Morphological and morphometric aspects of early life stages of piabanha Brycon gouldingi (Characidae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Histochemical and morphological features of biopsied and stripped oocytes from the Brazilian endangered teleost pirapitinga, Brycon nattereri (Characiformes)

The aim of the present study was to characterize biopsied and stripped oocytes from the Brazilian endangered teleost pirapitinga (Brycon nattereri) using histochemical and morphological analyses. Biopsied oocytes had a mean diameter of 2.225 mm (modal diameter: 2.312 mm), complete vitellogenesis and a central or slightly eccentric nucleus. Neutral polysaccharides were detected in the follicular cells, zona radiata and yolk globules, while acidic polysaccharides were detected in the follicular cells and cortical alveoli. Ten out of the 19 females treated with two doses of carp pituitary extract (cPE) released oocytes, which were also analysed. Stripping occurred 292 +/- 39 degree-hours after the second dose of cPE and led to a mean spawning weight of 36.2 g, 10% spawning index, 241 oocytes/g of ova, 8222 oocytes/female and 23 oocytes/g of body weight. Stripped oocytes had a mean diameter of 2.33 mm and a mode at 2.375 mm, were weakly adhesive and coloration ranged from wine to brown. Under scanning electron microscopy, stripped oocytes exhibited a single funnel-shaped micropyle located at the animal pole and a zona radiata that measured 7.7 m in thickness with eight pore canals/m(2). Oocyte morphology in Brycon nattereri is similar to that found in other species of the genus, except for the larger size and weaker adhesiveness. These findings provide essential information for a better understanding of the reproductive biology of B. nattereri and the establishment of conservation measures for this threatened species.

Morphological caste studies in the neotropical swarm-founding polistinae wasp Angiopolybia pattern (Lepeletier) (hymenoptera: Vespidae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Morphological patterns and community organization in leaf-litter ant assemblages

We present a new approach to determine the number and composition of guilds, using the hyperdiverse leaf-litter ant fauna as a model, based on appropriate morphological variables and species co-occurrence null models to describe the complex assemblages of interacting Species Community structure at the 1-m(2) scale. We obtained 18 linear morphometric measures from 949 workers of 171 leaf-litter ant species (18762 measurements) surveyed in four Atlantic Forest localities to test whether the assemblages are morphologically structured; the morphological characters were selected to indicate diet and foraging habits. Principal components analysis was used to characterize the morphospace and to describe the guild structure (number of species and composition). The guild proportionality assembly rule (significant tendency toward constant proportion of species in guilds) was assessed at the 1-m(2) scale. Our analysis indicates that the division of leaf-litter ants into guilds is based mainly on microhabitat distribution in the leaf-litter, body size and shape, eye size, and phylogeny. The same guild scheme applied to four more sites shows that different Atlantic Forest areas have the same leaf-fitter ant guilds. The guild proportionality assembly rule was confirmed for most guilds, Suggesting that there are guild-specific limitations on species coexistence within assemblages; on the other hand, in a few cases the variance in guild proportion was greater than expected under the null assumptions. Other studies on ant functional group classification are partially supported by our quantitative morphological analysis. Our results, however, imply that there are more compartments than indicated in previous models, particularly among cryptic species (confined to soil and litter) and tropical climate specialists. We argue that a general null model for the analysis of species association based oil morphology can reveal objectively defined groups and may thus contribute to a robust theory to explain community structure in general and have important consequences on studies of litter ant community ecology in particular.

The Ecological Basis for Biogeographic Classification: an Example in Orchid Bees (Apidae: Euglossini)

Biogeography has been difficult to apply as a methodological approach because organismic biology is incomplete at levels where the process of formulating comparisons and analogies is complex. The study of insect biogeography became necessary because insects possess numerous evolutionary traits and play an important role as pollinators. Among insects, the euglossine bees, or orchid bees, attract interest because the study of their biology allows us to explain important steps in the evolution of social behavior and many other adaptive tradeoffs. We analyzed the distribution of morphological characteristics in Colombian orchid bees from an ecological perspective. The aim of this study was to observe the distribution of these attributes on a regional basis. Data corresponding to Colombian euglossine species were ordered with a correspondence analysis and with subsequent hierarchical clustering. Later, and based on community proprieties, we compared the resulting hierarchical model with the collection localities to seek to identify a biogeographic classification pattern. From this analysis, we derived a model that classifies the territory of Colombia into 11 biogeographic units or natural clusters. Ecological assumptions in concordance with the derived classification levels suggest that species characteristics associated with flight performance, nectar uptake, and social behavior are the factors that served to produce the current geographical structure.

A New Subgeneric Classification of Rhipsalis (Cactoideae, Cactaceae)

Most Cactaceae have succulent stems and inhabit dry or arid areas, but some are epiphytes of humid regions. Rhipsalis is the largest genus of epiphytic cacti. Species of Rhipsalis are notoriously difficult to identify, and the subgeneric classification of the genus has remained controversial. Between 1837 and 1995, eight different subgeneric classifications have been proposed for Rhipsalis. The most comprehensive taxonomic treatment of the genus recognized five subgenera, Phyllarthrorhipsalis, Rhipsalis, Epallagogonium, Calamorhipsalis, and Erythrorhipsalis, characterized mainly by stem morphology. Here, molecular phylogenetic information combined with morphological data is used to re-evaluate the former subgeneric classifications proposed for the genus. Three monophyletic subgenera are recognized, Rhipsalis, Calamorhipsalis and Erythrorhipsalis, which are mainly characterized by floral traits. The changes proposed include expanding the circumscription of Rhipsalis by the inclusion of species previously included in Phyllarthrorhipsalis and Epallagogoniwn and recognizing a broader Calamorhipsalis, also including species from subgenus Epallagogonium. The circumscription of Erythrorhipsalis remains unchanged. For each subgenus a list of synonyms, a brief description and a list of species included are presented. A key for the identification of subgenera is also provided.

Image analysis in the morphological and morphometric study of teeth

The subject of this doctoral dissertation concerns the definition of a new methodology for the morphological and morphometric study of fossilized human teeth, and therefore strives to provide a contribution to the reconstruction of human evolutionary history that proposes to extend to the different species of hominid fossils. Standardized investigative methodologies are lacking both regarding the orientation of teeth subject to study and in the analysis that can be carried out on these teeth once they are oriented. The opportunity to standardize a primary analysis methodology is furnished by the study of certain early Neanderthal and preneanderthal molars recovered in two caves in southern Italy [Grotta Taddeo (Taddeo Cave) and Grotta del Poggio (Poggio Cave), near Marina di Camerata, Campania]. To these we can add other molars of Neanderthal and modern man of the upper Paleolithic era, specifically scanned in the paleoanthropology laboratory of the University of Arkansas (Fayetteville, Arkansas, USA), in order to increase the paleoanthropological sample data and thereby make the final results of the analyses more significant. The new analysis methodology is rendered as follows: 1. Standardization of an orientation system for primary molars (superior and inferior), starting from a scan of a sample of 30 molars belonging to modern man (15 M1 inferior and 15 M1 superior), the definition of landmarks, the comparison of various systems and the choice of a system of orientation for each of the two dental typologies. 2. The definition of an analysis procedure that considers only the first 4 millimeters of the dental crown starting from the collar: 5 sections parallel to the plane according to which the tooth has been oriented are carried out, spaced 1 millimeter between them. The intention is to determine a method that allows for the differentiation of fossilized species even in the presence of worn teeth. 3. Results and Conclusions. The new approach to the study of teeth provides a considerable quantity of information that can better be evaluated by increasing the fossil sample data. It has been demonstrated to be a valid tool in evolutionary classification that has allowed (us) to differentiate the Neanderthal sample from that of modern man. In a particular sense the molars of Grotta Taddeo, which up until this point it has not been possible to determine with exactness their species of origin, through the present research they are classified as Neanderthal.

Development of a new galaxy classification technique and its application to the zCOSMOS survey

The purpose of this Thesis is to develop a robust and powerful method to classify galaxies from large surveys, in order to establish and confirm the connections between the principal observational parameters of the galaxies (spectral features, colours, morphological indices), and help unveil the evolution of these parameters from $z \sim 1$ to the local Universe. Within the framework of zCOSMOS-bright survey, and making use of its large database of objects ($\sim 10\,000$ galaxies in the redshift range $0 < z \lesssim 1.2$) and its great reliability in redshift and spectral properties determinations, first we adopt and extend the \emph{classification cube method}, as developed by Mignoli et al. (2009), to exploit the bimodal properties of galaxies (spectral, photometric and morphologic) separately, and then combining together these three subclassifications. We use this classification method as a test for a newly devised statistical classification, based on Principal Component Analysis and Unsupervised Fuzzy Partition clustering method (PCA+UFP), which is able to define the galaxy population exploiting their natural global bimodality, considering simultaneously up to 8 different properties. The PCA+UFP analysis is a very powerful and robust tool to probe the nature and the evolution of galaxies in a survey. It allows to define with less uncertainties the classification of galaxies, adding the flexibility to be adapted to different parameters: being a fuzzy classification it avoids the problems due to a hard classification, such as the classification cube presented in the first part of the article. The PCA+UFP method can be easily applied to different datasets: it does not rely on the nature of the data and for this reason it can be successfully employed with others observables (magnitudes, colours) or derived properties (masses, luminosities, SFRs, etc.). The agreement between the two classification cluster definitions is very high. ``Early'' and ``late'' type galaxies are well defined by the spectral, photometric and morphological properties, both considering them in a separate way and then combining the classifications (classification cube) and treating them as a whole (PCA+UFP cluster analysis). Differences arise in the definition of outliers: the classification cube is much more sensitive to single measurement errors or misclassifications in one property than the PCA+UFP cluster analysis, in which errors are ``averaged out'' during the process. This method allowed us to behold the \emph{downsizing} effect taking place in the PC spaces: the migration between the blue cloud towards the red clump happens at higher redshifts for galaxies of larger mass. The determination of $M_{\mathrm{cross}}$ the transition mass is in significant agreement with others values in literature.

Time-lapse microscopy and classification of 2D human mesenchymal stem cells based on cell shape picks up myogenic from osteogenic and adipogenic differentiation

Current methods to characterize mesenchymal stem cells (MSCs) are limited to CD marker expression, plastic adherence and their ability to differentiate into adipogenic, osteogenic and chondrogenic precursors. It seems evident that stem cells undergoing differentiation should differ in many aspects, such as morphology and possibly also behaviour; however, such a correlation has not yet been exploited for fate prediction of MSCs. Primary human MSCs from bone marrow were expanded and pelleted to form high-density cultures and were then randomly divided into four groups to differentiate into adipogenic, osteogenic chondrogenic and myogenic progenitor cells. The cells were expanded as heterogeneous and tracked with time-lapse microscopy to record cell shape, using phase-contrast microscopy. The cells were segmented using a custom-made image-processing pipeline. Seven morphological features were extracted for each of the segmented cells. Statistical analysis was performed on the seven-dimensional feature vectors, using a tree-like classification method. Differentiation of cells was monitored with key marker genes and histology. Cells in differentiation media were expressing the key genes for each of the three pathways after 21 days, i.e. adipogenic, osteogenic and chondrogenic, which was also confirmed by histological staining. Time-lapse microscopy data were obtained and contained new evidence that two cell shape features, eccentricity and filopodia (= 'fingers') are highly informative to classify myogenic differentiation from all others. However, no robust classifiers could be identified for the other cell differentiation paths. The results suggest that non-invasive automated time-lapse microscopy could potentially be used to predict the stem cell fate of hMSCs for clinical application, based on morphology for earlier time-points. The classification is challenged by cell density, proliferation and possible unknown donor-specific factors, which affect the performance of morphology-based approaches. Copyright © 2012 John Wiley & Sons, Ltd.

The canine hair cycle - a guide for the assessment of morphological and immunohistochemical criteria

The hair follicle has a lifelong capacity to cycle through recurrent phases of controlled growth (anagen), regression (catagen) and quiescence (telogen), each associated with specific morphological changes. A comprehensive classification scheme is available for mice to distinguish the cycle stages anagen I-VI, catagen I-VIII and telogen. For dogs, such a classification system does not exist, although alopecia associated with hair cycle arrest is common. We applied analogous morphological criteria and various staining techniques to subdivide the canine hair cycle stages to the same extent as has been done in mice. Of all the staining techniques applied, haematoxylin and eosin stain, Sacpic, Masson Fontana and immunohistochemistry for vimentin and laminin proved to be most useful. To evaluate the applicability of our criteria, we investigated skin biopsies from healthy beagle dogs (n=20; biopsies from shoulder and thigh) kept in controlled conditions. From each biopsy, at least 50 hair follicles were assessed. Statistical analysis revealed that 30% of the follicles were in anagen (12% early and 18% late), 8% in catagen (2% early, 5% late and 1% not determinable) and 27% in telogen. Thirty-five per cent of hair follicles could not be assigned to a specific cycle stage because not all follicles within one biopsy were oriented perfectly. In conclusion, this guide will not only be helpful for the investigation of alopecic disorders and possibly their pathogenesis, but may also serve as a basis for research projects in which the comparison of hair cycle stages is essential, e.g. comparative analysis of gene expression patterns.

Defined morphological criteria allow reliable diagnosis of colorectal serrated polyps and predict polyp genetics.

Criteria for the diagnosis of serrated colorectal lesions (hyperplastic polyp, sessile serrated adenoma without or with dysplasia--which we called mixed polyp--and traditional serrated adenoma) for which consensus has been reached should be validated for applicability in daily practice in terms of inter-observer reproducibility and their association with clinical features and (epi)genetic events. A study set was created from a consecutive series of colorectal polyps (n = 1,926) by selecting all sessile serrated adenomas, traditional serrated adenomas and mixed polyps. We added consecutive series of hyperplastic polyps, classical adenomas and normal mucosa samples for a total of 200 specimens. With this series, we conducted an inter-observer study, encompassing ten pathologists with gastrointestinal pathology experience from five European countries, in three rounds in which all cases were microscopically evaluated. An assessment of single morphological criteria was included, and these were correlated with clinical parameters and the mutation status of KRAS, BRAF and PIK3CA and the methylation status of MLH1. Gender, age and localisation were significantly associated with certain types of lesions. Kappa statistics revealed moderate to good inter-observer agreement for polyp classification (κ = 0.56 to 0.63), but for single criteria, this varied considerably (κ = 0.06 to 0.82). BRAF mutations were frequently found in hyperplastic polyps (86 %, 62/72) and sessile serrated adenomas (80 %, 41/51). KRAS mutations occurred more frequently in traditional serrated adenomas (78 %, 7/9) and less so in classical adenomas (20 %, 10/51). Single morphological criteria for sessile serrated adenomas showed significant correlation with BRAF mutation (all p ≤ 0.001), and those for classical adenomas or traditional serrated adenoma correlated significantly with KRAS mutation (all p < 0.001). Therefore, single well-defined morphological criteria are predictive for genetic alterations in colorectal polyps.

Pinus nigra (European black pine) as the dominant species of the last glacial pinewoods in south-western to central Iberia: a morphological study of modern and fossil pollen

Aim Our aim was to discriminate different species of Pinus via pollen analysis in order to assess the responses of particular pine species to orbital and millennial-scale climate changes, particularly during the last glacial period. Location Modern pollen grains were collected from current pine populations along transects from the Pyrenees to southern Iberia and the Balearic Islands. Fossil pine pollen was recovered from the south-western Iberian margin core MD95-2042. Methods We measured a set of morphological traits of modern pollen from the Iberian pine species Pinus nigra, P. sylvestris, P. halepensis, P. pinea and P. pinaster and of fossil pine pollen from selected samples of the last glacial period and the early to mid-Holocene. Classification and regression tree (CART) analysis was used to establish a model from the modern dataset that discriminates pollen from the different pine species and allows identification of fossil pine pollen at the species level. Results The CART model was effective in separating pollen of P. nigra and P. sylvestris from that of the Mediterranean pine group (P. halepensis, P. pinea and P. pinaster). The pollen of Pinus nigra diverged from that of P. sylvestris by having a more flattened corpus. Predictions using this model suggested that fossil pine pollen is mainly from P. nigra in all the samples analysed. Pinus sylvestris was more abundant in samples from Greenland stadials than Heinrich stadials, whereas Mediterranean pines increased in samples from Greenland interstadials and during the early to mid-Holocene. Main conclusions Morphological parameters can be successfully used to increase the taxonomic resolution of fossil pine pollen at the species level for the highland pines (P. nigra and P. sylvestris) and at the group of species level for the Mediterranean pines. Our study indicates that P. nigra was the dominant component of the last glacial south-western/central Iberian pinewoods, although the species composition of these woodlands varied in response to abrupt climate changes.

Morphological variation within the diatom taxon Cyclotella comensis and its importance for quantitative temperature reconstructions

1. The morphologically complex taxon Cyclotella comensis Grunow had no clear relationship with environmental parameters in a study using sediment surface samples from the Swiss Alps. The morphological heterogeneity of the taxon was investigated by applying a principal component analysis (PCA) to 9000 presence/absence descriptions of valves from surface samples of six lakes from different altitudes (15 characteristics, 100 valves each lake). The PCA allowed the classification of six morphs, which differed mainly in size and length of striae. Photographs of the morphs are shown in this paper. 2. Sixty-eight sediment surface samples were analysed using these newly defined six morphs. Summer temperature explained a major part of the variance between the morphs as assessed by a redundancy analysis (RDA). Summer temperature optima and tolerances were estimated using weighted averaging. 3. The influence of the revised C. comensis taxonomy on the diatom inferred summer temperature of a high alpine lake is discussed in a multiproxy context for the past 800 years.

Classification of coral reef types in Torres Strait (GIS files in zip-archive 319 kB)

Coral reefs represent major accumulations of calcium carbonate (CaCO3). The particularly labyrinthine network of reefs in Torres Strait, north of the Great Barrier Reef (GBR), has been examined in order to estimate their gross CaCO3 productivity. The approach involved a two-step procedure, first characterising and classifying the morphology of reefs based on a classification scheme widely employed on the GBR and then estimating gross CaCO3 productivity rates across the region using a regional census-based approach. This was undertaken by independently verifying published rates of coral reef community gross production for use in Torres Strait, based on site-specific ecological and morphological data. A total of 606 reef platforms were mapped and classified using classification trees. Despite the complexity of the maze of reefs in Torres Strait, there are broad morphological similarities with reefs in the GBR. The spatial distribution and dimensions of reef types across both regions are underpinned by similar geological processes, sea-level history in the Holocene and exposure to the same wind/wave energetic regime, resulting in comparable geomorphic zonation. However, the presence of strong tidal currents flowing through Torres Strait and the relatively shallow and narrow dimensions of the shelf exert a control on local morphology and spatial distribution of the reef platforms. A total amount of 8.7 million tonnes of CaCO3 per year, at an average rate of 3.7 kg CaCO3 m-2 yr-1 (G), were estimated for the studied area. Extrapolated production rates based on detailed and regional census-based approaches for geomorphic zones across Torres Strait were comparable to those reported elsewhere, particularly values for the GBR based on alkalinity-reduction methods. However, differences in mapping methodologies and the impact of reduced calcification due to global trends in coral reef ecological decline and changing oceanic physical conditions warrant further research. The novel method proposed in this study to characterise the geomorphology of reef types based on classification trees provides an objective and repeatable data-driven approach that combined with regional census-based approaches has the potential to be adapted and transferred to different coral reef regions, depicting a more accurate picture of interactions between reef ecology and geomorphology.

Morphological, chemical and physical characteristics of cryosolic soils from Arctic Canada

Cryosols are permafrost-affected soils whose genesis is dominated by cryogenic processes, resulting in unique macromorphologies, micromorphologies, thermal characteristics, and physical and chemical properties. In addition, these soils are carbon sinks, storing high amounts of organic carbon collected for thousands of years. In the Canadian soil classification, the Cryosolic Order includes mineral and organic soils that have both cryogenic properties and permafrost within 1 or 2 m of the soil surface. This soil order is divided into Turbic, Static and Organic great groups on the basis of the soil materials (mineral or organic), cryogenic properties and depth to permafrost. The great groups are subdivided into subgroups on the basis of soil development and the resulting diagnostic soil horizons. Cryosols are commonly associated with the presence of ground ice in the subsoil. This causes serious problems when areas containing these soils are used for agriculture and construction projects (such as roads, town sites and airstrips). Therefore, where Cryosols have high ice content, it is especially important either to avoid these activities or to use farming and construction methods that maintain the negative thermal balance.