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opennotspecifiedSep 2013View details →

FIGURE 5. Bayesian tree inferred from SSU gene DNA sequences. Posterior probabilities exceeding 50 in A new species of the genus Tripylina Brzeski, 1963 (Nematoda: Enoplida: Trischistomatidae) from Zhejiang Province, eastern China

FIGURE 5. Bayesian tree inferred from SSU gene DNA sequences. Posterior probabilities exceeding 50% are given on appropriate clades. Nematode species and GenBank numbers are listed for each taxon.

opennotspecifiedJun 2013View details →

FIGURE 2 in DNA sequences and morphological variation in Lophiodes iwamotoi Ho, Serét & Shao, 2011 based on new material from New Caledonia

FIGURE 2. Polymorphic nucleotide sites at the cytochrome c oxidase subunit-I locus (A) and Rhodopsin locus (B) in two Lophiodes species collected from seamounts off New Caledonia. Diagnostic nucleotides of L. iwamotoi to L. mutilus are highlighted. Numeration of nucleotide sites starts from first nucleotide of the corresponding genes. The sequences used for the examination were deposited in NCBI Genbank. Their accession numbers are given.

opennotspecifiedJun 2013View details →

FIGURE 1 in DNA sequences and morphological variation in Lophiodes iwamotoi Ho, Serét & Shao, 2011 based on new material from New Caledonia

FIGURE 1. Freshly caught specimens of Lophiodes iwamotoi. A. ASIZP 73486, 248 mm SL. B. ASIZP 73489, 247 mm SL. C. ASIZP 73488, 154 mm SL. Not to scale.

opennotspecifiedJan 2013View details →

FIGURE 2. Phylogenetic results. A, Maximum likelihood tree from COI dataset rooted with Ophelia limacina. B, Maximum likelihood tree from ITS1 in Validation of three sympatric Thoracophelia species (Annelida: Opheliidae) from Dillon Beach, California using mitochondrial and nuclear DNA sequence data

FIGURE 2. Phylogenetic results. A, Maximum likelihood tree from COI dataset rooted with Ophelia limacina. B, Maximum likelihood tree from ITS1 dataset rooted according to the result for the COI dataset. Support values are shown as jackknife from parsimony analysis and bootstrap from maximum likelihood respectively separated by /. * indicates 100% values for each support measure.

opennotspecifiedJan 2013View details →

FIGURE 1. The three sympatric Thoracophelia spp. from Dillon Beach. A, Thoracophelia dillonensis. B in Validation of three sympatric Thoracophelia species (Annelida: Opheliidae) from Dillon Beach, California using mitochondrial and nuclear DNA sequence data

FIGURE 1. The three sympatric Thoracophelia spp. from Dillon Beach. A, Thoracophelia dillonensis. B, Pectinate branchiae of T. dillonensis. C, Thoracophelia williamsi. D, Bifurcated branchiae with pinnules of T. williamsi. E, Thoracophelia mucronata. F, Bifurcated branchiae of T. mucronata. Scale bars all 1 mm.

opennotspecifiedNov 2022View details →

Fig. 3 in Genetic variation in the spotted seal (Phoca largha Pallas, 1811) from the Rimsky-Korsakov Archipelago (Peter the Great Bay, western sea of Japan) as inferred from mitochondrial DNA control region sequences

Fig. 3. Consensus maximum likelihood tree demonstrating the matrilineal genealogy of some Phocidae species generated from the 460 bp mtDNA control region sequences. The numbers at branch nodes represent bootstrap support of 1000 replications for the maximum likelihood trees and posterior probabilities of 2,000,000 generations for the Bayesian trees with the same topology, respectively. The accession numbers of Phoca largha from Liaodong Bay are highlighted in bold. Scale bar indicates the relative branch lengths.

opennotspecifiedNov 2022View details →

Fig. 2 in Genetic variation in the spotted seal (Phoca largha Pallas, 1811) from the Rimsky-Korsakov Archipelago (Peter the Great Bay, western sea of Japan) as inferred from mitochondrial DNA control region sequences

Fig. 2. Minimum spanning network showing the mutational relationships among Phoca largha haplotypes detected in a sample of 32 spotted seal underyearlings. The tick marks on the branches indicate mutational changes. The circle sizes correspond to the number of haplotypes. The haplotypes of groups (A) and (B) are shown in gray and white circles, respectively. The median vectors are indicated by dark dots.

dryad32/100

Obovaria olivaria maf filtered vcf file from: RAD-tag and mitochondrial DNA sequencing reveal the genetic structure of a widespread and regionally imperiled freshwater mussel, Obovaria olivaria (Bivalvia: Unionidae)

<p><em>Obovaria olivaria</em> is a species of freshwater mussel native to the Mississippi River and Laurentian Great Lakes-St. Lawrence River drainages of North America. This mussel has experienced population declines across large parts of its distribution and is imperiled in many jurisdictions. <em>Obovaria olivaria </em>uses the similarly imperiled <em>Acipenser fulvescens</em> (Lake Sturgeon) as a host for its glochidia. We employed mitochondrial DNA sequencing and Restriction-site Associated DNA sequencing (RAD-seq) to assess patterns of genetic diversity and population structure of <em>O. olivaria</em> from 19 collection locations including the St. Lawrence River drainage, the Great Lakes drainage, the Upper Mississippi River drainage, the Ohioan River drainage and the Mississippi Embayment. Heterozygosity was highest in Upper Mississippi and Great Lakes populations, followed by a reduction in diversity and relative effective population size in the St. Lawrence populations. Pairwise <em>F</em><sub>ST</sub> ranged from 0.00 to 0.20, and analyses of genetic structure revealed two major ancestral populations, one including all St. Lawrence River/Ottawa River sites and the other including remaining sites; however, significant admixture and isolation by river distance across the range were evident. The genetic diversity and structure of <em>O. olivaria</em> is consistent with the existing literature on <em>Acipenser fulvescens</em> and suggest that, although northern and southern <em>O. olivaria</em> populations are genetically distinct, genetic structure in <em>O. olivaria</em> is largely clinal rather than discrete across its range. Conservation and restoration efforts of <em>O. olivaria</em> should prioritize the maintenance and restoration of locations where <em>O. olivaria </em>remain, especially in northern rivers, and to ensure connectivity that will facilitate dispersal of <em>Acipenser fulvescens</em> and movement of encysted glochidia.</p>

opencc-zeroFeb 2024View details →

dryad32/100

Data from: Estimating bloodstain age in the short term based on DNA fragment length using nanopore sequencer

<p>We used a nanopore sequencer to quantify DNA fragments > 10,000 bp in size and then evaluated their relationship with short-term bloodstain age. Moreover, DNA degradation was investigated after bloodstains were wetted once with water. Bloodstain samples on cotton gauze were stored at room temperature and low humidity for up to 6 months. Bloodstains stored for 1 day were wetted with nuclease-free water, allowed to dry, and stored at room temperature and low humidity for up to 1 week. The proportion of fragments > 20,000 bp in dry bloodstains tended to decrease over time, particularly for fragments > 50,000 bp in size. This trend was modeled using a power approximation curve, with the highest R2 value (0.6475) noted for fragments > 50,000 bp in size; lower values were recorded for shorter fragments. The proportion of longer fragments was significantly reduced in bloodstains that were dried after being wetted once, and there was significant difference in fragments > 50,000 bp between dry conditions and once-wetted. This result suggests that even temporary exposure to water causes significant DNA fragmentation, but not extensive degradation. Thus, bloodstains that appear fresh but have a low proportion of long DNA fragments may have been wetted previously. Our results indicate that evaluating the proportion of long DNA fragments yields information on both bloodstain age and the environment in which they were stored.</p>

opencc-zeroApr 2024View details →

Figure 4 in Genetic diversity of Undaria pinnatifida populations from China and their genetic relationship with those from Įapan and Korea as revealed by mitochondrial and nuclear DNA sequences

Figure 4: Maximum likelihood phylogenetic tree inferred from the alignment of ITS1 sequences. Support values are shown as in Figure 3. The ribotypes detected in the Chinese samples in the present study are indicated with bold italicized fonts. Alaria esculenta was used as an outgroup to root the tree. The branch length is proportional to the sequence divergence indicated by the scale bar (substitutions per site).

Figure 3 in Genetic diversity of Undaria pinnatifida populations from China and their genetic relationship with those from Įapan and Korea as revealed by mitochondrial and nuclear DNA sequences

Figure 3: Maximum likelihood phylogenetic tree inferred from the alignment of the combined cox3 and tatC–tLeu sequences. Bootstrap values and Bayesian posterior probabilities>50% are shown, and "-" indicates a value <50%. The branch length is proportional to the sequence divergence indicated by the scale bar (substitutions per site). Refer to Uwai et al. (2006a) for explanation of the haplotype names and classification of the clades I to IV. The haplotypes detected in the Chinese samples in the present study are indicated with bold italicized fonts. Lessoniopsis littoralis was used as an outgroup to root the tree.

Figure 2 in Genetic diversity of Undaria pinnatifida populations from China and their genetic relationship with those from Įapan and Korea as revealed by mitochondrial and nuclear DNA sequences

Figure 2: Geographic distribution of haplotypes in natural and farmed populations of Undaria pinnatifida from China (A) and statistical parsimony network (B) of ITS1 sequences. The color areas in the pie charts are proportional to the ribotype frequency in the map. Small circles indicate undetected ribotypes. Each line connecting ribotypes represents one base mutation. The ribotypes detected in the Chinese samples in the present study are indicated in the ribotype network by the same colors as those in the map.

Figure 1 in Genetic diversity of Undaria pinnatifida populations from China and their genetic relationship with those from Įapan and Korea as revealed by mitochondrial and nuclear DNA sequences

Figure 1: Geographic distribution of haplotypes in natural and farmed populations of Undaria pinnatifida from China (A) and statistical parsimony network (B) of the combined cox3 and tatC–tLeu sequences. The color areas in the pie charts are proportional to the haplotype frequency in the map. Refer to Uwai et al. (2006a) and Table 3 for explanation of the haplotype names and classification of the clades I to IV, which are enclosed by boxes with lines of different patterns. Small circles indicate undetected haplotypes. Each line connecting haplotypes represents one base mutation. The haplotypes detected in the Chinese samples in the present study are indicated in the haplotype network with the same colors as those in the map.

opencc-by-4.0Nov 2024View details →

Aligned DNA sequence matrix for phylogenetic analyses in the article "Systematics of the Dendropsophus leucophyllatus species group (Anura, Hylidae) from the Chocó region of Ecuador, with description of a new species"

<p>Aligned DNA sequence matrix for phylogenetic analyses of the article "Systematics of the <em>Dendropsophus leucophyllatus</em> species group (Anura, Hylidae) from the Chocó region of Ecuador, with description of a new species"</p> <p>The matrix is in NEXUS format and has 7691 bp and 203 terminals.</p> <p>Partitions are as follows:</p> <div> <div>charset 12S = 1-996;</div> <div> </div> <div>charset CO1codonPos1 =  997-1639\3;</div> <div>charset CO1codonPos2 =  998-1640\3;</div> <div>charset CO1codonPos3 =  999-1638\3;</div> <div> </div> <div>charset ND1nonCoding =  1641- 1713 2675- 2796 ;</div> <div>charset ND1codonPos1 =  1714-2674\3;</div> <div>charset ND1codonPos2 =  1715-2672\3;</div> <div>charset ND1codonPos3 =  1716-2673\3;</div> <div> </div> <div>charset CytbcodonPos1 =  2798-3686\3;</div> <div>charset CytbcodonPos2 =  2799-3687\3;</div> <div>charset CytbcodonPos3 =  2797-3685\3;</div> <div> </div> <div>charset RhodcodonPos1 =  3689-4001\3;</div> <div>charset RhodcodonPos2 =  3690-4002\3;</div> <div>charset RhodcodonPos3 =  3688-4003\3;</div> <div> </div> <div>charset TYRcodonPos1 =  4005-4539\3;</div> <div>charset TYRcodonPos2 =  4006-4537\3;</div> <div>charset TYRcodonPos3 =  4004-4538\3;</div> <div> </div> <div>charset RAG1codonPos1 =  4542-4965\3;</div> <div>charset RAG1codonPos2 =  4540-4966\3;</div> <div>charset RAG1codonPos3 =  4541-4964\3;</div> <div> </div> <div>charset POMCcodonPos1 =  4967-5441\3;</div> <div>charset POMCcodonPos2 =  4968-5439\3;</div> <div>charset POMCcodonPos3 =  4969-5440\3;</div> <div> </div> <div>charset SIAH1codonPos1 =  5443-5836\3;</div> <div>charset SIAH1codonPos2 =  5444-5837\3;</div> <div>charset SIAH1codonPos3 =  5442-5838\3;</div> <div> </div> <div>charset 16S_rec = 5839-7695;</div> </div>

Figure 16 in Rediscovery and description of Paramormyrops sphekodes (Sauvage, 1879) and a new cryptic Paramormyrops (Mormyridae: Osteoglossiformes) from the Ogooué River of Gabon using morphometrics, DNA sequencing and electrophysiology

Figure 16. Nine species of Paramormyrops from Lower Guinea showing, from left to right, head shape viewed from above, the outline of the body, and representative female and male EOD waveforms. Head shapes are camera lucida tracings of the holotypes for each species from the snout to end of opercular opening. The first six have sharp V-shaped head profiles and the last three have relatively blunt U-shaped heads. All but the last two have electric organs composed of Type NPp electrocytes (exhibiting Non-Penetrating stalks innervated on the posterior face). The last two have electric organs composed of Type Pa electrocytes (with Penetrating stalks innervated on the anterior face). All known mormyrids with Type Pa electrocytes have an initial, head-negative peak, P0, in the EOD waveform as illustrated here for P. kingsleyae. The P0 peak is absent in all species with Type NPp electrocytes. The EOD of P. batesii is unknown, but the electric organ is composed of Type Pa electrocytes.

Figure 9 in Rediscovery and description of Paramormyrops sphekodes (Sauvage, 1879) and a new cryptic Paramormyrops (Mormyridae: Osteoglossiformes) from the Ogooué River of Gabon using morphometrics, DNA sequencing and electrophysiology

Figure 9. Histology of para-sagittal section of paralectotype of P. sphekodes specimen MNHN 1998-1050 (Female, 98.7 mm, SL) shows electrocytes of type NPp (Non-Penetrating stalks with posterior innervation). The specimen, collected from Doumé Falls by Alfred Marche in 1876–1877 and preserved in alcohol, was embedded in plastic, sectioned with a tungsten carbide knife at 7 µm and stained with toluidine blue. E = main body of the electrocyte; anterior = anterior face of electrocyte; post = posterior face of same electrocyte; c = collagen layer separating two electrocytes; S = stalk of electrocyte which is innervated by the axons from the electromotor nerve (not shown); s = stalklets, or small branches from a dividing stalk that eventually fuse with posterior face of the electrocyte. Stalks are innervated on the posterior side of the electrocyte and all branches of the stalk system remain posterior to the main body of the electrocyte without crossing to the opposite or anterior side.

Figure 11 in Rediscovery and description of Paramormyrops sphekodes (Sauvage, 1879) and a new cryptic Paramormyrops (Mormyridae: Osteoglossiformes) from the Ogooué River of Gabon using morphometrics, DNA sequencing and electrophysiology

Figure 11. (A, B) Collection localities near the rapids at Doumé (0.84245°S, +12.96249°E) on the Ogooué River of Gabon, where P. sphekodes is sympatric with P. ntotom sp. nov. (B) shows local villagers fishing with hoop nets at Doumé. (C, D) View of the Sébé River (0.93494°S, 13.35767°E) where the two species are also sympatric. Both habitats are moderate-sized rivers with gentle flow or rapids over rocky outcroppings, interspersed with sandy beaches, surrounded by dense rain forest. The Ogooué River is 75–100 m wide at Doumé, 3 m in depth, and the water had low conductivity (13.9 µs/cm) at pH 7.04 and 6.66 mg/L O2 (83.1% saturated) at 26.7 °C. The Sébé River is 55–75 m wide, approximately 3.1 m deep, 16.0 µs conductivity, 7.08 pH and 7.5 mg/L O2 (93.6% saturation) at 26.6°C).

Figure 12 in Rediscovery and description of Paramormyrops sphekodes (Sauvage, 1879) and a new cryptic Paramormyrops (Mormyridae: Osteoglossiformes) from the Ogooué River of Gabon using morphometrics, DNA sequencing and electrophysiology

Figure 12. Holotype of P. ntotom sp. nov. CUMV 98138, tag number JPS-1189, male, 178 mm SL, from top to bottom photographed when alive, preserved in alcohol left and right sides, and radiograph. Scale bars = 1 cm.

Figure 4 in Rediscovery and description of Paramormyrops sphekodes (Sauvage, 1879) and a new cryptic Paramormyrops (Mormyridae: Osteoglossiformes) from the Ogooué River of Gabon using morphometrics, DNA sequencing and electrophysiology

Figure 4. The short EOD and SN4 Paramormyrops differ in the ratio of head length (HL) to head depth (HD) when measurements are taken from radiographs. (A) HLx/HDx is plotted against standard length for 41 specimens including short EOD specimens (n = 9, blue circles), SN4 specimens (n = 30, red squares) and the two existing types (* = lectotype of P. sphekodes and 'x' = the paralectotype). Solid lines show linear regression lines showing that head shape changes little with overall size. The measurements of the lectotype (LT) of P. sphekodes (MNHN-A893) and paralectotype (PLT) (MNHN 1998-1050) identify the short EOD individuals as P. sphekodes. The specimens with SN4-type EODs belong to a new species (red * indicates the new species holotype). Specimen 1185 is shown in x-ray in C. (B) Non-overlapping histograms of HLx/ HDx allow for good diagnosis of the two EOD types even if no EOD is available, as with the two types of P. sphekodes. (C) Radiographs of two specimens (Specimen CUMV 98134 tag number JPS-1185, an SN4 fish and MNHN-A893) illustrate landmarks used for measuring HLx and HDx (see Material and Methods). Scale bars = 1 cm.

Figure 10 in Rediscovery and description of Paramormyrops sphekodes (Sauvage, 1879) and a new cryptic Paramormyrops (Mormyridae: Osteoglossiformes) from the Ogooué River of Gabon using morphometrics, DNA sequencing and electrophysiology

Figure 10. Distribution map of West-Central Africa showing collection localities of specimens of P. sphekodes (blue), P. ntotom sp. nov. (red) and P. curvifrons (green). Stars mark collection locations of holotypes (or lectotype) and circles mark locations of other specimens.