Geometric morphometric analysis of the crown morphology of the lower first premolar of hominins, with special attention to Pleistocene Homo

This article is the third of a series that explores hominin dental crown morphology by means of geometric morphometrics. After the analysis of the lower second premolar and the upper first molar crown shapes, we apply the same technique to lower first premolar morphology. Our results show a clear distinction between the morphology seen in earlier hominin taxa such as Australopithecus and African early Homo, as well as Asian H. erectus, and more recent groups such as European H. heidelbergensis, H. neanderthalensis, and H. sapiens. The morphology of the earlier hominins includes an asymmetrical outline, a conspicuous talonid, and an occlusal polygon that tends to be large. The morphology of the recent hominins includes a symmetrical outline and a reduced or absent talonid. Within this later group, premolars belonging to H. heidelbergensis and H. neanderthalensis tend to possess a small and mesiolingually-displaced occlusal polygon, whereas H. sapiens specimens usually present expanded and centered occlusal polygons in an almost circular outline. The morphological differences among Paranthropus, Australopithecus, and African early Homo as studied here are small and evolutionarily less significant compared to the differences between the earlier and later homin taxa. In contrast to the lower second premolar and the upper first molar crown, the inclusion of a larger hominin sample of lower first premolars reveals a large allometric component.     

Highly resistant regression and object matching

In many disciplines, it is of great importance to match objects. Procrustes analysis is a popular method for comparing labeled point configurations based on a least squares criterion. We consider alternative procedures that are highly resistant to outlier points, and we describe an application in electrophoretic gel matching. We consider procedures based on S estimators, least median of squares, and least quartile difference estimators. Practical implementation issues are discussed, including random subset selection and intelligent subset selection (where subsets with small size or near collinear subsets are ignored). The relative performances of the resistant and Procrustes methods are examined in a simulation study.     

Geometric estimates of heritability in biological shape

The recently developed geometric morphometrics methods represent an important contribution of statistics and geometry to the study of biological shapes. We propose simple protocols using shape distances that incorporate geometric techniques into linear quantitative genetic models that should provide insights into the contribution of genetics to shape variation in organisms. The geometric approaches use Procrustes distances in a curved shape space and distances in tangent spaces within and among families to estimate shape heritability. We illustrate the protocols with an example of wing shape variation in the honeybee, Apis mellifera. The heritability of overall shape variation was small, but some localized components depicting shape changes on distal wing regions showed medium to large heritabilities. The genetic variance-covariance matrix of the geometric shape variables was significantly correlated with the phenotypic shape variance-covariance matrix. A comparison of the results of geometric methods with the traditional multivariate analysis of interlandmark distances indicated that even with a larger dimensionality, the interlandmark distances were not as rich in shape information as the landmark coordinates. Quantitative genetics studies of shape should greatly benefit from the application of geometric methods.     

Geometric morphometrics and leaf phenotypic plasticity: assessing fluctuating asymmetry and allometry in European white oaks (Quercus)

Because plants are unable to move away from unfavourable habitats and environmental perturbations, leaf phenotypic plasticity facilitates light absorption and gas exchange. Oaks (Quercus spp.) are particularly known for their adaptability and plastic phenotypes, and leaf allometry and developmental instability may represent important mechanisms for their adaptation to environments and evolution. Because of its important role in the adaptation of plant populations to different environments, allometry can be involved in diversifying selection. Developmental instability is related to environmental perturbations and stresses by producing random deviations in structures characterized by bilateral symmetry, such as oak leaves. In addition, developmental instability can also arise from genetic bottlenecks or as a result of hybridization. The splitting of symmetric and asymmetric components of variation and their separate analysis allows the variability in leaf shape traits to be summarized, reducing the variation produced by developmental instability. The geometric morphometric approach is a useful method for the study of leaf asymmetry and allometric patterns. This method provides an important tool for the visualization of shape attributes that characterize species with highly variable leaf phenotypic patterns. In this study, leaf shape and size variability of three white oak species was investigated by means of a two‐dimensional landmark‐based method providing improved knowledge of variance partitioning, species discrimination, fluctuating asymmetry and allometric patterns of variation resulting from the different analyses. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 335–348.     

Geometric morphometrics in entomology: Basics and applications

The recent expansion of a variety of morphometric tools has brought about a revolution in the comparison of morphology in the context of the size and shape in various fields including entomology. First, an overview of the theoretical issues of geometric morphometrics is presented with a caution about the usage of traditional morphometric measurements. Second, focus is then placed on two broad approaches as tools for geometric morphometrics; that is, the landmark‐based and the outline‐based approaches. A brief outline of the two methodologies is provided with some important cautions. The increasing trend of entomological studies in using the procedures of geometric morphometrics is then summarized. Finally, information is provided on useful toolkits such as computer software as well as codes and packages of the R statistical software that could be used in geometric morphometrics.     

Stereophotogrammetric analysis of occlusal morphology of extant hominoid molars: phenetics and function

Because teeth are commonly preserved in the fossil record, dental remains have often been employed in estimating evolutionary relationships among fossil hominoids. This is appropriate, however, only to the extent that dental morphology is phylogenetically informative. I have used phenetic analytic techniques to assess whether hominoid molars are likely to be useful for phylogenetic inference. Thirty-four occlusal landmarks for first and second molars were chosen; seven on each maxillary and ten on each mandibular tooth. Three-dimensional locations of these points were determined from stereophotographs of dental arcades of more than 260 specimens from six taxa (gorilla, chimpanzee, human, orangutan, siamang, and gibbon). Analytic emphasis was on canonical variates analyses of landmark coordinates for mandibular and maxillary second molars, adjusted for intergroup size differences. There is little correspondence between the systematic implications of hominoid molar morphometrics and reliable estimates of evolutionary propinquity based on interhominoid biomolecular similarities. The former seem to have been determined largely by dietary constraints. Although this suggests the possibility of using the protocol employed here to infer diets of fossil hominoids, molar crown measurements seem unlikely to serve well as phylogenetic indicators in the Hominoidea.     

Bootstrapped ordination: a method for estimating sampling effects in indirect gradient analysis

Indirect gradient analysis, or ordination, is primarily a method of exploratory data analysis. However, to support biological interpretations of resulting axes as vegetation gradients, or later confirmatory analyses and statistical tests, these axes need to be stable or at least robust into minor sampling effects. We develop a computer-intensive bootstrap (resampling) approach to estimate sampling effects on solutions from nonlinear ordination.We apply this approach to simulated data and to three forest data sets from North Carolina, USA and examine the resulting patterns of local and global instability in detrended correspondence analysis (DCA) solutions. We propose a bootstrap coefficient, scaled rank variance (SRV), to estimate remaining instability in species ranks after rotating axes to a common global orientation. In analysis of simulated data, bootstrap SRV was generally consistent with an equivalent estimate from repeated sampling. In an example using field data SRV, bootstrapped DCA showed good recovery of the order of common species along the first two axes, but poor recovery of later axes. We also suggest some criteria to use with the SRV to decide how many axes to retain and attempt to interpret.Abbreviations DCA= detrended correspondence analysis - SRV= scaled rank variance     

Cross-taxon congruence in benthic communities: Searching for surrogates in marine sediments

Cross-taxon congruence has been suggested as an efficient tool in conservation planning and biodiversity monitoring. It corresponds to the degree to which patterns in assemblage structure in a set of sites are similar among different taxonomic groups. If different groups ordinate the sampling sites similarly, they are concordant and this information is frequently used as an indicative that one group could be used as a surrogate for the other. Using spatiotemporal benthic data from a biodiverse coastal ecosystem (the Araçá Bay in southeast Brazil), we first assessed if macro- and meiofaunal assemblages inhabiting marine soft-sediments show concordant patterns. Then, we used multi- and univariate analysis to examine the relationship of both groups with the environment. Macro- and meiofaunal assemblages exhibited strong congruent patterns in all periods analyzed. Moreover, both groups responded to similar environmental features and their ordination patterns matched those generated by the environmental data. These results show that the patterns of concordance are probably mediated by similar responses to environmental gradients. Overall, our results suggest the potential for use of the surrogacy approach in conservation planning and monitoring purposes of marine benthic biodiversity, and that macro- and meiofauna can be used as a surrogate for each other.     

Anthropogenic land-use stress alters community concordance at the river-riparian interface

Organisms often respond in similar ways to environmental or spatial gradients, particularly at large spatial scales. Yet, while understanding these relationships is important for both basic and applied purposes, such as identifying surrogate taxa for conservation and monitoring purposes, patterns at finer scales and across ecotones are less certain. Our central aim was to explore patterns in community concordance at the river-riparian interface and examine whether concordance was decoupled by increasing anthropogenic stress (a gradient of local land-use intensity). We explored this at 15 sites over three years within the LTER site, Rhine-Main-Observatory, a low mountain river system in central Germany, assessing concordance between four organism groups: riparian spiders and carabid beetles, benthic macroinvertebrates, and combined aquatic macrophytes and riparian plants. This represented three different linkages: (1) predator–prey, (2) direct competition, and (3) habitat associations. While there were no correlations in richness patterns, multivariate community structure was highly concordant between all groups. Anthropogenic stress strongly reduced links between riparian spiders and carabid beetles, likely resulting from their shared resource requirements. However, increasing concordance generally occurred between plants and other groups, although inconsistently between the three groups. We posit that patterns may be resulting from two processes: (1) linkages between directly competing species decouple with increasing anthropogenic stress, and (2) stronger coupling may occur between habitat providers and dependent species when overall habitat complexity is reduced. Our results highlight the complex manner in which anthropogenic stress can influence ecosystem structure, particularly at small scales. Based on these complexities, we recommend considering the full suite of community data to adequately explore biodiversity patterns or when searching for surrogate taxa.     

Terrestrial and aquatic responses to climate change and human impact on the southeastern Tibetan Plateau during the past two centuries

Rapid population growth and economic development have led to increased anthropogenic pressures on the Tibetan Plateau, causing significant land cover changes with potentially severe ecological consequences. To assess whether or not these pressures are also affecting the remote montane‐boreal lakes on the SE Tibetan Plateau, fossil pollen and diatom data from two lakes were synthesized. The interplay of aquatic and terrestrial ecosystem response was explored in respect to climate variability and human activity over the past 200 years. Nonmetric multidimensional scaling and Procrustes rotation analysis were undertaken to determine whether pollen and diatom responses in each lake were similar and synchronous. Detrended canonical correspondence analysis was used to develop quantitative estimates of compositional species turnover. Despite instrumental evidence of significant climatic warming on the southeastern Plateau, the pollen and diatom records indicate very stable species composition throughout their profiles and show only very subtle responses to environmental changes over the past 200 years. The compositional species turnover (0.36–0.94 SD) is relatively low in comparison to the species reorganizations known from the periods during the mid‐ and early‐Holocene (0.64–1.61 SD) on the SE Plateau, and also in comparison to turnover rates of sediment records from climate‐sensitive regions in the circum arctic. Our results indicate that climatically induced ecological thresholds are not yet crossed, but that human activity has an increasing influence, particularly on the terrestrial ecosystem in our study area. Synergistic processes of post‐Little Ice Age warming, 20th century climate warming and extensive reforestations since the 19th century have initiated a change from natural oak‐pine forests to seminatural, likely less resilient pine‐oak forests. Further warming and anthropogenic disturbances would possibly exceed the ecological threshold of these ecosystems and lead to severe ecological consequences.