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Datasets for phylogenetic analyses and phylogenetic trees for: Genetic barcodes for species identification and phylogenetic estimation in ghost spiders (Araneae: Anyphaenidae: Amaurobioidinae). Invertebrate Systematics, 2024
<p>We combined the COI sequence data with legacy multigene sequence data to create a new, taxon-rich phylogeny for the Amaurobioidinae. We used sequences for four loci that have been used in previous studies on the subfamily: two mitochondrial loci, COI (658bp) and ribosomal subunit 16S (16S, 410bp); and two nuclear loci, Histone H3 (H3, 327bp) and ribosomal subunit 28S (28S, 839bp). We complemented the Amaurobioidinae data with sequences from several non-amaurobioidine anyphaenids and two clubionids as outgroups. Sequence alignment was performed using the MAFFT (ver. 7.308) plugin in Geneious, allowing MAFFT to automatically select an appropriate alignment strategy based on the properties of each locus, or with the online MAFFT server (https://mafft.cbrc.jp), which consistently selected the L-INS-i algorithm. Finally, alignments of the four loci were concatenated to construct a 2234 bp multigene sequence matrix containing 692 taxa, with about 55% missing/gap data (“full” matrix henceforth). To ensure that excessive missing data did not affect the resulting topology, we also constructed a reduced matrix by removing additional COI-only specimens so that each species and morphotype was represented by just one or two specimens for which all loci were available (where possible). After realignment, this reduced matrix was 2235 bp long, included 167 taxa, and had about 22% missing/gap data (“reduced” matrix henceforth). Phylogenetic analyses under maximum likelihood, including model selection, were then conducted with IQ-TREE 2. We performed phylogenetic analyses on both concatenated matrices (the full matrix and the reduced matrix) and on each individual locus. For model selection, we provided an initial scheme that partitioned the matrix by locus, and further partitioned the protein-coding loci (COI and H3) by codon position. We used ModelFinder and searched for the best partition scheme, all in IQ-TREE. The best models (partitions) for the full dataset were: GTR+F+I+G4 (16S), GTR+F+I+I+R4 (28S), TVM+F+I+I+R2 (COI-1), TIM2+F+R4 (COI-2), GTR+F+R5 (COI-3), TVMe+G4 (H3-1-H3-2), SYM+G4 (H3-3); and for the reduced dataset: GTR+F+I+G4 (16S), GTR+F+I+G4: (28S), GTR+F+I+G4: (COI-2), GTR+F+I+G4: (COI-3), TVM+F+I+G4: (COI-1, H3-2), GTR+F+I+G4: (H3-1), GTR+F+I+G4: (H3-3). For each dataset, once the best models and partitions were defined, we executed 10 independent replicates of tree calculations followed by 1000 ultrafast bootstrap replicates, and the replicate reaching the maximum likelihood was chosen. Phylogenetic analyses under parsimony were made with TNT, under equal weights, using the “new technology” search with default values, asking for 10 independent hits to the minimal length, and submitting the resulting trees to a round of TBR branch swapping. </p>
MACSE Barcode Alignments
<p>This page provides alignments of barcoding sequences obtained in April 2020 by using the <a href="https://github.com/ranwez/MACSE_V2_PIPELINES/tree/master/MACSE_BARCODE">MACSE barcoding pipelines</a> on sequences collected from the BOLD database. The pipeline is fully described in:</p> <ul> <li>Frédéric Delsuc and Vincent Ranwez (2020). Accurate alignment of (meta)barcoding data sets using MACSE. In Scornavacca, C., Delsuc, F., and Galtier, N., editors, Phylogenetics in the Genomic Era, chapter No. 2.3, pp. 2.3:1-2.3:31. No commercial publisher | Authors open access book. ( <a href="https://hal.inria.fr/PGE/hal-02541199">hal-02541199</a> ). (doi:<a href="https://doi.org/10.5281/zenodo.14185826">10.5281/zenodo.14185826</a>).</li> </ul> <p>Details of the individual files are provided in the file README.html.</p>
A reference library for Canadian invertebrates with 1.5 million barcodes, voucher specimens, and DNA samples
<p>[This repository contains the source data for the manuscript "A reference library for Canadian invertebrates with 1.5 million barcodes, voucher specimens, and DNA samples" by deWaard et al., 2019. BioRxiv]</p>
Examining ray and skate diversity in the Irish Sea using DNA barcodes: Research project data
<p>All of the supplementary material to accompany the 4th year research project 'Examining ray and skate diversity in the Irish Sea using DNA barcodes'. Data includes <em>Cytochrome c oxidase I</em> (COI) sequences generated in this project from <em>Raja </em>specimens, agarose gel electrophoresis images of DNA samples, DNA concentrations of DNA extractions from <em>Raja </em>specimens as well the accession numbers of sequences sourced from GenBank that were used to construct a maximum likelihood tree. </p>
FIG. 3 in First record and DNA Barcoding of Oman cownose ray, Rhinoptera jayakari Boulenger, 1895 from Andaman Sea, India
FIG. 3. — Rhinoptera jayakari Boulenger, 1895: A, underside of the head; B, location of prickles on dorsal surface of the head; C, nine series of teeth, upper jaw; D, dorsal fin along with spine. Size of specimen: 494 mm DW.
Figure 2 in Prospects for using DNA barcoding to identify spiders in species-rich genera
Figure 2. Box-and-whisker plots of average intraspecific divergence for 16 genera represented by more than 3 species (Neriene, Pimoa, and Theridion were excluded). The life history of each genus is also indicated.
Figure 1 in Prospects for using DNA barcoding to identify spiders in species-rich genera
Figure 1. Cumulative number of spider species described over time, including only species that are currently valid (description years for all valid species follow Platnick 2009).
Figure 5. A in Identity of the ailanthus webworm moth (Lepidoptera, Yponomeutidae), a complex of two species: evidence from DNA barcoding, morphology and ecology
Figure 5. A Neotype of Deiopeia [= Atteva] aurea, specimen CNCLEP00031092 (CNC) B–C Barcoded specimens of A. aurea from Maryland collected 4 Aug and 31 Jul 2006 respectively (specimens CNCLEP00027030 and CNCLEP00026910, CNC) D Aberrant specimen of A. aurea from Maryland collected 4 Aug 2006 (specimen CNCLEP00027027, CNC)
Figure 3. A in Identity of the ailanthus webworm moth (Lepidoptera, Yponomeutidae), a complex of two species: evidence from DNA barcoding, morphology and ecology
Figure 3. A The original figure of Atteva punctella from Plate 372 in Stoll (1781). Th e illustration is 25 mm wide in the work B Phalaena Tinea punctella Stoll (= A. pustulella Fabricius), specimen USNCN- CLEP00056027 (USNM) C Atteva hysginiella, specimen CNCLEP00060122 (CNC) D A. zebra, specimen CNCLEP00056033 (USNM).
Figure 4. A in Identity of the ailanthus webworm moth (Lepidoptera, Yponomeutidae), a complex of two species: evidence from DNA barcoding, morphology and ecology
Figure 4. A Holotype of A. edithella, specimen USNMENT00656111 (USNM) B Holotype of A. exquisita from Coahuila, Mexico, specimen USNMENT00656112 (USNM) C Holotype of A. ergatica, specimen CNCLEP00060676 (BMNH); due to markedly drooped wings, two half-photos were joined to show both sides D Holotype of A. microsticta, specimen USNMENT00656110 (USNM).
Figure 2 in Identity of the ailanthus webworm moth (Lepidoptera, Yponomeutidae), a complex of two species: evidence from DNA barcoding, morphology and ecology
Figure 2. Map showing the distribution of Atteva specimens examined as part of this study. Notable specimens are highlighted in red.
Figure 5 in Prospects for using DNA barcoding to identify spiders in species-rich genera
Figure 5. Maximum intraspecific divergence compared with nearest-neighbor distance using all data for the four categories of topology: A monophyletic (133 cases), B nested (23 cases), C paraphyletic (28 cases), and D intermingled (16 case). See Methods for definitions. 89.7% of monophyletic and nested species fall above the 1:1 line, indicating the presence of a barcode gap, while 90.9% of paraphyletic and intermingled species fall below this line.
Figure 4 in Prospects for using DNA barcoding to identify spiders in species-rich genera
Figure 4. Maximum intraspecific divergence compared with nearest-neighbour distance of monophyletic morphospecies for all data and using only new data, which have been identified by a single spider taxonomist. Most species (92.5%) fall above the 1:1 line, indicating the presence of a "barcode gap".
Appendix List of samples of deep frozen frog legs with purchase date, collection number, haplotype number, taxonomic identification, tibia length (TL) and estimated snout vent length (SVL). in Which frog's legs do froggies eat? The use of DNA barcoding for identification of deep frozen frog legs (Dicroglossidae, Amphibia) commercialized in France
Appendix List of samples of deep frozen frog legs with purchase date, collection number, haplotype number, taxonomic identification, tibia length (TL) and estimated snout vent length (SVL).
Fig. 2. Minimum spanning network depicting relationships among 16S in Which frog's legs do froggies eat? The use of DNA barcoding for identification of deep frozen frog legs (Dicroglossidae, Amphibia) commercialized in France
Fig. 2. Minimum spanning network depicting relationships among 16S haplotypes of Fejervarya cancrivora (Gravenhorst, 1829). The size of each circle is proportional to the haplotype frequency and the lengths of the connecting lines are proportional to the number of mutations. Colors refer to distinct regions (Indonesia: Java, Sumatra, Bali, Kalimantan, Bangka; Malaysia; Taiwan) and commercialized frogs of unknown origin are in black.
Fig. 3. Histograms. A in Which frog's legs do froggies eat? The use of DNA barcoding for identification of deep frozen frog legs (Dicroglossidae, Amphibia) commercialized in France
Fig. 3. Histograms. A. Snout vent length (in mm) in adult Fejervarya cancrivora (Gravenhorst, 1829) from samples collected for scientific purposes (Boulenger 1920) and collection specimens as mentioned in Material and methods. B. Snout vent length estimated from tibia length of genetically identified frog legs from French supermarkets (specimen list, see Appendix).
Fig. 1 in Which frog's legs do froggies eat? The use of DNA barcoding for identification of deep frozen frog legs (Dicroglossidae, Amphibia) commercialized in France
Fig. 1. Phylogeny of Indonesian species of Fejervarya and Limnonectes recovered by the Bayesian analysis (GTR + I + G model). Hoplobatrachus rugulosus (Wiegmann, 1834) and Occidozyga laevis (Günther, 1858) were used as outgroups. Numbers on nodes represent Bayesian posterior probabilities, * indicates a value higher than 0.98. Only values higher than 0.75 are represented. h01 to h18 indicate the 18 haplotypes from frozen frog legs recovered in this study.
Fig. 4 in Connecting systematic and ecological studies using DNA barcoding in a population survey of Drosophilidae (Diptera) from Mt Oku (Cameroon)
Fig. 4. Phylogenetic analysis of the subgenus Sophophora and Lissocephala aff. diola Tsacas & Lachaise, 1979. Conventions as for Fig. 3.
Fig. 2 in Connecting systematic and ecological studies using DNA barcoding in a population survey of Drosophilidae (Diptera) from Mt Oku (Cameroon)
Fig. 2. Percent divergence of the morphospecies DNA barcode from the closest neighbor found in the barcode database.
Fig. 3 in Connecting systematic and ecological studies using DNA barcoding in a population survey of Drosophilidae (Diptera) from Mt Oku (Cameroon)
Fig. 3. Phylogenetic analysis of the genus Zaprionus and Microdrosophila aff. mamaru (Burla, 1954). This tree is the neighbor-joining tree. The maximum likelihood tree gives the same topology. Nodes with a bootstrap value lower than 50% were merged. Bootstrap values were calculated over 1000 repeats. Above nodes: bootstrap values for maximum likelihood using a GTR + G + I model. Below nodes: bootstrap values for neighbor-joining using the Kimura-2p distance.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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