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opencc-by-nd-4.0Dec 2010View details →

FIGURE 1 in Voucher Specimens For Dna Sequences Of Phytoseiid Mites (Acari: Mesostigmata)

FIGURE 1: Slide-mounted females of Typhlodromus (Typhlodromus) exhilaratus and Neoseiulus idaeus after genomic DNA extraction using a Qiagen DNeasy kit. A – dorsal shield of T. (T.) exhilaratus; B – ventral shields of T. (T.) exhilaratus; C – dorsal shield of Neoseiulus idaeus; D – ventral shields of Neoseiulus idaeus.

FIGURE 6 in Holothyrids And Ticks: New Insights From Larval Morphology And Dna Sequencing, With The Description Of A New Species Of Diplothyrus (Parasitiformes: Neothyridae)

FIGURE 6: Diplothyrus lecorrei n. sp. Adult, idiosoma. (a) – male, ventral view; (b) – female, ventral view; (c) – male, Thon's organ; (d) – female, Thon's organ, detail view. Scale bars for a, b = 500 µm; scale bars for c, d = 200 µm.

FIGURE 5 in Holothyrids And Ticks: New Insights From Larval Morphology And Dna Sequencing, With The Description Of A New Species Of Diplothyrus (Parasitiformes: Neothyridae)

FIGURE 5: Diplothyrus lecorrei n. sp. Female. (a) – chelicera (details of whole chelicera and membranous outgrowth); (b) – palp, anterolateral (left) and posterolateral (right) views (setae drawn in dashed lines not consistently present); (c) – subcapitulum; (d) – genital area (arrow indicates presumed latigynal shield), open circles: setal bases, filled grey circles: pores; (e) – pretarsus II. Scale bars = 200 µm.

FIGURE 3 in Holothyrids And Ticks: New Insights From Larval Morphology And Dna Sequencing, With The Description Of A New Species Of Diplothyrus (Parasitiformes: Neothyridae)

FIGURE 3: Diplothyrus lecorrei n. sp. Larva, idiosoma, reconstructed. (a) – dorsal view; (b) – ventral view. Scale bar = 100 µm.

FIGURE 1 in Holothyrids And Ticks: New Insights From Larval Morphology And Dna Sequencing, With The Description Of A New Species Of Diplothyrus (Parasitiformes: Neothyridae)

FIGURE 1: Previous hypotheses of subordinal relationships in the Parasitiformes. (a) – Baker and Wharton (1952); (b) – Norton et al. (1993); (c) – Lehtinen (1991); (d) – Murrell et al. (2005)

FIGURE 2 in Holothyrids And Ticks: New Insights From Larval Morphology And Dna Sequencing, With The Description Of A New Species Of Diplothyrus (Parasitiformes: Neothyridae)

FIGURE 2: Diplothyrus lecorrei n. sp. Larva, gnathosoma. (a) – chelicera; (b) – palp, anterolateral view; (c) – palp tarsus, detail, anterolateral view; (d) – subcapitulum. Scale for a, b, d identical, scale bar = 100 µm; scale bar for c = 50 µm.

FIGURE 4 in Holothyrids And Ticks: New Insights From Larval Morphology And Dna Sequencing, With The Description Of A New Species Of Diplothyrus (Parasitiformes: Neothyridae)

FIGURE 4: Diplothyrus lecorrei n. sp. Larva, legs. (a) – leg I; (b) – detail tarsus I; (c) – leg II; (d) – leg III. Scale bar for a, c, d = 100 µm.

FIGURE 7 in Holothyrids And Ticks: New Insights From Larval Morphology And Dna Sequencing, With The Description Of A New Species Of Diplothyrus (Parasitiformes: Neothyridae)

FIGURE 7: Single most parsimonious tree using a combination of DNA sequence data for three genes (18S rRNA, 28S rRNA and EF-1α). Numbers above branches: Bremer support/jackknife support (parsimony analysis); below branches: posterior probability (Bayesian analysis). xx: branch not supported in Bayesian analysis.

opencc-by-4.0Sep 2021View details →

Aligned DNA sequence matrix for phylogenetic analyses in the article "Our unknown neighbor: a new species of rain frog of the genus Pristimantis (Amphibia: Anura: Strabomantidae) from the city of Loja, southern Ecuador"

The aligned matrix is in fasta format. Genes are arranged as follows: 12S = 1–909 16S = 910–1787 RAG-1 = 1788–2399

opencc-zeroNov 2022View details →

The topological nature of tag jumping in environmental DNA metabarcoding studies (sequencing raw data)

Metabarcoding of environmental DNA constitutes a state-of-the-art tool for environmental studies. One fundamental principle implicit in most metabarcoding studies is that individual sample amplicons can still be identified after being pooled with others – based on their unique combinations of tags – during the so-called demultiplexing step that follows sequencing. Nevertheless, it has been recognized that tags can sometimes be changed (i.e. tag jumping), which ultimately leads to sample crosstalk. Here, using four DNA metabarcoding datasets derived from the analysis of soils and sediments, we show that tag jumping follows very specific and systematic patterns. Specifically, we find a strong correlation between the number of reads in blank samples and their topological position in the tag matrix (described by vertical and horizontal vectors). This observed spatial pattern of artefactual sequences could be explained by polymerase activity, which leads to the exchange of the 3' tag of single stranded tagged sequences through the formation of heteroduplexes with mixed barcodes. Importantly, tag jumping substantially distorted our datasets – despite our use of methods suggested to minimize this error. We developed a topologic model to estimate the noise based on the counts in our blanks, which suggested that 40-80% of the taxa in our soil and sedimentary samples were likely false positives introduced through tag jumping. We highlight that the amount of false positive detections caused by tag jumping strongly biased our community analyses.

opencc-zeroDec 2022View details →

The phylogeny and global biogeography of Primulaceae based on high-throughput DNA sequence data

The angiosperm family Primulaceae is morphologically diverse and distributed nearly worldwide. However, phylogenetic uncertainty has limited the ability to identify major morphological and biogeographic transitions. We used target capture sequencing with the Angiosperms353 kit for over 300 species across Ericales, tree-based sequence curation, and multiple phylogenetic approaches to investigate the phylogenetics of the major clades of Primulaceae and their relationship to other Ericales. The study included 150 samples of Primulaceae comprising nearly all recognized genera of the family, with a particular focus on the most diverse subfamily, Myrsinoideae, for which previous phylogenetic knowledge was poor. We used fossil and secondary calibrations to generate dated phylogenetic trees and conducted broad-scale biogeographic analyses as well as ancestral state reconstructions of plant habit.

opencc-zeroJan 2023View details →

Chamaeleo africanus DNA sequencing purity results and statistics

Conservation of wildlife often depends on high quality molecular data to establish reliable species identification. Traditional approaches in extracting material (DNA) for phylogenetic studies on chameleons have relied on removed, euthanized or preserved/museum specimens, while field sampling usually takes the form of tail clippings from living individuals and their subsequent release. In this article, we propose an alternative to these approaches for field sampling, towards isolation of nuclear and mitochondrial DNA with oral (buccal) swabs, a methodology already been demonstrated as effective in other taxa. Options of sampling, storage, transport, extraction of DNA are presented and the quality and quantity of extracted material (using venipuncture as a positive control) was demonstrated as sufficient for downstream applications, including sequencing thereby presenting a practical field alternative. The advantages and limitations of this minimally invasive and non-destructive method applied to Chamaeleo africanus are further discussed.

opencc-zeroFeb 2023View details →

Aligned and curated mtDNA sequences from: Ancient DNA of narrow-headed voles reveals common features of the Late Pleistocene population dynamics in cold-adapted small mammals

Narrow-headed vole, together with collared lemming and common vole, was the most abundant small mammal species across Eurasian Late Pleistocene steppe-tundra environments. Previous ancient DNA studies of the latter two revealed dynamic past population histories shaped by climatic fluctuations. To investigate the extent to which species with similar adaptations share common evolutionary histories, we generated a dataset comprising mitochondrial genomes of 139 ancient and 6 modern narrow-headed voles from multiple sites across Europe and north-western Asia and covering the last ca. 100 thousand years (ka). We inferred Bayesian time-aware phylogenies using 11 radiocarbon-dated samples for calibration of the molecular clock. We found that across the three species, divergence of the main mtDNA lineages occurred during Marine Isotope Stages (MIS) 7 and MIS 5, suggesting a common response of species adapted to open habitat to the interglacial environments. In European narrow-headed voles, we identified multiple time-structured mtDNA lineages, implying lineage turnovers. Timing of some of these turnovers was synchronous across all three species, allowing us to identify the main drivers of the Late Pleistocene dynamics of steppe- and cold-adapted species.

opencc-zeroFeb 2023View details →

Perianth evolution and implications for generic delimitation in the Eucalypts (Myrtaceae): DNA sequences, morphological data

Eucalyptus was traditionally defined by the operculate perianth—hence the generic name (Latin, meaning "well-covered"). But after previous phylogenetic analysis placed Angophora, which has free sepals and petals, as sister to the bloodwood eucalypts, the latter were segregated into a new genus, Corymbia. We made a targeted capture of 101 low-copy nuclear exons from 392 samples representing 329 species-level taxa. The phylogeny was estimated using maximum likelihood (IQtree and RAxML) and the multi-species coalescent (Astral). We tested alternative relationships between four genera within Eucalypteae (Arillastrum, Angophora, Eucalyptus, Corymbia) at each of two nodes critical to generic delimitation using Shimodaira's Approximately Unbiased (AU) test. Monophyly of Arillastrum + (Corymbia + Angophora) relative to Eucalyptus sensu stricto was supported whereas monophyly of Corymbia relative to Angophora was decisively rejected. These results indicate that either Eucalyptus should be expanded to include all four genera or Corymbia should be split into two. All of the alternative relationships among the four currently recognised genera imply homoplasy in perianth evolution, specifically with respect to origins of the bud cap (operculum or calyptra), which has been traditionally used to define Eucalyptus. Inferred evolutionary transitions in perianth traits are generally congruent with divergences between major clades with a single exception: expression of separate sepals and petals in Angophora, which is nested within the operculate genus Corymbia, appears prima facie to be a reversal to the plesiomorphic perianth structure. Strictly, this is not a reversal because the petals of Angophora and Corymbia have a novel compound keel-and-limb structure that is absent in the outgroups. This structure is evident in early development, irrespective of whether the petals remain free or later become part of an operculum. Many of the currently recognised infrageneric taxa down to sectional level (and below in some cases) are well-supported by the sequence data and definable by morphological traits. Inclusion of Angophora within Eucalyptus was formally proposed two decades ago but did not gain acceptance. Here instead, we formally raise Corymbia subg. Blakella to genus rank and make the relevant new combinations.

opencc-by-4.0Dec 2022View details →

Aligned DNA sequence matrix for phylogenetic analyses in the article "A new species of spiny-backed tree frog, genus Osteocephalus (Anura: Hylidae), from the Yanachaga Chemillén National Park in central Peru"

Aligned DNA sequence matrix for phylogenetic analyses of the article "Systematics of Huicundomantis, a new subgenus of Pristimantis (Anura, Strabomantidae) with extraordinary cryptic diversity and eleven new species" The matrix is in NEXUS format and has 14791 bp and 38 terminals. Partitions are as follows: charset 12S_16S = 1-2442;     charset mtGenome_other_genes = 2443-9180;    charset nonCoding =  3132- 3138 4776- 4857 5203- 5214;     charset codonPos1 =  2443-3130\3 3139-4774\3 4858-5200\3 5215-9178\3;     charset codonPos2 =  2444-3131\3 3140-4775\3 4859-5201\3 5216-9179\3;     charset codonPos3 =  2445-3129\3 3141-4773\3 4860-5202\3 5217-9180\3;     charset 16S_ND1nonCoding =  9181- 9428 10390- 10506 ;     charset 16S_ND1codonPos1 =  9429-10389\3;     charset 16S_ND1codonPos2 =  9430-10387\3;     charset 16S_ND1codonPos3 =  9431-10388\3;     charset POMCcodonPos1 =  10507-11068\3;     charset POMCcodonPos2 =  10508-11066\3;     charset POMCcodonPos3 =  10509-11067\3;     charset CO1codonPos1 =  11069-12608\3;     charset CO1codonPos2 =  11070-12609\3;     charset CO1codonPos3 =  11071-12610\3;     charset CytbcodonPos1 =  12611-13757\3;     charset CytbcodonPos2 =  12612-13758\3;     charset CytbcodonPos3 =  12613-13759\3;     charset ND2codonPos1 =  13760-14789\3;     charset ND2codonPos2 =  13761-14790\3;     charset ND2codonPos3 =  13762-14791\3;

opencc-by-4.0Jan 2023View details →

The biodegaration of dimethoate by S. marcescens and DNA sequences

The biodegaration of  dimethoate by S. marcescens; DNA sequence; MBL gene expression; survival ship of bacteria to insects

opencc-zeroMay 2023View details →

DNA sequence data for two Roscoea species, R. stenophylla and R. australis (Zingiberaceae)

This dataset includes three genomic regions, nrITS (ITS1-5.8S–ITS2) and two chloroplast DNA (cpDNA) regions (psbA-trnH and trnL-F) for two Roscoea species R. stenophylla and R. australis (Zingiberaceae).

opencc-zeroJun 2023View details →

Fastq sequence files supporting: Assessing the degradation of environmental DNA and RNA based on genomic origin in a metabarcoding context

Molecular tools of species identification based on eNAs (environmental nucleic acids; eDNA and eRNA) have the potential to greatly transform biodiversity science. However, the ability of eNAs to obtain "real-time" biodiversity estimates may be complicated by the differential persistence and degradation dynamics of the molecular template (eDNA or eRNA) and the barcode marker used. Here, we collected water samples over a 28-day period to comparatively assess species detection using eDNA and eRNA metabarcoding of two distinct barcode markers—a mitochondrial mRNA marker (COI) and a nuclear rRNA marker (18S)—following complete removal of Arthropoda taxa in a semi-natural freshwater system. Our findings demonstrate that Arthropoda community composition was largely influenced by marker choice, rather than molecular template, individual microcosm, or sampling time point. Further, although eRNA may capture similar species diversity as the established eDNA method, this finding may be marker dependent. Although we found little to no difference in decay rates observed among sample groups (COI eDNA, COI eRNA, 18S eDNA, 18S eRNA), this result is likely due to limitations in the ability of eNA-based metabarcoding to provide a strong correlation between true eNA copy numbers present in the environment and final read counts obtained (following the metabarcoding workflow). Collectively, our findings provide further support for the use of multi-marker assessments in metabarcoding surveys to unravel the broadest taxonomic diversity possible, highlight the limitations of eNA metabarcoding methods in providing accurate decay rate estimates, as well as establish the need for further comparative studies using both metabarcoding and single-species detection methods to assess the persistence and degradation dynamics of eNAs for a diverse range of taxa.

opencc-by-4.0Mar 2023View details →

Review on Current Aspects of Technique in DNA Sequencing

International -E- Conference on Recent Trends in Chemical Science, Physical Science, Life Science and Computer Technology (ICRTCPLCT-2023) Organized by AIJ Degree College of Science Murud Janjira on 15th March 2023.