Reconstruction of the ancestral marsupial karyotype from comparative gene maps

BACKGROUND: The increasing number of assembled mammalian genomes makes it possible to compare genome organisation across mammalian lineages and reconstruct chromosomes of the ancestral marsupial and therian (marsupial and eutherian) mammals. However, the reconstruction of ancestral genomes requires genome assemblies to be anchored to chromosomes. The recently sequenced tammar wallaby (Macropus eugenii) genome was assembled into over 300,000 contigs. We previously devised an efficient strategy for mapping large evolutionarily conserved blocks in non-model mammals, and applied this to determine the arrangement of conserved blocks on all wallaby chromosomes, thereby permitting comparative maps to be constructed and resolve the long debated issue between a 2n=14 and 2n=22 ancestral marsupial karyotype. RESULTS: We identified large blocks of genes conserved between human and opossum, and mapped genes corresponding to the ends of these blocks by fluorescence in situ hybridization (FISH). A total of 242 genes was assigned to wallaby chromosomes in the present study, bringing the total number of genes mapped to 554 and making it the most densely cytogenetically mapped marsupial genome. We used these gene assignments to construct comparative maps between wallaby and opossum, which uncovered many intrachromosomal rearrangements, particularly for genes found on wallaby chromosomes X and 3. Expanding comparisons to include chicken and human permitted the putative ancestral marsupial (2n=14) and therian mammal (2n=19) karyotypes to be reconstructed. CONCLUSIONS: Our physical mapping data for the tammar wallaby has uncovered the events shaping marsupial genomes and enabled us to predict the ancestral marsupial karyotype, supporting a 2n=14 ancestor. Futhermore, our predicted therian ancestral karyotype has helped to understand the evolution of the ancestral eutherian genome.

Muramidases found in the foregut microbiome of the Tammar wallaby can direct cell aggregation and biofilm formation

We describe here the role of muramidases present in clones of metagenomic DNA that result in cell aggregation and biofilm formation by Escherichia coli. The metagenomic clones were obtained from uncultured Lachnospiraceae-affiliated bacteria resident in the foregut microbiome of the Tammar wallaby. One of these fosmid clones (p49C2) was chosen for more detailed studies and a variety of genetic methods were used to delimit the region responsible for the phenotype to an open reading frame of 1425 bp. Comparative sequence analysis with other fosmid clones giving rise to the same phenotype revealed the presence of muramidase homologues with the same modular composition. Phylogenetic analysis of the fosmid sequence data assigned these fosmid inserts to recently identified, but uncultured, phylogroups of Lachnospiraceae believed to be numerically dominant in the foregut microbiome of the Tammar wallaby. The muramidase is a modular protein containing putative N-acetylmuramoyl--alanine amidase and an endo-β-N-acetylglucosaminidase catalytic module, with a similar organization and functional properties to some Staphylococcal autolysins that also confer adhesive properties and biofilm formation. We also show here that the cloned muramidases result in the production of extracellular DNA, which appears to be the key for biofilm formation and autoaggregation. Collectively, these findings suggest that biofilm formation and cell aggregation in gut microbiomes might occur via the concerted action of carbohydrate-active enzymes and the production of extracellular DNA to serve as a biofilm scaffold.

A transcriptome resource for the koala (Phascolarctos cinereus) : insights into koala retrovirus transcription and sequence diversity

Background The koala, Phascolarctos cinereus, is a biologically unique and evolutionarily distinct Australian arboreal marsupial. The goal of this study was to sequence the transcriptome from several tissues of two geographically separate koalas, and to create the first comprehensive catalog of annotated transcripts for this species, enabling detailed analysis of the unique attributes of this threatened native marsupial, including infection by the koala retrovirus. Results RNA-Seq data was generated from a range of tissues from one male and one female koala and assembled de novo into transcripts using Velvet-Oases. Transcript abundance in each tissue was estimated. Transcripts were searched for likely protein-coding regions and a non-redundant set of 117,563 putative protein sequences was produced. In similarity searches there were 84,907 (72%) sequences that aligned to at least one sequence in the NCBI nr protein database. The best alignments were to sequences from other marsupials. After applying a reciprocal best hit requirement of koala sequences to those from tammar wallaby, Tasmanian devil and the gray short-tailed opossum, we estimate that our transcriptome dataset represents approximately 15,000 koala genes. The marsupial alignment information was used to look for potential gene duplications and we report evidence for copy number expansion of the alpha amylase gene, and of an aldehyde reductase gene. Koala retrovirus (KoRV) transcripts were detected in the transcriptomes. These were analysed in detail and the structure of the spliced envelope gene transcript was determined. There was appreciable sequence diversity within KoRV, with 233 sites in the KoRV genome showing small insertions/deletions or single nucleotide polymorphisms. Both koalas had sequences from the KoRV-A subtype, but the male koala transcriptome has, in addition, sequences more closely related to the KoRV-B subtype. This is the first report of a KoRV-B-like sequence in a wild population. Conclusions This transcriptomic dataset is a useful resource for molecular genetic studies of the koala, for evolutionary genetic studies of marsupials, for validation and annotation of the koala genome sequence, and for investigation of koala retrovirus. Annotated transcripts can be browsed and queried at http://koalagenome.org

The importance of ecological scale for wildlife conservation in naturally fragmented environments: A case study of the Brush-Tailed Rock-Wallaby (Petrogale Penicillata)

Determining the ecologically relevant spatial scales for predicting species occurrences is an important concept when determining species–environment relationships. Therefore species distribution modelling should consider all ecologically relevant spatial scales. While several recent studies have addressed this problem in artificially fragmented landscapes, few studies have researched relevant ecological scales for organisms that also live in naturally fragmented landscapes. This situation is exemplified by the Australian rock-wallabies’ preference for rugged terrain and we addressed the issue of scale using the threatened brush-tailed rock-wallaby (Petrogale penicillata) in eastern Australia. We surveyed for brush-tailed rock-wallabies at 200 sites in southeast Queensland, collecting potentially influential site level and landscape level variables. We applied classification trees at either scale to capture a hierarchy of relationships between the explanatory variables and brush-tailed rock-wallaby presence/absence. Habitat complexity at the site level and geology at the landscape level were the best predictors of where we observed brush-tailed rock-wallabies. Our study showed that the distribution of the species is affected by both site scale and landscape scale factors, reinforcing the need for a multi-scale approach to understanding the relationship between a species and its environment. We demonstrate that careful design of data collection, using coarse scale spatial datasets and finer scale field data, can provide useful information for identifying the ecologically relevant scales for studying species–environment relationships. Our study highlights the need to determine patterns of environmental influence at multiple scales to conserve specialist species such as the brush-tailed rock-wallaby in naturally fragmented landscapes.

Comparison of three expert elicitation methods for logistic regression on predicting the presence of the threatened brush-tailed rock-wallaby petrogale penicillata

Numerous expert elicitation methods have been suggested for generalised linear models (GLMs). This paper compares three relatively new approaches to eliciting expert knowledge in a form suitable for Bayesian logistic regression. These methods were trialled on two experts in order to model the habitat suitability of the threatened Australian brush-tailed rock-wallaby (Petrogale penicillata). The first elicitation approach is a geographically assisted indirect predictive method with a geographic information system (GIS) interface. The second approach is a predictive indirect method which uses an interactive graphical tool. The third method uses a questionnaire to elicit expert knowledge directly about the impact of a habitat variable on the response. Two variables (slope and aspect) are used to examine prior and posterior distributions of the three methods. The results indicate that there are some similarities and dissimilarities between the expert informed priors of the two experts formulated from the different approaches. The choice of elicitation method depends on the statistical knowledge of the expert, their mapping skills, time constraints, accessibility to experts and funding available. This trial reveals that expert knowledge can be important when modelling rare event data, such as threatened species, because experts can provide additional information that may not be represented in the dataset. However care must be taken with the way in which this information is elicited and formulated.

Inferring kangaroo phylogeny from incongruent nuclear and mitochondrial genes

The marsupial genus Macropus includes three subgenera, the familiar large grazing kangaroos and wallaroos of M. (Macropus) and M. (Osphranter), as well as the smaller mixed grazing/browsing wallabies of M. (Notamacropus). A recent study of five concatenated nuclear genes recommended subsuming the predominantly browsing Wallabia bicolor (swamp wallaby) into Macropus. To further examine this proposal we sequenced partial mitochondrial genomes for kangaroos and wallabies. These sequences strongly favour the morphological placement of W. bicolor as sister to Macropus, although place M. irma (black-gloved wallaby) within M. (Osphranter) rather than as expected, with M. (Notamacropus). Species tree estimation from separately analysed mitochondrial and nuclear genes favours retaining Macropus and Wallabia as separate genera. A simulation study finds that incomplete lineage sorting among nuclear genes is a plausible explanation for incongruence with the mitochondrial placement of W. bicolor, while mitochondrial introgression from a wallaroo into M. irma is the deepest such event identified in marsupials. Similar such coalescent simulations for interpreting gene tree conflicts will increase in both relevance and statistical power as species-level phylogenetics enters the genomic age. Ecological considerations in turn, hint at a role for selection in accelerating the fixation of introgressed or incompletely sorted loci. More generally the inclusion of the mitochondrial sequences substantially enhanced phylogenetic resolution. However, we caution that the evolutionary dynamics that enhance mitochondria as speciation indicators in the presence of incomplete lineage sorting may also render them especially susceptible to introgression.

The complete mitochondrial genome of the eastern grey kangaroo (Macropus giganteus)

We present the complete mitochondrial genome (accession number: LK995454) of an iconic Australian species, the eastern grey kangaroo (Macropus giganteus). The mitogenomic organization is consistent with other marsupials, encoding 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, an origin of light strand replication and a control region or Dloop. No repetitive sequences were detected in the control region. The M. giganteus mitogenome exemplifies a combination of tRNA gene order and structural peculiarities that appear to be unique to marsupials. We present a maximum likelihood phylogeny based on complete mitochondrial protein and RNA coding sequences that confirms the phylogenetic position of the grey kangaroo among macropodids.

How useful is expert opinion for predicting the distribution of a species within and beyond the region of expertise? A case study using brush-tailed rock-wallabiesPetrogale penicillata

1. Species' distribution modelling relies on adequate data sets to build reliable statistical models with high predictive ability. However, the money spent collecting empirical data might be better spent on management. A less expensive source of species' distribution information is expert opinion. This study evaluates expert knowledge and its source. In particular, we determine whether models built on expert knowledge apply over multiple regions or only within the region where the knowledge was derived. 2. The case study focuses on the distribution of the brush-tailed rock-wallaby Petrogale penicillata in eastern Australia. We brought together from two biogeographically different regions substantial and well-designed field data and knowledge from nine experts. We used a novel elicitation tool within a geographical information system to systematically collect expert opinions. The tool utilized an indirect approach to elicitation, asking experts simpler questions about observable rather than abstract quantities, with measures in place to identify uncertainty and offer feedback. Bayesian analysis was used to combine field data and expert knowledge in each region to determine: (i) how expert opinion affected models based on field data and (ii) how similar expert-informed models were within regions and across regions. 3. The elicitation tool effectively captured the experts' opinions and their uncertainties. Experts were comfortable with the map-based elicitation approach used, especially with graphical feedback. Experts tended to predict lower values of species occurrence compared with field data. 4. Across experts, consensus on effect sizes occurred for several habitat variables. Expert opinion generally influenced predictions from field data. However, south-east Queensland and north-east New South Wales experts had different opinions on the influence of elevation and geology, with these differences attributable to geological differences between these regions. 5. Synthesis and applications. When formulated as priors in Bayesian analysis, expert opinion is useful for modifying or strengthening patterns exhibited by empirical data sets that are limited in size or scope. Nevertheless, the ability of an expert to extrapolate beyond their region of knowledge may be poor. Hence there is significant merit in obtaining information from local experts when compiling species' distribution models across several regions.

Two cycles of voluminous pyroclastic volcanism and sedimentation related to episodic granite emplacement during the late Archean : Eastern Yilgarn Craton, Western Australia

The thick piles of late-Archean volcaniclastic sedimentary successions that overlie the voluminous greenstone units of the eastern Yilgarn Craton, Western Australia, record the important transition from the cessation in mafic-ultramafic volcanism to cratonisation between about 2690 and 2655 Ma. Unfortunately, an inability to clearly subdivide the superficially similar sedimentary successions and correlate them between the various geological terranes and domains of the eastern Yilgarn Craton has led to uncertainty about the timing and nature of the region's palaeogeographic and palaeotectonic evolution. Here, we present the results of some 2025 U–Pb laser-ablation-ICP-MS analyses and 323 Sensitive High-Resolution Ion Microprobe (SHRIMP) analyses of detrital zircons from 14 late-Archean felsic clastic successions of the eastern Yilgarn Craton, which have enabled correlation of clastic successions. The results of our data, together with those compiled from previous studies, show that the post-greenstone sedimentary successions include two major cycles that both commenced with voluminous pyroclastic volcanism and ended with widespread exhumation and erosion associated with granite emplacement. Cycle One commences with an influx of rapidly reworked feldspar-rich pyroclastic debris. These units, here-named the Early Black Flag Group, are dominated by a single population of detrital zircons with an average age of 2690–2680 Ma. Thick (up to 2 km) dolerite bodies, such as the Golden Mile Dolerite, intrude the upper parts of the Early Black Flag Group at about 2680 Ma. Incipient development of large granite domes during Cycle One created extensional basins predominantly near their southeastern and northwestern margins (e.g., St Ives, Wallaby, Kanowna Belle and Agnew), into which the Early Black Flag Group and overlying coarse mafic conglomerate facies of the Late Black Flag Group were deposited. The clast compositions and detrital-zircon ages of the late Black Flag Group detritus match closely the nearby and/or stratigraphically underlying successions, thus suggesting relatively local provenance. Cycle Two involved a similar progression to that observed in Cycle One, but the age and composition of the detritus were notably different. Deposition of rapidly reworked quartz-rich pyroclastic deposits dominated by a single detrital-zircon age population of 2670–2660 Ma heralded the beginning of Cycle Two. These coarse-grained quartz-rich units, are name here the Early Merougil Group. The mean ages of the detrital zircons from the Early Merougil Group match closely the age of the peak in high-Ca (quartz-rich) granite magmatism in the Yilgarn Craton and thus probably represent the surface expression of the same event. Successions of the Late Merougil Group are dominated by coarse felsic conglomerate with abundant volcanic quartz. Although the detrital zircons in these successions have a broad spread of age, the principal sub-populations have ages of about 2665 Ma and thus match closely those of the Early Merougil Group. These successions occur most commonly at the northwestern and southeastern margins of the granite batholiths and thus are interpreted to represent resedimented units dominted by the stratigraphically underlying packages of the Early Merougil Group. The Kurrawang Group is the youngest sedimentary units identified in this study and is dominated by polymictic conglomerate with clasts of banded iron formation (BIF), granite and quartzite near the base and quartz-rich sandstone units containing detrital zircons aged up to 3500 Ma near the top. These units record provenance from deeper and/or more-distal sources. We suggest here that the principal driver for the major episodes of volcanism, sedimentation and deformation associated with basin development was the progressive emplacement of large granite batholiths. This interpretation has important implication for palaeogeographic and palaeotectonic evolution of all late-Archean terranes around the world.

Evolution of sexual segregation in mammalian herbivores: kangaroos as marsupial models

Sexual segregation is best known in sexually dimorphic ungulates. Many hypotheses have been proposed to explain the evolution of sexual segregation in ungulates, but all are reducible to the influence of two factors: body size and sex-specific reproductive strategy. Definitive tests of these hypotheses are lacking in ungulates because these factors are confounded, all males being somewhat larger than females. Kangaroos represent a parallel radiation of terrestrial herbivores, but their populations are composed of a spectrum of adult body sizes, ranging from small males the same size as females to large males more than twice the size. We exploited this heteromorphism to assess the independent influences of size and sex in these ungulate analogues. We conducted a preliminary study of western grey kangaroos (Macropus fuliginosus) in north-western Victoria, Australia. Adult males predominately occupied grassland habitat, whereas females occurred mostly in lakebed, woodland and shrubland. Single-sex groups occurred more often than expected during the non-mating season. The diet of large males had the highest proportion of grass, and females had the least. These initial results indicate that both size and sex influence segregation in this species, confirming the worth of kangaroos as marsupial models for research into the evolution of sexual segregation.