Body size and risk of extinction in Australian mammals

The link between body size and risk of extinction has been the focus of much recent attention. For Australian terrestrial mammals this link is of particular interest because it is widely believed that species in the intermediate size range of 35-5500 g (the critical weight range) have been the most prone to recent extinction. But the relationship between body size and extinction risk in Australian mammals has never been subject to a robust statistical analysis. Using a combination of randomization tests and phylogenetic comparative analyses, we found that Australian mammal extinctions and declines have been nonrandom with respect to body size, but we reject the hypothesis of a critical weight range at intermediate sizes. Small species appear to be the least prone to extinction, but extinctions have not been significantly clustered around intermediate sizes. Our results suggest that hypotheses linking intermediate body size with high risk of extinction in Australian mammals are misguided and that the focus of future research should shift to explaining why the smallest species are the most resistant to extinction.

Arbovirus of marine mammals: a new alphavirus isolated from the elephant seal louse, Lepidophthirus macrorhini

A novel alphavirus was isolated from the louse Lepidophthirus macrorhini, collected from southern elephant seals, Mirounga leonina, on Macquarie Island, Australia. The virus displayed classic alphavirus ultrastructure and appeared to be serologically different from known Australasian alphaviruses. Nearly all Macquarie Island elephant seals tested had neutralizing antibodies against the virus, but no virus-associated pathology has been identified, Antarctic Division personnel who have worked extensively with elephant seals showed no serological evidence of exposure to the virus. Sequence analysis illustrated that the southern elephant seal (SES) virus segregates,vith the Semliki Forest group of Australasian alphaviruses. Phylogenetic analysis of known alphaviruses suggests that alphaviruses might be grouped according to their enzootic vertebrate host class, The SES virus represents the first arbovirus of marine mammals and illustrates that alphaviruses can inhabit Antarctica and that alphaviruses can be transmitted by lice.

Revision of Australian Clistoabdominalis (Diptera : Pipunculidae)

The 29 Australian species of Clistoabdominalis Skevington are revised and a phylogenetic analysis is presented. The following 23 new species are proposed: Clistoabdominalis ancylus, C. angelikae, C. capillifascis, C. carnatistylus, C. collessi, C. colophus, C. condylostylus, C. danielsi, C. dasymelus, C. digitatus, C. exallus, C. gaban, C. gremialis, C. lambkinae, C. lingulatus, C. mathiesoni, C. nutatus, C. octiparvus, C. scalenus, C. scintillatus, C. tasmanicus, C. tharra, and C. yeatesi. Pipunculus picrodes Perkins is proposed as a junior synonym of C. trochanteratus (Becker). Diagnoses and an illustrated key to species are provided. A summary of host records for all Australian species of Pipunculidae is presented to clarify confusion in the literature. Pipunculidae are documented hilltopping for the first time. This mating strategy is used by many species of Clistoabdominalis and patterns of hilltopping within the genus are examined.

Gulliver, a long terminal repeat retrotransposon from the genome of the oriental blood fluke Schistosoma japonicum

We characterized the consensus sequence and structure of a long terminal repeat (LTR) retrotransposon from the genome of the human blood fluke, Schistosoma japonicum, and have earned this element, Gulliver. The full length, consensus Gulliver LTR retrotransposon was 4788 bp, and it was flanked at its 5'- and 3'-ends by LTRs of 259 bp. Each LTR included RNA polymerase II promoter sequences, a CAAT signal and a TATA box, Gulliver exhibited features characteristic of a functional LTR retrotransposon including two read through (termination) ORFs encoding retroviral gag and pol proteins of 312 and 1071 amino acid residues, respectively. The gag ORF encoded motifs conserved in nucleic acid binding proteins, while the pol ORF encoded conserved domains of aspartic protease, reverse transcriptase (RT), RNaseH and integrase, in that order, a pol pattern conserved in the gypsy lineage of LTR retrotransposons. Whereas the sequence and structure of Gulliver was similar to that of gypsy, phylogenetic analysis revealed that Gulliver did not group particularly closely with the gypsy family. Rather, its closest relatives were a LTR retrotransposon from Caenorhabditis elegans, mag from Bombyx mori and, to a lesser extent, easel from the salmon Oncorhynchus keta. Dot blot hybridizations indicated that Gulliver was present at between 100 and several thousand copies in the S. japonicum genome, and Southern hybridization analysis suggested its probable presence in the genome of Schistosoma mansoni. Transcripts encoding the RT domain of Gulliver were detected by RT-PCR in larval and adult stages of S. japonicum, indicating that (at least) the RT domain of Gulliver is transcribed. This is the first report of the sequence and structure of an LTR retrotransposon from any schistosome or indeed from any species belonging to the phylum Platyhelminthes. (C) 2001 Elsevier Science B.V. All rights reserved.

Complete DNA sequence and gene organization of the mitochondrial genome of the liverfluke, Fasciola hepatica L. (Platyhelminthes; Trematoda)

The complete nucleotide sequence of the mitochondrial (mt) DNA molecule of the liverfluke, Fasciola hepatica (phylum Platyhelminthes, class Trematoda, family Fasciolidae), was determined, It comprises 14462 bp, contains 12 protein-encoding, 2 ribosomal and 22 transfer RNA genes, and is the second complete flatworm (and the first trematode) mitochondrial sequence to be described in detail. All of the genes are transcribed from the same strand. Of the genes typically found in mitochondrial genomes of eumetazoans, only atp8 is absent. The nad4L and nad4 genes overlap by 40 nt. Most intergenic sequences are very short. Two larger non-coding regions are present. The longer one (817 nt) is located between trnG and cox3 and consists of 8 identical tandem repeats of 85 nt, rich in G and C, followed by 1 imperfect repeat. The shorter non-coding region (187 nt) exhibits no special features and is separated from the longer region by trnG. The gene arrangement resembles that of some other trematodes including the eastern Asian Schistosoma species (and cyclophyllidean cestode species) but it is strikingly different from that of the African schistosomes, represented by Schistosoma mansoni. The genetic code is as inferred previously for flatworms. Transfer RNA genes range in length from 58 to 70 nt, their products producing characteristic 'clover leaf' structures, except for tRNA(S-VON) and tRNA(S-AGN) lacking the DHU arm.

Amino acid residues in conodont elements

Thermally unaltered conodont elements, brachiopods. and vertebrates were analyzed with reverse phase high profile liquid chromatography to locate and quantify amino acid remnants of the original organic matrix in the fossils. No consistent similarities in amino acid content were found in conodont taxa. and criteria based on organic residues appear to have no taxonomic significance in the fossils tested from these localities. However, hydroxyproline. an amino acid that is found in the collagen molecules of animals. as well as in the glycoproteins in the cell walls and reproductive tissues of certain plants, is represented in most taxa. The organic matter retained in the impermeable crowns of conodont elements might have been derived originally from a form of collagen. Biochemical analyses. correlated with histochemical tests, demonstrate that organic matter is an integral part of the hyaline tissue of the element crown and not the result of surface contamination. Tests of a range of vertebrate and invertebrate fossil hard tissues produced similar results. The analyses indicate that hyaline tissue in the conodont element crown is not a form of vertebrate enamel. which contains no collagen. Albid tissue. with little or no organic content. is not a form of vertebrate bone or dentine, both based on collagen and low in mineral. Although these results do not help to determine the phylogenetic affinities of conodont animals, they indicate teat conodont elements do not contain hard tissues characteristic of vertebrate animals.

Hyaline tissue of thermally unaltered conodont elements and the enamel of vertebrates

Comparison of the ultrastructure of the hyaline tissue of conodont elements and the enamel of vertebrates provides little support for a close phylogenetic relationship between conodonts and vertebrates. Transmission and scanning electron microscopy shows that the mineralised component of the hyaline tissue of Panderodus and of Cordylodus elements consists of large, flat, oblong crystals, arranged in layers that run parallel to the long axis of the conodont. Enamel in the dentition of a living vertebrate, the lungfish Neoceratodus forsteri, has crystals of calcium hydroxyapatite, arranged in layers, and extending in groups from the dentine-enamel junction; the crystals are slender, elongate spicules perpendicular to the surface of the tooth plate, Similar crystal arrangements to those of lungfish are found in other vertebrates, but none resembles the organisation of the hyaline tissue of conodont elements, The crystals of hydroxyapatite in conodont hyaline tissue are exceptionally large, perpendicular or parallel to the surface of the element, with no trace of prisms, unlike the protoprismatic radial crystallite enamel of fish teeth and scales, or the highly organised prismatic enamel of mammals.

The marginal dentition of the Australian lungfish, Neoceratodus forsteri (Osteichthyes : Dipnoi)

The dentary, a component of the transient marginal dentition found in the mandible of juveniles of the living Australian lungfish Neoceratodus forsteri, is a tooth plate exactly comparable to the tooth plates with radiating ridges that make up the marginal dentitions of Devonian dipnoans like Andreyevichthys, Orlovichthys and Ichnomylax. In N. forsteri, the dentary consists of two ridges, set almost in line with each other, and growing by the addition of cusps, of increasing sizes, to the extremity of each ridge. It is therefore equivalent to two ridges of a more normal tooth plate with radiating ridges. Despite its appearance, as a long row of sharp cusps ankylosed to a slender bone, and its position, embedded in soft tissue above the anterolabial margin of Meckel's cartilage, it is a tooth plate and is not comparable to the marginal dentitions of other vertebrates. Structure and development of the transient marginal dentition of this lungfish is another indication that dipnoans may not be the sister group of tetrapods.

The life-history basis of latitudinal diversity gradients: how do species traits vary from the poles to the equator.

1. Latitudinal variation among species in life-history traits is often suggested to contribute to high tropical species richness. However, traditional methods of analysing such variation rarely control for phylogeny and latitudinal range overlap between species, potentially giving misleading results. 2. Using a method of pairwise independent contrasts which overcomes these problems, I tested for latitudinal variation among bird species in a number of traits which have been linked, theoretically or empirically, with both latitude and species richness. 3. This method indicates strong support for Rapoport's Rule and decreasing clutch size towards the equator in both hemispheres, but only partial support for decreasing body size and ecological generalism towards the equator. 4. Indirect measures of sexual selection (sexual dichromatism and size dimorphism) show no variation with latitude; an apparent increase in dichromatism towards the equator is shown to be an artefact of phylogeny. 5. Many of the associations between life history and latitude were not detected by traditional cross-species analyses, highlighting the importance of incorporating phylogeny and overlap in studies of geographical life-history variation. Establishing associations between life-history traits and latitude does not prove, but is a necessary prerequisite for., a link between these traits and latitudinal diversity gradients.

Molecular clocks in reptiles: Life history influences rate of molecular evolution

Life history has been implicated as a determinant of variation in rate of molecular evolution amongst vertebrate species because of a negative correlation between bode size and substitution rate for many Molecular data sets. Both the generality and the cause of the negative bode size trend have been debated, and the validity of key studies has been questioned (particularly concerning the failure to account for phylogenetic bias). In this study, a comparative method has been used to test for an association between a range of life-history variables-such as body size age at maturity, and clutch size-and DNA substitution rate for three genes (NADH4, cytochrome b, and c-mos). A negative relationship between body size and rate of molecular evolution was found for phylogenetically independent pairs of reptile species spanning turtles. lizards. snakes, crocodile, and tuatara. Although this Study was limited by the number of comparisons for which both sequence and lite-history data were available, the results, suggest that a negative bode size trend in rate of molecular evloution may be a general feature of reptile molecular evolution. consistent with similar studies of mammals and birds. This observation has important implications for uncovering the mechanisms of molecular evolution and warns against assuming that related lineages will share the same substitution rate (a local molecular clock) in order to date evolutionary divergences from DNA sequences.

Evolution and developmental expression of nuclear receptor genes in the ascidian Herdmania

Nuclear receptors are a superfamily of metazoan transcription factors that have been shown to be involved in a wide range of developmental and physiological processes. A PCR-based survey of genomic DNA and developmental cDNAs from the ascidian Herdmania identifies eight members of this multigene family. Sequence comparisons and phylogenetic analyses reveal that these ascidian nuclear receptors are representative of five of the six previously defined nuclear receptor subfamilies and are apparent homologues of retinoic acid [NR1B], retinoid X [NR2B], peroxisome proliferator-activated [NR1C], estrogen related [NR3B], neuron-derived orphan (NOR) [NR4A3], nuclear orphan [NR4A], TR2 orphan [NR2C1] and COUP orphan [NR2F3] receptors. Phylogenetic analyses that include the ascidian genes produce topologically distinct trees that suggest a redefinition of some nuclear receptor subfamilies. These trees also suggest that extensive gene duplication occurred after the vertebrates split from invertebrate chordates. These ascidian nuclear receptor genes are expressed differentially during embryogenesis and metamorphosis.

The anammox case - A new experimental manifesto for microbiological eco-physiology

The anaerobic ammonium oxidation process is a new process for ammonia removal from wastewater. It is also a new microbial physiology that was previously believed to be impossible. The identification of Candidatus Brocadia anammoxidans and its relatives as the responsible bacteria was only possible with the development of a new experimental approach. That approach is the focus of this paper. The approach is a modernisation of the Winogradsky/Beyerinck strategy of selective enrichment and is based on the introduction of the molecular toolbox and modern bioreactor engineering to microbial ecology. It consists of five steps: (1) postulation of an ecological niche based on thermodynamic considerations and macro-ecological field data; (2) engineering of this niche into a laboratory bioreactor for enrichment culture; (3) black-box physiological characterisation of the enrichment culture as a whole; (4) phylogenetic characterisation of the enriched community using molecular tools; (5) physical separation of the dominant members of the enrichment culture using gradient centrifugation and the identification of the species of interest in accordance with Koch's postulates; (6) verification of the in situ importance of these species in the actual ecosystems. The power of this approach is illustrated with a case study: the identification of the planctomycetes responsible for anaerobic ammonium oxidation. We argue that this was impossible using molecular ecology or conventional 'cultivation based techniques' alone. We suggest that the approach might also be used for the microbiological study of many interesting microbes such as anaerobic methane oxidisers.

Evidence for an independent radiation of endosymbiotic litostome ciliates within Australian marsupial herbivores

The recent discovery of isotrichid-like ciliates occurring as endosymbionts in macropodid marsupials posed interesting questions in regard to both their phyletic origin (all previous records confined to eutherian mammals) and their morphological evolution (Australian forms possibly representing missing links between previously described genera). The SSU rRNA gene was sequenced for three species (Dasytricha dehorityi, D. dogieli, and Batricha tasmaniensis) and aligned against representatives of all major ciliate classes. The Australian species did not group with the other isotrichid species but instead formed an independent radiation. Discrepancies between recent global phylogenies of the phylum Ciliophora were examined by manipulation of the aligned sequence data set. Sources of conflict between these studies did not stem from differences in outgroup choice or phylogenetic reconstruction methods. Differences in the application of confidence limits and primary sequence alignment have probably resulted in the reporting of spurious associations which are not supported by more conservative confidence or alignment methodology. At present, the ciliate subphylum Intramacro-nucleata is an unresolved polytomy which may be due to deficiencies in the SSU rRNA gene sequence dataset or indicate that the ciliates radiated into their extant classes by rapid burst-like evolution. (C) 2001 academic Press.

Transpecific microsatellites for hard pines M. Shepherd, M. Cross, T. Maguire, M. Dieters, C. Williams, R. Henry

Microsatellites are difficult to recover from large plant genomes so cross-specific utilisation is an important source of markers. Fifty micro satellites were tested for cross-specific amplification and polymorphism to two New World hard pine species, slash pine (Pinus elliottii var. elliottii) and Caribbean pine (R caribaea var. hondurensis). Twenty-nine (58%) markers amplified in both hard pine species, and 23 of these 29 were polymorphic. Soft pine (subgenus Strobus) microsatellite markers did amplify, but none were polymorphic. Pinus elliottii var. elliottii and R caribaea var. hondurensis showed mutational changes in the flanking regions and the repeat motif that were informative for Pinus spp. phylogenetic relationships. Most allele length variation could be attributed to variability in repeat unit number. There was no evidence for ascertainment bias.

Convergent maternal care strategies in ungulates and macropods

Mammals show extensive interspecific variation in the form of maternal care. Among ungulates, there is a dichotomy between species in which offspring follow the mother (following strategy) versus species in which offspring remain concealed (hiding strategy). Here we reveal that the same dichotomy exists among macropods (kangaroos, wallabies and allies). We test three traditional adaptive explanations and one new life history hypothesis. and find very similar patterns among both ungulates and macropods. The three traditional explanations that we tested were that a ''following'' strategy is associated with (1) open habitat, (2) large mothers, and (3) gregariousness. Our new life-history hypothesis is that a following strategy'' is associated with delayed weaning, and thus with the slow end of the slow-fast mammalian life-history continuum, because offspring devote resources to locomotion rather than rapid growth. Our comparative test strongly supports the habitat structure hypothesis and provides some support for this new delayed weaning hypothesis for both ungulates and macropods. We propose that sedentary young in closed habitats benefit energetically by having milk brought to them. In open habitats, predation pressure will select against hiding. Followers will suffer slower growth to independence. Taken together, therefore, our results provide the first quantitative evidence that macropods and ungulates are convergent with respect to interspecific variation in maternal care strategy. In both clades, differences between species in the form of parental care are due to a similar interaction between habitat, social behavior, and life history.