Population structure in the barn swallow,Hirundo rustica: a comparison between neutral DNA markers and quantitative traits

Local adaptation to variable environments can generate clinal variation in morphological traits. Alternatively, similar patterns of clinal variation may be generated simply as a result of genetic drift/migration balance. Teasing apart these different processes is a continuing focus in evolutionary ecology. We compare genetic differentiation at molecular loci and quantitative traits to analyse the effect of these different processes in a morphological latitudinal cline of the barn swallow, Hirundo rustica, breeding across Europe. The results obtained show no structuring at neutral microsatellite loci, which contrasts with positive structuring at five quantitative morphometric traits. This supports the hypothesis that the observed morphometric cline in barn swallows is the result of selection acting in a spatially heterogeneous environment. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 306–314.     

Learning to see the wood for the trees: machine learning,decision trees,and the classification of isolated theropod teeth

Taxonomic identification of fossils based on morphometric data traditionally relies on the use of standard linear models to classify such data. Machine learning and decision trees offer powerful alternative approaches to this problem but are not widely used in palaeontology. Here, we apply these techniques to published morphometric data of isolated theropod teeth in order to explore their utility in tackling taxonomic problems. We chose two published datasets consisting of 886 teeth from 14 taxa and 3020 teeth from 17 taxa, respectively, each with five morphometric variables per tooth. We also explored the effects that missing data have on the final classification accuracy. Our results suggest that machine learning and decision trees yield superior classification results over a wide range of data permutations, with decision trees achieving accuracies of 96% in classifying test data in some cases. Missing data or attempts to generate synthetic data to overcome missing data seriously degrade all classifiers predictive accuracy. The results of our analyses also indicate that using ensemble classifiers combining different classification techniques and the examination of posterior probabilities is a useful aid in checking final class assignments. The application of such techniques to isolated theropod teeth demonstrate that simple morphometric data can be used to yield statistically robust taxonomic classifications and that lower classification accuracy is more likely to reflect preservational limitations of the data or poor application of the methods.     

Technical note: Quantification of neurocranial shape variation using the shortest paths connecting pairs of anatomical landmarks

Three‐dimensional geometric morphometric techniques have been widely used in quantitative comparisons of craniofacial morphology in humans and nonhuman primates. However, few anatomical landmarks can actually be defined on the neurocranium. In this study, an alternative method is proposed for defining semi‐landmarks on neurocranial surfaces for use in detailed analysis of cranial shape. Specifically, midsagittal, nuchal, and temporal lines were approximated using Bezier curves and equally spaced points along each of the curves were defined as semi‐landmarks. The shortest paths connecting pairs of anatomical landmarks as well as semi‐landmarks were then calculated in order to represent the surface morphology between landmarks using equally spaced points along the paths. To evaluate the efficacy of this method, the previously outlined technique was used in morphological analysis of sexual dimorphism in modern Japanese crania. The study sample comprised 22 specimens that were used to generate 110 anatomical semi‐landmarks, which were used in geometric morphometric analysis. Although variations due to sexual dimorphism in human crania are very small, differences could be identified using the proposed landmark placement, which demonstrated the efficacy of the proposed method. Am J Phys Anthropol 151:658–666, 2013. © 2013 Wiley Periodicals, Inc.     

DNA条形码(ITS2)在葫芦科鉴定中应用价值的评估

探讨在纳入分析数据时,数据信息的选择对ITS2序列作为DNA条形码在葫芦科植物中鉴定能力的影响。首先,建立由葫芦科植物ITS2序列组成的3个资料组,其中Dataset1为实验样本,Dataset2由实验样本及GenBank数据库样本组合,Dataset3为从Dataset2中去除部分序列后所得。通过比较3个资料组的种间、种内的变异、Barcoding Gap及鉴定成功率,评估纳入分析的数据选择差异对ITS2鉴定能力的影响。结果显示ITS2序列在3个资料组属水平上的鉴定成功率均达到100%;种水平上,用BLAST1法鉴定成功率分别为100%、 67.8%、 90.6%,Nearest Distance法鉴定成功率分别为100%、 52.5%、 66.5%。可见纳入分析的数据选择有差异时,会导致鉴定成功率的较大变化。3个资料组中,ITS2分析仅有Dataset2的Barcoding Gap不够显著。因此对于DNA条形码分析中的数据纳入标准,值得进一步研究。     

An illustration of variable precision rough set theory: the gender classification of the European barn swallow (Hirundo rustica)

This paper introduces a new technique in the investigation of object classification and illustrates the potential use of this technique for the analysis of a range of biological data, using avian morphometric data as an example. The nascent variable precision rough sets (VPRS) model is introduced and compared with the decision tree method ID3 (through a ‘leave n out’ approach), using the same dataset of morphometric measures of European barn swallows (Hirundo rustica) and assessing the accuracy of gender classification based on these measures. The results demonstrate that the VPRS model, allied with the use of a modern method of discretization of data, is comparable with the more traditional non-parametric ID3 decision tree method. We show that, particularly in small samples, the VPRS model can improve classification and to a lesser extent prediction aspects over ID3. Furthermore, through the ‘leave n out’ approach, some indication can be produced of the relative importance of the different morphometric measures used in this problem. In this case we suggest that VPRS has advantages over ID3, as it intelligently uses more of the morphometric data available for the data classification, whilst placing less emphasis on variables with low reliability. In biological terms, the results suggest that the gender of swallows can be determined with reasonable accuracy from morphometric data and highlight the most important variables in this process. We suggest that both analysis techniques are potentially useful for the analysis of a range of different types of biological datasets, and that VPRS in particular has potential for application to a range of biological circumstances.     

Technical note: A new method for measuring long bone curvature using 3D landmarks and semi‐landmarks

Here we describe and evaluate a new method for quantifying long bone curvature using geometric morphometric and semi‐landmark analysis of the human femur. The technique is compared with traditional ways of measuring subtense and point of maximum curvature using either coordinate calipers or projection onto graph paper. Of the traditional methods the graph paper method is more reliable than using coordinate calipers. Measurement error is consistently lower for measuring point of maximum curvature than for measuring subtense. The results warrant caution when comparing data collected by the different traditional methods. Landmark data collection proves reliable and has a low measurement error. However, measurement error increases with the number of semi‐landmarks included in the analysis of curvature. Measurements of subtense can be estimated more reliably using 3D landmarks along the curve than using traditional techniques. We use equidistant semi‐landmarks to quantify the curve because sliding the semi‐landmarks masks the curvature signal. Principal components analysis of these equidistant semi‐landmarks provides the added benefit of describing the shape of the curve. These results are promising for functional and forensic analysis of long bone curvature in modern human populations and in the fossil record. Am J Phys Anthropol, 2010. © 2010 Wiley‐Liss, Inc.     

Histomorphometric analysis of fibrosis in the renal interstitial compartment

The interstitium is the extravascular intertubular space of the renal parenchyma, which provides structural support to the functional renal units and is included at the same time in nearly all renal functions. Alterations to this renal compartment have been found in almost all glomerular diseases. During the last thirty years the studies of a few groups of investigators have shown that the degree of the renal dysfunction is strongly correlated with the changes in the tubulointerstitial compartment. We made a morphometric study of a group of 10 renal biopsies, previously diagnosed as IgA nephropathy or membranoproliferative glomerulonephritis. For morphometric analysis we made colour extraction of the interstitial area on tissue sections stained with trichrom Masson using the LUCIA M-NIKON image analysing system with integrated software for statistical analysis of the data. We measured the surface of the marked fields and the results were expressed as a percentage of the total scanned area. The results were correlated with the serum creatinine at the time of biopsy. We found fibrosis occupying more than 10% of the tubulointerstitial surface in all 10 patients. Six of them had a moderate level of fibrosis, occupying more that 20% of the tubulointerstitial space. The statistical analysis of these results showed a significant correlation between the degree of the interstitial expansion and the serum creatinine. The results showing the correlation between these parameters will enable the quantitative histological analyses to be included in the process of the nephropathological diagnosis in order to evaluate the histological risk factors in glomerular diseases.     

On the origin of DNA genomes: evolution of the division of labor between template and catalyst in model replicator systems

The division of labor between template and catalyst is a fundamental property of all living systems: DNA stores genetic information whereas proteins function as catalysts. The RNA world hypothesis, however, posits that, at the earlier stages of evolution, RNA acted as both template and catalyst. Why would such division of labor evolve in the RNA world? We investigated the evolution of DNA-like molecules, i.e. molecules that can function only as template, in minimal computational models of RNA replicator systems. In the models, RNA can function as both template-directed polymerase and template, whereas DNA can function only as template. Two classes of models were explored. In the surface models, replicators are attached to surfaces with finite diffusion. In the compartment models, replicators are compartmentalized by vesicle-like boundaries. Both models displayed the evolution of DNA and the ensuing division of labor between templates and catalysts. In the surface model, DNA provides the advantage of greater resistance against parasitic templates. However, this advantage is at least partially offset by the disadvantage of slower multiplication due to the increased complexity of the replication cycle. In the compartment model, DNA can significantly delay the intra-compartment evolution of RNA towards catalytic deterioration. These results are explained in terms of the trade-off between template and catalyst that is inherent in RNA-only replication cycles: DNA releases RNA from this trade-off by making it unnecessary for RNA to serve as template and so rendering the system more resistant against evolving parasitism. Our analysis of these simple models suggests that the lack of catalytic activity in DNA by itself can generate a sufficient selective advantage for RNA replicator systems to produce DNA. Given the widespread notion that DNA evolved owing to its superior chemical properties as a template, this study offers a novel insight into the evolutionary origin of DNA.     

Quantification of Surface Amorphous Content Using Dispersive Surface Energy: the Concept of Effective Amorphous Surface Area

We investigate the use of dispersive surface energy in quantifying surface amorphous content, and the concept of effective amorphous surface area is introduced. An equation is introduced employing the linear combination of surface area normalized square root dispersive surface energy terms. This equation is effective in generating calibration curves when crystalline and amorphous references are used. Inverse gas chromatography is used to generate dispersive surface energy values. Two systems are investigated, and in both cases surface energy data collected for physical mixture samples comprised of amorphous and crystalline references fits the predicted response with good accuracy. Surface amorphous content of processed lactose samples is quantified using the calibration curve, and interpreted within the context of effective amorphous surface area. Data for bulk amorphous content is also utilized to generate a thorough picture of how disorder is distributed throughout the particle. An approach to quantifying surface amorphous content using dispersive surface energy is presented. Quantification is achieved by equating results to an effective amorphous surface area based on reference crystalline, and amorphous materials.     

An eFTD-VP framework for efficiently generating patient-specific anatomically detailed facial soft tissue FE mesh for craniomaxillofacial surgery simulation

Accurate surgical planning and prediction of craniomaxillofacial surgery outcome requires simulation of soft tissue changes following osteotomy. This can only be achieved by using an anatomically detailed facial soft tissue model. The current state-of-the-art of model generation is not appropriate to clinical applications due to the time-intensive nature of manual segmentation and volumetric mesh generation. The conventional patient-specific finite element (FE) mesh generation methods are to deform a template FE mesh to match the shape of a patient based on registration. However, these methods commonly produce element distortion. Additionally, the mesh density for patients depends on that of the template model. It could not be adjusted to conduct mesh density sensitivity analysis. In this study, we propose a new framework of patient-specific facial soft tissue FE mesh generation. The goal of the developed method is to efficiently generate a high-quality patient-specific hexahedral FE mesh with adjustable mesh density while preserving the accuracy in anatomical structure correspondence. Our FE mesh is generated by eFace template deformation followed by volumetric parametrization. First, the patient-specific anatomically detailed facial soft tissue model (including skin, mucosa, and muscles) is generated by deforming an eFace template model. The adaptation of the eFace template model is achieved by using a hybrid landmark-based morphing and dense surface fitting approach followed by a thin-plate spline interpolation. Then, high-quality hexahedral mesh is constructed by using volumetric parameterization. The user can control the resolution of hexahedron mesh to best reflect clinicians’ need. Our approach was validated using 30 patient models and 4 visible human datasets. The generated patient-specific FE mesh showed high surface matching accuracy, element quality, and internal structure matching accuracy. They can be directly and effectively used for clinical simulation of facial soft tissue change.     

Allometric shape vector projection: a new method for the identification of allometric shape characters and trajectories applied to the human astragalus (talus)

The surface morphology of the human astragalus (talus) is difficult to represent accurately using landmarks as it is essentially globular in shape. Advances in laser scanning technology allow fast and accurate capture of bone surface morphology. However, methodologies to utilise these new accurate 3D data have not been fully developed. The present study uses canonical sampling of whole surface morphology attained through laser scanning and for the first time applies the technique to analysis of bone morphology. We introduce a new technique for identifying allometric shape characters in whole bone surface morphology. In a sample of adult human astragalus the new technique is successful in identifying and isolating intra-specific allometric shape characters in a bone which typically lacks landmarks and has, consequently, proved difficult to analyse using traditional 3D morphometric methods.     

Hexahedral meshing of subject-specific anatomic structures using mapped building blocks

To extend the use of computational techniques like finite element analysis to clinical settings, it would be beneficial to have the ability to generate a unique model for every subject quickly and efficiently. This work is an extension of two previously developed mapped meshing tools that utilised force and displacement control to map a template mesh to a subject-specific surface. The objective of this study was to map a template block structure, common to multiblock meshing techniques, to a subject-specific surface. The rationale is that the blocks are considerably less refined and may be readily edited after mapping, thereby yielding a mesh of high quality in less time than mapping the mesh itself. In this paper, the versatility and robustness of the method was verified by processing four data-sets. The method was found to be robust enough to cope with the variability of bony surface size, spatial position and geometry, producing building block structures (BBSs) that generated meshes comparable to those produced using BBSs that were created manually.     

Towards a solution for hepatitis C virus hypervariability: mimotopes of the hypervariable region 1 can induce antibodies cross-reacting with a large number of viral variants.

The hypervariable region 1 (HVR1) of the putative envelope protein E2 of hepatitis C virus (HCV) is the most variable antigenic fragment in the whole viral genome and is mainly responsible for the large inter-and intra-individual heterogeneity of the infecting virus. It contains a principal neutralization epitope and has been proposed as the major player in the mechanism of escape from host immune response. Since anti-HVR1 antibodies are the only species shown to possess protective activity up to date, developing an effective prevention therapy is a very difficult task. We have approached the problem of HVR1 variability by deriving a consensus profile from >200 HVR1 sequences from different viral isolates and used it as a template to generate a vast repertoire of synthetic HVR1 surrogates displayed on M13 bacteriophage. This library was affinity selected using many different sera from infected patients. Phages were identified which react very frequently with patients' sera and bind serum antibodies that cross-react with a large panel of HVR1 peptides derived from natural HCV variants. When injected into experimental animals, the 'mimotopes' with the highest cross-reactivity induced antibodies which recognized the same panel of natural HVR1 variants. In these mimotopes we identified a sequence pattern responsible for the observed cross-reactivity. These data may hold the key for future development of a prophylactic vaccine against HCV.     

Discrete and morphometric traits reveal contrasting patterns and processes in the macroevolutionary history of a clade of scorpions

Many palaeontological studies have investigated the evolution of entire body plans, generally relying on discrete character‐taxon matrices. In contrast, macroevolutionary studies performed by neontologists have mostly focused on morphometric traits. Although these data types are very different, some studies have suggested that they capture common patterns. Nonetheless, the tests employed to support this claim have not explicitly incorporated a phylogenetic framework and may therefore be susceptible to confounding effects due to the presence of common phylogenetic structure. We address this question using the scorpion genus Brachistosternus Pocock 1893 as case study. We make use of a time‐calibrated multilocus molecular phylogeny, and compile discrete and traditional morphometric data sets, both capturing the overall morphology of the organisms. We find that morphospaces derived from these matrices are significantly different, and that the degree of discordance cannot be replicated by simulations of random character evolution. Moreover, we find strong support for contrasting modes of evolution, with discrete characters being congruent with an ‘early burst’ scenario whereas morphometric traits suggest species‐specific adaptations to have driven morphological evolution. The inferred macroevolutionary dynamics are therefore contingent on the choice of character type. Finally, we confirm that metrics of correlation fail to detect these profound differences given common phylogenetic structure in both data sets, and that methods incorporating a phylogenetic framework and accounting for expected covariance should be favoured.     

Principles for the virtual reconstruction of hominin crania

Fossils are usually discovered broken or distorted, therefore reconstruction is inevitably the first step towards any comparative analysis. We outline a general methodological framework by which missing information about biological specimens can be estimated using geometric morphometric methods and discuss how this relates to effective paleoanthropological use of incomplete and distorted crania.Combining digital data resources with geometric morphometrics, we go beyond the assembly of fragments on the computer. As in a three-dimensional jigsaw puzzle, we first assemble the virtual pieces manually. Then we use landmarks, several hundred semilandmarks, and information from complete specimens to estimate missing coordinates and correct for distortion simultaneously. One can thus incorporate information from incomplete specimens in a comparative morphometric analysis while keeping track of the uncertainties that result from partial preservation or deformation. We exemplify our approach by reconstructing the fossil crania Arago XXI, Taung, and KNM-WT 15000. As different assumptions and algorithms lead to different estimations, there exists no “all-purpose” reconstruction. Instead one creates multiple reconstructions—a posterior distribution in a Bayesian sense. This distribution reflects uncertainty due to missing data values and sensitivity to prior assumptions. While there will typically be shape differences among equally plausible reconstructions, these different estimates might still support a single conclusion.     

A multiple-template approach to protein threading

Most threading methods predict the structure of a protein using only a single template. Due to the increasing number of solved structures, a protein without solved structure is very likely to have more than one similar template structures. Therefore, a natural question to ask is if we can improve modeling accuracy using multiple templates. This article describes a new multiple-template threading method to answer this question. At the heart of this multiple-template threading method is a novel probabilistic-consistency algorithm that can accurately align a single protein sequence simultaneously to multiple templates. Experimental results indicate that our multiple-template method can improve pairwise sequence-template alignment accuracy and generate models with better quality than single-template models even if they are built from the best single templates (P-value <10(-6)) while many popular multiple sequence/structure alignment tools fail to do so. The underlying reason is that our probabilistic-consistency algorithm can generate accurate multiple sequence/template alignments. In another word, without an accurate multiple sequence/template alignment, the modeling accuracy cannot be improved by simply using multiple templates to increase alignment coverage. Blindly tested on the CASP9 targets with more than one good template structures, our method outperforms all other CASP9 servers except two (Zhang-Server and QUARK of the same group). Our probabilistic-consistency algorithm can possibly be extended to align multiple protein/RNA sequences and structures.     

Regression equations for the estimation of stature and body mass using a Greek documented skeletal collection

Body size is an important variable in bioarchaeological and forensic studies, making the accurate calculation of stature and body mass imperative. Given that anatomical and morphometric approaches offer accurate results but require a particularly good preservation of the skeletal material, whereas mathematical and mechanical methods are more easily applicable but they are largely population-specific, the present paper uses a ‘hybrid’ approach in order to generate regression equations for the prediction of stature and body mass in a modern Greek sample. Specifically, anatomical and morphometric methods were used to calculate the stature and body mass of the individuals and regression equations using the Ordinary Least Squares and Reduced Major Axis methods were generated with long bone lengths and femoral head breadth as predictors. The obtained equations exhibit low random and directional error and perform better than existing equations designed using different samples from the United States, Europe, and the Balkans. Therefore, these equations are more appropriate for modern Greek material.     

Estimating and comparing thermal performance curves

I show how one can estimate the shape of a thermal performance curve using information theory. This approach ranks plausible models by their Akaike information criterion (AIC), which is a measure of a model's ability to describe the data discounted by the model's complexity. I analyze previously published data to demonstrate how one applies this approach to describe a thermal performance curve. This exemplary analysis produced two interesting results. First, a model with a very high r² (a modified Gaussian function) appeared to overfit the data. Second, the model favored by information theory (a Gaussian function) has been used widely in optimality studies of thermal performance curves. Finally, I discuss the choice between regression and ANOVA when comparing thermal performance curves and highlight a superior method called template mode of variation. Much progress can be made by abandoning traditional methods for a method that combines information theory with template mode of variation.