Dentaries of the 6 species of Myotis that occur in the eastern United States were analyzed using landmark-based geometric morphometrics. The species could be distinguished with a high degree of accuracy. Evidence was found of a phylogenetic signal in the morphology of the Neotropical and Nearctic Myotis sub-clades. There is also evidence of convergence in the morphology of the dentary among Myotis species that feed primarily by gleaning. When analyzed together there was no evidence of sexual dimorphism among the 6 eastern U.S. Myotis, but when analyzed individually some dimorphism may be present. A sample of fossil Myotis of unknown species from Bat Cave, Kentucky, was analyzed in an attempt to identify the specimens to species. Results indicate that Myotis austroriparius and M. sodalis predominate the sample, possibly with smaller numbers of M. grisescens and M. leibii. This study demonstrates the ability to differentiate Myotis taxa from historic and prehistoric sites and provides a tool for researchers to better understand and potentially conserve these species.

Eastern Newts (Notophthalmus viridescens) are a ubiquitous member of eastern North America’s caudate fauna. Unlike the typical amphibian, their life cycle is split into three phases instead of two, commonly called a triphasic life cycle. The larvae of N. viridescens are fully aquatic, eventually metamorphosing to become terrestrial juveniles, called efts. Upon sexual maturity, the eft will metamorphose into a semi-aquatic adult where its external morphology is typical of an aquatic salamander. Since there are apparent differences in their ecological niche, there are different forces acting on their skeletons. We hypothesize that due to differences in buoyancy, torsion, and locomotion, differences are expected in the morphology of the axial skeleton. Using image data generated on a SkyScan 1273 micro-computed tomography (µCT) scanner, 3D shape analyses will be used to quantify shape differences between vertebrae and test the hypothesis. Three dimensional digital models of each vertebrae of interest will be rendered from the scans in Dragonfly (Object Research Systems). Each 3D model is then loaded into SlicerMorph (3D Slicer), where landmarks are placed upon homologous structures on each vertebra. A Generalized Procrustes Analysis (GPA) followed by a Principal Component Analysis (PCA) is conducted for each vertebra to test for potential shape differences between each life stage. GPA and PCA analysis will be conducted on 10 terrestrial juveniles, 10 semi-aquatic adults, 5 aquatic juveniles, and 5 paedomorphic adults. The 5 aquatic juveniles and 5 paedomorphic adults, eastern newts that remain in the water through their entire lives, will validate if the semi-aquatic adult is truly adapting towards an aquatic lifestyle. If GPA and PCA indicate statistical shape differences between certain vertebrae, those vertebrae will be run through the Automated Landmarking through Pointcloud Alignment and Correspondence Analysis (ALPACA) module of SlicerMorph to produce heatmap data on the 3D models showing where exactly the shape changes are occurring in the vertebra.

OBJECTIVE: The objective of this study is to determine the earliest time point in growth when a difference in mandibular shape of dolichocephalic and brachycephalic subjects is distinguishable. MATERIALS & METHODS: 11 dolichocephalic and 14 brachycephalic subjects were selected using lateral cephalograms from the Forsyth/Moorrees Twin Study using a method described by Rocky Mountain Orthodontics. 23 landmarks outlining the mandible were identified on the lateral cephalograms of each subject from their earliest age (5-8 years) to their latest (16-18 years) using TPSdig software. The 2 dimensional coordinates for each landmark were then exported to TPSUtil. From TPSUtil, the TPS data was then converted to a .csv file in Microsoft Excel and imported into MorphoJ for analysis. Primary morphometric analysis consisted of generalized Procrustes analysis, principal component analysis, and discriminant function analysis. RESULTS: The first 5 principal components for both facial types accounted for the majority of the variance. Discriminant function analyses were not significant for any phenotype or age group pairing, suggesting that the overall shape difference was too small to be detected between groups and over time starting at age 7. A plot of the Procrustes coordinates for the brachycephalic group versus the dolichocephalic group revealed that there were differences in shape between the two phenotypes, but this difference was statistically insignificant. CONCLUSIONS: The mandible increases in size with age, with minimal change in shape. Mandibular shape is established by the age of 7. The difference in mandibular shapes of the two phenotypes was not statistically significant.

Clark’s Cave contains a large collection of late Pleistocene mammal material. In particular, it contains a sizable amount of Microtus spp. which can be valuable paleoclimate indicators. Identification techniques traditionally used to classify these species have been shown to be unreliable. Recent studies have shown that using geometric morphometric techniques on lower first molars can be more successful. By placing landmarks and running a discriminate analysis on new and previously collected material from the cave, significant differences in Microtus species proportions were found. Specifically, showing the deposit has a larger proportion of M. xanthognathus than previously reported; resulting in a subsequent drop in the number of M. pennsylvanicus and M. chrotorrhinus present. Moreover, previously unreported M. ochrogaster was determined to be an important component of the fauna. The results presented here show the importance of applying new techniques to previous studies.

Skeletal superstructure characteristics such as thick cranial vaults and well-developed supraorbital, infraorbital, zygomatic, temporal, and nuchal regions in hominins are collectively referred to as aspects of craniofacial robusticity. A better understanding of craniofacial robusticity is important because these features are regularly employed as individual traits in circumscribing fossil hominins as a means to separate other taxonomic groups from modern Homo sapiens even though the developmental and functional underpinnings of such traits are incompletely understood. The work of some researchers suggests that these features may be tied to a broader "robusticity complex", in which the expression of all the classically "robust" characteristics of the hominin cranium are intercorrelated and intrinsically linked. If true, then previous studies that have focused on characteristics of craniofacial robusticity as individual characters could be flawed. This study tests for the presence of an intercorrelated craniofacial robusticity complex in a geographically diverse sample of recent Homo sapiens using a morphological integration framework. Within this framework, significant levels of correlation between features of craniofacial robusticity are demonstrative of integration and thus a "robusticity complex", while non-significant levels of correlation provide evidence for modularity and therefore an independent expression of these traits. Craniofacial robusticity is examined among four anatomical areas of the human cranium including the frontal, zygomaxillary, temporal, and occipital regions. The expression of robusticity among these anatomical regions is quantified using three-dimensional coordinate landmark data in addition to classical discrete measures and is analyzed via two-block partial least squares regression analysis. The results show that levels of interaction between these major anatomical units are characterized by a range of correlation values with most obtaining statistical significance. These results frequently provide evidence for integration between subunits demonstrating at least partial evidence for a "robusticity complex" in the craniofacial skeleton of extant humans.

Objective: Variation in dental arch shape and arch relations from the primary to the permanent dentition were studied in an untreated longitudinal sample from the Iowa Fluoride Study and Growth Study data (55 females and 63 males). Methods: 3D coordinate data from 68 landmarks located on maxillary, mandibular, and occlusal dental cast scans from ages 5, 9, and 13 were submitted to a Procrustes fit prior to a Principal Component (PC) analysis to capture symmetric and asymmetric aspects of arch shape variation. Covariance pattern models were used to determine longitudinal arch shape changes from the primary to the permanent dentition and to correlate these changes with Angle class molar classification. Results: The first 3 principal components capture 52-78% of the variation in arch shape. PC1 explains 30-44% of the variance and captures changes in overall dentoalveolar height. PC2 explains 14-22% and shows mainly variation in dentoalveolar height and width at the canines. Lastly, PC3 explains 8-12% and captures overall arch width and perimeter differences and changes in anteroposterior arch relations. Results on symmetric shape variation for the occlusal data set captured significant differences (p < 0.0001) in morphology for PC2 and PC3. For PC2, initial morphology in the deciduous dentition for an individual classified as Class II was significantly different than a Class I individual. Initial shape characteristics for the Class II features stepped down maxillary incisors and an increased curve of Spee with deep overbite. For PC3, the initial morphology for both the distocclusion and Class II individuals demonstrated characteristics such as stepped up maxillary incisors and increased overjet relative to their flush terminal plane and Class I counterparts. The rate of arch shape changes at which the distal step group transitions to the mixed dentition was also significantly different from the flush terminal plane sample. Conclusions: Initial findings summarize the main aspects of arch shape variation throughout 3 dentition stages. The covariance pattern models estimated individual trajectories and dynamics of arch shape changes from the primary to the permanent dentition and correlated these changes with Angle molar classification. In the symmetric dataset, significant shape characteristic differences of both initial starting morphology and change in shape over time were discovered for two occlusal phenotypes highlighting differences primarily in the vertical and anteroposterior dimensions. The results found in the present study provide an excellent foundation for describing and identifying dental arch shape differences in the primary dentition that can aid in earlier detection, diagnosis, and treatment of malocclusion, or at a minimum warrant closer observation by the clinician.

The purpose of this study was to use geometric morphometrics (GM) to investigate the relationships between non-metric traits of the human hip bone: the greater sciatic notch (GSN), the ventral arc (VA), the subpubic contour (SPC), and the ischiopubic ramus ridge (IPRR), estimated skeletal sex, and shape. Fifty-nine undocumented left hip bone specimens were visually assessed for skeletal sex using recognized standards of sex estimation for the GSN (Buikstra and Ubelaker, 1994). The VA, SPC, and IPRR were assessed according to Klales et al., (2012). The Non-metric traits were scored on a five-scale scheme. Skeletal sex was classified as either male, possible male, indeterminate sex, possible female, or female. Three-dimensional computer models were created of the hip bones using the NextEngine 3D desktop surface scanner. Thirty landmarks were selected to represent the hip bone in three-dimensional shape for GM analysis. Twenty-seven of the selected landmarks were reliable according to suggested digitizing error measurements. The apex of the auricular surface, the arcurate eminence, and the anterior gluteal line were the least precise in the test for digitizing error. Geometric morphometric analysis of the computer models were performed using MorphoJ software. Principal component analysis identified the patterns of hip bone shape within the sex categories. A Procrustes ANOVA and a Spearman's correlation tested the significance between hip bone shape and estimated skeletal sex, and between hip bone shape and non-metric trait morphology. Patterns of hip bone shape in the ischium could not be identified by sex, however sex differences were identified in ischium size. Patterns of hip bone shape in the whole hip bone, segmented ilium and segmented pubis were distinguishable by larger sex groups (males = male and possible male categories; females = female and possible female categories). Shape patterns alluded to differences between females and possible females, however, shape patterns did not distinguish males from possible males. Individuals of indeterminate sex shared similar hip bone shapes as males and were therefore included in that larger sex group. Hip bone shape was also correlated with GSN, SPC, IPRR, and VA. However, the strength of the correlation differed between non-metric traits and certain components of hip bone shape. The GSN and SPC had the strongest correlation (p=<0.01) with the whole hip bone, the ilium and the pubis at distinguishing between larger male and female sex groups. The IPRR, and GSN had the strongest correlation (p=<0.01) with the pubis at distinguishing females and possible females. The results of the study suggest that non-metric traits can discern patterns of female shape better than patterns of male shape. Further research into discerning patterns of male hip bone shape and non-metric trait variation using GM is suggested. The results of the study also suggest that patterns of pubis shape might exist among females and could be identifiable using pubis non-metric trait scores. This result lends credence to the practice of estimating sex on a five-scale gradient rather than on a male/female dichotomous division, in order to capture the morphological variation of female hip bone better. / Graduate / 0327 / 0339 / heatherisobelrobertson@gmail.com

Geometric morphometrics, the science about the study of shape, has developed much in the last twenty years. In this thesis I first study the reliability of the phylogenies built using geometric morphometrics. The effect of different evolutionary models, branch-length combinations, dimensionality and degrees of integration is explored using computer simulations. Unfortunately in the most common situations (presence of stabilizing selection, short distance between internal nodes and presence of integration) the reliability of the phylogenies is very low. Different empirical studies are analysed to estimate the degree of evolutionary integration usually found in nature. This gives an idea about how powerful the effect of integration is over the reliability of the phylogenies in empirical studies. Evolutionary integration is studied looking at the decrease of variance in the principal components of the tangent shape space using the independent contrasts of shape. The results suggest that empirical data usually show strong degrees of integration in most of the organisms and structures analysed. These are bad news, since strong degree of integration has devastating effects over the phylogenetic reliability, as suggested by our simulations. However, we also propose the existence of other theoretical situations in which strong integration may not translate into convergence between species, like perpendicular orientation of the integration patterns or big total variance relative to the distance between species in the shape space. Finally, geometric morphometrics is applied to the study of the evolution of shape in proteins. There are reasons to think that, because of their modular nature and huge dimensionality, proteins may show different patterns of evolutionary integration. Unfortunately, proteins also show strong functional demands, which influence their evolution and that cause strong integration patterns. Integration is then confirmed as a widespread property in the evolution of shape, which causes poor phylogenetic estimates.

The limb skeleton of tapirs (Perissodactyla: Tapirus spp.) was traditionally thought to exhibit morphological variation only as a result of changes in body size. Here, we test whether forelimb variation exhibited by Tapirus is solely an artefact of size fluctuations through the tapir fossil record or whether it is influenced by habitat differences. We investigated the forelimb osteology of 12 species of Tapirus using three-dimensional geometric morphometrics on laser surface scans. Aligned shape coordinates were regressed against intrinsic bone size to account for allometry. Taxa of equivalent body mass exhibited significant differences in size-corrected bone shape. Stable carbon isotope values were averaged per species as a proxy for habitat density. Multivariate regressions of the humerus, pisiform, cuneiform, unciform, third and fourth metacarpals revealed no significant influence of size on shape. The lateral carpals (pisiform, cuneiform, unciform) demonstrated variation across the habitat density gradient. Observed variation is likely driven by species in the extinct subgenus Helicotapirus tapirs, which inhabited drier, more open woodland than modern taxa. We conclude that tapir forelimb variation is not exclusively an artefact of body size, with lateral wrist bones displaying notable differences across a habitat density gradient, beyond that resulting from size and phylogenetic effects.

Sex estimation is one of the most important, and arguably the first, parts of the biological profile that is estimated for purposes of human identification. This study will examine the utility of the distal humerus in sex estimation. The goal of this research is to corroborate the usefulness of the distal humerus in sex estimation and the usefulness of geometric morphometrics in sex estimation, as well as validate metric and visual methods for sex estimation using the distal humerus. Multiple methods of sex estimation are necessary because complete skeletons are rarely found, and often only fragments are discovered. Three methods of sex estimation utilizing the distal humerus are used in this study: epicondylar breadth (n=448), nonmetric traits per Rogers (1999) and Vance et al. (2011 (n=444)), and geometric morphometrics via a Microscribe digitizer and MorphoJ software (n=227). The sample was taken from the William M. Bass Donated Skeletal Collection and was primarily composed of White Americans. The male to female ratio was approximately equal. The results of the metric aspect of the study showed a classification accuracy of 88.84% with low intra-observer and inter-observer error rates. The results of the nonmetric aspect of the study showed a classification accuracy of 77% when all traits were combined with low intra-observer and high inter-observer error rates. The results of the geometric morphometric aspect of the study showed a classification accuracy of 55% for all landmarks, 57% for anterior landmarks, and 63% for posterior landmarks. The results show that not only is the epicondylar breadth a reliable and effective method of sex estimation, it is easily repeatable by other observers. The nonmetric method is useful when epicondylar breadth cannot be measured or when an observer is familiar with the method. The geometric morphometric method is not as strong as the other two methods, but with further research and modifications may become a feasible option for sex estimation using the distal humerus. The author concludes that the distal humerus is sexually dimorphic and can be used to estimate sex accurately.