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.     

The evolution of cranial form and function in theropod dinosaurs: insights from geometric morphometrics

Theropod dinosaurs, an iconic clade of fossil species including Tyrannosaurus and Velociraptor, developed a great diversity of body size, skull form and feeding habits over their 160+ million year evolutionary history. Here, we utilize geometric morphometrics to study broad patterns in theropod skull shape variation and compare the distribution of taxa in cranial morphospace (form) to both phylogeny and quantitative metrics of biting behaviour (function). We find that theropod skulls primarily differ in relative anteroposterior length and snout depth and to a lesser extent in orbit size and depth of the cheek region, and oviraptorosaurs deviate most strongly from the "typical" and ancestral theropod morphologies. Noncarnivorous taxa generally fall out in distinct regions of morphospace and exhibit greater overall disparity than carnivorous taxa, whereas large-bodied carnivores independently converge on the same region of morphospace. The distribution of taxa in morphospace is strongly correlated with phylogeny but only weakly correlated with functional biting behaviour. These results imply that phylogeny, not biting function, was the major determinant of theropod skull shape.     

Shell geometric morphometrics in Biomphalaria glabrata (Mollusca: Planorbidae) uninfected and infected with Schistosoma mansoni

Freshwater planorbid mollusks belonging to the genus Biomphalaria act as intermediate hosts for Schistosoma mansoni,the etiological agent of human intestinal schistosomiasis,in the Neotropical Region.Identification ofBiomphalaria spp.are carried out based on morphological characters,and the Schistosoma infection are determined by the presence of cercariae (verified through microscope preparation and mounting).Recently,the geometric morphometrics has proven to be a useful tool for determining shape differences in disease vectors arthropods.Due to this,we used geometric morphometrics to determine Biomphalaria glabrata shell differences (shape and size)between uninfected and infected specimens.We digitalized 12 anatomical points over the shell left side (from umbilicus to the last whorl) by combining type Ⅰ and Ⅱ landmarks and sliding semilandmarks;the coordinates were aligned by generalized Procrustes analysis.Principal component analyses were implemented for examining main variation axes,and discriminant analysis for testing group membership significance.We found significant separation between infected and uninfected shell conformation.All specimens were 100％correctly classified.The main differences occur in the peristome.The Kruskal-Wallis test finds significant differences in shell isometric size among infected and uninfected specimens.These findings correspond to other studies of traditional morphometrics,that infected snails showed the reduction in shell size in contrast to those uninfected specimens.     

Geographic and gender shape differences in the carapace of Liocarcinus depurator (Brachyura: Portunidae) using geometric morphometrics and the influence of a digitizing method

The current work describes the use of geometric morphometrics in the study of the portunid crab Liocarcinus depurator carapace shape variation along the Mediterranean coast of Spain. As a first step, the differences in shape induced by digitizing the carapace with either a digital camera or a flat bed scanner were investigated. Carapace shape information inferred from the camera images proved different from that obtained from the scanner images. This difference was greater than any shape variation because of crab gender or sample location. Carapace shape was analysed using multiple analysis of covariance (with centroid size as a covariate) of the partial warps and uniform components indicating differences between genders and between sample location; however, significant three-way interaction implied that such differences were gender and location specific. Landmarks identifying carapace width, carapace length and posterior carapace width showed greatest variation; hence gender and location differences were further analysed through the interrelationships between these linear measures. Regression analysis of the relationship between posterior carapace width and the ratio of carapace width to carapace length indicated clear differences between locations but not between genders. Crabs from the Alborán Sea had proportionally wider posterior carapaces than those from Alicante or North Catalonia. This finding may represent the difference between a southern influx of an Atlantic population distinguishable from a more northerly Mediterranean one, which would be in agreement with the overall oceanographic surface circulation pattern in the western Mediterranean.     

Testing evolutionary stasis and trends in first lower molar shape of extinct Italian populations of Terricola savii (Arvicolidae,Rodentia) by means of geometric morphometrics

Extinct populations of Terricola savii have been investigated in order to analyse evolutionary stasis and correlation of first lower molar shape with climatic proxies by means of geometric morphometrics. Evolutionary stasis, its recognition and explanation are central topics in evolutionary paleobiology. In this study, tooth shape variation of the arvicolid T. savii has been analysed through time. In addition to explicit multivariate tests of stasis based on landmark and semi‐landmark geometric morphometrics, first lower molar M₁ shape has been decomposed in orthogonal axes of variation and tested for correlation with climate changes. Multivariate tests were consistent with evolutionary stasis. Yet, according to univariate tests, the dominant dimension of shape variation shows a temporal trend well correlated with a climatic proxy, i.e. δ¹⁸O. The remaining variation does not show any trend. Adaptation to current climatic condition might occur even without affecting shape as a whole. Phenotypic plasticity of this species could be invoked to explain evolutionary stasis, as a long time pattern.     

Detecting taxonomic signal in an under-utilised character system: geometric morphometrics of the forcipular coxae of Scutigeromorpha (Chilopoda)

To date, the forcipules have played almost no role in determining the systematics of scutigeromorph centipedes though in his 1974 review of taxonomic characters Markus Würmli suggested some potentially informative variation might be found in these structures. Geometric morphometric analyses were used to evaluate Würmli's suggestion, specifically to determine whether the shape of the forcipular coxa contains information useful for diagnosing species. The geometry of the coxae of eight species from the genera Sphendononema, Scutigera, Dendrothereua, Thereuonema, Thereuopoda, Thereuopodina, Allothereua and Parascutigera was characterised using a combination of landmark- and semi-landmark-based sampling methods to summarize group-specific morphological variation. Canonical variates analysis of shape data characterizing the forcipular coxae indicates that these structures differ significantly between taxa at various systematic levels. Models calculated for the canonical variates space facilitate identification of the main shape differences between genera, including overall length/width, curvature of the external coxal margin, and the extent to which the coxofemoral condyle projects laterally. Jackknifed discriminant function analysis demonstrates that forcipular coxal training-set specimens were assigned to correct species in 61% of cases on average, the most accurate assignments being those of Parascutigera (Parascutigera guttata) and Thereuonema (Thereuonema microstoma). The geographically widespread species Thereuopoda longicornis, Sphendononema guildingii, Scutigera coleoptrata, and Dendrothereua linceci exhibit the least diagnostic coxae in our dataset. Thereuopoda longicornis populations sampled from different parts of East and Southeast Asia were significantly discriminated from each other, suggesting that, in this case, extensive synonymy may be obscuring diagnosable inter-species coxal shape differences.     

The distribution of stream-dwelling triclads (Platyhelminthes) in North Wales

This paper presents information collected during a survey of stream-dwelling triclads in two CO ntrasted areas of North Wales. The first study area was located in Caernarvon-shire on the mainland of North Wales and included a mountainous region rising to over 1000 m with abundant cold springs. In contrast, the study area on the nearby island of Anglesey was characterized by relatively warm, slow-flowing streams passing through gently undulating land which did not rise above 153 m. The object of the survey was to collect background data so that suitable streams could be chosen for more intensive studies on factors determining the distribution and abundance of stream-dwelling triclads. Distribution maps for the commonly occurring species were prepared and observations on the relationship between stream source-type and triclad fauna were obtained. The possible role of interspecific competition was of particular interest in this study and the results of this second phase of the work will be presented in a later paper.     

The interrelationships of proseriata (Platyhelminthes: seriata) tested with molecules and morphology

Proseriate flatworms are common members of the interstitial benthic fauna worldwide, predominantly occupying marine environments. As minute animals, having relatively few characters useful for cladistic analysis, they have been difficult to present in a phylogenetic framework using morphology alone. Here we present a new morphological matrix consisting of 16 putatively homologous characters and two molecular data sets to investigate further this major group of free-living members of the Platyhelminthes. Complete 18S rDNA (representing 277 parsimony-informative characters) from 17 ingroup taxa and partial 28S rDNA spanning variable expansion regions D1 to D3 and D1 to D6 (representing 219 and 361 parsimony-informative characters, respectively) from 27 and 14 ingroup taxa, respectively, were determined and aligned as complementary data sets. Morphological and molecular data sets were analyzed separately and together to determine underlying phylogenetic patterns and to resolve conflict between published scenarios based on morphology alone. The monophyly of the Proseriata cannot be confirmed categorically with any of these data sets. However, the constituent taxa are confirmed as basal members of the Neoophora, and a sister group relationship with Tricladida is rejected. Similarly, the monophyly of one of the two subtaxa of the Proseriata, the Lithophora, could not be confirmed with molecules. Concerning intragroup relationships, we could reject one of the two phylogenetic trees formerly proposed, as well as the clade Otoplanidae + Coelogynoporidae. However, a clade Otoplanidae + Archimonocelididae + Monocelididae (to which the Monotoplanidae belong) was supported, and the position of the genus Calviria shifted from the Archimonocelididae to the Coelogynoporidae.     

The ciliated epidermis of Xenoturbella bocki (Platyhelminthes, Xenoturbellida) with some phylogenetic considerations

The epidermis of Xenoturbella bocki Westblad was studied by scanning and transmission electron microscopy. Two cell types predominate in the epidermis: multiciliated epidermal cells and non-ciliated or monociliated gland cells. A conspicuous feature is the dense ciliary coverage and the numerous gland cell openings. Xenoturbella has a characteristic pattern of axonemal filament termination in the distal tips of their cilia. Each epidermal cilium has the typical 9 + 2 patten through the major part of its shaft. Near the tip there is a shelf at which doublets 4–7 terminate. Doublets 1, 2, 3, 8 and 9 continue into the thinner distal part of the cilium. A similar shelf in cilia is known only from the turbellarian orders Nemertodermatida and Acoela, and hence may be an apomorphic feature which indicates a close relationship between Xenoturbellida, Nemertoder-matida and Acoela. The basal body is provided with a so-called basal foot which has a cross-striated appearance and an expanded distal plate that seems to act as a microtubule organizing center. Approximately 15–25 microtubuli radiate from the endplate of the basal foot to the basal bodies caudally. The arrangement of basal foot and ciliary rootlets in Xenoturbella differs from that of Acoela and related orders in that there are two striated rootlets only (an anterior and a posterior one), rather than one main rootlet and two lateral rootlets.     

Floral and vegetative morphometrics of five Pleurothallis (Orchidaceae) species: correlation with taxonomy,phylogeny, genetic variability and pollination systems

Morphometric analyses of vegetative and floral characters were conducted in 21 populations of five Pleurothallis (Orchidaceae) species occurring in Brazilian 'campo rupestre' vegetation. A phylogenetic analysis of this species group was also carried out using nuclear ribosomal DNA internal transcribed spacers (ITS1 and ITS2). Results of the ordination and cluster analyses agree with species' delimitation revealed by taxonomic and allozyme studies. The groups formed in ordination analysis correspond to the pollinator groups determined in a previous pollination study. Relationships among the species in the cluster analysis using only vegetative characters are similar to those found in a previous allozyme study, but those indicated by cluster analysis using only floral characters differ. These results support the hypothesis that floral similarities are due to convergence driven by similar pollination mechanisms, and therefore floral traits may not be good indicators of phylogenetic relationships in this group. The results of the phylogenetic analysis support this conclusion to some extent. There is no correlation between genetic (allozyme) and morphological variability in the populations nor in the way this variability is distributed among conspecific populations. We describe a new subspecies of Pleurothallis ochreata based on differences in vegetative and chemical characters as well as geographic distribution. Absence of differentiation in floral characters, attraction of the same pollinator species, interfertility and genetic similarity support the argument for subspecific rather than specific status.     

The structures of L-rhamnose isomerase from Pseudomonas stutzeri in complexes with L-rhamnose and D-allose provide insights into broad substrate specificity

Pseudomonas stutzeril-rhamnose isomerase (P. stutzeri L-RhI) can efficiently catalyze the isomerization between various aldoses and ketoses, showing a broad substrate specificity compared to L-RhI from Escherichia coli (E. coli L-RhI). To understand the relationship between structure and substrate specificity, the crystal structures of P. stutzeri L-RhI alone and in complexes with l-rhamnose and d-allose which has different configurations of C4 and C5 from l-rhamnose, were determined at a resolution of 2.0 Å, 1.97 Å, and 1.97 Å, respectively. P. stutzeri L-RhI has a large domain with a (β/α)₈ barrel fold and an additional small domain composed of seven α-helices, forming a homo tetramer, as found in E. coli L-RhI and d-xylose isomerases (D-XIs) from various microorganisms. The β1-α1 loop (Gly60-Arg76) of P. stutzeri L-RhI is involved in the substrate binding of a neighbouring molecule, as found in D-XIs, while in E. coli L-RhI, the corresponding β1-α1 loop is extended (Asp52-Arg78) and covers the substrate-binding site of the same molecule. The complex structures of P. stutzeri L-RhI with l-rhamnose and d-allose show that both substrates are nicely fitted to the substrate -binding site. The part of the substrate-binding site interacting with the substrate at the 1, 2, and 3 positions is equivalent to E. coli L-RhI, and the other part interacting with the 4, 5, and 6 positions is similar to D-XI. In E. coli L-RhI, the β1-α1 loop creates an unique hydrophobic pocket at the the 4, 5, and 6 positions, leading to the strictly recognition of l-rhamnose as the most suitable substrate, while in P. stutzeri L-RhI, there is no corresponding hydrophobic pocket where Phe66 from a neighbouring molecule merely forms hydrophobic interactions with the substrate, leading to the loose substrate recognition at the 4, 5, and 6 positions.     

Structural insights into the assembly and shape of Type III restriction-modification (R-M) EcoP15I complex by small-angle X-ray scattering

EcoP15I is the prototype of the Type III restriction enzyme family, composed of two modification (Mod) subunits to which two (or one) restriction (Res) subunits are then added. The Mod subunits are responsible for DNA recognition and methylation, while the Res subunits are responsible for ATP hydrolysis and cleavage. Despite extensive biochemical and genetic studies, there is still no structural information on Type III restriction enzymes. We present here small-angle X-ray scattering (SAXS) and analytical ultracentrifugation analysis of the EcoP15I holoenzyme and the Mod(2) subcomplex. We show that the Mod(2) subcomplex has a relatively compact shape with a radius of gyration (R(G)) of ～37.4 ? and a maximal dimension of ～110 ?. The holoenzyme adopts an elongated crescent shape with an R(G) of ～65.3 ? and a maximal dimension of ～218 ?. From reconstructed SAXS envelopes, we postulate that Mod(2) is likely docked in the middle of the holoenzyme with a Res subunit at each end. We discuss the implications of our model for EcoP15I action, whereby the Res subunits may come together and form a "sliding clamp" around the DNA.     

Insight into the role of cetaceans in the life cycle of the tetraphyllideans (Platyhelminthes: Cestoda)

Four types of tetraphyllidean larvae infect cetaceans worldwide: two plerocercoids differing in size, ‘small’ (SP) and ‘large’ (LP), and two merocercoids referred to as Phyllobothrium delphini and Monorygma grimaldii. The latter merocercoid larvae parasitize marine mammals exclusively and exhibit a specialised cystic structure. Adult stages are unknown for any of the larvae and thus the role of cetaceans in the life cycle of these species has been a long-standing problem. The SP and LP forms are thought to be earlier stages of P. delphini and M. grimaldii that are presumed to infect large pelagic sharks that feed on cetaceans. A molecular analysis of the D2 variable region of the large subunit ribosomal DNA gene based on several individuals of each larval type collected from three Mediterranean species of cetaceans showed consistent and unique molecular signatures for each type regardless of host species or site of infection. The degree of divergence suggested that LP, P. delphini and M. grimaldii larvae may represent separate species, whereas SP may be conspecific with M. grimaldii. In all host species, individuals of SP accumulated in the gut areas in which the lymphoid tissue was especially developed. We suggest therefore that these larvae use the lymphatic system to migrate to the abdominal peritoneum and mesenteries where they develop into forms recognizable as M. grimaldii. The plerocercoid stage of P. delphini remains unknown. In a partial phylogenetic tree of the Tetraphyllidea, all larvae formed a clade that included a representative of the genus Clistobothrium, some species of which parasitize sharks such as the great white which is known to feed on cetaceans. A bibliographic examination of tetraphyllidean infections in marine mammals indicated that these larvae are acquired mostly offshore. In summary, the evidence suggests that cetaceans play a significant role in the life cycle of these larvae. In addition, it seems clear that cetaceans act as natural intermediate hosts for P. delphini and M. grimaldii, as within these hosts they undergo development from the plerocercoid stage to the merocercoid stage. Because tetraphyllidean species use fish, cephalopods and other marine invertebrates as intermediate hosts, the inclusion of cetaceans in the life cycle would have facilitated their transmission to apex predators such as the large, lamnid sharks. The biological significance of infections of LP in cetaceans is unclear, but infections do not seem to be accidental as such larvae show high prevalence and abundance as well as a high degree of site specificity, particularly in the anal crypts and bile ducts.     

The hydrophobic moment and its use in the classification of amphiphilic structures (review)

Amphiphilic alpha-helices play a major role in membrane dependent processes and are manifested in the primary structure of a protein by the periodic appearance of hydrophobic residues. Based on these periodic sequences, the hydrophobic moment was introduced, , which essentially treats the hydrophobicity of amino acid residues as a two-dimensional vector sum and provides a measure of amphiphilicity within regular repeat structures. To identify putative amphiphilic alpha-helix forming sequences, hydrophobic moment analysis assumes an amino acid residue periodicity of 100 and scans protein primary structures to find the 11-residue window with maximal . Taken with the window's mean hydrophobicity, , hydrophobic moment plot analysis uses the coordinate pair, [, ] to classify alpha-helices as either surface active, globular or transmembrane. More recently, this latter analysis has been extended to recognize candidate oblique orientated alpha-helices. Here, the hydrophobic moment is reviewed and data to query the logic of using a fixed window length and a fixed residue angular periodicity in hydrophobic moment analysis are provided. In addition, problems associated with the use of such analysis to predict alpha-helix structure/function relationships are considered.     

The pathogen-host interactions database (PHI-base) provides insights into generic and novel themes of pathogenicity

Fungal and oomycete pathogens of plants and animals are a major global problem. In the last 15 years, many genes required for pathogenesis have been determined for over 50 different species. Other studies have characterized effector genes (previously termed avirulence genes) required to activate host responses. By studying these types of pathogen genes, novel targets for control can be revealed. In this report, we describe the Pathogen-Host Interactions database (PHI-base), which systematically compiles such pathogenicity genes involved in pathogen-host interactions. Here, we focus on the biology that underlies this computational resource: the nature of pathogen-host interactions, the experimental methods that exist for the characterization of such pathogen-host interactions as well as the available computational resources. Based on the data, we review and analyze the specific functions of pathogenicity genes, the host-specific nature of pathogenicity and virulence genes, and the generic mechanisms of effectors that trigger plant responses. We further discuss the utilization of PHI-base for the computational identification of pathogenicity genes through comparative genomics. In this context, the importance of standardizing pathogenicity assays as well as integrating databases to aid comparative genomics is discussed.     

The choline binding site of phospholipase C (Bacillus cereus): insights into substrate specificity

The phosphatidylcholine-preferring phospholipase C from Bacillus cereus (PLC(Bc)) is a 28.5 kDa enzyme with three zinc ions in its active site. The roles that a number of amino acid residues play as zinc ligands and in binding and catalysis have been elucidated. Recent mechanistic studies indicate that the rate of the reaction is limited by a proton-transfer step during chemical hydrolysis and not substrate binding or product release. An X-ray structure of PLC(Bc) complexed with a phosphonate inhibitor related to phosphatidylcholine revealed that the three amino acid residues Glu4, Tyr56, and Phe66 comprise the choline binding pocket. However, because the contributions that these three residues make to substrate recognition and specificity were unknown, a series of site-specific mutants for Glu4, Tyr56, and Phe66 were constructed by PCR mutagenesis. On the basis of a comparison of their respective CD spectra and melting temperatures, it appears that the mutants adopt folded structures in solution that are virtually identical to that of wild-type PLC(Bc). The kinetic parameters k(cat) and K(m) for the hydrolysis of the three soluble substrates 1, 2-dihexanoyl-sn-glycero-3-phosphocholine (C6PC), 1, 2-dihexanoyl-sn-glycero-3-phosphoethanolamine (C6PE), and 1, 2-dihexanoyl-sn-glycero-3-phospho-L-serine (C6PS) at concentrations below their corresponding critical micelle concentration (cmc) values were determined for each mutant. Replacement of Phe66 with a nonaromatic residue dramatically decreased k(cat) (approximately 200-fold) and reduced PLC(Bc) activity toward C6PC, C6PE, and C6PS, whereas changes to Glu4 and Tyr56 typically led to much more modest losses in catalytic efficiencies. Mutations of Glu4 had relatively little effect upon k(cat) and K(m) for C6PS, but they significantly influenced K(m) for C6PC and C6PE. Replacing Tyr56 with nonaromatic residues also affects catalytic efficiency, albeit to a much lesser degree than the corresponding changes at position 66. However, the presence of an aromatic residue at position 56 seems to confer some substrate selectivity for C6PC and C6PE, which bear a positive charge on the headgroup, relative to C6PS, which has no net charge on the headgroup; this increase in specificity arises largely from a reduced k(cat) for C6PS.     

Phylogenetic insights into the correlates of dioecy in meadow-rues (Thalictrum, Ranunculaceae)

Numerous studies have examined the evolution of sexual systems in angiosperms, but few explore the interaction between these and the evolution of pollination mode. Wind pollination is often associated with unisexual flowers, but which evolved first and played a causative role in the evolution of the other is unclear. Thalictrum, meadow-rues (Ranunculaceae), provides a unique opportunity to study the evolution of these traits because it contains insect and wind pollination and four sexual systems. We used a phylogenetic approach to reconstruct ancestral states for sexual system, pollination mode, and geographic distribution in Thalictrum, and tested for correlations to uncover the factors involved in the evolution of unisexuality and wind pollination. Our results show that dioecy, andro- and gynomonoecy evolved at least twice from hermaphroditism. Wind pollination, unisexual flowers, and New World distribution were all significantly correlated. Wind pollination may have evolved early in the genus, followed by multiple losses and gains, and likely preceded the origin of unisexual flowers in several cases; we found no evidence for unisexual flowers evolving prior to wind pollination. Given a broad scale study showing the evolution of dioecy before wind pollination, our results from a finer scale analysis highlight that different evolutionary pathways are likely to occur throughout angiosperms.