Showing results for: [ Genetics not elsewhere classified ]
Genotypes from a 273 subset of spring or semi-winter varieties from an established global wheat diversity set, the Vavilov wheat diversity panel. Single nucleotide polymorphism (SNP) data were capture... mored using the Illumina iSelect 90K SNP array. SNP data were filtered on minor allele frequency > 3.5% and missing data < 30%, resulting in 26519 polymorphic SNPs for downstream analysis. This data set was published as supplementary material for the article "Evaluation of the impact of heat on wheat dormancy, late maturity alpha-amylase and grain size under control environmental conditions”, in Scientific Reports 2020.less
SIP 6: A functional genomics platform f - - Published 31 Jul 2020
This data collection contains the tabular data, R scripts and methods used to generate three indicators specific to vascular plants for the NSW Biodiversity Indicator Program's first assessment (prior... more to the date of commencement of the Biodiversity Conservation Act 2016): 1.2a expected survival of all known species; 2.1a within-species genetic diversity (for all known species); 2.1b extant area occupied (for all known species). These indicators use representative species sets (provided in a related data collection). The habitat condition indicators (related data collections) are used to infer reduction in geographic range size. These indicators are an application of the ‘expected diversity’ framework. Reduction in the geographic range size of a species due to habitat loss, alteration and fragmentation is well known to decrease within-species genetic diversity and increase extinction risk. Therefore, current range size and proportion of range lost from habitat loss, alteration and fragmentation were estimated for vascular plant species known to occur naturally in New South Wales. The area of effective habitat (i.e. high quality habitat able to support biodiversity) remaining for each species was estimated from two alternative habitat condition indicators (Love et al. 2020): ecological condition of terrestrial habitat and ecological carrying capacity of terrestrial habitat. Because most species in New South Wales have not been formally assessed for possible threatened status (i.e. at heightened risk of extinction), a provisional risk assessment using a limited set of criteria was completed for all NSW vascular plant species for which adequate data were available from the Atlas of Living Australia. For consistency with IUCN recommended Red List methods, the expected survival of all known species uses area of occupancy within 2km grids to classify all species into four categories: lowest risk, lower risk, higher risk and highest risk. Each category was assigned a probability of survival, allowing the proportion of NSW vascular plant species expected to survive in 100 years to be estimated. Extrapolating trends in the rate of biodiversity loss requires that the list of species used in analyses are representative of the overall biodiversity of New South Wales. A subset of NSW vascular plant species that uniformly represent the full variety of natural habitats for vascular plants in New South Wales (called the representative species set) was selected to represent all vascular plant species, including those yet to be discovered. Ecological environments defined by a generalised dissimilarity model of vascular plants were used as a surrogate for the variety of natural habitats. Based on the proportion of remaining effective habitat in each species’ original range, within-species genetic diversity is also estimated. A range of values is given because each species will respond to loss of range size differently, depending on factors like dispersal ability and degree of adaptation to local environmental conditions, and these differences are not precisely known. The data and scripts provided in the data collection will allow the pre-commencement analyses of these indicators to be re-run. The method as applied in the scripts is designed to allow future iterations of the indicators to be run using updated input data. Guidelines on how to re-run the analyses using the scripts and adapt the data package for future iterations of the indicators is provided in the implementation report (Nipperess DA, Faith DP, Williams KJ, King D, Manion G, Ware C, Schmidt R, Love J, Drielsma M, Allen S & Gallagher R 2020. Expected survival and state of all known species, first assessment. Department of Planning, Industry and Environment NSW, Sydney, Australia.). The relevant guidelines extracted from that report are provided with this data package.less
BBA2: Conduct the baseline assessment and prepare a state of NSW biodiversity report - Implementation of expected survival of all known species indicators(1.2a 2.1a 2.1b) - Published 21 May 2020
FASTA and FASTQ sequencing files from Sanger and MiSeq sequencing of good quality and degraded (formalin exposed) DNA from fish specimens in the Australian National Fish Collection. Data generated dur... moreing a CSIRO Environomics Future Science Platform project, stage 1.less
Collection Genomics Environomics FSP (SICOM) - Sanger and Illumina sequencing - Published 05 Mar 2020
Input files of mtDNA Control Region and NADH2 haplotype frequencies, Arlequin microsatellite genotypes, Diversity Array output files of SNPs and metadata of scalloped hammerheads (Sphyrna lewini) from... more Australia and Indo-Pacific. less
Exploring the status of Australia's hammerhead sharks - genetic population structure - - Published 03 Mar 2020
R generated, genlight file including genetic Single Nucleotide Polymorphism marker set used in Green et al (in press)- Novel multi-marker comparisons address the genetic population structure of silver... moretip sharks (Carcharhinus albimarginatus).
Data includes 92 individuals, from 3 locations and 6,461 SNPs.less
ACIAR Management of shark resources PNG - - Published 28 Dec 2018
The files used in the real data analyses of the paper entitled "Eagle: Making multiple-locus association mapping on a genome-wide scale routine". The original data comes from Nicod et al. (2016) Natu... morere Genetics who collected SNP dosages (continuous scores from 0 to1). We transformed these dosages into SNP genotypes (0,1,2).
Input files suitable for analysis by Eagle. The data were obtained from a large genome-wide association study (GWAS) performed in outbred mice and published on the Heterogeneous Stock Mouse web site. The data were reorganized to make it suitable for input into Eagle.
Acquired - Development of Statistical Methods - Published 12 Oct 2018
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
Eagle is an R package for genome-wide association mapping
Biological Data Science Group - Operating Cost - Genome-wide association mapping - Published 26 Sep 2017