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Showing results for: [ Biological Sciences ]
DNA sequence data to accompany:
Berry, O., Bulman, C., Bunce, M., Coghlan, M. Murray, D.C., and Ward, R.D. (in Press) Comparison of morphological and DNA metabarcoding analyses of diets in exploited m... morearine fishes. Marine Ecology Progress Series. doi: 10.3354/meps11524less
CLSD 1178.3 Biochemical Tracers 2012/13 - DNA Metabarcoding of SESSF Part 1 - Published 22 May 2018
From the first week in May 1987 until the end of 2017, when they were on their property "Koobabbie" in the Northern Wheatbelt of WA, Alison and John Doley collected data on every species of bird they ... moresaw each week. Data were recorded on a booklet prepared by CSIRO Division of Wildlife and Rangelands Research for its 1987-1990 bird atlas (Saunders and Ingram 1995). This booklet provided a list of all species known to have occurred in the central wheatbelt and divided the year into 12 months and each month into four weeks; that is, each year had 48 weeks of potential observations. Any species seen on "Koobabbie" that was not listed on the booklet was added to the list. The Doleys also made extensive notes about their observations at the back of each year’s booklet. These notes, together with the raw presence data, comprise this data set. The data recorded each week consisted of a tick for every species seen that week. For example, one Red-capped Robin seen once during a week was recorded as a tick, as were 100 Galahs seen every day of that week.less
Legacy data - Bird survey data from a private property - Published 16 Apr 2018
Analysed quality (viscosity and baking) data from 4way MAGIC trials in Yanco, Wongan Hills and Narrabri. Traits include equivalent Falling Number (eFN), relative expression of Ta-AMY1, total alpha amy... morelase activity, ELISA based LMA detection, crumb firmness, loaf volume, loaf weight, number of cells, oven spring, slice area and slice brightness.less
SIP-FY17_LMA Solutions_FY17 - - Published 10 Apr 2018
Magnified images of Eucalyptus seed from multiple accessions of multiple species were prepared. Automatic measurement tools used on the images then generated data for 35 different shape/image analysis... more parameters.less
Acquired - - Published 09 Apr 2018
A data set of 16S rDNA reference sequences from coal seam environments.
Onshore Gas_General Prog Operations - - Published 23 Mar 2018
Raw reads (and assembled transcriptome) of Cocos nucifera
Legacy data - Next Generation Sequencing - Published 22 Mar 2018
This dataset contains all the information and data collected as part of the work entitled "Natural selection on plasticity of thermal traits in a highly seasonal environment". Here, we included data f... morerom mark-recapture, Q10, and thermal performance parametersless
Legacy data - Mark-Capture-recapture - Published 16 Mar 2018
Bio-physical, ecological and social information have been used to parameterise two computer models able to simulate (ALCES and Ecopath with Ecosim [EwE]) land, coastal and marine processes. A careful ... moreexamination of a large volume of publications from the academic, private and public sector has also allowed us to identify a number of climate and social economic development scenarios the Kimberly region may experience in the decades to comeless
WAMSI-Kim 2.2.8 MSE Modelling Knowledge - MSE modelling and ecosystem modelling - Published 09 Mar 2018
Supplementary data for the BMC Genomics paper titled: "Chemosensory genes identified in the antennal transcriptome of the blowfly Calliphora stygia"
1023.1 FF Cybernose - strategic - Calliphora stygia transcriptome - Published 02 Mar 2018
The black soldier fly was unintentionally introduced to Australia in the middle of the 20th century, where it has since become established in every State and Territory. Specimen records of black soldi... moreer fly, held at the Australian National Insect Collection (ANIC) have had associated information contained on labels, transcribed and geo-referenced in the Atlas of Living Australia's transcription platform, DigiVol. This data-set adds to our knowledge about the distribution and diversity of Australia’s black soldier fly, helping ANIC researchers determine exactly where the black soldier fly occurs in Australia and identify any overlap with the native species. less
Australian National Insect Collection - Biological Specimen Collections - Published 23 Feb 2018
Raw single nucleotide polymorphism (SNP) genotypes obtained from samples collected in the Kimberley region of Western Australia. Genotypes derived from a "reduced representation" sequencing method as ... moreprovided by Diversity Arrays PTY LTD.
Also, covariates associated with each individual:
WAMSI-Kim 1.1.3 Ecological connectivity - DArTseq genotyping - Published 08 Feb 2018
Supplementary Data9: Allele Frequencies for 14 million SNPs MAF>0.05
OCE Post Doc - Conseq Animal Domesticati - - Published 06 Feb 2018
SNPs discovered in 20 farmed Tasmanian salmon from high covergae sequence analysis, SNps present in double haploid reference animal removed.
SIP 52 Salmon Genome & Tailored tools fo - - Published 29 Jan 2018
A program for analysing compositional heterogeneity across aligned sequence data.
Most model-based molecular phylogenetic methods assume evolution under stationary, reversible, and globally homogeneo... moreus conditions, implying that it would be unwise to use these methods if the data evolved under more complex conditions. Homo allows users to test whether pairs of sequences in alignments of nucleotides or amino acids are consistent with evolution under stationary, reversible, and globally homogeneous conditions (for details, see Ababneh et al. 2006b).
The output is a: Brief summary (printed to the terminal); Full summary (printed to a file); Five tables (printed to files), one with the p-values and four with the compositional distances.
The summaries allow users to determine whether some of the sequences violate the assumption of evolution under stationary, reversible, and globally homogeneous conditions.
For further details, see the manual, which is included with the software.less
CLSD Strategic: Solving Biodiversity Cha - Bioinformatics Software - Published 11 Jan 2018
Assembled genomic and tissue-specific transcriptomic data resources for two genetically distinct lines of Cowpea (Vigna unguiculata (L.) Walp). For each of two varieties of cowpea (IT97K-499-35, IT86D... more-1010) this collections contains the following datasets :
i) genomic survey assemblies based on Illumina sequencing
ii) transcriptome assemblies
iii) raw DNA and RNA sequence data feeding into the above assemblies
iv) In-silico gene predictions and predicted gene sequences derived from IT86D-1010 and IT97K-499-35
v) Mapping to the Vigna unguiculata v1.0 reference genome (http://phytozome.jgi.doe.gov/)
Capturing Heterosis for Smallholders, OPP1076280 - Crop genomics - Published 01 Dec 2017
Whole genome sequencing was performed on Gamarada debralockiae gen. nov. sp. nov. Following sequence assemblies, contigs greater than 1,000 nucleotides were subjected to gene annotation and analysis. ... moreWe provide here the remaining contigs which were less than 1,000 nucleotides in length.less
Onshore Gas_General Prog Operations - - Published 30 Nov 2017
Dugongs (Dugong dugon) are listed as vulnerable on the IUCN Red List of Threatened species and as other specially protected fauna in WA under Schedule 7 of the Wildlife Conservation (Specially Protect... moreed Fauna) Notice 2015). Gaps in our knowledge in Western Australia include having a good understanding of the species’ distribution, abundance and high use areas across the northwest.
This 3-year project (2014-2017) integrated Indigenous knowledge and scientific observations from field surveys to better understand the distribution, abundance and movements of dugong in the Kimberley region. The data collected also provides a baseline for future monitoring and management.
This medata record relates to raw and processed aerial survey data of marine fauna collected between 21st September 2015 and 8th October 2015 in Kimberley coastal waters to the 20m bathymetry line, comprising dugongs (Dugong dugon), Australian snubfin dolphins (Orcaella heinsohni), other dolphins (bottlenose, spinners, false killer whales), humpback whales (Megaptera novaeangliae) and large, mostly green turtles (Chelonia mydas).
The WA Department of Biodiversity Conservation and Attractions (DBCA, ex-DPaW) and CSIRO provided additional resources to extend the North Kimberley dugong aerial survey boundary westwards (Broome to just past Port Hedland) to cover the South Kimberley-Pilbara coastal regions, to close the last remaining knowledge gap of the dugong distribution and abundance in Australia. This additional survey was completed in May 2017.
Data from a trial movement study undertaken between 1-18th August 2016 also forms part of this metadata record. Five dugongs were tagged with Telonics manatee/dugong tags. GPS and ARGOS satellite detection locations and dive data were downloaded weekly from the ARGOS web site.less
WAMSI-Kim 1.2.5 Dugong Management - Dugong distribution and movement - Published 24 Nov 2017
Herbivory is a key ecological process that sustains food webs, and can regulate the biomass of primary producers in an ecosystem. It has long been hypothesized that rates of herbivory are greatest in ... morethe tropics, although strong evidence to support this is limited. The aim of this project was to identify the key species of herbivores, to identify the grazing rates of key herbivores, and in conjunction with project WAMSI 2 KMRP Project 2.2.4 (benthic primary productivity) provide estimates of the proportion of production that is consumed by herbivores. The research on herbivory was focused on the islands and coast of the Bardi Jawi Indigenous Protected Area in the Kimberley (Western Australia), encompassing Jalan (Tallon Island) and Iwany (Sunday Island). Focus of the herbivory study was on one type of habitat (seagrass meadows), and the diet of two species of herbivores (golden-lined rabbitfish and green turtle). Four surveys were conducted between October 2014 and April 2016. At these locations the following measurements or collections were made (not all measurements were made during each survey): (1) Rates of herbivory (three surveys). These data are presented in the report for WAMSI KMRP 2.2.4, here the focus is on assessing rates of herbivory as a proportion of primary production; (2) Collections of golden-lined rabbitfish (Siganus lineatus); and (3) Blood samples from green turtles (Chelonia mydas). Ten green turtles were tagged with satellite tags: 4 in April 2015, and 6 in April 2016. This data record only pertains to data held by CSIRO. For access to all other data generated by collaborative research partners of the KMRP 1.1.2 project refer to the additional metadata field.less
WAMSI-Kim 1.1.2 Key ecological pr - Rates of herbivory - Published 16 Nov 2017
In the absence of detailed functional annotation for any livestock genome, we used comparative genomics to predict ovine regulatory elements using human data. Reciprocal liftOver was used to predict t... morehe ovine genome location of ENCODE promoters and enhancers, along with 12 chromatin states built using 127 diverse epigenome.
Here we make available the following files:
a) Sheep_epigenome_predicted_features.tar.gz: contains the final reciprocal best alignment from ENCODE proximal as well as chromHMM ROADMAP features. The result of reciprocal liftOver.
b) liftOver_sheep_temporary_files.tar.gz: We have
added a new tar file with liftOver temporary files
i) LiftOver temporary files mapping human to sheep,
ii) LiftOver temporary files mapping sheep back to human and
iii) Dictionary files containing the link between human to sheep coordinates for exact best-reciprocal files.
OCE Post Doc - Conseq Animal Domesticati - - Published 09 Nov 2017
An in-house amplicon clustering and classification pipeline built around tools from USEARCH and RDP. It handles both 16S and 18S rDNA sequence data, and can be customised to use other reference sets a... morend marker genes.less
Onshore Gas_General Prog Operations - - Published 01 Nov 2017
Outdoor freshwater mesocosms spiked with varying concentrations of copper were sampled in order to profile microbial communities. Samples collected include water, sediment and cellulose baits. DNA was... more extracted from all sample types. In addition to this, RNA was extracted from sediment samples and reverse transcribed to get cDNA. The v4 region of the 16S ribosomal RNA gene was amplified using Earth Microbiome primers 515F and 806R.
The 16S rRNA gene amplicons were sequenced on the Illumina MiSeq platform with 250 base pair-end reads. Forward and reverse read alignments, quality filtering, chimera checking and OTU clustering were performed using USEARCH v9.
OTU sequences were submitted to GenBank, however, 130 were found to be too novel for submission and thus are made available here.less
Legacy data - Microbial community survey - Published 10 Oct 2017
Analysed data for the research paper "Turner et al: AUV-based classification of benthic communities of the Ningaloo shelf and mesophotic areas"
Ningaloo Outlook SRMP - AUV imagery data analysis - Published 06 Oct 2017
Eagle is an R package for genome-wide association mapping
Statistical Learning Group - Operating Cost - Genome-wide association mapping - Published 26 Sep 2017
This data set contains the genomes of Helicoverpa armigera and Helicoverpa zea and the relevant annotations.
Genomic innovations, transcriptional plasticity and gene loss underlying the evolution an... mored divergence of two highly polyphagous and invasive Helicoverpa pest species
Legacy data - Insect genomics - Published 11 Aug 2017
This collection contains 3-arcsecond gridded datasets (ESRI binary float format in WGS84) showing the baseline (1990-centred) predicted potential distribution of 102 (class numbers range between 1 and... more 125) "Keith" Vegetation Classes for New South Wales based on their correlation with baseline ecological environments (c.1990 climates, substrate and landform). The vegetation patterns and classification derive from a map for NSW compiled by David Keith. A kernel regression was used with a geographically even sample of 9,951 locations of training classes for the 102 classes attributed with 21 GDM-scaled environmental predictors for Vascular Plants representing baseline ecological environments. The training class data input to the kernel regression is provided with this package. The GDM-scaled environmental predictors, source biological data and model fit parameters are also provided with the data package. Using the 1990 baseline training class data, and without constraining the prediction to pre-existing map boundaries, the kernel regression predicted the potential distribution of the 102 Vegetation Classes using 1990-centred (30 year average) baseline climates derived from ANUCLIM v6.1 (Xu and Hutchinson 2011) and soil/geology/landform attributes. The kernel regression generates unconstrained probabilities varying in the range from 0 and up to 1 for each of the 102 classes. The data are provided as 3-arcsecond (approximately 90m), ESRI binary float grid format in WGS84. Each class is denoted “UNCON###”, where the number refers to the code originally assigned to that class in the vegetation map. A lookup table linking the vegetation classes to the output codes and descriptive title is provided. The methods are described in "Doerr, VAJ, Williams, KJ, Drielsma, M, Doerr, ED, Davies, MJ, Love, J, Langston, A, Low Choy, S, Manion, G, Cawsey, EM, McGinness, HM, Jovanovic, T, Crawford, D, Austin, M & Ferrier, S 2013, Designing landscapes for biodiversity under climate change: Final report, National Climate Change Adaptation Research Facility, Gold Coast, 260 pp.". A plain English description of the method used (but applied Nationally) can be found in the AdaptNRM Guide “Helping biodiversity adapt to climate change: a community-level modelling approach”, available online at: www.adaptnrm.org. Source of vegetation class data: KEITH, D. A. (2002) A compilation map of native vegetation for New South Wales. NSW Biodiversity Strategy, New South Wales Government. KEITH, D. A. (2004) Ocean shores to desert dunes, Hurstville, Department of Environment and Conservation (NSW).
1157.1 TB NARP Best Practice Landscape - Macroecological modelling of vegetation patterns using GDM and kernel regression - Published 01 Aug 2017