Receiver bias for colourful signals

Animals tend to respond more strongly to signals that are more colourful and such signals are also common in nature. This is the first study to explore experimentally the possibility that response biases arising in an animal's recognition mechanisms can explain these findings. We trained domestic fowls, Gallus gallus domesticus, to respond by pecking or not pecking to different colours displayed on a touch-sensitive computer screen. The colours changed in response to the birds' choices, which mimicked a simple evolutionary process. Discrimination training generated response biases for the colours more distinct from the nonrewarding colour. As a result the signals evolved towards distinct coloration. The biases developed in directions towards more intense and towards less intense colour, depending on the colour of the nonrewarding stimulus. The result may be applicable to all sorts of visual signals encountered during the same kind of experiences, that is, when one signal should be avoided and another should be approached. Copyright 2003 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved.      

Advancing the metabolic theory of biodiversity

A component of metabolic scaling theory has worked towards understanding the influence of metabolism over the generation and maintenance of biodiversity. Specific models within this ‘metabolic theory of biodiversity’ (MTB) have addressed temperature gradients in speciation rate and species richness, but the scope of MTB has been questioned because of empirical departures from model predictions. In this study, we first show that a generalized MTB is not inconsistent with empirical patterns and subsequently implement an eco‐evolutionary MTB which has thus far only been discussed qualitatively. More specifically, we combine a functional trait (body mass) approach and an environmental gradient (temperature) with a dynamic eco‐evolutionary model that builds on the current MTB. Our approach uniquely accounts for feedbacks between ecological interactions (size‐dependent competition and predation) and evolutionary rates (speciation and extinction). We investigate a simple example in which temperature influences mutation rate, and show that this single effect leads to dynamic temperature gradients in macroevolutionary rates and community structure. Early in community evolution, temperature strongly influences speciation and both speciation and extinction strongly influence species richness. Through time, niche structure evolves, speciation and extinction rates fall, and species richness becomes increasingly independent of temperature. However, significant temperature‐richness gradients may persist within emergent functional (trophic) groups, especially when niche breadths are wide. Thus, there is a strong signal of both history and ecological interactions on patterns of species richness across temperature gradients. More generally, the successful implementation of an eco‐evolutionary MTB opens the perspective that a process‐based MTB can continue to emerge through further development of metabolic models that are explicit in terms of functional traits and environmental gradients.     

Sustainability of culture-driven population dynamics

We consider models of the interactions between human population dynamics and cultural evolution, asking whether they predict sustainable or unsustainable patterns of growth. Phenomenological models predict either unsustainable population growth or stabilization in the near future. The latter prediction, however, is based on extrapolation of current demographic trends and does not take into account causal processes of demographic and cultural dynamics. Most existing causal models assume (or derive from simplified models of the economy) a positive feedback between cultural evolution and demographic growth, and predict unlimited growth in both culture and population. We augment these models taking into account that: (1) cultural transmission is not perfect, i.e., culture can be lost; (2) culture does not always promote population growth. We show that taking these factors into account can cause radically different model behavior, such as population extinction rather than stability, and extinction rather than growth. We conclude that all models agree that a population capable of maintaining a large amount of culture, including a powerful technology, runs a high risk of being unsustainable. We suggest that future work must address more explicitly both the dynamics of resource consumption and the cultural evolution of beliefs implicated in reproductive behavior (e.g., ideas about the preferred family size) and in resource use (e.g., environmentalist stances).     

Comparison of the Pseudorabies Virus Us9 Protein with Homologs from Other Veterinary and Human Alphaherpesviruses

Pseudorabies virus (PRV) Us9 is a small, tail-anchored (TA) membrane protein that is essential for axonal sorting of viral structural proteins and is highly conserved among other members of the alphaherpesvirus subfamily. We cloned the Us9 homologs from two human pathogens, varicella-zoster virus (VZV) and herpes simplex virus type 1 (HSV-1), as well as two veterinary pathogens, equine herpesvirus type 1 (EHV-1) and bovine herpesvirus type 1 (BHV-1), and fused them to enhanced green fluorescent protein to examine their subcellular localization and membrane topology. Akin to PRV Us9, all of the Us9 homologs localized to the trans-Golgi network and had a type II membrane topology (typical of TA proteins). Furthermore, we examined whether any of the Us9 homologs could compensate for the loss of PRV Us9 in anterograde, neuron-to-cell spread of infection in a compartmented chamber system. EHV-1 and BHV-1 Us9 were able to fully compensate for the loss of PRV Us9, whereas VZV and HSV-1 Us9 proteins were unable to functionally replace PRV Us9 when they were expressed in a PRV background.Alphaherpesviruses are classified by their variable host range, short reproductive cycle, and ability to establish latency in the peripheral nervous system (PNS) (36, 37). Commonly studied pathogens of this subfamily include herpes simplex virus (HSV) and varicella-zoster virus (VZV), as well as the veterinary pathogens pseudorabies virus (PRV), equine herpesvirus (EHV), and bovine herpesvirus (BHV). Initial infection begins with the virus entering the host mucosal surfaces and spreading between cells of the mucosal epithelium. Invariably, virus enters the PNS through the infection of peripheral nerves that innervate this region. The virus establishes a latent infection in PNS neurons that can be reactivated and that persists for the life of the host (36). In most natural infections, virus replication in the PNS never spreads to the central nervous system (CNS). However, on rare occasions, invasion of the CNS does occur, resulting in devastating encephalitis (46). Trafficking of virus particles from infected epithelial cells into the axon and subsequent transport to neuronal cell bodies is known as retrograde spread of infection. Trafficking of virus particles that are assembled in the neuronal cell body and subsequently sorted into axons for transport to epithelial cells at the initial site of infection (upon reactivation from latency) is known as anterograde spread of infection.Though the natural host of PRV is swine, the virus infects a wide variety of animals, including rodents, cats, dogs, rabbits, cattle, and chicken embryos, but not higher primates (1, 30, 47). In contrast to the well-contained spread of PRV within its natural host, infection of other mammals is usually lethal. Instead of stopping in the PNS, infection continues on to second-order and third-order neurons in the CNS (reviewed in reference 35). This facet of PRV infection makes it a useful tracer of neuronal connections (18). Work in our lab has identified three PRV proteins, Us9 and the gE/gI heterodimer, which are critical for efficient anterograde spread of infection in vivo (i.e., spread from presynaptic to postsynaptic neurons) (6, 45). The molecular mechanism by which these proteins function has been further elucidated in vitro using primary neuronal cultures of superior cervical ganglion (SCG) harvested from embryonic rat pups. PRV Us9 and, to a lesser extent, gE/gI are required for efficient axonal targeting of viral structural proteins, a necessary step for subsequent anterograde, transneuronal spread (10, 11, 27, 28, 42).PRV Us9 is a type II, tail-anchored (TA) membrane protein that is highly enriched in lipid raft microdomains and resides predominantly in or near the trans-Golgi network (TGN) inside infected cells (5-7, 27). It has homologs in most of the alphaherpesviruses, including VZV (16), HSV-1 (22), HSV-2 (17), EHV-1 (21, 40), EHV-4 (41), BHV-1 (25), and BHV-5 (14). Though several studies have examined individually the Us9 proteins encoded by VZV (16), HSV-1 (4, 22, 34, 39), BHV-1 (13), and BHV-5 (14), several gaps in our understanding of Us9 biology remain, namely, whether all of the PRV Us9 homologs are type II membrane proteins, if the proteins localize to similar subcellular compartments within different cell types, and if they can functionally substitute for the loss of PRV Us9 in axonal sorting and anterograde spread of infection. The aim of this study is to examine PRV Us9 in parallel assays with its homologs from VZV, HSV-1, EHV-1, and BHV-1 to identify potential similarities and differences between these highly conserved alphaherpesvirus proteins.     

Two modes of pseudorabies virus neuroinvasion and lethality in mice

We describe two distinct modes of neuroinvasion and lethality after murine flank inoculation with virulent and attenuated strains of pseudorabies virus (PRV). Mice infected with virulent (e.g., PRV-Becker, PRV-Kaplan, or PRV-NIA3) strains self-mutilate their flank skin in response to virally induced pruritus, die rapidly with no identifiable symptoms of central nervous system (CNS) infection such as behavioral abnormalities, and have little infectious virus or viral antigen in the brain. In distinct contrast, animals infected with an attenuated PRV vaccine strain (PRV-Bartha) survive approximately three times longer than wild-type PRV-infected animals, exhibit severe CNS abnormalities, and have an abundance of infectious virus in the brain at the time of death. Interestingly, these animals have no skin lesions and do not appear pruritic at any time during infection. The severe pruritus and relatively earlier time until death induced by wild-type PRV infection may reflect the peripheral nervous system (PNS) and immune responses to infection rather than a fatal, virally induced CNS pathology. Based on previously characterized afferent (sensory) and efferent (motor) neuronal pathways that innervate the skin, we deduced that wild-type virulent strains transit through the PNS via both afferent and efferent routes, whereas PRV-Bartha travels by only efferent routes in the PNS en route to the brain.     

Venation networks and the origin of the leaf economics spectrum

The leaf economics spectrum describes biome-invariant scaling functions for leaf functional traits that relate to global primary productivity and nutrient cycling. Here, we develop a comprehensive framework for the origin of this leaf economics spectrum based on venation-mediated economic strategies. We define a standardized set of traits - density, distance and loopiness - that provides a common language for the study of venation. We develop a novel quantitative model that uses these venation traits to model leaf-level physiology, and show that selection to optimize the venation network predicts the mean global trait-trait scaling relationships across 2548 species. Furthermore, using empirical venation data for 25 plant species, we test our model by predicting four key leaf functional traits related to leaf economics: net carbon assimilation rate, life span, leaf mass per area ratio and nitrogen content. Together, these results indicate that selection on venation geometry is a fundamental basis for understanding the diversity of leaf form and function, and the carbon balance of leaves. The model and associated predictions have broad implications for integrating venation network geometry with pattern and process in ecophysiology, ecology and palaeobotany.     

An empirical assessment of tree branching networks and implications for plant allometric scaling models

Several theories predict whole‐tree function on the basis of allometric scaling relationships assumed to emerge from traits of branching networks. To test this key assumption, and more generally, to explore patterns of external architecture within and across trees, we measure branch traits (radii/lengths) and calculate scaling exponents from five functionally divergent species. Consistent with leading theories, including metabolic scaling theory, branching is area preserving and statistically self‐similar within trees. However, differences among scaling exponents calculated at node‐ and whole‐tree levels challenge the assumption of an optimised, symmetrically branching tree. Furthermore, scaling exponents estimated for branch length change across branching orders, and exponents for scaling metabolic rate with plant size (or number of terminal tips) significantly differ from theoretical predictions. These findings, along with variability in the scaling of branch radii being less than for branch lengths, suggest extending current scaling theories to include asymmetrical branching and differential selective pressures in plant architectures.     

The taxonomic name resolution service: an online tool for automated standardization of plant names

Background

The digitization of biodiversity data is leading to the widespread application of taxon names that are superfluous, ambiguous or incorrect, resulting in mismatched records and inflated species numbers. The ultimate consequences of misspelled names and bad taxonomy are erroneous scientific conclusions and faulty policy decisions. The lack of tools for correcting this ‘names problem’ has become a fundamental obstacle to integrating disparate data sources and advancing the progress of biodiversity science.

Results

The TNRS, or Taxonomic Name Resolution Service, is an online application for automated and user-supervised standardization of plant scientific names. The TNRS builds upon and extends existing open-source applications for name parsing and fuzzy matching. Names are standardized against multiple reference taxonomies, including the Missouri Botanical Garden's Tropicos database. Capable of processing thousands of names in a single operation, the TNRS parses and corrects misspelled names and authorities, standardizes variant spellings, and converts nomenclatural synonyms to accepted names. Family names can be included to increase match accuracy and resolve many types of homonyms. Partial matching of higher taxa combined with extraction of annotations, accession numbers and morphospecies allows the TNRS to standardize taxonomy across a broad range of active and legacy datasets.

Conclusions

We show how the TNRS can resolve many forms of taxonomic semantic heterogeneity, correct spelling errors and eliminate spurious names. As a result, the TNRS can aid the integration of disparate biological datasets. Although the TNRS was developed to aid in standardizing plant names, its underlying algorithms and design can be extended to all organisms and nomenclatural codes. The TNRS is accessible via a web interface at http://tnrs.iplantcollaborative.org/ and as a RESTful web service and application programming interface. Source code is available at https://github.com/iPlantCollaborativeOpenSource/TNRS/.     

Directional transneuronal infection by pseudorabies virus is dependent on an acidic internalization motif in the Us9 cytoplasmic tail

The Us9 gene is conserved among most alphaherpesviruses. In pseudorabies virus (PRV), the Us9 protein is a 98-amino-acid, type II membrane protein found in the virion envelope. It localizes to the trans-Golgi network (TGN) region in infected and transfected cells and is maintained in this compartment by endocytosis from the plasma membrane. Viruses with Us9 deleted have no observable defects in tissue culture yet have reduced virulence and restricted spread to retinorecipient neurons in the rodent brain. In this report, we demonstrate that Us9-promoted transneuronal spread in vivo is dependent on a conserved acidic motif previously shown to be essential for the maintenance of Us9 in the TGN region and recycling from the plasma membrane. Mutant viruses with the acidic motif deleted have an anterograde spread defect indistinguishable from that of Us9 null viruses. Transneuronal spread, however, is not dependent on a dileucine endocytosis motif in the Us9 cytoplasmic tail. Through alanine scanning mutagenesis of the acidic motif, we have identified two conserved tyrosine residues that are essential for Us9-mediated spread as well as two serine residues, comprising putative consensus casein kinase II sites, that modulate the rate of PRV transneuronal spread in vivo.