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opencc-zeroSep 2020View details →

Effects of taphonomic deformation on geometric morphometric analysis of fossils: a case study using the dicynodont Diictodon feliceps (Therapsida, Anomodontia)

Taphonomic deformation, the distortion of fossils as a result of geological processes, poses problems for the use of geometric morphometrics in addressing paleobiological questions. Signal from biological variation, such as ontogenetic trends and sexual dimorphism, may be lost if variation from deformation is too high. Here, we investigate the effects of taphonomic deformation on geometric morphometric analyses of the abundant, well known Permian therapsid Diictodon feliceps. Distorted Diictodon crania can be categorized into seven typical styles of deformation: lateral compression, dorsoventral compression, anteroposterior compression, 'saddle-shape' deformation (localized collapse at cranial mid-length), anterodorsal shear, anteroventral shear, and right/left shear. In simulated morphometric datasets incorporating known 'biological' signals and subjected to uniform shear, deformation was typically the main source of variance but accurate 'biological' information could be recovered in most cases. However, in empirical datasets, not only was deformation the dominant source of variance, but little structure associated with allometry and sexual dimorphism was apparent, suggesting that the more varied deformation styles suffered by actual fossils overprint biological variation. In a principal component analysis of all anomodont therapsids, deformed Diictodon specimens exhibit significant dispersion around the 'true' position of this taxon in morphospace based on undistorted specimens. The overall variance associated with deformation for Anomodontia as a whole is minor, and the major axes of variation in the study sample show a strong phylogenetic signal instead. Although extremely problematic for studying variation in fossil taxa at lower taxonomic levels, the cumulative effects of deformation in this study are shown to be random, and inclusion of deformed specimens in higher-level analyses of morphological disparity are warranted. Mean morphologies of distorted specimens are found to approximate the morphology of undistorted specimens, so we recommend use of species-level means in higher-level analyses when possible.

opencc-zeroOct 2020View details →

Geometric morphometric wing analysis represents a robust tool to identify female mosquitoes (Diptera: Culicidae) in Germany

Accurate species identification is the prerequisite to assess the relevance of mosquito specimens, but is often hindered by missing or damaged morphological features. The present study analyses the applicability of wing geometric morphometrics as a low-cost and practical alternative to identify native mosquitoes in Germany. Wing pictures were collected for 502 female mosquitoes of five genera and 19 species from 80 sampling sites. The reliable species identification based on interspecific wing geometry of 18 landmarks per specimen was tested. Leave-one-out cross validation revealed an overall accuracy of 99% for the genus and 90% for the species identification. Misidentifications were mainly due to three pairings of Aedes species: Aedes annulipes vs. Aedes cantans, Aedes cinereus vs. Aedes rossicus and Aedes communis vs. Aedes punctor. Cytochrome oxidase subunit I (COI) gene region was sequenced to validate the morphological and morphometric identification. Similar to the results of the morphometric analysis, the same problematic three Aedes-pairs clustered, but most other species could be well separated. Overall, our study underpins that morphometric wing analysis is a robust tool for reliable mosquito identification, which reach the accuracy of COI barcoding.

opencc-by-4.0Nov 2020View details →

Fig. 1 in Morphometric Analysis Of Сapillaria Anatis (Nematoda, Capillariidae) From Anas Platyrhynchos Domesticus

Fig. 1. Head end of Сapillaria anatis.

opencc-zeroJan 2024View details →

Morphometric analysis of the Late Cretaceous Placenticeras of Alabama, USA: Sexual dimorphism, allometry, and implications for taxonomy

A traditional typological approach to taxonomy often does not adequately account for intraspecific variation and can result in taxonomic oversplitting. For many groups, including ammonoids of the Placenticeras genus, intraspecific variation documented in recent studies (e.g., ontogenetic changes, sexual dimorphism, polymorphism) challenges the historic proliferation of species names. Here, we used a population approach to taxonomy and quantitatively evaluated morphometric variation in a sample of Late Cretaceous (Santonian -Campanian) Placenticeras from Alabama and adjacent counties. We used linear mixed models (LMMs) to characterize how morphological variables scale with conch size across the sample, exploiting mixed longitudinal data to evaluate individual variation in growth and inform interpretations of multivariate analyses. Extended LMMs incorporating geological formation evaluated morphological changes through time. Principal component analysis and clustering analysis were then used to evaluate the number of distinct clusters that emerged in multivariate morphospace independent of previous taxon name assignments. Discontinuous scaling relationships and distinct clusters in multivariate space suggest sexual dimorphism characterized by differences in adult size, and secondarily, shape. Previous Stantonoceras and Placenticeras assignments broadly overlap in our morphospace, failing to justify this historic distinction (as sexual dimorphs, or as genera or subgenera). Placenticeras conch morphology and ornament placement changed through time, suggesting a potential utility for coarse (stage-level) biostratigraphy. However, temporal changes were not associated with distinct clusters in morphospace and our data fail to support the plethora of reported species names. As few as one or two (successive) species may be present in our sample (representing 130 years of collection effort). In addition to highlighting the need for a significant taxonomic revision of the Placenticeras genus, this study demonstrates the utility of LMMs for distinguishing between different sources of morphological variation, improving interpretations of morphospace under a population approach to taxonomy, and maximizing the amount of ontogenetic information that can be obtained non-destructively.

opencc-zeroMar 2022View details →

Why the long teeth? Morphometric analysis suggests different selective pressures on functional occlusal traits in Plio-Pleistocene African suids

Neogene and Pleistocene African suids displayed convergent evolutionary trends in the third molar (M3) morphology, with increasingly elongated and higher crowns through time. While these features can prevent premature loss of masticatory functionality and potentially increase long-term reproductive success, changes in dental occlusal traits such as enamel complexity and thickness can also improve chewing efficiency and increase short-term energetic return. While both long-term and short-term benefits can contribute to the thriving of a lineage, the selective pressures associated with each category can be different. To examine how crown elongation correlates with these functional occlusal traits, we selected M3s of Kolpochoerus, Notochoerus, and Metridiochoerus from Kenya and South Africa, dated between 3.0 Ma and 0.4 Ma. To account for dental wear, we used micro-CT imaging of unworn/slightly worn M3s to simulate wear progression within each tooth. We compared morphometric representatives of occlusal enamel complexity and thickness among the specimens following their respective wear trajectories. We found that M3 elongation correlates with higher occlusal complexity and thinner enamel in Notochoerus and Metridiochoerus lineages through time. In Kolpochoerus, enamel complexity and thickness were generally maintained through time, despite M3 elongation. The differences in M3 morphometric trends suggest that Kolpochoerus likely experienced a different set of selective pressures on functional occlusal traits compared to Notochoerus and Metridiochoerus. The shared evolutionary trends of M3 specialization among Notochoerus and Metridiochoerus suggest similar selective pressures on their chewing efficiency and the possibility of a dietary niche overlap in more xeric habitats.

opencc-by-4.0Mar 2022View details →

Research compendium for 'Practical and technical aspects for the 3D scanning of lithic artefacts using micro-computed tomography techniques and laser light scanners for subsequent geometric morphometric analysis. Introducing the StyroStone protocol'

Abstract: Here, we present a new method to scan a large number of lithic artefacts using three-dimensional (3D) scanning technology. Despite the rising use of high-resolution 3D surface scanners in archaeological sciences, no virtual studies have focused on the 3D digitization and analysis of small lithic implements such as bladelets, microblades, and microflakes. This is mostly due to difficulties in creating reliable 3D meshes of these artefacts resulting from several inherent features (i.e., size, translucency, and acute edge angles), which compromise the efficiency of structured light or laser scanners and photogrammetry. Our new protocol StyroStone addresses this problem by proposing a step-by-step procedure relying on the use of micro-computed tomographic technology, which is able to capture the 3D shape of small lithic implements in high detail. We tested a system that enables us to scan hundreds of artefacts together at once within a single scanning session lasting a few hours. As also bigger lithic artefacts (i.e., blades) are present in our sample, this protocol is complemented by a short guide on how to effectively scan such artefacts using a structured light scanner (Artec Space Spider). Furthermore, we estimate the accuracy of our scanning protocol using principal component analysis of 3D Procrustes shape coordinates on a sample of meshes of bladelets obtained with both micro-computed tomography and another scanning device (i.e., Artec Micro). A comprehensive review on the use of 3D geometric morphometrics in lithic analysis and other computer-based approaches is provided in the introductory chapter to show the advantages of improving 3D scanning protocols and increasing the digitization of our prehistoric human heritage. Content List: <ul> <li>S1. Step-by-step protocol entitled ‘StyroStone: A protocol for scanning and extracting three-dimensional meshes of stone artefacts using Micro-CT scanners’. Also available on protocols.io (dx.doi.org/10.17504/protocols.io.bzbfp2jn);</li> <li>S2. Dataset with all raw semilandmark coordinate data (in .xlsx format) used in the validation study;</li> <li>S3. AGMT3D project. The file “Validation Protocol-MorphoProject.mat” can be used to open the project in the software AGMT3D;</li> <li>S4. Dataset in .csv format of the principal component score data of the validation study;</li> <li>S5. R script used to create Figure 2 using the R package ggplot2;</li> <li>S6. 3D models of the experimental bladelets obtained with the Micro-CT scanner used in the validation study. Both .ply and .wrl formats are provided;</li> <li>S7. 3D models of the experimental bladelets obtained with the Artec Micro scanner used in the validation study. Both .ply and .wrl formats are provided.</li> </ul>

opencc-zeroApr 2022View details →

Data from: Morphometric analysis of Skiagia-plexus acritarchs from the early Cambrian of North Greenland

The Cambrian evolutionary radiations are marked by spectacular biotic turnovers and the establishment of increasingly tiered food chains. At their base are primary producers, which in the Cambrian fossil record are chiefly represented among organic-walled microfossils. The majority of these microfossil remains have traditionally been attributed to an informal category of incertae sedis called "acritarchs", based entirely on form taxonomy. Acritarch form-taxa have been intensely used for biostratigraphy, and in large-scale studies of phytoplankton diversity. However, both prospects have been challenged by cases of taxonomic inconsistencies and over-splitting arising from the large phenotypic plasticity seen among these microfossils. The acritarch form-genus Skiagia stands as an ideal case-study to explore these taxonomic challenges, since it encompasses a number of form-species widely used in lower Cambrian biostratigraphy. Moreover, subtle morphological differences among Skiagia species were suggested to underlie key evolutionary innovations towards complex reproduction strategies. Here we apply a multivariate morphometric approach to investigate the morphological variation of Skiagia-plexus acritarchs using an assemblage sourced from the Buen Formation (Cambrian Series 2, Stage 3–4) of North Greenland. Our analysis showed that the specific-level classification of Skiagia discretizes a continuous spectrum of morphologies. While these findings bring important taxonomic and biostratigraphic hurdles to light, the unequal frequency distribution of life cycle stages among Skiagia species suggests that certain elements of phytoplankton paleobiology are nonetheless captured by Skiagia form-taxonomy. These results demonstrate the value of using morphometric tools to explore acritarch phenotypic plasticity and its potential ontogenetic and paleoecological drivers in Cambrian ecosystems.

opencc-zeroAug 2022View details →

Morphometric analysis of lungfish endocasts elucidates early dipnoan palaeoneurological evolution

Lungfish (Dipnoi) are lobe-finned fish (Sarcopterygii) that have persisted for over 400 million years from the Devonian Period to present day. They are the extant sister group to tetrapods and thus have the ability to provide unique insight into the condition of the earliest tetrapods as well as their own evolutionary history. The evolution of their dermal skull and dentition is relatively well understood, but this is not the case for the central nervous system. While the brain itself has very poor preservation potential and is not currently known in any fossil lungfish, substantial indirect information about it and associated structures such as the inner ears can be obtained from the cranial endocast. However, before the recent development of X-ray tomography as a palaeontological tool, these endocasts could not be studied non-destructively, and few detailed studies were undertaken. Here we describe and illustrate the endocasts of six Palaeozoic lungfish (Iowad ipterus halli, Gogodipterus paddyensis, Pillararhynchus longi, Griphognathus whitei, Orlovichthys limnatis, and Rhinodipterus ulrichi) from tomographic scans. We combine these with six previously described digital lungfish endocasts (4 fossil and 2 recent taxa) into a 12-taxon data set for multivariate morphometric analysis using 17 variables. We find that the olfactory region appears to be more highly plastic than the hindbrain, and undergoes significant elongation in several taxa. Further, while the semicircular canals covary as an integrated module, the utriculus and sacculus of the inner ear instead vary independently of each other. Functional interpretation suggests that olfaction has remained a dominant sense throughout lungfish evolution, and that changes seen in the labyrinth system may potentially reflect a change from a nektonic niche in older marine lungfish to more near-shore environments over time. Phylogenetic implications propose that endocranial form fails to support the monophyly of the 'chirodipterids'. Those with elongated crania similarly fail to form a distinct clade, suggesting that these are two paraphyletic groups that have converged either towards head elongation or truncation driven by constraints other than phylogeny.

opencc-zeroAug 2022View details →

A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component

Over the last six decades, populations of the bumblebees Bombus sylvicola and Bombus balteatus in Colorado have experienced decreases in tongue length, a trait important for plant-pollinator mutualisms. It has been hypothesized that this observation reflects selection resulting from shifts in floral composition under climate change. Here we used morphometrics and population genomics to determine whether morphological change is ongoing, investigate the genetic basis of morphological variation, and analyse population structure in these populations. We analysed whole-genome sequencing data and morphometric measurements of 580 samples of both species from seven high-altitude localities. Out of 281 samples originally identified as B. sylvicola, 67 formed a separate genetic cluster comprising a newly-discovered cryptic species ("incognitus"). However, an absence of genetic structure within species suggests that gene flow is common between mountains. We did not discover any genetic associations with tongue length, but a SNP related to production of a proteolytic digestive enzyme was implicated in body size variation. We identified evidence of covariance between kinship and both tongue length and body size, which is suggestive of a genetic component of these traits, although it is possible that shared environmental effects between colonies are responsible. Our results provide evidence for ongoing modification of a morphological trait important for pollination and indicate that this trait probably has a complex genetic and environmental basis. This archive contains genetic variation data derived from genome sequencing of 580 bumblebee samples collected from high-elevation locations in Colorado. The species are Bombus sylvicola (n=214), Bombus balteatus (n=299) and "incognitus" (n=67).

opencc-zeroMay 2024View details →

Data from: A 3D geometric morphometric analysis of the bovid distal humerus, with special reference to Rusingoryx atopocranion (Pleistocene, Eastern Africa)

The family Bovidae [Mammalia: Artiodactyla] is speciose and has extant representatives on every continent, forming key components of mammal communities. For these reasons, bovids are ideal candidates for studies of ecomorphology. In particular, the morphology of the bovid humerus has been identified as highly related to functional variables such as body mass and habitat. This study investigates the functional morphology of the bovid distal humerus in isolation due to its increased likelihood of preservation in the fossil record, and the resulting opportunity for better understanding the ecomorphology of extinct bovids. A landmark scheme of 30 landmarks was used to capture the 3D distal humerus morphology in 111 extant bovid specimens. We find that the distal humerus has identifiable morphologies associated with body mass, habitat preference, and tribe affiliation, and that some characteristics are shared between high body mass bovids and those living on hard, flat terrain which is likely due to the high stress on the bone in both cases. We directly apply our findings regarding extant bovids to the extinct alcelaphine bovid, Rusingoryx atopocranion from the mid to late Pleistocene (>33-45 ka) Lake Victoria region of Kenya. This species is known for some peculiar morphologies including a domed cranium with hollow nasal crests, and having small hooves for a bovid of its size. Another interesting aspect of Rusingoryx's skeletal morphology which has not been addressed is an unusual protrusion on the lateral epicondyle of the distal humerus. Despite considerable individual variation in the Rusingoryx specimens, we find evidence to support its historical assignment to the tribe Alcelaphini, and that it likely preferred open grassland habitats, which is consistent with independent reconstructions of the paleoenvironment. We also provide the most accurate body mass estimate for Rusingoryx to date, based on distal humerus centroid size. Overall, we are able to conclude that the distal humerus in extant bovids is highly informative regarding body mass, habitat preference and tribe, and that this can be applied directly to a fossil taxon with promising results.

opencc-by-4.0Dec 2022View details →

Fig. 2. 60 in Identification and Distribution of Wedge Clams (Donacidae: Bivalvia) in Thailand by Geometric Morphometric and Molecular Analysis.

Fig. 2. 60 Outline digitized landmarks along the inner edge of left valve. Scale bar = 5 mm.

opencc-by-4.0Aug 2018View details →

Fig. 7. Reconstructed denticles shapes using a in Geometric morphometric on a new species of Trichodinidae. A tool to discriminate trichodinid species combined with traditional morphology and molecular analysis

Fig. 7. Reconstructed denticles shapes using a range of 20 harmonic.

opencc-by-4.0Aug 2018View details →

Fig. 6 in Geometric morphometric on a new species of Trichodinidae. A tool to discriminate trichodinid species combined with traditional morphology and molecular analysis

Fig. 6. Fourier harmonic power spectrum based on Elliptical Fourier analysis.

opencc-by-4.0Dec 2007View details →

Fig. 6 in Fractal analysis of ostracod shell variability: A comparison with geometric and classic morphometrics

Fig. 6. Location of landmarks chose on Krithe valve for shape analysis.

opencc-by-4.0Sep 2024View details →

Linear morphometric analysis data of lithic points from Lovedale, Free State, South Africa

Linear morphometric analysis data of lithic points from the Middle Stone Age site of Lovedale and other Middle Stone Age localities in the Modder River basin, Free State, South Africa.

Fig. 4 in A morphometric analysis of Hedera L. (the ivy genus, Araliaceae) and its taxonomic implications

Fig. 4. — Plot of principal components one and two for Hedera species with stellate trichomes.

Fig. 1. — A in A morphometric analysis of Hedera L. (the ivy genus, Araliaceae) and its taxonomic implications

Fig. 1. — A juvenile Hedera leaf.

Fig. 5 in A morphometric analysis of Hedera L. (the ivy genus, Araliaceae) and its taxonomic implications

Fig. 5. — Plot of principal components one and two for Hedera species with scale trichomes.

Fig. 3 in A morphometric analysis of Hedera L. (the ivy genus, Araliaceae) and its taxonomic implications

Fig. 3. — Plot of principal components one and two for all Hedera species.

Fig. 2 in A morphometric analysis of Hedera L. (the ivy genus, Araliaceae) and its taxonomic implications

Fig. 2. — UPGMA cluster dendrogram of Hedera based on 30 morphological characters.