Methods for studying allometry in geometric morphometrics: a comparison of performance

Evolutionary Ecology - Allometry has been the focus of growing interest in studies using geometric morphometric methods to address a wide range of research questions at the interface of ecology and...     

Integrative species delimitation in Nearctic ambush bugs (Heteroptera: Reduviidae: Phymatinae): insights from molecules,geometric morphometrics and ecological associations

Ambush bugs (Hemiptera: Reduviidae: Phymatinae) are sit-and-wait predators of flower-visiting insects including pollinators. Broad species distribution ranges, intraspecific polymorphism, sexual dimorphism and subtle interspecific differences all contribute to making species delimitation especially difficult in this group, which is used as a model in the study of interactions between sexual dimorphism and sexual selection. Species boundaries among Nearctic ambush bugs in the common and frequently collected erosa species group (11 species, nine subspecies) have therefore remained unclear, resulting in a complex and poorly justified taxonomy. Recent molecular phylogenetic research suggested that several widespread Nearctic species are para- or polyphyletic. We here build on this research, integrating geometric morphometrics, molecular species delimitation approaches and host plant association data to provide a comprehensive dataset with respect to both taxon and character sampling with the goal of teasing apart evolutionary lineages of Nearctic Phymata Latreille. Although molecular-based species delimitation analyses suggested a variety of species hypotheses, probably as a result of striking discordance between mitochondrial and nuclear ribosomal genes, the combination of these with geometric morphometric data enabled us to confidently delimit several of these problematic taxa. In addition, geometric morphometric analysis of pronotal shape revealed undocumented morphological patterns that appear to be useful in the diagnosis of many of the surveyed taxa. The results from this study provide an objective foundation for the much-needed taxonomic revision of the most ubiquitous ambush bugs in North America.     

Geometric morphometrics and ecological niche modelling for delimitation of near-sibling triatomine species

Identifying morphologically similar triatomine species is key to Chagas' disease vector control and surveillance, but remains challenging when only qualitative phenotypic data are available. We investigated whether morphometric and ecological variation can provide additional criteria for species delimitation by combining geometric morphometrics and ecological niche modelling to characterize two near-sibling triatomine species, Triatoma sordida and Triatoma garciabesi (Reduviidae: Triatominae). We analysed size and shape variation in 231 wings and 123 heads from one T. garciabesi and three T. sordida populations. Predicted distribution maps (21 climatic variables, 324 vector occurrence points) were produced using the Maxent method. Multivariate analyses summarized morphological and ecological variation. Wings and heads of T. sordida were significantly larger and more elongated than those of T. garciabesi. Discriminant analyses separated the species, with a partial overlap between Argentinean populations. The predicted distribution of T. garciabesi included northwest Argentina (mainly arid Chaco), whereas that of T. sordida included northeast Argentina (humid Chaco) and the Brazilian Cerrado and Caatinga ecoregions. Clear ecological niche differences were observed, with T. garciabesi occupying colder and drier areas than T. sordida. Our results show how morphometric variation and niche divergence can be used to enhance operational criteria for the delimitation of phenotypically similar triatomine species.     

Correction to: Methods for studying allometry in geometric morphometrics: a comparison of performance

Evolutionary Ecology -     

Heterochrony and geometric morphometrics: a comparison of cranial growth in Pan paniscus versus Pan troglodytes

Heterochrony, the classic framework in which to study ontogeny and phylogeny, in essence relies on a univariate concept of shape. Though principal component (PC) plots of multivariate shape data seem to resemble classical bivariate allometric plots, the language of heterochrony cannot be translated directly into general multivariate methodology. We simulate idealized multivariate ontogenetic trajectories and explore their appearance in PC plots of shape space and size-shape space. Only if the trajectories of two related species lie along exactly the same path in shape space can the classic terminology of heterochrony apply and pure dissociation of size change against shape change be detected. Regional heterochrony--the variation of apparent heterochrony by region--implies a dissociation of local growth fields and cannot be identified in an overall PC analysis. We exemplify a geometric morphometric approach to these issues using adult and subadult crania of 48 Pan paniscus and 47 Pan troglodytes specimens. On each specimen, we digitized 47 landmarks and 144 semilandmarks on facial curves and the external neurocranial surface. We reject the hypothesis of global heterochrony in the cranium of Pan as well as regional heterochrony for the lower face, the upper face, and the neurocranium.     

Seed morphology in the tribe Chloraeeae (Orchidaceae): combining traditional and geometric morphometrics

Previous work on orchid seeds has shown that characters associated with the seed coat may be useful for classification and phylogeny at a suprageneric level. The seed morphology of several species of the tribe Chloraeeae was analysed using traditional morphometrics, and the seed shape was studied, for the first time, using tools of geometric morphometrics. Seed characters were evaluated by their discriminative power and the information they may provide in a phylogenetic context. By contrast with previous findings, seed shape resulted in a continuum among the taxa studied, and in only a few cases could genera or groups of species be discriminated on the basis of shape. However, seed size, expressed as centroid size, was a variable character and informative at a phylogenetic level. Traditional measures of seed coat, mainly those of seed coat cells, were also helpful for the discrimination of genera and species, agreeing with previous statements about their utility in taxonomy and phylogeny. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 160 , 171–183.     

Plant species delimitation: A comparison of morphological and molecular markers

Abstract

Species delimitation is fundamental in many areas of biology. Despite its importance, there is no agreement on criteria for species delimitation mostly due to divergence on the point of view adopted by the different biological disciplines. Two main groups of diagnostic characters are commonly used to distinguish species: the traditional morphological ones and the molecular ones. Field species recognition and sampling are generally based on morphological characters, but they can either fail to discriminate species and mask the presence of cryptic species or discriminate different species while in reality there is only one. To overcome this problem it is common to compare clusters obtained on the basis of the observed polymorphism of both characters, and to analyse their agreement. Here we compile a set of studies that have examined species delimitation with both markers. This provides a review of the different morphological and molecular markers, and of the sampling strategy and clustering methodology generally employed to delimitate species. Some conclusions are drawn with regard to species delimitation, when comparing diagnostic morphological and molecular markers.     

Interspecific comparison of growth and shape within Diapterus (Gerreidae: Perciformes) using geometric morphometrics

Morphometric analyses can generate useful information to solve taxonomic problems by direct comparison of each species representative’s shape or by analyzing its growth patterns. In this study, growth patterns and shape variation of the four fish species belonging to the genus Diapterus (Gerreidae) were analyzed using geometric morphometrics. We examined 287 specimens, D. auratus (n = 65), D. aureolus (n = 76), D. brevirostris (n = 87) and D. rhombeus (n = 59). For the exploration of growth trajectories of each species, the standard length was used as a size measurement, and the Procrustes distance as a morphological variation measurement. We also compared averages of the morphological change direction within each species through a pairwise comparison between vector angles. These analyses were also used to select those fishes whose increase in size did not lead to a significant change in Procrustes distance. Once this subsample was selected, the body shapes of the four species were compared using Canonical variate Analysis and Multivariate Analysis of Variance. Diapterus aureolus showed the most different morphological trajectory and the most divergent vector within the genus. An average of 93% of correct classification was estimated from Mahalanobis distances. The Canonical Variate Analysis generated three statistically significant canonical variates (p < 0.001) and indicated that D. auratus, D. brevirostris, and D. rhombeus presented a more related shape between them than D. aureolus, as indicated in previous studies. In this context, we considered the shape and growth of D. aureolus with regard to its congeners can be an important element for suggesting a taxonomic rearrangement. However, our interpretation should be supported by phylogenetic analysis. Based in our study, we suggest that trajectories analyses can be directly used in morphometric comparisons to detect those specimens affected by allometry.     

Morphological evolution of the lizard skull: a geometric morphometrics survey

Patterns of diversity among lizard skulls were studied from a morphological, phylogenetic, and functional perspective. A sample of 1,030 lizard skulls from 441 species in 17 families was used to create a lizard skull morphospace. This morphospace was combined with a phylogeny of lizard families to summarize general trends in the evolution of the lizard skull. A basal morphological split between the Iguania and Scleroglossa was observed. Iguanians are characterized by a short, high skull, with large areas of attachment for the external adductor musculature, relative to their sister group. The families of the Iguania appear to possess more intrafamilial morphological diversity than families of the Scleroglossa, but rarefaction of the data reveals this to be an artifact caused by the greater number of species represented in Iguanian families. Iguanian families also appear more dissimilar to one another than families of the Scleroglossa. Permutation tests indicate that this pattern is real and not due to the smaller number of families in the Iguanidae. Parallel and convergent evolution is observed among lizards with similar diets: ant and termite specialists, carnivores, and herbivores. However, these patterns are superimposed over the more general phylogenetic pattern of lizard skull diversity. This study has three central conclusions. Different clades of lizards show different patterns of disparity and divergence in patterns of morphospace occupation. Phylogeny imposes a primary signal upon which a secondary ecological signal is imprinted. Evolutionary patterns in skull metrics, taken with functional landmarks, allow testing of trends and the development of new hypotheses concerning both shape and biomechanics.     

House mouse dispersal in Iron Age Spain: a geometric morphometrics appraisal

During the Iron Age, sea trade in the Mediterranean increased, particularly with the expansion of Phoenician and Greek colonies in the Western Mediterranean. A side effect of these human movements was the involuntary dispersion of commensal species, such as the house mouse (Mus musculus domesticus). One archaeological layer dated from the 4th Century BC, coming from an Iberian village located in the Mediterranean coast of Spain, contained a large and reliable accumulation of small mammals. The presence of the house mouse was highly suspected within this layer. To assess its abundance quantitatively, we used a geometric morphometrics approach of the first lower molar contour using elliptical Fourier analysis. We also increased the power of the discrimination between the Algerian mouse (Mus spretus) and the house mouse by combining a dimension reduction approach together with different validation procedures. The relative importance of age, sex, and geographical origin onto the shape and form of the lower molar contour was also investigated. The results obtained demonstrate the presence and the dominance of the house mouse in the landscape surrounding the Iberian village in the 1st Millennium BC, only a few centuries after its arrival in the Western Mediterranean Basin. A cross‐validated linear discriminant function considering different Mediterranean populations suggest Morocco and France as the most probable geographical origins for the Algerian mouse, and Tunisia for the origin of house mice in North‐Eastern Spain. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 483–497.     

Drivers of moth species richness on tropical altitudinal gradients: a cross-regional comparison

Aims We examine the role of species–area relationships (SARs), climatic parameters and phylogeny in shaping the altitudinal species richness patterns of moths. With respect to SARs, we investigate whether habitat heterogeneity is a probable mechanism for mediating area effects. We investigate the consistency of patterns by comparing several discrete regions. Location Nine mountainous regions in tropical Asia and the Malay Archipelago. Methods Presence‐only records for 292 species of the Lepidopteran family Sphingidae were used to measure interpolated species richness in 200‐m altitudinal bands. Species richness was correlated with area measures, which were calculated from both two‐dimensional map projections and three‐dimensional digital elevation models (DEMs). We used data simulations of homogeneous communities to test for effects of sample (i.e. habitat) heterogeneity as a mechanism causing SARs. Species richness patterns were compared among regions and between the two major sphingid clades, and were related to regional climatic characteristics. Results The area of altitudinal bands was a strong (statistical) explanation of species richness, particularly if area was calculated from three‐dimensional DEMs, but SARs often over‐predict species richness in lowland areas. There was no evidence for habitat heterogeneity as a mechanism of altitudinal SARs (tested for Borneo only). Species richness patterns varied considerably between the nine regions, which may, as an alternative to SARs, be explained by climatic differences such as (temperature) seasonality. Phylogenetic clades differed in species richness patterns exhibited. Main conclusion SARs provide strong empirical explanations for (regional) altitudinal patterns of species richness, but lack of evidence for the most likely mechanism cautions against a priori ‘corrections’ of species richness data for area. Furthermore, SARs are often not a sufficient explanation for the drop in species richness towards lowlands. Climate, or other collinear variables, may offer alternative explanations for altitudinal SARs. More research is needed to understand the mechanisms for SARs in an altitudinal context in order to evaluate their importance in the face of parameter collinearity.     

Inter- and intraspecific variation in grass phytolith shape and size: a geometric morphometrics perspective

Background and AimsThe relative contributions of inter- and intraspecific variation to phytolith shape and size have only been investigated in a limited number of studies. However, a detailed understanding of phytolith variation patterns among populations or even within a single plant specimen is of key importance for the correct taxonomic identification of grass taxa in fossil samples and for the reconstruction of vegetation and environmental conditions in the past. In this study, we used geometric morphometric analysis for the quantification of different sources of phytolith shape and size variation.MethodsWe used landmark-based geometric morphometric methods for the analysis of phytolith shapes in two extant grass species (Brachypodium pinnatum and B. sylvaticum). For each species, 1200 phytoliths were analysed from 12 leaves originating from six plants growing in three populations. Phytolith shape and size data were subjected to multivariate Procrustes analysis of variance (ANOVA), multivariate regression, principal component analysis and linear discriminant analysis.Key ResultsInterspecific variation largely outweighed intraspecific variation with respect to phytolith shape. Individual phytolith shapes were classified with 83 % accuracy into their respective species. Conversely, variation in phytolith shapes within species but among populations, possibly related to environmental heterogeneity, was comparatively low.ConclusionsOur results imply that phytolith shape relatively closely corresponds to the taxonomic identity of closely related grass species. Moreover, our methodological approach, applied here in phytolith analysis for the first time, enabled the quantification and separation of variation that is not related to species discrimination. Our findings strengthen the role of grass phytoliths in the reconstruction of past vegetation dynamics.     

A comparison of trunk muscle activation: Ab Circle vs. traditional modalities

The purpose of this study was to compare the activation of the rectus abdominis (RA), external oblique abdominis (EO), lower abdominal stabilizers (LASs), and lumbar erector spinae (LES) during performance of 3 traditional trunk exercises vs. exercise on the Ab Circle device. Surface electromyography was used to assess 12 subjects (6 men, 6 women) for 6 exercise conditions, including: abdominal crunch, side bridge, quadruped, and Ab Circle levels 1-3. For the RA, the abdominal crunch elicited significantly greater activity vs. the Ab Circle level 1, and the side bridge elicited significantly greater activity vs. the Ab Circle levels 1 and 2. For the EO, the side bridge elicited significantly greater activity vs. the quadruped. No significant differences were noted between conditions for the LASs. For the LES, the side bridge and quadruped elicited significantly greater activity vs. the abdominal crunch. The results of this study indicate that the anterior, posterior, and lateral trunk musculature can be activated to similar or even greater levels by performing the 3 traditional trunk exercises vs. the Ab Circle. This was particularly evident for the side bridge exercise, which elicited significantly greater activity of the RA vs. the Ab Circle levels 1 and 2, and elicited similar activity of the EO, LASs, and LES at all 3 Ab Circle levels.     

Three-dimensional geometric morphometrics of Arvicanthis: implications for systematics and taxonomy

Arvicanthis is an African murid, found throughout sub-Saharan Africa, Sudan and Egypt. Although in the past 10 years several studies have been carried out to assess its systematics, there is still a need for a general revision of the genus. In this study the morphometric relationships between 71 populations throughout the range were investigated. A three-dimensional geometric morphometric approach was used to assess differences in the size and shape of the skull. These were related to the different biogeographical domains characterizing the range of the genus and to molecular and karyotypic phylogenies. Results agree only in part with phylogeny, and show a close relationship with the environmental backgrounds of each species. It is therefore suggested that the adaptation of Arvicanthis to local environment has played an important role in the phenotypic evolution of the skull. This leads to problems in taxonomic definitions based on morphometrics, which should not be used without comparison with other independently derived characters such as the DNA and the karyotype.     

Phenotypic evolution of human craniofacial morphology after admixture: a geometric morphometrics approach

An evolutionary, diachronic approach to the phenotypic craniofacial pattern arisen in a human population after high levels of admixture and gene flow was achieved by means of geometric morphometrics. Admixture has long been studied after molecular data. Nevertheless, few efforts have been made to explain the morphological outcome in human craniofacial samples. The Spanish-Amerindian contact can be considered a good scenario for such an analysis. Here we present a comparative analysis of craniofacial shape changes observed between two putative ancestor groups, Spanish and precontact Aztecs, and two diachronic admixed groups, corresponding to early and late colonial periods from the Mexico's Central Valley. Quantitative shape comparisons of Amerindian, Spanish, and admixed groups were used to test the expectations of quantitative genetics for admixture events. In its simplest form, this prediction states that an admixed group will present phenotypic values falling between those of both parental groups. Results show that, in general terms, although the human skull is a complex, integrated structure, the craniofacial morphology observed fits the theoretical expectations of quantitative genetics. Thus, it is predictive of population structure and history. In fact, results obtained after the craniofacial analysis are in accordance with previous molecular and historical interpretations, providing evidence that admixture is a main microevolutionary agent influencing modern Mexican gene pool. However, expectations are not straightforward when moderate shape changes are considered. Deviations detected at localized structures, such as the upper and lower face, highlight the evolution of a craniofacial pattern exclusively inherent to the admixed groups, indicating that quantitative characters might respond to admixture in a complicated, nondirectional way.     

SpedeSTEM: a rapid and accurate method for species delimitation

We describe a software package (SpedeSTEM) that allows researchers to conduct a species delimitation analysis using intraspecific genetic data. Our method operates under the assumption that a priori information regarding group membership is available, for example that samples are drawn from some number of described subspecies, races or distinct morphotypes. SpedeSTEM proceeds by calculating the maximum likelihood species tree from all hierarchical arrangements of the sampled alleles and uses information theory to quantify the model probability of each permutation. SpedeSTEM is tested here against empirical and simulated data; results indicate that evolutionary lineages that diverged as few as 0.5N generations in the past can be validated as distinct using sequence data from little as five loci. This work enables speciation investigations to identify lineages that are evolutionarily distinct and thus have the potential to form new species before these lineages acquire secondary characteristics such as reproductive isolation or morphological differentiation that are commonly used to define species.     

Morphological disparity in theropod jaws: comparing discrete characters and geometric morphometrics

Disparity, the diversity of form and function of organisms, can be assessed from cladistic or phenetic characters, and from discrete characters or continuous characters such as landmarks, outlines, or ratios. But do these different methods of assessing disparity provide comparable results? Here we provide evidence that all metrics correlate significantly with each other and capture similar patterns of morphological variation. We compare three methods of capturing morphological disparity (discrete characters, geometric morphometric outlines and geometric morphometric landmarks) in coelurosaurian dinosaurs. We standardize our study by focusing all our metrics on the mandible, so avoiding the risk of confounding disparity methods with anatomical coverage of the taxa. The correlation is strongest between the two geometric morphometric methods, and weaker between the morphometric methods and the discrete characters. By using phylogenetic simulations of discrete character and geometric morphometric data sets, we show that the strength of these correlations is significantly greater than expected from the evolution of random data under Brownian motion. All disparity metrics confirm that Maniraptoriformes had the highest disparity of all coelurosaurians, and omnivores and herbivores had higher disparity than carnivores.