Approximating persistence in a general class of population processes

We provide a general framework for estimating persistence in populations which may be affected by catastrophic events, and which are either unbounded or have very large ceilings. We model the population using a birth-death process modified to allow for downward jumps of arbitrary size. For such processes, it is typically necessary to truncate the process in order to make the evaluation of expected extinction times (and higher-order moments) computationally feasible. Hence, we give particular attention to the selection of a cut-off point at which to truncate the process, and we present a simple method for obtaining quantitative indicators of the suitability of a chosen cut-off. (c) 2005 Elsevier Inc. All rights reserved.

Novel mitochondrial gene content and gene arrangement indicate illegitimate inter-mtDNA recombination in the chigger mite, Leptotrombidium pallidum

To better understand the evolution of mitochondrial (mt) genomes in the Acari (mites and ticks), we sequenced the mt genome of the chigger mite, Leptotrombidium pallidum (Arthropoda: Acari: Acariformes). This genome is highly rearranged relative to that of the hypothetical ancestor of the arthropods and the other species of Acari studied. The mt genome of L. pallidum has two genes for large subunit rRNA, a pseudogene for small subunit rRNA, and four nearly identical large noncoding regions. Nineteen of the 22 tRNAs encoded by this genome apparently lack either a T-arm or a D-arm. Further, the mt genome of L. pallidum has two distantly separated sections with identical sequences but opposite orientations of transcription. This arrangement cannot be accounted for by homologous recombination or by previously known mechanisms of mt gene rearrangement. The most plausible explanation for the origin of this arrangement is illegitimate inter-mtDNA recombination, which has not been reported previously in animals. In light of the evidence from previous experiments on recombination in nuclear and mt genomes of animals, we propose a model of illegitimate inter-mtDNA recombination to account for the novel gene content and gene arrangement in the mt genome of L. pallidum.

Effects of Photosystem II inhibiting herbicides on mangroves - preliminary toxicology trials

Mangroves are sensitive to the root application of Photosystem II inhibiting herbicides and Avicennia marina is more sensitive than other mangroves tested. Seedlings of four mangrove species, including two salt-excreting species (A. marina and Aegiceras corniculatum) and two salt-excluding species (Rhizophora stylosa and Ceriops australis) were treated with a range of concentrations of the herbicides diuron, ametryn and atrazine. Assessment of responses required the separation of seedlings into two groups: those that had only their roots exposed to the herbicides through the water (A. marina and R. stylosa) and those that had both roots and leaves exposed to herbicides through the water (A. corniculatum and C australis). Salt-excreting species in each group were more susceptible to all herbicide treatments than salt-excluding species, indicating that root physiology was a major factor in the uptake of toxic pollutants in mangroves. Submergence of leaves appeared to facilitate herbicide uptake, having serious implications for seedling recruitment in the field. Each herbicide was ranked by its toxicity to mangrove seedlings from most damaging to least effective, with diuron > ametryn > atrazine. The relative sensitivity of A. marina found in these pot trials was consistent with the observed sensitivity of this species in the field, notably where severe dieback had specifically affected A. marina in the Mackay region, north eastern Australia. (c) 2004 Elsevier Ltd. All rights reserved.

Sociality and the rate of molecular evolution

The molecular clock does not tick at a uniform rate in all taxa but maybe influenced by species characteristics. Eusocial species (those with reproductive division of labor) have been predicted to have faster rates of molecular evolution than their nonsocial relatives because of greatly reduced effective population size; if most individuals in a population are nonreproductive and only one or few queens produce all the offspring, then eusocial animals could have much lower effective population sizes than their solitary relatives, which should increase the rate of substitution of nearly neutral mutations. An earlier study reported faster rates in eusocial honeybees and vespid wasps but failed to correct for phylogenetic nonindependence or to distinguish between potential causes of rate variation. Because sociality has evolved independently in many different lineages, it is possible to conduct a more wide-ranging study to test the generality of the relationship. We have conducted a comparative analysis of 25 phylogenetically independent pairs of social lineages and their nonsocial relatives, including bees, wasps, ants, termites, shrimps, and mole rats, using a range of available DNA sequences (mitochondrial and nuclear DNA coding for proteins and RNAs, and nontranslated sequences). By including a wide range of social taxa, we were able to test whether there is a general influence of sociality on rates of molecular evolution and to test specific predictions of the hypothesis: (1) that social species have faster rates because they have reduced effective population sizes; (2) that mitochondrial genes would show a greater effect of sociality than nuclear genes; and (3) that rates of molecular evolution should be correlated with the degree of sociality. We find no consistent pattern in rates of molecular evolution between social and nonsocial lineages and no evidence that mitochondrial genes show faster rates in social taxa. However, we show that the most highly eusocial Hymenoptera do have faster rates than their nonsocial relatives. We also find that social parasites (that utilize the workers from related species to produce their own offspring) have faster rates than their social relatives, which is consistent with an effect of lower effective population size on rate of molecular evolution. Our results illustrate the importance of allowing for phylogenetic nonindependence when conducting investigations of determinants of variation in rate of molecular evolution.

Genotoxicity of inorganic lead salts and disturbance of microtubule function

Lead compounds are known genotoxicants, principally affecting the integrity of chromosomes. Lead chloride and lead acetate induced concentration-dependent increases in micronucleus frequency in V79 cells, starting at 1.1 μ M lead chloride and 0.05 μ M lead acetate. The difference between the lead salts, which was expected based on their relative abilities to form complex acetato-cations, was confirmed in an independent experiment. CREST analyses of the micronuclei verified that lead chloride and acetate were predominantly aneugenic (CREST-positive response), which was consistent with the morphology of the micronuclei (larger micronuclei, compared with micronuclei induced by a clastogenic mechanism). The effects of high concentrations of lead salts on the microtubule network of V79 cells were also examined using immunofluorescence staining. The dose effects of these responses were consistent with the cytotoxicity of lead(II), as visualized in the neutral-red uptake assay. In a cell-free system, 20-60 μ M lead salts inhibited tubulin assembly dose-dependently. The no-observed-effect concentration of lead(II) in this assay was 10 μ M. This inhibitory effect was interpreted as a shift of the assembly/disassembly steady-state toward disassembly, e.g., by reducing the concentration of assembly-competent tubulin dimers. The effects of lead salts on microtubule-associated motor-protein functions were studied using a kinesin-gliding assay that mimics intracellular transport processes in vitro by quantifying the movement of paclitaxel-stabilized microtubules across a kinesin-coated glass surface. There was a dose-dependent effect of lead nitrate on microtubule motility. Lead nitrate affected the gliding velocities of microtubules starting at concentrations above 10 μ M and reached half-maximal inhibition of motility at about 50 μ M. The processes reported here point to relevant interactions of lead with tubulin and kinesin at low dose levels. Environ. Mal. Mutagen. 45:346-353, 2005. © 2005 Wiley-Liss, Inc.

Small regulatory RNAs in mammals

Mammalian cells harbor numerous small non-protein-coding RNAs, including small nucleolar RNAs (snoRNAs), microRNAs (miRNAs), short interfering RNAs (siRNAs) and small double-stranded RNAs, which regulate gene expression at many levels including chromatin architecture, RNA editing, RNA stability, translation, and quite possibly transcription and splicing. These RNAs are processed by multistep pathways from the introns and exons of longer primary transcripts, including protein-coding transcripts. Most show distinctive temporal- and tissue-specific expression patterns in different tissues, including embryonal stem cells and the brain, and some are imprinted. Small RNAs control a wide range of developmental and physiological pathways in animals, including hematopoietic differentiation, adipocyte differentiation and insulin secretion in mammals, and have been shown to be perturbed in cancer and other diseases. The extent of transcription of non-coding sequences and the abundance of small RNAs suggests the existence of an extensive regulatory network on the basis of RNA signaling which may underpin the development and much of the phenotypic variation in mammals and other complex organisms and which may have different genetic signatures from sequences encoding proteins.

Phylogeography of an east Australian wet-forest bird, the satin bowerbird (Ptilonorhynchus violaceus), derived from mtDNA, and its relationship to morphology

Australian wet forests have undergone a contraction in range since the mid-Tertiary, resulting in a fragmented distribution along the east Australian coast incorporating several biogeographical barriers. Variation in mitochondrial DNA and morphology within the satin bowerbird was used to examine biogeographical structure throughout almost the entire geographical extent of these wet forest fragments. We used several genetic analysis techniques, nested clade and barrier analyses, that use patterns inherent in the data to describe the spatial structuring. We also examined the validity of the two previously described satin bowerbird subspecies that are separated by well-defined biogeographical barriers and tested existing hypotheses that propose divergence occurs within each subspecies across two other barriers, the Black Mountain corridor and the Hunter Valley. Our data showed that the two subspecies were genetically and morphologically divergent. The northern subspecies, found in the Wet Tropics region of Queensland, showed little divergence across the Black Mountain corridor, a barrier found to be significant in other Wet Tropics species. Biogeographical structure was found through southeastern Australia; three geographically isolated populations showed genetic differentiation, although minimal divergence was found across the proposed Hunter Valley barrier. A novel barrier was found separating inland and coastal populations in southern New South Wales. Little morphological divergence was observed within subspecies, bar a trend for birds to be larger in the more southerly parts of the species' range. The results from both novel and well-established genetic analyses were similar, providing greater confidence in the conclusions about spatial divergence and supporting the validity of these new techniques.

Water quality condition and trend in North Queensland waterways

The Queensland Environmental Protection Agency monitored water quality at 133 sites in North Queensland waterways between Cooktown and Bundaburg from 1992 to 2001. Condition of the waterways was rated by comparing recent data with the Queensland Water Quality Guidelines. Long-term trends were analysed using a censored regression technique that incorporates the effects of flow, temperature, seasonality and allows for long-term non-linear trends. Many sites were in good condition; those in poor condition were usually impacted by point source discharges; those in moderate condition were usually impacted by agricultural land use. There were no consistent long-term trends across the whole region. Recommendations for future programs include incorporating pressure indicators, ensuring high standards of quality assurance, including covariates such as rainfall in trend assessment and continuing programs over more than 10 years to allow detection of trends due to changes in land-use. (c) 2004 Elsevier Ltd. All rights reserved.

Ecosystem response to antibiotics entering the aquatic environment

Awareness of antibiotics in wastewaters and aquatic ecosystems is growing as investigations into alternate pollutants increase and analytical techniques for detecting these chemicals improve. The presence of three antibiotics (ciproffoxacin, norfloxacin and cephalexin) was evaluated in both sewage effluent and environmental waters downstream from a sewage discharge. Bacteria cultured from the sewage bioreactor and receiving waters were tested for resistance against six antibiotics (ciprofloxacin, tetracycline, ampicillin, trimethoprim, erythromycin and trimethoprim/sulphamethoxazole) and effects of short term exposure (24h) to antibiotics on bacterial denitrification rates were examined. Antibiotics were detected entering the sewage treatment plant with varying levels of removal during the treatment process. Antibiotics were also detected in effluent entering receiving waters and detectable 500m from the source. Among the bacteria cultured from the sewage bioreactor, resistance was displayed against all six antibiotics tested and bacteria cultured from receiving waters were resistant against two of the antibiotics tested. Rates of denitrification were observed to decrease in response to some antibiotics and not to others, though this was only observed at concentrations exceeding those likely to be found in the environment. Findings from this preliminary research have indicated that antibiotics are entering our aquatic systems and pose a potential threat to ecosystem function and potentially human health. (c) 2004 Elsevier Ltd. All rights reserved.

Water quality in the Great Barrier Reef region: responses of mangrove, seagrass and macroalgal communities

Marine plants colonise several interconnected ecosystems in the Great Barrier Reef region including tidal wetlands, seagrass meadows and coral reefs. Water quality in some coastal areas is declining from human activities. Losses of mangrove and other tidal wetland communities are mostly the result of reclamation for coastal development of estuaries, e.g. for residential use, port infrastructure or marina development, and result in river bank destabilisation, deterioration of water clarity and loss of key coastal marine habitat. Coastal seagrass meadows are characterized by small ephemeral species. They are disturbed by increased turbidity after extreme flood events, but generally recover. There is no evidence of an overall seagrass decline or expansion. High nutrient and substrate availability and low grazing pressure on nearshore reefs have lead to changed benthic communities with high macroalgal abundance. Conservation and management of GBR macrophytes and their ecosystems is hampered by scarce ecological knowledge across macrophyte community types. (c) 2004 Elsevier Ltd. All rights reserved.

Application of a novel phytotoxicity assay for the detection of herbicides in Hervey Bay and the Great Sandy Straits

A novel phytotoxicity assay was incorporated into an environmental assessment of Hervey Bay and the Great Sandy Straits, to investigate the role of run-off associated herbicides in the deteriorated health of intertidal seagrass meadows. Dose response curves of common herbicides were performed and their toxicity equivalents elucidated to assist in analysis. The results of the assay were reproducible and corresponded strongly with results of chemical analyses. The incorporation of the assay into the assessment of surface waters added an important aspect to the study by allowing investigation of the toxicity of cumulative herbicide concentrations and yielding biologically relevant data. The highest herbicide concentration detected during the study was equivalent to 0.23 mu g 1(-1) diuron; a concentration known to inhibit photosynthetic efficiency of the assay biomaterial by approximately 3%. (c) 2004 Elsevier Ltd. All rights reserved.

Effects of the herbicide diuron on the early life history stages of coral

The effects of the herbicide diuron on the early life history stages of broadcast spawning and brooding corals were examined in laboratory experiments. Fertilisation of Acropora millepora and Montipora aequituberculata oocytes were not inhibited at diuron concentrations of up to 1000 mu gl(-1). Metamorphosis of symbiont-free A. millepora larvae was only significantly inhibited at 300 mu gl(-1) diuron. Pocillopora damicornis larvae, which contain symbiotic dinoflagellates, were able to undergo metamorphosis after 24h exposure to diuron at 1000 mu gl(-1). Two-week old P. damicornis recruits on the other hand were as susceptible to diuron as adult colonies, with expulsion of symbiotic dinoflagellates (bleaching) evident at 10 mu gl(-1) diuron after 96 h exposure. Reversible metamorphosis was observed at high diuron concentrations, with fully bleached polyps escaping from their skeletons. Pulse amplitude modulation (PAM) chlorophyll fluorescence techniques demonstrated a reduction in photosynthetic efficiency (Delta F/F'(m)) in illuminated P. dami- cornis recruits after a 2h exposure to 1 mu gl(-1) diuron. The dark-adapted quantum yields (F-v/F-m also declined, indicating chronic photoinhibition and damage to photosystem H. Crown Copyright (c) 2004 Published by Elsevier Ltd. All rights reserved.

Evolution of duplicate control regions in the mitochondrial genomes of metazoa: A case study with Australasian Ixodes ticks

To investigate the evolution pattern and phylogenetic utility of duplicate control regions (CRs) in mitochondrial (mt) genomes, we sequenced the entire mt genomes of three Ixodes species and part of the mt genomes of another I I species. All the species from the Australasian lineage have duplicate CRs, whereas the other species have one CR. Sequence analyses indicate that the two CRs of the Australasian Ixodes ticks have evolved in concert in each species. In addition to the Australasian Ixodes ticks, species from seven other lineages of metazoa also have mt genomes with duplicate CRs. Accumulated mtDNA sequence data from these metazoans and two recent experiments on replication of mt genomes in human cell lines with duplicate CRs allowed us to re-examine four intriguing questions about the presence of duplicate CRs in the mt genomes of metazoa: (1) Why do some mt genomes, but not others, have duplicate CRs? (2) How did mt genomes with duplicate CRs evolve? (3) How could the nucleotide sequences of duplicate CRs remain identical or very similar over evolutionary time? (4) Are duplicate CRs phylogenetic markers? It appears that mt genomes with duplicate CRs have a selective advantage in replication over mt genomes with one CR. Tandem duplication followed by deletion of genes is the most plausible mechanism for the generation of mt genomes with duplicate CRs. Once duplicate CRs occur in an mt genome, they tend to evolve in concert, probably by gene conversion. However, there are lineages where gene conversion may not always occur, and, thus, the two CRs may evolve independently in these lineages. Duplicate CRs have much potential as phylogenetic markers at low taxonomic levels, such as within genera, within families, or among families, but not at high taxonomic levels, such as among orders.