Two distinct forms of Chlamydia psittaci associated with disease and infertility in Phascolarctos cinereus (Koala)

While several diseases associated with Chlamydia psittaci infection have been reported in Phascolarctos cinereus (koala), it is still unclear whether one or more chlamydial strains are responsible. In this study, we provide evidence, obtained by restriction enzyme and gene probe analysis, that two quite distinct strains of C. psittaci infect koalas; one strain was isolated from the conjunctivae, and the other was isolated from the urogenital tract and the rectum. A gene probe, pFEN207, containing the coding sequence for an enzyme involved in the biosynthesis of the chlamydial genus-specific lipopolysaccharide antigen, and a separate probe, pCPML-4N, prepared from a DNA fragment of a koala-infecting strain of C. psittaci, were used to determine the patterns of hybridization in the koala-infecting strains; these patterns were found to be quite distinct from those observed with C. psittaci isolates from other animals. We also demonstrated by hybridization analysis with an avian strain plasmid that all three koala urogenital isolates contain a plasmid and that there is no evidence for the presence of a homologous plasmid in any of the ocular isolates

Unexpected high abyssal ophiuroid diversity in polymetallic nodule fields of the Northeast Pacific Ocean, and implications for conservation

The largest and commercially appealing mineral deposits can be found in the abyssal seafloor of the Clarion-Clipperton Zone (CCZ), a polymetallic nodule province, in the NE Pacific Ocean, where experimental mining is due to take place. In anticipation of deep-sea mining impacts, it has become essential to rapidly and accurately assess biodiversity. For this reason, ophiuroid material collected during seven scientific cruises from five exploration license areas within CCZ, one area protected from mining (APEI3, Area of Particular Environmental Interest) in the periphery of CCZ and the DIS-turbance and re-COLonisation (DISCOL) Experimental Area (DEA), in the SE Pacific Ocean, was examined. Specimens were genetically analysed using a fragment of the mitochondrial cytochrome c oxidase subunit I (COI). Maximum Likelihood and Neighbour Joining trees were constructed, while four tree-based and distance-based methods of species delineation (ABGD, BINs, GMYC, mPTP) were employed to propose Secondary Species Hypotheses (SSHs) within the ophiuroids collected. The species delimitations analyses concordant results revealed the presence of 43 deep-sea brittle stars SSHs, revealing an unexpectedly high diversity and showing that the most conspicuous invertebrates in abyssal plains have been so far considerably under-estimated. The number of SSHs found in each area varied from 5 (IFREMER area) to 24 (BGR area), while 13 SSHs were represented by singletons. None of the SSHs was found to be present in all 7 areas, while the majority of species (44.2 %) had a single-area presence (19 SSHs). The most common species were Ophioleucidae sp. (Species 29), Amphioplus daleus (Species 2) and Ophiosphalma glabrum (Species 3), present in all areas except APEI3. The biodiversity patterns could be mainly attributed to POC fluxes that could explain the highest species numbers found in BGR (German contractor area) and UKSRL (UK contractor area) areas. The five exploration contract areas belong to a mesotrophic province, while in contrary the APEI3 is located in an oligotrophic province which could explain the lowest diversity as well as very low similarity with the other six study areas. Based on these results the representativeness and the appropriateness of APEI3 to meet its purpose of preserving the biodiversity of the CCZ fauna are questioned. Finally, this study provides the foundation for biogeographic and functional analyses that will provide insight into the drivers of species diversity and its role in ecosystem function

Unexpected high abyssal ophiuroid diversity in polymetallic nodule fields of the Northeast Pacific Ocean, and implications for conservation

The largest and commercially appealing mineral deposits can be found in the abyssal seafloor of the Clarion-Clipperton Zone (CCZ), a polymetallic nodule province, in the NE Pacific Ocean, where experimental mining is due to take place. In anticipation of deep-sea mining impacts, it has become essential to rapidly and accurately assess biodiversity. For this reason, ophiuroid material collected during seven scientific cruises from five exploration license areas within CCZ, one area protected from mining (APEI3, Area of Particular Environmental Interest) in the periphery of CCZ and the DIS-turbance and re-COLonisation (DISCOL) Experimental Area (DEA), in the SE Pacific Ocean, was examined. Specimens were genetically analysed using a fragment of the mitochondrial cytochrome c oxidase subunit I (COI). Maximum Likelihood and Neighbour Joining trees were constructed, while four tree-based and distance-based methods of species delineation (ABGD, BINs, GMYC, mPTP) were employed to propose Secondary Species Hypotheses (SSHs) within the ophiuroids collected. The species delimitations analyses concordant results revealed the presence of 43 deep-sea brittle stars SSHs, revealing an unexpectedly high diversity and showing that the most conspicuous invertebrates in abyssal plains have been so far considerably under-estimated. The number of SSHs found in each area varied from 5 (IFREMER area) to 24 (BGR area), while 13 SSHs were represented by singletons. None of the SSHs was found to be present in all 7 areas, while the majority of species (44.2 %) had a single-area presence (19 SSHs). The most common species were Ophioleucidae sp. (Species 29), Amphioplus daleus (Species 2) and Ophiosphalma glabrum (Species 3), present in all areas except APEI3. The biodiversity patterns could be mainly attributed to POC fluxes that could explain the highest species numbers found in BGR (German contractor area) and UKSRL (UK contractor area) areas. The five exploration contract areas belong to a mesotrophic province, while in contrary the APEI3 is located in an oligotrophic province which could explain the lowest diversity as well as very low similarity with the other six study areas. Based on these results the representativeness and the appropriateness of APEI3 to meet its purpose of preserving the biodiversity of the CCZ fauna are questioned. Finally, this study provides the foundation for biogeographic and functional analyses that will provide insight into the drivers of species diversity and its role in ecosystem function

Phylogeny of snakes (Serpentes): combining morphological and molecular data in likelihood Bayesian and parsimony analyses

Copyright © 2007 The Natural history MuseumThe phylogeny of living and fossil snakes is assessed using likelihood and parsimony approaches and a dataset combining 263 morphological characters with mitochondrial (2693 bp) and nuclear (1092 bp) gene sequences. The ‘no common mechanism’ (NCMr) and ‘Markovian’ (Mkv) models were employed for the morphological partition in likelihood analyses; likelihood scores in the NCMr model were more closely correlated with parsimony tree lengths. Both models accorded relatively less weight to the molecular data than did parsimony, with the effect being milder in the NCMr model. Partitioned branch and likelihood support values indicate that the mtDNA and nuclear gene partitions agree more closely with each other than with morphology. Despite differences between data partitions in phylogenetic signal, analytic models, and relative weighting, the parsimony and likelihood analyses all retrieved the following widely accepted groups: scolecophidians, alethinophidians, cylindrophiines, macrostomatans (sensu lato) and caenophidians. Anilius alone emerged as the most basal alethinophidian; the combined analyses resulted in a novel and stable position of uropeltines and cylindrophiines as the second-most basal clade of alethinophidians. The limbed marine pachyophiids, along with Dinilysia and Wonambi, were always basal to all living snakes. Other results stable in all combined analyses include: Xenopeltis and Loxocemus were sister taxa (fide morphology) but clustered with pythonines (fide molecules), and Ungaliophis clustered with a boine-erycine clade (fide molecules). Tropidophis remains enigmatic; it emerges as a basal alethinophidian in the parsimony analyses (fide molecules) but a derived form in the likelihood analyses (fide morphology), largely due to the different relative weighting accorded to data partitions.Michael S. Y. Lee, Andrew F. Hugall, Robin Lawson & John D. Scanlo

Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle

As top predators, falcons possess unique morphological, physiological and behavioral adaptations that allow them to be successful hunters: for example, the peregrine is renowned as the world's fastest animal. To examine the evolutionary basis of predatory adaptations, we sequenced the genomes of both the peregrine (Falco peregrinus) and saker falcon (Falco cherrug), and we present parallel, genome-wide evidence for evolutionary innovation and selection for a predatory lifestyle. The genomes, assembled using Illumina deep sequencing with greater than 100-fold coverage, are both approximately 1.2 Gb in length, with transcriptome-assisted prediction of approximately 16,200 genes for both species. Analysis of 8,424 orthologs in both falcons, chicken, zebra finch and turkey identified consistent evidence for genome-wide rapid evolution in these raptors. SNP-based inference showed contrasting recent demographic trajectories for the two falcons, and gene-based analysis highlighted falcon-specific evolutionary novelties for beak development and olfaction and specifically for homeostasis-related genes in the arid environment–adapted saker

Variation in Phenotype, Parasite Load and Male Competitive Ability across a Cryptic Hybrid Zone

BackgroundMolecular genetic studies are revealing an increasing number of cryptic lineages or species, which are highly genetically divergent but apparently cannot be distinguished morphologically. This observation gives rise to three important questions: 1) have these cryptic lineages diverged in phenotypic traits that may not be obvious to humans; 2) when cryptic lineages come into secondary contact, what are the evolutionary consequences: stable co-existence, replacement, admixture or differentiation and 3) what processes influence the evolutionary dynamics of these secondary contact zones?Methodology/principal findingsTo address these questions, we first tested whether males of the Iberian lizard Lacerta schreiberi from two highly genetically divergent, yet morphologically cryptic lineages on either side of an east-west secondary contact could be differentiated based on detailed analysis of morphology, coloration and parasite load. Next, we tested whether these differences could be driven by pre-copulatory intra-sexual selection (male-male competition). Compared to eastern males, western males had fewer parasites, were in better body condition and were more intensely coloured. Although subtle environmental variation across the hybrid zone could explain the differences in parasite load and body condition, these were uncorrelated with colour expression, suggesting that the differences in coloration reflect heritable divergence. The lineages did not differ in their aggressive behaviour or competitive ability. However, body size, which predicted male aggressiveness, was positively correlated with the colour traits that differed between genetic backgrounds.Conclusions/significanceOur study confirms that these cryptic lineages differ in several aspects that are likely to influence fitness. Although there were no clear differences in male competitive ability, our results suggest a potential indirect role for intra-sexual selection. Specifically, if lizards use the colour traits that differ between genetic backgrounds to assess the size of potential rivals or mates, the resulting fitness differential favouring western males could result in net male-mediated gene flow from west to east across the current hybrid zone.Devi Stuart-Fox, Raquel Godinho, Joëlle Goüy de Bellocq, Nancy R. Irwin, José Carlos Brito, Adnan Moussalli, Pavel Široký, Andrew F. Hugall and Stuart J. E. Bair

Phylogenetic evidence for mid-Cenozoic turnover of a diverse continental biota

Rapid climatic change at the beginning of the Oligocene epoch is concordant with global biotic turnover in the fossil record. However, while Southern Hemisphere geological movement played a key role in shaping these global climatic shifts, given generally poor terrestrial fossil records, evidence for matching turnover in entire Austral biotas is lacking. Emerging comprehensive phylogenetic frameworks provide alternative avenues to explore for signals of mass turnover or restructuring. Here, we combine phylogenetic data with empirical and simulation-based approaches to understand the temporal dynamics of the origins of a diverse and highly endemic continental biota (Australian lizards and snakes). These analyses indicate that the temporal clustering of major radiation ages in Gondwanan endemic lineages and immigration into Australia is narrower than expected under time-continuous models assuming no overarching external perturbation. Independent phylogenetic dating analyses further indicate that the timing of both processes is concentrated in the period post-dating the Eocene–Oligocene transition (~34 million years ago). Epoch-defining processes around the start of the Oligocene appear to have also played a decisive role in reshaping a diverse Southern Hemisphere biota—by both re-setting Gondwanan endemic diversity and opening the way to successful immigration from the north.P.M.O. was supported by a McKenzie Postdoctoral Fellowship from the University of Melbourne and an Australian Reseach Council Early Career Researcher Fellowship

Phylogénie des Megascolecidae et Crassiclitellata (Annelida, Oligochaeta) : analyse combinée contre analyse partitionée, utilisant l'ADNr nucléaire (28S) et mitochondrial (12S, 16S)

Chez les oligochètes mégascolécoides, une analyse de l\u27ADNr nucléaire (28S) et mitochondrial (12S et 16S), utilisant la parcimonie et la vraisemblance, le soutien des partitions et les tests de taux de vraisemblance, indique que toutes les classifications supragénériques des Megascolecidae sont incompatibles avec les données moléculaires. Les deux jeux de données, nucléaire et mitochondrial, peuvent présenter des incompatibilités historiques ou méthodologiques et nous explorons donc l\u27effet du soutien et du conflit sur les mesures, à trois niveaux : 1) analyses séparées ; 2) combinaison des données avec un seul modèle ; et 3) combinaison des soutiens pour des topologies en compétition en utilisant des modèles séparés. La puissance de résolution est identifiée par le soutien des partitions, le consensus, et quatre tests de taux de vraisemblance en compétition. L\u27analyse combinée identifie le soutien caché et le conflit ; des modèles plus complexes réduisent ce conflit, probablement parce qu\u27ils suppriment une hétérogénéité dynamique et produisent un consensus mieux résolu. Ceci est incompatible avec les classifications morphologiques, qui sont plus ou moins rejetées en fonction du test de taux de vraisemblance utilisé. La congruence et le soutien de pouvoir combiné soutiennent nos conclusions : la plupart des groupements ont été basés sur des homoplasies, par exemple l\u27origine multiple des prostates racémeuses et de la méronéphridie de « type Dichogastrinae ». La classification largement utilisée des Megascolescidae non-Ocnerodrelinae en trois groupes (Acanthodrilidae, avec prostate tubulaire et holonéphridie ; Octochaetidae, avec prostate tubulaire et méronéphridie ; Megascolescidae, avec prostate racémeuse) n\u27est pas soutenue par les données moléculaires. La monophylie des Crassiclitellata Jamieson, 1988, oligochètes avec un clitellum à plusieurs couches, est confirmée. Les résultats fournissent des arguments pour l\u27inclusion des branchiobdellides et des hirudinées dans les oligochètes.Analysis of megascolecoid oligochaete (earthworms and allies) nuclear 28S rDNA and mitochondrial 12S and 16S rDNA using parsimony and likelihood, partition support and likelihood ratio tests, indicates that all higher, suprageneric, classifications within the Megascolecidae are incompatible with the molecular data. The two data-sets (nuclear and mitochondrial) may have historical or methodological incompatabilities therefore we explore the effect on measures of support and conflict at three levels: 1) separate analysis; 2) combining the data with single model; and 3) combining the relative support for competing topologies using separate models. Resolving power is identified via partition support, consensus and four competing likelihood ratio tests. Combined analysis identifies hidden support and conflict; more complex models reduce this conflict, possibly owing to removal of dynamic heterogeneity, and give a more resolved consensus. This is incompatible with morphological classifications, rejection of which varies among likelihood ratio tests. Both congruence and combined power support our conclusions: most of the groupings are based on homoplasies, for instance, multiple origin of racemose prostates or of "dichogastrin" meronephridia. The widely used classification of the non-ocnerodrilin Megascolecidae into three groups (Acanthodrilidae, with tubular prostates and holonephridia; Octochaetidae, with tubular prostates and meronephridia; and Megascolecidae, with racemose prostates) is not supported by molecular data. Monophyly of the Crassiclitellata Jamieson, 1988, oligochaetes with a multilayered clitellum, is confirmed. The results provide support for including the branchiobdellids and leeches in the Oligochaeta.</p

Samples 3 gene alignment

Genbank details for samples used in new phylogenetic analyses presented in this study