1,720,975 research outputs found
FIGURE 3 in Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River
No full textFIGURE 3. Admixture plots from the population genetics data set. Number of genetic clusters (K) presented for K = 2–6 from all samples (n = 318) analyzed in a population genetics framework. Admixture analysis was conducted in NGSAdmix with an optimal K = 3. Labeling of x-axis is according to Group as in Table 1: CAGT, California Golden Trout; KRRT, Kern River Rainbow Trout; LKGT, Little Kern Golden Trout; CRT, Coastal Rainbow Trout; EGLK, Eagle Lake Rainbow Trout; HRNB, Hatchery Rainbow Trout; MRRB, McCloud River Redband Trout; REDB, all other Redband Trout.Published as part of Campbell, Matthew A., Habibi, Ensieh, Auringer, Grace, Stephens, Molly, Rodzen, Jeff, Conway, Kevin W. & Finger, Amanda J., 2023, Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River, pp. 1-29 in Zootaxa 5254 (1) on page 14, DOI: 10.11646/zootaxa.5254.1.1, http://zenodo.org/record/771076
FIGURE 4 in Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River
No full textFIGURE 4. Admixture plots from McCloud river trout and other Redband Trout in population genetics dataset. Admixture results from NGSAdmix for genetic clusters (K) from 2-4 with the subset of samples collected as Redband Trout. Sample size of 204, optimal K = 2. The x-axis labels are labeled according to watershed.Published as part of Campbell, Matthew A., Habibi, Ensieh, Auringer, Grace, Stephens, Molly, Rodzen, Jeff, Conway, Kevin W. & Finger, Amanda J., 2023, Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River, pp. 1-29 in Zootaxa 5254 (1) on page 17, DOI: 10.11646/zootaxa.5254.1.1, http://zenodo.org/record/771076
FIGURE 6 in Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River
No full textFIGURE 6. Species tree produced by SVDQuartets. The species tree branch lengths are equal and bootstrap support was maximal for all nodes and not shown. Each subspecies of Rainbow Trout (Oncorhynchus mykiss) is indicated with McCloud River Redband Trout (O. m. calisulat, ssp. nov.) and Sacramento Redband Trout (O. m. stonei) in bold text. For Rainbow Trout subspecies, sampling locations are labeled with a four-letter code corresponding to Figure 1 and Table 1. The two samples of Lahontan Cutthroat Trout (O. clarkii henshawi) are labeled as LCT.Published as part of Campbell, Matthew A., Habibi, Ensieh, Auringer, Grace, Stephens, Molly, Rodzen, Jeff, Conway, Kevin W. & Finger, Amanda J., 2023, Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River, pp. 1-29 in Zootaxa 5254 (1) on page 19, DOI: 10.11646/zootaxa.5254.1.1, http://zenodo.org/record/771076
FIGURE 7 in Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River
No full textFIGURE 7. Phylogenetic network of individuals examined in this study produced by the neighbor net algorithm. Tips are labeled by individual codes described in Table 1. Each subspecies of Rainbow Trout (Oncorhynchus mykiss) is indicated. McCloud River Redband Trout (O. m. calisulat, ssp. nov.) and Sacramento River Redband Trout (O. m. stonei) are show in bold. The outgroup species, Lahontan Cutthroat Trout (O. clarkii henshawi) is indicated.Published as part of Campbell, Matthew A., Habibi, Ensieh, Auringer, Grace, Stephens, Molly, Rodzen, Jeff, Conway, Kevin W. & Finger, Amanda J., 2023, Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River, pp. 1-29 in Zootaxa 5254 (1) on page 20, DOI: 10.11646/zootaxa.5254.1.1, http://zenodo.org/record/771076
FIGURE 5 in Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River
No full textFIGURE 5. Maximum Likelihood (ML) tree (A) and ML consensus tree (B). In both panels subspecies of Rainbow Trout (Oncorhynchus mykiss) are indicated along with members of the Golden Trout Complex. McCloud River Redband Trout (O. m. calisulat, ssp. nov.) and Sacramento Redband Trout (O. m. stonei) are indicated with bold text. Individual sample names are provided at tips and further described in Table 1. In 5A, nodes receiving Shimodaira-Hasegawa approximate Likelihood Ratio Test scores> 80 and bootstrap support (BS)> 95% are indicated with a diamond. In 5B, two spans of bootstrap support are presented, with 100%> BS> 95% as solid black circles and 95%> BS> 90% as grey circles at nodes.Published as part of Campbell, Matthew A., Habibi, Ensieh, Auringer, Grace, Stephens, Molly, Rodzen, Jeff, Conway, Kevin W. & Finger, Amanda J., 2023, Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River, pp. 1-29 in Zootaxa 5254 (1) on page 18, DOI: 10.11646/zootaxa.5254.1.1, http://zenodo.org/record/771076
FIGURE 1 in Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River
No full textFIGURE 1. Map of key features and distributions of key lineages in this study. The distribution of Coastal Rainbow Trout (Oncorhynchus mykiss irideus) is shown in grey shading. Other lineages are labeled in different colors. Distributions were retrieved from the PISCES database (pisces.ucdavis.edu, "Historic Range—Expert Opinion") except for Warner Lakes Redband Trout (O. m. ssp.), which is represented by a polygon of hydrologic unit code (HUC) 17120007. Sampling locations used in phylogenetic analyses are indicated with a four-letter code that corresponds to Table 1 and Supplemental Table S1. Samples of O. m. gairdnerii from Idaho are not shown.Published as part of Campbell, Matthew A., Habibi, Ensieh, Auringer, Grace, Stephens, Molly, Rodzen, Jeff, Conway, Kevin W. & Finger, Amanda J., 2023, Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River, pp. 1-29 in Zootaxa 5254 (1) on page 6, DOI: 10.11646/zootaxa.5254.1.1, http://zenodo.org/record/771076
FIGURE 2 in Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River
No full textFIGURE 2. Principal Component Analyses. The first two Principal Components (PCs) are presented for all samples (n = 318) in the population genetics analysis in A and Redband Trout samples (n = 204) in B. Genotype likelihoods were generated separately for the PCs presented in each panel. In A points are color coded by Group corresponding broadly to lineage, and further condensed into a Major Group by consolidating the California Golden Trout Complex and represented by shape (Table 1). In B, points are colored by watershed and the same shape applied to the Major Group (MRRB and REDB). Abbreviations for Major Group are explained in the text.Published as part of Campbell, Matthew A., Habibi, Ensieh, Auringer, Grace, Stephens, Molly, Rodzen, Jeff, Conway, Kevin W. & Finger, Amanda J., 2023, Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River, pp. 1-29 in Zootaxa 5254 (1) on page 13, DOI: 10.11646/zootaxa.5254.1.1, http://zenodo.org/record/771076
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Genotyping by sequencing in wildlife forensics: Using high-throughput microsatellite sequencing to identify allele variants in American black bears (Ursus americanus)
No full textBlack bears (Ursus americanus) are an ecologically and economically important species requiring protection from the threats of illegal wildlife trade. DNA analysis techniques such as genotyping by sequencing can reveal allele sequence variation (also referred to as novel alleles). These novel alleles can identify genetic distinctions among populations and improve our ability to determine the location of origin of evidence seized in poaching and wildlife trafficking cases. This can aid in locating poaching hotspots, identifying criminal networks, and preventing illegal take of wildlife. The objectives of this research were to 1) identify novel alleles in U. americanus populations in California and 2) identify all genetically distinct populations of U. americanus populations in California to better determine an individual black bear's location of origin. To accomplish these objectives, 1,544 black bear DNA samples were sequenced at nine microsatellite loci and three sex markers using the Illumina MiSeq high-throughput sequencing (HTS) platform. Allele counts and a genotype concordance for samples with allele calls at a minimum of six of the nine microsatellite loci (n = 635) were performed to compare 1) the total number of alleles identified and 2) the genotype assignments made through HTS vs. those previously assigned through capillary electrophoresis (CE), a genotyping method commonly used in wildlife forensics. Novel allele variants were detected at eight of the nine loci in the analysis panel and 29.9% of alleles identified through HTS were novel variants. HTS methods detected a total of 137 alleles across all loci while CE detected 96, a 42.7% increase in known alleles. An analysis of the genetic population structure using genotypes assigned through HTS identified seven genetic clusters (populations) of black bears in California, an increase compared to the six identified using CE genotyping for the same sample set. This population structure analysis may serve as a reference for future method development to match black bear DNA samples to their region of origin. The HTS methods developed for black bears through this research will serve as a reference for method development and optimization for other species, such as deer and mountain lion, commonly analyzed in wildlife forensics
- …
