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

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

Categorical versus geometric morphometric approaches to characterizing the evolution of morphological disparity in Osteostraci (Vertebrata,stem Gnathostomata)

Morphological variation (disparity) is almost invariably characterized by two non-mutually exclusive approaches: (1) quantitatively, through geometric morphometrics; and (2) in terms of discrete, ‘cladistic’, or categorical characters. Uncertainty over the comparability of these approaches diminishes the potential to obtain nomothetic insights into the evolution of morphological disparity and the few benchmarking studies conducted so far show contrasting results. Here, we apply both approaches to characterizing morphology in the stem-gnathostome clade Osteostraci in order to assess congruence between these alternative methods as well as to explore the evolutionary patterns of the group in terms of temporal disparity and the influence of phylogenetic relationships and habitat on morphospace occupation. Our results suggest that both approaches yield similar results in morphospace occupation and clustering, but also some differences indicating that these metrics may capture different aspects of morphology. Phylomorphospaces reveal convergence towards a generalized ‘horseshoe’-shaped cranial morphology and two strong trends involving major groups of osteostracans (benneviaspidids and thyestiids), which probably reflect adaptations to different lifestyles. Temporal patterns of disparity obtained from categorical and morphometric approaches appear congruent, however, disparity maxima occur at different times in the evolutionary history of the group. The results of our analyses indicate that categorical and continuous data sets may characterize different patterns of morphological disparity and that discrepancies could reflect preservational limitations of morphometric data and differences in the potential of each data type for characterizing more or less inclusive aspects of overall phenotype.     

Do different disparity proxies converge on a common signal? Insights from the cranial morphometrics and evolutionary history of Pterosauria (Diapsida: Archosauria)

Disparity, or morphological diversity, is often quantified by evolutionary biologists investigating the macroevolutionary history of clades over geological timescales. Disparity is typically quantified using proxies for morphology, such as measurements, discrete anatomical characters, or geometric morphometrics. If different proxies produce differing results, then the accurate quantification of disparity in deep time may be problematic. However, despite this, few studies have attempted to examine disparity of a single clade using multiple morphological proxies. Here, as a case study for this question, we examine the disparity of the volant Mesozoic fossil reptile clade Pterosauria, an intensively studied group that achieved substantial morphological, ecological and taxonomic diversity during their 145+ million-year evolutionary history. We characterize broadscale patterns of cranial morphological disparity for pterosaurs for the first time using landmark-based geometric morphometrics and make comparisons to calculations of pterosaur disparity based on alternative metrics. Landmark-based disparity calculations suggest that monofenestratan pterosaurs were more diverse cranially than basal non-monofenestratan pterosaurs (at least when the aberrant anurognathids are excluded), and that peak cranial disparity may have occurred in the Early Cretaceous, relatively late in pterosaur evolution. Significantly, our cranial disparity results are broadly congruent with those based on whole skeleton discrete character and limb proportion data sets, indicating that these divergent approaches document a consistent pattern of pterosaur morphological evolution. Therefore, pterosaurs provide an exemplar case demonstrating that different proxies for morphological form can converge on the same disparity signal, which is encouraging because often only one such proxy is available for extinct clades represented by fossils. Furthermore, mapping phylogeny into cranial morphospace demonstrates that pterosaur cranial morphology is significantly correlated with, and potentially constrained by, phylogenetic relationships.     

JOINED AT THE HIP: LINKED CHARACTERS AND THE PROBLEM OF MISSING DATA IN STUDIES OF DISPARITY

Paleontological investigations into morphological diversity, or disparity, are often confronted with large amounts of missing data. We illustrate how missing discrete data affect disparity using a novel simulation for removing data based on parameters from published datasets that contain both extinct and extant taxa. We develop an algorithm that assesses the distribution of missing characters in extinct taxa, and simulates data loss by applying that distribution to extant taxa. We term this technique “linkage.” We compare differences in disparity metrics and ordination spaces produced by linkage and random character removal. When we incorporated linkage among characters, disparity metrics declined and ordination spaces shrank at a slower rate with increasing missing data, indicating that correlations among characters govern the sensitivity of disparity analysis. We also present and test a new disparity method that uses the linkage algorithm to correct for the bias caused by missing data. We equalized proportions of missing data among time bins before calculating disparity, and found that estimates of disparity changed when missing data were taken into account. By removing the bias of missing data, we can gain new insights into the morphological evolution of organisms and highlight the detrimental effects of missing data on disparity analysis.     

Getting into Shape: An Empirical Comparison of Traditional Truss-Based Morphometric Methods with a Newer Geometric Method Applied to New World Cichlids

Body shape is a difficult, but important, trait to quantify. Researchers have traditionally used multivariate analysis of several linear measures ('trusses') across the body form to quantify shape. Newer geometric morphometric methods claim to better estimate shape because they analyze the geometry among the locations of all landmarks simultaneously rather than the linear distances between pairs of landmarks. We tested this claim by comparing the results of several traditional morphometric analyses against a newer geometric analysis involving thin-plate splines (TPS), all applied to a common data set of morphologically variable new world cichlids Amphilophus citrinellus and A. zaliosus. The TPS method yielded slightly stronger evidence of morphological differences among forms, although traditional methods also distinguished the two species. Perhaps our most important result was the idiosyncratic interpretation of shape variation among the traditional truss-based methods, whereas the generation of deformation grids using the TPS approach yielded clear and visually interpretable figures. Our results indicate that geometric morphometrics can be a more effective way to analyze and interpret body form, but also that traditional methods can be relied upon to provide statistical evidence of shape differences, although not necessarily accurate information about the nature of variation in shape.     

Integration of cytochrome c oxidase I barcodes and geometric morphometrics to delimit species in the genus Gnopharmia (Lepidoptera: Geometridae,Ennominae)

We tested the hypothesis of species taxonomy in the genus Gnopharmia (Macariini, Ennominae) that was recently established in a review based on discrete morphological characters. For this objective we integrated both DNA‐based and morphometric approaches in order to infer species boundaries. A 658‐bp fragment of the mitochondrial cytochrome c oxidase subunit 1 (CO1) (DNA barcode) was analysed from populations of five species distributed throughout the Middle East to assess their consistency with traditionally defined morphospecies. Signals in the morphological variation of the aedeagus of all relevant populations were evaluated using geometric landmarks. Consistent groupings compatible with the current taxonomic classification were found with both approaches. The results strongly support the distinction of seven closely related species. © 2013 The Linnean Society of London     

三维几何形态测量方法在石制品分析中的应用

几何形态测量方法是生物学研究中用于形态特征分析和形态比较研究的一种常用方法。其核心思想是利用空间坐标点获取研究对象的形态数据,再通过坐标数据的多元统计分析,定量探讨研究对象的形态特征及影响其形态变异的因素。近年来,随着三维扫描技术的广泛应用以及对于石制品形态特征量化分析要求的提高,基于三维模型的几何形态测量方法开始出现在相关的旧石器考古研究中。本文首先对三维几何形态测量分析方法及其在石制品研究中的应用情况进行介绍,随后具体阐述了该方法的分析流程。为便于国内学者更好地了解这一方法,本文进一步以广西百色盆地南坡山遗址发现的手斧为例,利用三维几何形态测量方法对这些手斧的几何形态特征进行了初步探讨。三维几何形态测量方法为石制品形态研究提供了新思路和新视角,有望成为今后中国旧石器考古研究中一个重要的发展方向。     

Discrete and morphometric traits reveal contrasting patterns and processes in the macroevolutionary history of a clade of scorpions

Many palaeontological studies have investigated the evolution of entire body plans, generally relying on discrete character‐taxon matrices. In contrast, macroevolutionary studies performed by neontologists have mostly focused on morphometric traits. Although these data types are very different, some studies have suggested that they capture common patterns. Nonetheless, the tests employed to support this claim have not explicitly incorporated a phylogenetic framework and may therefore be susceptible to confounding effects due to the presence of common phylogenetic structure. We address this question using the scorpion genus Brachistosternus Pocock 1893 as case study. We make use of a time‐calibrated multilocus molecular phylogeny, and compile discrete and traditional morphometric data sets, both capturing the overall morphology of the organisms. We find that morphospaces derived from these matrices are significantly different, and that the degree of discordance cannot be replicated by simulations of random character evolution. Moreover, we find strong support for contrasting modes of evolution, with discrete characters being congruent with an ‘early burst’ scenario whereas morphometric traits suggest species‐specific adaptations to have driven morphological evolution. The inferred macroevolutionary dynamics are therefore contingent on the choice of character type. Finally, we confirm that metrics of correlation fail to detect these profound differences given common phylogenetic structure in both data sets, and that methods incorporating a phylogenetic framework and accounting for expected covariance should be favoured.     

How reliable are morphological and anatomical characters to distinguish European wildcats,domestic cats and their hybrids in France?

Phenotypic variation in hybridizing species or subspecies is a prerequisite for allowing conservation ecologists and wildlife managers to identify parental populations and their hybrids in the field. We assessed the reliability of a set of eight morphological (body size and pelage characters) and four anatomical criteria (skull and intestine morphometric measurements) to distinguish between 302 French specimens classified as wildcat, domestic cat or hybrid on the basis of a Bayesian analysis (STRUCTURE) of their multilocus microsatellite genotypes. This aim was achieved by performing a set of multivariate analyses on morphological, anatomical and genetic data sets (Hill and Smith's analysis, co‐inertia analysis and discriminant analysis of principal components). Wildcats and domestic cats were very satisfactorily distinguished, even when using simple non‐invasive morphological criteria easily usable in the field like the morphology of the tail, dorsal line or flank stripes. Using anatomical instead of morphological characters slightly increased the discriminating power. Many more difficulties arose when we tried to distinguish hybrid specimens from both wildcat and domestic ones. Anatomical characters performed better than morphological ones in recognizing hybrids, but the assignment success rate remained very low, about 31.6% and 1.5%, respectively. Overall, the most discriminating characters were two continuous, derived anatomical characters: the cranial index followed by the intestinal index. Classification of specimens in three classes based on their microsatellite genotypes appeared to be inadequate for identifying hybrid specimens, as hybrid specimens seemed to be distributed along an anatomical continuum. With this observation in mind, we assessed the linear relationships between a proxy of the individual level of hybridization (q_ik) and the cranial and intestinal indices, respectively. Both relationships were highly significant. The greatest correlation was found with the cranial index (R² = 60.4%). Altogether, our results suggest that future work should be geared towards enhancing the measure of hybridization using more discriminating molecular markers and improving morphometric skull measurements through the use of modern geometric morphometric methods, using landmarks rather than skull dimension.     

早期生命形态演化研究中的定量方法

定量古生物学是现代古生物学的一个分支,提倡用定量的手段来研究地质历史时期生命的演化过程。我国从事定量古生物研究的群体较小,特别是对前寒武纪早期生命演化的定量研究还没有系统地展开。这篇文章将主要介绍如何利用定量手段来研究前寒武纪化石的形态演化。对于前寒武纪化石,由于大部分化石分类属性的不确定性,通常使用几何性状对化石的最基本形态结构进行分析,并用存在/缺失(1/0)这种离散变量对每个性状进行量化。非参数多维标量分析方法[Non-parametric multidimensional scaling analysis(MDS)]可以将高维度的离散数据投影到二维或者三维的形态空间上,进而探讨生物群在形态空间中所占有的范围;由离散变量计算得出的生物群的表形分异度(morphological disparity)可以用MDS方差或者平均差异参数[Mean dissimilarity coeffi-cient(MDC)]来计算。形态空间的范围(morphospace range)和表形分异度是相互联系的,如果形态空间范围是固定的,那么表形分异度实际上代表了生物群在形态空间中的分布密度。在解释数据之前,需要对可能存在的样本效应进行测试。常用的方法包括稀释法(rarefaction)、随机取样法(randomization)和自举法(bootstrapping)等。为了帮助读者进一步了解这些方法的使用,文中列举了三个实例:伊迪卡拉生物的形态演化,元古代宏观藻类的形态演化和元古代及寒武纪疑源类的演化。     

Morphological divergence of lake and stream Phoxinus of Northern Italy and the Danube basin based on geometric morphometric analysis

Minnows of the genus Phoxinus are promising candidates to investigate adaptive divergence, as they inhabit both still and running waters of a variety of altitudes and climatic zones in Europe. We used landmark‐based geometric morphometric methods to quantify the level of morphological variability in Phoxinus populations from streams and lakes of Northern Italy and the Danube basin. We analyzed body shape differences of populations in the dorsal, lateral, and ventral planes, using a large array of landmarks and semilandmarks. As the species identification of Phoxinus on morphological characters is ambiguous, we used two mitochondrial genes to determine the genetic background of the samples and to ensure we are comparing homogenous groups. We have found significant body shape differences between habitats: Minnow populations inhabiting streams had a deeper body and caudal peduncle and more laterally inserted pectoral fins than minnows inhabiting lakes. We have also found significant body shape differences between genetic groups: Italian minnows had deeper bodies, deeper and shorter caudal peduncles, and a shorter and wider gape than both groups from the Danube. Our results show that the morphology of Phoxinus is highly influenced by habitat and that body shape variation between habitats was within the same range as between genetic groups. These morphological differences are possibly linked to different modes of swimming and foraging in the respective habitats and are likely results of phenotypic plasticity. However, differences in shape and interlandmark distances between the groups suggest that some (though few) morphometric characters might be useful for separating Phoxinus species.     

GEOMETRIC MORPHOMETRICS OF DEVELOPMENTAL INSTABILITY: ANALYZING PATTERNS OF FLUCTUATING ASYMMETRY WITH PROCRUSTES METHODS

Although fluctuating asymmetry has become popular as a measure of developmental instability, few studies have examined its developmental basis. We propose an approach to investigate the role of development for morphological asymmetry by means of morphometric methods. Our approach combines geometric morphometrics with the two-way ANOVA customary for conventional analyses of fluctuating asymmetry and can discover localized features of shape variation by examining the patterns of covariance among landmarks. This approach extends the notion of form used in studies of fluctuating asymmetry from collections of distances between morphological landmarks to an explicitly geometric concept of shape characterized by the configuration of landmarks. We demonstrate this approach with a study of asymmetry in the wings of tsetse flies (Glossina palpalis gambiensis). The analysis revealed significant fluctuating and directional asymmetry for shape as well as ample shape variation among individuals and between the offspring of young and old females. The morphological landmarks differed markedly in their degree of variability but multivariate patterns of landmark covariation identified by principal component analysis were generally similar between fluctuating asymmetry (within-individual variability) and variation among individuals. Therefore there is no evidence that special developmental processes control fluctuating asymmetry. We relate some of the morphometric patterns to processes known to be involved in the development of fly wings.     

Cranial morphological variation of Dromiciops gliroides (Microbiotheria) along its geographical distribution in south-central Chile: A three-dimensional analysis

We analyzed the variation in cranial morphology of the marsupial Dromiciops gliroides along its distribution in south-central Chile. We evaluated whether the cranial morphological variation is congruent with the phylogeographic structure previously observed in this species. We built three-dimensional models of 69 crania on which we digitized 30 landmarks. We used standard geometric morphometric methods to extract and analyze the shape and size components of the crania. Our data showed a subtle but consistent cranial size and shape variation along the studied distributional range, suggesting a geographic variation pattern rather than a phylogeographic structuring. Indeed, our multivariate analyses recovered a subtle morphological differentiation between island and mainland populations, contrary to what is suggested by a former phylogeographic study. We detected that either the cranial size variation, as well as the insularity and the latitude could be important factors underlying the cranial shape changes. We suggest that an interplay of historical and contemporary processes could be shaping the morphological pattern observed in this marsupial.     

A web based tool to merge geometric morphometric data from multiple characters

Geometric morphometrics (GM) is an important method of shape analysis and increasingly used in a wide range of scientific disciplines.Presently,a single character comparison system of geometric morphometric data is used in almost all empirical studies,and this approach is sufficient for many scientific problems.However,the estimation of overall similarity among taxa or objects based on multiple characters is crucial in a variety of contexts (e.g.(semi-)automated identification,phenetic relationships,tracing of character evolution,phylogenetic reconstruction).Here we propose a new web-based tool for merging several geometric morphometrics data files from multiple characters into a single data file.Using this approach information from multiple characters can be compared in combination and an overall similarity estimate can be obtained in a convenient and geometrically rigorous manner.To illustrate our method,we provide an example analysis of 25 dung beetle species with seven Procrustes superimposed landmark data files representing the morphological variation of body features:the epipharynx,right mandible,pronotum,elytra,hindwing,and the metendosternite in dorsal and lateral view.All seven files were merged into a single one containing information on 649 landmark locations.The possible applications of such merged data files in different fields of science are discussed.     

An Expanded Combined Evidence Approach to the Gavialis Problem Using Geometric Morphometric Data from Crocodylian Braincases and Eustachian Systems

The phylogenetic position of the Indian gharial (Gavialis gangeticus) is disputed - morphological characters place Gavialis as the sister to all other extant crocodylians, whereas molecular and combined analyses find Gavialis and the false gharial (Tomistoma schlegelii) to be sister taxa. Geometric morphometric techniques have only begun to be applied to this issue, but most of these studies have focused on the exterior of the skull. The braincase has provided useful phylogenetic information for basal crurotarsans, but has not been explored for the crown group. The Eustachian system is thought to vary phylogenetically in Crocodylia, but has not been analytically tested. To determine if gross morphology of the crocodylian braincase proves informative to the relationships of Gavialis and Tomistoma, we used two- and three-dimensional geometric morphometric approaches. Internal braincase images were obtained using high-resolution computerized tomography scans. A principal components analysis identified that the first component axis was primarily associated with size and did not show groupings that divide the specimens by phylogenetic affinity. Sliding semi-landmarks and a relative warp analysis indicate that a unique Eustachian morphology separates Gavialis from other extant members of Crocodylia. Ontogenetic expansion of the braincase results in a more dorsoventrally elongate median Eustachian canal. Changes in the shape of the Eustachian system do provide phylogenetic distinctions between major crocodylian clades. Each morphometric dataset, consisting of continuous morphological characters, was added independently to a combined cladistic analysis of discrete morphological and molecular characters. The braincase data alone produced a clade that included crocodylids and Gavialis, whereas the Eustachian data resulted in Gavialis being considered a basally divergent lineage. When each morphometric dataset was used in a combined analysis with discrete morphological and molecular characters, it generated a tree that matched the topology of the molecular phylogeny of Crocodylia.     

Where to Live? How Morphology and Evolutionary History Predict Microhabitat Choice by Tropical Tadpoles

Tadpoles have diverse morphologies and occupy diverse habitats. The morphological differences between tadpoles can be represented by linear and geometric measurements and used to explain the organization of tadpole assemblages. However, the effects of evolutionary history must be isolated from the morphological differences before we can determine which patterns result from the use and sharing of common ecological resources. Here, we aimed to determine how morphological similarities and phylogenetic distances affect microhabitat choice by tadpoles. We analyzed the tadpoles of 101 anuran species and classified them according to ecomorphological guild, habitat use, position in the water column, and floor substrate. We used geometric and traditional morphometric approaches to describe the morphological variation among tadpoles and calculated the patristic distance for each species. Afterwards, we used morphometric and phylogenetic matrices as predictors of the variance in the ecological matrix, using a partial redundancy analysis. When we used traditional morphometric data, phylogeny explained a large amount of the ecological variation. By contrast, when we used geometric morphometric data, morphology and phylogeny explained similar amounts of the ecological variation, showing that the technique used to extract morphological variation affects the results. We provide evidence that both morphology, as a surrogate for contemporary factors, and evolutionary inertia are important in determining the behavior of tadpoles. Thus, niche conservatism can be important in modeling the behavior of tadpoles, but does not explain all the preferences of tadpoles.     

Evolutionary patterns of shape and functional diversification in the skull and jaw musculature of triggerfishes (Teleostei: Balistidae)

The robust skull and highly subdivided adductor mandibulae muscles of triggerfishes provide an excellent system within which to analyze the evolutionary processes underlying phenotypic diversification. We surveyed the anatomical diversity of balistid jaws using Procrustes‐based geometric morphometric analyses and a phylomorphospace approach to quantifying morphological transformation through evolution. We hypothesized that metrics of interspecific cranial shape would reveal patterns of phylogenetic diversification that are congruent with functional and ecological transformation. Morphological landmarks outlining skull and adductor mandibulae muscle shape were collected from 27 triggerfish species. Procrustes‐transformed skull shape configurations revealed significant phylogenetic and size‐influenced structure. Phylomorphospace plots of cranial shape diversity reveal groupings of shape between different species of triggerfish that are mostly consistent with phylogenetic relatedness. Repeated instances of convergence upon similar cranial shape by genetically disparate taxa are likely due to the functional demands of shared specialized dietary habits. This study shows that the diversification of triggerfish skulls occurs via modifications of cranial silhouette and the positioning of subdivided jaw adductor muscles. Using the morphometric data collected here as input to a biomechanical model of triggerfish jaw function, we find that subdivided jaw adductors, in conjunction with a unique cranial skeleton, have direct biomechanical consequences that are not always congruent with phylomorphospace patterns in the triggerfish lineage. The integration of geometric morphometrics with biomechanical modeling in a phylogenetic context provides novel insight into the evolutionary patterns and ecological role of muscle subdivisions in triggerfishes. J. Morphol. 277:737–752, 2016. © 2016 Wiley Periodicals, Inc.     

Geometric morphometric analyses provide evidence for the adaptive character of the Tanganyikan cichlid fish radiations

The cichlids of East Africa are renowned as one of the most spectacular examples of adaptive radiation. They provide a unique opportunity to investigate the relationships between ecology, morphological diversity, and phylogeny in producing such remarkable diversity. Nevertheless, the parameters of the adaptive radiations of these fish have not been satisfactorily quantified yet. Lake Tanganyika possesses all of the major lineages of East African cichlid fish, so by using geometric morphometrics and comparative analyses of ecology and morphology, in an explicitly phylogenetic context, we quantify the role of ecology in driving adaptive speciation. We used geometric morphometric methods to describe the body shape of over 1000 specimens of East African cichlid fish, with a focus on the Lake Tanganyika species assemblage, which is composed of more than 200 endemic species. The main differences in shape concern the length of the whole body and the relative sizes of the head and caudal peduncle. We investigated the influence of phylogeny on similarity of shape using both distance-based and variance partitioning methods, finding that phylogenetic inertia exerts little influence on overall body shape. Therefore, we quantified the relative effect of major ecological traits on shape using phylogenetic generalized least squares and disparity analyses. These analyses conclude that body shape is most strongly predicted by feeding preferences (i.e., trophic niches) and the water depths at which species occur. Furthermore, the morphological disparity within tribes indicates that even though the morphological diversification associated with explosive speciation has happened in only a few tribes of the Tanganyikan assemblage, the potential to evolve diverse morphologies exists in all tribes. Quantitative data support the existence of extensive parallelism in several independent adaptive radiations in Lake Tanganyika. Notably, Tanganyikan mouthbrooders belonging to the C-lineage and the substrate spawning Lamprologini have evolved a multitude of different shapes from elongated and Lamprologus-like hypothetical ancestors. Together, these data demonstrate strong support for the adaptive character of East African cichlid radiations.     

3D geometric morphometrics and missing-data. Can extant taxa give clues for the analysis of fossil primates?

Geometric morphometric methods constitute a powerful and precise tool for the quantification of morphological differences. The use of geometric morphometrics in palaeontology is very often limited by missing data. Shape analysis methods based on landmarks are very sensible but until now have not been adapted to this kind of dataset. To analyze the prospective utility of this method for fossil taxa, we propose a model based on prosimian cranial morphology in which we test two methods of missing data reconstruction. These consist of generating missing-data in a dataset (by increments of five percent) and estimating missing data using two multivariate methods. Estimates were found to constitute a useful tool for the analysis of partial datasets (to a certain extent). These results are promising for future studies of morphological variation in fossil taxa.