Extrinsic versus intrinsic factors in the decline and extinction of Australian marsupials

Recent attempts to explain the susceptibility of vertebrates to declines worldwide have largely focused on intrinsic factors such as body size, reproductive potential, ecological specialization, geographical range and phylogenetic longevity. Here, we use a database of 145 Australian marsupial species to test the effects of both intrinsic and extrinsic factors in a multivariate comparative approach. We model five intrinsic (body size, habitat specialization, diet, reproductive rate and range size) and four extrinsic (climate and range overlap with introduced foxes, sheep and rabbits) factors. We use quantitative measures of geographical range contraction as indices of decline. We also develop a new modelling approach of phylogenetically independent contrasts combined with imputation of missing values to deal simultaneously with phylogenetic structuring and missing data. One extrinsic variable-geographical range overlap with sheep-was the only consistent predictor of declines. Habitat specialization was independently but less consistently associated with declines. This suggests that extrinsic factors largely determine interspecific variation in extinction risk among Australian marsupials, and that the intrinsic factors that are consistently associated with extinction risk in other vertebrates are less important in this group. We conclude that recent anthropogenic changes have been profound enough to affect species on a continent-wide scale, regardless of their intrinsic biology.

Visual biology of Hawaiian coral reef fishes. II. Colors of Hawaiian coral reef fish

The colors of 51 species of Hawaiian reef fish have been measured using a spectrometer and therefore can be described in objective terms that are not influenced by the human visual experience. In common with other known reef fish populations, the colors of Hawaiian reef fish occupy spectral positions from 300-800nm; yellow or orange with blue, yellow with black, and black with white are the most frequently combined colors; and there is no link between possession of ultraviolet (UV) reflectance and UV visual sensitivity or the potential for UV visual sensitivity. In contrast to other reef systems, blue, yellow, and orange appear more frequently in Hawaiian reef fish. Based on spectral quality of reflections from fish skin, trends in fish colors can be seen that are indicative of both visually driven selective pressures and chemical or physical constraints on the design of colors. UV-reflecting colors can function as semiprivate communication signals. White or yellow with black form highly contrasting patterns that transmit well through clear water. Labroid fishes display uniquely complex colors but lack the ability to see the UV component that is common in their pigments. Step-shaped spectral curves are usually long-wavelength colors such as yellow or red, and colors with a peak-shaped spectral curves are green, blue, violet, and UV.

Expression, purification, crystallization, and NMR studies of the helicase interaction domain of Escherichia coli DnaG primase

in Escherichia coli, the DnaG primase is the RNA polymerase that synthesizes RNA primers at replication forks. It is composed of three domains, a small N-terminal zinc-binding domain, a larger central domain responsible for RNA synthesis, and a C-terminal domain comprising residues 434-581 [DnaG(434-581)] that interact with the hexameric DnaB helicase. Presumably because of this interaction, it had not been possible previously to express the C-terminal domain in a stably transformed E coli strain. This problem was overcome by expression of DnaG(434-581) under control of tandem bacteriophage gimel-promoters, and the protein was purified in yields of 4-6 mg/L of culture and studied by NMR. A TOCSY spectrum of a 2 mM solution of the protein at pH 7.0, indicated that its structured core comprises residues 444-579. This was consistent with sequence conservation among most-closely related primases. Linewidths in a NOESY spectrum of a 0.5 mM sample in 10 mM phosphate, pH 6.05, 0.1 M NaCl, recorded at 36 degreesC, indicated the protein to be monomeric. Crystals of selenomethionine-substituted DnaG(434-581) obtained by the hanging-drop vapor-diffusion method were body-centered tetragonal, space group I4(1)22, with unit cell parameters a = b 142.2 Angstrom, c = 192.1 Angstrom, and diffracted beyond 2.7 Angstrom resolution with synchrotron radiation. (C) 2003 Elsevier Inc. All rights reserved.

Generic delimitation and phylogenetic uncertainty: An example from a group that has undergone an explosive radiation

Phylogenetic trees can provide a stable basis for a higher-level classification of organisms that reflects evolutionary relationships. However, some lineages have a complex evolutionary history that involves explosive radiation or hybridisation. Such histories have become increasingly apparent with the use of DNA sequence data for phylogeny estimation and explain, in part, past difficulties in producing stable morphology-based classifications for some groups. We illustrate this situation by using the example of tribe Mirbelieae (Fabaceae), whose generic classification has been fraught for decades. In particular, we discuss a recent proposal to combine 19 of the 25 Mirbelieae genera into a single genus, Pultenaea sens. lat., and how we might find stable and consistent ways to squeeze something as complex as life into little boxes for our own convenience. © CSIRO.

Implications of current ecological thinking for biodiversity conservation: A review of the salient issues

Given escalating concern worldwide about the loss of biodiversity, and given biodiversity's centrality to quality of life, it is imperative that current ecological knowledge fully informs societal decision making. Over the past two decades, ecological science has undergone many significant shifts in emphasis and perspective, which have important implications for how we manage ecosystems and species. In particular, a shift has occurred from the equilibrium paradigm to one that recognizes the dynamic, non-equilibrium nature of ecosystems. Revised thinking about the spatial and temporal dynamics of ecological systems has important implications for management. Thus, it is of growing concern to ecologists and others that these recent developments have not been translated into information useful to managers and policy makers. Many conservation policies and plans are still based on equilibrium assumptions. A fundamental difficulty with integrating current ecological thinking into biodiversity policy and management planning is that field observations have yet to provide compelling evidence for many of the relationships suggested by non-equilibrium ecology. Yet despite this scientific uncertainty, management and policy decisions must still be made. This paper was motivated by the need for considered scientific debate on the significance of current ideas in theoretical ecology for biodiversity conservation. This paper aims to provide a platform for such discussion by presenting a critical synthesis of recent ecological literature that (1) identifies core issues in ecological theory, and (2) explores the implications of current ecological thinking for biodiversity conservation.

Ecology, values, and objectivity: Advancing the debate

We add to current discussions about the interface between ecology, values, and objectivity by reporting on a novel Delphi-based study of the scientific reasoning employed by a group of eight ecologists as they collectively considered current ecological thinking. We rely on contextual empiricism, with its features of multiple ways of relating theory to reality and science as a social activity, to provide a richer understanding of scientific objectivity. This understanding recognizes the place and contributions of values and, in so doing, moves the discussion beyond whether or not science is value neutral.

An evaluation of the evidence for linkages between mangroves and fisheries: A synthesis of the literature and identification of research directions

There is a widely held paradigm that mangroves are critical for sustaining production in coastal fisheries through their role as important nursery areas for fisheries species. This paradigm frequently forms the basis for important management decisions on habitat conservation and restoration of mangroves and other coastal wetlands. This paper reviews the current status of the paradigm and synthesises the information on the processes underlying these potential links. In the past, the paradigm has been supported by studies identifying correlations between the areal and linear extent of mangroves and fisheries catch. This paper goes beyond the correlative approach to develop a new framework on which future evaluations can be based. First, the review identifies what type of marine animals are using mangroves and at what life stages. These species can be categorised as estuarine residents, marine-estuarine species and marine stragglers. The marine-estuarine category includes many commercial species that use mangrove habitats as nurseries. The second stage is to determine why these species are using mangroves as nurseries. The three main proposals are that mangroves provide a refuge from predators, high levels of nutrients and shelter from physical disturbances. The recognition of the important attributes of mangrove nurseries then allows an evaluation of how changes in mangroves will affect the associated fauna. Surprisingly few studies have addressed this question. Consequently, it is difficult to predict how changes in any of these mangrove attributes would affect the faunal communities within them and, ultimately, influence the fisheries associated with them. From the information available, it seems likely that reductions in mangrove habitat complexity would reduce the biodiversity and abundance of the associated fauna, and these changes have the potential to cause cascading effects at higher trophic levels with possible consequences for fisheries. Finally, there is a discussion of the data that are currently available on mangrove distribution and fisheries catch, the limitations of these data and how best to use the data to understand mangrove-fisheries links and, ultimately, to optimise habitat and fisheries management. Examples are drawn from two relatively data-rich regions, Moreton Bay (Australia) and Western Peninsular Malaysia, to illustrate the data needs and research requirements for investigating the mangrove-fisheries paradigm. Having reliable and accurate data at appropriate spatial and temporal scales is crucial for mangrove-fisheries investigations. Recommendations are made for improvements to data collection methods that would meet these important criteria. This review provides a framework on which to base future investigations of mangrove-fisheries links, based on an understanding of the underlying processes and the need for rigorous data collection. Without this information, the understanding of the relationship between mangroves and fisheries will remain limited. Future investigations of mangrove-fisheries links must take this into account in order to have a good ecological basis and to provide better information and understanding to both fisheries and conservation managers.

The systematics and biology of the south African gall-inducing scale insect, Calycicoccus merwei brain (Hemiptera : Coccoidea : Eriococcidae)

The scale insect genus Calycicoccus Brain has a single described species, C. merwei Brain, which is endemic to southeastern South Africa. Females of C. merwei induce small, mostly conical galls on the foliage of their host tree, Apodytes dimidiata E. Meyer ex Arn. (Icacinaceae), which has a wider, mostly coastal distribution, than that currently known for the scale insect. Calycicoccus has been placed in the family Eriococcidae and may be related to the South American genus Aculeococcus Lepage. No other native eriococcid species have been described so far in South Africa, although the family is diverse in other Gondwanan regions. This paper summarizes the biology of C. merwei, redescribes the adult female, describes the adult male, the second-instar female and the first-instar nymphs for the first time, and reconsiders the phylogenetic relationships of the genus. The adult female is shown to have unusual abdominal segmentation, in that segment I is present both dorsally and ventrally, but a segment is absent ventrally on the middle abdomen. First-instar nymphs are sexually dimorphic; males have a larger and relatively narrower body, larger mouthparts, longer antennae and legs, and more thoracic dorsal setae compared with females. Molecular data from nuclear small-subunit ribosomal DNA (18S) and elongation factor 1 alpha (EF-1a) show C. merwei to have no close relatives among the Eriococcidae sampled to date. Instead, the Calycicoccus lineage is part of a polytomy near the base of the Eriococcidae. Molecular dating of the node suggests that the Calycicoccus lineage diverged from other eriococcids more than 100 Mya. These data support the placement of Calycicoccus as the only genus in the subfamily Calycicoccinae Brain.

The myosin-I-binding protein Acan125 binds the SH3 domain and belongs to the superfamily of leucine-rich repeat proteins

The SH3 domains of src and other nonreceptor tyrosine kinases have been shown to associate with the motif PXXP, where P and X stand for proline and an unspecified amino acid, but a motif that binds to the SH3 domain of myosin has thus far not been characterized. We previously showed that the SH3 domain of Acanthamoeba myosin-IC interacts with the protein Acan125. We now report that the Acan125 protein sequence contains two tandem consensus PXXP motifs near the C terminus. To test for binding, we expressed a polypeptide, AD3p, which includes 344 residues of native C-terminal sequence and a mutant polypeptide, AD3 Delta 977-994p, which lacks the sequence RPKPVPPPRGAKPAPPPR containing both PXXP motifs. The SH3 domain of Acanthamoeba myosin-IC bound AD3p and not AD3 Delta 977-994p, showing that the PXXP motifs are required for SH3 binding. The sequence of Acan125 is related overall to a protein of unknown function coded by Caenorhabditis elegans gene K07G5.1. The K07G5.1 gene product contains a proline-rich segment similar to the SH3 binding motif found in Acan125. The aligned sequences show considerable conservation of leucines and other hydrophobic residues, including the spacing of these residues, which matches a motif for leucine-rich repeats (LRRs). LRR domains have been demonstrated to be sites for ligand binding. Having an LRR domain and an SH3-binding domain, Acan125 and the C. elegans homologue define a novel family of bifunctional binding proteins.

The cell biology of atherosclerosis - new developments

In the development of atherosclerotic lesions, three basic processes occur: 1) invasion of the artery wall by leucocytes, particularly monocytes and T-lymphocytes; 2) smooth muscle phenotypic modulation, proliferation, and synthesis of extracellular matrix; and 3) intracellular (macrophage and smooth muscle) lipoprotein uptake and lipid accumulation. Invasion of the vessel wall by leucocytes is mediated through the expression of adhesion molecules on both leucocytes and the endothelium making them 'sticky'. The adhesion molecules are induced by high serum cholesterol levels or complement fragments. Leucocytes which have adhered to the endothelium are chemo-attracted into the vessel wall by cytokines produced by early arriving leucocytes or by low density lipoprotein which has passively passed into the wall, in the process being trapped and oxidised. The oxidised low density lipoprotein is taken up by scavenger receptors (which are not subject to down-regulation) on both macrophages and smooth muscle cells. The overaccumulation of lipid is toxic to the cells and they die contributing to the central necrotic core. The macrophages and T-lymphocytes produce substances which induce smooth muscle cells of the artery wall to change from a 'contractile' (high volume fraction of myofilaments [V(v)myo]) to a 'synthetic' (low V(v)myo) phenotype. In this altered state they respond to growth factors released from macrophages, platelets, regenerating endothelial cells and smooth muscle cells; produce large amounts of matrix; express lipoprotein scavenger receptors; express adhesion molecules for leucocytes; and express HLA-DR following exposure to the T-lymphocyte product, IFN-delta, suggesting that they can become involved in a generalised immune reaction.

Structural analysis of three His32 mutants of DsbA: Support for an electrostatic role of His32 in DsbA stability

DsbA, a 21-kDa protein from Escherichia coli, is a potent oxidizing disulfide catalyst required for disulfide bond formation in secreted proteins. The active site of DsbA is similar to that of mammalian protein disulfide isomerases, and includes a reversible disulfide bond formed from cysteines separated by two residues (Cys3O-Pro31-His32-Cys33). Unlike most protein disulfides, the active-site disulfide of DsbA is highly reactive and the oxidized form of DsbA is much less stable than the reduced form at physiological pH. His32, one of the two residues between the active-site cysteines, is critical to the oxidizing power of DsbA and to the relative instability of the protein in the oxidized form. Mutation of this single residue to tyrosine, serine, or leucine results in a significant increase in stability (of similar to 5-7 kcal/mol) of the oxidized His32 variants relative to the oxidized wild-type protein. Despite the dramatic changes in stability, the structures of all three oxidized DsbA His32 Variants are very similar to the wild-type oxidized structure, including conservation of solvent atoms near the active-site residue, Cys3O. These results show that the His32 residue does not exert a conformational effect on the structure of DsbA. The destabilizing effect of His32 on oxidized DsbA is therefore most likely electrostatic in nature.