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Data from: Multilocus phylogeny and revised classification for mountain dragons of the genus Japalura s.l. (Reptilia: Agamidae: Draconinae) from Asia
Although the genus Japalura s.l. has long been recognized as paraphyletic based on limited genetic sampling, its problematic taxonomy has not been revised, and phylogenetic relationships among the majority of congeners remain unknown. Here we utilize a densely sampled dataset of both multilocus genetic and morphological data to provide the first phylogenetic inference of relationships among Japalura s.l.species. Our results show that Japalura s.l. is paraphyletic, consisting of four major clades that are scattered across the phylogeny of the subfamily Draconinae: the first clade from the western, central and middle-eastern Trans-Himalayas, the second clade from the far eastern Trans-Himalayas, the third clade from East Asia and the last clade from Indochina. To address this widespread paraphyly of the genus and to stabilize the taxonomy within the family Draconinae, we revise the current taxonomy and split Japalura s.l. into four genera. By doing so, we recognize two existing generic names, Japalura sensu stricto and Pseudocalotes, resurrect one name available in the literature, Diploderma, and describe one new genus, Cristidorsa gen. nov. We discuss phylogenetic relationships and taxonomy within Japalura s.l. and present a diagnostic key to all recognized genera of the subfamily Draconinae.
Data from: Plastid and seed morphology data support revised infrageneric classification and African origin of the pantropical genus Xylopia (Annonaceae)
The floristic treatment of Engler and Diels, published in 1901, provides the only infrageneric classification of the pantropical genus Xylopia (Annonaceae). Here we test and extend that classification using molecular and seed morphology characters. Phylogenetic relationships were reconstructed using data from four plastid regions obtained from 44 of the approximately 165 species in the genus, recovering four well-supported major clades. Seed characters were examined for these taxa, and six aril morphologies, three previously undocumented, were distinguished; we also document the presence of a sarcotesta on the seeds of many species. Molecular and seed data support recognition of five sections within the genus; one, Xylopia sect. Rugosperma, is proposed here as new. Our phylogenetic results suggest an African origin for the genus and reveal complex biogeographic patterns, likely facilitated by long-distance dispersal.
Data from: A molecular phylogeny and revised higher-level classification for the leaf-mining moth family Gracillariidae and its implications for larval host-use evolution
Gracillariidae are one of the most diverse families of internally feeding insects, and many species are economically important. Study of this family has been hampered by lack of a robust and comprehensive phylogeny. In the present paper, we sequenced up to 22 genes in 96 gracillariid species, representing all previously recognized subfamilies and genus groups, plus 20 outgroups representing other families and superfamilies. Following objective identification and removal of two rogue taxa, two datasets were constructed: dataset 1, which included 12 loci totalling 9927 bp for 94 taxa, and dataset 2, which supplemented dataset 1 with 10 additional loci for 10 taxa, for a total of 22 loci and 16 167 bp. Maximum likelihood analyses strongly supported the monophyly of Gracillariidae and most previously recognized subfamilies and genus groups. On this basis, we propose a new classification consisting of eight subfamilies, four of which are newly recognized or resurrected: Acrocercopinae Kawahara & Ohshima subfam. n.; Gracillariinae Stainton; Lithocolletinae Stainton; Marmarinae Kawahara & Ohshima subfam. n.; Oecophyllembiinae Réal & Balachowsky; Parornichinae Kawahara & Ohshima subfam. n.; Ornixolinae Kuznetzov & Baryshnikova stat. rev.; and Phyllocnistinae Zeller. The subfamily Gracillariinae is restricted to the monophyletic group comprising Gracillaria Haworth and closely related genera. We also formally transfer Acrocercops scriptulata Meyrick to Ornixolinae and use the name Diphtheroptila Vári, creating Diphtheroptila scriptulata comb. n. An exploratory mapping of larval host-use traits on the phylogeny shows strong conservation of modes of leaf mining but much higher lability of associations with host plant orders and families, suggesting that host shifts could play a significant role in gracillariid diversification.
FIGURE 2 in Taxonomic status of Andersen's fruit-eating bat (Artibeus jamaicensis aequatorialis) and revised classification of Artibeus (Chiroptera: Phyllostomidae)
FIGURE 2. Unrooted neighbor-joining phylogram based on 414 AFLP bands. Numbers along branches indicate bootstrap support values (top score) and Bayesian posterior probabilities (bottom score). Bold clade identifies specimens traditionally recognized as Artibeus jamaicensis aequatorialis.
FIGURE 3 in Taxonomic status of Andersen's fruit-eating bat (Artibeus jamaicensis aequatorialis) and revised classification of Artibeus (Chiroptera: Phyllostomidae)
FIGURE 3. Map of the distribution of Artibeus aequatorialis. Star indicates the type locality of A. aequatorialis (Zaruma [3°40'60"S, 79°37'0"W], Ecuador). The distributional range is based on literature references (hollow squares; Andersen 1906 and Marques-Aguiar 2008) and specimens examined in the Species Account (star and solid squares). The northernmost (western Colombia; Valle del Cauca, Cali [3°26'14"N, 76°31'21"W], and Rio Raposo [3°43'0"N, 77°7'60"W]) and southernmost (western Peru; Tumbes, Faical [3°44'57"S, 80°45'2"W]) extent of A. aequatorialis remains to be defined. Shaded areas represent areas of the Andes Mountains higher than 1800 meters.
FIGURE 1. A in A revised classification of the jumping plant-lice (Hemiptera: Psylloidea)
FIGURE 1. A schematic representation of the classification proposed including all recognised families and subfamilies of Psylloidea.
FIGURES 44–49 in The new Andean jumping spider genus Urupuyu and its placement within a revised classification of the Amycoida (Araneae: Salticidae)
FIGURES 44–49. Male palpal bulbs of different groups of Amycoida, cleared, ventral view. Colonus: 44. Breda: 45, rotated about 180° for comparison. Psecas: 46 (non-amycoid). Sitticus: 47. Agelista: 48, slightly rotated. Amycus: 49, slightly rotated. Light green shows path of spermophore; darker red shows the loop seen in most amycoid lineages, a possible synapomorphy for the group; blue rings show articulation between subtegulum and tegulum.
FIGURES 18–21 in The new Andean jumping spider genus Urupuyu and its placement within a revised classification of the Amycoida (Araneae: Salticidae)
FIGURES 18–21. Urupuyu antisana: 18 male spinnerets; 19 right anterior lateral spinneret; 20 posterior median spinnerets; 21 left posterior lateral spinneret.
FIGURES 1–5. Urupuyu spp. U in The new Andean jumping spider genus Urupuyu and its placement within a revised classification of the Amycoida (Araneae: Salticidae)
FIGURES 1–5. Urupuyu spp. U. antisana: 1 male from Papallacta; 2 female from Papallacta; 3 female from Sendero Jumandy. U. edwardsi: 4 male; 5 same, sitting on fern leaf. Figs 1-5 © 2015 W. Maddison, released under a Creative Commons Attribution (CC-BY) 3.0 license.
FIGURES 14–17 in The new Andean jumping spider genus Urupuyu and its placement within a revised classification of the Amycoida (Araneae: Salticidae)
FIGURES 14–17. Urupuyu antisana: 14 epiandric region (arrows show fusules); 15 male left tarsus II; 16 detail of same, showing modified white setae; 17 same.
FIGURES 6–8 in The new Andean jumping spider genus Urupuyu and its placement within a revised classification of the Amycoida (Araneae: Salticidae)
FIGURES 6–8. Urupuyu antisana: 6 male carapace; 7 same, showing depressions (larger, arrowed) and punctuations (smaller); 8 same, detail showing perforation in depression.
FIGURES 37–38 in The new Andean jumping spider genus Urupuyu and its placement within a revised classification of the Amycoida (Araneae: Salticidae)
FIGURES 37–38. Maximum likelikhood phylogenies from Chimera and Non-chimera matrices, combined 5 gene analyses. Numbers show likelihood bootstrap % for Amycoids only; in parenthesis are bootstrap percentages for analysis without Nilakantha and Gypogyna (shown for deep amycoid branches only). Rectangles at nodes indicate bootstrap support in parsimony analysis (filled rectangle at least 75%; open 50% to 74%). Sites partitioned as per PartitionFinder analysis.
FIGURES 32–35 in The new Andean jumping spider genus Urupuyu and its placement within a revised classification of the Amycoida (Araneae: Salticidae)
FIGURES 32–35. Urupuyu occidentale: 32 male left palp, ventral view; 33 same, palpal tibia, retrolateral view; 34 same, dorsal view; Urupuyu spp: 35 distributional records in Ecuador.
FIGURES 27–31 in The new Andean jumping spider genus Urupuyu and its placement within a revised classification of the Amycoida (Araneae: Salticidae)
FIGURES 27–31. Urupuyu edwardsi: 27 male left palp, ventral view; 28 same, palpal tibia, retrolateral view; 29 same, dorsal view; 30 epigyne, ventral view; 31 same, cleared, dorsal view (arrow indicates initial portion of copulation duct dilated as a chamber).
FIGURES 22–26 in The new Andean jumping spider genus Urupuyu and its placement within a revised classification of the Amycoida (Araneae: Salticidae)
FIGURES 22–26. Urupuyu antisana: 22 male left palp, ventral view; 23 same, palpal tibia, retrolateral view; 24 same, dorsal view; 25 epigyne, ventral view; 26 same, cleared, dorsal view (arrow indicates initial portion of copulation duct dilated as a chamber).
FIGURE 36 in The new Andean jumping spider genus Urupuyu and its placement within a revised classification of the Amycoida (Araneae: Salticidae)
FIGURE 36. Summary of molecular phylogeny results. Numbers show likelihood bootstrap percentages, in format / ().
FIGURES 9–13 in The new Andean jumping spider genus Urupuyu and its placement within a revised classification of the Amycoida (Araneae: Salticidae)
FIGURES 9–13. Urupuyu antisana: 9 male left palp, ventral view (white arrow shows projection on embolus; black arrow in white triangle shows tegular cleft); 10 detail of same; 11 chelicerae, frontal view; 12 right chelicera, promarginal teeth (arrows); 13 left chelicera, promarginal teeth (arrows).
FIGURES 50–52 in The new Andean jumping spider genus Urupuyu and its placement within a revised classification of the Amycoida (Araneae: Salticidae)
FIGURES 50–52. Morphological characters of Amycoida. 50 divided lorum present in Gophoinae (arrow shows area with thin cuticle). 51 fused lorum (Amycinae), as that present in non-gophoine Amycoida. 52 expanded left male palp (Cotinusa) showing developed distal hematodocha articulating the embolus with the rest of the bulb.
FIGURES 14–19 in A revised phylogenetic classification of the ant subfamily Formicinae (Hymenoptera: Formicidae), with resurrection of the genera Colobopsis and Dinomyrmex
FIGURES 14–19. Selected species of Camponotus (Figs. 14–17) and New Caledonia Colobopsis (Figs. 18–19), full-face view of head of minor worker. 14, Camponotus (Pseudocolobopsis) claviscapus, Costa Rica (CASENT0249388); 15, C. (Myrmentoma) decipiens, Texas, USA (CASENT0249367); 16. C. (Tanaemyrmex) chloroticus, Fiji (CASENT0171139); 17, C. (Myrmamblys) pulchellus_cf, New Caledonia (CASENT0280237); 18, Colobopsis indet. (CASENT0280248); 19, Colobopsis camela (CASENT0280242). Images from AntWeb (www.antweb.org); photographers Will Ericson (14–15), Eli Sarnat (16) and Shannon Hartman (17–19).
FIGURES 8–13 in A revised phylogenetic classification of the ant subfamily Formicinae (Hymenoptera: Formicidae), with resurrection of the genera Colobopsis and Dinomyrmex
FIGURES 8–13. Species of Colobopsis from Fiji. Full-face view of head of minor worker (Figs. 8–11) and lateral view of minor worker (Figs. 12–13). 8, Colobopsis vitiensis (CASENT0280250); 9, C. polynesica (CASENT0280252); 10. C. schmelzi (CASENT0280259); 11, C. bryani (CASENT0280258); 12, C. schmelzi (CASENT0280259); 13, C. bryani (CASENT0280258). Images from AntWeb (www.antweb.org); photographers Shannon Hartman (8–9) and Estella Ortega (10– 13).
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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.