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Figure 14 from: Hatch AS, Liew H, Hourdez S, Rouse GW (2020) Hungry scale worms: Phylogenetics of Peinaleopolynoe (Polynoidae, Annelida), with four new species. ZooKeys 932: 27-74. https://doi.org/10.3897/zookeys.932.48532
Figure 14 Macro photos and micrographs of P. goffrediae sp. nov. holotype SIO-BIC A5485 and paratype SIO-BIC A5464 A dorsal view, holotype B ventral view, holotype. Segments 12–15 are marked to indicate the presence of four pairs of papillae C frontal view of proboscis showing papillae and jaws, holotype. Numbers mark the papillae on the dorsal (seven papillae) and ventral (six papillae) surfaces D loose elytron, holotype E dorsal view of anterior, holotype F ventral view of anterior, paratype G left side branchiae on segments 12–15, holotype H ventral papillae on segments 12–15 (four pairs) indicated by white arrows, holotype. Ventral lamellae on segments 16–17 (two pairs) indicated by black arrows, holotype I dorsal view of posterior, holotype J ventral view of posterior, holotype. Abbreviations: XII, segment 12; XIII, segment 13; XIV, segment 14; XV, segment 15; j, jaws; ma, median antenna; la, lateral antenna; pa, palp; dac, dorsal anterior cirrus; vac, ventral anterior cirrus; el, elytrophore; br, single large group of branchiae on elytrigerous segment; noc, notochaetae; dc, dorsal cirrus; br1, branchiae small group 1 attached to dorsal tubercle on cirrigerous segment; br2, branchiae large group 2 attached near base of notopodium on cirrigerous segment; no, notopodium; vc, ventral cirrus; bc, buccal cirrus; ne, neuropodium; dt, dorsal tubercle; anc, anal cirrus. Scale bars: 4 mm (A, B); 2 mm (C–F, H–J); 1 mm (G).
Supplementary material 1 from: Hatch AS, Liew H, Hourdez S, Rouse GW (2020) Hungry scale worms: Phylogenetics of Peinaleopolynoe (Polynoidae, Annelida), with four new species. ZooKeys 932: 27-74. https://doi.org/10.3897/zookeys.932.48532
Figures S1, S2
Figure 10 from: Hatch AS, Liew H, Hourdez S, Rouse GW (2020) Hungry scale worms: Phylogenetics of Peinaleopolynoe (Polynoidae, Annelida), with four new species. ZooKeys 932: 27-74. https://doi.org/10.3897/zookeys.932.48532
Figure 10 Micrographs of Peinaleopolynoe spp. jaws APeinaleopolynoe orphanae sp. nov. paratype SIO-BIC A9996 BPeinaleopolynoe elvisi sp. nov. holotype SIO-BIC A8488 CPeinaleopolynoe goffrediae sp. nov. holotype SIO-BIC A5485 DPeinaleopolynoe mineoi sp. nov. paratype SIO-BIC A9709. Scale bars: 3 mm (A, C); 2 mm (B, D).
Figure 11 from: Hatch AS, Liew H, Hourdez S, Rouse GW (2020) Hungry scale worms: Phylogenetics of Peinaleopolynoe (Polynoidae, Annelida), with four new species. ZooKeys 932: 27-74. https://doi.org/10.3897/zookeys.932.48532
Figure 11 Live dorsal views of P. orphanae sp. nov. Arrows indicate elytral bite marks from the fighting behavior A paratype SIO-BIC A10020 with blue elytra B paratype SIO-BIC A10024 with pink elytra C paratype SIO-BIC A6312 with white elytra D paratype SIO-BIC A6166 with black elytra E paratype SIO-BIC A10023 with red elytra. Scale bars: 5 mm (A, B, D, E); 3 mm (C).
Figure 1 from: Hatch AS, Liew H, Hourdez S, Rouse GW (2020) Hungry scale worms: Phylogenetics of Peinaleopolynoe (Polynoidae, Annelida), with four new species. ZooKeys 932: 27-74. https://doi.org/10.3897/zookeys.932.48532
Figure 1 Maximum likelihood (ML) tree of the combined analysis from six genes (COI, 16S, 18S, 28S, H3, CytB) aligned with MAFFT and then concatenated. Numbers next to nodes are ML bootstrap percentages from RAxML, Bayesian inference (BI) posterior probability, and maximum parsimony (MP) jackknife support values, separated by slashes. Key: * indicates 95% bootstrap/jackknife or greater and 0.95 posterior probability or greater. – indicates the node was not found. Branchiae drawings at terminals indicate presence of arborescent or plicate branchiae; ~ indicates that on segments with two groups of branchiae, the position in T. branchiata is split into anterior and posterior groups, as opposed to upper and lower groups in remaining taxa. The seven paraphyletic groups of Branchinotogluma are highlighted in a yellow-orange gradient.
Figure 17 from: Hatch AS, Liew H, Hourdez S, Rouse GW (2020) Hungry scale worms: Phylogenetics of Peinaleopolynoe (Polynoidae, Annelida), with four new species. ZooKeys 932: 27-74. https://doi.org/10.3897/zookeys.932.48532
Figure 17 Micrographs of P. mineoi sp. nov. holotype SIO-BIC A10071 A right parapodium from segment 10 B right parapodium from segment 11 C notochaetae D superior neurochaetae (supra-acicular) E inferior neurochaetae (subacicular). Abbreviations: br1, branchiae small group 1 attached to dorsal tubercle; br2, branchiae large group 2 attached near base of notopodium; noc, notochaetae; dc, dorsal cirrus; no, notopodium; snec, superior neurochaetae; ne, neuropodium; neap, neuroacicular process; noap, notoacicular process; vc, ventral cirrus; inec, inferior neurochaetae; el, elytrophore; br, single large group of branchiae on elytrigerous segment. Scale bars: 0.5 mm (A, B); 15 μm (C); 5 μm (D, E).
Figure 5 from: Hatch AS, Liew H, Hourdez S, Rouse GW (2020) Hungry scale worms: Phylogenetics of Peinaleopolynoe (Polynoidae, Annelida), with four new species. ZooKeys 932: 27-74. https://doi.org/10.3897/zookeys.932.48532
Figure 5 Peinaleopolynoe santacatalina specimens ASIO-BIC A8487, live dorsal view BPeinaleopolynoe santacatalina observed on the Rosebud Whalefall off the coast of San Diego, CA CSIO-BIC A8489, live dorsal view without elytra. Numbers next to the elytrophores indicate the pairs of elytra (ten total) DSIO-BIC A10927, live ventral view. Arrows indicate the four pairs of papillae on segments 12–15. Abbreviations: el, elytrophore; br, single large group of branchiae on elytrigerous segment; br1, branchiae small group 1 attached to dorsal tubercle on cirrigerous segment; br2, branchiae large group 2 attached near base of notopodium on cirrigerous segment. Scale bars: 5 mm (A, C, D); 10 mm (B).
Figure 16 from: Hatch AS, Liew H, Hourdez S, Rouse GW (2020) Hungry scale worms: Phylogenetics of Peinaleopolynoe (Polynoidae, Annelida), with four new species. ZooKeys 932: 27-74. https://doi.org/10.3897/zookeys.932.48532
Figure 16 Micrographs of P. mineoi sp. nov. holotype SIO-BIC A10071 and paratype SIO-BIC A9709 A dorsal view, holotype B ventral view, holotype. Segments 12–15 are marked to indicate the presence of four pairs of papillae C frontal view of proboscis showing papillae and jaws, paratype. Numbers mark the papillae on the dorsal (seven papillae) and ventral (six papillae) surfaces D loose elytron, holotype E dorsal view of anterior, holotype F ventral view of anterior, holotype G right side branchiae on segments 8–13, holotype H ventral papillae on segments 12–15 (four pairs) indicated by arrows, holotype I dorsal view of posterior, holotype J ventral view of posterior, holotype. Abbreviations: XII, segment 12; XIII, segment 13; XIV, segment 14; XV, segment 15; j, jaws; ma, median antenna; la, lateral antenna; pa, palp; dac, dorsal anterior cirrus; vac, ventral anterior cirrus; el, elytrophore; br, branchiae; nec, neurochaetae; noc, notochaetae; dc, dorsal cirrus; no, notopodium; vc, ventral cirrus; bc, buccal cirrus; ne, neuropodium; dt, dorsal tubercle; anc, anal cirrus. Scale bars: 1 mm (A, B, D); 0.5 mm (C, E–J).
Figure 4 from: Hatch AS, Liew H, Hourdez S, Rouse GW (2020) Hungry scale worms: Phylogenetics of Peinaleopolynoe (Polynoidae, Annelida), with four new species. ZooKeys 932: 27-74. https://doi.org/10.3897/zookeys.932.48532
Figure 4 Maximum likelihood tree topology from concatenated data (COI, 16S, 18S, 28S, H3, CytB) for Peinaleopolynoe and its sister clade (B. bipapillata and B. sp. nov. 1), with the transformation for A ventral segmental papillae and/or lamellae and B elytral pairs. 'Pie charts' at the nodes represent probabilities for the relevant states.
Figure 9 from: Hatch AS, Liew H, Hourdez S, Rouse GW (2020) Hungry scale worms: Phylogenetics of Peinaleopolynoe (Polynoidae, Annelida), with four new species. ZooKeys 932: 27-74. https://doi.org/10.3897/zookeys.932.48532
Figure 9 Micrographs of P. orphanae sp. nov. holotype SIO-BIC A6151 A left parapodium from segment 6 B left parapodium from segment 9 C notochaeta D superior neurochaeta (supra-acicular) E inferior neurochaeta (subacicular). Abbreviations: br1, branchiae small group 1 attached to dorsal tubercle; br2, branchiae large group 2 attached near base of notopodium; noc, notochaetae; dc, dorsal cirrus; no, notopodium; snec, superior neurochaetae; ne, neuropodium; neap, neuroacicular process; vc, ventral cirrus; inec, inferior neurochaetae; el, elytrophore; br, single large group of branchiae on elytrigerous segment. Scale bars: 2 mm (A, B); 15 μm (C); 10 μm (D, E).
Figure 13 from: Hatch AS, Liew H, Hourdez S, Rouse GW (2020) Hungry scale worms: Phylogenetics of Peinaleopolynoe (Polynoidae, Annelida), with four new species. ZooKeys 932: 27-74. https://doi.org/10.3897/zookeys.932.48532
Figure 13 Micrographs of P. elvisi sp. nov. holotype SIO-BIC A8488 A right parapodium from segment 10 B right parapodium from segment 7 C notochaetae D superior neurochaetae (supra-acicular) E inferior neurochaetae (subacicular). Abbreviations: br1, branchiae small group 1 attached to dorsal tubercle; br2, branchiae large group 2 attached near base of notopodium; noc, notochaetae; dc, dorsal cirrus; no, notopodium; snec, superior neurochaetae; ne, neuropodium; neap, neuroacicular process; noap, notoacicular process; vc, ventral cirrus; inec, inferior neurochaetae; el, elytrophore; br, single large group of branchiae on elytrigerous segment. Scale bars: 1 mm (A, B); 15 μm (C); 10 μm (D, E).
Figure 3 from: Hatch AS, Liew H, Hourdez S, Rouse GW (2020) Hungry scale worms: Phylogenetics of Peinaleopolynoe (Polynoidae, Annelida), with four new species. ZooKeys 932: 27-74. https://doi.org/10.3897/zookeys.932.48532
Figure 3 Haplotype networks from COI data with geographic locality coding; each colored circle represents a single individual APeinaleopolynoe santacatalina network includes four individuals, three from the Rosebud Whalefall off San Diego, California and one from the Del Mar Seeps, California BPeinaleopolynoe mineoi sp. nov. network includes four individuals, three from Mound 12, Costa Rica and one from Mound 11, Costa Rica CPeinaleopolynoe elvisi sp. nov. includes five individuals, two from Jaco Scar, Costa Rica, two from Seamount 1, Costa Rica, and one from the Patrick Whalefall in Monterey Canyon, California. The small black circle represents a missing haplotype.
Figure 12 from: Hatch AS, Liew H, Hourdez S, Rouse GW (2020) Hungry scale worms: Phylogenetics of Peinaleopolynoe (Polynoidae, Annelida), with four new species. ZooKeys 932: 27-74. https://doi.org/10.3897/zookeys.932.48532
Figure 12 Macro photos and micrographs of P. elvisi sp. nov. holotype SIO-BIC A8488 A dorsal view B ventral view. Segments 12–15 are marked to indicate the presence of four pairs of papillae C frontal view of proboscis showing papillae and jaws. Numbers mark the papillae on the dorsal (six papillae) surface D left elytron from segment 2 E dorsal view of anterior F ventral view of anterior G left side branchiae on segments 7–11 H ventral papillae on segments 12–15 (four pairs) indicated by white arrows. Ventral lamellae on segments 16–17 (two pairs) indicated by black arrows I dorsal view of posterior J ventral view of posterior. Abbreviations: XII, segment 12; XIII, segment 13; XIV, segment 14; XV, segment 15; j, jaws; ma, median antenna; pa, palp; la, lateral antenna; vac, ventral anterior cirrus; el, elytrophore; br, single large group of branchiae on elytrigerous segment; noc, notochaetae; dc, dorsal cirrus; br1, branchiae small group 1 attached to dorsal tubercle on cirrigerous segment; br2, branchiae large group 2 attached near base of notopodium on cirrigerous segment; no, notopodium; nec, neurochaetae; vc, ventral cirrus; ne, neuropodium; dt, dorsal tubercle; anc, anal cirrus. Scale bars: 4 mm (A, B); 0.5 mm (C); 1 mm (D, H–J); 2 mm (E–G).
Figure 8 from: Hatch AS, Liew H, Hourdez S, Rouse GW (2020) Hungry scale worms: Phylogenetics of Peinaleopolynoe (Polynoidae, Annelida), with four new species. ZooKeys 932: 27-74. https://doi.org/10.3897/zookeys.932.48532
Figure 8 Macro photos and micrographs of P. orphanae sp. nov. holotype SIO-BIC A6151 and paratype SIO-BIC A9996 A dorsal view, holotype B ventral view, holotype. Segments 12–15 are marked to indicate the presence of four pairs of papillae C frontal view of proboscis showing papillae, paratype. Numbers mark the papillae on the dorsal (seven papillae) and ventral (six papillae) surfaces D right elytron from segment 5, holotype E dorsal view of anterior, holotype F ventral view of anterior, holotype G right side branchiae on segments 8–11, holotype H ventral papillae on segments 12–15 (four pairs) indicated by arrows, holotype I dorsal view of posterior, holotype J ventral view of posterior, holotype. Abbreviations: XII, segment 12; XIII, segment 13; XIV, segment 14; XV, segment 15; ma, median antenna; la, lateral antenna; pa, palp; dac, dorsal anterior cirrus; vac, ventral anterior cirrus; el, elytrophore; br, single large group of branchiae on elytrigerous segment; noc, notochaetae; dc, dorsal cirrus; vc, ventral cirrus; bc, buccal cirrus; br1, branchiae small group 1 attached to dorsal tubercle on cirrigerous segment; br2, branchiae large group 2 attached near base of notopodium on cirrigerous segment; no, notopodium; ne, neuropodium; nec, neurochaetae; dt, dorsal tubercle; anc, anal cirrus. Scale bars: 4 mm (A, B); 2 mm (C–J).
Figure 7 from: Hatch AS, Liew H, Hourdez S, Rouse GW (2020) Hungry scale worms: Phylogenetics of Peinaleopolynoe (Polynoidae, Annelida), with four new species. ZooKeys 932: 27-74. https://doi.org/10.3897/zookeys.932.48532
Figure 7 Live dorsal views of the new Peinaleopolynoe spp. APeinaleopolynoe orphanae sp. nov. holotype SIO-BIC A6151 BPeinaleopolynoe elvisi sp. nov. holotype SIO-BIC A8488 CPeinaleopolynoe goffrediae sp. nov. holotype SIO-BIC A5485 DPeinaleopolynoe mineoi sp. nov. holotype SIO-BIC A10071. Scale bars: 6 mm (A); 8 mm (B, C); 1 mm (D).
Figure 1 from: Antoł A, Kozłowski J (2020) Scaling of organ masses in mammals and birds: phylogenetic signal and implications for metabolic rate scaling. ZooKeys 982: 149-159. https://doi.org/10.3897/zookeys.982.55639
Figure 1 PGLS (solid lines) and OLS (dashed lines) interspecific scaling of tissue/organ masses in mammals with log fat-free-body mass as the independent variable. For the scaling with log body mass as an independent variable, see Suppl. material 1: Figure S3
Figure 2 from: Antoł A, Kozłowski J (2020) Scaling of organ masses in mammals and birds: phylogenetic signal and implications for metabolic rate scaling. ZooKeys 982: 149-159. https://doi.org/10.3897/zookeys.982.55639
Figure 2 PGLS (solid lines) and OLS (dashed lines) interspecific scaling of tissue/organ masses in birds with log fat-free-body mass as the independent variable. For the scaling with log body mass as an independent variable, see Suppl. material 1: Figure S5.
Data from: High-throughput identification of informative nuclear loci for shallow-scale phylogenetics and phylogeography
One of the major challenges for researchers studying phylogeography and shallow-scale phylogenetics is the identification of highly-variable and informative nuclear loci for the question of interest. Previous approaches to marker generation have generally required extensive testing of loci of unknown utility from other systems or development of markers from the nearest model organism with genomic resources. Here, we present a fast and economical approach to generating thousands of variable, single-copy nuclear loci for any system using next-generation sequencing. We performed Illumina paired-end sequencing of three reduced-representation libraries (RRLs) in chorus frogs (Pseudacris) to identify orthologous, single-copy loci across libraries and to estimate sequence divergence at multiple taxonomic levels. We also conducted PCR testing of these loci across the genus Pseudacris and outgroups to determine whether loci developed for phylogeography can be extended to deeper phylogenetic levels. Prior to sequencing, we conducted in silico digestion of the most closely-related reference genome (Xenopus tropicalis) to generate expectations for the number of loci and degree of coverage for a particular experimental design. Using the RRL approach, we: (1) identified >100,000 single-copy nuclear loci, 6,339 of which were shared across individuals within species and 904 of which were shared between species, (2) estimated average nuclear sequence divergence at 0.1% between alleles within an individual, 1.1% between conspecific individuals, and 1.8% between species, and (3) determined from PCR testing that 53% of the loci successfully amplify within-species and also many amplify to the genus-level and beyond (16%). Our study effectively identified nuclear loci present in the genome that have levels of sequence divergence on par with mitochondrial markers commonly used in phylogeography. Specifically, we estimated that ~7% of loci in the chorus frog genome are >3% divergent within species; this translates to ~50,000 single-copy loci in the genome with >3% divergence. Moreover, successful amplification of many loci at deeper phylogenetic levels indicates that the RRL approach represents an efficient method for rapid generation of informative markers for both phylogenetics and phylogeography. We conclude by making recommendations for minimizing the cost and maximizing the efficiency of marker development for future studies in this field.
◂Fig. 5 Cells of phylogenetically related strains (light microscopy). a Thecate cell in dorsal view. b Thecate cell in ventral view, note the sulcus extending onto the epitheca (arrow). c Putatively necrotic, thecate cell. d Thecate cell with one bulge on the epitheca (arrow), note that this was the only such cell among thousands of inspected cells. e, f Coccoid cells, apparently without thecae. g Two thecate cells enclosed in the parental theca. h Two connected, immotile cells enclosed in the parental thecae. j Lid of epitheca in dorsal-apical view (mirrored), composed of plates 2′‒4′, all intercalary plates and plates 2′′‒6′′. l‒m Same opened theca in ventral view (l) and dorsal view (m), note the sulcus extending onto the epitheca (arrow), the dorsal opening and all apical and all intercalary plates and plates 3′′‒5′′ remaining with the hypotheca. n Chloroplasts (as inferred from autofluorescence), note the space occupied by the nucleus. Plate labelling follows the Kofoidean notation, n′: apical plate; n′′: precingular plate; n′′′: postcingular plate; na: anterior intercalary plate. Scale= 10 µm in Bumps on the back: An unusual morphology in phylogenetically distinct Peridinium aff. cinctum (= Peridinium tuberosum; Peridiniales, Dinophyceae)
◂Fig. 5 Cells of phylogenetically related strains (light microscopy). a Thecate cell in dorsal view. b Thecate cell in ventral view, note the sulcus extending onto the epitheca (arrow). c Putatively necrotic, thecate cell. d Thecate cell with one bulge on the epitheca (arrow), note that this was the only such cell among thousands of inspected cells. e, f Coccoid cells, apparently without thecae. g Two thecate cells enclosed in the parental theca. h Two connected, immotile cells enclosed in the parental thecae. j Lid of epitheca in dorsal-apical view (mirrored), composed of plates 2′‒4′, all intercalary plates and plates 2′′‒6′′. l‒m Same opened theca in ventral view (l) and dorsal view (m), note the sulcus extending onto the epitheca (arrow), the dorsal opening and all apical and all intercalary plates and plates 3′′‒5′′ remaining with the hypotheca. n Chloroplasts (as inferred from autofluorescence), note the space occupied by the nucleus. Plate labelling follows the Kofoidean notation, n′: apical plate; n′′: precingular plate; n′′′: postcingular plate; na: anterior intercalary plate. Scale= 10 µm
Text-fig. 7. Maxillary (labial view) with maxillary foramen (arrows) from A – Cyprinus carpio (Cyprininae) showing the schematic reconstruction of the nervus trigeminus and the rostral barbel, B – Ctenopharyngodon idella (Xenocyprininae), C – Tinca tinca (Tincinae), (images not to scale). in Revision Of The Cyprinids From The Early Oligocene Of The České Středohoří Mountains, And The Phylogenetic Relationships Of Protothymallus Laube, 1901 (Teleostei, Cyprinidae, Gobioninae)
Text-fig. 7. Maxillary (labial view) with maxillary foramen (arrows) from A – Cyprinus carpio (Cyprininae) showing the schematic reconstruction of the nervus trigeminus and the rostral barbel, B – Ctenopharyngodon idella (Xenocyprininae), C – Tinca tinca (Tincinae), (images not to scale).
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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.