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opennotspecifiedNov 2022View details →

FIG. 2 in New records, neotype designation and DNA sequences of three species of Chaetonotus (Gastrotricha: Chaetonotidae) from Brazil

FIG. 2. Chaetonotus dadayi, light microscopy photomicrographs (DIC). A. Dorsal view of the body - habitus, B. Dorsal view of the anterior region, C. Ventral view of the anterior region, D. Dorsolateral view of the denticulate spines, E. Ventral view of the interciliary area. Ct: Cephalic cilia tuft, Ds: Dorsal spines, Lt: lateral spined scale, Mo: Mouth, Pe: Pleurae, Vs: Ventral spined scales. Scale bars: A–B, D–E, 15 μm; C, 20 μm.

opennotspecifiedNov 2022View details →

FIG.1 in New records, neotype designation and DNA sequences of three species of Chaetonotus (Gastrotricha: Chaetonotidae) from Brazil

FIG.1. Location of sampling points in the State of São Paulo and Minas Gerais, Brazil. 1. Água Limpa Stream, Diamantina; 2. Serra do Japi, Jundiaí; 3. Urban lagoon, Paulínia; 4. Broa Dam, São Carlos; 5. Billings dam, Santo André.

opencc-by-4.0Dec 2022View details →

Combinatorial Barcode Scripts for the manuscript 'Scalable Combinatorial Synthesis of Synthetic DNA Barcode Sequences'

Raw data and custom Python code for the manuscript 'Scalable Combinatorial Synthesis of Synthetic DNA Barcode Sequences'.

opennotspecifiedJan 2023View details →

FIGURE 1. A in A note on the identity of the spikenard (Nardostachys jatamansi, Caprifoliaceae) based on DNA sequence data

FIGURE 1. A photograph of N. jatamansi with pink-colored flowers. Inset shows close-up of flowers. bar=10cm.

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

FIGURE 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.

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

FIGURE 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.

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

FIGURE 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.

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

FIGURE 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.

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

FIGURE 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.

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

FIGURE 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.

FIGURE 8 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

FIGURE 8. McCloud River Redband Trout, Onchorhynchus mykiss calisulat, ssp. nov., Sheepheaven Creek. A. WFB 5020, holotype, 120 mm SL. B. same specimen as in A, radiograph. C. TCWC 28772.01, paratype, 144 mm SL. D. Illustration of O. m. calisulat, ssp. nov., showing life colors, © J. Tomelleri, used with permission.

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

FIGURE 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.

Figure 6 in Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements

Figure 6. Hypothetical radiation schemes for Uromastyx and possibly relevant geological events. Approximate distribution range for each taxon (Wilms, 2001) is shown with its abbreviated name: Hard (Uromastyx hardwickii), Aca (U. acanthinura), Mali (U. d. maliensis), Gey (U. geyri), Dis (U. d. dispar), Oce (U. ocellata), Mac (U. macfadyeni), Aeg (U. a. aegyptia), Mic (U. a. microlepis), Orn (U. ornata) and Ben (U. benti).

Figure 5 in Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements

Figure 5. Neighbour-joining tree constructed based on maximum likelihood distances from 1503 alignable nucleotide sites (the HKY model and transition/transversion ratio of 3.48). The tree was rooted with Chamaeleo africanus as an outgroup. Bootstrap probabilities are shown for neighbour joining, maximum likelihood and maximum parsimony analyses (from left to right). Underlined values mean that the branch was not reconstructed in the best tree topology by the corresponding analyses. Note that two distinct sequence haplotypes are included for Uromastyx acanthinura and U. ocellata. See Material and methods for more details on the analytical conditions. The nucleotide sequences taken from the database are: Chamaeleo africanus (accession No., AF448743), Chlamydosaurus kingii (AF128469), Physignathus lesueurii (AF128463), Acanthosoura capra (AF128498), Salea horsfieldii (AF128490), Trapelus savignii (AF128512), Leiolepis guentherpetersi (AF128461), Leiolepis belliana (U82689), Laudakia caucasia (AF028681) and Laudakia lehmanni (AF028677).

Figure 4 in Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements

Figure 4. Secondary structures of the inserted sequences found between tRNAGln and tRNAIle genes. The 128 bp insert for Uromastyx ornata can assume alternative secondary structures either with an extremely stable and long stem region (A) or with a clover-leaf structure for the second tRNAGln gene (or pseudogene) and a stable stem-and-loop structure (B). The 59 bp inserted for U. ocellata may also assume a somewhat less stable stem-and-loop structure (C). Heavy-strand sequences are shown and numbers refer to the corresponding positions in their light-strand sequences shown in Fig. 3A. Bars in stems represent Watson–Crick base pairs and dots stand for wobble G–U pairs for RNA.

Figure 2 in Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements

Figure 2. Evolution of mitochondrial gene organization in Uromastyx. A, typical vertebrate organization plesiomorphic to lizards. B, typical organization for acrodont lizards including Leiolepis and likely the direct common ancestor of Leiolepis and Uromastyx. C, typical Uromastyx organization in which the putative origin of light-strand replication (black box) disappeared from the WANCY tRNA gene cluster. D, organization for U. ornata and likely for the direct common ancestor of U. ornata and U. ocellata, which has an insertion containing a stem-and-loop structure (hatched box) and the second tRNAGln gene or pseudogene (Q*). E, organization for U. ocellata in which Q* disappeared. See Figs 3 and 4 for sequences and secondary structures of the inserted region in U. ornata and U. ocellata.

Figure 3 in Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements

Figure 3. Nucleotide sequences of the inserted region between the tRNA Gln and tRNAIle genes. A, alignment between the 128 bp insertion in Uromastyx ornata and the 59 bp insertion in U. ocellata (65% identity). B, alignment between the original tRNAGln gene and its second copy within the inserted region for U. ornata (49% identity). Light-strand and heavystrand sequences are shown for A and B, respectively. Dots indicate identity with the first sequence and dashes denote a gap.

Figure 1 in Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements

Figure 1. Position of primers used for amplification and/or sequencing. See Table 1 for the primer sequences; numbers of primers correspond to those in Table 1.

opencc-zeroApr 2023View details →

dryad32/100

Complete organelle genomes of Korean fir, Abies koreana and phylogenomics of the gymnosperm genus Abies using nuclear and cytoplasmic DNA sequence data

Background Abies koreana E. H. Wilson is an endangered evergreen coniferous tree that is native to high altitudes in South Korea and susceptible to the effects of climate change. Hybridization and reticulate evolution have been reported in the genus; therefore, multigene datasets from nuclear and cytoplasmic genomes are needed to better understand its evolutionary history. Results Using Illumina NovaSeq6000 and Oxford Nanopore Technologies (ONT) PromethION platforms, we generated complete mitochondrial (1,174,803 bp) and plastid (121,341 bp) genomes from A. koreana. The mitochondrial genome is highly dynamic, transitioning from cis- to trans-splicing and breaking the conserved gene clusters. In the case of the plastome, the ONT reads revealed two structural conformations of A. koreana. The short inverted repeats (1,186 bp) of the A. koreana plastome are associated with the different structural types. Transcriptomic sequencing revealed 1,356 sites of C-to-U RNA editing in the 41 mitochondrial genes. Using A. koreana as a reference, we additionally produced nuclear ribosomal DNA and organelle genomic sequences from eight Abies species and generated multiple datasets for maximum likelihood and network analyses. Three sections (Balsamea, Momi, and Pseudopicea) were well grouped in the nuclear phylogeny, but the phylogenomic relationships showed conflicting signals in the mitochondrial and plastid genomes, indicating a complicated evolutionary history that may have included introgressive hybridization. Conclusions These results illustrate that phylogenomic analyses based on the sequences from differently inherited organelle genomes resulted in conflicting trees. Organellar capture, organellar genome recombination, and incomplete lineage sorting in an ancestral heteroplasmic individual can contribute to phylogenomic discordance. We provide strong support for the relationships within Abies and new insights into the phylogenomic complexity of this genus.