ORCID Profile
0000-0002-9906-0673
Current Organisations
University of Melbourne
,
Murdoch University
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Publisher: Museums Victoria
Date: 2006
Publisher: Public Library of Science (PLoS)
Date: 16-04-2008
Publisher: Portico
Date: 21-01-2013
Publisher: Wiley
Date: 17-11-2015
DOI: 10.1111/GEB.12255
Publisher: Springer Science and Business Media LLC
Date: 31-07-2014
Publisher: CSIRO Publishing
Date: 2012
DOI: 10.1071/SB10049
Abstract: Although the Australasian grass genus Austrostipa is species rich, abundant and ecologically significant, the subgeneric classification of its 62 species has not been comprehensively tested with molecular data. We used three molecular markers from 51 species to determine a phylogeny of the genus and found strong support for the following seven of the existing subgenera: Falcatae, Austrostipa, Aulax, Lobatae, Bambusina, Lancea and Longiaristatae. The molecular data do not support Tuberculatae and Eremophilae, which could be combined with subgenus Austrostipa. The data are equivocal or insufficient regarding monophyly of Ceres, Arbuscula, Petaurista and Lanterna. Data from the nuclear internal transcribed spacer region appear to be suitable for phylogenetic analysis of this group, and the degree of sequence variability resolves species-level relationships with good levels of support. In contrast, chloroplast sequence data from the matK and rbcL genes do not resolve most relationships at the species level, and the inferred phylogeny hints at gene duplication, chloroplast capture, or deep coalescence in the evolutionary history of Austrostipa.
Publisher: GigaScience Press
Date: 20-12-2021
DOI: 10.46471/GIGABYTE.36
Abstract: Organelle genomes are typically represented as single, static, circular molecules. However, there is evidence that the chloroplast genome exists in two structural haplotypes and that the mitochondrial genome can display multiple circular, linear or branching forms. We sequenced and assembled chloroplast and mitochondrial genomes of the Golden Wattle, Acacia pycnantha, using long reads, iterative baiting to extract organelle-only reads, and several assembly algorithms to explore genomic structure. Using a de novo assembly approach agnostic to previous hypotheses about structure, we found that different assemblies revealed contrasting arrangements of genomic segments a hypothesis supported by mapped reads spanning alternate paths.
Publisher: Oxford University Press (OUP)
Date: 09-2019
DOI: 10.1093/GIGASCIENCE/GIZ109
Abstract: Bioinformatics software tools are often created ad hoc, frequently by people without extensive training in software development. In particular, for beginners, the barrier to entry in bioinformatics software development is high, especially if they want to adopt good programming practices. Even experienced developers do not always follow best practices. This results in the proliferation of poorer-quality bioinformatics software, leading to limited scalability and inefficient use of resources lack of reproducibility, usability, adaptability, and interoperability and erroneous or inaccurate results. We have developed Bionitio, a tool that automates the process of starting new bioinformatics software projects following recommended best practices. With a single command, the user can create a new well-structured project in 1 of 12 programming languages. The resulting software is functional, carrying out a prototypical bioinformatics task, and thus serves as both a working ex le and a template for building new tools. Key features include command-line argument parsing, error handling, progress logging, defined exit status values, a test suite, a version number, standardized building and packaging, user documentation, code documentation, a standard open source software license, software revision control, and containerization. Bionitio serves as a learning aid for beginner-to-intermediate bioinformatics programmers and provides an excellent starting point for new projects. This helps developers adopt good programming practices from the beginning of a project and encourages high-quality tools to be developed more rapidly. This also benefits users because tools are more easily installed and consistent in their usage. Bionitio is released as open source software under the MIT License and is available at ionitio-team/bionitio.
Publisher: Wiley
Date: 11-04-2011
DOI: 10.1111/J.1095-8649.2011.02962.X
Abstract: This study investigated the feeding ecology of King George whiting Sillaginodes punctatus recruits to determine how diet composition varies between habitat types (seagrass and unvegetated habitats), and between sites separated by distance. Broad-scale s ling of seagrass and unvegetated habitats at nine sites in Port Phillip Bay (Australia) indicated the diet composition varied more by distance into the bay than by habitat. Near the entrance to the bay the diet was dominated by harpacticoids and gammarid hipods, in the middle reaches of the bay the diet was completely dominated by harpacticoids, while at sites furthest into the bay, mysids and crab zoea were also important. Abundances of prey in guts was significantly higher between 1000 and 2200 hours compared with other times, indicating diurnal feeding. Laboratory determined gut evacuation rate (based on an exponential model) was estimated to be -0·54. Daily rations were highly variable among sites and habitat types. Sillaginodes punctatus recruits consumed much higher quantities of prey on unvegetated habitat than seagrass habitat at some middle reach sites with prey consumption of harpacticoid copepods on unvegetated habitat approaching 3000 in iduals per day at one site. The results of this study provide insight into why habitat associations of S. punctatus recruits within mosaics of seagrass and unvegetated habitat show high spatial variation.
Publisher: MDPI AG
Date: 17-02-2022
DOI: 10.3390/ANI12040501
Abstract: Lamb growth can be optimised with genetic selection using sire Australian sheep breeding values, however, breeding value expression has been shown to be reduced with poor nutrition. It was therefore hypothesised that the genetic potential for lamb growth would also be reduced, where production factors such as multiple births limit growth. Live weights at birth, weaning, and post-weaning were collected from more than 18,000 lambs produced over five years and eight locations of the Sheep Cooperative Research Centre Information Nucleus Flock experiment, and the impact of environment, production factors, and genotype was determined using mixed effects regression. The genetic potential for lamb growth was moderated by environment, multiple births, and sire type (p 0.05). Twin lambs achieved 76% of the expected weight gain at weaning and 58% post-weaning. For triplet lambs weight gains were drastically less at approximately 30% of the expected gain at the same time points. Lambs born to maternal sires consistently had the poorest response to genetic selection, achieving approximately half the expected weight gain. Hence, producers need to temper expectations for growth based on genetic selection, or employ mitigation strategies such as precision feeding, the use of alternate breeds, or place emphasis on the genetic merit of other desirable traits.
Publisher: Elsevier BV
Date: 11-2019
DOI: 10.1016/J.FOODRES.2019.108528
Abstract: This study investigated the effect of three ageing methods (dry, wet and stepwise wet-then-dry) and ageing time on pH, colour, yield, lipid and protein oxidation and eating quality of beef loins using Meat Standards Australia (MSA) sensory protocols with 900 and 540 consumers in Australia and Japan, respectively. Australian beef loins (Longissimus thoracis et lumborum) at four days post mortem were subjected to wet ageing (boneless for 7, 21, 35 or 56 days), dry ageing (bone-in for 35 or 56 days) or a wet-then-dry ageing method (bone-in 21 days wet ageing followed by 35 days dry ageing). The pH was higher in dry aged than wet aged beef loins (P < .001). Instrumental measurement of surface colour of trimmed dry and wet aged steaks showed significant differences in a*, b* and hue angle. Weight loss was higher in dry aged primals (P < .001), however, total water content was similar among the two ageing methods (P = .934). Retail yield did not differ between 35 and 56 days dry aged primals. Lipid (TBARS) and protein (total carbonyl content) oxidation between the dry and wet aged s les differed depending on the ageing time. When comparing the wet-then-dry and 56 days dry aged s les, only pH and retail yield differed. Australian and Japanese consumers rated dry aged steaks significantly higher (P < .001) than the wet aged counterparts for tenderness, juiciness, flavour, overall liking and weighted palatability scores. The wet-then-dry steaks were also rated higher than the 56 days wet aged steaks for flavour, overall liking and palatability within the Japanese sensory panels. The Japanese consumers also consistently rated all MSA sensory attributes lower (P < .001) than the Australian consumers. The results from this study show dry ageing provides a value adding opportunity for the meat industry in both domestic and export markets.
Publisher: Cold Spring Harbor Laboratory
Date: 23-12-2020
DOI: 10.1101/2020.12.22.423164
Abstract: Although organelle genomes are typically represented as single, static, circular molecules, there is evidence that the chloroplast genome exists in two structural haplotypes and that the mitochondrial genome can display multiple circular, linear or branching forms. We sequenced and assembled chloroplast and mitochondrial genomes of the Golden Wattle, Acacia pycnantha, using long reads, iterative baiting to extract organelle-only reads, and several assembly algorithms to explore genomic structure. Using a de novo assembly approach agnostic to previous hypotheses about structure, we found different assemblies revealed contrasting arrangements of genomic segments a hypothesis supported by mapped reads spanning alternate paths.
Publisher: Cold Spring Harbor Laboratory
Date: 03-06-2022
DOI: 10.1101/2022.06.02.494505
Abstract: There is an ongoing explosion of scientific datasets being generated, brought on by recent technological advances in many areas of the natural sciences. As a result, the life sciences have become increasingly computational in nature, and bioinformatics has taken on a central role in research studies. However, basic computational skills, data analysis and stewardship are still rarely taught in life science educational programs [1], resulting in a skills gap in many of the researchers tasked with analysing these big datasets. In order to address this skills gap and empower researchers to perform their own data analyses, the Galaxy Training Network (GTN) has previously developed the Galaxy Training Platform ( training.galaxyproject.org ) an open access, community-driven framework for the collection of FAIR training materials for data analysis utilizing the user-friendly Galaxy framework as its primary data analysis platform [2]. Since its inception, this training platform has thrived, with the number of tutorials and contributors growing rapidly, and the range of topics extending beyond life sciences to include topics such as climatology, cheminformatics and machine learning. While initially aimed at supporting researchers directly, the GTN framework has proven to be an invaluable resource for educators as well. We have focused our efforts in recent years on adding increased support for this growing community of instructors. New features have been added to facilitate the use of the materials in a classroom setting, simplifying the contribution flow for new materials, and have added a set of train-the-trainer lessons. Here, we present the latest developments in the GTN project, aimed at facilitating the use of the Galaxy Training materials by educators, and its usage in different learning environments.
Publisher: Springer Science and Business Media LLC
Date: 20-09-2011
Publisher: Elsevier BV
Date: 2019
Publisher: Informa UK Limited
Date: 03-2012
DOI: 10.3852/11-092
Abstract: Australian collections of sequestrate Agaricaceae were examined with morphological and molecular data (nuclear DNA from ITS and LSU), and the majority were found to belong to the genera Agaricus and Macrolepiota. Previously described Australian species of Endoptychum are transferred to the appropriate agaricoid genera and several new combinations proposed. Descriptions and illustrations are provided for these and eight new species: Agaricus eburneocanus sp. nov., A. chartaceus sp. nov., A. erythrosarx sp. nov., A. inilleasper sp. nov., A. pachydermus sp. nov., Macrolepiota gasteroidea sp. nov., M. vinaceofibrillosa sp. nov. and M. turbinata sp. nov. The sequestrate genus Barcheria is retained as a distinct taxon. Timing of evolution of sequestrate sporocarp forms in Macrolepiota, Chlorophyllum and Agaricus seems to have occurred in the past 15 000 000 y, and a stem age is approximately 65 000 000 y for Barcheria.
Publisher: CSIRO Publishing
Date: 2016
DOI: 10.1071/SB16013
Abstract: Pimelea Banks & Sol. ex Gaertn. is a genus of flowering plants comprising an estimated 90 species in Australia and ~35 species in New Zealand. The genus is economically important, with the inflorescences of some species having floricultural applications, and the presence of toxic compounds in several species proving poisonous to livestock. Pimelea grows in a variety of habitats ranging from arid to alpine, suggesting a complicated biogeographic history. The relationships within Pimelea remain largely uncertain, despite previous attempts at clarification using molecular phylogenetics. However, it is clear that Pimelea is closely related to Thecanthes Wikstr., with the two genera comprising the subtribe Pimeleinae. We used Bayesian and maximum-likelihood phylogenetic analyses of four plastid markers (matK, rbcL, rps16, trnL–F) and one nuclear ribosomal marker (ITS) to examine the evolutionary relationships within Pimeleinae. We found strong support for the monophyly of Pimeleinae but, similar to previous studies, Pimelea was paraphyletic with respect to Thecanthes. Our results also indicated that P. longiflora R.Br. subsp. longiflora and P. longiflora subsp. eyrei (F.Muell.) Rye are best considered as distinct species. Therefore, we reduce Thecanthes to synonymy with Pimelea, making the necessary new combination Pimelea filifolia (Rye) C.S.P.Foster et M.J.Henwood (previously Thecanthes filifolia Rye), and also reinstate Pimelea eyrei F.Muell.
Publisher: American Society for Microbiology
Date: 26-02-2019
Abstract: S. pneumoniae is a component of the commensal nasopharyngeal microflora of humans, but from this reservoir, it can progress to localized or invasive disease with a frequency that translates into massive global morbidity and mortality. However, the factors that govern the switch from commensal to pathogen, as well as those that determine disease tropism, are poorly understood. Here we show that capacity to utilize raffinose can determine the nature of the disease caused by a given pneumococcal strain. Moreover, our findings provide an interesting ex le of convergent evolution, whereby pneumococci belonging to two unrelated serotypes/lineages exhibit SNPs in separate genes affecting raffinose uptake and utilization that correlate with distinct pathogenic profiles in vivo . This further underscores the critical role of differential carbohydrate metabolism in the pathogenesis of localized versus invasive pneumococcal disease.
Publisher: Oxford University Press (OUP)
Date: 21-04-2022
DOI: 10.1093/NAR/GKAC247
Abstract: Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute to the project, with support from multiple national infrastructure providers that enable freely accessible analysis and training services. The Galaxy Training Network supports free, self-directed, virtual training with & integrated tutorials. Project engagement metrics have continued to grow over the last 2 years, including source code contributions, publications, software packages wrapped as tools, registered users and their daily analysis jobs, and new independent specialized servers. Key Galaxy technical developments include an improved user interface for launching large-scale analyses with many files, interactive tools for exploratory data analysis, and a complete suite of machine learning tools. Important scientific developments enabled by Galaxy include Vertebrate Genome Project (VGP) assembly workflows and global SARS-CoV-2 collaborations.
Publisher: Springer Science and Business Media LLC
Date: 30-04-2010
Abstract: Duplication and ergence of genes and genetic networks is hypothesized to be a major driver of the evolution of complexity and novel features. Here, we examine the history of genes and genetic networks in the context of eye evolution by using new approaches to understand patterns of gene duplication during the evolution of metazoan genomes. We hypothesize that 1) genes involved in eye development and phototransduction have duplicated and are retained at higher rates in animal clades that possess more distinct types of optical design and 2) genes with functional relationships were duplicated and lost together, thereby preserving genetic networks. To test these hypotheses, we examine the rates and patterns of gene duplication and loss evident in 19 metazoan genomes, including that of Daphnia pulex - the first completely sequenced crustacean genome. This is of particular interest because the pancrustaceans (hexapods+crustaceans) have more optical designs than any other major clade of animals, allowing us to test specifically whether the high amount of disparity in pancrustacean eyes is correlated with a higher rate of duplication and retention of vision genes. Using protein predictions from 19 metazoan whole-genome projects, we found all members of 23 gene families known to be involved in eye development or phototransduction and deduced their phylogenetic relationships. This allowed us to estimate the number and timing of gene duplication and loss events in these gene families during animal evolution. When comparing duplication/retention rates of these genes, we found that the rate was significantly higher in pancrustaceans than in either vertebrates or non-pancrustacean protostomes. Comparing patterns of co-duplication across Metazoa showed that while these eye-genes co-duplicate at a significantly higher rate than those within a randomly shuffled matrix, many genes with known functional relationships in model organisms did not co-duplicate more often than expected by chance. Overall, and when accounting for factors such as differential rates of whole-genome duplication in different groups, our results are broadly consistent with the hypothesis that genes involved in eye development and phototransduction duplicate at a higher rate in Pancrustacea, the group with the greatest variety of optical designs. The result that these genes have a significantly high number of co-duplications and co-losses could be influenced by shared functions or other unstudied factors such as synteny. Since we did not observe co-duplication/co-loss of genes for all known functional modules (e.g. specific regulatory networks), the interactions among suites of known co-functioning genes (modules) may be plastic at the temporal scale of analysis performed here. Other factors in addition to gene duplication - such as cis-regulation, heterotopy, and co-option - are also likely to be strong factors in the ersification of eye types.
Publisher: Oxford University Press (OUP)
Date: 24-08-2011
Abstract: Complex organs such as eyes are commonly lost during evolution, but the timescale on which lost phenotypes could be reactivated is a matter of long-standing debate, with important implications for the molecular mechanisms of trait loss. Two phylogenetic approaches have been used to test whether regain of traits has occurred. One way is by comparison of nested, continuous-time Markov models of trait evolution, approaches that we term tree-based tests. A second way to demonstrate statistical support for trait regain is through use of node-based tests that employ explicit estimation of ancestral node states. Here, we estimate new molecular and morphological phylogenies and use them to examine the possibility of eye regain and dispersal between abyssal and shallow seas during the history of cylindroleberidid ostracods, a family of about 200 species, comprising both eyeless and sighted species. First, we confirmed that eye presence/absence is correlated with habitat depth. Parameter estimates from a phylogenetic model indicate that speciation is more rapid in deep-sea eyeless clades compared with shallow-water sighted clades. In addition, we found that tree-based statistical tests usually indicated reversals, including both transitions from deep to shallow seas and regain of eyes. In contrast, node-based statistical tests usually failed to show significant support for reversals. These results also hold for simulated phylogenies, indicating that they are not unique to the current data set. We recommend that both tree-based and node-based tests should be examined before making conclusions about character reversal and that ideally, alternative character histories should be tested using additional data, besides just the phylogenetic distribution of presence/absence of the characters.
No related grants have been discovered for Anna Syme.