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The Middle Miocene Ape Pierolapithecus catalaunicus Exhibits Extant Great Ape-Like Morphometric Affinities on Its Patella: Inferences on Knee Function and Evolution  [PDF]
Marta Pina, Sergio Almécija, David M. Alba, Matthew C. O'Neill, Salvador Moyà-Solà
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0091944
Abstract: The mosaic nature of the Miocene ape postcranium hinders the reconstruction of the positional behavior and locomotion of these taxa based on isolated elements only. The fossil great ape Pierolapithecus catalaunicus (IPS 21350 skeleton; 11.9 Ma) exhibits a relatively wide and shallow thorax with moderate hand length and phalangeal curvature, dorsally-oriented metacarpophalangeal joints, and loss of ulnocarpal articulation. This evidence reveals enhanced orthograde postures without modern ape-like below-branch suspensory adaptations. Therefore, it has been proposed that natural selection enhanced vertical climbing (and not suspension per se) in Pierolapithecus catalaunicus. Although limb long bones are not available for this species, its patella (IPS 21350.37) can potentially provide insights into its knee function and thus on the complexity of its total morphological pattern. Here we provide a detailed description and morphometric analyses of IPS 21350.37, which are based on four external dimensions intended to capture the overall patellar shape. Our results reveal that the patella of Pierolapithecus is similar to that of extant great apes: proximodistally short, mediolaterally broad and anteroposteriorly thin. Previous biomechanical studies of the anthropoid knee based on the same measurements proposed that the modern great ape patella reflects a mobile knee joint while the long, narrow and thick patella of platyrrhine and especially cercopithecoid monkeys would increase the quadriceps moment arm in knee extension during walking, galloping, climbing and leaping. The patella of Pierolapithecus differs not only from that of monkeys and hylobatids, but also from that of basal hominoids (e.g., Proconsul and Nacholapithecus), which display slightly thinner patellae than extant great apes (the previously-inferred plesiomorphic hominoid condition). If patellar shape in Pierolapithecus is related to modern great ape-like knee function, our results suggest that increased knee mobility might have originally evolved in relation to enhanced climbing capabilities in great apes (such as specialized vertical climbing).
Facial Morphogenesis of the Earliest Europeans  [PDF]
Rodrigo S. Lacruz, José María Bermúdez de Castro, María Martinón-Torres, Paul O’Higgins, Michael L. Paine, Eudald Carbonell, Juan Luis Arsuaga, Timothy G. Bromage
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0065199
Abstract: The modern human face differs from that of our early ancestors in that the facial profile is relatively retracted (orthognathic). This change in facial profile is associated with a characteristic spatial distribution of bone deposition and resorption: growth remodeling. For humans, surface resorption commonly dominates on anteriorly-facing areas of the subnasal region of the maxilla and mandible during development. We mapped the distribution of facial growth remodeling activities on the 900–800 ky maxilla ATD6-69 assigned to H. antecessor, and on the 1.5 My cranium KNM-WT 15000, part of an associated skeleton assigned to African H. erectus. We show that, as in H. sapiens, H. antecessor shows bone resorption over most of the subnasal region. This pattern contrasts with that seen in KNM-WT 15000 where evidence of bone deposition, not resorption, was identified. KNM-WT 15000 is similar to Australopithecus and the extant African apes in this localized area of bone deposition. These new data point to diversity of patterns of facial growth in fossil Homo. The similarities in facial growth in H. antecessor and H. sapiens suggest that one key developmental change responsible for the characteristic facial morphology of modern humans can be traced back at least to H. antecessor.
The Coefficient of Covariation  [PDF]
S. M. Seeletse
Journal of Applied Sciences , 2001,
Abstract: The coefficient of Variation (CV) measures the closeness of observed values of a phenomenon, and is limited to data sets of univariate random variables. This article introduces a CV extension to multivariate cases, a measure which we shall call the coefficient of covariation (CCV). The CCV comes in the form of a matrix, the diagonal elements of which are the CVs. The off-diagonal elements of the CCV matrix are CV generalisations derived from covariances and means of the two involved variables. CV measures of the closeness of elements of single data set, and the CCV is intended to measure the closeness of data sets.
The Mandibular Landmarks about the Facial Artery and Vein with Multidetector Computed Tomography Angiography (MDCTA): an Anatomical and Radiological Morphometric Study
Cicekcibasi,Aynur Emine; Yilmaz,Mehmet Tugrul; Kiresi,Demet; Seker,Muzaffer;
International Journal of Morphology , 2012, DOI: 10.4067/S0717-95022012000200024
Abstract: the aim of this study was to investigate the course of the facial vessels according to several mandibular landmarks in living individuals using multidetector computed tomography angiography (mdcta) to determine these related to sex and side. this study was conducted in the radiology department, meram faculty of medicine, necmettin erbakan university (konya, turkey). in total, sixty faces from 30 specimens (15 males and 15 females) with symptoms and signs of vascular disease were evaluated for the facial vessels by mdcta scan. the facial vessel parameters were measured according to the reference points (mandibular angle, mental protuberance, mental foramen and facial midline). the distance from the point at which the facial artery first appears in the lower margin of the mandible to the mandibular angle for right and left facial artery were observed as 3.53±0.66 cm and 3.31±0.73 cm in males, respectively. these distances were determined as 2.91±0.52 cm and 3.35±0.48 cm in females. mdcta is a new, powerful, safe and noninvasive test to demonstrate the vasculature of the head. bony structures and neighboring vessel morphology can be evaluated by this technique in cases of trauma with suspected vessel injuries and when considering patient selection for flap surgery.
Does Sympathy Motivate Prosocial Behaviour in Great Apes?  [PDF]
Katja Liebal, Amrisha Vaish, Daniel Haun, Michael Tomasello
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0084299
Abstract: Prosocial behaviours such as helping, comforting, or sharing are central to human social life. Because they emerge early in ontogeny, it has been proposed that humans are prosocial by nature and that from early on empathy and sympathy motivate such behaviours. The emerging question is whether humans share these abilities to feel with and for someone with our closest relatives, the great apes. Although several studies demonstrated that great apes help others, little is known about their underlying motivations. This study addresses this issue and investigates whether four species of great apes (Pongo pygmaeus, Gorilla gorilla, Pan troglodytes, Pan paniscus) help a conspecific more after observing the conspecific being harmed (a human experimenter steals the conspecific’s food) compared to a condition where no harming occurred. Results showed that in regard to the occurrence of prosocial behaviours, only orangutans, but not the African great apes, help others when help is needed, contrasting prior findings on chimpanzees. However, with the exception of one population of orangutans that helped significantly more after a conspecific was harmed than when no harm occurred, prosocial behaviour in great apes was not motivated by concern for others.
Shared Pattern of Endocranial Shape Asymmetries among Great Apes, Anatomically Modern Humans, and Fossil Hominins  [PDF]
Antoine Balzeau, Emmanuel Gilissen, Dominique Grimaud-Hervé
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0029581
Abstract: Anatomical asymmetries of the human brain are a topic of major interest because of their link with handedness and cognitive functions. Their emergence and occurrence have been extensively explored in human fossil records to document the evolution of brain capacities and behaviour. We quantified for the first time antero-posterior endocranial shape asymmetries in large samples of great apes, modern humans and fossil hominins through analysis of “virtual” 3D models of skull and endocranial cavity and we statistically test for departures from symmetry. Once based on continuous variables, we show that the analysis of these brain asymmetries gives original results that build upon previous analysis based on discrete traits. In particular, it emerges that the degree of petalial asymmetries differs between great apes and hominins without modification of their pattern. We indeed demonstrate the presence of shape asymmetries in great apes, with a pattern similar to modern humans but with a lower variation and a lower degree of fluctuating asymmetry. More importantly, variations in the position of the frontal and occipital poles on the right and left hemispheres would be expected to show some degree of antisymmetry when population distribution is considered, but the observed pattern of variation among the samples is related to fluctuating asymmetry for most of the components of the petalias. Moreover, the presence of a common pattern of significant directional asymmetry for two components of the petalias in hominids implicates that the observed traits were probably inherited from the last common ancestor of extant African great apes and Homo sapiens. These results also have important implications for the possible relationships between endocranial shape asymmetries and functional capacities in hominins. It emphasizes the uncoupling between lateralized activities, some of them well probably distinctive to Homo, and large-scale cerebral lateralization itself, which is not unique to Homo.
-Geometric morphometric analysis of snout shape in extant ruminants (Ungulata, Artiodactyla)  [PDF]
Jonathan P. Tennant,Norman MacLeod
PeerJ , 2015, DOI: 10.7287/peerj.preprints.176v1
Abstract: Snout shape is a prominent aspect of herbivore feeding ecology, controlling both forage selectivity and intake rate. Many previous investigations have suggested that ruminant feeding classes can be discriminated via snout shape, with grazing and browsing species attributed ‘blunt’ and ‘pointed’ snouts respectively, with an intermediate sub-grouping. This aspect of functional ecology is analysed for the first time using a statistically rigorous geometry-based framework to compare the two-dimensional profiles of the premaxilla in ventral aspect for a large sample of ruminant species. Our results suggest that, when a sample of browsing and grazing ruminants are classified ecologically based on a range of independent indicators of their feeding strategy, they cannot be fully discriminated on the basis of their premaxilla profile shape. Instead, our sample forms a shape variation continuum with overlap between groupings, but with a 78 percent chance of successful categorisation. Moreover, previously used terminology such as ‘pointed’ and ‘blunt’ are largely inadequate for delimiting snout shape varieties, insofar as these terms lack the descriptive power to define the morphological disparity demonstrated. These results suggest that previous attempts to use snout shape as a proxy for feeding style in ruminants may have been biased due to under-sampling of this highly diverse group and to lack of geometric rigour in the assessment of shape data. Alternatively, conflicting or inadequate evidence in defining ‘browsers’ and ‘grazers’ could have caused incorrect assignment to ecological groups, distorting our analyses. The relation between snout shape and body mass are also documented.
On spectral distribution of high dimensional covariation matrices  [PDF]
Claudio Heinrich,Mark Podolskij
Mathematics , 2014,
Abstract: In this paper we present the asymptotic theory for spectral distributions of high dimensional covariation matrices of Brownian diffusions. More specifically, we consider $N$-dimensional Ito integrals with time varying matrix-valued integrands. We observe $n$ equidistant high frequency data points of the underlying Brownian diffusion and we assume that $N/n\rightarrow c\in (0,\infty)$. We show that under a certain mixed spectral moment condition the spectral distribution of the empirical covariation matrix converges in distribution almost surely. Our proof relies on method of moments and applications of graph theory.
Structural Constraints Identified with Covariation Analysis in Ribosomal RNA  [PDF]
Lei Shang, Weijia Xu, Stuart Ozer, Robin R. Gutell
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0039383
Abstract: Covariation analysis is used to identify those positions with similar patterns of sequence variation in an alignment of RNA sequences. These constraints on the evolution of two positions are usually associated with a base pair in a helix. While mutual information (MI) has been used to accurately predict an RNA secondary structure and a few of its tertiary interactions, early studies revealed that phylogenetic event counting methods are more sensitive and provide extra confidence in the prediction of base pairs. We developed a novel and powerful phylogenetic events counting method (PEC) for quantifying positional covariation with the Gutell lab’s new RNA Comparative Analysis Database (rCAD). The PEC and MI-based methods each identify unique base pairs, and jointly identify many other base pairs. In total, both methods in combination with an N-best and helix-extension strategy identify the maximal number of base pairs. While covariation methods have effectively and accurately predicted RNAs secondary structure, only a few tertiary structure base pairs have been identified. Analysis presented herein and at the Gutell lab’s Comparative RNA Web (CRW) Site reveal that the majority of these latter base pairs do not covary with one another. However, covariation analysis does reveal a weaker although significant covariation between sets of nucleotides that are in proximity in the three-dimensional RNA structure. This reveals that covariation analysis identifies other types of structural constraints beyond the two nucleotides that form a base pair.
Construction and use of gene expression covariation matrix
Jér?me Hennetin, Petri Pehkonen, Michel Bellis
BMC Bioinformatics , 2009, DOI: 10.1186/1471-2105-10-214
Abstract: We describe here how single-channel techniques can be treated like double-channel techniques and used to generate both gene expression changes and covariation measures. We also present a new method that allows the calculation of both positive and negative correlation coefficients between genes. First, we perform systematic comparisons between two given biological conditions and classify, for each comparison, genes as increased (I), decreased (D), or not changed (N). As a result, the original series of n gene expression level measures assigned to each gene is replaced by an ordered string of n(n-1)/2 symbols, e.g. IDDNNIDID....DNNNNNNID, with the length of the string corresponding to the number of comparisons. In a second step, positive and negative covariation matrices (CVM) are constructed by calculating statistically significant positive or negative correlation scores for any pair of genes by comparing their strings of symbols.This new method, applied to four different large data sets, has allowed us to construct distinct covariation matrices with similar properties. We have also developed a technique to translate these covariation networks into graphical 3D representations and found that the local assignation of the probe sets was conserved across the four chip set models used which encompass three different species (humans, mice, and rats). The application of adapted clustering methods succeeded in delineating six conserved functional regions that we characterized using Gene Ontology information.Since the introduction of microarray technology in the 1990s, a large number of data sets have been produced in the field of transcriptome profiling and made publicly accessible through specialised repositories like the Gene Expression Omnibus (GEO) at NIH[1,2] or ArrayExpress at EBI [3,4]. Based upon the massive analysis of these types of data, a number of different approaches have been taken to develop integrated knowledge about the coexpression of genes [5], to search
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