Geometric craniometric analysis of sexual dimorphism and ontogenetic variation: A case study based on two geographically disparate species, Aethomys ineptus from southern Africa and Arvicanthis niloticus from Sudan (Rodentia: Muridae)

Non-geographic morphometric variation, particularly at the level of sexual dimorphism and ontogenetic (age-related) variation, has been documented in rodents, and useful for establishing whether to analyse sexes separately or together, and for selecting adult specimens for subsequent data recording and analysis. However, such studies have largely been based on traditional morphometric analyses of linear measurements that mainly focus on overall size, rather than shape-related morphometric variation. Unit-free, landmark/outline-based geometric morphometric analyses are considered to offer a more appropriate tool for assessing shape-related morphometric variation. In this study, we used geometric cranial morphometric analysis to assess the nature and extent of sexual dimorphism and age variation within the Tete veld rat, Aethomys ineptus (Thomas and Wroughton, 1908) from southern Africa and the African Nile rat, Arvicanthis niloticus (Desmarest, 1822) from Sudan. The results obtained were in turn compared with previously published results based on independent geometric and traditional cranial morphometric data from the same sampled populations examined in the present study. While our geometric morphometric results detected statistically significant sexual dimorphism in cranial shape within Ar. niloticus only, previously published results based on traditional morphometric data failed to detect significant sexual dimorphism within this species. However, similar to previously published traditional morphometric data, our geometric morphometric results detected statistically significant age-related variation in cranial shape and size within both Ae. ineptus and Ar. niloticus, with individuals of age classes 5 and 6 being considered to represent adult specimens. Our results highlight the importance of carefully evaluating both size- and shape-related non-geographic morphometric variation prior to the analysis of geographic variation and the delineation of species. Erroneous conclusions of non-geographic variation may have implications in the interpretation of geographic and evolutionary processes that may be responsible for morphological differences at both the inter- and intra-specific levels.     

Geographic phenetic variation of two eastern-Mediterranean non-commensal mouse species, Mus macedonicus and M. cypriacus (Rodentia: Muridae) based on traditional and geometric approaches to morphometrics

We tested the hypothesis that skull shape within the genus Mus may vary with geographic location by assessing the extent and spatial distribution of phenotypic skull variation within and among two wild mouse species, M. macedonicus and M. cypriacus, using traditional and geometric morphometrics including a rather novel application of sliding semilandmarks. Shape was shown to be significantly correlated both with longitude and latitude in M. macedonicus, yet the correlation between morphometric and geographic distances was not significant, and morphometric differences between Asian and European populations were not higher than those within the particular continents. The phylogenetic signal was found to be stronger in dental characters than in cranial ones, however, overall concordance between the pattern of morphometric variation and the presumed history of M. macedonicus was rather weak. In both species, the dorsal and ventral sides of the skull were shown to covary in many aspects though there were also some differences between them, making the functional interpretation of these differences difficult. Discrimination between M. cypriacus and M. macedonicus as well as discrimination between two M. macedonicus subspecies was highly reliable using both traditional and geometric morphometric tools to analyze skull measurements.     

Towards the automated identification of Chrysomya blow flies from wing images

The Old World screwworm fly (OWSF), Chrysomya bezziana (Diptera: Calliphoridae), is an important agent of traumatic myiasis and, as such, a major human and animal health problem. In the implementation of OWSF control operations, it is important to determine the geographical origins of such disease‐causing species in order to establish whether they derive from endemic or invading populations. Gross morphological and molecular studies have demonstrated the existence of two distinct lineages of this species, one African and the other Asian. Wing morphometry is known to be of substantial assistance in identifying the geographical origin of individuals because it provides diagnostic markers that complement molecular diagnostics. However, placement of the landmarks used in traditional geometric morphometric analysis can be time‐consuming and subject to error caused by operator subjectivity. Here we report results of an image‐based approach to geometric morphometric analysis for delivering wing‐based identifications. Our results indicate that this approach can produce identifications that are practically indistinguishable from more traditional landmark‐based results. In addition, we demonstrate that the direct analysis of digital wing images can be used to discriminate between three Chrysomya species of veterinary and forensic importance and between C. bezziana genders.     

Fused traditional and geometric morphometrics demonstrate pinniped whisker diversity

Vibrissae (whiskers) are important components of the mammalian tactile sensory system, and primarily function as detectors of vibrotactile information from the environment. Pinnipeds possess the largest vibrissae among mammals and their vibrissal hair shafts demonstrate a diversity of shapes. The vibrissae of most phocid seals exhibit a beaded morphology with repeating sequences of crests and troughs along their length. However, there are few detailed analyses of pinniped vibrissal morphology, and these are limited to a few species. Therefore, we comparatively characterized differences in vibrissal hair shaft morphologies among phocid species with a beaded profile, phocid species with a smooth profile, and otariids with a smooth profile using traditional and geometric morphometric methods. Traditional morphometric measurements (peak-to-peak distance, crest width, trough width and total length) were collected using digital photographs. Elliptic Fourier analysis (geometric morphometrics) was used to quantify the outlines of whole vibrissae. The traditional and geometric morphometric datasets were subsequently combined by mathematically scaling each to true rank, followed by a single eigendecomposition. Quadratic discriminant function analysis demonstrated that 79.3, 97.8 and 100% of individuals could be correctly classified to their species based on vibrissal shape variables in the traditional, geometric and combined morphometric analyses, respectively. Phocids with beaded vibrissae, phocids with smooth vibrissae, and otariids each occupied distinct morphospace in the geometric morphometric and combined data analyses. Otariids split into two groups in the geometric morphometric analysis and gray seals appeared intermediate between beaded- and smooth-whiskered species in the traditional and combined analyses. Vibrissal hair shafts modulate the transduction of environmental stimuli to the mechanoreceptors in the follicle-sinus complex (F-SC), which results in vibrotactile reception, but it is currently unclear how the diversity of shapes affects environmental signal modulation.     

Ecotypes and genetic divergence among sympatrically distributed populations of Hordeum vulgare and Hordeum spontaneum from the xeric region of Jordan

Summary The progeny of paired samples of Hordeum vulgare L. and Hordeum spontaneum C. Koch, collected from Jordan's xeric region was used in this study. Statistical analyses of seven easily measured morphometric traits were used to elucidate the relationships and distances between populations of both species, to detect any ecogeographical races, and to study the interrelationships and adjustments in the morphometric traits under study. Flag leaf area and plant height were the two most important discriminating variables which totally separated Hordeum vulgare from Hordeum spontaneum and accounted for 85.3% of total phenotypic variance in the collection. Cluster analysis indicated that the level of divergence among populations of both species was considerably different. Populations of Hordeum vulgare clustered at a maximum Euclidean distance of 2.08, while the maximum distance at which populations of Hordeum spontaneum clustered was 1.49. Three ecotypes each of Hordeum vulgare and Hordeum spontaneum were identified. These ecotypes corresponded to the environmental range of the collection sites. The interrelationships between the seven morphometric traits were adjusted in different ways as revealed by the principal components analysis. Sampling from the different clusters identified in this analysis is expected to increase the allelic diversity for selection and breeding purposes.     

Morphometric analyses of Staurosira inflata comb. nov. (Bacillariophyceae) and the morphologically related Staurosira tabellaria from north-western Russia

The morphology and ontogenetic allometric trends of a rare diatom Fragilaria heidenii Østrup and the morphologically related Staurosira tabellaria (W. Smith) Leuduger-Fortmorel were compared using conventional and semilandmark-based geometric morphometric analyses. Fragilaria heidenii was studied in detail by light and electron microscopy using type material and recent samples from Lake Ladoga and Lake Ilmen (north-western Russia). The taxon is transferred into the genus Staurosira Ehrenberg as Staurosira inflata comb. nov. on the basis of its valve morphology. This taxon is characterized by the absence of rimoportulae, lack of perforated copulae, spines located on the interstriae, internal vola occlusion in the areolae and the features of the areolae and apical pore fields. Conventional morphometric analysis showed considerable overlapping of S. inflata and S. tabellaria in their frustule characteristics such as length, width, length-to-width ratio and striae density. Moreover, at later stages of the vegetative life cycle, S. inflata has a tendency to resemble S. tabellaria by its valve outline that makes it difficult to separate these two taxa. The geometric morphometric analysis revealed two shape groups corresponding to S. inflata and S. tabellaria that were separated by a clear gap. Semilandmarks representing shape of the middle part of the valve were primarily responsible for discrimination between species. Apart from differences in valve shapes, S. inflata and S. tabellaria also differed significantly in their ontogenetic allometric trajectories. Overall, our results demonstrate that the semilandmark-based geometric morphometrics is sensitive enough to distinguish species by their outlines, when traditional morphometric parameters are not able to discriminate them with confidence.     

Artificial neural networks and geometric morphometric methods as a means for classification: A case‐study using teeth from Carcharhinus sp. (Carcharhinidae)

Over the past few decades, geometric morphometric methods have become increasingly popular and powerful tools to describe morphological data while over the same period artificial neural networks have had a similar rise in the classification of specimens to preconceived groups. However, there has been little research into how well these two systems operate together, particularly in comparison to preexisting techniques. In this study, geometric morphometric data and multilayer perceptrons, a style of artificial neural network, were used to classify shark teeth from the genus Carcharhinus to species. Three datasets of varying size and species differences were used. We compared the performance of this combination with geometric morphometric data in a linear discriminate function analysis, linear measurements in a linear discriminate function analysis, and a preexisting methodology from the literature that incorporates linear measurements and a two‐layered discriminate function analysis. Across datasets, geometric morphometric data in a multilayer perceptron tended to yield modest accuracies but accuracies that varied less across species whereas other methods were able to achieve higher accuracies in some species at the expense of lower accuracies in others. Further, the performance of the two‐layered discriminate function analysis illustrates that constraining what material is classified can increase the accuracy of a method. Based on this tradeoff, the best methodology will then depend on the scope of the study and the amount of material available. J. Morphol. 278:131–141, 2017. ©© 2016 Wiley Periodicals,Inc.     

Patterns of bilateral asymmetry and allometry in Late Devonian Polygnathus conodonts

Conodont animals were early jawless vertebrates equipped with a feeding apparatus composed of several tooth‐like elements. The P1 elements, at the rear of the apparatus, were characterized by a robust shape and rapid morphological evolution. Occlusion occurred between paired right and left P1 elements, occasioning some bilateral asymmetry, which, together with allometric growth, may partially obliterate the temporal differences. The present study aims to disentangle these different components of morphological variation in Late Devonian Polygnathus P1 conodont elements. An extensive 2D geometric morphometric analysis of the platform shape was performed through the Famennian record of two outcrops. This analysis was completed by a 3D study on a subset of conodont elements. The 2D and 3D morphometric quantifications provided highly congruent results, showing that the 2D shape constitutes a good approximation of the element geometry. The 3D analysis delivered further insights into the relationship between the geometry of the elements and the constraints related to occlusion. The 2D analysis allowed a quantitative assessment of the variation among species and through time. Allometry and bilateral asymmetry were differently expressed depending on the species considered, suggesting that constraints imposed on pairing by the morphology of the elements varied even among related species. The within‐species variation was so important that it largely obliterated temporal trends; a relationship of Polygnathus shape and conodont biofacies variations through the Famennian nevertheless suggested an evolution driven by ecological interactions between conodont genera.     

Species concept and morphological differentiation of strains traditionally assigned to Micrasterias truncata

The morphological and molecular differentiation of the Micrasterias truncata (Corda) ex Bréb species complex was investigated. In total, 17 strains traditionally assigned to M. truncata were isolated from different European localities (Czech Republic, southwest France, Ireland), and obtained from public culture collections. In addition, strains of the morphologically similar species, M. decemdentata (Nägeli) W. Archer and M. zeylanica F. E. Fritsch, were also included. Molecular phylogenetic analysis based on trnG^ucc intron sequences revealed five well supported clades. Two Australian strains assigned to M. truncata var. pusilla G. S. West formed a lineage sister to M. zeylanica. This was evident from a concatenated phylogeny based on small subunit rDNA and trnG^ucc intron sequences. The isolated position of these strains was also illustrated by parallel landmark‐based geometric morphometric analysis of cell shapes. The strains NIES 783 and NIES 784 probably represent a separate species. Particular analysis, including additional strains, is needed to resolve the relationship inside this lineage. The second phylogenetic lineage, containing two strains of M. truncata var. semiradiata (Kützing) Wolle, was also different from other strains on the basis of morphometric data. We suggest recognizing this variety as a separate species, Micrasterias semiradiata L.A. Brébisson ex F. T. Kützing. The remaining three clades formed a firmly supported group of the ‘core’M. truncata recognized by both molecular markers. However, neither any morphological, morphometric, nor geographical pattern was detected among members of these three clades. This pattern could be caused by a relatively recent origin of these lineages that may represent a sympatric, truly cryptic species. Strains attributable to traditional morphologically defined variety M. truncata var. neodamensis were nested within the ‘core’M. truncata.     

Can members of the south‐western Gila robusta species complex be distinguished by morphological features?

The goal for this project was to re‐examine key morphological characters hypothesized to differentiate Gila intermedia, Gila robusta and Gila nigra and outline methods better suited for making species designations based on morphology. Using a combination of meristic counts, morphological measurements and geometric morphometrics, morphological dissimilarities were quantified among these three putative species. Traditional meristic counts and morphological measurements (i.e. distances between landmarks) were not useful for species identification. Geometric morphometrics, however, identified differences among species, while also suggesting an effect of geographic location on morphological variation. Using canonical variate analysis for the 441 fish sampled in this study, geometric morphometrics accurately predicted true group membership 100% of the time for G. nigra, 97% of the time for G. intermedia and 91% of the time for G. robusta. These results suggest that geometric morphometric analysis is necessary to identify morphological differences among the three species. Geometric morphometric analysis used in this study can be adopted by management officials as a tool to classify unidentified individuals.     

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.     

Shape and size variations in the cranium of elephant-shrews: a morphometric contribution to a phylogenetic debate

A geometric morphometric analysis was carried out on the crania of 13 species of elephant-shrews (Macroscelidea), a group of African mammals whose phylogeny is still debated. The material examined consisted of 313 crania and included all the genera of Macroscelididae, the unique family recognized by taxonomists. The results obtained from the analysis of the cranium shape and size, either from dorsal or lateral view, were very similar. The first one appeared more reliable because of the higher number of intersection points fixed between the cranial sutures. All the cranial features that distinguished the genus Rhynchocyon were a consequence of the extreme enlargement of frontal bones. Instead, within the subfamily Macroscelidinae, the differences between genera were based on modification involving other bones, mainly mastoids and nasals, as shown by the deformation grids. A cluster analysis confirmed the traditional subdivision in two subfamilies (Rhynchocyoninae and Macroscelidinae) but suggested a different relationship among the recognized genera belonging to Macroscelidinae. Our results are congruent with data obtained from previous biochemical research and support the traditional subdivision in two subfamilies, the monophily of the genus Elephantulus and its closeness with Petrodromus, relating to their similar cranium shapes. The latter presumably is a case of gigantism as adaptation to forest habitats. Further studies on all the species of Elephantulus could provide new evidence for assessing the relationships within this clade, including Macroscelides that by the present analysis appeared as a well-distinguished taxonomic entity.     

Leaf morphological analyses in four European oak species (Quercus) and their hybrids: A comparison of traditional and geometric morphometric methods

Abstract

In this study, leaf morphology was assessed in a mixed oak stand (western France) using two geometric morphometric (landmark and outline) datasets and one dataset of 19 leaf measures. Adult oaks (817 oaks), comprising four white oak species (Quercus petraea, Q. robur, Q. pubescens and Q. pyrenaica), were sampled for DNA extraction and genetic analysis (nuclear microsatellites). Leaf morphology was assessed on 336 oaks, comprising pure species and hybrids as determined by genetic assignment. This comparative study of oak leaf morphology, based on the use of two free size geometric morphometric methods and a set of leaf measurements, combined with the genetic assignment of individuals to pure species or hybrids, provided information about the differences among species and the intermediate leaf morphology of their hybrids.     

Evolution of opercle bone shape along a macrohabitat gradient: species identification using mtDNA and geometric morphometric analyses in neotropical sea catfishes (Ariidae)

Transitions between the marine and freshwater macrohabitat have occurred repeatedly in the evolution of teleost fishes. For example, ariid catfishes have moved from freshwater to marine environments, and vice versa. Opercles, a skeletal feature that has been shown to change during such transitions, were subjected to 2D geometric morphometric analyses in order to investigate evolutionary shape changes during habitat transition in ariid catfishes and to test the influence of habitat on shape changes. A mtDNA marker, which proved useful in previous studies, was used to verify species identities. It greatly improved the assignment of specimens to a species, which are difficult to assign by morphology alone. The application of a mtDNA marker confirmed the occurrence of Notarius biffi in Central America, South of El Salvador. Molecular identification together with principal component analysis (PCA) and further morphological inspection of neurocrania indicated the existence of a cryptic species within Bagre pinnimaculatus. Principal component (PC) scores of individual specimens clustered in morphospace by genus rather than by habitat. Strong phylogenetic structure was detected using a permutation test of PC scores of species means on a phylogenetic tree. Calculation of Pagel's λ suggested that opercle shape evolved according to a Brownian model of evolution. Yet canonical variate analysis (CVA) conducted on the habitat groups showed significant differences in opercle shapes among freshwater and marine species. Overall, opercle shape in tropical American Ariidae appears to be phylogenetically constrained. This verifies the application of opercle shape as a taxonomic tool for species identification in fossil ariid catfishes. At the same time, adaptation to freshwater habitats shows characteristic opercle shape trajectories in ariid catfishes, which might be used to detect habitat preferences in fossils.     

Morphologic variation of two key biostratigraphical proteaceous-like pollen taxa across the Cretaceous–Paleogene boundary in northern South America

Echitriporites trianguliformis and E. suescae comb. nov. are two species of proteaceous-like triaperturate pollen that have been widely reported in several sedimentary sequences from northern South America, especially in Colombia and Venezuela. Despite their biostratigraphic significance and because of their morphological similarity, distinction between the two species has been difficult, leading to a biased understanding of their chronostratigraphic ranges. In this study, we compare 75 pollen grains spanning the Maastrichtian–Danian time interval through traditional and geometric morphometrics, and a newly proposed Procrustes-based method (index of pollen curvature). Traditional assessments show subtle variation between specimens; however, geometric morphometrics and the curvature index allow quantifying morphological differences in the degree of concavity-convexity through time. Therefore, geometric morphometrics and curvature index results enable us to constrain the stratigraphic ranges of both taxa. We suggest a coetaneous range for E. trianguliformis and E. suescae comb. nov. during the Late Cretaceous, but the presence of only E. trianguliformis after the Cretaceous–Paleogene boundary event. In addition, we propose a threshold value of 1.5 µm for the curvature index as a tool for distinguishing between these two taxa. We conclude that the combination of geometric morphometrics and the curvature index provides a powerful tool to distinguish between morphological closely-related pollen taxa that are difficult to distinguish through both light microscope visual comparisons and statistical analysis of morphometric measurements.     

Geometric morphometrics as a tool for identifying emperor fish (Lethrinidae) larvae and juveniles

The aim of this study was to evaluate the efficiency of geometric morphometrics for describing the body shape of fish larvae and juveniles, and identifying them to species, in comparison with traditional linear measurements. Species of emperor fishes (Perciformes: Lethrinidae, genus Lethrinus) were chosen as the model group, as the late larval and early juvenile stages in this genus are particularly difficult to identify. Forty‐five individuals of different species of Lethrinus were collected from the south‐western lagoon of New Caledonia between May 2005 and March 2006. The individuals were first identified to species by their partial cytochrome‐b gene sequence. They were then morphologically characterized using eight linear measurements and 23 landmarks recorded on digital photographs. Except for a small proportion of individuals, geometric morphometrics gave better results to distinguish the different species than linear measurements. A ‘leave one out’ approach confirmed the nearly total discrimination of recently settled Lethrinus genivittatus and Lethrinus nebulosus, whereas traditional identification keys failed to distinguish them. Therefore, geometric morphometrics is a promising tool for identifying fish larvae and juveniles to species. An effective approach would require building image databases of voucher specimens associated with their DNA barcodes. These images could be downloaded by the operator and processed with the specimens to be identified.     

Effectiveness of modern leaf analysis tools for the morpho‐ecological study of plants: the case of Primula albenensis

Scientific and technological progress has led to the creation of analysis tools that have revolutionized traditional studies in morphology and plant ecology. Recently developed methods and tools which, on the basis of leaf samples, allow for geometric morphometric analyses and the evaluation of functional strategies are good examples. These methods, still little used, have never been applied on leaf samples to simultaneously obtain information on their morphometry and the ecology of the plants. This article discusses the effectiveness of modern leaf analysis tools for geometric morphometrics (outline analysis) and studies of functional strategies based on the competitor‐stress tolerator‐ruderal (CSR) scheme, using a study of a steno‐endemic plant of the Alps, Primula albenensis Banfi et Ferl. as an example. These aspects were analyzed using leaf samples collected in the only two areas where this species grows. CSR analyses revealed that P. albenensis is not a stress‐tolerant species (C:S:R = 37:1:62), as previously thought. Moreover, no significant intraspecific differences in functional strategy were revealed. Instead, outline analysis highlighted a significant difference (p < 0.001) between leaves collected from the two sampling areas. The results of this study and others reported in the literature therefore suggest that these modern methods of leaf analysis are cheap, effective and relatively simple to perform. Furthermore, researchers are able to carry out geometric morphometric and CSR analysis using the same samples of leaves in order to maximize the information content provided by the analysis of a plant material which may not be easily available.     

Identifying hybridizing taxa within the <Emphasis Type="Italic">Daphnia longispina</Emphasis> species complex: a comparison of genetic methods and phenotypic approaches

Daphnia galeata Sars, D. longispina O. F. Müller and D. cucullata Sars (Crustacea: Cladocera) are closely related species which often produce interspecific hybrids in natural populations. Several marker systems are available for taxon determination in this hybridizing complex, but their performance and reliability has not been systematically assessed. We compared results from identifications by three molecular methods. More than 1,200 individuals from 10 localities in the Czech Republic were identified as parental species or hybrids by allozyme electrophoresis and the analysis of the restriction fragment length polymorphism of the internal transcribed spacer (ITS-RFLP); over 440 of them were additionally analyzed and identified by 12 microsatellite loci. Identification by microsatellite markers corresponded well with allozyme analyses. However, consistent discrepancies between ITS-RFLP and other markers were observed in two out of 10 studied localities. Although some marker discrepancies may have been caused by occasional recent introgression, consistent deviations between ITS-RFLP and other markers suggest a long-term maintenance of introgressed alleles. These results warn against its use as a sole identification method in field studies. Additionally, we quantitatively evaluated the discriminatory power of geometric morphometric (elliptic Fourier) analysis of body shapes based on photos of over 1,300 individuals pre-classified by allozyme markers. Furthermore, a randomly selected subset of 240 individuals was independently determined from photos by several experts. Despite a tendency for morphological divergence among parental Daphnia species, some taxa (especially D. galeata, D. longispina, and their hybrids) substantially overlapped in their body shapes. This was reflected in different determination success for particular species and hybrids in discriminant analysis based on shape data as well as from photographs.