Andrea Cardini

Leaf Morphology, Taxonomy and Geometric Morphometrics: A Simplified Protocol for Beginners

Taxonomy relies greatly on morphology to discriminate groups. Computerized geometric morphometric methods for quantitative shape analysis measure, test and visualize differences in form in a highly effective, reproducible, accurate and statistically powerful way. Plant leaves are commonly used in taxonomic analyses and are particularly suitable to landmark based geometric morphometrics. However, botanists do not yet seem to have taken advantage of this set of methods in their studies as much as zoologists have done. Using free software and an example dataset from two geographical populations of sessile oak leaves, we describe in detailed but simple terms how to: a) compute size and shape variables using Procrustes methods; b) test measurement error and the main levels of variation (population and trees) using a hierachical design; c) estimate the accuracy of group discrimination; d) repeat this estimate after controlling for the effect of size differences on shape (i.e., allometry). Measurement error was completely negligible; individual variation in leaf morphology was large and differences between trees were generally bigger than within trees; differences between the two geographic populations were small in both size and shape; despite a weak allometric trend, controlling for the effect of size on shape slighly increased discrimination accuracy. Procrustes based methods for the analysis of landmarks were highly efficient in measuring the hierarchical structure of differences in leaves and in revealing very small-scale variation. In taxonomy and many other fields of botany and biology, the application of geometric morphometrics contributes to increase scientific rigour in the description of important aspects of the phenotypic dimension of biodiversity. Easy to follow but detailed step by step example studies can promote a more extensive use of these numerical methods, as they provide an introduction to the discipline which, for many biologists, is less intimidating than the often inaccessible specialistic literature.

Sample size and sampling error in geometric morphometric studies of size and shape

Geometric morphometric studies are increasingly becoming common in systematics and palaeontology. The samples in such studies are often small, due to the paucity of material available for analysis. However, very few studies have tried to assess the impact of sampling error on analytical results. Here, this issue is addressed empirically using repeated randomized selection experiments to build progressively smaller samples from an original dataset of ∼400 vervet monkey (Cercopithecus aethiops) skulls. Size and shape parameters (including mean size and shape, size and shape variances, angles of allometric trajectories) that are commonly used in geometric morphometric studies, are estimated first in the original sample and then in the random subsamples. Estimates are then compared to give an indication of what is the minimum desirable sample size for each parameter. Mean size, standard deviation of size and variance of shape are found to be fairly accurate even in relatively small samples. In contrast, mean shapes and angles between static allometric trajectories are strongly affected by sampling error. If confirmed in other groups, our findings may have substantial implications for studies of morphological variation in present and fossil species. By performing rarefaction analyses like those presented in our study, morphometricians can be easily provided with important clues on how a simple but crucial factor like sample size can alter results of their studies.

Estimation of sex from sternal measurements in a Western Australian population

In Australia, particularly Western Australia, there is a relative paucity of contemporary population-specific morphometric standards for the estimation of sex from unknown skeletal remains. This is largely a historical artefact from lacking, or poorly documented, repositories of human skeletons available for study. However, medical scans, e.g. MSCT (multislice spiral computed tomography) are an ingenious and practical alternative source for contemporary data. To that end, this study is a comprehensive analysis of sternal sexual dimorphism in a sample of modern Western Australian (WA) individuals with a main purpose to develop a series of statistically robust standards for the estimation of sex. The sample comprises thoracic MSCT scans, with a mean of 0.9 millimeter (mm) slice thickness, on 187 non-pathological sterna. Following 3D volume rendering, 10 anatomical landmarks were acquired using OsiriX(®) (version 3.9) and a total of 8 inter landmark linear measurements were calculated using Morph Db (an in-house developed database application). Measurements were analyzed using basic descriptive statistics and discriminant function analyses, with statistical analyses performed using SPSS 19.0. All measurements are sexually dimorphic and sex differences explain 9.8-47.4% of sample variance. The combined length of the manubrium and body, sternal body length, manubrium width, and corpus sterni width at first sternebra contribute significantly to sex discrimination and yield the smallest sex-biases. Cross-validated classification accuracies, i.e., univariate, stepwise and direct function, are 72.2-84.5%, with a sex bias of less than 5%. We conclude that the sternum is a reliable element for sex estimation among Western Australians.

The Geometry of the Marmot (Rodentia: Sciuridae) Mandible: Phylogeny and Patterns of Morphological Evolution

Marmots have a prominent role in the study of mammalian social evolution, but only recently has their systematics received the attention it deserves if sociobiological studies are to be placed in a phylogenetic context. Sciurid morphology can be used as model to test the congruence between morphological change and phylogeny because sciurid skeletal characters are considered to be inclined to convergence. However, no morphological study involving all marmot species has ever been undertaken. Geometric morphometric techniques were applied in a comparative study of the marmot mandible. The adults of all 14 living marmot species were compared, and mean mandible shape were used to investigate morphological evolution in the genus Marmota. Three major trends were observed. First, the phylogenetic signal in the variation of landmark geometry, which describes mandible morphology, seems to account for the shape differences at intermediate taxonomic levels. The subgenera Marmota and Petromarmota, recently proposed on the basis of mitochondrial cytochrome b sequence, receive support from mandible morphology. When other sciurid genera were included in the analysis, the monophyly of the genus Marmota and that of the tribe Marmotini (i.e., marmots, prairie dogs, and ground squirrels) was strengthened by the morphological data. Second, the marmotine mandible may have evolved as a mosaic of characters and does not show convergence determined by size similarities. Third, allopatric speciation in peripheral isolates may have acted as a powerful force for modeling shape. This hypothesis is strongly supported by the peculiar mandible of M. vancouverensis and, to a lesser degree, by that of M. olympus, both thought to have originated as isolated populations in Pleistocene ice-free refugia.

Larger mammals have longer faces because of size-related constraints on skull form

Facial length is one of the best known examples of heterochrony. Changes in the timing of facial growth have been invoked as a mechanism for the origin of our short human face from our long-faced extinct relatives. Such heterochronic changes arguably permit great evolutionary flexibility, allowing the mammalian face to be remodelled simply by modifying postnatal growth. Here we present new data that show that this mechanism is significantly constrained by adult size. Small mammals are more brachycephalic (short faced) than large ones, despite the putative independence between adult size and facial length. This pattern holds across four phenotypic lineages: antelopes, fruit bats, tree squirrels and mongooses. Despite the apparent flexibility of facial heterochrony, growth of the face is linked to absolute size and introduces what seems to be a loose but clade-wide mammalian constraint on head shape.

The application of traditional and geometric morphometric analyses for forensic quantification of sexual dimorphism: preliminary investigations in a Western Australian population

A current limitation of forensic practice in Western Australia is a lack of contemporary population-specific standards for biological profiling; this directly relates to the unavailability of documented human skeletal collections. With rapidly advancing technology, however, it is now possible to acquire accurate skeletal measurements from 3D scans contained in medical databases. The purpose of the present study, therefore, is to explore the accuracy of using cranial form to predict sex in adult Australians. Both traditional and geometric morphometric methods are applied to data derived from 3D landmarks acquired in CT-reconstructed crania. The sample comprises multi-detector computed tomography scans of 200 adult individuals; following 3D volume rendering, 46 anatomical landmarks are acquired using OsiriX (version 3.9). Centroid size and shape (first 20 PCs of the Procrustes coordinates) and the inter-landmark (ILD) distances between all possible pairs of landmarks are then calculated. Sex classification effectiveness of the 3D multivariate descriptors of size and shape and selected ILD measurements are assessed and compared; robustness of findings is explored using resampling statistics. Cranial shape and size and the ILD measurements are sexually dimorphic and explain 3.2 to 54.3 % of sample variance; sex classification accuracy is 83.5–88.0 %. Sex estimation using 3D shape appears to have some advantages compared to approaches using size measurements. We have, however, identified a simple and biologically meaningful single non-traditional linear measurement (glabella–zygion) that classifies Western Australian individuals according to sex with a high degree of expected accuracy (87.5–88 %).

Variation in guenon skulls (I): species divergence, ecological and genetic differences

Guenons are the most diverse clade of African monkeys. They have varied ecologies, include arboreal and terrestrial species, and can be found in nearly every region of sub-Saharan Africa. Species boundaries are often uncertain, with a variable number of species and subspecies mostly recognised on the basis of their geographic distribution and pelage. If guenon soft tissue patterns show high variability, the same does not seem to hold for skull morphology. Guenon skulls are traditionally considered relatively undifferentiated and homogeneous. However, patterns of variation in skulls have never been examined using a large number of specimens sampled across the breadth of species diversity. Thus, in the present study, skulls of adult guenons and two outgroup species are analysed using three-dimensional geometric morphometrics. Three-dimensional coordinates of 86 anatomical landmarks were measured on 1,315 adult specimens belonging to all living guenon species except Cercopithecus dryas. Species are well-discriminated using shape but the best discrimination occurs when species have either a long evolutionary history (e.g., Allenopithecus nigroviridis) or represent extremes of size variation (Miopithecus sp. and Erythrocebus patas). Interspecific phenetic relationships reflect size differences. Four main clusters are found that mainly correspond to four size groups: the smallest species (Miopithecus sp.), the largest species (E. patas plus the study outgroups), a group of medium-small arboreal guenons, and a group of medium-large arboreal and terrestrial guenons. Correlations between interspecific shape distances and interspecific differences in size are higher than between shape distances and genetic distances. However, if only the component of interspecific shape variation which is not correlated to evolutionary allometry is used in the comparison with genetic distances, correlations are up to 1.4 times larger than those including allometric shape. The smallest correlations are those between shape and ecological distances, which is consistent with the lack of clusters clearly reflecting broad ecological specialisations (e.g., arboreality versus terrestriality). Thus, size, which is generally considered more evolutionarily labile than shape, seems to have played a major role in the evolution of the guenons. The incongruence between interspecific shape differences and phylogeny might be explained by a large proportion of shape changes having occurred along allometric trajectories that tend to be conserved within this clade.

Post-natal ontogeny of the mandible and ventral cranium in Marmota species (Rodentia, Sciuridae): allometry and phylogeny

Post-natal ontogenetic variation of the marmot mandible and ventral cranium is investigated in two species of the subgenus Petromarmota (M. caligata, M. flaviventris) and four species of the subgenus Marmota (M. caudata, M. himalayana, M. marmota, M. monax). Relationships between size and shape are analysed using geometric morphometric techniques. Sexual dimorphism is negligible, allometry explains the main changes in shape during growth, and males and females manifest similar allometric trajectories. Anatomical regions affected by size-related shape variation are similar in different species, but allometric trajectories are divergent. The largest modifications of the mandible and ventral cranium occur in regions directly involved in the mechanics of mastication. Relative to other anatomical regions, the size of areas of muscle insertion increases, while the size of sense organs, nerves and teeth generally decreases. Epigenetic factors, developmental constraints and size variation were found to be the major contributors in producing the observed allometric patterns. A phylogenetic signal was not evident in the comparison of allometric trajectories, but traits that allow discrimination of the Palaearctic marmots from the Nearctic species of Petromarmota are present early in development and are conserved during post-natal ontogeny.

Extreme climate, rather than population history, explains mid-facial morphology of northern asians

Previous studies have examined mid-facial cold adaptation among either widely dispersed and genetically very diverse groups of humans isolated for tens of thousands of years, or among very closely related groups spread over climatically different regions. Here we present a study of one East Asian and seven North Asian populations in which we examine the evidence for convergent adaptations of the mid-face to a very cold climate. Our findings indicate that mid-facial morphology is strongly associated with climatic variables that contrast the temperate climate of East Asians and the very cold and dry climate of North Asians. This is also the case when either maxillary or nasal cavity measurements are considered alone. The association remains significant when mtDNA distances among populations are taken into account. The morphological contrasts between populations are consistent with physiological predictions and prior studies of mid-facial cold adaptation in more temperate regions, but among North Asians there appear to be some previously undescribed morphological features that might be considered as adaptive to extreme cold. To investigate this further, analyses of the seven North Asian populations alone suggest that mid-facial morphology remains strongly associated with climate, particularly winter precipitation, contrasting coastal Arctic and continental climates. However, the residual covariation among North Asian mid-facial morphology and climate when genetic distances are considered, is not significant. These findings point to modern adaptations to extreme climate that might be relevant to our understanding of the mid-facial morphology of fossil hominins that lived during glaciations.

Morphometrics and phylogenetics: principal components of shape from cranial modules are neither appropriate nor effective cladistic characters.

Department of Ecology, Evolution, and Organismal Biology, and Department of Statistics, Iowa State University, Ames, IA 50011 USA Anatomical and Human Sciences, Hull York Medical School, The University of York, York Y010 5DD, UK Museo di Paleobiologia e dell’Orto Botanico, Universita di Modena e Reggio Emilia, via Universita 4, 41100, Modena, Italy Department of Biological Sciences, The University of Hull, Hull HU6 7RX, UK Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794 USA