Efficacy of diffeomorphic surface matching and 3D geometric morphometrics for taxonomic discrimination of Early Pleistocene hominin mandibular molars.

Morphometric assessments of the dentition have played significant roles in hypotheses relating to taxonomic diversity among extinct hominins. In this regard, emphasis has been placed on the statistical appraisal of intraspecific variation to identify morphological criteria that convey maximum discriminatory power. Three-dimensional geometric morphometric (3D GM) approaches that utilize landmarks and semi-landmarks to quantify shape variation have enjoyed increasingly popular use over the past twenty-five years in assessments of the outer enamel surface (OES) and enamel-dentine junction (EDJ) of fossil molars. Recently developed diffeomorphic surface matching (DSM) methods that model the deformation between shapes have drastically reduced if not altogether eliminated potential methodological inconsistencies associated with the a priori identification of landmarks and delineation of semi-landmarks. As such, DSM has the potential to better capture the geometric details that describe tooth shape by accounting for both homologous and non-homologous (i.e., discrete) features, and permitting the statistical determination of geometric correspondence. We compare the discriminatory power of 3D GM and DSM in the evaluation of the OES and EDJ of mandibular permanent molars attributed to Australopithecus africanus, Paranthropus robustus and early Homo sp. from the sites of Sterkfontein and Swartkrans. For all three molars, classification and clustering scores demonstrate that DSM performs better at separating the A. africanus and P. robustus samples than does 3D GM. The EDJ provided the best results. P. robustus evinces greater morphological variability than A. africanus. The DSM assessment of the early Homo molar from Swartkrans reveals its distinctiveness from either australopith sample, and the "unknown" specimen from Sterkfontein (Stw 151) is notably more similar to Homo than to A. africanus.

Sexual dimorphism in sister species of Leucoraja skate and its relationship to reproductive strategy and life history.

Instances of sexual dimorphism occur in a great variety of forms and manifestations. Most skates (Batoidea: Rajoidei) display some level of body shape dimorphism in which the pectoral fins of mature males develop to create a distinct bell-shaped body not found in females. This particular form of dimorphism is present in each of the sister species Leucoraja erinacea and Leucoraja ocellata, but differences between sexes are much greater in the former. In order to understand the nature and potential causes of pectoral dimorphism, we used geometric morphometrics to investigate allometry of fin shape in L. erinacea and L. ocellata and its relationship to the development of reproductive organs, based on previous work on the bonnethead shark, Sphyrna tiburo. We found that allometric trajectories of overall pectoral shape were different in both species of skate, but only L. erinacea varied significantly with respect to endoskeleton development. Male maturation was characterized by a number of sex-specific morphological changes, which appeared concurrently in developmental timing with elongation of cartilage-supported claspers. We suggest that external sexual dimorphism of pectoral fins in skates is a byproduct of skeletal growth needed for clasper development. Further, the magnitude of male shape change appears to be linked to the differential life histories of species. This work reports for the first time that pectoral dimorphism is a persistent feature in rajoid fishes, occurring in varying degrees across several genera. Lastly, our results suggest that pectoral morphology may be useful as a relative indicator of reproductive strategy in some species.

Ocular Deformations in Spaceflight-Associated Neuro-Ocular Syndrome and Idiopathic Intracranial Hypertension.

Purpose: Spaceflight-associated neuro-ocular syndrome (SANS) shares several clinical features with idiopathic intracranial-hypertension (IIH), namely disc edema, globe-flattening, hyperopia, and choroidal folds. Globe-flattening is caused by increased intracranial pressure (ICP) in IIH, but the cause in SANS is uncertain. If increased ICP alone causes SANS, then the ocular deformations should be similar to IIH; if not, alternative mechanisms would be implicated. Methods: Using optical coherence tomography (OCT) axial images of the optic nerve head, we compared "pre to post" ocular deformations in 22 patients with IIH to 25 crewmembers with SANS. We used two metrics to assess ocular deformations: displacements of Bruch's membrane opening (BMO-displacements) and Geometric Morphometrics to analyze peripapillary shape changes of Bruch's membrane layer (BML-shape). Results: We found a large disparity in the mean retinal nerve-fiber layer thickness between SANS (108 um; 95% confidence interval [CI] = 105-111 um) and IIH (300 um; 95% CI = 251-350.1 um). The pattern of BML-shape and BMO-displacements in SANS were significantly different from IIH (P < 0.0001). Deformations in IIH were large and preponderantly anterior, whereas the deformations in SANS were small and bidirectional. The degree of disc edema did not explain the differences in ocular deformations. Conclusions: This study showed substantial differences in the degree of disc edema and the pattern of ocular deformations between IIH and SANS. The precise cause for these differences is unknown but suggests that there may be fundamental differences in the underlying biomechanics of each consistent with the prevailing hypothesis that SANS is consequent to multiple factors beyond ICP alone. We propose a hypothetical model to explain the differences between IIH and SANS based on the pattern of indentation loads.

The shape of human evolution: a geometric morphometrics perspective.

Study of morphological form is fundamental to the discipline of paleoanthropology. The size and shape of our ancestors' anatomical features have long been the focus of research on hominin systematics, phylogeny, functional morphology, ontogeny, variation, and evolutionary change. Early physical anthropologists relied on both qualitative descriptions of anatomical shape and linear measurements to assess variation among hominins. The seminal works of W. W. Howells and C. E. Oxnard helped to bring multivariate techniques to the forefront of physical anthropology. Howells' intention was the objective delineation of components of shape, which could then fuel further analyses and interpretations, as well as clarification of the ways that growth influences interindividual and interpopulational differences in shape. He expressed concern that previous comparisons of individual measurements did not capture the overall shape of the skull, which is "expressed by the relations between measurements." Similarly, Oxnard recognized that a multivariate approach to the study of complex shapes allows "for such perturbations (e.g., variation and covariation)…that are difficult to evaluate by eye and impossible to reveal by measurement and simple analysis alone." While multivariate methods offered clear advantages over univariate or bivariate representations of shape, the analysis of traditional morphometric measures such as linear distances, angles, and ratios, has limitations when it comes to quantifying the complex geometry of some anatomical structures.

Biometric morphing: a novel technique for the analysis of morphologic outcomes after facial surgery.

The results of facial surgery are intuitively judged in terms of the visible changes in facial features or proportions. However, describing these morphologic outcomes objectively remains a challenge. Biometric morphing addresses this issue by merging statistical shape analysis and image processing. This study describes the implementation of biometric morphing in describing the average morphologic result of facial surgery. The biometric morphing protocol was applied to pre- and postoperative images of the following: (1) 40 dorsal hump reduction rhinoplasties and (2) 20 unilateral enophthalmos repairs. Pre- and postoperative average images (average morphs) were generated. The average morphs provided an objective rendering of nasal and periorbital morphology, which summarized the average features and extent of deformity in a population of patients. Subtle alterations in morphology after surgery, which would otherwise be difficult to identify or demonstrate, were clearly illustrated. Biometric morphing is an effective instrument for describing average facial morphology in a population of patients.

Cranial shape differentiation in three closely related delphinid cetacean species: insights into evolutionary history.

The present study investigates the pattern of differentiation of cranial shape in three closely related delphinid cetacean species of the complex Delphinus-Stenella-Tursiops: Delphinus delphis, Stenella coeruleoalba and Tursiops truncatus. Dorsal and ventral aspects of the cranium were analysed using landmark-based geometric morphometric methods. While there was no evidence of sexual dimorphism for shape or size, multivariate statistical analyses showed that there were interspecific differences in skull morphology. Skull shape differences between the three studied species were related with cranial width and differences in the length of the rostrum relative to the cranial portion of the skull. D. delphis and S. coeruleoalba showed high cranial shape similarity, which is indicative of their evolutionary proximity when compared with T. truncatus. Phenetic clusters based on cranial shape similarities were found to be concordant with the molecular phylogenetic clades obtained from mitochondrial DNA genes. Geometric morphometric methods can thus be an exceptionally useful tool for the study of differentiation of delphinid cetacean species and therefore provide some insights into their evolutionary history.

Development of sizing structure for fall arrest harness design.

Updated harness designs are needed to accommodate diverse populations in the current workforce. This paper determined an improved fall-arrest harness sizing scheme and strap-length configurations for harness design. A 3-D elliptic Fourier analysis (EFA) procedure with 123 coefficients was developed to quantify torso-shape effect on harness fit, based on 3-D data of 108 women and 108 men. The EFA coefficients were then applied to 600 representative body scans from a national database of 2382 participants to establish an improved sizing system. Study outcomes suggested a more upward back D-ring location for women than current unisex designs to accommodate female torso form and mitigate their fit problem. Results also suggested an improved system of three sizes for women and three sizes for men. New harness sizing charts for women and men were proposed accordingly. Using the most current 3-D whole-body digital scanning technology, this study assembled data from a US workforce to establish an improved fall-arrest harness sizing system and strap configurations for men and women. The information is useful for new generation harness designs to reduce the risk of worker injury.

A comment on phylogenetic correction.

Statistical methods are now commonly used to take into account the expected lack of independence of observations across different species (due to their phylogenetic relatedness) when computing correlations or regressions among traits. The methods are often interpreted as removing that part of the regression or correlation that is an artifact due to phylogeny and there is an expectation that the corrected regression or correlation coefficients will usually be closer to zero. It is shown here that this is not an accurate way to interpret these methods. The effect of taking phylogeny into account is to reduce the variance of the estimated regression or correlation coefficients. Their means are not because since estimates of regression coefficients are unbiased whether or not the correct phylogeny is taken into account. Estimates of correlations are only slightly biased (and in the opposite direction that many expect).

Re-evaluation of batoid pectoral morphology reveals novel patterns of diversity among major lineages.

Batoids (Chondrichthyes: Batoidea) are a diverse group of cartilaginous fishes which comprise a monophyletic sister lineage to all neoselachians or modern sharks. All species in this group possess anteroposteriorly expanded-pectoral fins, giving them a unique disc-like body form. Reliance on pectoral fins for propulsion ranges from minimal (sawfish) to almost complete dependence (skates and rays). A recent study on the diversity of planform pectoral fin shape in batoids compared overall patterns of morphological variation within the group. However, inconsistent pectoral homology prevented the study from accurately representing relationships within and among major batoid taxa. With previous work in mind, we undertook an independent investigation of pectoral form in batoids and evaluated the implications of shape diversity on locomotion and lifestyle, particularly in the skates (Rajoidei) and rays (Myliobatoidei). We used geometric morphometrics with sliding semilandmarks to analyze pectoral fin outlines and also calculate fin aspect ratios (AR), a functional trait linked to locomotion. In agreement with previous work, our results indicated that much of the evolution of batoid pectoral shape has occurred along a morphological axis that is closely related to AR. For species where kinematic data were available, both shape and AR were associated with swimming mode. This work further revealed novel patterns of shape variation among batoids, including strong bimodality of shape in rays, an intermediate location of skate species in the morphospace between benthic/demersal and pelagic rays, and approximately parallel shape trajectories in the benthic/demersal rays and skates. Finally, manipulation of landmarks verified the need for a consistent and accurate definition of homology for the outcome and efficacy of analyses of pectoral form and function in batoids.

Effects of lowering cerebrospinal fluid pressure on the shape of the peripapillary retina in intracranial hypertension.

PURPOSE: To analyze the deformations of the peripapillary retinal pigment epithelium-basement membrane (ppRPE/BM) layer in response to procedures that lower intracranial pressure (ICP). Second, to demonstrate how shape changes may complement the mean retinal nerve fiber layer (RNFL) thickness as a measure of intracranial hypertension (ICH) and papilledema. METHODS: We used geometric morphometrics on spectral-domain optical coherence tomography images to analyze shape change of the ppRPE/BM layer after several interventions that lower cerebrospinal fluid (CSF) pressure. We also evaluated the effects of pressure-lowering interventions on both the anterior-posterior displacement of ppRPE/BM and the mean RNFL thickness. Forty-one patients with ICH and papilledema were studied before and after lumbar puncture (20), CSF shunt (9), and medical treatment of idiopathic ICH (23). We also compared the shape of 30 normal subjects to 23 patients whose papilledema resolved after medical treatment. RESULTS: The ppRPE/BM-layer in ICH and papilledema is characterized by an asymmetric anterior deformation that moves posteriorly and becomes more V-shaped after each pressure-lowering intervention. The differences were statistically significant for all three groups. These shape changes also occur in patients with ongoing ICH who have secondary optic atrophy (without papilledema). Posterior displacement at the margin of the ppRPE/BM layer correlated strongly with overall shape changes. CONCLUSIONS: The subsurface contour of the ppRPE/BM layer is a dynamic property that changes with CSF pressure-lowering interventions. It can supplement the RNFL thickness as an indirect gauge of ICP and is particularly helpful in patients with secondary optic atrophy. Direct measurements of displacement at the basement membrane opening may serve as a more convenient office-based surrogate for shape analysis.

Phylogenetic, ecological, and allometric correlates of cranial shape in Malagasy lemuriforms.

Adaptive radiations provide important insights into many aspects of evolution, including the relationship between ecology and morphological diversification as well as between ecology and speciation. Many such radiations include divergence along a dietary axis, although other ecological variables may also drive diversification, including differences in diel activity patterns. This study examines the role of two key ecological variables, diet and activity patterns, in shaping the radiation of a diverse clade of primates, the Malagasy lemurs. When phylogeny was ignored, activity pattern and several dietary variables predicted a significant proportion of cranial shape variation. However, when phylogeny was taken into account, only typical diet accounted for a significant proportion of shape variation. One possible explanation for this discrepancy is that this radiation was characterized by a relatively small number of dietary shifts (and possibly changes in body size) that occurred in conjunction with the divergence of major clades. This pattern may be difficult to detect with the phylogenetic comparative methods used here, but may characterize not just lemurs but other mammals.

Host genes related to paneth cells and xenobiotic metabolism are associated with shifts in human ileum-associated microbial composition.

The aim of this study was to integrate human clinical, genotype, mRNA microarray and 16 S rRNA sequence data collected on 84 subjects with ileal Crohn's disease, ulcerative colitis or control patients without inflammatory bowel diseases in order to interrogate how host-microbial interactions are perturbed in inflammatory bowel diseases (IBD). Ex-vivo ileal mucosal biopsies were collected from the disease unaffected proximal margin of the ileum resected from patients who were undergoing initial intestinal surgery. Both RNA and DNA were extracted from the mucosal biopsy samples. Patients were genotyped for the three major NOD2 variants (Leufs1007, R702W, and G908R) and the ATG16L1T300A variant. Whole human genome mRNA expression profiles were generated using Agilent microarrays. Microbial composition profiles were determined by 454 pyrosequencing of the V3-V5 hypervariable region of the bacterial 16 S rRNA gene. The results of permutation based multivariate analysis of variance and covariance (MANCOVA) support the hypothesis that host mucosal Paneth cell and xenobiotic metabolism genes play an important role in host microbial interactions.

Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition.

We tested the hypothesis that Crohn's disease (CD)-related genetic polymorphisms involved in host innate immunity are associated with shifts in human ileum-associated microbial composition in a cross-sectional analysis of human ileal samples. Sanger sequencing of the bacterial 16S ribosomal RNA (rRNA) gene and 454 sequencing of 16S rRNA gene hypervariable regions (V1-V3 and V3-V5), were conducted on macroscopically disease-unaffected ileal biopsies collected from 52 ileal CD, 58 ulcerative colitis and 60 control patients without inflammatory bowel diseases (IBD) undergoing initial surgical resection. These subjects also were genotyped for the three major NOD2 risk alleles (Leu1007fs, R708W, G908R) and the ATG16L1 risk allele (T300A). The samples were linked to clinical metadata, including body mass index, smoking status and Clostridia difficile infection. The sequences were classified into seven phyla/subphyla categories using the Naïve Bayesian Classifier of the Ribosome Database Project. Centered log ratio transformation of six predominant categories was included as the dependent variable in the permutation based MANCOVA for the overall composition with stepwise variable selection. Polymerase chain reaction (PCR) assays were conducted to measure the relative frequencies of the Clostridium coccoides - Eubacterium rectales group and the Faecalibacterium prausnitzii spp. Empiric logit transformations of the relative frequencies of these two microbial groups were included in permutation-based ANCOVA. Regardless of sequencing method, IBD phenotype, Clostridia difficile and NOD2 genotype were selected as associated (FDR ≤ 0.05) with shifts in overall microbial composition. IBD phenotype and NOD2 genotype were also selected as associated with shifts in the relative frequency of the C. coccoides--E. rectales group. IBD phenotype, smoking and IBD medications were selected as associated with shifts in the relative frequency of F. prausnitzii spp. These results indicate that the effects of genetic and environmental factors on IBD are mediated at least in part by the enteric microbiota.

Shape analysis of the peripapillary RPE layer in papilledema and ischemic optic neuropathy.

PURPOSE: Geometric morphometrics (GM) was used to analyze the shape of the peripapillary retinal pigment epithelium-Bruch's membrane (RPE/BM) layer imaged on the SD-OCT 5-line raster in normal subjects and in patients with papilledema and ischemic optic neuropathy. METHODS: Three groups of subjects were compared: 30 normals, 20 with anterior ischemic optic neuropathy (AION), and 25 with papilledema and intracranial hypertension. Twenty equidistant semilandmarks were digitized on OCT images of the RPE/BM layer spanning 2500 µm on each side of the neural canal opening (NCO). The data were analyzed using standard GM techniques, including a generalized least-squares Procrustes superimposition, principal component analysis, thin-plate spline (to visualize deformations), and permutation statistical analysis to evaluate differences in shape variables. RESULTS: The RPE/BM layer in normals and AION have a characteristic V shape pointing away from the vitreous; the RPE/BM layer in papilledema has an inverted U shape, skewed nasally inward toward the vitreous. The differences were statistically significant. There was no significant difference in shapes between normals and AION. Pre- and posttreatment OCTs, in select cases of papilledema, showed that the inverted U-shaped RPE/BM moved posteriorly into a normal V shape as the papilledema resolved with weight loss or shunting. CONCLUSIONS: The shape difference in papilledema, absent in AION, cannot be explained by disc edema alone. The difference is a consequence of both the translaminar pressure gradient and the material properties of the peripapillary sclera. GM offers a novel way of statistically assessing shape differences of the peripapillary optic nerve head.

Bias and error in estimates of mean shape in geometric morphometrics.

Sampling experiments were performed to investigate mean square error and bias in estimates of mean shape produced by different geometric morphometric methods. The experiments use the isotropic error model, which assumes equal and independent variation at each landmark. The case of three landmarks in the plane (i.e., triangles) was emphasized because it could be investigated systematically and the results displayed on the printed page. The amount of error in the estimates was displayed as RMSE surfaces over the space of all possible configurations of three landmarks. Patterns of bias were shown as vector fields over this same space. Experiments were also performed using particular combinations of four or more landmarks in both two and three dimensions. It was found that the generalized Procrustes analysis method produced estimates with the least error and no pattern of bias. Averages of Bookstein shape coordinates performed well if the longest edge was used as the baseline. The method of moments (Stoyan, 1990, Model. Biomet. J. 32, 843) used in EDMA (Lele, 1993, Math. Geol. 25, 573) exhibits larger errors. When variation is not small, it also shows a pattern of bias for isosceles triangles with one side much shorter than the other two and for triangles whose vertices are approximately collinear causing them to resemble their own reflections. Similar problems were found for the log-distance method of Rao and Suryawanshi (1996, Proc. Nat. Acad. Sci. 95, 4121). These results and their implications for the application of different geometric morphometric methods are discussed.

Computing the uniform component of shape variation.

Any change in shape of a configuration of landmark points in two or three dimensions includes a uniform component, a component that is a wholly linear (affine) transformation. The formulas for estimating this component have been standardized for two-dimensional data but not for three-dimensional data. We suggest estimating the component by way of the complementarity between the uniform component and the space of partial warps. The component can be estimated by regression in either one space or the other: regression on the partial warps, followed by their removal, or regression on a basis for the uniform component itself. Either of the new methods can be used for both two- and three-dimensional landmark data and thus generalize Bookstein's (1996, pages 153-168 in Advances in morphometrics [L. F. Marcus et al., eds.], Plenum, New York) linearized Procrustes formula for estimating the uniform component in two dimensions.

EVALUATION OF THE RESTRICTED MAXIMUM-LIKELIHOOD METHOD FOR ESTIMATING PHYLOGENETIC TREES USING SIMULATED ALLELE-FREQUENCY DATA.

Comparisons are made of the accuracy of the restricted maximum-likelihood, Wagner parsimony, and UPGMA (unweighted pair-group method using arithmetic averages) clustering methods to estimate phylogenetic trees. Data matrices were generated by constructing simulated stochastic evolution in a multidimensional gene-frequency space using a simple genetic-drift model (Brownian-motion, random-walk) with constant rates of divergence in all lineages. Ten differentphylogenetic tree topologies of 20 operational taxonomic units (OTU's), representing a range of tree shapes, were used. Felsenstein's restricted maximum-likelihood method, Wagner parsimony, and UPGMA clustering were used to construct trees from the resulting data matrices. The computations for the restricted maximum-likelihood method were performed on a Cray-1 supercomputer since the required calculations (especially when optimized for the vector hardware) are performed substantially faster than on more conventional computing systems. The overall level of accuracy of tree reconstruction depends on the topology of the true phylogenetic tree. The UPGMA clustering method, especially when genetic-distance coefficients are used, gives the most accurate estimates of the true phylogeny (for our model with constant evolutionary rates). For large numbers of loci, all methods give similar results, but trends in the results imply that the restricted maximum-likelihood method would produce the most accurate trees if sample sizes were large enough.

THE ACCURACY OF PHYLOGENETIC ESTIMATION USING THE NEIGHBOR-JOINING METHOD.

We studied the factors affecting the accuracy of the neighbor-joining (NJ) method for estimating phylogenies by simulating character change under different evolutionary models applied to twenty different 8-OTU tree topologies that varied widely with respect to tree imbalance and stemminess. The models incorporated three evolutionary rates-constant, varying among lineages, varying among characters-and three evolutionary contexts concerning patterns of character change relative to speciation events-phyletic, speciational, and punctuational. All combinations of the rate and context models were studied. In addition, three different absolute rates of change were investigated. To measure the accuracy, the strict consensus index was computed between the estimated tree and the tree topology along which the data had been generated. The results were analyzed by analysis of variance and compared to a previous study that evaluated UPGMA clustering and maximum parsimony (MP) as phylogenetic estimation techniques. We found evolutionary context and tree imbalance to be the most important factors affecting the accuracy of the NJ method. NJ was more accurate than UPGMA or MP in terms of the average strict consensus index over all treatments. However, no one method was more accurate than the other two for all combinations of treatments. Higher absolute rate of change generally resulted in higher accuracy for all three methods.

ACCURACY OF ESTIMATED PHYLOGENIES: EFFECTS OF TREE TOPOLOGY AND EVOLUTIONARY MODEL.

A simulation study was carried out to investigate the relative importance of tree topology (both balance and stemminess), evolutionary rates (constant, varying among characters, and varying among lineages), and evolutionary models in determining the accuracy with which phylogenetic trees can be estimated. The three evolutionary context models were phyletic (characters can change at each simulated time step), speciational (changes are possible only at the time of speciation into two daughter lineages), and punctuational (changes occur at the time of speciation but only in one of the daughter lineages). UPGMA clustering and maximum parsimony ("Wagner trees") methods for estimating phylogenies were compared. All trees were based on eight recent OTUs. The three evolutionary context models were found to have the largest influence on accuracy of estimates by both methods. The next most important effect was that of the stemminess × context interaction. Maximum parsimony and UPGMA performed worst under the punctuational models. Under the phyletic model, trees with high stemminess values could be estimated more accurately and balanced trees were slightly easier to estimate than unbalanced ones. Overall, maximum parsimony yielded more accurate trees than UPGMA-but that was expected for these simulations since many more characters than OTUs were used. Our results suggest that the great majority of estimated phylogenetic trees are likely to be quite inaccurate; they underscore the inappropriateness of characterizing current phylogenetic methods as being for reconstruction rather than for estimation.