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DNA barcode analyses improve accuracy in fungal species distribution models
<p class="western"><span>Species distribution models based on environmental predictors are useful to explain a species geographic range. For many groups of organisms, including fungi, the increase of occurrence data sets has generalized their use. However, fungal species are not always easy to distinguish, and taxonomy of many groups is not completely settled. This study explores the effect of taxonomic uncertainty in databases used for modeling fungal distributions. We analyze distribution models for three morphospecies from the corticioid genus <i>Xylodon</i> (Hymenochaetales, Basidiomycota), comparing models based on species names on vouchers specimens with models derived from species identified by DNA barcode. Differences in the contribution of predictors driving the distribution of each modeled taxon and the extent of their ranges were studied. Records under <i>X</i><i>ylodon</i><i> paradoxus</i>, <i>X</i>.<i> flaviporus</i> and <i>X</i>. <i>raduloides</i> were obtained from fungarium collections and GenBank repository. Two grouping criteria were used: (1) specimens were grouped by their collection or sequence voucher names and (2) specimens were grouped following molecular identification using ITS sequences through barcoding gap species recognition (BGSR). Climatic, geographic and biotic variables were used to predict the potential distribution of each taxon through MaxEnt algorithm. From the three morphospecies selected according to voucher names, up to 19 species candidates were detected using BGSR. Climatic variables were the most important predictors in distribution models made from names on voucher specimens, but their importance decreased when BGSR was applied. In general, the extent of species distributions was more restricted for taxa under BGSR. Our results show that taxonomic uncertainty has a strong effect in <i>Xylodon</i> species distribution models. Misleading results can be obtained when cryptic species or identification errors mask the actual diversity of the presence records. Preserved specimens in natural history collections offer the possibility to assess if the species name on labels matches the current species recognition criteria.</span></p>
FIGURE 6 in Comparisons of two cryptic Ampedus species (Coleoptera: Elateridae) by using classical systematics, ecological niche modeling, and DNA barcoding
FIGURE 6. MaxEnt model outputs for Ampedus samedovi. Minimum Training Presence threshold is applied to outputs.
FIGURE 5 in Comparisons of two cryptic Ampedus species (Coleoptera: Elateridae) by using classical systematics, ecological niche modeling, and DNA barcoding
FIGURE 5. MaxEnt model outputs for Ampedus platiai. Minimum Training Presence threshold is applied to outputs.
FIGURE 2 in Comparisons of two cryptic Ampedus species (Coleoptera: Elateridae) by using classical systematics, ecological niche modeling, and DNA barcoding
FIGURE 2. Distributions and collecting localities of Ampedus platiai and Ampedus samedovi. Red: Distribution of only A. platiai in the provinces, Blue: Distribution of only A. samedovi in the provinces, Yellow: Distribution of A. platiai and A. samedovi in the provinces (The map is designed in ArcGis 10.2).
FIGURE 1 in Comparisons of two cryptic Ampedus species (Coleoptera: Elateridae) by using classical systematics, ecological niche modeling, and DNA barcoding
FIGURE 1. Habitus and aedeagi photos of examined species. A–B. Ampedus platiai, C–D. A. samedovi, E–F. A. pomonae (Aedeagi of A. platiai and A. samedovi are redrawn from Kabalak 2010 and aedeagus of A. pomonae is redrawn from Platia 1994.). BML: Basal struts of median lobe, BP: Basal piece, ML: Median Lobe, PDT: Paramere distal tooth, PR: Paramere.
FIGURE 12 in Morphological description of a new species of Capnia (Plecoptera: Capniidae) with DNA barcoding of genus members from the Russian Far East
FIGURE 12. Bayesian inference (BI) tree based on the cytochrome c oxidase I (COI) nucleotide sequence data of the genus Capnia and outgroup Zwicknia rupprechti Bayesian posterior probabilities (≥0.7) are given above tree nodes and bootstrap support values found in the ML analysis (≥70 %) are shown below nodes. Specimens obtained in this study are in Bold.
FIGURES 4–7 in Morphological description of a new species of Capnia (Plecoptera: Capniidae) with DNA barcoding of genus members from the Russian Far East
FIGURES 4–7. Female of Capnia yavorskayae sp. nov. Paratype. 4. Mesothoracic sclerite, ventral: Bs—basisternum; Fs— furcasternum; Fsa—furcasternal arm; Fsp—furcasternal pit; Kes—katepisternum; Pfs—postfurcasternum; Prs—presternum; PPfs—prothoracic postfurcasternum; Sc—spinasternum; Tn—trochantin. 5–6. Abdominal tip, variation of the subgenital plate. 7. Vaginal complex (cleared) with genital opening, membranous genital cavity, inner tooth-shaped black sclerite.
FIGURES 1–3 in Morphological description of a new species of Capnia (Plecoptera: Capniidae) with DNA barcoding of genus members from the Russian Far East
FIGURES 1–3. Female of Capnia yavorskayae sp. nov. Paratype. 1. Habitus, dorsal. 2. Right forewing. 3. Right hindwing.
FIGURE 19 in Morphology, molecular phylogenetics, and DNA barcoding revealed a new unusual species of the aphid genus Pleotrichophorus from the USA (Insecta, Hemiptera Aphididae)
FIGURE 19. Maximum-likelihood bootstrap consensus tree of Macrosiphini taxa. Pleotrichophorus samples new to this study are highlighted by the peach-colored box. Capitophorus species are highlighted by the blue box. The misidentified specimen of Pleotrichophorus glandulosus specimen reported by Choi et al. (2018) was recovered in a clade along with members of the genus Capitophorus. Support values from left to right are ML ultrafast bootstrap (>95; blue dot), standard non-parametric ML bootstrap (>75; red dot), and MP ultrafast bootstrap (>95; green dot). Nodes without labeled support values indicate that the support value was not significant for that analysis or was not recovered by that analysis.
FIGURE 18. K2P in Morphology, molecular phylogenetics, and DNA barcoding revealed a new unusual species of the aphid genus Pleotrichophorus from the USA (Insecta, Hemiptera Aphididae)
FIGURE 18. K2P neighbor-joining tree of Capitophorus and Pleotrichophorus COI barcodes with auto-collapsed clades with 0.005> average branch length. Collapsed terminal clusters are indicated by red, green, blue, or orange circles. Bootstrap values higher than 80% are indicated on branches with gray circles. Capitophorus species are indicated by blue branches. Pleotrichophorus glandulosus sensu Choi et al. 2018 and Capitophorus sp. from South Korea, China, and California are indicated in orange. Pleotrichophorus species are indicated by red branches. Pleotrichophorus blackmani sp. n., is indicated in green. COI barcodes identified as Pleotrichophorus glandulosus, P. pseudoglandulosus, and P. sp. from France, Russian Far East, and Eastern Canada are indicated in purple.
FIGURE 15 in Morphology, molecular phylogenetics, and DNA barcoding revealed a new unusual species of the aphid genus Pleotrichophorus from the USA (Insecta, Hemiptera Aphididae)
FIGURE 15. SEM of Pleotrichophorus glandulosus (Kaltenbach, 1846): head and body surface: (a) head and pronotum; (b) head trichoid sensilla; (c) trichoid sensilla of abdomen; (d) structure of the sensillum; (e) ultrastructure of the trichoid sensillum socket; (f, g) ultrastructure of the apices of trichoid sensilla; (h) abdominal cuticle surface; (i) ultrastructure of the cuticle surface.
FIGURE 17 in Morphology, molecular phylogenetics, and DNA barcoding revealed a new unusual species of the aphid genus Pleotrichophorus from the USA (Insecta, Hemiptera Aphididae)
FIGURE 17. SEM of Pleotrichophorus glandulosus (Kaltenbach, 1846): apterous viviparous female. mouthparts and legs sensilla: (a, b) URS with trichoid sensilla of two lengths (arrows) and very short type III basiconic sensilla (asterisk); (c) seven pairs of type III basiconic sensilla on the very apical end of URS; (d, e) trichoid sensilla on III FEMUR; (f) trichoid sensilla on the proximal part of III TIBIA; (g) trichoid sensilla on the distal part of III TIBIA; (h) HT I with three ventral setae setae and basal part of HT II with campaniform on the dorsal side (arrow); (i) distal end of HT II with long empodial setae (arrow).
FIGURE 16 in Morphology, molecular phylogenetics, and DNA barcoding revealed a new unusual species of the aphid genus Pleotrichophorus from the USA (Insecta, Hemiptera Aphididae)
FIGURE 16. SEM of Pleotrichophorus glandulosus (Kaltenbach, 1846): apterous viviparous female. antennal sensilla: (a) small multiporous placoid sensilla (red) and type I trichoid sensilla (blue) on ANT III; (b) structure of the type I trichoid sensillum; (c, d, e) structure of small multiporous placoid sensilla; (f) large multiporous placoid sensillum (yellow) on ANT V general view; (g) ultrastructure of the large multiporous placoid sensillum; (h) large multiporous placoid sensillum (yellow), small multiporous placoid sensilla (green) and sunken coeloconic sensilla (pink) on ANT VI BASE; (i) type II trichoid sensilla on the PT.
FIGURE 12 in Morphology, molecular phylogenetics, and DNA barcoding revealed a new unusual species of the aphid genus Pleotrichophorus from the USA (Insecta, Hemiptera Aphididae)
FIGURE 12. SEM of general characters of the alate viviparous female of Pleotrichophorus blackmani sp. n.: (a) head and pronotum; (b) compound eye and ocellus; (c) frontal ocellus and trichoid sensilla; (d) cuticle surface; (e) ultrastructure of the cuticle surface; (f) fore wing; (g) distal end of pterostigma and radial sector; (h) ultrastructure of wing surface and the scale-like element; (i) hind wing with hamuli enlarged; (j) abdomen; (k) SIPH; (l) cauda, s-siphunculi, c-cauda.
FIGURE 13 in Morphology, molecular phylogenetics, and DNA barcoding revealed a new unusual species of the aphid genus Pleotrichophorus from the USA (Insecta, Hemiptera Aphididae)
FIGURE 13. SEM of Pleotrichophorus blackmani sp. n. alate viviparous female. head and antennal sensilla: (a) frontal ocellus and trichoid sensilla; (b, c) structure of trichoid sensilla of different lengths; (d) small multiporous placoid sensilla (red) and type I trichoid sensilla (blue) on ANT III; (e) structure of type I trichoid sensillum; (f) structure of the small multiporous placoid sensilla; (g-i) ultrastructure of small multiporous placoid sensillum and the secretion; (j) large multiporous placoid sensillum (yellow) on ANT V; (k) ultrastructure of the large multiporous placoid sensillum; (l) large multiporous placoid sensillum (yellow), small multiporous placoid sensilla (green) and sunken coeloconic sensilla (pink) on ANT VI BASE; (m) ultrastructure of the small multiporous placoid sensillum; (n, o) ultrastructure of sunken coeloconic sensilla.
FIGURE 14 in Morphology, molecular phylogenetics, and DNA barcoding revealed a new unusual species of the aphid genus Pleotrichophorus from the USA (Insecta, Hemiptera Aphididae)
FIGURE 14. SEM of apterous viviparous female of Pleotrichophorus glandulosus (Kaltenbach, 1846): (a) dorsal habitus; (b) head and pronotum; (c) end of dorsal side of abdomen; (d) surface of SIPH; (e) distal tip of SIPH; (f) lateral side of the end of abdomen; (g) cauda, H-head, Pr-pronotum, MS-mesonotum, Mt-metanotum, I-VIII-abd. tergites I-VIII, s-siphunculi, c-cauda, ap-anal plate, gp-genital plate.
FIGURE 11 in Morphology, molecular phylogenetics, and DNA barcoding revealed a new unusual species of the aphid genus Pleotrichophorus from the USA (Insecta, Hemiptera Aphididae)
FIGURE 11. SEM of Pleotrichophorus blackmani sp. n. apterous viviparous female. sensilla on legs: (a) III FEMUR with very short trichoid sensilla; (b) structure of femoral trichoid sensillum; (c) proximal part of III TIBIA with trichoid sensilla; (d) structure of trichoid sensillum with visible molting pore (star); (e) ultrastructure of the molting pore; (f) trichoid sensilla on the middle part of III TIBIA; (g) structure of trichoid sensillum from the middle part; (h) trichoid sensilla on the proximal part of III TIBIA; (i, j) structure of the sensilla from the distal part; (k) hind tarsus with visible campaniform sensillum (arrow); (l) HT I with three ventral setae; (m) structure of the campaniform sensillum; (n) distal end of HT II with short empodial seta; (o) structure of an empodial seta.
FIGURE 4 in Morphology, molecular phylogenetics, and DNA barcoding revealed a new unusual species of the aphid genus Pleotrichophorus from the USA (Insecta, Hemiptera Aphididae)
FIGURE 4. Pleotrichophorus blackmani sp. n. slide-mounted specimen of oviparous female: (a) habitus; (b) arrangement of pseudosensoria on hind tibiae; (c) shape of pseudosensoria.
FIGURE 10 in Morphology, molecular phylogenetics, and DNA barcoding revealed a new unusual species of the aphid genus Pleotrichophorus from the USA (Insecta, Hemiptera Aphididae)
FIGURE 10. SEM of Pleotrichophorus blackmani sp. n. apterous viviparous female. mouthparts sensilla: (a) ventral view of URS with well-visible trichoid sensilla (arrows); (b) lateral view of URS with well-visible trichoid sensilla (arrow); (c) distal end of URS with long trichoid sensilla and very short type III basiconic sensilla (asterisk); (d) structure of type I trichoid sensillum; (e) structure of type II basiconic sensillum; (f) ultrastructure of the socket of trichoid sensillum; (g, h) ventral and lateral view of the apical tip of URS with six pairs of type III basiconic sensilla; (i) ultrastructure of the basiconic sensillum with molting pore (star) on the base.
FIGURE 5 in Morphology, molecular phylogenetics, and DNA barcoding revealed a new unusual species of the aphid genus Pleotrichophorus from the USA (Insecta, Hemiptera Aphididae)
FIGURE 5. Scanning electron microscopy (SEM) of apterous viviparous female of Pleotrichophorus blackmani sp. n.: (a) dorsal habitus; (b) head and pronotum; (c) posterior part of abdomen dorsally; (d) surface of SIPH; (e) distal tip of SIPH; (f) lateral side of the end of abdomen; (g) cauda, H—head, Pr—pronotum, MS—mesonotum, Mt—metanotum, I-VIII-abd. tergites I-VIII, s—siphunculi, c—cauda, ap—anal plate, gp—genital plate.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.