion of a general correspondence between anthropometric and geographic distances separating villages. The mean stature of the Yanomama is smaller than that of most other South American tribes which have been measured, and the Yanomama are genetically distinct from the other small Indians as shown by genetic distances based on allele frequencies for a variety of genetic markers. Since some subjects were measured more than once by the same and by different observers, it was possible to calculate approximate estimates of variance within and between observers. Univariate analysis indicates that face height and nose height are especially susceptible to systematic differences in technique between observers. The variances obtained in this field study compare favorably with those of some classical laboratory studies described in the literature. It was found that measurement error nevertheless probably makes a substantial contribution to anthropometric distance between villages. The median error variance as a fraction of that of Herskovits ('30) is 0.62 for the seven measurements in common with this study. The median value of the error variance for the 12 variables in this study is between 16% and 17% of the total variance.     

山苍子天然种群叶片和种实性状的表型多样性

为揭示山苍子(Litsea cubeba)天然种群叶片和种实性状的表型变异程度及其变异规律,调查了长江以南7个省份共10个天然种群的叶片和种实性状,并对其多样性进行分析。结果表明:1)山苍子的叶片和种实性状在种群间和种群内存在极其丰富的多样性,各性状表型分化系数(Vst)均值为60.19%,种群表型性状分化以种群间变异为主;2)果实形态、叶片形态、果实重和种子重4类性状的Vst均值分别为51.27%、66.66%、54.57%和72.29%;平均变异系数(CV)分别为6.60%、16.91%、19.71%和13.40%;果实形态的表型分化系数和变异系数最小,表明其性状最为稳定;3)10个表型性状间多数呈显著或极显著相关,性状与地理气候因子的相关性较差;4)系统聚类将10个种群共分为4类,种群间的分类并没有依地理距离而聚类,表型性状的Mahalanobis距离与地理距离的相关不显著(r=0.042,P=0.821),进一步表明山苍子叶片和种实性状的变异在空间上是不连续性的。研究结果为今后山苍子种质资源的保存和育种策略的制定奠定基础。     

Ecogeographical patterns of morphological variation in pygmy shrews Sorex minutus (Soricomorpha: Soricinae) within a phylogeographical and continental‐and‐island framework

Ecogeographical patterns of morphological variation were studied in the Eurasian pygmy shrew Sorex minutus aiming to understand the species’ morphological diversity in a continental and island setting, and within the context of previous detailed phylogeographical studies. In total, 568 mandibles and 377 skulls of S. minutus from continental and island populations from Europe and Atlantic islands were examined using a geometric morphometrics approach, and the general relationships of mandible and skull size and shape with geographical and environmental variables were studied. Samples were then pooled into predefined geographical groups to evaluate the morphological differences among them using analyses of variance, aiming to contrast the morphological and genetic relationships based on morphological and genetic distances and ancestral state reconstructions, as well as assess the correlations of morphological, genetic, and geographical distances with Mantel tests. We found significant relationships of mandible size with geographical and environmental variables, fitting the converse Bergmann's rule; however, for skull size, this was less evident. Continental groups of S. minutus could not readily be differentiated from each other by shape. Most island groups of S. minutus were easily discriminated from the continental groups by being larger, indicative of an island effect. Moreover, morphological and genetic distances differed substantially and, again, island groups were distinctive morphologically. Morphological and geographical distances were significantly correlated, although this was not the case for morphological and genetic distances, indicating that morphological variation does not reflect genetic subdivision in S. minutus. Our analyses showed that environmental variables and insularity had important effects on the morphological differentiation of S. minutus.     

A quantitative genetic analysis of localized morphology in mandibles of inbred mice using finite element scaling analysis.

We analyzed patterns of mandibular genetic and phenotypic morphological integration and the relationship of genealogy to interstrain molecular and morphological differences in ten inbred strains of mice. Positions of mandibular landmarks in two-dimensional space were used to construct a finite element mesh for each individual, then all individuals from the ten strains were compared to the average mandible from a standard strain (SEA/GnJ). Measures of size and shape associated with finite element scaling analysis were then used in a quantitative genetic analysis of mandibular variation. Significant genetic variation for mandibular size and shape was uncovered. Patterns of both genetic and phenotypic correlation for measures of landmark-specific sizes were consistent with models of morphological integration based on the developmental origin of parts of the mandible and on the effects of muscle attachment on mandibular morphology. Shape differences local to particular landmarks did not show these forms of morphological integration. Although interstrain distances based on local shape magnitudes were significantly correlated with genealogical relationship, distances based on local size differences were not. Even higher than the correlation of genealogy with distances based on local shape magnitude was the genealogical-molecular distance correlation. Patterns of morphometric mandibular variation corresponded to expected effects of epigenetic developmental processes. Also, when detailed shape differences were considered, morphology served as a rough guide to genealogy, although molecular distances showed a stronger relationship.     

Genetic, geographic, and environmental correlates of human temporal bone variation

Temporal bone shape has been shown to reflect molecular phylogenetic relationships among hominoids and offers significant morphological detail for distinguishing taxa. Although it is generally accepted that temporal bone shape, like other aspects of morphology, has an underlying genetic component, the relative influence of genetic and environmental factors is unclear. To determine the impact of genetic differentiation and environmental variation on temporal bone morphology, we used three-dimensional geometric morphometric techniques to evaluate temporal bone variation in 11 modern human populations. Population differences were investigated by discriminant function analysis, and the strength of the relationships between morphology, neutral molecular distance, geographic distribution, and environmental variables were assessed by matrix correlation comparisons. Significant differences were found in temporal bone shape among all populations, and classification rates using cross-validation were relatively high. Comparisons of morphological distances to molecular distances based on short tandem repeats (STRs) revealed a significant correlation between temporal bone shape and neutral molecular distance among Old World populations, but not when Native Americans were included. Further analyses suggested a similar pattern for morphological variation and geographic distribution. No significant correlations were found between temporal bone shape and environmental variables: temperature, annual rainfall, latitude, or altitude. Significant correlations were found between temporal bone size and both temperature and latitude, presumably reflecting Bergmann's rule. Thus, temporal bone morphology appears to partially follow an isolation by distance model of evolution among human populations, although levels of correlation show that a substantial component of variation is unexplained by factors considered here.     

Correlation between genetic distances based on single loci and on skeletal morphology in inbred mice

Genetic and morphometric distances between 12 inbred strains of mice ranging from closely related substrains to a sub-species were estimated using published data on single locus polymorphisms, and on the basis of up to 44 measurements on seven different bones, respectively. Simulation was also used to investigate sampling effects for the single loci. There were strong and statistically highly significant correlations among all measures of genetic distance ranging from 0.58 for the comparison of single loci with the logarithm of the Mahalanobis distance based on 24 measurements on four bones, to 0.72 for estimates of genetic distance based on single loci and the morphology of the mandible. These findings are in sharp contrast with those of Wayne & O'Brien (1986) who claimed that 'structural gene and morphometric variation of mandible traits are uncoupled between mouse strains'. Their failure to find such a correlation is probably because their sample of inbred strains included only a single pair of closely related substrains, and no substrains separated for less than 40 years, and because they failed to correct for non-linearity between morphometric and single-locus measurement scales. Simulations and regression analysis suggested that genetic distances could be estimated with approximately equal precision using morphological data on bone measurements or about 10 cladistically informative single loci, which would usually involve sampling about 50 loci. Data based on single-gene markers is usually more informative than morphometric data for studying the similarity of independently-derived strains. However, similarities among closely related populations such as sublines of an inbred strain can usually be studied more efficiently using morphometry.     

Behavioral and Social Structure Effects on Seed Dispersal Curves of a Forest‐Interior Bulbul (Pycnonotidae) in a Tropical Evergreen Forest

Movement patterns of animals can vary dramatically as a function of their reproductive cycle or social structure; however, little is known about how changes in the social structure of dispersers affect patterns of seed dispersal. We examined the movement patterns of the forest‐dwelling and cooperatively breeding Puff‐throated Bulbul (Alophoixus pallidus) in relation to different stages of their reproductive cycle, time of day, and group size, to determine potential impacts on the shape and scale of dispersal curves generated using a combination of gut passage time and displacement distance data. There were significant differences in dispersal distances depending on group size, season (breeding, non‐breeding), incubation (vs. other times of the year), and time of the day. The estimated median seed dispersal distance was 28 m. The median dispersal distances produced by birds in larger groups were longer than those of smaller groups (29 m vs. 25 m). During the breeding season, median dispersal distances were longer than during the non ‐ breeding season (31 m vs. 25 m), but the median dispersal distances were significantly shorter during incubation than during outside incubation (24 m vs. 28 m). The median dispersal distance produced in the early morning (30 m) was also longer than that of other times of the day (23 m late morning, 28 m early afternoon, and 26 m late afternoon). This study suggests that various aspects of an animal's behavior are likely to have significant effects on seed shadows and that this may vary significantly even among individuals of the same species.     

Multivariate analysis of anthropometric data and classifications of British Columbian natives

Anthropometric data collected in native populations of British Columbia in the late 19th century by Franz Boas were analyzed by two multivariate techniques. Multivariate analysis of variance was used to test physical classificatory units devised by Boas and an ad hoc classification based on local cultural units. Both were found to have some empirical validity. Mahalanobis' D (Mahalanobis, '30) was computed between pairs of local groups, for both sexes. From these a matrix of differences was prepared and diagrams drawn to illustrate phenetic relationships among samples. By this means one cluster of groups, Interior B.C. peoples, could be distinguished and other local samples appeared distinctly different from each other. It was concluded that in the absence of genealogical data by which to identify local populations, local cultural units are preferable to more inclusive units for making empirical comparisons and classifications.     

MULTIVARIATE PHENOTYPIC DIFFERENTIATION AMONG BOTTLENECK LINES OF THE HOUSEFLY

Multivariate phenotypic differentiation in eight morphometric traits was examined in bottleneck lines of the housefly initiated with one, four, or 16 pairs of flies from a natural outbred population. Differentiation was assessed using a Mahalanobis' distance metric in units of additive genetic variance and covariance estimated from the ancestral population (i.e., generalized genetic distance). This distance metric was partitioned into contributions of size and shape to total distance. Bottleneck lines of all sizes diverged significantly from the ancestral line, but the direction of these shifts differed among the lines of different initial founding size. Those populations founded with single pairs diverged from the ancestral line mostly in shape; the 16-pair lines differentiated almost entirely in size, and the four-pair lines were intermediate in the relative contribution of shape to differentiation from the control. Bottlenecks serve to alter the genetic relationships among traits within the derived populations and in doing so could promote speciation by permitting differentiation of the populations along evolutionary trajectories less accessible to the base population.     

Some remarks on the interpretation of Penrose's size and shape components. Craniometrical similarities of African groups

The present paper deals with cranial data of different African races and shows how far the components “size” and “shape” of the Penrose distance express biological distances as well as the kind of changes occurring when different groups of variables are used. The stability of the distances between the populations was further studied by exchanging the reference group on a racial and subracial level. The analyses supply a differentiated picture according to the affinities, especially between the reference populations of the major races. Europoid and Negroid populations can often be separated only by shape distance, while the size distance is more suitable for separating Bushmen and Hottentots.     

Genetic structure and essential oil composition in wild populations of Salvia multicaulis Vahl.

The phytochemical study on ten populations of Salvia multicaulis Vahl. revealed that their essential oil qualitative profiles contained a significant amount of monoterpene hydrocarbons, which were the most abundant compounds. Besides, α-Pinene was the major constituent in all studied populations' essential oils. Significant correlations were observed between edaphic parameters and some major essential oil compounds. According to clustering analyses of the chemical data, the S. multicaulis populations were divided into three chemotypes: β-caryophyllene, camphene and camphor, and limonene. The population genetics study showed significant molecular differences among the populations. The Mantel test indicated a significant positive correlation between the geographical distances and genetic diversity, exhibiting a low amount of gene flow and a considerable genetic differentiation value. We also detected four genotypes based on the Nei's genetic distance and structure analysis. The identified chemical and genetic similarities/differences among these populations were correlated with edaphic parameters and geographic distances, suggesting that environmental factors are the primary drivers of the chemical polymorphism of essential oils in S. multicaulis populations.     

Systematics and evolution of the Jacchus group of marmosets (Platyrrhini)

Interspecific differentiation and geographic variation patterns in 39 skull traits of eastern Brazilian marmosets are analyzed. Eastern Callithrix taxa are distinct morphologically, and no evidence of intergradation among taxa is observed. Instead, there are sharp, stepped morphological boundaries among taxa, consistent with species‐level distinction. The morphological similarity cluster diagram obtained from Mahalanobis distances is different from available molecular trees, and the general picture emerging is that the eastern Callithrix taxa should be considered as good species arising recently in South American history. In particular, C. kuhlii is morphologically distinct from other marmoset taxa, including C. geoffroyi and C. penicillata, which were previously hypothesized to be the parental populations that formed C. kuhlii by hybridization. Furthermore, C. kuhlii populations from southeastern Bahia do not overlap morphologically with any C. penicillata population, including the upper São Francisco River populations that display skin colors and pelage patterns to some extent similar to true Kuhli's marmosets. There is a negative, though insignificant, correlation between the morphological distance matrix and a Mahalanobis distance matrix estimated from nine climatic variables, a pattern opposite to that expected under a parapatric speciation model. This result, together with the lack of clinal variation in skull traits, suggests that an allopatric model of speciation might best explain eastern marmoset diversification. Am J Phys Anthropol 2003. © 2002 Wiley‐Liss, Inc.     

Ecogeographic analysis of morphological and life-history variation in the Italian treefrog

We describe the spatial pattern of variation in body size, body shape, and adult population age structure of the Italian treefrog (Hyla intermedia). By means of a non-parametric test of matrix association (the Partial Mantel Test), we investigate the role of climate and geography in explaining the patterns of phenotypic variation. Body size is the most important source of morphometric variation, both at intra- and inter-populational levels. Body shape, despite its secondary role in explaining variation, still maintains high discriminative power among populations. Age structure differs significantly among populations, since body size correlates positively to age, these differences partly explain geographic variation of body size. The patterns of variation in both age and body size are congruent with climate variation, suggesting causal relationship. However, we find no evidence for adaptive explanations and suggest that climate-induced demographically differential survivorship might be the proximate cause responsible for the associations observed. Unlike body size, body shape varies congruently with the pattern of between-population geographic distances, which we show to be highly correlated with their genetic distances, thus suggesting isolation by distance as the proximate cause of the association.     

A critical review of the mean measure of divergence and Mahalanobis distances using artificial data and new approaches to the estimation of biodistances employing nonmetric traits

This article reviews the two most common distance measures employed for the calculation of biodistances based on nonmetric traits, the mean measure of divergence (MMD) and the tetrachoric Mahalanobis D² distance (TMD). In addition, two new approaches for the estimation of biodistances from nonmetric traits are proposed and assessed. The first (OMD) is based on the direct application of the Mahalanobis distance to ordinally recorded data before their transformation to binary dichotomies. The second (RMD) approximates the covariances of the Mahalanobis distance by the Pearson correlation coefficients calculated in the binary dataset. The application of all four methods to artificial datasets demonstrates that they overall provide a satisfactory estimation of the biodistance among samples especially when the number of statistically non significant distances is very limited. However, the best performance is observed by the OMD, whereas special attention should be paid to the TMD since its values might come out of an ill‐conditioned system. The influence of the number of traits, the effect of missing values, as well as the validity of the test statistics used to assess biodistance significance are also examined and discussed. Am J Phys Anthropol 157:284–294, 2015. © 2015 Wiley Periodicals, Inc.     

Multivariate statistical analysis on the physical interrelationship of native tribes in Sarawak, Malaysia

An anthropometric survey was made on the seven tribes in Sarawak, Malaysia. In order to study their physical interrelationship, the data obtained were used for multivariate statistical analysis including Mahalanobis's distance and two-dimensional representation of group configuration with canonical variates. The conclusions were as follows; the Land Dayak are different from other tribes; the Kayan and Kenyah resemble each other; the Iban, Malay and Kedayan are close enough to make a cluster; and the Land Dayak, Kedayan and Melanau, being different from one another, do not seem to be of the same origin.     

Effects of landscape and history on diversification of a montane, stream-breeding amphibian

Aim The aim of this study was to understand the roles of landscape features in shaping patterns of contemporary and historical genetic diversification among populations of the Andean tree frog (Hypsiboas andinus) across spatial scales. Location Andes mountains, north‐western Argentina, South America. Methods Mitochondrial DNA control region sequences were utilized to assess genetic differentiation among populations and calculate population pair‐wise genetic distances. Three models of movement, namely traditional straight‐line distance and two effective distances based on habitat classification, were examined to determine which of these explained the most variation in pair‐wise population genetic differentiation. The two habitat classifications were based on digital vegetation and hydrology layers that were generated from a 90‐m resolution digital elevation model (DEM) and known relationships between elevation and habitat. Mantel tests were conducted to test for correlations between geographic and genetic distance matrices and to estimate the percentage variation explained by each type of geographic distance. To investigate the location of possible barriers to gene flow, we used Monmonier’s maximum difference algorithm as implemented in barrier 2.2. Results At both geographic scales, effective distances explained more variation in genetic differentiation than did straight‐line distance. The least‐cost distances based on the simple classification performed better than the more detailed habitat classification. We controlled for the effects of historical range fragmentation determined from previous nested clade analyses, and therefore evaluated the effect of different distances on the genetic variation attributable to more recent factors. Effective distances identified populations that were highly divergent as a result of isolation in unsuitable habitats. The proposed locations of barriers to gene flow identified using Monmonier’s maximum difference algorithm corresponded well with earlier analyses and supported findings from our partial Mantel tests. Main conclusions Our results indicate that landscape features have been important in both historical and contemporary genetic structuring of populations of H. andinus at both large and small spatial scales. A landscape genetic perspective offers novel insights not provided by traditional phylogeographic studies: (1) effective distances can better explain patterns of differentiation in populations, especially in heterogeneous landscapes where barriers to dispersal may be common; and (2) least‐cost path analysis can help to identify corridors of movement between populations that are biologically more realistic.     

Microsatellite diversity among the primitive tribes of India

The present study was undertaken to determine the extent of diversity at 12 microsatellite short tandem repeat (STR) loci in seven primitive tribal populations of India with diverse linguistic and geographic backgrounds. DNA samples of 160 unrelated individuals were analyzed for 12 STR loci by multiplex polymerase chain reaction (PCR). Gene diversity analysis suggested that the average heterozygosity was uniformly high ( >0.7) in these groups and varied from 0.705 to 0.794. The Hardy-Weinberg equilibrium analysis revealed that these populations were in genetic equilibrium at almost all the loci. The overall G(ST) value was high (G(ST) = 0.051; range between 0.026 and 0.098 among the loci), reflecting the degree of differentiation/heterogeneity of seven populations studied for these loci. The cluster analysis and multidimensional scaling of genetic distances reveal two broad clusters of populations, besides Moolu Kurumba maintaining their distinct genetic identity vis-à-vis other populations. The genetic affinity for the three tribes of the Indo-European family could be explained based on geography and Language but not for the four Dravidian tribes as reflected by the NJT and MDS plots. For the overall data, the insignificant MANTEL correlations between genetic, linguistic and geographic distances suggest that the genetic variation among these tribes is not patterned along geographic and/or linguistic lines.