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PLANT SPECIES RECOGNITION USING LEAF IMAGES AND CONVOLUTIONAL NEURAL NETWORKS (CAAR dataset, version 1)

<p>The CAAR dataset contains leaf images from plants obtained from the Arboreal Collection at Augusto Ribas Agricultural College (CAAR/UEPG). This plant collection is situated in Augusto Ribas College, located at the Ponta Grossa State University, Ponta Grossa, Paraná, Brasil. The images were taken using a smartphone camera with a resolution of 1659 x 2658 pixels and 24 bits of color depth. For each plant, images samples were collected using a white paper sheet background, varying the leaf orientation. The<br>number of plant species used to build the dataset is equal to 35. Data augmentation, using rotation and zoom, were used to increase the data size from 730 to 1986 images in this dataset.</p>

FIGURE 6 in Redescription of Mastigias papua (Scyphozoa, Rhizostomeae) with designation of a neotype and recognition of two additional species

FIGURE 6. nMDS analysis of the morphological variation of Mastigias medusae including data from all historically described species. A. Analysis including Mastigias from both lake (open colored symbols) and ocean (filled colored symbols) samples, and also from historical descriptions (black filled symbols). B. Analysis including only Mastigias from ocean habitats and from the historical descriptions. Circle emphasizes the close morphological match between new samples from the Philippines and historical descriptions of M. albipuntatus.

FIGURE 5 in Redescription of Mastigias papua (Scyphozoa, Rhizostomeae) with designation of a neotype and recognition of two additional species

FIGURE 5. Adult Mastigias papua medusa (103 mm bell diameter) from the type locality: waigeo, west Papua (specifically from Mastigias Papua Cove). A. Profile view of M. papua, with details of the oral arm and margin of the bell. Two rhopalia are marked with arrows, delineating an octant. B. Details of the subumbrellar view of the terminals clubs, showing the typical 'tricorn' cross-section of lagoonal animals. C. Details of the contracted bell margin and oral arm. Note the patches of endosymbiontic zooxanthellae (here most easily visible as tan tiny dots in the unwinged part of oral arm). D. Subumbrellar view of canals dyed in the laboratory, note the perradial canal (p) and the interradial canal (i) which are both generally simple canals originating at the gastrovascular cavity and ending at the ring canal; the origins of the highly anastomosing adradial canals are marked with yellow circles where they join the gastrovascular cavity. E. Subumbrellar view of the bell margin, with velar lappets in between the two pairs of rhopalar lappets (r).

FIGURE 4 in Redescription of Mastigias papua (Scyphozoa, Rhizostomeae) with designation of a neotype and recognition of two additional species

FIGURE 4. Mastigias papua from the type locality: waigeo, west Papua (specifically from Mastigias Papua Cove, November 2007) showing ontogenetic variation within species. A. Mature medusa, 150 mm bell diameter B. Juvenile medusa, 16 mm bell diameter. (i) unwinged portion of the oral arm, (ii) winged portion of oral arm, and (iii) terminal club.

FIGURE 3 in Redescription of Mastigias papua (Scyphozoa, Rhizostomeae) with designation of a neotype and recognition of two additional species

FIGURE 3. nMDS analysis of morphological variation of 229 Mastigias samples collected in 5 regions in the western Pacific and China Sea. Lake samples are represented by unfilled symbols; ocean samples are represented by filled symbols. The type specimen is represented by a filled star.

FIGURE 2 in Redescription of Mastigias papua (Scyphozoa, Rhizostomeae) with designation of a neotype and recognition of two additional species

FIGURE 2. Bayesian phylogenetic reconstruction using COI of Mastigias. Branches are labeled with symbols that represent the Bayesian posterior probability for the alignments 1, 2 and 3 respectively; * 0.95–1.00, ^ 0.90–0.95, + 0.80–0.90. Branches in black are present in all three alignments (i.e. 1—keeping missing data, 2—excluding sequences with missing data, 3— excluding sites with ambiguous base calls); branches in grey are present in alignment 1 only or alignments 1 and 2, or 1 and 3. Points in the map represent the locations of the three monophyletic clades, named primarily following Swift et al. (2016): the 'China Sea' clade with samples from Berau, Japan, Komodo and Philippines; the 'Solomon Sea' clade with samples from Tufi; and a 'Tropical western Pacific Islands' clade with samples from Palau, Papua, and Enewetak.

FIGURE 1 in Redescription of Mastigias papua (Scyphozoa, Rhizostomeae) with designation of a neotype and recognition of two additional species

FIGURE 1. Map of the Indo-west Pacific showing the samples considered in this study (see also Table 1). Symbols represent the samples available from each location for each category of analysis (see key, top right). Locations for the museum samples are approximate as specific locations for those samples were not available. Type locality is shown for Mastigias papua as described by Lesson (1830).

FIGURE 1 in Morphological and phylogenetic evidence for recognition of a new species of Kirschsteiniothelia, K. agumbensis and validation of five new combinations in Kirschsteiniotheliaceae

FIGURE 1. Maximum likelihood (ML) phylogenetic tree obtained from an IQ-TREE analysis of species from Kirschsteiniotheliaceae and closely related taxa based on ITS, LSU and SSU sequences. Strains of the species under study is shown in bold text. Families and orders are indicated on the right side of the tree in blocks, as well as the name of new species in bold text. Branch support values from 1000 non-parametric bootstraps for IQ-TREE (ML-BS) and posterior probability values from the Bayesian analysis (PP) are shown at the nodes (ML-BS>70%/ PP>0.9). The tree is rooted with Stemphylium vesicarium MFLUCC 14-0920 and Stemphylium vesicarium CBS 191.86.

FIGURE 3 in Morphological and phylogenetic evidence for recognition of a new species of Kirschsteiniothelia, K. agumbensis and validation of five new combinations in Kirschsteiniotheliaceae

FIGURE 3. Kirschsteiniothelia agumbensis (AMH 10646). a–c Conidia with attachment. d–i Conidia. Scale bars: a–i = 20 µm.

FIGURE 5 in Morphological and phylogenetic evidence for recognition of a new species of Kirschsteiniothelia, K. agumbensis and validation of five new combinations in Kirschsteiniotheliaceae

FIGURE 5. The results of the pairwise homoplasy index (PHI) test for the closely related species of Kirschsteiniothelia agumbensis using both LogDet transformation and splits decomposition. PHI test results (фw) <0.05 indicate significant recombination within the dataset.

FIGURE 2 in Morphological and phylogenetic evidence for recognition of a new species of Kirschsteiniothelia, K. agumbensis and validation of five new combinations in Kirschsteiniotheliaceae

FIGURE 2. Kirschsteiniothelia agumbensis (AMH 10646). a–c Conidiomata on natural substrate. d Colonies on MEA obverse. e Colonies on MEA reverse. Scale bars: a = 1000 µm. b–c = 100 µm.

FIGURE 4 in Morphological and phylogenetic evidence for recognition of a new species of Kirschsteiniothelia, K. agumbensis and validation of five new combinations in Kirschsteiniotheliaceae

FIGURE 4. Kirschsteiniothelia agumbensis (AMH 10646). a–f SEM of conidia. Scale bars: a–b = 20 µm. c–d = 2 µm. e–f = 20 µm.

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Fig. 6 in Generic Recognition for a Neglected Lineage of South American Pitvipers (Squamata: Viperidae: Crotalinae), with the Description of a New Species from the Colombian Chocó

Fig. 6. Hypothesis of relationships for species of Bothrocophias based on parsimony analyses of 76 anatomical characters.

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Fig. 1 in Generic Recognition for a Neglected Lineage of South American Pitvipers (Squamata: Viperidae: Crotalinae), with the Description of a New Species from the Colombian Chocó

Fig. 1. Alternative hypotheses of relationships among species of Bothrops, Bothriopsis, Lachesis, and Bothrocophias new genus. (A) Recovered in six of eight different analyses of anatomical data only (Gutberlet and Harvey, in press); (B) recovered in one reanalysis of Kraus et al.'s ND4 sequence data (Gutberlet, 1998b); (C) recovered in one of eight analyses of anatomical data only (Gutberlet and Harvey, in press) and in all analyses of sequence data from four mitochondrial genes (Parkinson et al., in press); (D) recovered in one of eight analyses of anatomical data only (Gutberlet and Harvey, in press).

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Fig. 5 in Generic Recognition for a Neglected Lineage of South American Pitvipers (Squamata: Viperidae: Crotalinae), with the Description of a New Species from the Colombian Chocó

Fig. 5. Lateral view of snout of Bothrocophias hyoprora (FMNH 56171), showing canthorostral scales (shaded).

Fig. 57 in Molecular and morphological recognition of species boundaries in the neglected ant genus Brachymyrmex (Hymenoptera: Formicidae): toward a taxonomic revision

Fig. 57 Maximum clade credibility tree of Brachymyrmex and Myrmelachista based on five gene fragments (see Supplementary material Table S1). Analyses were run under maximum parsimony (MP), maximum likelihood (ML), and Bayesian inference (BI) with bootstrap support values and Bayesian posterior probabilities indicated above

Fig. 56 in Molecular and morphological recognition of species boundaries in the neglected ant genus Brachymyrmex (Hymenoptera: Formicidae): toward a taxonomic revision

Fig. 56 Boxplots representing intraspecific variation and interspecific differences for eight morphometric traits. Interspecific differences are tested with Benjamini-Hochberg corrected pairwise Dunn's tests, with sig- nificance levels indicated by letter codes (if species carry at least one identical letter than observed dif- ferences are insignificant, if they carry no identical letter, the ob- served differences for the studied trait are significant)

Fig. 55 in Molecular and morphological recognition of species boundaries in the neglected ant genus Brachymyrmex (Hymenoptera: Formicidae): toward a taxonomic revision

Fig. 55 Boxplots representing intraspecific variation and interspecific differences for eight morphometric traits. Interspecific differences are tested with Benjamini-Hochberg corrected pairwise Dunn's tests, with sig- nificance levels indicated by letter codes (if species carry at least one identical letter than observed dif- ferences are insignificant, if they carry no identical letter, the ob- served differences for the studied trait are significant)

Fig. 54 in Molecular and morphological recognition of species boundaries in the neglected ant genus Brachymyrmex (Hymenoptera: Formicidae): toward a taxonomic revision

Fig. 54 Morphospace occupation of 38 of the here studied Brachymyrmex species as reconstructed with non-metric multidimensional scaling. The limited stress (5.70) indicates that the ordination is robust

Fig. 46 in Molecular and morphological recognition of species boundaries in the neglected ant genus Brachymyrmex (Hymenoptera: Formicidae): toward a taxonomic revision

Fig. 46 Brachymyrmex patagonicus: a, c, e head, dorsal, and lateral view of the lectotype worker; b, d, f B. laevis n. syn.: head, dorsal, and lateral view of a syntype worker