S. Ivan Perez

Differences between sliding semi-landmark methods in geometric morphometrics, with an application to human craniofacial and dental variation

Over the last decade, geometric morphometric methods have been applied increasingly to the study of human form. When too few landmarks are available, outlines can be digitized as series of discrete points. The individual points must be slid along a tangential direction so as to remove tangential variation, because contours should be homologous from subject to subject whereas their individual points need not. This variation can be removed by minimizing either bending energy (BE) or Procrustes distance (D) with respect to a mean reference form. Because these two criteria make different assumptions, it becomes necessary to study how these differences modify the results obtained. We performed bootstrapped‐based Goodalls F‐test, Footes measurement, principal component (PC) and discriminant function analyses on human molars and craniometric data to compare the results obtained by the two criteria. Results show that: (1) F‐scores and P‐values were similar for both criteria; (2) results of Footes measurement show that both criteria yield different estimates of within‐ and between‐sample variation; (3) there is low correlation between the first PC axes obtained by D and BE; (4) the percentage of correct classification is similar for BE and D, but the ordination of groups along discriminant scores differs between them. The differences between criteria can alter the results when morphological variation in the sample is small, as in the analysis of modern human populations.

Geometric morphometric approach to sex estimation of human pelvis

Sex estimation of skeletal remains is an important issue in both forensics and bioarchaeology. The chance of attaining a high level of accuracy regarding sex allocations is related to the skeletal component analyzed and the ability of the techniques employed to describe shape and size differences among the sexes. Current opinion regards the hip bone as the most reliable sex indicator because it is the most dimorphic bone, particularly in adult individuals. The aim of this study was therefore to analyze the greater sciatic notch and the ischiopubic complex morphology by employing geometric morphometric techniques, based on semilandmark and multivariate statistical methods, in order to develop a reliable and accurate technique for adult sex estimation. The sample analyzed consisted of 121 adult left hip bones randomly selected from the collection of documented skeletons housed at the Museu Antropologico de Coimbra. Morphometric analysis was based on coordinates of landmarks and semilandmarks of the ilium and ischiopubic regions that were digitized on 2D photographic images. Discriminant analysis with leave-one-out cross-validation and k-means clustering of shape and shape-size variables were used in order to classify individuals by sex. For the greater sciatic notch, average accuracy of 90.9% was achieved with both multivariate analyses based on shape variables. For the ischiopubic complex, the values obtained with shape variables were 93.4% and 90.1% for discriminant and k-means, respectively. Females were misclassified more frequently than males, especially for the ischiopubic complex. When multivariate statistical analyses were performed using shape-size variables, the percentages of correct classifications were lower than those obtained with shape variables. We conclude that the use of geometric morphometrics and multivariate statistics is a reliable method to quantify pelvic shape differences between the sexes and could be applied to discriminate between females and males.

Nonrandom factors in modern human morphological diversification: a study of craniofacial variation in southern South american populations.

The causes of craniofacial variation among human populations have been the subject of controversy. In this work, we studied aboriginal populations from southern South America, the last continental region peopled by humans and with a wide range of ecological conditions. Because of these characteristics, southern South America provides a unique opportunity to study the relative importance of random and nonrandom factors in human diversification. Previous craniometric studies recognized remarkable differences among populations from this region, usually resorting to random factors as the main explanation. In contrast, here we suggest, using tests based on quantitative genetic models, that: (1) the rate of craniofacial divergence among these populations is too high and (2) the patterns of variation within and between populations are too different to be explained by genetic drift alone. In addition, the among-sample craniofacial variation is correlated with climate and diet but not with mtDNA variation. We suggest that the influence of nonrandom factors (e.g., plasticity, selection) on human craniofacial diversification in regions with large ecological variation is more important than generally acknowledged and capable to generate large craniofacial divergence in a short period of time. These results bring nonrandom factors into focus for the interpretation of human craniofacial variation.

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.

Ontogeny of Robusticity of Craniofacial Traits in Modern Humans: A Study of South American Populations

To date, differences in craniofacial robusticity among modern and fossil humans have been primarily addressed by analyzing adult individuals; thus, the developmental basis of such differentiation remains poorly understood. This article aims to analyze the ontogenetic development of craniofacial robusticity in human populations from South America. Geometric morphometric methods were used to describe cranial traits in lateral view by using landmarks and semilandmarks. We compare the patterns of variation among populations obtained with subadults and adults to determine whether population-specific differences are evident at early postnatal ontogeny, compare ontogenetic allometric trajectories to ascertain whether changes in the ontogeny of shape contribute to the differentiation of adult morphologies, and estimate the amount of size change that occurs during growth along each population-specific trajectory. The results obtained indicate that the pattern of interpopulation variation in shape and size is already established at the age of 5 years, meaning that processes acting early during ontogeny contribute to the adult variation. The ontogenetic allometric trajectories are not parallel among all samples, suggesting the divergence in the size-related shape changes. Finally, the extension of ontogenetic trajectories also seems to contribute to shape variation observed among adults.

Molecular phylogenetic relationships and phenotypic diversity in miniaturized toadlets, genus Brachycephalus (Amphibia: Anura: Brachycephalidae)

Toadlets of the genus Brachycephalus are endemic to the Atlantic rainforests of southeastern and southern Brazil. The 14 species currently described have snout-vent lengths less than 18 mm and are thought to have evolved through miniaturization: an evolutionary process leading to an extremely small adult body size. Here, we present the first comprehensive phylogenetic analysis for Brachycephalus, using a multilocus approach based on two nuclear (Rag-1 and Tyr) and three mitochondrial (Cyt b, 12S, and 16S rRNA) gene regions. Phylogenetic relationships were inferred using a partitioned Bayesian analysis of concatenated sequences and the hierarchical Bayesian method (BEST) that estimates species trees based on the multispecies coalescent model. Individual gene trees showed conflict and also varied in resolution. With the exception of the mitochondrial gene tree, no gene tree was completely resolved. The concatenated gene tree was completely resolved and is identical in topology and degree of statistical support to the individual mtDNA gene tree. On the other hand, the BEST species tree showed reduced significant node support relative to the concatenate tree and recovered a basal trichotomy, although some bipartitions were significantly supported at the tips of the species tree. Comparison of the log likelihoods for the concatenated and BEST trees suggests that the method implemented in BEST explains the multilocus data for Brachycephalus better than the Bayesian analysis of concatenated data. Landmark-based geometric morphometrics revealed marked variation in cranial shape between the species of Brachycephalus. In addition, a statistically significant association was demonstrated between variation in cranial shape and genetic distances estimated from the mtDNA and nuclear loci. Notably, B. ephippium and B. garbeana that are predicted to be sister-species in the individual and concatenated gene trees and the BEST species tree share an evolutionary novelty, the hyperossified dorsal plate.

Species tree estimation for a deep phylogenetic divergence in the New World monkeys (Primates: Platyrrhini)

The estimation of a robust phylogeny is a necessary first step in understanding the biological diversification of the platyrrhines. Although the most recent phylogenies are generally robust, they differ from one another in the relationship between Aotus and other genera as well as in the relationship between Pitheciidae and other families. Here, we used coding and non-coding sequences to infer the species tree and embedded gene trees of the platyrrhine genera using the Bayesian Markov chain Monte Carlo method for the multispecies coalescent (*BEAST) for the first time and to compared the results with those of a Bayesian concatenated phylogenetic analysis. Our species tree, based on all available sequences, shows a closer phylogenetic relationship between Atelidae and Cebidae and a closer relationship between Aotus and the Cebidae clade. The posterior probabilities are lower for these conflictive tree nodes compared to those in the concatenated analysis; this finding could be explained by some gene trees showing no concordant topologies between Aotus and the other genera. Moreover, the topology of our species tree also differs from the findings of previous molecular and morphological studies regarding the position of Aotus. The existence of discrepancies between morphological data, gene trees and the species tree is widely reported and can be related to processes such as incomplete lineage sorting or selection. Although these processes are common in species trees with low divergence, they can also occur in species trees with deep and rapid divergence. The sources of the inconsistency of morphological and molecular traits with the species tree could be a main focus of further research on platyrrhines.

Modeling lineage and phenotypic diversification in the New World monkey (Platyrrhini, Primates) radiation

Adaptive radiations that have taken place in the distant past can now be more thoroughly studied with the availability of large molecular phylogenies and comparative data drawn from extant and fossil species. Platyrrhines are a good example of a major mammalian evolutionary radiation confined to a single continent, involving a relatively large temporal scale and documented by a relatively small but informative fossil record. Here, we present comparative evidence using data on extant and fossil species to explore alternative evolutionary models in an effort to better understand the process of platyrrhine lineage and phenotypic diversification. Specifically, we compare the likelihood of null models of lineage and phenotypic diversification versus various models of adaptive evolution. Moreover, we statistically explore the main ecological dimension behind the platyrrhine diversification. Contrary to the previous proposals, our study did not find evidence of a rapid lineage accumulation in the phylogenetic tree of extant platyrrhine species. However, the fossil-based diversity curve seems to show a slowdown in diversification rates toward present times. This also suggests an early high rate of extinction among lineages within crown Platyrrhini. Finally, our analyses support the hypothesis that the platyrrhine phenotypic diversification appears to be characterized by an early and profound differentiation in body size related to a multidimensional niche model, followed by little subsequent change (i.e., stasis).

Ontogenetic Allometry and Cranial Shape Diversification Among Human Populations From South America

Modifications of ontogenetic allometries play an important role in patterning the shape differentiation among populations. This study evaluates the influence of size variation on craniofacial shape disparity among human populations from South America and assesses whether the morphological disparity observed at the interpopulation level resulted from a variable extension of the same ontogenetic allometry, or whether it arose as a result of divergences in the pattern of size‐related shape changes. The size and shape of 282 adult and subadult crania were described by geometric morphometric‐based techniques. Multivariate regressions were used to evaluate the influence of size on shape differentiation between and within populations, and phylogenetic comparative methods were used to take into account the shared evolutionary history among populations. The phylogenetic generalized least‐squares models showed that size accounts for a significant amount of shape variation among populations for the vault and face but not for the base, suggesting that the three modules did not exhibit a uniform response to changes in overall growth. The common slope test indicated that patterns of evolutionary and ontogenetic allometry for the vault and face were similar and characterized by a heightening of the face and a lengthening of the vault with increasing size. The conservation of the same pattern of shape changes with size suggests that differences in the extent of growth contributed to the interpopulation cranial shape variation and that certain directions of morphological change were favored by the trait covariation along ontogeny. Anat Rec, 2011.

Spatial patterns and evolutionary processes in southern South America: A study of dental morphometric variation

The purpose of this article is to examine the patterns of evolutionary relationships between human populations from the later Late Holocene (1,500-100 years BP) of southern South America on the basis of dental morphometric data. We tested the hypotheses that the variation observed in this region would be explained by the existence of populations with different phylogenetic origin or differential action of gene flow and genetic drift. In this study, we analyzed permanent teeth from 17 samples of male and female adult individuals from throughout southern South America. We measured mesiodistal and buccolingual diameters at the base of the crown, along the cement-enamel junction. The results of multiple regression analysis and a mantel correlogram indicate the existence of spatial structure in dental shape variation, as the D(2) Mahalanobis distance between samples increases with increasing geographical distance between them. In addition, the correlation test results show a trend toward reduction of the internal variation of samples with increasing latitude. The detected pattern of dental variation agrees with the one expected as an outcome of founder serial effects related to an expansion of range during the initial occupation of southern South America.