Evidence for Morphometric Differentiation of Wild and Captively Reared Adult Coho Salmon: A Geometric Analysis

As part of a comprehensive genetic evaluation of reproduction in naturally spawning coho salmon, Oncorhynchus kisutch, we examined morphometric variation in captively reared and wild adults from Hood Canal, Washington (U.S.A.) for evidence of differentiation between these groups. We collected captively reared fish as parr from two stocks and reared to adulthood at a freshwater hatchery, maturing in 1995 and 1996; we sampled closely size-matched wild fish as they returned to a neighboring stream in both years. Multivariate analysis of shape variation by Procrustes coordinates, visualized by thin-plate splines, indicated that the captively reared adults were differentiated from the wild fish by sharply reduced sexual dimorphism as well as smaller heads and less hooked snouts, increased trunk depth, larger caudal peduncles, shorter dorsal fins, larger hindbodies and a reduction in body streamlining. The differences between the captively reared and wild fish were similar to but more pronounced than some differences previously reported between hatchery and wild coho salmon. The magnitude and pattern of differences suggested that at least some of them were environmentally induced. Shape variation showed an allometric relationship with variation in body (measured as centroid) size. Morphometric variation was a poor correlate of most spawning behaviors. Nevertheless, our results suggest that the morphometric consequences of captive rearing for mate selection and reproductive activity of spawning fish may limit its effectiveness as a restorative tool.     

Studying Developmental Variation with Geometric Morphometric Image Analysis (GMIA)

The ways in which embryo development can vary across individuals of a population determine how genetic variation translates into adult phenotypic variation. The study of developmental variation has been hampered by the lack of quantitative methods for the joint analysis of embryo shape and the spatial distribution of cellular activity within the developing embryo geometry. By drawing from the strength of geometric morphometrics and pixel/voxel-based image analysis, we present a new approach for the biometric analysis of two-dimensional and three-dimensional embryonic images. Well-differentiated structures are described in terms of their shape, whereas structures with diffuse boundaries, such as emerging cell condensations or molecular gradients, are described as spatial patterns of intensities. We applied this approach to microscopic images of the tail fins of larval and juvenile rainbow trout. Inter-individual variation of shape and cell density was found highly spatially structured across the tail fin and temporally dynamic throughout the investigated period.     

A Geometric Morphometric Approach to the Analysis of Lip Shape during Speech: Development of a Clinical Outcome Measure

Objective assessments of lip movement can be beneficial in many disciplines including visual speech recognition, for surgical outcome assessment in patients with cleft lip and for the rehabilitation of patients with facial nerve impairments. The aim of this study was to develop an outcome measure for lip shape during speech using statistical shape analysis techniques. Lip movements during speech were captured from a sample of adult subjects considered as average using a three-dimensional motion capture system. Geometric Morphometrics was employed to extract three-dimensional coordinate data for lip shape during four spoken words decomposed into seven visemes (which included the resting lip shape). Canonical variate analysis was carried out in an attempt to statistically discriminate the seven visemes. The results showed that the second canonical variate discriminated the resting lip shape from articulation of the utterances and accounted for 17.2% of the total variance of the model. The first canonical variate was significant in discriminating between the utterances and accounted for 72.8% of the total variance of the model. The outcome measure was created using the 95% confidence intervals of the canonical variate scores for each subject plotted as ellipses for each viseme. The method and outcome model is proposed as reference to compare lip movement during speech in similar population groups.     

Homo floresiensis Contextualized: A Geometric Morphometric Comparative Analysis of Fossil and Pathological Human Samples

The origin of hominins found on the remote Indonesian island of Flores remains highly contentious. These specimens may represent a new hominin species, Homo floresiensis, descended from a local population of Homo erectus or from an earlier (pre-H. erectus) migration of a small-bodied and small-brained hominin out of Africa. Alternatively, some workers suggest that some or all of the specimens recovered from Liang Bua are pathological members of a small-bodied modern human population. Pathological conditions proposed to explain their documented anatomical features include microcephaly, myxoedematous endemic hypothyroidism (“cretinism”) and Laron syndrome (primary growth hormone insensitivity). This study evaluates evolutionary and pathological hypotheses through comparative analysis of cranial morphology. Geometric morphometric analyses of landmark data show that the sole Flores cranium (LB1) is clearly distinct from healthy modern humans and from those exhibiting hypothyroidism and Laron syndrome. Modern human microcephalic specimens converge, to some extent, on crania of extinct species of Homo. However in the features that distinguish these two groups, LB1 consistently groups with fossil hominins and is most similar to H. erectus. Our study provides further support for recognizing the Flores hominins as a distinct species, H. floresiensis, whose affinities lie with archaic Homo.     

Brain Networks Responsible for Sense of Agency: An EEG Study

BackgroundSelf-agency (SA) is a person’s feeling that his action was generated by himself. The neural substrates of SA have been investigated in many neuroimaging studies, but the functional connectivity of identified regions has rarely been investigated. The goal of this study is to investigate the neural network related to SA.MethodsSA of hand movements was modulated with virtual reality. We examined the cortical network relating to SA modulation with electroencephalography (EEG) power spectrum and phase coherence of alpha, beta, and gamma frequency bands in 16 right-handed, healthy volunteers.ResultsIn the alpha band, significant relative power changes and phase coherence of alpha band were associated with SA modulation. The relative power decrease over the central, bilateral parietal, and right temporal regions (C4, Pz, P3, P4, T6) became larger as participants more effectively controlled the virtual hand movements. The phase coherence of the alpha band within frontal areas (F7-FP2, F7-Fz) was directly related to changes in SA. The functional connectivity was lower as the participants felt that they could control their virtual hand. In the other frequency bands, significant phase coherences were observed in the frontal (or central) to parietal, temporal, and occipital regions during SA modulation (Fz-O1, F3-O1, Cz-O1, C3-T4L in beta band; FP1-T6, FP1-O2, F7-T4L, F8-Cz in gamma band).ConclusionsOur study suggests that alpha band activity may be the main neural oscillation of SA, which suggests that the neural network within the anterior frontal area may be important in the generation of SA.     

An Evidence-Based Combining Classifier for Brain Signal Analysis

Nowadays, brain signals are employed in various scientific and practical fields such as Medical Science, Cognitive Science, Neuroscience, and Brain Computer Interfaces. Hence, the need for robust signal analysis methods with adequate accuracy and generalizability is inevitable. The brain signal analysis is faced with complex challenges including small sample size, high dimensionality and noisy signals. Moreover, because of the non-stationarity of brain signals and the impacts of mental states on brain function, the brain signals are associated with an inherent uncertainty. In this paper, an evidence-based combining classifiers method is proposed for brain signal analysis. This method exploits the power of combining classifiers for solving complex problems and the ability of evidence theory to model as well as to reduce the existing uncertainty. The proposed method models the uncertainty in the labels of training samples in each feature space by assigning soft and crisp labels to them. Then, some classifiers are employed to approximate the belief function corresponding to each feature space. By combining the evidence raised from each classifier through the evidence theory, more confident decisions about testing samples can be made. The obtained results by the proposed method compared to some other evidence-based and fixed rule combining methods on artificial and real datasets exhibit the ability of the proposed method in dealing with complex and uncertain classification problems.     

An Expanded Combined Evidence Approach to the Gavialis Problem Using Geometric Morphometric Data from Crocodylian Braincases and Eustachian Systems

The phylogenetic position of the Indian gharial (Gavialis gangeticus) is disputed - morphological characters place Gavialis as the sister to all other extant crocodylians, whereas molecular and combined analyses find Gavialis and the false gharial (Tomistoma schlegelii) to be sister taxa. Geometric morphometric techniques have only begun to be applied to this issue, but most of these studies have focused on the exterior of the skull. The braincase has provided useful phylogenetic information for basal crurotarsans, but has not been explored for the crown group. The Eustachian system is thought to vary phylogenetically in Crocodylia, but has not been analytically tested. To determine if gross morphology of the crocodylian braincase proves informative to the relationships of Gavialis and Tomistoma, we used two- and three-dimensional geometric morphometric approaches. Internal braincase images were obtained using high-resolution computerized tomography scans. A principal components analysis identified that the first component axis was primarily associated with size and did not show groupings that divide the specimens by phylogenetic affinity. Sliding semi-landmarks and a relative warp analysis indicate that a unique Eustachian morphology separates Gavialis from other extant members of Crocodylia. Ontogenetic expansion of the braincase results in a more dorsoventrally elongate median Eustachian canal. Changes in the shape of the Eustachian system do provide phylogenetic distinctions between major crocodylian clades. Each morphometric dataset, consisting of continuous morphological characters, was added independently to a combined cladistic analysis of discrete morphological and molecular characters. The braincase data alone produced a clade that included crocodylids and Gavialis, whereas the Eustachian data resulted in Gavialis being considered a basally divergent lineage. When each morphometric dataset was used in a combined analysis with discrete morphological and molecular characters, it generated a tree that matched the topology of the molecular phylogeny of Crocodylia.     

Dietary Ecology of Murinae (Muridae,Rodentia): A Geometric Morphometric Approach

Murine rodents represent a highly diverse group, which displays great ecological versatility. In the present paper we analyse the relationship between dental morphology, on one hand, using geometric morphometrics based upon the outline of first upper molar and the dietary preference of extant murine genera, on the other. This ecomorphological study of extant murine rodents demonstrates that dietary groups can be distinguished with the use of a quantitative geometric morphometric approach based on first upper molar outline. A discriminant analysis of the geometric morphometric variables of the first upper molars enables us to infer the dietary preferences of extinct murine genera from the Iberian Peninsula. Most of the extinct genera were omnivore; only Stephanomys showed a pattern of dental morphology alike that of the herbivore genera.     

中华姬鼠与大林姬鼠头骨的几何形态学研究

中华姬鼠Apodemus draco和大林姬鼠A.peninsulae形态与习性相似,北京地区的这两种鼠都存在还是只有大林姬鼠存在一直存在争议.通过新兴的几何形态测量技术对北京地区捕获的137只姬鼠头骨与黑龙汀的9只大林姬鼠头骨进行背面和侧面的形态对比分析.系统聚类分析结果、主成分分析结果和判别函数分析结果显示,北京地...     

QuorUM: An Error Corrector for Illumina Reads

Motivation

Illumina Sequencing data can provide high coverage of a genome by relatively short (most often 100 bp to 150 bp) reads at a low cost. Even with low (advertised 1%) error rate, 100 × coverage Illumina data on average has an error in some read at every base in the genome. These errors make handling the data more complicated because they result in a large number of low-count erroneous k-mers in the reads. However, there is enough information in the reads to correct most of the sequencing errors, thus making subsequent use of the data (e.g. for mapping or assembly) easier. Here we use the term “error correction” to denote the reduction in errors due to both changes in individual bases and trimming of unusable sequence. We developed an error correction software called QuorUM. QuorUM is mainly aimed at error correcting Illumina reads for subsequent assembly. It is designed around the novel idea of minimizing the number of distinct erroneous k-mers in the output reads and preserving the most true k-mers, and we introduce a composite statistic π that measures how successful we are at achieving this dual goal. We evaluate the performance of QuorUM by correcting actual Illumina reads from genomes for which a reference assembly is available.

Results

We produce trimmed and error-corrected reads that result in assemblies with longer contigs and fewer errors. We compared QuorUM against several published error correctors and found that it is the best performer in most metrics we use. QuorUM is efficiently implemented making use of current multi-core computing architectures and it is suitable for large data sets (1 billion bases checked and corrected per day per core). We also demonstrate that a third-party assembler (SOAPdenovo) benefits significantly from using QuorUM error-corrected reads. QuorUM error corrected reads result in a factor of 1.1 to 4 improvement in N50 contig size compared to using the original reads with SOAPdenovo for the data sets investigated.

Availability

QuorUM is distributed as an independent software package and as a module of the MaSuRCA assembly software. Both are available under the GPL open source license at http://www.genome.umd.edu.

Contact

ude.dmu@siacramg.     

A Geometric Morphometric Analysis of Geographic Mandibular Variation in the Dwarf Gerbil Gerbillus nanus (Gerbillinae,Rodentia)

Journal of Mammalian Evolution - Previous studies have demonstrated the pliability and adaptability of mammalian mandibles in response to different ecological demands such as food availability. The...     

Getting into Shape: An Empirical Comparison of Traditional Truss-Based Morphometric Methods with a Newer Geometric Method Applied to New World Cichlids

Body shape is a difficult, but important, trait to quantify. Researchers have traditionally used multivariate analysis of several linear measures ('trusses') across the body form to quantify shape. Newer geometric morphometric methods claim to better estimate shape because they analyze the geometry among the locations of all landmarks simultaneously rather than the linear distances between pairs of landmarks. We tested this claim by comparing the results of several traditional morphometric analyses against a newer geometric analysis involving thin-plate splines (TPS), all applied to a common data set of morphologically variable new world cichlids Amphilophus citrinellus and A. zaliosus. The TPS method yielded slightly stronger evidence of morphological differences among forms, although traditional methods also distinguished the two species. Perhaps our most important result was the idiosyncratic interpretation of shape variation among the traditional truss-based methods, whereas the generation of deformation grids using the TPS approach yielded clear and visually interpretable figures. Our results indicate that geometric morphometrics can be a more effective way to analyze and interpret body form, but also that traditional methods can be relied upon to provide statistical evidence of shape differences, although not necessarily accurate information about the nature of variation in shape.     

Brain Deactivation in the Outperformance in Bimodal Tasks: An fMRI Study

While it is known that some individuals can effectively perform two tasks simultaneously, other individuals cannot. How the brain deals with performing simultaneous tasks remains unclear. In the present study, we aimed to assess which brain areas corresponded to various phenomena in task performance. Nineteen subjects were requested to sequentially perform three blocks of tasks, including two unimodal tasks and one bimodal task. The unimodal tasks measured either visual feature binding or auditory pitch comparison, while the bimodal task required performance of the two tasks simultaneously. The functional magnetic resonance imaging (fMRI) results are compatible with previous studies showing that distinct brain areas, such as the visual cortices, frontal eye field (FEF), lateral parietal lobe (BA7), and medial and inferior frontal lobe, are involved in processing of visual unimodal tasks. In addition, the temporal lobes and Brodmann area 43 (BA43) were involved in processing of auditory unimodal tasks. These results lend support to concepts of modality-specific attention. Compared to the unimodal tasks, bimodal tasks required activation of additional brain areas. Furthermore, while deactivated brain areas were related to good performance in the bimodal task, these areas were not deactivated where the subject performed well in only one of the two simultaneous tasks. These results indicate that efficient information processing does not require some brain areas to be overly active; rather, the specific brain areas need to be relatively deactivated to remain alert and perform well on two tasks simultaneously. Meanwhile, it can also offer a neural basis for biofeedback in training courses, such as courses in how to perform multiple tasks simultaneously.     

Bat Species Comparisons Based on External Morphology: A Test of Traditional versus Geometric Morphometric Approaches

External morphology is commonly used to identify bats as well as to investigate flight and foraging behavior, typically relying on simple length and area measures or ratios. However, geometric morphometrics is increasingly used in the biological sciences to analyse variation in shape and discriminate among species and populations. Here we compare the ability of traditional versus geometric morphometric methods in discriminating between closely related bat species – in this case European horseshoe bats (Rhinolophidae, Chiroptera) – based on morphology of the wing, body and tail. In addition to comparing morphometric methods, we used geometric morphometrics to detect interspecies differences as shape changes. Geometric morphometrics yielded improved species discrimination relative to traditional methods. The predicted shape for the variation along the between group principal components revealed that the largest differences between species lay in the extent to which the wing reaches in the direction of the head. This strong trend in interspecific shape variation is associated with size, which we interpret as an evolutionary allometry pattern.     

Protocol for Three-dimensional Confocal Morphometric Analysis of Astrocytes

As glial cells in the brain, astrocytes have diverse functional roles in the central nervous system. In the presence of harmful stimuli, astrocytes modify their functional and structural properties, a condition called reactive astrogliosis. Here, a protocol for assessment of the morphological properties of astrocytes is presented. This protocol includes quantification of 12 different parameters i.e. the surface area and volume of the tissue covered by an astrocyte (astrocyte territory), the entire astrocyte including branches, cell body, and nucleus, as well as total length and number of branches, the intensity of fluorescence immunoreactivity of antibodies used for astrocyte detection, and astrocyte density (number/1,000 µm²). For this purpose three-dimensional (3D) confocal microscopic images were created, and 3D image analysis software such as Volocity 6.3 was used for measurements. Rat brain tissue exposed to amyloid beta_1-40 (Aβ_1-40) with or without a therapeutic intervention was used to present the method. This protocol can also be used for 3D morphometric analysis of other cells from either in vivo or in vitro conditions.