Population genetics of the mangrove Rhizophora stylosa in northern Australia
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Starch gel electrophoresis was used to examine genetic variation in five widely separated populations of the mangrove Rhizophora stylosa Griff. Shoots containing leaves and well developed apical buds were collected between March and August 1987 from Darwin, the Daintree River, 2 sites at Missionary Bay (Hinchinbrook Island), Chunda Bay (Cape Ferguson) and Lardelli Creek (Ayr). No two trees at each sampling site were separated by more than 1km, except for the Daintree River site, which was sampled over 2km.A suitable extraction buffer was developed by modifying a buffer developed by Dr Gavin Moran (CSIRO) for eucalypts and acacias.Twenty eight enzymes were investigated for the Rhizophora stylosa samples (ACP, ACON, AK, ADH, ALD, AAT, EST(FL), FH, BetaGAL, G6PD, GPI, GDH, GSR, GAPDH, HK, IDH, LAP, LGGP, LTP, LPP, MDH, ME, MDR, PER, PGM, 6PGD, SKDH, TPI). Fourteen enzymes were resolved adequately for these samples (ACON, AAT, GPI, GDH, GSR, HK, IDH, LAP, LTP, MDH, ME, PER, 6PGD, TPI).Other Rhizophoraceae successfully tested for enzyme activity in leaf and apical bud tissue, using the same methods were Rhizophora apiculata Blume, R. lamarckii Montr., R. mucronata Lamarck, Bruguiera gymnorhiza Lamarck, Ceriops decandra (Griff.) Ding Hou, C. tagal (Perr.) C.B. Rob. var. tagal and C. tagal var. australis C.T. White. Other mangrove species producing clear repeatable results included Lumnitzera racemosa Willdenow, Xylocarpus australasicus Ridley, Sonneratia alba J.E. Smith, Acrostichum speciosum Willdenow, Avicennia marina (Forssk.) Vierh. and A. officinalis Linnaeus.While leaves and buds were chosen initially, due to their year round availability, whole anthers and the plumule of the progagule of Rhizophora stylosa were also successfully tested for enzyme activity. This research was undertaken to:1. develop an effective extraction buffer to counteract the effect of complex secondary metabolites in mangroves, which denature proteins during enzyme extraction.2. develop techniques for the electrophoresis of mangrove tissue and to use these to investigate genetic variability in Rhizophora stylosa and other Rhizophoraceae.
Campylorhynchus brunneicapillus single nucleotide polymorphism genotype data from southern California, USA
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This dataset contains 184 single nucleotide polymorphism (SNP) genotypes of Campylorhynchus brunneicapillus (Cactus Wren) sampled in southern California. Genomic markers were generated from ddRAD loci and analyzed using the Stacks v2.60 pipeline. The genotypes for all samples are provided in a VCF file with 40,707 independent loci. A companion sample data file is provided with sample names, location, and other data. These files may be opened and edited in a text editor program, such as Notepad (PC) or BBEdit (Mac). The .vcf file can be loaded into the Stacks population program to calculate genetic diversity statistics, or loaded into R, using vcfR, for further analysis.
EPA-Generated Data for Banerji et al. Ecological Role of MC
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Data used to generate Figures 2, 3, and 4 as we ll as Table 3. This dataset is associated with the following publication: Banerji, A., M. Bagley, J. Shoemaker, D. Tettenhorst, C. Nietch, J. Allen, and J. Santodomingo. Evaluating putative ecological drivers of microcystin spatiotemporal dynamics using metabarcoding and environmental data. Harmful Algae. Elsevier B.V., Amsterdam, NETHERLANDS, 86: 84-95, (2019).
Genomic variation in the genus Pimephales: raw sequence data and single-nucleotide polymorphisms.
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The fathead minnow (Pimephales promelas) is a key model of vertebrate toxicity. Standardized tests of toxicity in fathead minnow have been developed to support regulatory science, and much is known about the response of the species to various environmental pollutants. However, there is little data on genetic variation within the species, despite the potential influence of genetic background on toxicological outcomes. Furthermore, the phylogenetic relationships among Pimephales species are not fully established and rates of evolutionary divergence within the species and genus have not been investigated. This study examined patterns of genetic variation across the genome within a single wild population of fathead minnow from the San Juan River of the southwestern U.S. These patterns were contrasted with variation in an inbred, captive population reared by the U.S. Environmental Protection Agency. The study also examined variation in two specimens each of the congeners bluntnose minnow (P. notatus), slim minnow (P. tenellus), and the bullhead minnow (P. vigilax). This data release describes the availability of the raw sequence data, the methods for identifying genetic polymorphisms among the samples, and provides the called polymorphisms in a standardized format (the variant call format, or VCF).
Neodiprion lecontei Official Gene Set v1.1
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,This dataset presents the Neodiprion Official Gene Set (OGS) v1.1. It was generated using Maker v2.31.8, followed by CrossMap re-mapping of coordinates to genome assembly Nlec1.1 (https://www.ncbi.nlm.nih.gov/assembly/GCA_001263575.2/).,This dataset is now obsolete - a new genome assembly, iyNeoleco1.1 (https://www.ncbi.nlm.nih.gov/assembly/GCF_021901455.1) has been produced by the Ag100Pest project, with annotations from NCBI's RefSeq resource.,,