Fluctuating asymmetry in the honey bee,Apis mellifera: effects of ploidy and hybridization

We present a new measure of morphological asymmetry that avoids most of the statistical problems inherent in character-by-character analysis of size or shape. The method is an application of Procrustes analysis, which computes best-fitting super-positions of configurations of landmarks to the left and right sides of a single specimen. The Procrustes method combines subtle deviations in all aspects of the landmark configuration into one net asymmetry score. Directional asymmetry is separated from fluctuating asymmetry in a simple partition of a net sum-of-squares, and geometrical details of either component can be inspected by traditional methods of multivariate statistical analysis of landmarks. We demonstrate this method in a comparison of wing venation asymmetry in male (haploid) and female (diploid) honey bees (Apis mellifera). In addition we investigate the effects of ploidy and inter-subspecies hybridization on asymmetry and wing venation abnormalities, using the subspecies A. m. mellifera, A. m. carnica, and the hybrid strain “Nigra”. Results suggest that while the haploid males showed a higher frequency of wing venation abnormalities and greater total asymmetry than the diploid females, most of the asymmetry difference between males and females was in the form of directional, not fluctuating, asymmetry. Hybrid females had a higher frequency of wing venation abnormalities than females of either subspecies, but there were no significant differences in the mean level of asymmetry among females of A. m. mellifera, A. m. carnica and hybrid Nigra. Hybrid males had higher absolute frequency of wing venation abnormalities and asymmetry than males of either subspecies. However the mean frequency of venation abnormalities did not differ significantly between Nigra and A. m. carnica males, and mean asymmetries were not significantly different between Nigra and A. m. mellifera males. We discuss the relationship which is assumed to exist between developmental stability and fluctuating asymmetry in light of our result.     

Combining geometric morphometrics with pattern recognition for the investigation of species complexes

The parasitoid Hymenoptera contain a large number of species complexes that are as yet unresolved by traditional taxonomic studies. Evolutionary studies as well as biological control programmes often require further investigations which cannot rely on simple qualitative morphological characters; in many cases, particularly with dried specimens housed in museums, molecular approaches cannot be used. Recent developments in geometric morphometrics and statistical exploratory approaches open new perspectives for the objective evaluation of morphological characters in this taxonomic context. In this study, geometric morphometrics and pattern recognition approaches were applied to the wing shape and venation of two closely related braconid species considered to differ by subtle qualitative morphological head characters. Exploratory analyses such as kernel density estimates and Gaussian mixture analyses were used to explore the structure of the data in the multivariate morphometric space. Discrimination techniques (linear discriminant functions and neural networks combined with cross‐validations) were used to estimate the taxonomic value of qualitative characters. Gaussian mixtures highlighted the existence of two non‐overlapping groups. A good congruence was found between one of the two groups and the a priori defined Bassus tumidulus. The misclassification rate was higher for B. tegularis specimens, which also appeared morphometrically heterogeneous. Discrimination between the two a priori defined species was incomplete with misclassification rates higher than, or equal to, 6%. In most cases, the lack of congruence between species and morphometrically defined subgroups could be related to specimens that exhibited ambiguous qualitative character states. In summary, if two entities are present, they still need to be defined morphologically, while B. tegularis heterogeneity calls for further investigation of specimens of known origin and hosts. © 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 80, 89–98.     

The bootstrapped ordination re-examined

Abstract. A method is described to determine the number of significant dimensions in metric ordination of a sample. The method is probabilistic, based on bootstrap resampling. An iterative algorithm takes bootstrap samples with replacement from the sample. It finds in each bootstrap sample ordination coordinates and computes, after Procrustean adjustments, the correlation between observed and bootstrap ordination scores. It compares this correlation to the same parameter generated in a parallel bootstrapped ordination of randomly permuted data, which upon many iterations will generate a probability. The method is assessed in principal coordinates analysis of simulated data sets that have varying number of variables and correlation levels, uniform or patterned correlation structure. The results suggest the method is more reliable than other available methods in recovering the true intrinsic dimensionality. Examples with grassland data illustrate utility.     

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.     

Genes mirror geography in Daphnia magna

Identifying the presence and magnitude of population genetic structure remains a major consideration in evolutionary biology as doing so allows one to understand the demographic history of a species as well as make predictions of how the evolutionary process will proceed. Next‐generation sequencing methods allow us to reconsider previous ideas and conclusions concerning the distribution of genetic variation, and what this distribution implies about a given species evolutionary history. A previous phylogeographic study of the crustacean Daphnia magna suggested that, despite strong genetic differentiation among populations at a local scale, the species shows only moderate genetic structure across its European range, with a spatially patchy occurrence of individual lineages. We apply RAD sequencing to a sample of D. magna collected across a wide swath of the species' Eurasian range and analyse the data using principle component analysis (PCA) of genetic variation and Procrustes analytical approaches, to quantify spatial genetic structure. We find remarkable consistency between the first two PCA axes and the geographic coordinates of individual sampling points, suggesting that, on a continent‐wide scale, genetic differentiation is driven to a large extent by geographic distance. The observed pattern is consistent with unimpeded (i.e. no barriers, landscape or otherwise) migration at large spatial scales, despite the fragmented and patchy nature of favourable habitats at local scales. With high‐resolution genetic data similar patterns may be uncovered for other species with wide geographic distributions, allowing an increased understanding of how genetic drift and selection have shaped their evolutionary history.     

Fish Shape Analysis Using Landmarks

Landmarks are used to summarize the shapes of ten haddock and nine whiting. Error variance models, after generalized Procrustes analysis, are compared using simulation tests. The power to discriminate between fish species is shown to be increased by permitting non-affine transformations that correct for fish curvature.     

Epiphytic vegetation on Acer macrophyllum: a multivariate study of species-habitat relationships

Multivariate methods were used to examine epiphytic species composition on the lower trunk of Acer macrophyllum at five sites in south-coastal British Columbia, Canada. Differences in species composition and abundance between sites were attributed mainly to variation in relative humidity and light conditions. Bark chemistry differences accounted for only a small portion of the observed variation in epiphytic composition between sites. Within sites, compositional variation was examined over 0.5–5 m from ground level on the upper, vertical, and lower trunk surfaces of leaning trees. Compositional variation of the epiphytic vegetation with height and inclination tended to be more strongly developed at drier sites. Furthermore, at all sites compositional variation tended to be greater on upper (wetter) than on lower (drier) surfaces. Particular epiphytic species tended to occur in similar locations on the trunk surface at different sites, suggesting that some microhabitat specialization has occurred. Observed distributional shifts of epiphytic species appeared to be greatest among sites differing widely in prevailing microenvironmental conditions.Nomenclature follows Hitchcock & Cronquist (1973) Flora of the Pacific Northwest for vascular plants, Schofield (1976) Bryophytes of British Columbia for mosses, Stotler & Crandall-Stotler (1977) A checklist of the liverworts and hornworts of North America for hepatics, and Hale & Culberson (1970) A fourth Checklist of the lichens of the continental United States and Canada for lichens.Support from the Natural Sciences and Engineering Research Council, through an operating grant to G.E.B. and a scholarship to N.C.K., is gratefully acknowledged. We thank Dr. H. Kimmins for providing facilities and technical expertise for the analysis of bark nutrients.