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Figure 6 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 6. Relevant portion of the phylogram produced from maximum likelihood analysis in RAxML of cyt-b sequences from nine individuals of the 'short EOD' form (blue), eight specimens of species 'SN4' from the Doumé and Sébé sites (red) aligned to data matrix (73 Paramormyrops individuals) of Sullivan et al. (2002), rooted with sequence of M. ntemensis (not shown). Sequence of P. curvifrons individual is shown in green. For species codes, follow Sullivan et al. (2002). Bootstrap values are shown at nodes (filled circles). Haplotypes of SN4 and 'short EOD' do not constitute monophyletic groups. However, no haplotypes are shared between these forms and nowhere on the tree do haplotypes from the two forms appear as nearest relatives. This result is consistent with the hypothesis of heterospecificity of the two forms.

Figure 7 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 7. Five specimens of P. sphekodes from Ogooué basin of Gabon. From top to bottom: specimen tag number 1192, female, 113.5 mm; 1201, female, 111 mm from the Ogooué River at Doumé; 1214, male, 112.5 mm; 1230, male, 133 mm and 1238, male, 119 mm from the Sébé River nearby. Scale bars = 1 cm.

Figure 3 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 3. The Paramormyrops specimens with short EODs, and those called SN4 have overlapping meristics but differ in a number of morphometric ratios. Here, the short EOD specimens are shown as blue circles, while '*' indicates the lectotype of P. sphekodes and '+' indicates the paralectotype. The red circles show those with longer EODs referred to as SN4 specimens. The short EOD forms have elevated ratios of interorbital width to snout length and correspondingly blunter snout angles than the SN4 specimens. They also have slightly reduced caudal peduncle depth to length ratios. There is overlap in each ratio taken separately, but combined they provide a convenient morphological basis for diagnosis between these two EOD types. EOD traces are 10 ms long.

Figure 1 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 1. (A) Paramormyrops sphekodes (Sauvage, 1877) MNHN A.893 photographed in 1984 by W. Harder at which time the lot contained two specimens, suspended vertically in a tall jar from a glass floater. The original MNHN catalogue shows two specimens accessioned in 1878 under this number. The larger specimen (SL = 113.8 mm) is currently catalogued as A 893; the smaller specimen (SL = 98.7 mm) was subsequently catalogued in 1998 as MNHN 1050-1998. Sauvage's original description indicates multiple specimens with a largest of 140 mm total length, but he designated no holotype. We regard these specimens as syntypes prior to our designation of the larger as lectotype. (B) Radiograph of MNHN A893.

Figure 2 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 2. Electric organ discharge (EOD) waveforms recorded from 40 specimens of P. sphekodes-like mormyrids from the Ogooué River Basin of Gabon suggest the possibility of two species with distinct EOD waveforms. (A) For each specimen, EOD duration is plotted against standard length (SL). (B) Histogram of EOD durations reveals two modal peaks: one for short EODs, <2 ms duration, and one for longer EODs,> 2 ms. (C) EOD waveforms of longer (above) and shorter duration (below) are superimposed after each EOD's amplitude is normalized to the same peak-to-peak height and centred on the zero-crossing between positive and negative peaks. Blue lines are males and red lines are females. Head positivity is upward. EOD duration is measured between T1 and T2 (in E), first and last points of the waveform that deviate above or below the baseline by more than 2% of the peak-to-peak height. In previous publications, the longer EOD type was referred to by the code name 'SN4'. The fish with the 'short EOD' waveform is new to this study. (D) Histograms of SLs of all 40 specimens separated by EOD-type and by sex/age class show that within each EOD type there are males recognized by their dimorphic anal fins. Within each group, males tend to have the longest duration waveforms. This sex difference is especially pronounced for SN4 males recorded during the breeding season. Fish of both EOD types co-occur at two sites in Gabon: the main channel of the Ogooué River at Doumé and the Sébé River nearby (see map). (E) EOD waveform of specimen CUMV 98177 tag JPS-1238 showing how EOD duration is measured.

Figure 5 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 5. Morphometrics and ratios from the three species of Paramormyrops included in this study. (A–C) and (E–G) show measurement ratios useful in diagnosis of these three species. Snout angle measurements (see Material and Methods) are compared in (D) and (G). (D) plots snout angle against IOW/SNL. Holotypes or lectotypes are indicated by '*' symbols and paratypes are indicated by 'x' symbols. (H) compares IOW/SNL for specimens of differing standard lengths. Superimposed on the data points in (A–C) and (E–G) are box plots showing range, 25% quartile, median and 75% quartile. Black bars above box plots span samples where means differ significantly (P ≤ 0.05) using Tukey–Kramer multiple comparison tests for differences in sample means. See Table 1 for abbreviations.

Figure 1. A in Systematics and phylogeography of the Taiwanese endemic minnow Candidia barbatus (Pisces: Cyprinidae) based on DNA sequence, allozymic, and morphological analyses

Figure 1. A, image of Candidia barbatus; B, map of Taiwan showing the late Pleistocene (dashed line) shoreline, the current shoreline (solid line) (modified from Boggs et al., 1979 and Wu et al., 2007), the sampling sites of Candidia barbatus, the native species range (shaded area), and mtDNA lineages recovered. Geographical ranges of allozyme clusters are demarcated by arrows. Numerical codes for each sampling site: 1, Wulaokeng River (WL); 2, Shuangshi River (SS); 3, Masu River (MS); 4, Shandiaoling River (SD); 5, Sifen River (SF); 6, Waishuangshi River (WS); 7, Dahan River (DH); 8, Beishi River (BS); 9, Ayu River (AY); 10, Hapen River (HP); 11, Chingmei River (CM); 12, Fengshan River (FES); 13, Houlong River (HL); 14, Daan River (DA); 15, Dajia River (DJ); 16, Dadu River (DD); 17, Choshui River (CS); 18, Puzi River (PZ); 19, Tsengwen River (TW); 20, Nanzishan River (NZ); 21, Laonong River (LN); 22, Ailiao River (AL); 23, Lili River (LL); 24, Fanshan River (FAS); 25, Fengang River (FG); 26, Sichong River (SH) (also see Table 1).

Figure 4 in Systematics and phylogeography of the Taiwanese endemic minnow Candidia barbatus (Pisces: Cyprinidae) based on DNA sequence, allozymic, and morphological analyses

Figure 4. The marginal posterior probability distributions for the migration rate of Candidia barbatus between northern and central Taiwan.

Figure 3 in Systematics and phylogeography of the Taiwanese endemic minnow Candidia barbatus (Pisces: Cyprinidae) based on DNA sequence, allozymic, and morphological analyses

Figure 3. Detection of the number of groups by STRUCTURE. A, L(K) as a function of K; B, DK following Evanno et al. (2005) as a function of K.

Figure 2 in Systematics and phylogeography of the Taiwanese endemic minnow Candidia barbatus (Pisces: Cyprinidae) based on DNA sequence, allozymic, and morphological analyses

Figure 2. The neighbor-joining (NJ) tree corrected by the Hasegawa–Kishino–Yano (HKY) + Gamma (0.1719) model based on the complete mitochondrial cytochrome b sequence. The times to the most recent common ancestor for major splitting events are shown below branches with their 95% highest posterior density in parentheses. Numbers above the branches, from top to bottom, are bootstrap values derived from maximum likelihood, Bayesian, NJ, and maximum parsimony methods, respectively. Candidia sieboldii and Candidia temminckii were included as outgroups. H01–H05: lineage A, recovered from Masu River, Shandiaoling River, Sifen River, Waishuangshi River, Dahan River, Beishi River, Hapen River, and Chingmei River. H06, H07: Lineage B, recovered from Wulaokeng River, Shuangshi River, Masu River, Ayu River, Chingmei River, Fengshan River, Houlong River, and Daan River. H08: Lineage C, recovered from Masu River, Shandiaoling River, Sifen River, Beishi River, Ayu River, Dajia River, Dadu River, and Choshui River. H09–H11: Lineage D, recovered from Puzi River, Tsengwen River, and Nanzishan River. H12: Lineage E, recovered from Nanzishan River and Laonong River. H13–H19: Lineage F, recovered from Ailiao River, Lili River, Fanshan River, Fengang River, and Sichong River.

opennotspecifiedMar 2022View details →

FIGURE 3 in Two new species of Hypoxylon (Hypoxylaceae) from China based on morphological and DNA sequence data analyses

FIGURE 3. Hypoxylon jianfengense (Holotype FACATAS 845). A. Stromata on wood. B. Stromatal surface and ostioles. C, D. Stroma in vertical section showing the perithecia and tissue below the perithecial layer. E. KOH-extractable pigments. F. Stromatal granules in water. G. Mature and immature asci in water. H. Asci in Melzer's reagent. I. Immature asci in water. J, K. Mature asci in water. L. Apical apparatus in Melzer' s reagent. M. Ascospore in water showing germ slit. N. Ascospores in water. O. Ascospores in 10% KOH. P. Ascospore under SEM. Bars: A = 5 mm; B = 0.3 mm; C = 0.5 mm; D = 0.1 mm; G, I–K = 20 µm; H, L–O = 10 µm; P = 2.5 µm.

opennotspecifiedMar 2022View details →

FIGURE 1 in Two new species of Hypoxylon (Hypoxylaceae) from China based on morphological and DNA sequence data analyses

FIGURE 1. Phylogenetic tree of Hypoxylon based on the multigene alignment of ITS-LSU-RPB2-TUB2 in the Maximum Likelihood analyses (RaxML). Support values of Maximum Likelihood (ML), Maximum Parsimony (MP) and Bayesian (B) analyses (bootstrap support above 50%, posterior probability value above 0.95) are displayed above or below the respective branches (ML/MP/BA).

opennotspecifiedMar 2022View details →

FIGURE 2 in Two new species of Hypoxylon (Hypoxylaceae) from China based on morphological and DNA sequence data analyses

FIGURE 2. Hypoxylon larissae (Holotype FACATAS 844). A. Stromata on wood. B, C. Stromatal surface and ostioles. D, E. Stroma in vertical section showing the perithecia and tissue below the perithecial layer. F. KOH-extractable pigments. G. Stromatal granules in water. H. Mature and immature asci in Melzer's reagent. I. Asci in Melzer's reagent. J. Immature asci in water. K. Mature asci in water. L. Ascospores in water. M. Ascospores in 10% KOH. N. Ascospores in water showing germ slit. O. Apical apparatus in Melzer's reagent. P. Ascospore under SEM. Bars: A = 5 mm;B, C, E = 0.4 mm; D = 1 mm; H–K = 20 µm; L–O = 10 µm; P = 5 µm.

opencc-by-4.0Mar 2022View details →

Raw data of sequencing results of our study: Bovine milk microbiota: Evaluation of different DNA extraction protocols in challenging samples

Clean reads of the repeated milk samples with used Primer Pairs V1V2 and V3V4 Raw data of sequencing results (amplicon single variants)

dryad32/100

Blast output from: Lost in dead wood? Environmental DNA sequencing from dead wood shows little signs of saproxylic beetles

eDNA metabarcoding has become a standard method for assessing wood-inhabiting fungi and bacteria, yet determination of dead-wood-inhabiting beetles still relies on time-consuming collection of beetle specimens. We thus tested whether beetle species can be identified by eDNA sequencing of wood in a mesocosm experiment that manipulated species assemblages. Dead wood samples were taken at exit holes of beetles and DNA was extracted and analyzed using two comparative methods: (i) metabarcoding with standard arthropod primers (421 bp) and (ii) using short species-specific primers (120-264 bp) with Sanger sequencing. Results showed that beetle DNA was amplified by each of the two approaches, however, with (i) we detected only one non-target saproxylic beetle species. In addition, we identified 80 different OTUs with four non-targeted species of arthropods. For (ii) we detected the targeted species in two fresh beetle exit holes out of 20 samples. We suggest that, in contrast to fungi and bacteria, this eDNA metabarcoding approach is not able to reliably detect saproxylic beetles from wood samples, likely due to rapid degradation of their target DNA. Adapting such an approach for large scale analyses thus requires a better knowledge of degradation processes affecting DNA quality and quantity in wood.

opencc-zeroApr 2022View details →

FIGURE 12 in Colour patterns to sequences: a perspective on the systematics of the Hyperolius viridiflavus group (Anura: Hyperoliidae) using mitochondrial DNA

FIGURE 12. Ranges of the species based on existing information. A—H. spatzi, B—H. nitidulus, C—H. dintelmanni, D—H. sp. 1, E—H. tuberculatus, F—H. bangwae, G—H. parallelus, H—H. marmoratus, I—H. marginatus, J—H. noblei, K—H. goetzei, L—H. glandicolor, M—H. mariae, N—H. viridiflavus.

FIGURE 11 in Colour patterns to sequences: a perspective on the systematics of the Hyperolius viridiflavus group (Anura: Hyperoliidae) using mitochondrial DNA

FIGURE 11. Illustrations of typical colour patterns in the Hyperolius viridiflavus complex: A—H. viridiflavus, from an illustration of 1845 by J. Vignaud; B—H. marmoratus, Storms River, South Africa, photo A. Channing; C—H. marginatus, North Luangwa National Park, Zambia, photo A. Channing; D—H. parallelus, PEM A12451, Cuanavale Source, Angola, photo W. Conradie; E—H. nitidulus, Lamto, Côte d'Ivoire, photo M.-O. Rödel; F—H. glandicolor, Kinangop, Kenya, photo A. Channing; G—H. tuberculatus, ZMB 91677, Dja Reserve, Cameroon, photo M.-O. Rödel; H—H. mariae, Kiloza, Tanzania, photo A. Channing; I—H. noblei, PEM A10608, Quinonga, Mozambique, photo W. Conradie; J—H. goetzei, Iringa, Tanzania, photo A. Channing; K—H. spatzi, Senegal, photo A. Hillers; L—H. dintelmanni, CAS 254137, Edib Hills, Cameroon, photo D. Portik.

FIGURE 10 in Colour patterns to sequences: a perspective on the systematics of the Hyperolius viridiflavus group (Anura: Hyperoliidae) using mitochondrial DNA

FIGURE 10. Localities of sequences (black circles), type localities (stars) and location of junior synonyms of Hyperolius noblei (A), H. goetzei (B), H. spatzi (C) and H. dintelmanni (D). Locality codes are explained in Table 3.

FIGURE 8 in Colour patterns to sequences: a perspective on the systematics of the Hyperolius viridiflavus group (Anura: Hyperoliidae) using mitochondrial DNA

FIGURE 8. Localities of sequences (black circles), type localities (stars) and location of junior synonyms of Hyperolius nitidulus (A), H. mariae (B) and H. sp 1 (C). Locality codes are explained in Table 3.

FIGURE 9 in Colour patterns to sequences: a perspective on the systematics of the Hyperolius viridiflavus group (Anura: Hyperoliidae) using mitochondrial DNA

FIGURE 9. Localities of sequences (black circles), type localities (stars) and location of junior synonyms of Hyperolius bangwae (A), H. tuberculatus (B), and H. glandicolor (C). Locality codes are explained in Table 3.