Association of candidate genes with flowering time and water-soluble carbohydrate content in Lolium perenne (L.)

Sk?t, L., Humphreys, J., Humphreys, M. O., Thorogood, D., Gallagher, J. A., Sanderson, R., Armstead, I. P., Thomas, I. D. (2007). Association of candidate genes with flowering time and water-soluble carbohydrate content in Lolium perenne (L.). Genetics, 177 (1), 535-547. Sponsorship: BBSRC RAE2008

The Terrorism Virus: Contemporary Traits and Mechanisms

In order to present and understand the nature of modern terrorism it is important to realize its key properties as well the mechanisms that shape terrorism. Selected properties and mechanisms shaping modern terrorism which can be exemplified by the following: evolutionary nature of terrorism, asymmetry of terrorism, interferentiality of terrorism, multitude of components of terrorism, diffusion of terrorism, duality of terrorism, positive dimension of terrorism, terrorist as the system, diversity of terrorist activity goals, changeability of terrorist threat, the broad and narrow dimension of terrorism, counter-anti-terrorism, the confrontational and cooperational character of relations, calculation and operational strategy, disintegrational nature of terrorism, multidisciplinarity of terrorism, horizontal and vertical dimension of terrorism and a the few other traits or mechanisms.

Retrieval by Shape Population: An Index Tree Approach

Based on our previous work in deformable shape model-based object detection, a new method is proposed that uses index trees for organizing shape features to support content-based retrieval applications. In the proposed strategy, different shape feature sets can be used in index trees constructed for object detection and shape similarity comparison respectively. There is a direct correspondence between the two shape feature sets. As a result, application-specific features can be obtained efficiently for shape-based retrieval after object detection. A novel approach is proposed that allows retrieval of images based on the population distribution of deformed shapes in each image. Experiments testing these new approaches have been conducted using an image database that contains blood cell micrographs. The precision vs. recall performance measure shows that our method is superior to previous methods.

Scalable Overlay Multicast Tree Construction for QoS-Constrained Media Streaming

Overlay networks have become popular in recent times for content distribution and end-system multicasting of media streams. In the latter case, the motivation is based on the lack of widespread deployment of IP multicast and the ability to perform end-host processing. However, constructing routes between various end-hosts, so that data can be streamed from content publishers to many thousands of subscribers, each having their own QoS constraints, is still a challenging problem. First, any routes between end-hosts using trees built on top of overlay networks can increase stress on the underlying physical network, due to multiple instances of the same data traversing a given physical link. Second, because overlay routes between end-hosts may traverse physical network links more than once, they increase the end-to-end latency compared to IP-level routing. Third, algorithms for constructing efficient, large-scale trees that reduce link stress and latency are typically more complex. This paper therefore compares various methods to construct multicast trees between end-systems, that vary in terms of implementation costs and their ability to support per-subscriber QoS constraints. We describe several algorithms that make trade-offs between algorithmic complexity, physical link stress and latency. While no algorithm is best in all three cases we show how it is possible to efficiently build trees for several thousand subscribers with latencies within a factor of two of the optimal, and link stresses comparable to, or better than, existing technologies.

Nutrient enrichment effects on mangrove sediments from differing tree height zones in Bocas del Toro, Panama

Red mangrove (Rhizophora mangle L.) forests have distinct tree-height zones, with tall trees fringing the ocean and shorter trees in interior stands. A long-term nitrogen (N) and phosphorus (P) fertilization experiment in Almirante Bay, Bocas del Toro Province, Panama has shown that tree-height zonation is primarily related to nutrient limitation. This experiment was used to test the effects of in-situ nutrient additions and tree zonation on mangrove sediments. The sediments underlying the experimental R. mangle trees were sampled and N₂ fixation, ¹⁵N, chlorophyll a, percent N and P, and percent organic biomass were quantified. Both N and P additions significantly affected almost every parameter measured in both zones within this experiment. These results are likely to have implications for management since N and P inputs are predicted to increase throughout the tropics and subtropics worldwide.

Independent evolutionary origins of landlocked alewife populations and rapid parallel evolution of phenotypic traits.

Alewife, Alosa pseudoharengus, populations occur in two discrete life-history variants, an anadromous form and a landlocked (freshwater resident) form. Landlocked populations display a consistent pattern of life-history divergence from anadromous populations, including earlier age at maturity, smaller adult body size, and reduced fecundity. In Connecticut (USA), dams constructed on coastal streams separate anadromous spawning runs from lake-resident landlocked populations. Here, we used sequence data from the mtDNA control region and allele frequency data from five microsatellite loci to ask whether coastal Connecticut landlocked alewife populations are independently evolved from anadromous populations or whether they share a common freshwater ancestor. We then used microsatellite data to estimate the timing of the divergence between anadromous and landlocked populations. Finally, we examined anadromous and landlocked populations for divergence in foraging morphology and used divergence time estimates to calculate the rate of evolution for foraging traits. Our results indicate that landlocked populations have evolved multiple times independently. Tests of population divergence and estimates of gene flow show that landlocked populations are genetically isolated, whereas anadromous populations exchange genes. These results support a 'phylogenetic raceme' model of landlocked alewife divergence, with anadromous populations forming an ancestral core from which landlocked populations independently diverged. Divergence time estimates suggest that landlocked populations diverged from a common anadromous ancestor no longer than 5000 years ago and perhaps as recently as 300 years ago, depending on the microsatellite mutation rate assumed. Examination of foraging traits reveals landlocked populations to have significantly narrower gapes and smaller gill raker spacings than anadromous populations, suggesting that they are adapted to foraging on smaller prey items. Estimates of evolutionary rates (in haldanes) indicate rapid evolution of foraging traits, possibly in response to changes in available resources.

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.

BACKGROUND: Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great "Tree of Life" (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user's needs. Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces. RESULTS: With the aim of building such a "phylotastic" system, the NESCent Hackathons, Interoperability, Phylogenies (HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012. During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations, documentation, presentations, and tests including: (1) a generalized scheme for integrating components; (2) proof-of-concept pruners and controllers; (3) a meta-API for taxonomic name resolution services; (4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying; (5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodes; and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a website (http://www.phylotastic.org), and a server image. CONCLUSIONS: Approximately 9 person-months of effort (centered on a software development hackathon) resulted in the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3 end-user demonstration tools. While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality assessment.

Mainland size variation informs predictive models of exceptional insular body size change in rodents.

The tendency for island populations of mammalian taxa to diverge in body size from their mainland counterparts consistently in particular directions is both impressive for its regularity and, especially among rodents, troublesome for its exceptions. However, previous studies have largely ignored mainland body size variation, treating size differences of any magnitude as equally noteworthy. Here, we use distributions of mainland population body sizes to identify island populations as 'extremely' big or small, and we compare traits of extreme populations and their islands with those of island populations more typical in body size. We find that although insular rodents vary in the directions of body size change, 'extreme' populations tend towards gigantism. With classification tree methods, we develop a predictive model, which points to resource limitations as major drivers in the few cases of insular dwarfism. Highly successful in classifying our dataset, our model also successfully predicts change in untested cases.

Synchrony between sensory and cognitive networks is associated with subclinical variation in autistic traits

© 2015 Young, Smith, Coutlee and Huettel.Individuals with autistic spectrum disorders exhibit distinct personality traits linked to attentional, social, and affective functions, and those traits are expressed with varying levels of severity in the neurotypical and subclinical population. Variation in autistic traits has been linked to reduced functional and structural connectivity (i.e., underconnectivity, or reduced synchrony) with neural networks modulated by attentional, social, and affective functions. Yet, it remains unclear whether reduced synchrony between these neural networks contributes to autistic traits. To investigate this issue, we used functional magnetic resonance imaging to record brain activation while neurotypical participants who varied in their subclinical scores on the Autism-Spectrum Quotient (AQ) viewed alternating blocks of social and nonsocial stimuli (i.e., images of faces and of landscape scenes). We used independent component analysis (ICA) combined with a spatiotemporal regression to quantify synchrony between neural networks. Our results indicated that decreased synchrony between the executive control network (ECN) and a face-scene network (FSN) predicted higher scores on the AQ. This relationship was not explained by individual differences in head motion, preferences for faces, or personality variables related to social cognition. Our findings build on clinical reports by demonstrating that reduced synchrony between distinct neural networks contributes to a range of subclinical autistic traits.

CPAG: software for leveraging pleiotropy in GWAS to reveal similarity between human traits links plasma fatty acids and intestinal inflammation.

Meta-analyses of genome-wide association studies (GWAS) have demonstrated that the same genetic variants can be associated with multiple diseases and other complex traits. We present software called CPAG (Cross-Phenotype Analysis of GWAS) to look for similarities between 700 traits, build trees with informative clusters, and highlight underlying pathways. Clusters are consistent with pre-defined groups and literature-based validation but also reveal novel connections. We report similarity between plasma palmitoleic acid and Crohn's disease and find that specific fatty acids exacerbate enterocolitis in zebrafish. CPAG will become increasingly powerful as more genetic variants are uncovered, leading to a deeper understanding of complex traits. CPAG is freely available at www.sourceforge.net/projects/CPAG/.

Conversion of natural forests to managed forest plantations decreases tree resistance to prolonged droughts

© 2015 Published by Elsevier B.V.Throughout the southern US, past forest management practices have replaced large areas of native forests with loblolly pine plantations and have resulted in changes in forest response to extreme weather conditions. However, uncertainty remains about the response of planted versus natural species to drought across the geographical range of these forests. Taking advantage of a cluster of unmanaged stands (85-130year-old hardwoods) and managed plantations (17-20year-old loblolly pine) in coastal and Piedmont areas of North Carolina, tree water use, cavitation resistance, whole-tree hydraulic (Ktree) and stomatal (Gs) conductances were measured in four sites covering representative forests growing in the region. We also used a hydraulic model to predict the resilience of those sites to extreme soil drying. Our objectives were to determine: (1) if Ktree and stomatal regulation in response to atmospheric and soil droughts differ between species and sites; (2) how ecosystem type, through tree water use, resistance to cavitation and rooting profiles, affects the water uptake limit that can be reached under drought; and (3) the influence of stand species composition on critical transpiration that sets a functional water uptake limit under drought conditions. The results show that across sites, water stress affected the coordination between Ktree and Gs. As soil water content dropped below 20% relative extractable water, Ktree declined faster and thus explained the decrease in Gs and in its sensitivity to vapor pressure deficit. Compared to branches, the capability of roots to resist high xylem tension has a great impact on tree-level water use and ultimately had important implications for pine plantations resistance to future summer droughts. Model simulations revealed that the decline in Ktree due to xylem cavitation aggravated the effects of soil drying on tree transpiration. The critical transpiration rate (Ecrit), which corresponds to the maximum rate at which transpiration begins to level off to prevent irreversible hydraulic failure, was higher in managed forest plantations than in their unmanaged counterparts. However, even with this higher Ecrit, the pine plantations operated very close to their critical leaf water potentials (i.e. to their permissible water potentials without total hydraulic failure), suggesting that intensively managed plantations are more drought-sensitive and can withstand less severe drought than natural forests.

Identification of dopamine receptors across the extant avian family tree and analysis with other clades uncovers a polyploid expansion among vertebrates.

Dopamine is an important central nervous system transmitter that functions through two classes of receptors (D1 and D2) to influence a diverse range of biological processes in vertebrates. With roles in regulating neural activity, behavior, and gene expression, there has been great interest in understanding the function and evolution dopamine and its receptors. In this study, we use a combination of sequence analyses, microsynteny analyses, and phylogenetic relationships to identify and characterize both the D1 (DRD1A, DRD1B, DRD1C, and DRD1E) and D2 (DRD2, DRD3, and DRD4) dopamine receptor gene families in 43 recently sequenced bird genomes representing the major ordinal lineages across the avian family tree. We show that the common ancestor of all birds possessed at least seven D1 and D2 receptors, followed by subsequent independent losses in some lineages of modern birds. Through comparisons with other vertebrate and invertebrate species we show that two of the D1 receptors, DRD1A and DRD1B, and two of the D2 receptors, DRD2 and DRD3, originated from a whole genome duplication event early in the vertebrate lineage, providing the first conclusive evidence of the origin of these highly conserved receptors. Our findings provide insight into the evolutionary development of an important modulatory component of the central nervous system in vertebrates, and will help further unravel the complex evolutionary and functional relationships among dopamine receptors.

Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds".

Mitchell et al. argue that divergence-time estimates for our avian phylogeny were too young because of an "inappropriate" maximum age constraint for the most recent common ancestor of modern birds and that, as a result, most modern bird orders diverged before the Cretaceous-Paleogene mass extinction event 66 million years ago instead of after. However, their interpretations of the fossil record and timetrees are incorrect.

Tree species-area and species-diameter relationships at three lowland rain forest sites in Sumatra

Data from three forest sites in Sumatra (Batang Ule, Pasirmayang and Tebopandak) have been analysed and compared for the effects of sample area cut-off, and tree diameter cut-off. An 'extended inverted exponential model' is shown to be well suited to fitting tree-species-area curves. The model yields species carrying capacities of 680 for Batang Ule, 380 species for Pasirmayang, and 35 for Tebopandak (tree diameter >10cm). It would seem that in terms of species carrying capacity, Tebopandak and Pasirmayang are rather similar, and both less diverse than the hilly Batang Ule site. In terms of conservation policy, this would mean that rather more emphasis should be put on conserving hilly sites on a granite substratum. For Pasirmayang with tree diameter >3cm, the asymptotic species number estimate is 567, considerably higher than the estimate of 387 species for trees with diameter >10cm. It is clear that the diameter cut-off has a major impact on the estimate of the species carrying capacity. A conservative estimate of the total number of tree species in the Pasirmayang region is 632 species! In sampling exercises, the diameter cut-off should not be chosen lightly, and it may be worth adopting field sampling procedures which involve some subsampling of the primary sample area, where the diameter cut-off is set much lower than in the primary plots.

A new parameterization of Johnson's SB distribution with application to fitting forest tree diameter data

The SB distributional model of Johnson's 1949 paper was introduced by a transformation to normality, that is, z ~ N(0, 1), consisting of a linear scaling to the range (0, 1), a logit transformation, and an affine transformation, z = γ + δu. The model, in its original parameterization, has often been used in forest diameter distribution modelling. In this paper, we define the SB distribution in terms of the inverse transformation from normality, including an initial linear scaling transformation, u = γ′ + δ′z (δ′ = 1/δ and γ′ = �γ/δ). The SB model in terms of the new parameterization is derived, and maximum likelihood estimation schema are presented for both model parameterizations. The statistical properties of the two alternative parameterizations are compared empirically on 20 data sets of diameter distributions of Changbai larch (Larix olgensis Henry). The new parameterization is shown to be statistically better than Johnson's original parameterization for the data sets considered here.