A new global biome reconstruction and data-model comparison for the Middle Pliocene

Aim To produce a robust, comprehensive global biome reconstruction for the Middle Pliocene (c. 3.6–2.6 Ma), which is based on an internally consistent palaeobotanical data set and a state‐of‐the‐art coupled climate–vegetation model. The reconstruction gives a more rigorous picture of climate and environmental change during the Middle Pliocene and provides a new boundary condition for future general circulation model (GCM) studies. Location Global. Methods Compilation of Middle Pliocene vegetation data from 202 marine and terrestrial sites into the comprehensive GIS data base TEVIS (Tertiary Environmental Information System). Translation into an internally consistent classification scheme using 28 biomes. Comparison and synthesis of vegetation reconstruction from palaeodata with the outputs of the mechanistically based BIOME4 model forced by climatology derived from the HadAM3 GCM. Results The model results compare favourably with available palaeodata and highlight the importance of employing vegetation–climate feedbacks and the anomaly method in biome models. Both the vegetation reconstruction from palaeobotanical data and the BIOME4 prediction indicate a general warmer and moister climate for the Middle Pliocene. Evergreen taiga as well as temperate forest and grassland shifted northward, resulting in much reduced tundra vegetation. Warm‐temperate forests (with subtropical taxa) spread in mid and eastern Europe and tropical savannas and woodland expanded in Africa and Australia at the expense of deserts. Discrepancies which occurred between data reconstruction and model simulation can be related to: (1) poor spatial model resolution and data coverage; (2) uncertainties in delimiting biomes using climate parameters; or (3) uncertainties in model physics and/or geological boundary conditions. Main conclusions The new global biome reconstruction combines vegetation reconstruction from palaeobotanical proxies with model simulations. It is an important contribution to the further understanding of climate and vegetation changes during the Middle Pliocene warm interval and will enhance our knowledge about how vegetation may change in the future.     

Genetic tests of ancient asexuality in Root Knot Nematodes reveal recent hybrid origins

Background  

The existence of "ancient asexuals", taxa that have persisted for long periods of evolutionary history without sexual recombination, is both controversial and important for our understanding of the evolution and maintenance of sexual reproduction. A lack of sex has consequences not only for the ecology of the asexual organism but also for its genome. Several genetic signatures are predicted from long-term asexual (apomictic) reproduction including (i) large "allelic" sequence divergence (ii) lack of phylogenetic clustering of "alleles" within morphological species and (iii) decay and loss of genes specific to meiosis and sexual reproduction. These genetic signatures can be hard to assess since it is difficult to demonstrate the allelic nature of very divergent sequences, divergence levels may be complicated by processes such as inter-specific hybridization, and genes may have secondary roles unrelated to sexual reproduction. Apomictic species of Meloidogyne root knot nematodes have been suggested previously to be ancient asexuals. Their relatives reproduce by meiotic parthenogenesis or facultative sexuality, which in combination with the abundance of nematode genomic sequence data, makes them a powerful system in which to study the consequences of reproductive mode on genomic divergence.     

Behavior of free-ranging common dolphins (Delphinus sp.) in the Hauraki Gulf, New Zealand

Here we present the first data describing the behavior of common dolphins ( Delphinus sp.) in the Hauraki Gulf, New Zealand. Activity budgets are used to assess the effects of diel, season, depth, sea surface temperature, group size, and composition on dolphin behavior. Additionally, the presence/absence of Bryde's whale ( Balaenoptera brydei ) and Australasian gannet ( Morus serrator ) is examined in relation to dolphin behavior. Behavioral data were collected from 686 independent dolphin groups during boat-based surveys conducted between February 2002 and January 2005. Foraging (46.7%) and social (7.2%) were the most and least frequently observed behaviors, respectively. Travel (28.9%), mill (9.5%), and rest (7.7%) accounted for the remainder of the activity budget. Behavior varied seasonally, with the highest proportion of foraging and resting groups observed during the spring and autumn, respectively. Behavior also varied with water depth, with foraging animals observed in the deepest and resting groups recorded in the shallowest regions of the Hauraki Gulf. A correlation between group size and behavior was evident, although behavior did not vary with the composition of dolphin groups. Resting, milling, and socializing animals were more frequently observed in smaller group sizes. Foraging behavior was prevalent in both small and large group sizes, suggesting foraging plasticity exists within this population. Behavior differed between single- and multispecies groups, with foraging more frequent in multispecies groups. Resting, milling, or socializing was rarely observed in the presence of any associated species, indicating the primary mechanism for association is likely prey related.     

Requirements for the valid quantification of immunostains on tissue microarray materials using image analysis

Antibody‐based proteomics applied to tissue microarray (TMA) technology provides a very efficient means of visualizing and locating antigen expression in large collections of normal and pathological tissue samples. To characterize antigen expression on TMAs, the use of image analysis methods avoids the effects of human subjectivity evidenced in manual microscopical analysis. Thus, these methods have the potential to significantly enhance both precision and reproducibility. Although some commercial systems include tools for the quantitative evaluation of immunohistochemistry‐stained images, there exists no clear agreement on best practices to allow for correct and reproducible quantification results. Our study focuses on practical aspects regarding (i) image acquisition (ii) segmentation of staining and counterstaining areas and (iii) extraction of quantitative features. We illustrate our findings using a commercial system to quantify different immunohistochemistry markers targeting proteins with different expression patterns (cytoplasmic, nuclear or membranous) in colon cancer or brain tumor TMAs. Our investigations led us to identify several steps that we consider essential for standardizing computer‐assisted immunostaining quantification experiments. In addition, we propose a data normalization process based on reference materials to be able to compare measurements between studies involving different TMAs. In conclusion, we recommend certain critical prerequisites that commercial or in‐house systems should satisfy in order to permit valid immunostaining quantification.     

The Role of Gender in Public Perception of Whether Animals Can Experience Grief and Other Emotions

Gender plays a significant role in influencing people's attitudes toward animals, however, little is known about how it influences their attribution of emotions to animals. To investigate the role that gender plays in public attitudes toward animals' experience of emotions and beliefs about whether animals can grieve, a face-to-face survey of 1,000 members of the general public was carried out in Brisbane, Australia. Potential respondents were asked to complete a 10-min “social attitudinal” survey. Males were significantly less likely than females to believe that animals experience complex emotions, including depression (p < 0.05), anxiety (p < 0.05), love (p < 0.01), and grief (p < 0.05), but did not differ in regard to basic emotions including distress, fear, happiness, anger, sadness, and fear. Males were also less likely to believe that animals show some behavioral (eating p < 0.05; vocalizing p < 0.01) changes when they experience grief (p < 0.05) and that animals grieve as a result of separation from a conspecific (p < 0.005). These results demonstrate a greater skepticism in males, compared with females, regarding the attribution of emotions to animals.     

The Evolution of Tyrosine-Recombinase Elements in Nematoda

Transposable elements can be categorised into DNA and RNA elements based on their mechanism of transposition. Tyrosine recombinase elements (YREs) are relatively rare and poorly understood, despite sharing characteristics with both DNA and RNA elements. Previously, the Nematoda have been reported to have a substantially different diversity of YREs compared to other animal phyla: the Dirs1-like YRE retrotransposon was encountered in most animal phyla but not in Nematoda, and a unique Pat1-like YRE retrotransposon has only been recorded from Nematoda. We explored the diversity of YREs in Nematoda by sampling broadly across the phylum and including 34 genomes representing the three classes within Nematoda. We developed a method to isolate and classify YREs based on both feature organization and phylogenetic relationships in an open and reproducible workflow. We also ensured that our phylogenetic approach to YRE classification identified truncated and degenerate elements, informatively increasing the number of elements sampled. We identified Dirs1-like elements (thought to be absent from Nematoda) in the nematode classes Enoplia and Dorylaimia indicating that nematode model species do not adequately represent the diversity of transposable elements in the phylum. Nematode Pat1-like elements were found to be a derived form of another Pat1-like element that is present more widely in animals. Several sequence features used widely for the classification of YREs were found to be homoplasious, highlighting the need for a phylogenetically-based classification scheme. Nematode model species do not represent the diversity of transposable elements in the phylum.     

Methyllycaconitine: a selective probe for neuronal α-bungarotoxin binding sites

The ability of methyllycaconitine (MLA) to inhibit the binding of [¹²⁵I]α-bungarotoxin to rat brain membranes, frog and human muscle extracts and the human muscle cell line TE671 has been measured. MLA showed a markedly higher affinity for the rat brain site (K_i 1.4 × 10⁻⁹ M) than for the muscle receptors (K_i; 10⁻⁵-10⁻⁶ M). Structure modelling techniques were used to fit the structure of MLA to a nicotinic pharmacophore model. MLA is the first low molecular weight ligand to be shown to discriminate between muscle nicotinic receptors and their α-bungarotoxinbinding counterpart in the brain, and as such may be a useful structural probe for pursuing the structural and functional properties of the neuronal protein.     

Scale-dependent habitat selection by wintering geese: implications for landscape management

The management of Arctic migrant geese is complex, because they frequently use landscapes under intensive human use, and are conflict species in multiple respects. Some populations are of high conservation concern, but they also cause agricultural damage, are quarry for hunters, and may be particularly sensitive to infrastructure developments. In Bulgarian Dobrudzha, large wintering populations of greater white-fronted geese Anser albifrons and red-breasted geese Branta ruficollis feed in agricultural land, and cause management dilemmas. We developed linear models to investigate fine- and meso-scale foraging habitat selection of geese foraging on winter wheat in the area, and used these models to make suggestions for zoning landscape use in order to reduce conflict and conserve geese. Habitat selection was scale-dependent. Geese selected fields that were near to major roosts and had low proximity to roads and tree-lines, which may be a proxy for hunting disturbance. We found some evidence for selection of wheat fields with high nutritional quality. Within fields, geese strongly avoided features which cause landscape ‘clutter’: power-lines, tree-lines and wind-turbines, but primarily over distances of less than a few hundred metres. Optimal management might involve encouraging goose populations to feed in areas close to roosts, by means of agri-environmental measures and creation of hunting-free refuges. This would allow efficient use of agri-environment funds, might reduce conflict with farmers, and would mean that infrastructure development—notably wind farms—could be sited at greater distance from roosts with relatively minor impact on foraging habitat availability.