ORCID Profile
0000-0003-3955-6674
Current Organisations
Deakin University - Melbourne Burwood Campus
,
Aberystwyth University
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Publisher: Informa UK Limited
Date: 03-02-2016
DOI: 10.3109/19401736.2014.880897
Abstract: The complete mitochondrial genome of Cherax glaber was sequenced using the HiSeq platform. The mitogenome consists of 15,806 base pairs containing 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The Cherax glaber has a base composition of 32.39% for T, 22.42% for C, 33.73% for A and 11.46% for G, with an AT bias of 66.12%.
Publisher: Informa UK Limited
Date: 29-04-2014
Publisher: Informa UK Limited
Date: 29-04-2016
DOI: 10.3109/19401736.2014.913162
Abstract: The complete mitochondrial genome of the iconic Australian freshwater fish, the Murray Cod, Maccullochella peelii, was recovered from partial genome sequencing data using the HiSeq platform (Illumina, San Diego, CA). The mitogenome consists of 16,442 bp (58% A + T content) containing 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 768 bp non-coding AT-rich region. This is the first mitogenome sequence for the genus Maccullochella, and the fourth for the family Percichthyidae.
Publisher: Springer Science and Business Media LLC
Date: 08-12-2010
Publisher: Informa UK Limited
Date: 19-02-2016
DOI: 10.3109/19401736.2015.1007348
Abstract: The complete mitogenome of the ray Taeniura lymma was recovered from genome skimming using the HiSeq sequencing system. The T. lymma mitogenome has 17,652 base pairs (59.13% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a 1906 bp non-coding AT-rich region. This mitogenome sequence is the second for a ray from Australian waters, the first for the genus Taeniura and the ninth for the family Dasyatidae.
Publisher: Oxford University Press (OUP)
Date: 10-2015
DOI: 10.1093/GBE/EVV186
Publisher: Springer Science and Business Media LLC
Date: 28-11-2017
Publisher: Informa UK Limited
Date: 17-01-2016
DOI: 10.3109/19401736.2013.878907
Abstract: The complete mitochondrial genome of Cherax cainii was recovered from partial genome sequencing data using the HiSeq platform. The mitogenome consists of 15,801 base pairs (69% A + T content) containing 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a 783 bp non-coding AT-rich region. This is the second completely sequenced mitogenome from the genus Cherax after the first reported Cherax destructor mitogenome nearly a decade ago.
Publisher: Informa UK Limited
Date: 08-08-2016
DOI: 10.3109/19401736.2014.947586
Abstract: The complete mitogenome of the ray Pastinachus atrus was recovered from a partial genome scan using the HiSeq sequencing system. The P. atrus mitogenome has 18,162 base pairs (61% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 2516 bp non-coding AT-rich region. This mitogenome sequence is the first for a ray from Australian waters, the first for the Genus Pastinachus, and the 6th for the family Dasyatidae.
Publisher: Wiley
Date: 02-11-2016
DOI: 10.1111/EVO.13091
Publisher: Elsevier BV
Date: 04-2015
DOI: 10.1016/J.YMPEV.2015.02.009
Abstract: The increased rate at which complete mitogenomes are being sequenced and their increasing use for phylogenetic studies have resulted in a bioinformatic bottleneck in preparing and utilising such data for phylogenetic analysis. Hence, we present MitoPhAST, an automated tool that (1) identifies annotated protein-coding gene features and generates a standardised, concatenated and partitioned amino acid alignment directly from complete artial GenBank/EMBL-format mitogenome flat files, (2) generates a maximum likelihood phylogenetic tree using optimised protein models and (3) reports various mitochondrial genes and sequence information in a table format. To demonstrate the capacity of MitoPhAST in handling a large dataset, we used 81 publicly available decapod mitogenomes, together with eight new complete mitogenomes of Australian freshwater crayfishes, including the first for the genus Gramastacus, to undertake an updated test of the monophyly of the major groups of the order Decapoda and their phylogenetic relationships. The recovered phylogenetic trees using both Bayesian and ML methods support the results of studies using fragments of mtDNA and nuclear markers and other smaller-scale studies using whole mitogenomes. In comparison to the fragment-based phylogenies, nodal support values are generally higher despite reduced taxon s ling suggesting there is value in utilising more fully mitogenomic data. Additionally, the simple table output from MitoPhAST provides an efficient summary and statistical overview of the mitogenomes under study at the gene level, allowing the identification of missing or duplicated genes and gene rearrangements. The finding of new mtDNA gene rearrangements in several genera of Australian freshwater crayfishes indicates that this group has undergone an unusually high rate of evolutionary change for this organelle compared to other major families of decapod crustaceans. As a result, freshwater crayfishes are likely to be a useful model for studies designed to understand the evolution of mtDNA rearrangements. We anticipate that our bioinformatics pipeline will substantially help mitogenome-based studies increase the speed, accuracy and efficiency of phylogenetic studies utilising mitogenome information. MitoPhAST is available for download at ht85/MitoPhAST.
Publisher: Wiley
Date: 13-03-2014
DOI: 10.1002/ECE3.1016
Publisher: Springer Science and Business Media LLC
Date: 11-09-2016
Publisher: Elsevier BV
Date: 2018
DOI: 10.1016/J.YMPEV.2017.09.022
Abstract: To further understand the evolutionary history and mitogenomic features of Australia's highly distinctive freshwater crayfish fauna, we utilized a recently described rapid mitogenome sequencing pipeline to generate 24 new crayfish mitogenomes including a ersity of burrowing crayfish species and the first for Astacopsis gouldi, the world's largest freshwater invertebrate. Whole mitogenome-based phylogeny estimates using both Bayesian and Maximum Likelihood methods substantially strengthen existing hypotheses for systematic relationships among Australian freshwater crayfish with evidence of pervasive ersifying selection and accelerated mitochondrial substitution rate among the members of the clade representing strongly burrowing crayfish that may reflect selection pressures for increased energy requirement for adaptation to terrestrial environment and a burrowing lifestyle. Further, gene rearrangements are prevalent in the burrowing crayfish mitogenomes involving both tRNA and protein coding genes. In addition, duplicated control regions were observed in two closely related Engaeus species, together with evidence for concerted evolution. This study significantly adds to the understanding of Australian freshwater crayfish evolutionary relationships and suggests a link between mitogenome evolution and adaptation to terrestrial environments and a burrowing lifestyle in freshwater crayfish.
Publisher: Informa UK Limited
Date: 14-04-2016
DOI: 10.3109/19401736.2014.908361
Abstract: The complete mitochondrial genome of the enigmatic freshwater crayfish Engaeus lyelli was sequenced using the MiSeq Personal Sequencer (Illumina, San Diego, CA). The mitogenome has 16,027 bp consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 23 transfer RNAs, and a non-coding AT-rich region. The base composition of E. lyelli is 29.01% for T, 27.13% for C, 31.43% for A, and 12.44% for G, with an AT bias of 60.44%. The species has the distinctive gene order characteristic of parastacid crayfish with the exception of some minor rearrangements involving the tRNA genes.
Publisher: Springer Science and Business Media LLC
Date: 20-07-2010
Publisher: Elsevier BV
Date: 08-2020
Publisher: Elsevier BV
Date: 06-2015
Publisher: Informa UK Limited
Date: 20-05-2016
DOI: 10.3109/19401736.2014.919460
Abstract: The mitogenome of the black yabby, Geocharax gracilis, was sequenced using the MiSeq Personal Sequencer. It has 15,924 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 23 transfer RNAs, and a non-coding AT-rich region. The base composition of G. gracilis mitogenome is 32.18% for T, 22.32% for C, 34.83% for A, and 10.68% for G, with an AT bias of 67.01%. The mitogenome gene order is typical for that of parastacid crayfish with the exception of some minor rearrangements involving tRNA genes.
Publisher: Cambridge University Press (CUP)
Date: 04-2003
DOI: 10.1017/S0031182002002925
Abstract: The use of naturally infected hosts in studies attempting to identify parasite-induced changes in host biology is problematical because it does not eliminate the possibility that infection may be a consequence, rather than a cause, of host trait variation. In addition, uncontrolled concomitant infections may confound results. In this study we experimentally infected in idual laboratory-bred female three-spined sticklebacks Gasterosteus aculeatus L. with the pseudophyllidean cestode Schistocephalus solidus [Müller], and compared the morphology and growth patterns of infected females with sham-exposed controls over a 16-week period. Fish were fed a ration of 8% body weight per day. Non-invasive image analysis techniques allowed the growth of in idual plerocercoids to be tracked in vivo throughout the course of infection, and patterns of host and parasite growth were determined. Females that developed infections erged morphometrically from unexposed control females and exposed-uninfected females at 6 weeks post-infection, with the width of the body at the pectoral fins giving the earliest indication of infection success. When including the plerocercoid, infected females gained weight more quickly than controls, but when plerocercoid weight was removed this trend was reversed. There was no effect of infection on the increase in fish length. Plerocercoids grew at different rates in in idual hosts, and exhibited measurable sustained weight increases of up to 10% per day. Final estimates of plerocercoid weight from morphometric analysis prior to autopsy were accurate to within +/−17% of actual plerocercoid weight. At autopsy, infected female sticklebacks had significantly lower perivisceral fat reserves but had developed significantly larger ovaries than controls. The results are discussed in relation to previous studies examining natural infections, and the value of utilizing experimental infections to examine ecological aspects of host–parasite interactions is discussed.
Publisher: Elsevier BV
Date: 12-2018
Abstract: In this era of unprecedented growth in aquaculture and trade, aquatic parasite cultures are essential to better understand emerging diseases and their implications for human and animal health. Yet culturing parasites presents multiple challenges, arising from their complex, often multihost life cycles, multiple developmental stages, variable generation times and reproductive modes. Furthermore, the essential environmental requirements of most parasites remain enigmatic. Despite these inherent difficulties, in vivo and in vitro cultures are being developed for a small but growing number of aquatic pathogens. Expanding this resource will facilitate diagnostic capabilities and treatment trials, thus supporting the growth of sustainable aquatic commodities and communities.
Publisher: Brill
Date: 2004
Publisher: The Royal Society
Date: 10-07-2023
Abstract: The primary function of animal nests is to protect developing offspring from hostile and fluctuating environments. Animal builders have been shown to adjust nest construction in response to changes in their environment. However, the extent of this plasticity, and its dependence on an evolutionary history of environmental variability, is not well understood. To test whether an evolutionary history with flowing water impacts male ability to adjust nests in response to flow regime, we collected three-spined sticklebacks ( Gasterosteus aculeatus ) from three lakes and three rivers, and brought them into reproductive condition in controlled laboratory aquaria. Males were then allowed to nest under both flowing and static conditions. Nest building behaviour, nest structure and nest composition were all recorded. In comparison to males building nests under static conditions, males building in flowing water took longer to construct their nests and invested more in nesting behaviour. Moreover, nests built in flowing water contained less material, were smaller, more compact, neater and more elongated than nests built under static conditions. Whether males came from rivers or lakes had little impact on nesting activities, or male capacity to adjust behaviours in response to flow treatment. Our findings suggest that aquatic animals which have experienced a stable environment over a long period of time retain plasticity in nest-building behaviours that allow them to adjust nests to ambient flow conditions. This ability may prove crucial in coping with the increasingly unpredictable flow regimes found in anthropogenically altered waterways and those resulting from global climate change. This article is part of the theme issue ‘The evolutionary ecology of nests: a cross-taxon approach’.
Publisher: Wiley
Date: 19-08-2018
DOI: 10.1111/JEB.13358
Publisher: Informa UK Limited
Date: 24-02-2015
DOI: 10.3109/19401736.2015.1018209
Abstract: The mitogenome of Paranephrops planifrons, was obtained by next generation sequencing. This crayfish has a mitochondrial genome of 16,174 base pairs with 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs (tRNA), and a non-coding AT-rich region of 771 bp. The P. planifrons nucleotide composition is: 33.63% for T, 21.92% for C, 34.46% for A, and 9.98% for G and has a 68.09% AT bias. While the mitogenome gene order for this species is consistent with aspects of the highly distinctive parastacid crayfish mitogenome gene arrangement, it has a novel gene order involving the rearrangements of a protein coding and several tRNA genes.
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Iain Barber.