Do we need the third dimension? Quantifying the effect of the z-axis in 3D geometric morphometrics based on sailfin silversides (Telmatherinidae)

Sample Size and Geometric Morphometrics Methodology Impact the Evaluation of Morphological Variation

Geometric morphometrics has had a profound impact on our understanding of morphological evolution. However, factors such as sample size and the views and elements selected for two-dimensional geometric morphometric (2DGM) analyses, which are often dictated by specimen availability and time rather than study design, may affect the outcomes of those analyses. Leveraging large intraspecific sample sizes (n > 70) for two bat species, Lasiurus borealis and Nycticeius humeralis, we evaluate the impact of sample size on calculations of mean shape, shape variance, and centroid size. Additionally, we assessed the concordance of multiple skull 2D views with one another and characterized morphological variation in skull shape in L. borealis and N. humeralis, as well as a closely related species, Lasiurus seminolus. Given that L. seminolus is a morphologically cryptic species with L. borealis, we assessed whether differences in skull shape and in 2DGM approach would allow species discrimination. We found that reducing sample size impacted mean shape and increased shape variance, that shape differences were not consistent across views or skull elements, and that trends shown by the views and elements were not all strongly associated with one another. Further, we found that L. borealis and L. seminolus were statistically different in shape using 2DGM in all views and elements. These results underscore the importance of selecting appropriate sample sizes, 2D views, and elements based on the hypothesis being tested. While there is likely not a generalizable sample size or 2D view that can be employed given the wide variety of research questions and systems evaluated using 2DGM, a generalizable solution to issues with 2DGM presented here is to run preliminary analyses using multiple views, elements, and sample sizes, thus ensuring robust conclusions.

Entropy-Driven, Integrative Bioinformatics Approaches Reveal the Recent Transmission of the Monkeypox Virus from Nigeria to Multiple Non-African Countries

Monkeypox virus (mpox) has currently affected multiple countries around the globe. This study aims to analyze how the virus spread globally. The study uses entropy-driven bioinformatics in five directions to analyze the 60 full-length complete genomes of mpox. We analyzed the topological entropy distribution of the genomes, principal component analysis (PCA), the dissimilarity matrix, entropy-driven phylogenetics, and genome clustering. The topological entropy distribution showed genome positional entropy. We found five clusters of the mpox genomes through the two PCA, while the three PCA elucidated the clustering events in 3D space. The clustering of genomes was further confirmed through the dissimilarity matrix and phylogenetic analysis which showed the bigger size of Cluster 1 and size similarity between Clusters 2 and 4 as well as Clusters 3 and 5. It corroborated with the phylogenetics of the genomes, where Cluster 1 showed clear segregation from the other four clusters. Finally, the study concluded that the spreading of the mpox is likely to have originated from African countries to the rest of the non-African countries. Overall, the spreading and distribution of the mpox will shed light on its evolution and pathogenicity of the mpox and help to adopt preventive measures to stop the spreading of the virus.

Dots on a screen: The past, present, and future of morphometrics in the study of nonavian dinosaurs

Using morphometrics to study nonavian dinosaur fossils is a practice that predates the origin of the word "dinosaur." By the 1970s, linear morphometrics had become established as a valuable tool for analyzing intra- and interspecific variation in nonavian dinosaurs. With the advent of more recent techniques such as geometric morphometrics and more advanced statistical approaches, morphometric analyses of nonavian dinosaurs have proliferated, granting unprecedented insight into many aspects of their biology and evolution. I outline the past, present, and future of morphometrics as applied to the study of nonavian dinosaurs zeroing in on five aspects of nonavian dinosaur paleobiology where morphometrics has been widely utilized to advance our knowledge: systematics, sexual dimorphism, locomotion, macroevolution, and trackways. Morphometric methods are especially susceptible to taphonomic distortion. As such, the impact of taphonomic distortion on original fossil shape is discussed as are current and future methods for quantifying and accounting for distortion with the goal of reducing the taphonomic noise to biological signal ratio. Finally, the future of morphometrics in nonavian dinosaur paleobiology is discussed as paleobiologists move into a "virtual paleobiology" framework, whereby digital renditions of fossils are captured via methods such as photogrammetry and computed tomography. These primary data form the basis for three-dimensional (3D) geometric morphometric analyses along with a slew of other forms of analyses. These 3D specimen data form part of the extended specimen and help to democratize paleobiology, unlocking the specimen from the physical museum and making the specimen available to researchers across the world.

Hide and seek shark teeth in Random Forests: machine learning applied to Scyliorhinus canicula populations

Shark populations that are distributed alongside a latitudinal gradient often display body size differences at sexual maturity and vicariance patterns related to their number of tooth files. Previous works have demonstrated that Scyliorhinus canicula populations differ between the northeastern Atlantic Ocean and the Mediterranean Sea based on biological features and genetic analysis. In this study, we sample more than 3,000 teeth from 56 S. canicula specimens caught incidentally off Roscoff and Banyuls-sur-Mer. We investigate population differences based on tooth shape and form by using two approaches. Classification results show that the classical geometric morphometric framework is outperformed by an original Random Forests-based framework. Visually, both S. canicula populations share similar ontogenetic trends and timing of gynandric heterodonty emergence but the Atlantic population has bigger, blunter teeth, and less numerous accessory cusps than the Mediterranean population. According to the models, the populations are best differentiated based on their lateral tooth edges, which bear accessory cusps, and the tooth centroid sizes significantly improve classification performances. The differences observed are discussed in light of dietary and behavioural habits of the populations considered. The method proposed in this study could be further adapted to complement DNA analyses to identify shark species or populations based on tooth morphologies. This process would be of particular interest for fisheries management and identification of shark fossils.

Sexual dimorphism in an adaptive radiation: Does intersexual niche differentiation result in ecological character displacement?

Evolutionary radiations are one plausible explanation for the rich biodiversity on Earth. Adaptive radiations are the most studied form of evolutionary radiations, and ecological opportunity has been identified as one factor permitting them. Competition among individuals is supposedly highest in populations of conspecifics. Divergent modes of resource use might minimize trophic overlap, and thus intersexual competition, resulting in ecological character displacement between sexes. However, the role of intersexual differentiation in speciation processes is insufficiently studied. The few studies available suggest that intersexual niche differentiation exists in adaptive radiations, but their role within the radiation, and the extent of differentiation within the organism itself, remains largely unexplored. Here, we test the hypothesis that multiple morphological structures are affected by intersexual niche differentiation in "roundfin" Telmatherina, the first case where intersexual niche differentiation was demonstrated in an adaptive fish radiation. We show that sexes of two of the three morphospecies differ in several structural components of the head, all of these are likely adaptive. Sexual dimorphism is linked to the respective morphospecies-specific ecology and affects several axes of variation. Trait variation translates into different feeding modes, processing types, and habitat usages that add to interspecific variation in all three morphospecies. Intrasexual selection, that is, male-male competition, may contribute to variation in some of the traits, but appears unlikely in internal structures, which are invisible to other individuals. We conclude that intersexual variation adds to the adaptive diversity of roundfins and might play a key role in minimizing intersexual competition in emerging radiations.

Alligator appendicular architecture across an ontogenetic niche shift

A variety of species undergo ontogenetic niche shifts in either diet, habitat, or both. As a result, multiple ontogenetic stages are able to take advantage of different resources and live in sympatry without competing with one another. The American alligator (Alligator mississippiensis) begins to undergo an ontogenetic niche shift in both diet and habitat at a length of 1.2 m. They transition from a terrestrial wetland environment to a riverine environment and take advantage of different dietary resources. At 1.8 m, A. mississippiensis reaches sexual maturity. Ontogenetic shifts in habitat have the capacity to alter morphology, especially limb morphology, as different age classes traverse different ecological systems. We evaluated shape trends in the scapulae, humeri, ilia, and femora using geometric morphometrics to test whether there were punctuated changes in limb shape, shape disparity, and integration corresponding to either the ontogenetic habitat shift or onset of sexual maturity. We found size to strongly correlate with limb shape but found a continuous size gradient rather than punctuated changes in size. Furthermore, we found that adults (total length > 1.8 m) had significantly higher limb shape disparity than juveniles or subadults, likely related to ontogenetic decreases in limb use and a reduction in limb constraints. Finally, we found that the forelimb and hindlimb acted as a single integrated unit and that neither the forelimb nor hindlimb was significantly more integrated than the other. Therefore, the ontogenetic niche shift itself did not impact limb morphology in A. mississippiensis.

Patterns of Body Shape Diversity and Evolution in Intertidal and Subtidal Lineages of Combtooth Blennies (Blenniidae)

Marine intertidal zones can be harsher and more dynamic than bordering subtidal zones, with extreme and temporally variable turbulence, water velocity, salinity, temperature, and dissolved oxygen levels. Contrasting environmental conditions and ecological opportunities in subtidal versus intertidal habitats may generate differing patterns of morphological diversity. In this study we used phylogenetic comparative methods, measurements of body length, and two-dimensional landmarks to characterize body shape and size diversity in combtooth blennies (Ovalentaria: Blenniidae) and test for differences in morphological diversity between intertidal, subtidal, and supralittoral zones. We found that subtidal combtooth blennies have significantly higher body shape disparity and occupy a region of morphospace three times larger than intertidal lineages. The intertidal morphospace was almost entirely contained within the subtidal morphospace, showing that intertidal combtooth blennies did not evolve unique body shapes. We found no significant differences in body size disparity between tidal zones, no correlations between body shape and tidal zone or body size and tidal zone, and no body shape convergence associated with tidal zone. Our findings suggest that a subset of combtooth blenny body shapes are suitable for life in both subtidal and intertidal habitats. Many species in regions of morphospace unique to subtidal combtooth blennies exhibit distinct microhabitat use, which suggests subtidal environments promoted morphological diversification via evolutionary microhabitat transitions. In contrast, limited intertidal body shape diversity may be due to strong selective pressures that constrained body shape evolution and environmental filtering that prevented colonization of intertidal zones by certain subtidal body shapes.