Estimating phylogenetic inertia in Tithonia (Asteraceae): a comparative approach

Abstract.— Phylogenetic inertia is a difficult issue in evolutionary biology because we have yet to reach a consensus about how to measure it. In this study a comparative approach is used to evaluate phylogenetic inertia in 14 demographic and morphological characters in 10 species and one subspecies of the genus Tithonia (Asteraceae). Three different methods, autocorrelational analysis, phylogenetic correlograms, and ancestor-state reconstruction, were used to evaluate phylogenetic inertia in these traits. Results were highly dependent on the method applied. Autoregression and phylogenetic eigenvector regression (PVR) methods found more inertia in morphological traits. In contrast, phylogenetic correlograms and ancestor-state reconstruction suggest that morphological characters exhibit less phylogenetic inertia than demographic ones. The differences between results are discussed and methods are compared in an effort to understand phylogenetic inertia more thoroughly.     

WFS1 and non-syndromic low-frequency sensorineural hearing loss: A novel mutation in a Portuguese case

Low-frequency sensorineural hearing loss (LFSNHL) is an unusual type of HL in which frequencies at 2000 Hz and below are predominantly affected. Most of the families with LFSNHL carry missense mutations in WFS1 gene, coding for wolframin.     

Technical note: interpreting stable carbon isotopes in human tooth enamel: an examination of tissue spacings from South Africa

Stable isotope analysis of skeletal tissues is widely used in archeology and paleoanthropology to reconstruct diet. In material that is poorly preserved or very old, the tissue of choice is frequently tooth enamel, since this is less susceptible to diagenesis. The relationships between carbon isotope ratios in tooth enamel (δ(13) C(enamel) ), bone collagen (δ(13) C(collagen) ), and bone apatite (δ(13) C(bone apatite) ) are, however, not well understood. To elucidate these, we have measured all three indicators in archeological humans from the western and southern Cape coastal regions of South Africa. The correlation between δ(13) C(enamel) and δ(13) C(collagen) is good (R(2) = 0.71 if two outliers are excluded, n = 79). The correlation between δ(13) C(enamel) and δ(13) C(bone apatite) is weaker (R(2) = 0.37, n = 33) possibly due to bone diagenesis. No systematic offset between δ(13) C(bone apatite) and δ(13) C(enamel) was observed in this sample of archeological humans. Intertooth comparisons of δ(13) C(enamel) in three individuals showed little variation, despite the different ages of crown formation. Carbon isotope ratios in both enamel and bone collagen are good proxies for δ(13) C(diet) .     

Isotropic high resolution optoacoustic imaging with linear detector arrays in bi‐directional scanning

Optoacoustic (photoacoustic) imaging is often performed with one‐dimensional transducer arrays, in analogy to ultrasound imaging. Optoacoustic imaging using linear arrays offers ease of implementation but comes with several performance drawbacks, in particular poor elevation resolution, i.e. the resolution along the axis perpendicular to the focal plane. Herein, we introduce and investigate a bi‐directional scanning approach using linear arrays that can improve the imaging performance to quasi‐isotropic transverse resolution. We study the approach theoretically and perform numerical simulations and phantom measurements to evaluate its performance under defined conditions. Finally, we discuss the features and the limitations of the proposed method.

The poor elevation resolution in a linear scan (left image) is overcome by the proposed bi‐directional scanning approach that yields isotropic transverse resolution (right).     

Evolution of venom delivery structures in madtom catfishes (Siluriformes: Ictaluridae)

The use of venom to subdue prey or deter predators has evolved multiple times in numerous animal lineages. Catfishes represent one of the most easily recognized, but least studied groups of venomous fishes. Venom glands surround spines on the dorsal and pectoral fins that serve as venom delivery structures. Species of madtom catfishes in the genus Noturus were found to each have one of four venom delivery morphologies: (1) smooth spine with no venom gland; (2) smooth spine with venom gland associated with shaft of spine; (3) serrated spine with venom gland associated with shaft of spine; and (4) serrated spine with venom gland associated with shaft of spine and posterior serrations. Analyses accounting for the phylogenetic history of Noturus species suggest that a serrated pectoral spine with a venom gland is the ancestral condition for the genus. The presence of serrations and a venom gland have been largely conserved among Noturus species, but sting morphology has changed at least five times within the genus. Four of these changes have resulted in a loss of morphological complexity, including the loss of posterior serrations, loss of venom glands associated with the posterior serrations, and one complete loss of the venom gland. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 115–129.     

Subunit arrangement in the dodecameric chloroplast small heat shock protein Hsp21

Unfolding proteins are prevented from irreversible aggregation by small heat shock proteins (sHsps) through interactions that depend on a dynamic equilibrium between sHsp subunits and sHsp oligomers. A chloroplast-localized sHsp, Hsp21, provides protection to client proteins to increase plant stress resistance. Structural information is lacking concerning the oligomeric conformation of this sHsp. We here present a structure model of Arabidopsis thaliana Hsp21, obtained by homology modeling, single-particle electron microscopy, and lysine-specific chemical crosslinking. The model shows that the Hsp21 subunits are arranged in two hexameric discs, similar to a cytosolic plant sHsp homolog that has been structurally determined after crystallization. However, the two hexameric discs of Hsp21 are rotated by 25° in relation to each other, suggesting a role for global dynamics in dodecamer function.     

A new approach to blood flow simulation in vascular networks

A proper analysis of blood flow is contingent upon accurate modelling of the branching pattern and vascular geometry of the network of interest. It is challenging to reconstruct the entire vascular network of any organ experimentally, in particular the pulmonary vasculature, because of its very high number of vessels, complexity of the branching pattern and poor accessibility in vivo. The objective of our research is to develop an innovative approach for the reconstruction of the full pulmonary vascular tree from available morphometric data. Our method consists of the use of morphometric data on those parts of the pulmonary vascular tree that are too small to reconstruct by medical imaging methods. This method is a three-step technique that reconstructs the entire pulmonary arterial tree down to the capillary bed. Vessels greater than 2 mm are reconstructed from direct volume and surface analysis using contrast-enhanced computed tomography. Vessels smaller than 2 mm are reconstructed from available morphometric and distensibility data and rearranged by applying Murray's laws. Implementation of morphometric data to reconstruct the branching pattern and applying Murray's laws to every vessel bifurcation simultaneously leads to an accurate vascular tree reconstruction. The reconstruction algorithm generates full arterial tree topography down to the ?rst capillary bifurcation. Geometry of each order of the vascular tree is generated separately to minimize the construction and simulation time. The node-to-node connectivity along with the diameter and length of every vessel segment is established and order numbers, according to the diameter-de?ned Strahler system, are assigned. In conclusion, the present model provides a morphological foundation for future analysis of blood flow in the pulmonary circulation     

Applying a multiobjective metaheuristic inspired by honey bees to phylogenetic inference

The development of increasingly popular multiobjective metaheuristics has allowed bioinformaticians to deal with optimization problems in computational biology where multiple objective functions must be taken into account. One of the most relevant research topics that can benefit from these techniques is phylogenetic inference. Throughout the years, different researchers have proposed their own view about the reconstruction of ancestral evolutionary relationships among species. As a result, biologists often report different phylogenetic trees from a same dataset when considering distinct optimality principles. In this work, we detail a multiobjective swarm intelligence approach based on the novel Artificial Bee Colony algorithm for inferring phylogenies. The aim of this paper is to propose a complementary view of phylogenetics according to the maximum parsimony and maximum likelihood criteria, in order to generate a set of phylogenetic trees that represent a compromise between these principles. Experimental results on a variety of nucleotide data sets and statistical studies highlight the relevance of the proposal with regard to other multiobjective algorithms and state-of-the-art biological methods.     

50年来山东塔山植被与物种多样性的变化

为分析塔山植被与物种多样性50a自然演替和动态变化,2009-2010年,采用系统勘踏法和典型取样法进行了调查。当前塔山主要植被类型为"黑松林-赤松林-栓皮栎林"。50a间,该区针叶林从黑松(Pinus thunbergii)林演替为黑松林、赤松(P. densiflora)林和油松林(P. tabulaeformis)为主的混合针叶林,但针叶林的整体优势度下降,以栓皮栎(Quercus variabilis)和麻栎(Q. acutissima)为建群种的阔叶林面积明显增大,由针叶林向阔叶林的演替趋势明朗。物种丰富度为草本层>灌木层>乔木层,Shannon-wiener指数和Simpson指数为灌木层>草本层>乔木层,物种多样性较低,处于森林演替初期。     

Genome reduction as the dominant mode of evolution

A common belief is that evolution generally proceeds towards greater complexity at both the organismal and the genomic level, numerous examples of reductive evolution of parasites and symbionts notwithstanding. However, recent evolutionary reconstructions challenge this notion. Two notable examples are the reconstruction of the complex archaeal ancestor and the intron‐rich ancestor of eukaryotes. In both cases, evolution in most of the lineages was apparently dominated by extensive loss of genes and introns, respectively. These and many other cases of reductive evolution are consistent with a general model composed of two distinct evolutionary phases: the short, explosive, innovation phase that leads to an abrupt increase in genome complexity, followed by a much longer reductive phase, which encompasses either a neutral ratchet of genetic material loss or adaptive genome streamlining. Quantitatively, the evolution of genomes appears to be dominated by reduction and simplification, punctuated by episodes of complexification.