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Figure 94 in Phylogeny of the spider genus Ixchela Huber, 2000 (Araneae: Pholcidae) based on morphological and molecular evidence (CO1 and 16S), with a hypothesized diversification in the Pleistocene

Figure 94. Chronogram with the molecular dating for the genus Ixchela using the lognormal relaxed clock model. Bars at nodes indicate the 95% highest posterior density interval (HPD) to each tmrca (time of the most recent common ancestor). Numbers on bars indicate the mean age for each node in millions of years (Mya). Gradient of colours indicates ages of nodes, from the older nodes (darker) toward more recent nodes (lighter).

Figure 95 in Phylogeny of the spider genus Ixchela Huber, 2000 (Araneae: Pholcidae) based on morphological and molecular evidence (CO1 and 16S), with a hypothesized diversification in the Pleistocene

Figure 95. Biogeographical provinces of Mexico following the scheme of Morrone (2004, 2005), showing the distribution of the genus Ixchela. Red background colour indicates the Mexican Montane biotic component and its provinces: 1, Sierra Madre Occidental (no records of Ixchela); 2, Transmexican Volcanic Belt (species recorded in green); 3, Sierra Madre Oriental (species recorded in yellow); 4, Cuenca del Balsas (no records of Ixchela); 5, Sierra Madre del Sur (species recorded in dark blue). Yellow background colour indicates the Province of Chiapas (species recorded in light blue) which belongs to the Mesoamerican biotic component and is extended toward mountainous zones of Central America (Guatemala, Honduras, El Salvador and Nicaragua).

Figure 93 in Phylogeny of the spider genus Ixchela Huber, 2000 (Araneae: Pholcidae) based on morphological and molecular evidence (CO1 and 16S), with a hypothesized diversification in the Pleistocene

Figure 93. Majority consensus tree derived from the Bayesian analysis using the (morphology + CO1 + 16S) data set. Numbers above branches indicate posterior probabilities. Numbers below branches: (+) indicates clades found with PA/ Jackknife support values and/or with significant PA/Bremer support values. Black squares below branches indicate clades found with PA using different concavity values (K) using implied weighting; white squares indicate clades not recovered with some concavity values (see inset). Numbers and arrows indicate clades that are discussed in the text.

Figure 91 in Phylogeny of the spider genus Ixchela Huber, 2000 (Araneae: Pholcidae) based on morphological and molecular evidence (CO1 and 16S), with a hypothesized diversification in the Pleistocene

Figure 91. Consensus tree of the five most parsimonious trees obtained by the morphological cladistic analysis with equal weighting of characters (L = 59, CI = 0.72, RI = 0.84). Black squares indicate synapomorphic or apomorphic states, whereas white squares indicate homoplastic character states. Small numbers above squares indicate character number; small numbers below squares indicate character state. Larger numbers above branches indicate Jackknife support values; larger numbers below branches indicate Bremer support values. Black squares below branches indicate clades recovered with PA using different concavity values (K) using implied weighting; white squares indicate clades not recovered with some concavity values (see inset).

Figure 92 in Phylogeny of the spider genus Ixchela Huber, 2000 (Araneae: Pholcidae) based on morphological and molecular evidence (CO1 and 16S), with a hypothesized diversification in the Pleistocene

Figure 92. Majority consensus tree derived from the Bayesian analysis using the morphology + CO1 data set. Numbers above branches indicate posterior probabilities. Numbers below branches: (+) indicates clades found with PA/Jackknife support values and/or with statistically significant PA/Bremer support values. Black squares below branches indicate clades found with PA using different concavity values (K) using implied weighting; white squares indicate clades not recovered with some concavity values (see inset). Numbers and arrows indicate clades that are discussed in the text.

Figures 79–89 in Phylogeny of the spider genus Ixchela Huber, 2000 (Araneae: Pholcidae) based on morphological and molecular evidence (CO1 and 16S), with a hypothesized diversification in the Pleistocene

Figures 79–89. Ixchela tlayuda sp. nov. Male: 79, 80, Habitus, lateral and dorsal views, respectively. 81, Carapace and chelicerae, frontal view. 82, Chelicerae, frontal view. 83–84, Left palp, retrolateral and prolateral views, respectively. 85, Chelicera, lateral view. Female: 86, Epigynum, left lateral view. 87, Epigynum, ventral view. 88, Epigynum, dorsal view. 89, Epigynum, frontal view. Scale bars: 0.5 mm (Figs 82, 85, 88), 1 mm (Figs 79–81, 83, 84, 86, 87, 89).

Figures 68–78 in Phylogeny of the spider genus Ixchela Huber, 2000 (Araneae: Pholcidae) based on morphological and molecular evidence (CO1 and 16S), with a hypothesized diversification in the Pleistocene

Figures 68–78. Ixchela purepecha sp. nov. Male: 68, 69, Habitus, lateral and dorsal views, respectively. 70, Carapace and chelicerae, frontal view. 71, Chelicerae, frontal view. 72, 73, Left palp, retrolateral and prolateral views, respectively. 74, Chelicera, lateral view. Female: 75, Epigynum, left lateral view. 76, Epigynum, ventral view. 77, Epigynum, anterior–dorsal view. 78, Epigynum, frontal view. Scale bars: 0.5 mm (Figs 71, 74, 75, 77), 1 mm (Figs 68, 69, 72, 73, 76, 78).

Figures 45–55 in Phylogeny of the spider genus Ixchela Huber, 2000 (Araneae: Pholcidae) based on morphological and molecular evidence (CO1 and 16S), with a hypothesized diversification in the Pleistocene

Figures 45–55. Ixchela jalisco sp. nov. Male: 45, 46, Habitus, lateral and dorsal views, respectively. 47, Carapace and chelicerae, frontal view. 48, Chelicerae, frontal view. 49, 50, Left palp, retrolateral and prolateral views, respectively. 51, Chelicera, lateral view. Female: 52, Epigynum, left lateral view. 53, Epigynum, ventral view. 54, Epigynum, dorsal view. 55, Epigynum, frontal view. Scale bars: 0.5 mm (Figs 48, 51, 52, 54, 55), 1 mm (Figs 45–47, 49, 50, 53).

Figures 56–67 in Phylogeny of the spider genus Ixchela Huber, 2000 (Araneae: Pholcidae) based on morphological and molecular evidence (CO1 and 16S), with a hypothesized diversification in the Pleistocene

Figures 56–67. Ixchela mendozai sp. nov. Male: 56, 57, Habitus, lateral and dorsal views, respectively. 58, Carapace and chelicerae, frontal view. 59, Chelicerae, frontal view. 60, 61, Left palp, retrolateral and prolateral views, respectively. 62, Chelicera, lateral view. 63, Bulb and embolus, prolatero-dorsal view (arrow indicates the curved and sharp subdistally sclerotized spine). Female: 64, Epigynum, ventral view. 65, Epigynum, dorsal view. 66, Epigynum, left lateral view. 67, Epigynum, frontal view. Scale bars: 0.5 mm (Figs 58, 59, 62–67), 1 mm (Figs 56, 57, 60, 61).

Figures 34–44 in Phylogeny of the spider genus Ixchela Huber, 2000 (Araneae: Pholcidae) based on morphological and molecular evidence (CO1 and 16S), with a hypothesized diversification in the Pleistocene

Figures 34–44. Ixchela azteca sp. nov. Male: 34, 35, Habitus, lateral and dorsal views, respectively. 36, Carapace and chelicerae, frontal view. 37, Chelicerae, frontal view. 38, 39, Left palp, retrolateral and prolateral views, respectively. 40, Chelicera, lateral view. Female: 41, Epigynum, left lateral view. 42, Epigynum, ventral view. 43, Epigynum, dorsal view. 44, Epigynum, frontal view. Scale bars: 0.5 mm (Figs 42, 43), 1 mm (Figs 34–41, 44).

Figures 26–33 in Phylogeny of the spider genus Ixchela Huber, 2000 (Araneae: Pholcidae) based on morphological and molecular evidence (CO1 and 16S), with a hypothesized diversification in the Pleistocene

Figures 26–33. Ixchela azteca sp. nov. Male. 26, Chelicerae, ventral view. 27, Left chelicerae, frontal view. 28, Right chelicerae, posterior view. 29, Left endite, ventral view (arrow indicates the serrated margin). 30, Detail of the serrated margin on endite. 31, Spinnerets, ventral view. 32, Detail of one anterior lateral spinneret (arrows indicate the slightly pointed spigot and the wide spigot). 33, Detail of one posterior median spinneret (arrows indicate the acciniform gland spigots). Scale bars: 50 μm (Figs 30, 32, 33), 100 μm (Figs 28, 29), 200 μm (Fig. 27), 300 μm (Fig. 31), 500 μm (Fig. 26).

opennotspecifiedMar 2013View details →

Fig. 2 in Use of Morphology and CO1 Barcoding to Test the Validity ofTetraopes huetheriSkillman (Coleoptera: Cerambycidae)

Fig. 2. Neighbor-Joining tree of 22 Tetraopes specimens and data from Farrell (2001). Scale indicates 1% difference.

opencc-by-4.0Dec 2021View details →

NanoClass-compatible BOLD CO1 databases

BOLD CO1 databases reformatted to use in NanoClass (https://github.com/ejongepier/NanoClass; version 0.3.0-beta or higher) and QIIME2. Three separate databases are included for use in combination with primers mtD, LCO-HCO and CI. Databases include reference sequences and reference taxonomies for the use in NanoClass, as well as pre-trained classifiers for use in QIIME2. See usage instructions below. For questions, please contact e.jongepier@uva.nl. ========================================== WARNING ========================================== Please note this version of a custom BOLD CO1 db comes with absolutely no warranties. When using this db in NanoClass, mind that it has only been tested with methods: ["megablast","minimap","spingo"] NanoClass cannot be run in combination with these BOLD CO1 databases using methods ["mothur","centrifuge","kraken"]. Compatibility with ["blast","dcmegablast","qiime","rdp"] is untested. Just remove the tools you want to skip from the NanoClass/config.yaml (see also the NanoClass documentation here: https://ejongepier.github.io/NanoClass/) Never use this data base in combination with the NanoClass snakemake -F parameter or this BOLD CO1 database will be overwriten by the default 16S SILVA database. ========================================== DESCRIPTION ========================================== BOLD CO1 database (last) downloaded on 20210420 and reformatted for use in QIIME2 and NanoClass. To clean-up BOLD CO1 db these steps were taken (step 7 to 11 were repeated for each of the 3 primers): - remove identical duplicates [3597874] - drop seqs with non-IUPAC characters [3597839] - remove leading and trailing ambiguous bases [3597839] - remove low quality reads - remove reads with homopolymer runs - filter by length - extract fragments between primer sequences [mtD:112450; CI:121391; LCO-HCO:65307] - dereplicate / cluster [mtD:55075; CI:46470; LCO-HCO:24835] - remove uninformative taxonomic labels [mtD:55073; CI:46466; LCO-HCO:24832] - reformat db for use in NanoClass - train classifier based on fragments   ========================================== HOW TO USE THESE DBS ========================================== Use in NanoClass: Unzip the database and copy the reference taxonomy and (unzipped) reference sequences to the NanoClass/db/common directory, like so: $ cp mtD/bold-v20210421-taxonomy-mtD.tsv /path/to/NanoClass/db/common/ref-taxonomy.txt $ gzip -d -c  mtD/bold-v20210421-frags-mtD.fa.gz > /path/to/NanoClass/db/common/ref-seqs.fna Something similar can be done for the other two primers (CI or LCO-HCO). Only these three primers are supported at this point. Next, create an (empty) ref-seqs.aln file just to prevent NanoClass from automatically downloading the default 16S SILVA database, which would overwrite the BOLD db you just copied into NanoClass/db/common. $ touch /path/to/NanoClass/db/common/ref-seqs.aln Finally, you need to make a change to the NanoClass/Snakefile (i.e change first line into the second). optrules.extend(["plots/precision.pdf"] if len(config["methods"]) > 2 else []) optrules.extend(["plots/precision.pdf"] if len(config["methods"]) > 200 else []) This will disable the computation of precision plots by NanoClass as this is not supported in combination with the custom BOLD CO1 databases. Also mind that you need to change the nanofilt minlen and maxlen in the NanoClass/config.yaml to capture the appropriate fragment length for your primer. For the mtD primer I used minlen 600 and maxlen 900 for testing. Use in QIIME2: You can use the trained classifier directly in QIIME2, like so: $ qiime feature-classifier classify-sklearn \   --i-classifier mtD/bold-v20210421-classifier-mtD.qza \   --i-reads <your-reprseqs>.qza \   --o-classification <your-classification>.qza \   --verbose Something similar can be done for the other two primers (CI or LCO-HCO). Only these three primers are supported at this point. The classifiers have only been tested with with the sklearn algorithm.

opencc-by-4.0Jul 2015View details →

Supplementary material 1 from: Arriaga-Jiménez A, Roy L (2015) Co1 DNA supports conspecificity of Geomyphilus pierai and G. barrerai (Coleoptera, Scarabaeidae, Aphodiinae) and is a good marker for their phylogeographic investigation in Mexican mountains. ZooKeys 512: 77-88. https://doi.org/10.3897/zookeys.512.9646

EMBL accession numbers of beetle DNA sequences: Explanation note: accession numbers (EMBL) of each Co1 and ITS DNA sequence obtained from beetle individuals and integrated into analyses in the present study.

FIGURE 3 in Validation of the status of a species with high CO1 and low nuclear genetic divergences: the scab mite Caparinia ictonyctis stat. res. (Acariformes: Psoroptidae) parasitizing the African hedgehog Atelerix albiventris

FIGURE 3. Details of Caparinia spp. A—Position of seta si, female of C. ictonyctis stat. res.; B—Same, female of C. tripilis; C—Coxal field III, male of C. ictonyctis stat. res.; D—Same, females of C. tripilis; E - Anal region, female of C. tripilis; F— Adanal shields, male of C. tripilis.

FIGURE 6. Caparinia ictonyctis Lawrence, 1955, protonymph. A in Validation of the status of a species with high CO1 and low nuclear genetic divergences: the scab mite Caparinia ictonyctis stat. res. (Acariformes: Psoroptidae) parasitizing the African hedgehog Atelerix albiventris

FIGURE 6. Caparinia ictonyctis Lawrence, 1955, protonymph. A—dorsal view; B—ventral view; C—tarsus I in dorsal view, D—same in ventral view; E—tarsus II in dorsal view; F—same in ventral view; G—leg III in ventral view; H—leg IV in ventral view. Scale bars: 100 µm = A, B; 50 µm = C–H.

FIGURE 5. Caparinia ictonyctis Lawrence, 1955, larva. A in Validation of the status of a species with high CO1 and low nuclear genetic divergences: the scab mite Caparinia ictonyctis stat. res. (Acariformes: Psoroptidae) parasitizing the African hedgehog Atelerix albiventris

FIGURE 5. Caparinia ictonyctis Lawrence, 1955, larva. A—dorsal view; B—ventral view; C—leg I in dorsal view, D—same in ventral view; E—leg II in dorsal view; F—same in ventral view; G—leg III in ventral view. Scale bars: 100 µm = A, B; 50 µm = C–G.

FIGURE 2 in Validation of the status of a species with high CO1 and low nuclear genetic divergences: the scab mite Caparinia ictonyctis stat. res. (Acariformes: Psoroptidae) parasitizing the African hedgehog Atelerix albiventris

FIGURE 2. SEM images of Caparinia ictonyctis stat. res. A—Tibia and tarsus IV of male, dorsal view; B—Tarsus IV of male, ventral view; C—Female, dorsal view; D—Posterior opisthosoma, dorsal view; E—Trochanter I, dorsal view; F—Tibia and tarsus III, dorsal view.

FIGURE 4 in Validation of the status of a species with high CO1 and low nuclear genetic divergences: the scab mite Caparinia ictonyctis stat. res. (Acariformes: Psoroptidae) parasitizing the African hedgehog Atelerix albiventris

FIGURE 4. Anal region of females (left column) and adanal shields of males (right column) of Caparinia spp. A and B—C. setifera; C and D—C. erinacei; E and F—C. algirus; G and H—C. lophiomys.