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FIGURE 1 in The unexpected gecko: A new cryptic species within Urocotyledon inexpectata (Stejneger, 1893) from the northern granitic Seychelles
FIGURE 1. Molecular evidence for the existence of cryptic species. A) Cyt-B (mtDNA) tree depicting the divergence between northern and southern lineages (from Rocha et al., 2011); B) posterior probability distributions of gdi values calculated from BPP analyses for each lineage/species. Gdi <0.2 suggests a single species, gdi> 0.7 supports distinct species, and gdi values between 0.2 and 0.7 represent ambiguous species status. * Note that this study confirmed the specimens from the northern island of Felicité are nested within the northern-island genetic lineage but new sequences are not included in this analysis.
FIGURE 5 in The unexpected gecko: A new cryptic species within Urocotyledon inexpectata (Stejneger, 1893) from the northern granitic Seychelles
FIGURE 5. Skull of Urocotyledon inexpectata (BMNH 1907.10.15.7) in A—lateral, B—dorsal, C—ventral, and mandible in D—lateral, dorsal, medial and ventral view (from up to down). Each color represents a different bone present in the head.
FIGURE 2. A in The unexpected gecko: A new cryptic species within Urocotyledon inexpectata (Stejneger, 1893) from the northern granitic Seychelles
FIGURE 2. A—PCA plots of the first principal component (PC 1) versus the second (PC 2) of morphometric analysis between the two geographic groups of Seychelles Urocotyledon. Pale orange polygons denote distribution within PCAs of U. inexpectata (Southern clade) and pink polygons U. norzilensis sp. nov. (Northern clade). B—Separate PCA plots for males (above) and females (below). C—Plot of the body size (SVL) and linear measurements (hindlimbs length-HLL, Head width–HW, eye diameter–OD, and snout-eye distance-SED), that differed significantly between northern and southern clades. Values in all the variables with the exception of SVL, are represented using Least-squares means interaction plot (function Lsmip, package lsmeans) based on a lnSVL value of 1.590. For abbreviations and further details see Material and Methods section.
FIGURE 3. A in The unexpected gecko: A new cryptic species within Urocotyledon inexpectata (Stejneger, 1893) from the northern granitic Seychelles
FIGURE 3. A—Photographs of dorsal views showing morphological variability found in live Urocotyledon inexpectata and U. norzilensis sp. nov.; circles depict records of U. inexpectata from Silhouette (green) and Mahé (orange), while triangles depict records of U. norzilensis sp. nov. from Praslin (pink) and Felicité (blue). B—distributional records of live material used for morphological analyses; C—Photos of habitat in southern islands. D & E—Photos of habitat in northern granitic islands. Photos by Ana Perera.
FIGURE S1 in The unexpected gecko: A new cryptic species within Urocotyledon inexpectata (Stejneger, 1893) from the northern granitic Seychelles
FIGURE S1. Dorsal and ventral view of skull of Urocotyledon inexpectata and U. norzilensis sp. nov. used for this work.
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 7 in Cryptic Species of Freshwater Sculpin (Cottidae: Cottus) in California, USA
FIGURE 7. Phylogenetic hypotheses generated by TreeMix from genotype calls with Cottus beldingii designated as the root, permitting no migration (A), one migration edge (B) and two migration edges (C). A minimum-spanning network is shown in panel D generated from cytochrome b data from Inland Riffle Sculpin individuals. Color-coding of taxa is shown in the figure key.
FIGURE 6 in Cryptic Species of Freshwater Sculpin (Cottidae: Cottus) in California, USA
FIGURE 6. Species tree generated from genotype calls with SVDQuartets. The tree is rooted by Cottus asper and C. beldingii. Circles at tips are proportional to sample size and colored by taxon. Nodal support was maximal (bootstrap support = 100%) for all nodes, and is not indicated.
FIGURE 4 in Cryptic Species of Freshwater Sculpin (Cottidae: Cottus) in California, USA
FIGURE 4. Principal Components analyses of genome-wide SNP data from all sampling locations in study (A) and from locations where the fish were only identified as Riffle or Pit Sculpin when collected (B). Points are color coded by taxon as indicated in the legend with sampling locations indicated corresponding to Table 2. The total variance explained by each Principal Component is indicated in the axis labels.
FIGURE 5 in Cryptic Species of Freshwater Sculpin (Cottidae: Cottus) in California, USA
FIGURE 5. Admixture analysis of all sampling locations from K = 2 to 6 genetic clusters. Sampling locations along the x-axis are color coded by sampling location as in Figure 4 and correspond to Table 2. Cottus taxa are designated on the x-axis.
FIGURE 3 in Cryptic Species of Freshwater Sculpin (Cottidae: Cottus) in California, USA
FIGURE 3. (A) Distribution of Cottus pitensis in northeastern California (light green). This distribution is mostly in streams of the Pit River basin in California but extends into Oregon tributaries of Goose Lake (upper right corner of map). (B) Drawing of C. pitensis holotype from Bailey and Bond (1963), collected from the North Fork Pit River, Modoc County, CA.
FIGURE 2 in Cryptic Species of Freshwater Sculpin (Cottidae: Cottus) in California, USA
FIGURE 2. Distribution of Riffle Sculpin taxa in California, described in the text. Pit Sculpin (Cottus pitensis) is found in the northeast (light green). Inland Riffle Sculpin (Cottus gulosus) is found mainly in streams of the Central Valley (blue/orange), while Coastal Riffle Sculpin (Cottus ohlone) is confined to coastal and South San Francisco Bay watersheds (yellow/pink).
FIGURE 1 in Cryptic Species of Freshwater Sculpin (Cottidae: Cottus) in California, USA
FIGURE 1. Inland (A, B) and Coastal (C, D) Riffle Sculpins from the UC Davis Museum of Wildlife and Fish Biology. (A) San Joaquin Riffle Sculpin, Cottus gulosus gulosus. WFB-277-08-09. Kaweah River, Tulare County, California (68 mm SL, 82 mm TL). Coll. Larry Brown, September 10, 1985. Holotype is same as for C. gulosus (USNM 291). (B) Sacramento Riffle Sculpin, Cottus gulosus wintu. Holotype WFB-3464. North Fork Feather River, Butte County, California (78 mm SL, 96 mm TL). Coll. Jason Baumsteiger, October 5, 2017. (C) Coastal Riffle Sculpin, Cottus ohlone. Holotype. WFB-3402. Also, holotype for Ohlone Sculpin, C. o. ohlone. Guadalupe River, Santa Clara County, California (65 mm SL, 79 mm TL). Coll: J. J. Smith, November 18, 1986. (D) Pomo Riffle Sculpin, Cottus ohlone pomo. Holotype. WFB-3396. Pieta Creek near mouth on Russian River, Mendocino County, California (90 mm SL, 105 mm TL). Coll. P Moyle, J. Baumsteiger, August 2, 2017.
Figure 1 in First use of acoustic calls to distinguish cryptic members of a fish species complex
Figure 1. Background shading indicates the geographical distribution of the three populations (Liu et al., 2014) from the Dascyllus aruanus complex. A, in each geographical area, dots correspond to sampling locations. B, scatterplot of principal component PC1 versus PC2, performed with individual mean values of the six acoustic properties of calls corresponding to the signal jump for the three suggested species: D. abudafur (blue ●), D. aruanus (turquoise +) and D. emamo (pink▲). Ellipses correspond to 90% of the observations, dots correspond to the ellipse centra.
FIG. 4 in Towards Navigating the Minotaur's Labyrinth: Cryptic Diversity and Taxonomic Revision within the Speciose Genus Hipposideros (Hipposideridae)
FIG. 4. Morphological comparisons of the frontal sacs and noseleaves in A — Macronycteris commersonii (FMNH 213588, ♀), Madagascar, Province d'Antsiranana, Réserve Spéciale d'Ankarana [now Parc National], near Andrafiabe Cave, 31 October 2010; B — M. gigas (FMNH 128212, ♀), Senegal, Casmance, Diabane, 12 km SW of Adeane, 15 January 1983; C — M. vittatus (FMNH 192800, ♀, sequenced for Cyt-b), Tanzania, Pemba Island, Kaskazini Region, Micheweni District, Kilijini Village, 3 August 2006; and D — Doryrhina cyclops (FMNH 164973), Uganda, Masindi District, Budongo Forest, 25 June 1998. The form of M. cryptovalorona is similar to M. commersonii and no comparative specimen material was available for M. thomensis. Drawing by Velizar Simeonovski
FIG. 3 in Towards Navigating the Minotaur's Labyrinth: Cryptic Diversity and Taxonomic Revision within the Speciose Genus Hipposideros (Hipposideridae)
FIG. 3. Time tree resulting from MCMCTREE analysis in PAML using the MrBayes topology shown in Fig. 1. The analysis was constrained using two calibrations, one applied to the root and a fossil calibration applied to the split between Rhinonicteris and Cloeotis (see Materials and Methods for details). Numbers at nodes are divergence time estimates in millions of years. 95% confidence intervals for each node are denoted by grey bars. See Table 1 for definitions of acronyms
FIG. 2 in Towards Navigating the Minotaur's Labyrinth: Cryptic Diversity and Taxonomic Revision within the Speciose Genus Hipposideros (Hipposideridae)
FIG. 2. Resulting MrBayes tree from Bayesian analysis of the Cyt-b dataset under a GTR+G model of sequence evolution. The analysis was rooted using Doryrhina cyclops (not shown). Support values for both the ML and BA analysis are shown, with posterior probabilities converted to percentages. Clades referring to the commersonii species groups identified in Rakotoarivelo et al. (2015) are highlighted. Samples sequenced as part of this study, including a re-sequenced sample of H. vittatus FMNH 192857 from Pemba, are highlighted in bold. See Table 1 for definitions of acronyms. Where sampling sites are known for Malagasy samples, the site is given followed by the code MG to indicate Madagascar
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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)
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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.