Variation in cranial morphology of bottlenose dolphins (genus Tursiops) off South Africa

Taxonomy plays an important role in conservation biology. Despite the variety of methods used to differentiate units, some groups, such as Delphinidae within the Cetacea have proven difficult to untangle. This study aimed to shed light on morphological variation of the genus Tursiops in South African waters using geometric morphometrics and to distinguish morphological groups and variation in these groups. A total of 241 crania of Tursiops spp. were analyzed using a suite of 2‐dimensional landmarks defined on photographs of the specimens. Results revealed two distinct morphological groups, with the smaller cluster comprised mainly of specimens from the cold temperate region off the west coast and the larger cluster comprised of specimens mainly from the warm temperate and subtropical regions off the south and east coast, respectively. We suggest that these groups correspond to different species of Tursiops, but this result requires further support. These groups were treated as separate entities and sexual dimorphism and geographic variation were assessed within each group. While sexual dimorphism and geographic variation were not significant within Cluster D1 and V1, they were significant within Clusters D2 and V2. The few Cluster 1 specimens found in the warm temperate and subtropical regions, relative to the number of Cluster 2 specimens, could be an indication of an offshore distribution for this group in these regions. Alternatively, the smaller cluster may also be indicative of a potentially small population size.     

Classifying behavior from short‐interval biologging data: An example with GPS tracking of birds

1. Recent advances in digital data collection have spurred accumulation of immense quantities of data that have potential to lead to remarkable ecological insight, but that also present analytic challenges. In the case of biologging data from birds, common analytical approaches to classifying movement behaviors are largely inappropriate for these massive data sets.
2. We apply a framework for using K‐means clustering to classify bird behavior using points from short time interval GPS tracks. K‐means clustering is a well‐known and computationally efficient statistical tool that has been used in animal movement studies primarily for clustering segments of consecutive points. To illustrate the utility of our approach, we apply K‐means clustering to six focal variables derived from GPS data collected at 1–11 s intervals from free‐flying bald eagles (Haliaeetus leucocephalus) throughout the state of Iowa, USA. We illustrate how these data can be used to identify behaviors and life‐stage‐ and age‐related variation in behavior.
3. After filtering for data quality, the K‐means algorithm identified four clusters in >2 million GPS telemetry data points. These four clusters corresponded to three movement states: ascending, flapping, and gliding flight; and one non‐moving state: perching. Mapping these states illustrated how they corresponded tightly to expectations derived from natural history observations; for example, long periods of ascending flight were often followed by long gliding descents, birds alternated between flapping and gliding flight.
4. The K‐means clustering approach we applied is both an efficient and effective mechanism to classify and interpret short‐interval biologging data to understand movement behaviors. Furthermore, because it can apply to an abundance of very short, irregular, and high‐dimensional movement data, it provides insight into small‐scale variation in behavior that would not be possible with many other analytical approaches.

     

Parameterization and classification of the protein universe via geometric techniques

We present a scheme for the classification of 3487 non-redundant protein structures into 1207 non-hierarchical clusters by using recurring structural patterns of three to six amino acids as keys of classification. This results in several signature patterns, which seem to decide membership of a protein in a functional category. The patterns provide clues to the key residues involved in functional sites as well as in protein-protein interaction. The discovered patterns include a "glutamate double bridge" of superoxide dismutase, the functional interface of the serine protease and inhibitor, interface of homo/hetero dimers, and functional sites of several enzyme families. We use geometric invariants to decide superimposability of structural patterns. This allows the parameterization of patterns and discovery of recurring patterns via clustering. The geometric invariant-based approach eliminates the computationally explosive step of pair-wise comparison of structures. The results provide a vast resource for the biologists for experimental validation of the proposed functional sites, and for the design of synthetic enzymes, inhibitors and drugs.     

Allometric and nonallometric components of Drosophila wing shape respond differently to developmental temperature

Phenotypic plasticity of wing size and shape of Drosophila simulans was analyzed across the entire range of viable developmental temperatures with Procrustes geometric morphometric method. In agreement with previous studies, size clearly decreases when temperature increases. Wing shape variation was decomposed into its allometric (24%) and nonallometric (76%) components, and both were shown to involve landmarks located throughout the entire wing blade. The allometric component basically revealed a progressive, monotonous variation along the temperature. Surprisingly, nonallometric shape changes were highly similar at both extremes of the thermal range, suggesting that stress, rather than temperature per se, is the key developmental factor affecting wing shape.     

Morphological intergration between development compartments in the Drosophila wing

Abstract. Developmental integration is the covariation among morphological structures due to connections between the developmental processes that built them. Here we use the methods of geometric morphometrics to study integration in the wing of Drosophila melanogaster . In particular, we focus on the hypothesis that the anterior and posterior wing compartments are separate developmental units that vary independently. We measured both variation among genetically diverse individuals and random differences between body sides of single individuals (fluctuating asymmetry, FA). For both of these sources of variation, the patterns of variation identified by principal component analyses all involved landmarks in both the anterior and posterior compartments simultaneously. Analyses focusing exclusively on the covariation between the anterior and posterior compartments, by the partial least-squares method, revealed pervasive integration of the two compartments, for both individual variation and FA. These analyses clearly indicate that the anterior and posterior compartments are not separate units of variation, but that the covariation between compartments is sufficient to account for nearly all the variation throughout the entire wing. We conclude that variation among individuals as well as the developmental perturbations responsible for FA generate shape variation primarily through developmental processes that are integrated across both compartments. In contrast, much less of the shape variation in our sample can be attributed to the localized processes that establish the identity of particular wing veins.     

Darkling beetle communities in two geologically contrasting biotopes: testing biodiversity patterns by microsite comparisons

Studies at a microsite scale, where most of the environmental variation can be reduced to a few factors, may help to identify the actual contribution of a particular environmental factor to community organization. Climate is known to be an important factor for regulating animal diversity. However, for soil‐dwelling animals, the role of soil characteristics can hardly be extracted out because of the inter‐relationships between climate and soil. The community structure of soil‐dwelling darkling beetles inhabiting the two geologically highly contrasting west‐ and east‐facing slopes (WFS and EFS, respectively) of the Mediterranean island of Santorini (Greece) was investigated in a case study aiming to assess the separate influence of soil characteristics and climate. Eroded pumice soils of EFS allowed a higher abundance of darkling beetle individuals and biomass, hosting more productive vegetation and being more penetrable to fossorial larvae. Moreover, the two slopes differed significantly with respect to the abundance of certain species that are characterized by a peculiar morphological adaptation to different soil characteristics. Thus, local geological sharp divergence led to darkling beetle interslope community differences as a result of local selection towards certain species. However, the two communities are similar in terms of darkling beetle diversity, evenness, and species niche‐breadth. This demonstrates that sites sharing the same climatic conditions tend to have similarly structured darkling beetle communities, even if there are marked differences in soil characteristics that promote differences in species composition, thus suggesting that climate is the major factor for regulating species diversity. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98 , 787–793.     

Allometry,merism, and tooth shape of the upper deciduous M2 and permanent M1

The aims of this study were to investigate the effect of allometry on the shape of dm² and M¹ crown outlines and to examine whether the trajectory and magnitude of scaling are shared between species. The sample included 160 recent Homo sapiens, 28 Upper Paleolithic H. sapiens, 10 early H. sapiens, and 33 H. neanderthalensis (Neandertal) individuals. Of these, 97 were dm²/M¹ pairs from the same individuals. A two‐block partial least squares analysis of paired individuals revealed a significant correlation in crown shape between dm² and M¹. A principal component analysis confirmed that Neandertal and H. sapiens dm² and M¹ shapes differ significantly and that this difference is primarily related to hypocone size and projection. Allometry accounted for a small but significant proportion of the total morphological variance. We found the magnitude of the allometric effect to be significantly stronger in Neandertals than in H. sapiens. Procrustes distances were significantly different between the two tooth classes in Neandertals, but not among H. sapiens groups. Nevertheless, we could not reject the null hypothesis that the two species share the same allometric trajectory. Although size clearly contributes to the unique shape of the Neandertal dm² and M¹, the largest H. sapiens teeth do not exhibit the most Neandertal‐like morphology. Hence, additional factors must contribute to the differences in dm² and M¹ crown shape between these two species. We suggest an investigation of the role of timing and rate of development on the shapes of the dm² and M¹ may provide further answers. Am J Phys Anthropol 154:104–114, 2014. © 2014 Wiley Periodicals, Inc.     

Towards a biogeographic regionalization of the European biota

Aim To determine if it is possible to generate analytically derived regionalizations for multiple groups of European plants and animals and to explore potential influences on the regions for each taxonomic group. Location Europe. Methods We subjected range maps of trees, butterflies, reptiles, amphibians, birds and mammals to k‐means clustering followed by v‐fold cross‐validation to determine the pattern and number of regions (clusters). We then used the mean range sizes of species in each group as a correlate of the number of regions obtained for each taxon, and climate and species richness gradients as correlates of the spatial arrangement of the group‐specific regions. We also included the pattern of tree clusters as a predictor of animal clusters in order to test the ‘habitat templet’ concept as an explanation of animal distribution patterns. Results Spatially coherent clusters were found for all groups. The number of regions ranged from three to eight and was strongly associated with the mean range sizes of the species in each taxon. The cluster patterns of all groups were associated with various combinations of climate, underlying species richness gradients and, in the case of animals, the arrangement of tree clusters, although the rankings of the correlates differed among groups. In four of five groups the tree pattern was the strongest single predictor of the animal cluster patterns. Main conclusions Despite a long history of human disturbance and habitat modification, the European biota retains a discernable biogeographic structure. The primary driver appears to be aspects of climate related to water–energy balance, which also influence richness gradients. For many animals, the underlying habitat structure, as measured by tree distributions, appears to have a strong influence on their biogeographic structure, highlighting the need to preserve natural forest formations if we want to preserve the historical signal found in geographic distributions.