Are geometric morphometric analyses replicable? Evaluating landmark measurement error and its impact on extant and fossil Microtus classification.

Geometric morphometric analyses are frequently employed to quantify biological shape and shape variation. Despite the popularity of this technique, quantification of measurement error in geometric morphometric datasets and its impact on statistical results is seldom assessed in the literature. Here, we evaluate error on 2D landmark coordinate configurations of the lower first molar of five North American Microtus (vole) species. We acquired data from the same specimens several times to quantify error from four data acquisition sources: specimen presentation, imaging devices, interobserver variation, and intraobserver variation. We then evaluated the impact of those errors on linear discriminant analysis-based classifications of the five species using recent specimens of known species affinity and fossil specimens of unknown species affinity. Results indicate that data acquisition error can be substantial, sometimes explaining >30% of the total variation among datasets. Comparisons of datasets digitized by different individuals exhibit the greatest discrepancies in landmark precision, and comparison of datasets photographed from different presentation angles yields the greatest discrepancies in species classification results. All error sources impact statistical classification to some extent. For example, no two landmark dataset replicates exhibit the same predicted group memberships of recent or fossil specimens. Our findings emphasize the need to mitigate error as much as possible during geometric morphometric data collection. Though the impact of measurement error on statistical fidelity is likely analysis-specific, we recommend that all geometric morphometric studies standardize specimen imaging equipment, specimen presentations (if analyses are 2D), and landmark digitizers to reduce error and subsequent analytical misinterpretations

Translational genetic modelling of 3D craniofacial dysmorphology: elaborating the facial phenotype of neurodevelopmental disorders through the prism of schizophrenia

Purpose of Review: In the context of human developmental conditions, we review the conceptualisation of schizophrenia as a neurodevelopmental disorder, the status of craniofacial dysmorphology as a clinically accessible index of brain dysmorphogenesis, the ability of genetically modified mouse models of craniofacial dysmorphology to inform on the underlying dysmorphogenic process and how geometric morphometric techniques in mutant mice can extend quantitative analysis. Recent Findings: Mutant mice with disruption of neuregulin-1, a gene associated meta-analytically with risk for schizophrenia, constitute proof-of-concept studies of murine facial dysmorphology in a manner analogous to clinical studies in schizophrenia. Geometric morphometric techniques informed on the topography of facial dysmorphology and identified asymmetry therein. Summary: Targeted disruption in mice of genes involved in individual components of developmental processes and analysis of resultant facial dysmorphology using geometric morphometrics can inform on mechanisms of dysmorphogenesis at levels of incisiveness not possible in human subjects

Do cladistic and morphometric data capture common patterns of morphological disparity?

The distinctly non-random diversity of organismal form manifests itself in discrete clusters of taxa that share a common body plan. As a result, analyses of disparity require a scalable comparative framework. The difficulties of applying geometric morphometrics to disparity analyses of groups with vastly divergent body plans are overcome partly by the use of cladistic characters. Character-based disparity analyses have become increasingly popular, but it is not clear how they are affected by character coding strategies or revisions of primary homology statements. Indeed, whether cladistic and morphometric data capture similar patterns of morphological variation remains a moot point. To address this issue, we employ both cladistic and geometric morphometric data in an exploratory study of disparity focussing on caecilian amphibians. Our results show no impact on relative intertaxon distances when different coding strategies for cladistic characters were used or when revised concepts of homology were considered. In all instances, we found no statistically significant difference between pairwise Euclidean and Procrustes distances, although the strength of the correlation among distance matrices varied. This suggests that cladistic and geometric morphometric data appear to summarize morphological variation in comparable ways. Our results support the use of cladistic data for characterizing organismal disparity

A comparison of traditional and geometric morphometric techniques for the study of basicranial morphology in horses: a case study of the Araucanian horse from Colombia

Skull size and shape have been widely used to study domestic animal populations and breeds. Although several techniques have been proposed to quantify cranial form, few attempts have been made to compare the results obtained by di erent techniques. While linear morphometrics has traditionally been used in breed characterization, recent advances in geometric morphometrics have created new techniques for specifically quantifying shape and size. The objective of this study was to compare two morphometric methods for their ability to describe external morphology. For this purpose, 20 skull specimens of adult male Araucanian horses were examined. Two age categories were established (the 'mature group',M3 not fully erupted to moderately worn, n = 7; and the 'senile group', M3 totally erupted and highly worn, n = 13). Both methods showed that there were statistical di erences between generations, but discrimination rates were di erent between methods with the geometric morphometric analysis obtaining a rate of 97.5%. Although linear morphometrics was found to be compatible with geometric morphometrics, the latter was better able to discriminate the two groups and it also provides more information on shape.This research was funded by Cooperative University of Colombia, project 2378

Asymmetry of Caddo Ceramics from the Washington Square Mound Site: An Exploratory Analysis

While pursuing a study of 3D geometric morphometrics for ceramic burial vessels that often articulate with the Native American Graves Protection and Repatriation Act (NAGPRA) from the ancestral Caddo region, there have been no shortage of potentially meaningful observations, one of which--rotational asymmetry in coil-built vessels--is discussed here. Using Geomagic Design X (reverse-engineering software) and Geomagic Control X (inspection software), metrics associated with rotational asymmetry were generated then analyzed. Results indicate variable asymmetry among the different vessel shapes (i.e., bottles, jars, etc.), which may augment and strengthen studies and discussion of vessel form. Future directions include the incorporation of directional and--possibly--fluctuating asymmetry measures for the widest vessel profiles. Preliminary results point toward substantive analytical gains that can be used to augment more traditional ceramic analyses as well as geometric morphometric studies of ceramic vessel shape

Tools for quantitative form description : an evaluation of different software packages for semi-landmark analysis

The challenging complexity of biological structures has led to the development of several methods for quantitative analyses of form. Bones are shaped by the interaction of historical (phylogenetic), structural, and functional constrains. Consequently, bone shape has been investigated intensively in an evolutionary context. Geometric morphometric approaches allow the description of the shape of an object in all of its biological complexity. However, when biological objects present only few anatomical landmarks, sliding semi-landmarks may provide good descriptors of shape. The sliding procedure, mandatory for sliding semi-landmarks, requires several steps that may be time-consuming. We here compare the time required by two different software packages ('Edgewarp' and 'Morpho') for the same sliding task, and investigate potential differences in the results and biological interpretation. 'Morpho' is much faster than 'Edgewarp,' notably as a result of the greater computational power of the 'Morpho' software routines and the complexity of the 'Edgewarp' workflow. Morphospaces obtained using both software packages are similar and provide a consistent description of the biological variability. The principal differences between the two software packages are observed in areas characterized by abrupt changes in the bone topography. In summary, both software packages perform equally well in terms of the description of biological structures, yet differ in the simplicity of the workflow and time needed to performthe analyses

Integrating species distribution models, genetics and morphology to infer species dynamics of New Zealand Phaulacridium grasshoppers : a thesis presented in partial fulfilment of the requirements for the degree of Masters of Science in Zoology at Massey University, Palmerston North, New Zealand

Species comparison studies have used a number of different methods that can contribute to our understanding of processes that influence the differences and similarities observed between species. This thesis describes the geographic distribution, spatial genetics, and morphology of two New Zealand Phaulacridium grasshoppers, the widespread P. marginale and the restricted P. otagoense. The primary focus was on Phaulacridium populations from the region of the southern South Island where the two species ranges overlap, for the purpose of examining the evolutionary and ecological interactions of the species. The geographic distribution of the two species was analysed using the recorded and potential modern distribution of Phaulacridium grasshoppers. Models of environmental envelopes for each species demonstrated that the potential distribution of P. marginale covered the majority of New Zealand. In contrast, the potential distribution of P. otagoense is restricted to patches of land primarily in the southern South Island where this species is known to occur. The phylogeographic structure of Phaulacridium species was analysed using dense population samples. Two main mtDNA COI sequence groups were found, one was shallow but geographically widespread, while the other was more diverse but geographically restricted. Within the southern South Island region both mitochondrial lineages co-occur within a single location. Demographic history analysis suggested that the widespread range of P. marginale is the result of recent population, and the restricted P. otagoense was recently represented in large populations. The morphological variation of Phaulacridium grasshoppers was explored using traditional and geometric techniques. Two distinct morphotypes were apparent, the larger morph was geographically widespread and the smaller morph was restricted to the southern South Island. Both morphotypes co-occur in locations within the southern South Island region. Furthermore, several individuals could not be classified into a discreet morphotype, suggesting that these individuals had a mixture of morphological features, as expected of a hybrid. Comparing the morphological and genetic data from the current study demonstrates the first reported case of introgression between P. marginale and P. otagoense. It is evident that Phaulacridium F1 hybrids exist in the wild, however it is unknown whether these F1 hybrids are fertile and also if F2 hybrids (backcrossed from parental species or F1 hybrids) are viable and fertile