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Morphometrics, Homology, and Phylogenetics: Quantified Characters as Synapomorphies
Abstract
It has been claimed that quantified features are inappropriate for phylogenetic analysis. We consider that claim to be true under most conditions for characters discovered by commonly used morphometric methods, including outline-based and conventional multivariate methods. The most important reason these characters are unsuitable is that one of the tests of homology, the test of similarity, may be difficult to apply to them. This test is not even possible if the methods for comparing forms, such as outline-based techniques, do not ensure that the characters are located in the same part of the anatomy. Conventional methods, including principal components analysis, have no explicit basis for localizing characters. In addition, unless the transformation between forms is homogeneous, conventional methods cannot dissect transformations region by region to discover characters. However, one morphometric method, the thin-plate spline decomposed by its partial warps (TPS), finds characters that can be subjected to the same tests of homology (conjunction, similarity, and congruence) that we would apply to all other characters. Among available methods, TPS is unique in being able to locate the center and spatial extent of regional differences in shape and ensures that the same regions are compared among forms. We provide an example using the teleost fishes piranhas, in which tests of homology are applied to a synapomorphy found by the method.
... However, as Adams [54] points out, this Klingenberg-Gidaszewski method (i.) relies on ancestral-state reconstruction which usually involves high levels of uncertainty [93] and (ii.) is unsuitable for use in evaluating phenotypic traits owing the the fact that geometric scaling is not taken into consideration and changes systematically as trait variation among species and/or with the number of traits increases. The ...
... Moreover, given the constraint (observed in our results) that estimated ancestral wing morphologies tend to occupy regions closer to the origin of the Procrustes PC space than the terminal taxa, the range of shape variation displayed by the former group is such that it is di cult for us to imagine any con guration of inferred hypothetical ancestral wing shapes that would be consistent with the expectations of a strongly supported phylogenetic covariation pattern. This ordination geometry indicates that our results, and our interpretations, are robust to the imprecision of ancestral node inferences, as noted by Losos [93]. ...
... The nding that many biological datasets do not exhibit signi cant patterns of phylogenetic covariation is well established -including for morphometric datasets -and can arise for many different reasons (see [93] and references therein). Notwithstanding the results reported by Outomuro et al. [1], Trithemis forewing and hindwing morphology appears to fall into this broad category. ...
The phylogenetic ecology and wing ecomorphology of the Afro-Asian dragonfly genus Trithemis have been investigated previously. Curiously, results reported for the forewing and hindwing shape variation in the latter were, in some ways, at odds with expectations given the mapping of landscape and water-body preferences over the Trithemis cladogram. To confirm these results we conducted a wing-shape investigation of 27 Trithemis species that employed a robust statistical test for phylogenetic covariation, more comprehensive representation of Trithemis wing morphology and a wider range of morphometric data-analysis procedures. Contrary to results published previously, statistical comparisons of forewing and hindwing mean shapes with the Trithemis cladogram revealed no statistically significant pattern of phylogenetic covariation. Moreover, landmark-based and image-based geometric morphometric analysis results, as well as embedded image-contrast deep learning analysis results, all demonstrated that both wings exhibit substantial convergent wing-shape similarities among, and differences between, species that inhabit open and forested landscapes and species that hunt over temporary/standing or running water bodies. Geometric morphometric data and data-analysis methods yielded the worst performance in identifying wing shape distinctions between Trithemis habitat guilds and the direct analysis of wing images using an embedded, image-contrast, convolution (deep learning) neural network delivered the best performance. Bootstrap and jackknife tests confirmed that our results are not artifacts of overtrained discriminant systems or the “curse of dimensionality”. In addition to our conclusions pertaining to Trithemis ecomorphology, the discrepancy between the previous investigation’s results and ours appears to reflect decisions made with regard to the manner in which complex morphological structures are sampled and analyzed. Naturally, results and interpretations of patterns in morphometric data pertain only to the data collected, not necessarily to other aspects of the structures from which those data were collected. For samples of morphologically similar taxa, landmark-based sampling strategies may be effective provided a sufficient number of landmark points distributed across all structures of potential interest exist. However, in a large number of instances analysis of full digital images of the structures under consideration may prove to be a more robust and effective sampling strategy, especially when coupled with analysis via machine learning procedures.
... In order to address these questions, several protocols have been tested in the past. One consisted of using partial distortion scores for landmarks that were "identical" between all the specimens/taxa included in an analysis (e.g., Zelditch et al., 1995;. This method was highly controversial (e.g., Bookstein, 1994;2002;Monteiro, 2000; and was subsequently abandoned (Zelditch et al., 2004), as the choice of data was considered to be too arbitrary. ...
... While the issue of trait definition and independence is at the root of many controversies surrounding the use of morphometric data (Rohlf, 1998;Monteiro, 2000;Bookstein, 2002), it should be noted that it is also a problem when using "traditional" discrete morphological character because their definitions vary widely (e.g., Thiele, 1993) as it is often difficult to assess their independence (e.g., Mounier et al., 2009). Finally, according to Adams et al. (2011), methods consisting of forcing multivariate shape variables into a form compatible with cladistic software (Zelditch et al., 1995;Gonzalez-Jose et al., 2008) would distort the information present in these variables and this would severely limit the useful biological conclusions that can be made. This is in fact the case for all implementations of discontinuous coding from a continuous dataset and is therefore not specific to geometric morphometric data. ...
Ces 30 dernières années, plusieurs protocoles permettant d’utiliser des données 3D de morphométrie géométrique en cladistique ont été proposés. Fortement critiqués, ces protocoles ne sont qu’occasionnellement utilisés en paléoanthropologie, malgré le potentiel évident d’une telle approche. Dans cette étude, nous avons testé deux protocoles différents afin d’évaluer l’information phylogénétique dérivée des données de morphométrie géométrique, que nous avons appliqué à 23 unités taxonomiques opérationnelles (UTOs) représentant les genres Pongo, Gorilla, Pan, Australopithecus et Homo. Ces 23 UTOs sont issues de la moyenne des coordonnées procrustes alignées (analyse procruste généralisée) de trois configurations de points-repères (148, 347 et 636 points-repères) décrivant la morphologie du calvarium de 78 spécimens. Le premier protocole utilise les coordonnées des composantes principales, obtenues après une analyse en composantes principales, comme variables décrivant les UTOs. La seconde approche utilise directement les coordonnées 3D alignées des points-repères. Ces deux ensembles de données ont ensuite été analysés à l’aide des algorithmes "heuristic" et "branch-and-bound" implémentés dans le logiciel TNT. Ces analyses ont produit un arbre cladistique unique pour chaque jeu de données. Indépendamment de la matrice utilisée pour obtenir les arbres, ces résultats préliminaires sont phylogénétiquement cohérents et soutiennent des hypothèses paléoanthropologiques intéressantes.
... In terms of classification, Hylobatidae and Cebidae are easy to distinguish, but Atelidae and Cercopithecidae are difficult to distinguish, and so on ( Supplementary Fig. 1e). This shape similarity may be hypothesized to be determined based on evolutionary distance; however, the relationship between morphological similarity and evolutionary distance has long been a topic of debate [69][70][71][72][73][74][75][76] . This is because other factors, such as diet (carnivore, herbivore, or omnivore), sexual dimorphism, and predator presence, may have a greater influence on morphology than evolutionary distance. ...
... Although we examined whether or not there is some link between this distinguishability and the evolutionary distance, no clear correlation between the latentspace and phylogenetic distances was detected ( Supplementary Fig. 3). As was seen in our result, the longstanding debate regarding the correlation between phylogenetic and morphological distances has been extensively discussed, as the relationship is not always straightforward [69][70][71][72][73][74][75][76] . Several studies have successfully demonstrated that phylogenetic relationships can be inferred from morphological differences. ...
Shape measurements are crucial for evolutionary and developmental biology; however, they present difficulties in the objective and automatic quantification of arbitrary shapes. Conventional approaches are based on anatomically prominent landmarks, which require manual annotations by experts. Here, we develop a machine-learning approach by presenting morphological regulated variational AutoEncoder (Morpho-VAE), an image-based deep learning framework, to conduct landmark-free shape analysis. The proposed architecture combines the unsupervised and supervised learning models to reduce dimensionality by focusing on morphological features that distinguish data with different labels. We applied the method to primate mandible image data. The extracted morphological features reflected the characteristics of the families to which the organisms belonged, despite the absence of correlation between the extracted morphological features and phylogenetic distance. Furthermore, we demonstrated the reconstruction of missing segments from incomplete images. The proposed method provides a flexible and promising tool for analyzing a wide variety of image data of biological shapes even those with missing segments.
... Clovis points were described originally from a small collection recovered from the Blackwater Draw locality near Clovis, New Mexico between 1936 and 1938. They have been described as pointed, fluted, lanceolate blades made from a variety of fine-grained materials (e.g., stone, crystalline minerals, bone) with subparallel or convex (excurvate) sides, a maximum width at or below the lateral midpoint, a lenticular cross section, and a concave base (Fig. 1, see Wormington, 1957;Howard, 1990;Morrow, 1996;Haynes, 2002). Owing to the presence of a variably sized excavated area, the flute, at the base of many Clovis points, it has been inferred that these tools were bound to a notched wooden handle or shaft and functioned as a knife and/or dart tip (Kay, 1996) that was either thrust manually (Frison, 1986) or thrown, quite possibly with the aid of a "thrower" or atl-atl (Hutchings, 1997). ...
... This approach to the characterization of artifact outlines is essentially identical to that proposed by MacLeod (1999) as a core part of the extended eigenshape analysis procedure. While the morphometric analysis of archaeological objects need not proceed under the same constraints as for biological specimens (Bookstein, 1991;Zelditch et al., 1995, but see MacLeod, 1999 for a critical rejoinder), the merits of taking advantage of the locations topologically comparable structures both on, and internal to, the Column 1, three representative colour images of fluted projectile points. In each case these images have been scaled to a common size and oriented to minimize deviations from the pooled-sample mean shape. ...
Archaeologists often wish to distinguish between groups of cultural artifacts using information collected from descriptions or measurements of their morphological forms. Morphometric methods have played an increasingly large role in such quantitative assessments. However, standard approaches to morphometric analyses are often poorly suited to many artifact types as much variation of interest to archeologists cannot be quantified adequately by sparse sets of landmarks or semilandmarks. Use of measurement conventions also requires that investigators know which aspects of the artifacts under consideration are important to include at the outset of an investigation. In this review results obtained from landmark-semilandmark-based, and image pixel-based assessments of a common set of Paleoindian fluted projectile points are compared. Results confirm that, by itself, PCA is unsuited for the assessment of between-group differences irrespective of data type, but can be useful as a transformation to reduce the dimensionality of a morphological dataset while retaining its effective information content. Landmark-semilandmark data analysed using geometric morphometric methods delivered the lowest-quality results whereas image pixel data analysed by the Naïve Bayes machine-learning classifier delivered the highest. Direct analyses of artifact images using geometric morphometric methods delivered very good results. These findings suggest that the direct analyses of digital images and 3D scans, using either geometric morphometric data-analysis methods or machine-learning procedures, can provide archaeologists with tools that improve and extend the scope of their assessments of a wide range of artifact types.
... Investigations of the morphological aspects of growth and development have increased in number and in sophistication in recent decades. In part, this increase is due to the appreciation that evolutionary changes in adult form are the consequence of changes to the ontogenetic routes that lead to that form (Gould, 1977;Hall, 2003;Zelditch et al., 2004;McNulty, 2012). The availability of advanced methodologies for data collection (e.g., 3D digitizers and scanners) and analysis (typified by the 'geometric morphometric revolution'; Rohlf and Marcus, 1993;Adams et al., 2004) have also provided researchers with improved means to quantify and evaluate relationships between ontogeny and biological form. ...
... The majority of these investigations focused on analyzing ontogenetic sequences, rather than phenotypic trajectories in shape space. However, some have argued that ontogenetic trajectories of shape change (i.e., not just the sequence of character ontogeny) may provide insights into phylogeny Zelditch et al., 1995; but see Adams and Rosenberg, 1998;Rohlf, 1998). ...
While the analysis of ontogenetic trajectories is common in geometric morphometrics (GM), the simultaneous comparison of several trajectories can be unwieldy and is, in some cases, unable to make use of one of the main advantages of GM, visualization. Furthermore, due to the paucity of the paleontological record, analyses of trajectories are often limited to extant taxa. We address these issues by presenting a method for visualizing the similarities and differences of cranial ontogenetic trajectories among taxa and a method for reconstructing ancestral ontogenetic trajectories, so that these differences can be investigated in a phylogenetic context. We also tested for the presence of phylogenetic signal in the ontogenetic trajectories themselves. Using an ontogenetic series of 522 crania, representing 17 cercopithecine species from 8 genera, we first calculated ontogenetic trajectories of cranial shape change for each species, and then entered these trajectories into a principal components analysis to produce a developmental shape-change trajectory PCA (δPCA). Then, through an augmentation of the phylomorphospace approach, we projected a molecular phylogeny onto the major axes of trajectory shape variation from the δPCA to produce an 'ontophylomorphospace,' using squared-change parsimony to reconstruct interior nodes. Through these procedures, we were able to determine that the δPCAs illustrate patterns of variation in these developmental trajectories in a visually intuitive manner that allows for easier comparisons among taxa. Through examination of the ontophylomorphospace, we found that African papionins exhibit extensive homoplasy in the evolution of cranial ontogenetic trajectories, and that Asian species of Macaca show highly derived ontogenetic trajectories relative to other cercopithecines. Additionally, we found no support for the presence of a phylogenetic signal in cranial ontogenetic trajectories. The δPCA and the ontophylomorphospace are ways in which to visualize and compare complex, multivariate shape transformations, both among extant taxa and over evolutionary time, respectively.
... In bivalves-as it is for most biological forms-outline shape is of fundamental importance to the taxonomy, life history, and functional range of the organism. It is, therefore, no coincidence that, despite the actively antagonistic stance taken by many 'landmark-centric' theorists and practitioners (e.g., Bookstein et al., 1982;Bookstein, 1990Bookstein, , 1991Zelditch et al., 1995;Zelditch et al., 2004), most applied morphometric investigations employ landmark configurations that are dominated by semilandmark points that lie on the specimens' outline (e.g., see example analyses in Bookstein, 1990Bookstein, , 1991Marcus et al., 1993;Marcus et al., 1996;Zelditch et al., 2004). Landmark data were collected from the 3D scan files in the form of sets of 3D point coordinates. ...
... Because the rationale for using semilandmarks to represent a specimen's outline has often been misunderstood (e.g., Bookstein et al., 1982;Bookstein, 1990Bookstein, , 1991Zelditch et al., 1995;Zelditch et al., 2004) and because the eigenshape sampling strategy will be extended to 3D surfaces in the following section, it is worth taking a moment to review the difference between strictly landmark-based and outline-based morphometric analyses. As noted above, landmarks represent positions that can be located unambiguously on each shape in the sample. ...
... Our work also opens a new chapter of research in evolutionary biology by using generative models to visualize evolutionary changes directly from images, which can serve a variety of biological use-cases. For example, Phylo-Diffusion can help biologists automate the discovery of synapomorphies, which are distinctive traits that emerge on specific evolutionary branches and are crucial for systematics and classification [33]. Our proposed experiments of trait masking and swapping can also be viewed as novel image-based counterparts to genetic experiments, which traditionally take years. ...
A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of large-scale image repositories in biology and recent advances in generative modeling, there is an opportunity to accelerate the discovery of evolutionary traits automatically from images. Toward this goal, we introduce Phylo-Diffusion, a novel framework for conditioning diffusion models with phylogenetic knowledge represented in the form of HIERarchical Embeddings (HIER-Embeds). We also propose two new experiments for perturbing the embedding space of Phylo-Diffusion: trait masking and trait swapping, inspired by counterpart experiments of gene knockout and gene editing/swapping. Our work represents a novel methodological advance in generative modeling to structure the embedding space of diffusion models using tree-based knowledge. Our work also opens a new chapter of research in evolutionary biology by using generative models to visualize evolutionary changes directly from images. We empirically demonstrate the usefulness of Phylo-Diffusion in capturing meaningful trait variations for fishes and birds, revealing novel insights about the biological mechanisms of their evolution. (Model and code can be found at imageomics.github.io/phylo-diffusion )
... Desde hace años ha habido diferentes intentos de articular los métodos filogenéticos con aquellos de morfometría geométrica (e.g. Bookstein, 2002;Cannon y Manos, 2001;Rohlf, 2002;Zelditch et al., 1995), no existiendo un consenso sobre cómo llevar a cabo tal articulación. Algunos autores muy importantes dentro de la morfometría geométrica (ej. ...
... La morfometría multivariada tradicional tiene limitaciones técnicas para extraer de las matrices de distancias la información sobre la conformación biológica (Zelditch et al., 1995). Por el contrario, una nueva metodología conocida como morfometría geométrica revolucionó el estudio de la variación de la conformación (Rohlf y Marcus, 1993). ...
Se emplearon análisis morfométricos tradicionales para cuantificar las diferencias en la variación morfológica entre Bothrops atrox y Bothrops asper, cuya posición taxonómica es controversial. Para ello se examinaron doce hembras y dieciséis machos B. atrox y diecinueve hembras y once machos B. asper. Se seleccionó un conjunto de cinco distancias entre puntos anatómicos para utilizarlas en análisis de componentes principales multigrupo (ACPmg). El primer componente principal (CPmg-1) dio cuenta de la mayor porción de la variación en el nivel intragrupo y fue tomado como un estimador de tamaño. La proyección ortogonal de los individuos sobre el CPmg-1 rindió unos residuos que se consideraron representantes de la conformación biológica libre de tamaño, ya que por construcción matemática ellos son libres de alometría intragrupo. Tales residuos se emplearon en análisis discriminantes, utilizando la primera variable canónica resultante para representar la conformación libre del tamaño. Además, los análisis discriminantes permitieron evaluar la capacidad de reclasificar correctamente los individuos en sus grupos. En ambos sexos los resultados revelaron diferencias significativas de tamaño y conformación libre de tamaño entre B. atrox y B. asper. A causa de la técnica utilizada (ACPmg) se pudo asignar al componente genético de la varianza fenotípica total una porción alta de las diferencias morfométricas, lo que sugiere un nivel importante de divergencia genética entre ambas entidades biológicas. Sin embargo, la separación morfométrica no fue total, existiendo un nivel bajo pero significativo de individuos que no se pudieron asignar correctamente a sus respectivas taxa. Para llegar a conclusiones más definidas con relación a la posición taxonómica se requieren estudios con más poblaciones, utilizando herramientas analíticas adicionales como las de la morfometría geométrica.
... Their approach reflected conventions that have grown up around GM which prioritizes the representation of complex structures thorough the digitization of small sets of independently defined landmark points. Originally, some GM practitioners even objected to the collection and use of boundary outline semilandmarks (e.g., [12,60]) though these data are now collected and analysed routinely by GM practitioners, largely for practical reasons (e.g., [61]). But even given the (belated) acceptance of semilandmark points as useful means of sampling complex morphologies, we suspect few morphometricians would have been entirely comfortable with the sampling scheme devised by Outomuro et al. [47] as either a comprehensive, or geometrically accurate, representation of a Trithemis dragonfly wing. ...
Background
The phylogenetic ecology of the Afro-Asian dragonfly genus Trithemis has been investigated previously by Damm et al. (in Mol Phylogenet Evol 54:870–882, 2010) and wing ecomorphology by Outomuro et al. (in J Evol Biol 26:1866–1874, 2013). However, the latter investigation employed a somewhat coarse sampling of forewing and hindwing outlines and reported results that were at odds in some ways with expectations given the mapping of landscape and water-body preference over the Trithemis cladogram produced by Damm et al. (in Mol Phylogenet Evol 54:870–882, 2010). To further explore the link between species-specific wing shape variation and habitat we studied a new sample of 27 Trithemis species employing a more robust statistical test for phylogenetic covariation, more comprehensive representations of Trithemis wing morphology and a wider range of morphometric data-analysis procedures.
Results
Contrary to the Outomuro et al. (in J Evol Biol 26:1866–1874, 2013) report, our results indicate that no statistically significant pattern of phylogenetic covariation exists in our Trithemis forewing and hindwing data and that both male and female wing datasets exhibit substantial shape differences between species that inhabit open and forested landscapes and species that hunt over temporary/standing or running water bodies. Among the morphometric analyses performed, landmark data and geometric morphometric data-analysis methods yielded the worst performance in identifying ecomorphometric shape distinctions between Trithemis habitat guilds. Direct analysis of wing images using an embedded convolution (deep learning) neural network delivered the best performance. Bootstrap and jackknife tests of group separations and discriminant-function stability confirm that our results are not artifacts of overtrained discriminant systems or the “curse of dimensionality” despite the modest size of our sample.
Conclusion
Our results suggest that Trithemis wing morphology reflects the environment’s “push” to a much greater extent than phylogeny’s “pull”. In addition, they indicate that close attention should be paid to the manner in which morphologies are sampled for morphometric analysis and, if no prior information is available to guide sampling strategy, the sample that most comprehensively represents the morphologies of interest should be obtained. In many cases this will be digital images (2D) or scans (3D) of the entire morphology or morphological feature rather than sparse sets of landmark/semilandmark point locations.
... Another important aspect for understanding the relationship between molecular and morphological evolution is the phylogenetic signal (Felsenstein, 1988, Zelditch et al., 1995, MacLeod, 2002, Klingenberg and Gidaszewski, 2010, Zelditch et al., 2012b. With a null hypothesis of not having any phylogenetic signal in the data set, the morphological variation of penaeid prawn body shape is tested by mapping the body shape onto an independently derived molecular phylogeny (Klingenberg and Gidaszewski, 2010). ...
This study reports on the phylogeny of selected penaieds and population genetics of the commercially important Green Tiger Prawn (Penaeus semisulcatus) in the Malaysian waters. In the first part of this study, morphological shape variations among 12 species of family Penaeidae, mainly from northwest coast of Peninsular Malaysia were investigated. This was achieved based on the Geometric Morphometrics (GM) of 18 homologous landmarks, analysed with Principal Component Analysis (PCA) and Canonical Variate Analysis (CVA) in Morpho J software. The shape variations was attributed to body shape, carapace head and telson tail among individuals. The first four components accounted for 76.24% and 78.47% for PCA and CVA, respectively. There is a tendency for closely related species to cluster together, although not absolutely consistent. To assess the phylogenetic signal, the morphometric data was mapped onto three phylogenetic trees (Neighbour Joining -NJ, Maximum Likelihood- ML and Bayesian Inference- BI) generated from the partial mitochondrial Cytochrome oxidase Subunit 1 (COI) on the same 12 species. Results revealed non significance (no phylogenetic signal) for NJ but significant phylogenetic signal (evolutionary significance) for ML and BI which suggest shape difference among all 12 penaeid prawn species was related to their evolutionary history. This discrepancy could be explained due to NJ tree are prone to errors when dealing with deeper divergence times, whereas ML and BI tree are ideal for phylogeny tree reconstruction which apply a model of sequence evolution on the data. In the second part of the study, a population genetics study was conducted on P. semisulcatus from Strait of Malacca (SOM), South China Sea (SCS), Sulu Sea (SS) and Celebes Sea (CS). A 548 base pair region of mitochondrial COI and 571 base pair of control region (CR) were analysed among 263 specimens from 15 locations. Genetic divergences (Tamura 3-parameter) for COI was 0.1% to 7.2% and CR 2.3% to 21.7% among the populations, with Bagan Pasir (BGP) in central SOM being most genetically different from other populations (COI: 3.3-4.2%; CR: 7.1-16.5%). Genetic data differentiated the populations into two groups; Lineage 1 (East coast of Peninsular Malaysia, Sarawak and Sabah) and Lineage II (west Coast of Peninsular populations with the exception of BGP and Batu Pahat (BPT)) as revealed by all related statistical analyses. The west coast populations of Bagan Pasir (BGP) and Batu Pahat (BPT) unexpectedly clustered in Lineage 1. The Bagan Pasir population is believed to be a mixed gene pool between the two Lineages. The genetic diversity analysis showed high nucleotide diversity, π (Lineage I: COI: 3.4%; CR: 7.4%) (Lineage II: COI: 3.8%; CR: 12.6%) and high haplotype diversity, h (Lineage I: COI: 0.81; CR: 1.0) (Lineage II: COI: 0.57; CR: 0.99). A mismatch analysis produced a unimodal distribution of pairwise differences between haplotypes in both Lineages, supporting evidence from other demographic statistics that both Lineages had undergone sudden expansion. The findings of this study are not only important for the strategic management plan of wild and cultured stocks of P. semisulcatus but also for the management and conservation of species family Penaidae in Malaysian water.
... The emergence of geometric morphometrics in the 1980's appeared promising (Rohlf and Marcus 1993). Although there was substantial optimism during this time for the development of a fully statistical, quantitative framework for morphological phylogenetics (Felsenstein 1988), the following years witnessed substantial controversy over the usability of quantitative traits generated through geometric approaches in phylogenetics (Zelditch et al. 1995;Adams and Rosenberg 1998;Rohlf 1998;Felsenstein 2002;MacLeod 2002;Rohlf 2002). Since this time, new approaches to morphometrics have reignited the potential for a data-rich future in morphology (Boyer et al. 2015(Boyer et al. , 2016Pomidor et al. 2016). ...
During the modern synthesis, researchers merged insights from natural history, evolutionary genetics, and paleontology to develop a cohesive theoretical foundation for evolutionary theory. Since then, the rapid emergence of genomic resources has revolutionized our understanding of evolutionary processes. Despite neontological successes, paleobiology has lagged behind, due in part to perceived challenges in collecting and analyzing morphological data. As a result, the earlier synthetic evolutionary view developed between neo- and paleontology has not kept pace with the current data-centric landscape. To address these issues, I aim to integrate morphological data representing fossil and living taxa into the modern evolutionary framework through the development of novel statistical approaches that leverage sources of data previously thought to be unconventional. These developments follow two main threads: 1) development of a statistical framework through which to infer phylogeny among fossil taxa by merging increasingly large and high-throughput quantitative morphological datasets with stratigraphic information, and 2) developing empirical applications of new approaches to comprehensively examine long-hypothesized but under-studied patterns in evolutionary rate throughout time, and mosaic change by integrating morphological, stratigraphic, and developmental data.
... Selection of landmarks in the landmark-based studies relate to the existence of shape variation between species and population (Dujardin 2008). GM based investigations generally used to explore shape variation in an evolutionary pathway that have focused on vertebrates to understand transformations in skull shape, scapula shape, body form and so on (Swiderski 1993;Zelditch et al. 1995;Oettle et al. 2005;Stayton 2005). However, the present investigation highlights the usefulness of the Geometric morphometric based analysis for easy and quick identification of the fishes, which can be beneficial for fisheries recourse management. ...
Landmark-based geometric morphometric (GM) analysis was carried out in the present study on the species of the family Leiognathidae. Pattern of shape variation along the axes of the principal components and canonical variates were analyzed after the General Procrustes analysis. Canonical variates analysis confirmed the occurrence of eleven species of the family Leiognathidae along the Gopalpur-on-Sea, Odisha coast. Further, inter-specific shape variation among the species of the family were carried out using Discriminant function
analysis, which would help us to understand the morphological divergence with respect to
shape.
... During the last two decades, several proposals for estimating phylogenies from morphometric data have been discussed contentiously. Some authors have suggested phylogenetic analyses based on cladistic characters derived from partial warp scores Zelditch et al. 1995Zelditch et al. , 1998Swiderski et al. 1998;Bogdanowicz et al. 2005;Clouse et al. 2011) or principal component (PC) scores (MacLeod 2002;González-José et al. 2008Aguilar-Medrano et al. 2011;Brocklehurst et al. 2016). These proposals, however, have been criticized for various reasons, especially the decomposition of phenotypic spaces into distinct characters (Bookstein 1994;Naylor 1996;Adams and Rosenberg 1998;Rohlf 1998;Monteiro 2000;Adams et al. 2011;Zelditch et al. 2012). ...
In recent years, there has been controversy whether multidimensional data such as geometric morphometric data or information on gene expression can be used for estimating phylogenies. This study uses simulations of evolution in multidimensional phenotype spaces to address this question and to identify specific factors that are important for answering it. Most of the simulations use phylogenies with four taxa, so that there are just three possible unrooted trees and the effect of different combinations of branch lengths can be studied systematically. In a comparison of methods, squared-change parsimony performed similarly well as maximum likelihood, and both methods outperformed Wagner and Euclidean parsimony, neighbor-joining and UPGMA. Under an evolutionary model of isotropic Brownian motion, phylogeny can be estimated reliably if dimensionality is high, even with relatively unfavorable combinations of branch lengths. By contrast, if there is phenotypic integration such that most variation is concentrated in one or a few dimensions, the reliability of phylogenetic estimates is severely reduced. Evolutionary models with stabilizing selection also produce highly unreliable estimates, which are little better than picking a phylogenetic tree at random. To examine how these results apply to phylogenies with more than four taxa, we conducted further simulations with up to eight taxa, which indicated that the effects of dimensionality and phenotypic integration extend to more than four taxa, and that convergence among internal nodes may produce additional complications specifically for greater numbers of taxa. Overall, the simulations suggest that multidimensional data, under evolutionary models that are plausible for biological data, do not produce reliable estimates of phylogeny.
... Some studies also used GM combined with genetic approaches for species discrimination (Gómez and Correa, 2017;Altamiranda-Saavedra et al., 2017) or even to compare both markers for genetic and phenetic structure of specific populations (Gómez et al., 2014). Furthermore, studies have been conducted using morphometric data to construct phylogenies (Zelditch et al., 1995(Zelditch et al., , 1998Swiderski et al., 2000;Guerrero et al., 2003). This is only possible if there is a strong phylogenetic signal (Cole and Lele, 2002) in the morphometric data. ...
... However, the use of these data has been historically limited. Several methods have been proposed for the phylogenetic analysis of landmark data (Zelditch, Fink & Swiderski, 1995;Caumul & Polly, 2005;González-José et al., 2008;Klingenberg & Gidaszewski, 2010), but for the most part they have been controversial (Rohlf, 1998;Zelditch et al., 2004;Adams et al., 2011) and failed to gain significant acceptance. ...
Background
In the last 20 years, a general picture of the evolutionary relationships between geoemydid turtles (ca. 70 species distributed over the Northern hemisphere) has emerged from the analysis of molecular data. However, there is a paucity of good traditional morphological characters that correlate with the phylogeny, which are essential for the robust integration of fossil and molecular data. Part of this problem might be due to intrinsic limitations of traditional discrete characters. Here, we explore the use of continuous data in the form of 3D coordinates of homologous landmarks on the turtle shell for phylogenetic inference and the phylogenetic placement of single species on a scaffold molecular tree. We focus on the performance yielded by sampling the carapace and/or plastral lobes and using various phylogenetic methods.
Methods
We digitised the landmark coordinates of the carapace and plastron of 42 and 46 extant geoemydid species, respectively. The configurations were superimposed and we estimated the phylogenetic tree of geoemydids with landmark analysis under parsimony, traditional Farris parsimony, unweighted squared-change parsimony, maximum likelihood with a Brownian motion model, and neighbour-joining on a matrix of pairwise Procrustes distances. We assessed the performance of those analyses by comparing the trees against a reference phylogeny obtained from seven molecular markers. For comparisons between trees we used difference measures based on quartets and splits. We used the same reference tree to evaluate phylogenetic placement performance by a leave-one-out validation procedure.
Results
Whatever method we used, similarity to the reference phylogeny was low. The carapace alone gave slightly better results than the plastron or the complete shell. Assessment of the potential for placement of single species on the reference tree with landmark data gave much better results, with similar accuracy and higher precision compared to the performance of discrete characters with parsimony.
... In this study, low spatial scales might feature compression only in the region of landmarks representing the inner lateral teeth, whereas more global spatial scales might show gradual compressions that span many widely separated landmarks. The methodology's strength is parsing these changes into scale-based components (as discussed by Zelditch et al. 1995). In most ontogenetic studies, shape and size are plotted against one another to determine allometries. ...
Determining the connection between ontogeny and phylogeny continues to be a major theme in biology. However, few studies have combined dissection of pattern and process that lead to transformation of complex morphological structures. Here we examine the patterns and processes of shape change in a model system-the gastropod radula. This system is a simple one having only two processes: initial secretion and postsecretional movement of teeth. However, it produces a tremendous amount of shape variability and fusion patterns. To determine both pattern and mechanism of shape change in an evolutionary context, we use three complementary approaches and datasets. First, we use a phylogenetic hypothesis to determine the polarity of developmental events. Second, we perform a morphometric analysis of shape change using relative warp analysis that allows us to locate and compare the direction and magnitude of ontogenetic and phylogenetic shape divergence. These comparisons are the basis for testing hyptheses of heterochrony and heterotopy, and we show how our results do not conform to expectations of pure heterochrony. The rejection of heterochrony as a hypothesis is based on empirically demonstrating (1) initial shape differs in each taxon; (2) a single dimension of shape variability does not simultaneously describe ontogenetic and evolutionary shape changes; and (3) a significantly different shape and size covariance between taxa. This rejection is probably based on spatial changes in initial conditions and not spatial changes caused by the process itself. Finally, we construct a mechanistic model that explains how shape change happens based on the sequence of events during ontogeny. By using the parameters in the model as characters in the phylogenetic dataset, we show that different parts of the system have arisen at different times and become co-opted into the process. By integrating our analyses together we show that spatial process parameters can be responsible for our nonspatial patterns and that different ontogenetic processes can create similar end morphologies.
... prior to the development of methods (e.g., [33,35,36]) that, to a greater-or-lesser extent, addressed the criticisms geometric morphometricians had levelled at such data (see [15,63]). Despite this initial near-rejection, today boundary outline semilandmark data are one of the most common subjects for geometric morphometric analysis because these data capture important aspects of morphological variation that cannot be represented through the use of landmark data alone. ...
... Let us first examine the theoretical reasons for using geometric morphometrics. The interlandmark distances used by the traditional approach are limited to providing information regarding differences between specimens that are aligned with its axis (Zelditch et al. 1995), whereas the rectangular coordinates associated with landmarks capture variation in all possible directions of figure space. For interlandmark distances to have the same amount of information concerning shape and size variation present in landmark coordinates, one has to include all possible interlandmark directions in the analysis. ...
The recently developed geometric morphometrics methods represent an important contribution of statistics and geometry to the study of biological shapes. We propose simple protocols using shape distances that incorporate geometric techniques into linear quantitative genetic models that should provide insights into the contribution of genetics to shape variation in organisms. The geometric approaches use Procrustes distances in a curved shape space and distances in tangent spaces within and among families to estimate shape heritability. We illustrate the protocols with an example of wing shape variation in the honeybee, Apis mellifera. The heritability of overall shape variation was small, but some localized components depicting shape changes on distal wing regions showed medium to large heritabilities. The genetic variance-covariance matrix of the geometric shape variables was significantly correlated with the phenotypic shape variance-covariance matrix. A comparison of the results of geometric methods with the traditional multivariate analysis of interlandmark distances indicated that even with a larger dimensionality, the interlandmark distances were not as rich in shape information as the landmark coordinates. Quantitative genetics studies of shape should greatly benefit from the application of geometric methods.
... Despite the antiquity and generally narrow context of the concept, the issue of homology and its practical application remain the subject of substantial controversy (Rieppel, 1980(Rieppel, , 1992(Rieppel, , 1994Roth, 1984Roth, , 1988Roth, , 1991Sattler, 1984). Subsequently, however, the concept and criteria for the diagnosis of homology have been recognized as equally vital and challenging for phylogenetic interpretation of characters as diverse as DNA sequences (Patterson, 1988;Mindell, 1991;Hillis, 1994;Brower and Schawaroch, 1996), proteins (Fitch, 1970), metric abstractions (Bookstein, 1994;Fink and Zelditch, 1995;Zelditch et al., 1995Adams and Rosenberg, 1998;Rohlf, 1998;Swiderski et al., 1998;, and behavioral repertoires (Wenzel, 1992;Greene, 1994). In that Owen (1843) originally contrasted "analogues" --phylogenetically independent structures having common functions in different taxa^ -from "homologues," it is not surprising that an emphasis on function persists in the diagnosis of homology and the utility of characters for phylogenetic reconstruction (Bock, 1967(Bock, , 1977(Bock, , 1979(Bock, , 1989; but see Cracraft, 1981Z?). ...
Two landmarks of the temporal region of the skull in most birds are the zygomatic process (processus zygomaticus) and the postorbital process (processus postorbitalis). The morphology and homology of these processes in gallinaceous birds (Galliformes) and waterfowl (Anseriformes), however, are not clear. Anseriformes usually are said to lack a processus zygomaticus. By contrast, the processus zygomaticus of many Galliformes often is described as connected to the tip of the processus postorbitalis, forming a temporal arch. Olson and Feduccia (1980a) cited these cranial differences as evidence opposing a hypothesis of sister relationship between the two orders, an hypothesis having a substantial history of advocacy (Seebohm, 1889; Shufeldt, 1901; Delacour, 1954; Johnsgard, 1965; Cracraft, 1981a, 1986; Schulin, 1987). Dzerzhinsky (1982, 1995) contradicted the proposal by Olson and Feduccia (1980a), interpreting the two processes as completely fused in Anseriformes, forming a unique 'sphenotemporal process,' which he averred to have been derived evolutionarily from the condition found in the Galliformes. In the present study, we examined skulls and jaw muscles of juvenile and adult specimens of selected taxa from both orders to test these opposing hypotheses, and found that: (a) the processus zygomaticus is small or lacking in adult Galliformes, and absent in all Anseriformes; (b) the processus zygomaticus is connected to the tip of the processus postorbitalis by an ossified aponeurosis of m. adductor mandibulae externus (aponeurosis zygomatica) in adults of most galliforms, whereas the aponeurosis zygomatica of anseriforms has a linear origin along the os squamosum as far as the processus postorbitalis; the aponeurosis zygomatica is ossified in Anhimidae and unossified in Anatidae; (c) a laterally exposed fossa of the temporal region (fossa musculorum temporalium) is reduced in Galliformes and absent in Anseriformes; (d) pars superficialis and pars zygomatica of m. adductor mandibulae externus are shifted rostrad in Galliformes and Anseriformes, and (e) pars articularis of m. adductor mandibulae externus is much enlarged in both orders. Based on these observations, we conclude that the parts of musculus adductor mandibulae externus of Anseriformes have been misinterpreted in a number of previous studies, perhaps reflecting confusion about associated processes and fossae. These findings are interpreted with respect to the homology of the osteological features and their associated muscles. The distribution of the included states supports the growing consensus for a sister relationship between the Galliformes and Anseriformes.
... Some attempts to treat geometric morphometric data as phylogenetic characters have been made (e.g. Zelditch et al., 1995;Caumul and Polly, 2005;Gonz alez-Jos e et al., 2008) and heavily criticized (Adams and Rosenberg, 1998;Monteiro, 2000;Adams et al., 2011). Recently, a new method of "landmark analysis under parsimony" (here abbreviated as LAUP) has been proposed to treat landmark configurations, a set of landmarks each defined by two (2D) or three (3D) coordinates, as such in cladistic analyses (Catalano et al., 2010;Goloboff and Catalano, 2011). ...
Wing venation provides useful characters with which to classify extant and fossil insects. Recently, quantification of its shape using landmarks has increased the potential of wing venation to distinguish taxa. However, the use of wing landmarks in phylogenetic analyses remains largely unexplored. Here, we tested landmark analysis under parsimony (LAUP) to include wing shape data in a phylogenetic analysis of hornets and yellow jackets. Using 68 morphological characters, nine genes and wing landmarks, we produced the first total-evidence phylogeny of Vespinae. We also tested the influence of LAUP parameters using simulated landmarks. Our data confirmed that optimization parameters, alignment method, landmark number and, under low optimization parameters, the initial orientation of aligned shapes can influence LAUP results. Furthermore, single landmark configurations never accurately reflected the topology used for data simulation, but results were significantly close when compared to random topologies. Thus, wing landmark configurations were unreliable phylogenetic characters when treated independently, but provided some useful insights when combined with other data. Our phylogeny corroborated the monophyly of most groups proposed on the basis of morphology and showed the fossil Palaeovespa is distantly related to extant genera. Unstable relationships among genera suggest that rapid radiations occurred in the early history of the Vespinae.
... In contrast to previous metric methods, eigenshape analysis is an outline-based technique for testing explicit shape based hypotheses [17][18] [20]. Outline-based approaches have been criticised because semilandmarks are not homologous to one another across outlines; that is, the point-to-point homology that characterises landmark-based approaches is absent [21]. This issue, though valid, is of limited concern unless biological variables are one-to-one mapped to individual points, and in most instances this is not the case, but rather the entire outline itself represents a biologically homologous or functionally meaningful form (e.g. ...
The role of ontogeny in the generation of adult orphological diversity is poorly understood. The aims of this study are to investigate the developmental bases for the extraordinary level of anatomical and ecological diversity and differing life strategy displayed by hystricognath rodents (e.g. guinea pigs, porcupines, capybaras) compared with muroids (mice and rats). The complementary methodological frameworks of heterochrony and allometry are used as a base to explore patterns of cranial growth at different points in developmental time. Developmental series of 58 rodent species were examined for this work, including prenatal and postnatal specimens.
In one part of this thesis I examine the importance of equence heterochrony in morphological evolution. Two time windows are investigated: the onset of skeletal formation, beginning prenatally, and the point of suture closure, occurring during the latter part of postnatal growth. equence heterochrony was analysed using the Parsimov ethod. In the first comprehensive assay of heterochronies in cranial suture growth for a mammalian clade, we find that numerous heterochonies in suture closure have occurred in the evolutionary history of hystricognaths. Sutures are of particular interest because they serve as major sites of bone expansion during postnatal craniofacial growth in the vertebrate skull, and we show that their sequence of closure represents an aspect of ontogeny with functional and phylogenetic correlates. In complement, we present the most comprehensive sampling of rodent ossification sequences to date, including data for non‐model organisms nd several representatives from both muroid and hystricognath clades. This study contributes considerably to improving the amount of data that presently exist on skeletal development across mammalian clades. We find, in ontrast to the results for suture closure patterns, that heterochrony is not a common mode of evolutionary change during skeletal formation. We additionally present data on intraspecific variation in cranial, postcranial, and autopodial ossification sequences for Rhabdomys pumilio, to further expand the extremely limited literature regarding this topic.
It has been hypothesized that most morphological evolution occurs by allometric differentiation. Hence the second part of this thesis focuses upon the evolution and patterning of ontogenetic allometry in rodents. The evolution of postnatal growth trajectories is examined across major clades; prenatal skull growth is comprehensively recorded morphometrically for the first time for the muroid rodent, R. pumilio. Studies directed towards examining the evolution of allometry are few and of small scope. We investigated the influence of phylogenetic relations and ecological factors on the results of the first quantification of allometric disparity among rodents by exploring allometric space, a multivariate morphospace that, in this study, was derived from the ontogenetic trajectories of 17 muroids and 17 hystricognaths. Disparity was quantified using angles between ontogenetic trajectories. We found an overlapping occupation of allometric space for muroids and hystricognaths, indicating similar abilities to evolve in different directions of phenotypic space. We show changes to covariance structure were common during rodent evolution and anatomic diversity was not found to constrain the labile nature of allometric patterning. Grouping of taxa in allometric space was found to be related to dietary habit; rodents sharing morphological features considered to be associated with the processing of particular dietary materials were found to group most closely with one another, showing the evolution of allometry in rodents has an adaptive basis. Whilst postnatal ontogenetic allometry has been documented for many species, there are very few studies that compare the dynamics of prenatal and postnatal growth. From this standpoint, trends regarding the linearity of prenatal allometry and its association to postnatal growth patterns are relatively unknown. Using a reflex microscope to measure cleared and stained specimens of R. pumilio, I performed the first study of prenatal ontogenetic allometry in a rodent, providing a crucial base for future comparative studies. Bivariate and multivariate estimates of allometry were coupled with matrix comparison methods to assess growth trends. The results indicate that prenatal growth is characterized by rapid lengthening of cranial elements. Ontogenetic allometric trends are found to shift between the prenatal and postnatal period, and localized variation in growth relationships occurs among cranial elements.
... there is no doubt that the recent rapprochement of morphometrics a n d phylogenetics has opened up a broad array of new auestions. It has also raised the standards to which answers will be held (Zelditch et al. 1992Zelditch et al. , 1995). ...
... Landmarks were then superimposed by generalized Procrustes analysis, which allows calculating variability between the taxa after aligning their landmark configurations in a specific process that ensures homology (Rohlf 1990, Rohlf and Slice 1990, Rohlf and Marcus 1993, Zelditch et al. 1995. This was conducted in TpsRelw 1.53 (Rohlf 2013). ...
The genus Ablattaria Reitter, 1884 (Coleoptera: Silphidae: Silphinae) is revised. Four taxa are recognized as valid species: Ablattaria arenaria (Kraatz, 1876), A. cribrata (Ménétries, 1832), A. laevigata (Fabricius, 1775) and A. subtriangula Reitter, 1905. Ablattaria laevigata var. meridionalis Ganglbauer, 1899 is newly treated as a junior subjective synonym of A. laevigata. Lectotypes are designated for Phosphuga arenaria Kraatz, 1876, Ablattaria arenaria var. punctigera Reitter, 1884, Ablattaria arenaria var. alleoni Portevin, 1926, Silpha cribrata Ménétries, 1832, Silpha laevigata Fabricius, 1775, Silpha gibba Brullé, 1832, Ablattaria gibba var. costulata Portevin, 1926, Ablattaria gibba var. distinguenda Portevin, 1926, Ablattaria gibba var. punctata Portevin, 1926 and Ablattaria subtriangula Reitter, 1905. The distribution of all taxa is mapped, based on material examined. Geometric morphometric methods were used to evaluate shape variability in Ablattaria. Results indicated sexual dimorphism in all species. Shape inconsistency was found between the sexes of all taxa when tested independently. The first two relative warp axes indicated 65.17% shape variation in males and 65.72% in females. Canonical variate analysis separated the taxa studied. There was minimal overlap between some groups in both sexes. Differences in body shape between populations of A. laevigata from Central Europe, Italy and Greece + Turkey were also examined. Relative warps implied 58.01% shape variability on both axes in males and 64.78% in females. CVA
revealed noticeable overlaps between the groups, although the Italian population demonstrated a higher separation in both sexes.
... In this study, we analyze the patterns of the caudal bursa of males Enterobiinae using the thin plate spline approaches of Bookstein (1991). Applications of morphometrics whether geometric or multivariate in phylogeny has long been and still remain controversial (Felsenstein, 1988(Felsenstein, , 2002(Felsenstein, , 2004Zelditch et al., 1995;Bookstein, 1994Bookstein, , 2002Naylor, 1996;Monteiro, 2000;Rohlf, 2001Rohlf, , 2002MacLeod, 2002). In this paper we do not use morphometric data to infer phylogenetic relationships within a clade, a procedure that is at the root of most controversies (see McLeod, 2002 for a recent synthesis). ...
The Enterobiinae includes 47 species of pinworms parasite of primates. A previous cladistic analysis of this subfamily supported its monophyly and its subdivision into three genera. Based on morphological characters, this cladistic analysis excluded characters describing the shape of the genital papillae of male pinworms, because the corresponding patterns could not be descri-bed using discrete characters. In this study, the shape of the genital papillae of the males of 35 within the 47 species is analyzed using geometric morphometric approaches. The aims of this study are to investigate: (i) the relationships between the phylogeny and the shape patterns of the caudal bursa, (ii) the shape differences between and within monophyletic groups, and, (iii) the functional implications of the shape patterns observed within the subfamily. Results de-monstrate that different patterns of evolution of the caudal bursa, each one characterized by a particular spatial distribution of the phasmids and genital papillae may be recognized, which are consistent with the classification of the Enterobiinae into three groups. On the whole, these patterns may be related to particular mating behavior of the pinworms. When lacks of congruence are observed between shape patterns distribution and species distribution into monophyletic groups, they are found to correspond to homoplasic events; this suggesting that convergent selective pressures are involved in the evolution of the shape of the genital papillae. This analy-sis also confirms that morphometric shape patterns cannot be interpreted unequivocally without the support of a preexisting phylogenetic framework. Jean-Pierre Hugot, UR 034, Institut de Recherche pour le Développement, RCEVD-CVD, Mahidol Uni-versity, 25/25 Phuttamonthon 4, Nakhon Pathom 73170, Thailand.
... Three-dimensional geometric morphometric techniques can be used to quantitatively capture shape morphology and variation between taxa (Zelditch et al., 2004;Klingenberg, 2010), and are a potential avenue for testing phylogenetic hypotheses with complex morphological structures. The utility of geometric morphometric data in phylogenetic analyses has been discussed by many authors (Bookstein, 1994;Zelditch et al., 1995;Rohlf, 1998;Montiero, 2000;MacLeod, 2002), with Klingenberg and Gidaszewski (2010) introducing the use of a permutation test of shape mean to test for a significant phylogenetic signal in shape data. Using the methods of Klingenberg and Gidaszewski (2010), two phylogenetic hypotheses of the relationships within Procyonidae will be examined in light of new brain shape data from endocasts. ...
Endocasts provide a proxy for brain morphology but are rarely incorporated in phylogenetic analyses despite the potential for new suites of characters. The phylogeny of Procyonidae, a carnivoran family with relatively limited taxonomic diversity, is not well resolved because morphological and molecular data yield conflicting topologies. The presence of phylogenetic and ecologic signals in the endocasts of procyonids will be determined using three-dimensional geometric morphometrics. Endocasts of seven ingroup species and four outgroup species were digitally rendered and 21 landmarks were collected from the endocast surface. Two phylogenetic hypotheses of Procyonidae will be examined using methods testing for phylogenetic signal in morphometric data. In analyses of all taxa, there is significant phylogenetic signal in brain shape for both the morphological and molecular topologies. However, the analyses of ingroup taxa recover a significant phylogenetic signal for the morphological topology only. These results indicate support for the molecular outgroup topology, but not the ingroup topology given the brain shape data. Further examination of brain shape using principal components analysis and wireframe comparisons suggests procyonids possess more developed areas of the brain associated with motor control, spatial perception, and balance relative to the basal musteloid condition. Within Procyonidae, similar patterns of variation are present, and may be associated with increased arboreality in certain taxa. Thus, brain shape derived from endocasts may be used to test for phylogenetic signal and preliminary analyses suggest an association with behavior and ecology. Anat Rec, 2014. © 2014 Wiley Periodicals, Inc.
... This technique has been demonstrated to be both objective and efficient compared to traditional methods (e.g. Zelditch, Fink & Swiderski, 1995;Rohlf, Loy & Corti, 1996;Rohlf, 1998), including in studies on bats (e.g. Velazco, Gardner & Patterson, 2010). ...
The taxonomic status of bent‐winged bats (Miniopterus) in the Western Palaearctic and adjacent regions is unclear, particularly in some areas of the eastern Mediterranean, Middle East and Arabia. To address this, we analysed an extensive collection of museum materials from all principal parts of this distribution range, i.e. North Africa, Europe and southwest Asia, using morphological (skull) and genetic approaches (mitochondrial DNA). Linear and geometric morphometric analysis of cranial and dental characteristics, together with molecular phylogeny, suggested that Miniopterus populations comprise four separate species: (1) M. schreibersii sensu strictissimo (s.str.) – occurring in Europe, coastal Anatolia, Levant, Cyprus, western Transcaucasia, and North Africa; (2) M. pallidus – occurring in inland Anatolia, Jordan, eastern Transcaucasia, Turkmenistan, Iran and southern Afghanistan (Kandahar); (3) a Miniopterus sp. – recorded from Nangarhar province in eastern Afghanistan, which we tentatively assign to M. cf. fuliginosus; and (4) a Miniopterus sp. with Afro‐tropic affinities confirmed from south‐western Arabia and Ethiopia, which we tentatively name M. cf. arenarius. The latter two species are well differentiated by skull morphology, while M. pallidus possesses very similar skull morphology to M. schreibersii. The results also suggest the existence of a possible new taxon (subspecies) within M. schreibersii s.str. inhabiting the Atlas Mountains of Morocco. © 2012 The Linnean Society of London
... Most studies that have used geometric morphometrics to explore shape variation in an evolutionary framework have focused on vertebrates: for example, to study transformations in skull shape, scapula shape, body form, etc. (Swiderski, 1993;Zelditch, Fink & Swiderski, 1995;Oettlé, Pretorius & Steyn, 2005;Stayton, 2005). In contrast, relatively few such studies have focused on insects. ...
A geometric morphometric analysis was conducted on wing-vein landmarks on exemplar species of the family
Simuliidae of the following genera: Parasimulium, Gymnopais, Twinnia, Helodon, Prosimulium, Greniera,
Stegopterna, Tlalocomyia, Cnephia, Ectemnia, Metacnephia, Austrosimulium, and Simulium. Generalized least
squares superimposition was performed on landmarks, followed by a principal component analysis on resulting Procrustes distances. Patterns of shape change along the principal component axes were visualized using the thin-plate spline. The analysis revealed wing shape diversity through (1) the insertion points of the subcosta and R1, resulting in the terminus of the costa exhibiting a trend towards a more apical position on the wing, and (2) the insertion point of the humeral cross vein, resulting in the anterior branch of the media exhibiting a trend toward a more basal position on the wing. Canonical variates analysis of Procrustes distances successfully assigned all exemplar species into their a priori taxonomic groupings. The diversity in wing shape reveals a trend towards decreased length of basal radial cell and increased costalization of anterior wing veins in the evolutionary transition from plesiomorphic prosimuliines to more derived simuliines. The functional significance of these evolutionary transitions is discussed.
Sound detection in fishes relies on the inner ear and peripheral structures, such as calcareous otoliths, which play a crucial role in perceiving movement, orientation, and balance. Otoliths, in particular, respond to various environmental factors including temperature, salinity, and food availability, making them valuable indicators of ecological conditions. This study applies geometric morphometrics (GMM) to analyze the otolith shape of Diplodus annularis (Linnaeus, 1758) from two distinct populations located in the Gulf of Asinara (Porto Torres, Sardinia) and the northern Adriatic Sea (Le Tegnue). By using GMM techniques, precise and quantifiable differences in otolith morphology were revealed between the two populations, demonstrating significant shape variation. In addition, fluctuating asymmetry (FA), which serves as a marker for developmental stability and environmental stress, was assessed. The results show marked disparities in FA between the populations: samples from Porto Torres exhibited posterior asymmetry, while samples from Le Tegnue showed asymmetry in the anterior region of the otoliths. These findings underscore the sensitivity of GMM in detecting even subtle morphological differences, making it a powerful tool for studying environmental and genetic influences on marine species.
The present study was conducted to evaluate the differences related to area of males and females of Akis costitubera Marseul by using morphometric geometric technique. The study was accomplished by using photographic records of each individual in ventral views by using a CELES- TRON X-150 digital camera. A matrix of photographs for each view was constructed using the TpsUtil program. In each view, we used 26 homologous landmarks which were digitized in the TPSdig2 program. 30 males and 30 females individuals were collected, photographed, and 26 land- marks from ventral views were digitized. We used a multivariate analysis of morphological variation. The results revealed significant differences between male and female (P<0.005), and the surface area of females was larger than that for males. The study concludes that sexual dimorphism occurred in the population of A. costitubera Marseul where these differences raise the question of whether sexual dimorphism may be modulated by natural selection.
Phylogenetic relationships within the helcionelloid molluscs have been difficult to establish. One of the reasons for this is that qualitative approaches to investigating morphological variation in this group have struggled to identify clear patterns. An alternative method of identifying these patterns is to study these organisms quantitatively. Here this approach is exemplified by employing morphometric methods to investigate patterns of subtle morphological variation in two species of Mackinnonia Runnegar in Bengtson et al. from Cambrian Series 2, Stages 3–4. Specifically, a combination of elliptical Fourier and multivariate analyses were conducted to study intra‐ and interspecific variation in protoconch form as well as variation in ontogenetic trajectory of the teleoconch of two species of Mackinnonia. The material used consists of two assemblages of Mackinnonia rostrata (Zhou & Xiao), from the Shackleton Limestone of Antarctica and Ajax Limestone of Australia, and an assemblage of Mackinnonia taconica (Landing & Bartowski) from the Bastion Formation of Greenland. Results of this study show significant (p < 0.0001) differences in protoconch shape between all three groups. Ontogenetic sequences of outline curves truncated at successive rugae significantly (p < 0.05) discriminate between M. rostrata and M. taconica. These techniques uncovered significant intraspecific morphological variation of disparate assemblages of M. rostrata despite shared qualitative features and structure a conceptual framework for understanding such patterns of variation and put this in the context of the incipient species concept
Geometric Morphometrics (GM) is a method originally applied in Evolutionary Biology studies, using the analysis of change in size and shape in order to better understand ontogenetic sequences, phylogenetic relations, among other issues. The application of GM in archaeological materials has seen a sharp increase in the last decade, mostly associated with theoretical approaches from Evolutionary Archaeology. This is not an isolated case, since most methods used by Evolutionary Archaeologists have been borrowed from Biology, provoking discussion with regard to the future development of Evolutionary Archaeology and its methods (Lycett, 2015). This article aims to discuss some concepts that have been directly borrowed from the application of GM in Biological Sciences and that have not been subject to much thought when used in Archaeology. Such concepts include homology and landmark types, the concept of modularity, as well as the idea of allometry. As much as archaeologists using GM can learn from past discussions held by biologists regarding the above mentioned concepts, it is high time for archaeologists to further discuss ideas concerning the use of these concepts in archaeological studies.
Cerion mumia is a complex of eight subspecies distributed along the north coast of Cuba from Pinar del Rio to Camaguey provinces. The geometric morphometric analysis presented here was aimed at identifying patterns of shell shape variation to test the hypothesis of colonisation through land bridges during the Eocene-Oligocene. C. mumia cuspidatum, the easternmost population, was similar in shape to the subspecies from the north coast of Havana, but showed morphometric differences suggesting allopatric speciation followed by dispersal. The shells from the west were more globose than those from Havana or the east, which tended to be more cylindrical, as shown by the thin-plate spline analysis. As a result of the morphometric analysis I propose to elevate C. noriae comb. nov. and C. wrighti comb. nov. to species rank and to include C. noriae hondanum comb. nov. as a subspecies of C. noriae comb. nov. I report a second locality of C. noriae comb. nov. at Playa Santa Fe formation from the late upper Pleistocene. Geometric morphometric techniques are useful in species identification through comparing new samples with type material.
Para conocer las divergencias y/o convergencias en la forma del cuerpo entre el híbrido yaque pintado y sus progenitores, se evaluó por medio de un análisis exploratorio, el contorno corporal total y distintas regiones del cuerpo. Para ello se utilizó un análisis de componentes principales (ACP) con las matrices de covarianza y correlación, valiéndose del método jackknife, con el propósito de verificar cuándo un coeficiente dentro del componente es estadísticamente diferente de cero. Los análisis demuestran que el híbrido exhibe la forma corporal general de la especie progenitora P. fasciatum. Se confirma además, que el ACP con la matriz de
correlación, si bien logró extraer en la mayoría de los casos un mejor vector de tamaño isométrico, no permitió verificar las relaciones dentro de los grupos de estudio, ya que sus gráficas por lo general ubicaron a los híbridos en posición intermedia en relación a sus progenitores, dando la impresión de que éstos heredan los caracteres de uno y otro padre prácticamente en la misma proporción. Mientras que al aplicar el ACP con matriz de covarianza, las gráficas sí permitieron visualizar las relaciones entre los grupos.
This study represents the first in a series tracing the early evolution of a dominant Caribbean reef coral, the Montastraea “annularis” species complex, using a combination of morphometric and phylogenetic approaches. It focuses on Costa Rica and Panama; additional geographic locations and reef environments will be treated in subsequent work. To distinguish species, new landmark methods are developed by comparisons with genetically characterized modern colonies from Panama. The fossil material consists of transverse thin-sections of 94 well-preserved specimens of M. annularis -like corals collected in Plio-Pleistocene reef sequences in the Limón basin of Costa Rica and the Bocas del Toro basin of Panama. The landmarks comprise 27 spatially homologous points, which define the thickness and structure of the corallite wall and associated costosepta. Bookstein size and shape coordinates are analyzed using cluster analysis and canonical discriminant analysis, and a total of 10 morphotypes are distinguished. Cladistic analyses are performed using characters derived partially from morphometric data. A matrix consisting of 16 taxa and eight characters is analyzed using global parsimony and a sister group of two species as the outgroup. The results reveal two distinct evolutionary groups, which are distinguished by the new corallite wall characters. One group contains one modern species, and the other contains a second; the relationships of the third are poorly resolved. Despite the low number of equally parsimonious trees, high numbers of plesiomorphic taxa, long range extensions, and lack of agreement with genetic data indicate that the new characters alone are inadequate for completely interpreting evolutionary relationships, and more samples and characters are needed. Nevertheless, these preliminary results do show that three modern species of the M. “annularis” complex arose prior to accelerated extinction at the end of late Pliocene to early Pleistocene faunal turnover of Caribbean reef corals, and two may have originated younger than 4 Ma. Six or more new species may be represented in upper Pliocene to lower Pleistocene sequences in Costa Rica and Panama. Coexistence of predominantly pre- and post-turnover clades may have been responsible for the high diversity observed within the species complex in these two sequences.
The power of landmark-based morphometries lies in their potential for comparative description. Description has been the cornerstone of comparative biology for the past 200 years, so it might seem at least superficially, that the new landmark-based methods don’t provide biologists with anything they didn’t have already. Ironically, nothing could be further from the truth. Geometric morphometries allow us to recognize features of organisms that we may previously not have noticed by providing analytical and graphical means to decompose variation into components that reflect differences at different spatial scales. At one end of the scale, these components reflect shape differences that are restricted to highly localized subregions, at the other, they reflect differences that are globally and diffusely spread over the entire form. In essence the new methods provide a set of filters that can be used, individually or in combination, to sequester particular aspects of the ensemble morphological variation so as to leave a clearer, less confounded view of the aspects that remain.
The use of quantitative shape data in phylogenetic studies has been challenged on several grounds, the most important being that hypotheses of homology cannot apply to them. Two premises underlie that argument: (1) quantitative data comprise a single homogeneous class, and (2) qualitative and quantitative data are fundamentally different. The first premise is problematic because some morphometric variables are constrained to compare homologous features of organisms, whereas others are not. Those that are so constrained, including traditional measurement data, shape coordinates and partial warps, yield features that can be assessed for their similarities and differences, and the resulting hypotheses of homology can be tested for their congruence with the cladogram. Those variables that are not so constrained, including most outline-based variables as well as multivariate constructs such as principal components and canonical variates, may be useful tools discriminating and sorting taxa by overall similarities in shape, but not for dis-covering characters. The second premise is also problematic because the same logic and methods apply to both qualitative and quantitative data alike. Thus, if care is taken to ensure that morphometric comparisons are framed in terms of homology, there is no barrier to using quantitative variables in phylogenetic studies, especially those produced by geometric morphometrics. Not only are they tools for describing shape differences, they are also tools for understanding the evolutionary history of shape.
A single-plane structured light range-sensor was tested to establish its usefulness in acquiring 3-D measurements of fish skulls. Twenty-one distances among 22 landmark points for each of 12 neurocrania of the scorpaenid fish Neomerinthe hemingway were taken with digital calipers, with a video-based 2-D imaging system widely used in systematic studies, and with a single-plane structured-light range sensor of inexpensive and simple design. Measures taken by 3-D sensor are highly correlated with those obtained from caliper measurement (r = 0.9995, P << 0.001 ), with a precision ranging from 0.08–0.43 mm. Like caliper-based measurements, they are less strongly correlated with measurements derived from projected video-imaging. Most skulls were scanned in just over 3 minutes each. Range maps, typically establishing the (x,y,z) coordinates of more than 75,000 points per scan, can be obtained in about 40–50 CPU seconds using software running on multiple platforms. Sensor data taken from different views can be merged to build a more complete 3-D reconstruction. System design, calibration, and use are discussed. By eliminating error due to perspective effects inherent in measuring from projected video images, such sensors hold considerable promise in quantifying biological shape in 3-D for comparative and functional studies.
It has always been obvious that organisms have properties making them ‘different’ from each other. Historically, taxonomists have sought to register these differences and similarities by assigning species to subjectively-delimited groups within hierarchical classifications. Many current methods in sys-tematics still have a subjective component, and classifications often reflect biases inherent in their construction (Hull 1988).
Zelditch et al. (1995) have recently proposed that partial warp scores derived from shape differences among organisms can be used as cladistic characters for phylogenetic inference. The current study represents a test of Zelditch et al.’s proposal. A group of different—shaped imaginary fishes, interrelated by a known phylogeny, was artificially generated by subjecting an ancestral fish to evolutionary change along a predetermined tree. Care was taken to ensure that invoked shape changes occurred only once on the tree and that shape changes occurred independently of each other. These conditions were set in order to maximally predispose any emergent “shape characters,” which might be derived from shape differences among terminals, to cladistic analysis. Thirty-eight landmarks were recorded for each of the eight terminals resulting from the contrived evolutionary tree. These landmarks were transformed into shape coordinates. The shape coordinates for each of the terminals were then individually contrasted with those of the ancestor by means of the computer program TPSPLINE (Rohlf, 1994). The resulting partial warp scores were recoded as cladistic characters following the protocol of Fink et al.(1994) and subjected to cladistic analysis. Two most parsimonious trees (MPTs) resulted, one of which matched the “true” tree. Although this tree matched the true tree in topology, the reconstructed ancestral shape states implied by parsimony for this tree were quite different from those of the true tree. Whereas the true tree contained no homoplasy whatsoever, the two inferred MPTs implied considerable shape homoplasy (Retention Index = 0.48). An UPGMA of raw partial warp scores also retrieved the correct tree topology.
The new morphometrics, or geometric morphometrics, is a rapidly evolving field. “Morphometrics” has been used to describe a number of fields that study measurements of organisms, and that is why the modifier “new” or “geometric” is necessary to set aside the special subject matter discussed here: the shape of biological organisms as it is studied using as data, point coordinates in two or three dimensions. This includes landmark and outline coordinates. Landmarks are specific points on an organism that correspond in a sensible way over the forms being studied, that is they are homologs; while outline points do not share this notion of homology. The data of morphometrics is now being extended to include tangent directions at coordinates as well (see Bookstein and Green, 1993; Little and Mardia, this volume). Shape is primarily concerned with properties of coordinates that are invariant to scale, location and orientation (see Appendix I, Glossary). The current status of morphometrics together with some future objectives are summarized in a review by Rohlf and Marcus (1993a).
This article provides an overview of recent methods of ancestral character state reconstruction and phenotypic evolution using examples drawn largely from vertebrate nervous systems. The evolutionary meaning of key concepts is reviewed, including homology, convergence, parallelism, reversal, adaptation, polarity, and phylogenetic tree. Parsimony-based methods for reconstructing ancestral states and analyzing the evolution of character or trait data include maximum parsimony optimization for discrete traits, and squared-change and linear parsimony for continous traits. Descriptions of likelihood, Bayesian, and correlative comparative methods are also reviewed. The strengths and weaknesses of these alternative methods are evaluated in light of different classes of data being examined and the different assumptions they make.
Cell lineage studies in the clade Eutrochozoa. and especially the Spiralia. remains a rich and relatively untapped source for understanding broad evolutionary developmental problems; including (1) the utility of cell timing formation for phylogenetic hypotheses: (2) the evolution of cell timing changes and its relation to heterochronic patterns (3) stereotypy or lack thereof in rates of change of cell growth during evolution and its relation to both evolutionary history and current usage and (4) how mosaic cleavage timing variation may be expected to differ from other groups. A compilation of available cell timing information was made from previous studies where each division Was explicitly followed and the total number of cells followed was greater than 24. From that compilation, we performed a series of heuristic and quantitative analyses, including a phylogenetic analysis using cell timing data as characters and analyses of timing variation across all taxa. Our results show that: (1) cell lineage data reconstructs a phylogenetic hypothesis that has similarities, especially among the Mollusca, to the patterns found in morphological and molecular analyses (2) the mesentoblast (4d) is a unique cell compared to other cell in that it speeds up and slows down relative to other cells in taxa with both unequal and equal cell sizes; (3) some cells that form in the same quartet at the same point in the cell lineage hierarchy have much lower variations than analogous other cells. arguing for architectural constraint or stabilizing selection acting on those cells; and (4) although variation in cell timing generally increases during development, timing of formation of progeny cells in the first quartet has lower variation than the parent cells, arguing that some regulation-like behavior might be present.
Body weight, length, width and depth at two growth stages were observed for a total of 5015 individuals of GIFT strain, along with a pedigree including 5588 individuals from 104 sires and 162 dams was collected. Multivariate animal models and a random regression model were used to genetically analyse absolute and relative growth scales of these growth traits. In absolute growth scale, the observed growth traits had moderate heritabilities ranging from 0.321 to 0.576, while pairwise ratios between body length, width and depth were lowly inherited and maximum heritability was only 0.146 for length/depth. All genetic correlations were above 0.5 between pairwise growth traits and genetic correlation between length/width and length/depth varied between both growth stages. Based on those estimates, selection index of multiple traits of interest can be formulated in future breeding program to improve genetically body weight and morphology of the GIFT strain. In relative growth scale, heritabilities in relative growths of body length, width and depth to body weight were 0.257, 0.412 and 0.066, respectively, while genetic correlations among these allometry scalings were above 0.8. Genetic analysis for joint allometries of body weight to body length, width and depth will contribute to genetically regulate the growth rate between body shape and body weight.
© 2015 Blackwell Verlag GmbH.
Determining the connection between ontogeny and phylogeny continues to be a major theme in biology. However, few studies have combined dissection of pattern and process that lead to transformation of complex morphological structures. Here we examine the patterns and processes of shape change in a model system-the gastropod radula. This system is a simple one having only two processes: initial secretion and postsecretional movement of teeth. However, it produces a tremendous amount of shape variability and fusion patterns. To determine both pattern and mechanism of shape change in an evolutionary context, we use three complementary approaches and datasets. First, we use a phylogenetic hypothesis to determine the polarity of developmental events. Second, we perform a morphometric analysis of shape change using relative warp analysis that allows us to locate and compare the direction and magnitude of ontogenetic and phylogenetic shape divergence. These comparisons are the basis for testing hyptheses of heterochrony and heterotopy, and we show how our results do not conform to expectations of pure heterochrony. The rejection of heterochrony as a hypothesis is based on empirically demonstrating (1) initial shape differs in each taxon; (2) a single dimension of shape variability does not simultaneously describe ontogenetic and evolutionary shape changes; and (3) a significantly different shape and size covariance between taxa. This rejection is probably based on spatial changes in initial conditions and not spatial changes caused by the process itself. Finally, we construct a mechanistic model that explains how shape change happens based on the sequence of events during ontogeny. By using the parameters in the model as characters in the phylogenetic dataset, we show that different parts of the system have arisen at different times and become co-opted into the process. By integrating our analyses together we show that spatial process parameters can be responsible for our nonspatial patterns and that different ontogenetic processes can create similar end morphologies.
Heterochrony, change in developmental rate and timing, is widely recognized as an agent of evolutionary change. Heterotopy, evolutionary change in spatial patterning of development, is less widely known or understood. Although Haeckel coined the term as a complement to heterochrony in 1866, few studies have detected heterotopy or even considered the possibility that it might play a role in morphological evolution. We here review the roles of heterochrony and heterotopy in evolution and discuss how they can be detected. Heterochrony is of interest in part because it can produce novelties constrained along ancestral ontogenies, and hence result in parallelism between ontogeny and phylogeny. Heterotopy can produce new morphologies along trajectories different from those that generated the forms of ancestors. We argue that the study of heterochrony has been bound to an analytical formalism that virtually precludes the recognition of heterotopy, so we provide a new framework for the construction of ontogenetic trajectories and illustrate their analysis in a phylogenetic context. The study of development of form needs tools that capture not only rates of development but the space in which the changes are manifest. The framework outlined here provides tools applicable to both. When appropriate tools are used and the necessary steps are taken, a more comprehensive interpretation of evolutionary change in development becomes possible. We suspect that there will be very few cases of change solely in developmental rate and timing or change solely in spatial patterning; most ontogenies evolve by changes of spatiotemporal pattern.
The analysis of morphology is crucial to the study of phylogeny in many ancient and modern organismal groups. Recently a number of arguments have been made in favor of regarding certain kinds of morphometric variables as putatively homologous characters and allowing them to participate, along with other non-morphometric variables, in parsimony-based cladistic analyses. These arguments rest on the assumptions that geometric landmarks incorporate the concept of biological homology and that partial warp and principal warp morphometric variables uniquely incorporate and operationalize the concept of spatial localization, thus providing investigators with the ability to assess patterns and directions of geometrical variation in unmeasured regions of organic forms. Literature review, coupled with empirical investigations of similarities and differences among three different morphometric data analysis methods on two different datasets suggest that there is no support for these assertions. Geometric landmarks, which form the basis for all morphometric measurements and latent shape variables, have no necessary correspondence to biological homology. Partial warp variables, coordinate-point eigenshape variables, and inter-landmark distance-based singular vector shape-change variables all express localized (= regionally-weighted) geometric deformations. However, none of these deformation patterns are localized in the sense of being truly independent from globally-distributed aspects of shape change. All three of the morphometric
In recent years, advances in our understanding of feline relationships have cast light on their evolutionary history. In contrast, there have been no phylogenetic analyses on machairodont felids, making it difficult to develop an evolutionary hypothesis based on the recent surge of studies on their craniomandibular morphology and functional anatomy. In this paper, I provide the first phylogenetic hypothesis of machairodont relationships based on 50 craniomandibular and dental characters from a wide range of sabercats spanning more 11 Myr. Exact searches produced 19 most-parsimonious trees, and a strict consensus was well resolved. The Machairodontinae comprise a number of basal taxa (Promegantereon, Machairodus, Nimravides, Dinofelis, Metailurus) and a well-supported clade of primarily Plio-Pleistocene taxa (Megantereon, Smilodon, Amphimachairodus, Homotherium, Xenosmilus) for which the name Eumachairodontia taxon novum is proposed. Previous phenetic grouping of machairodont taxa into three distinct groups, the Smilodontini, Homotherini and Metailurini, was not supported by cladistic parsimony analysis, and forcing monophyly of these groups was significantly incompatible with character distribution. Machairodonts as a clade are not characterized by saberteeth, i.e. hypertrophied, blade-like upper canines, but by small lower canines, as well as small M1; and large P3 parastyle. True saberteeth arose later and are a synapomorphy of the Eumachairodontia.
Analyses of craniodental measurement data from 15 wild-collected population samples of the Neotropical muroid rodent genus Zygodontomys reveal consistent patterns of relative variability and correlation that suggest a common latent structure. Eigenanalysis of each sample covariance matrix of logarithms yields a first principal component that accounts for a large fraction of the total variance. Variances of subsequent sample principal components are much smaller, and the results of bootstrap resampling together with asymptotic statistics suggest that characteristic roots of the covariance matrix after the first are seldom distinct. The coefficients of normalized first principal components are strikingly similar from sample to sample: inner products of these vectors reveal an average between-sample correlation of 0.989, and the mean angle of divergence is only about eight degrees. Since first principal component coefficients identify the same contrasts among variables as comparisons of relative variability and correlation, we conclude that a single factor accounts for most of the common latent determination of these sample dispersions. Analyses of variance based on toothwear (a coarse index of age) and sex in the wild-collected samples, and on known age and sex in a captive-bred population, reveal that specimen scores on sample first principal components are age- and sex-dependent; residual sample dispersion, however, is essentially unaffected by age, sex, or age x sex interaction. The sample first principal component therefore reflects the covariance among measured dimensions induced by general growth, and its coefficients are interpretable as exponents of postnatal growth allometry. Path-analytic models that incorporate prior knowledge of the equivalent allometric effects of general growth within these samples can be used to decompose the between-sample variance by factors corresponding to other ontogenetic mechanisms of form change. The genetic or environmental determinants of differences in sample mean phenotypes induced by such mechanisms, however, can be demonstrated only by experiment.
First principal components extracted from covariance matrices of log-transformed craniodental measurements closely approximate general size factors within field-collected samples representing 14 species in seven Neotropical muroid genera; because these samples are mixed-cross-sectional, scores are age-correlated and coefficients reflect postweaning growth allometries. Compared between congeners, sample first principal component coefficients are very similar, an observation that implies a nearly parallel orientation of ontogenetic trajectories in log-measurement space. On the assumption that a common general size factor (estimated as the first principal component of the pooled-within covariance matrix) accounts for most of the observed measurement covariance within samples, size-adjusted differences between congeneric species were estimated variable-by-variable in separate analyses of covariance; these differences reflect developmental adjustments of craniodental morphology that precede the measured interval of postweaning ontogeny. Vectors of size-adjusted difference coefficients are not similar from genus to genus, and a diversity of causal mechanisms is probably responsible. Analyses of captive-bred samples from two "species" of Zygodontomys provide prima facie evidence that size-adjusted differences estimated from field-collected samples have a genetic basis. Postweaning growth allometries in the muroid head skeleton may be conserved due to the biomechanical constraints of masticatory function; the apparent evolutionary plasticity of earlier ontogenetic adjustments may reflect the absence of such constraints in the fetus or suckling pup. The relevance of these results for current theories concerning the developmental genetics of mammalian morphometric evolution is discussed.
Multivariate discrimination by shape in relation to size. Syst. Zool., 30:291–308.—The diverse methods for analyzing size-free shape differences tend to be guided by computational expediency rather than
geometric principles. We question the use of ratios and ad hoc combinations of spatially unrelated measures. Neither are linear
discriminant functions or series of independent regressions helpful to the visualization of shape differences. A bridge is
needed between traditional quantitative methods and thegeometrical analysis of shape.
In principle any measured transects between landmarks of a form can serve as characters in a morphometric analysis. Systematic
studies use a highly non-random sample of these, particularly biased regarding geometrical information. We suggest defining
size and shape in terms of factors—estimates of information common to a universe of measured distances.
The model presented here calculates a linear combination of variables that quantifies shape differences among populations,
independent of size. In analyses in which the first two principal components confound size and shape, size is removed from
one axis with shear coefficients derived from regression of general size on principal components centered by group. The general
size factor is estimated by the principal axis of the within-group covariancematrix of the log-transformed data. Residuals
from the regression of general size onthe transformed axes approximate a shape-discriminating factor that is uncorrelated
with size within group and displays the interpopulation shape differences borne by the first two principal components. The
results bear a direct and interpretable correspondence to biorthogonal analysis of shape difference.
The truss: body form reconstruction in morphometrics. Syst. Zool., 31:113–135.—In principle, any measured distances between landmarks of a form may serve as characters for morphometric analyses. Systematic studies typically are based on a highly biased and repetitious sample of these. But collections of landmarks and the distances among them must be homologous from form to form for comparisons to be meaningful, and an adequate character set should at least permit the full reconstruction of the original configuration of landmarks.
We describe a geometric protocol for character selection, the truss network, which enforces systematic coverage of the form and which exhaustively and redundantly archives the landmark configuration. Reconstruction of the form from truss measures provides Cartesian coordinates for landmarks and allows estimation of, and compensation for, measurement error. Samples of forms may be averaged and standardized to one or more common reference sizes by regression of measured distances on a composite measure of body size, followed by reconstruction of the form using distance values predicted by the regression functions at some standard body size.
Principal component loadings of distance measures may be indicated directly on the truss network to display patterns of within-group allometry or between-group shape differences. Because the truss enforces use of cross measurements, discrimination among groups may be enhanced. Composite mapped forms are useful in biorthogonal analyses of differences in shape because they allow the comparison of averaged forms among samples. Certain patterns of principal component loadings are concordant with, and provide an initial sampling of, the biorthogonal grids for these deformations.
Because development is epigenetic, diverse aspects of morphology are integrated during ontogeny. Using the method of thin-plate splines, and the decomposition of these splines by their principal warps, we examine the ontogeny of integrated features of skull growth of the cotton rat, Sigmodon fulviventer as observed in landmark locations in the ventral view. Postnatal growth of the skull in Sigmodon is not adequately described by the familiar contrast between relatively rapid facial elongation and slow, precocial growth of the cranial base. No developmental units corresponding to "facial skull" and "cranial base" emerge from analysis of geometric shape change. Rather, skull growth is both more integrated and more complex, exhibiting both skull-wide integration and locally individualized regions. Like skull shape, integration has an ontogeny; different regions of the skull can be partitioned into developmentally individualized parts in different ways at different ages. The effective count of individualized parts decreases substantially before weaning occurs, suggesting that the integration required by the functionally demanding activity of chewing gradually develops before the functional transition occurs. Our description of skull growth and integration does not depend upon arbitrary a priori choices about what to measure; rather, we base our decomposition of the whole into parts upon results of the data analysis. Our approach complicates the study of heterochrony, but, because it expresses the spatiotemporal organization of ontogeny, it enables the study of heterotopy.
Abstract— Cladistic data are the characters of organisms. Character is defined as a feature that can be evaluated as a variable with two or more mutually exclusive and ordered states. Cladistic characters must be treated as multistate variables, and coded as sequential numbers or in additive binary fashion. Any other interpretation and handling of cladistic data will introduce error into analysis. Character states cannot be treated independently as present or absent, i.e., as nominal variables, because redundancy is introduced into the data and information content is sacrificed. Non-additive binary coding demonstrates that treating cladistic variables as nominal data will lead to multiple, equally parsimonious solutions. Defining characters found universally in a group of organisms, but unknown outside those organisms have no alternative state that can be designated as absent. Absence, however, is valid as a character state if it can be shown to be apomorphic. When two or more character states occur within a taxon, that taxon must be coded as having an unknown state for that character, or the taxon must be split in two or more taxa. Continuously varying quantitative data are not suitable for cladistic analysis because there is no justifiable basis for recognizing discrete states among them. Quantitative data are questionable even when they exhibit mutually exclusive states because the states can be interpreted only in reference to an archetype, i.e., as implied homologies not subject to test.
Developmental constraint is a theoretically important construct bridging ontogenetic and evolutionary studies. We propose a new operationalization of this notion that exploits the unusually rich measurement structure of landmark data. We represent landmark configurations by their partial warps, a basis for morphospace that represents a set of localized features of form. A finding of developmental constraint arises from the interplay between age-varying means and age-specific variances in these subspaces of morphospace. Examination of variances and means in 16 ventral skull landmarks in the cotton rat S. fulviventer at ages 1, 10, 20, and 30 days yielded three types of developmental constraint: canalization (constraint to relatively constant form age by age); chreods (reduction of variance orthogonal to the mean trajectory over ages); and opposition (reduction of age-specific variance along the mean trajectory over ages). While canalization and chreodic constraints have been noted previously, the oppositional type of constraint appears novel. Only one of our characters, relative length and orientation of the incisive foramen, appears to be canalized. Although skull growth becomes increasingly integrated through ontogeny, our characters display a remarkable spatiotemporal complexity in patterns of variance reduction. The specific assortment of constraints observed may be related to the precociality of Sigmodon. We suggest that Waddington's diagrammatic presentation of the “epigenetic landscape” may be misleading in quantitative studies of developmental regulation.
Despite the potential information that may lie in phylogenetic analyses of ontogenies of body form, few studies have examined methods for extracting and analyzing ontogenetic shape characters. We propose and exemplify a procedure for phylogenetic shape analysis. We use the thin-plate spline decomposed by its partial warps, a method that has several critical advantages over available alternatives. Most notably, shape variables extracted by this method refer to localizable features of the morphology. We demonstrate how these characters can be coded and include them in a phylogenetic analysis of the piranha genus Pygocentrus , using a data set also comprising meristic, myological, and osteological characters. Using ontogenies of these localized shape variables, we have corroborated the monophyly of Pygocentrus . Although we found no new characters corroborating the proposed sister-group relationship of P. nattereri and P. cariba , our characters are all congruent with this hypothesis. Several ontogenetic shape characters serve to diagnose the previously undiagnosed P. nattereri . Independence of ontogenetic shape features is assessed in the same manner as for any other features: by examination of their distributions on the corroborated cladogram. In addition to inspecting associations among characters that changed multiple times, character independence was assessed using the information in the kinds of ontogenetic modifications (gain, loss, reorientation, reversal) and the information in observed development. Most of the geometrically independent features extracted during this study are phylogenetically independent of each other. We also found that region-specific ontogenetic allometries are phylogenetically independent of each other. In addition, localized ontogenetic changes along orthogonal body axes (anteroposterior and dorsoventral in this case) are usually phylogenetically independent. Although these findings of character independence may be specific to this study, the method for assessing this independence can be applied generally. Evolution of both spatial and temporal patterns of growth is an inference that depends upon using methods, such as the one employed here, capable of describing the spatial patterning of ontogeny.
Homology in morphometrics and phylogenetics. Pages 325-338 in Proceedings of the Michigan morphometrics workshop
- G R Smith
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Morphometric tools for land-mark data: Geometry and biology Can biometrical shape be a homologous character? Pages 197-227 in Homology: The hierarchical basis of comparative biology
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Can biometrical shape be a homologous character? Pages 197-227 in Homology: The hierarchical basis of comparative biology
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