Find research datasets worth reusing

opencc-by-4.0Jun 2017View details →

Twelve thousand recent limpets (Mollusca, Patellogastropoda) from a northeastern Pacific latitudinal gradient

Provided here is an image and 2D shape library of 12,035 Recent patellogastropod limpet (Mollusca, Patellogastropoda) shells collected from the northeastern Pacific along a latitudinal gradient ranging from Alaska to Baja, California. 2D outline coordinate data and morphometric measurements were generated using macroscopic high-throughput imaging methods (AutoMorph: https://github.com/HullLab/AutoMorph) developed in P.M. Hull’s lab at Yale University. This dataset is composed of patellogastropoda from 1,256 University of California Museum of Paleontology (UCMP) sample lots (metadata.tar.gz: Table 1). These lots represent multi-species assemblages collected from 353 unique localities along the western coast of North America (metadata.tar.gz: Table 2), ranging from Cape Yakataga, Alaska, United States (60°06’11N) to Cabo San Lucas, Baja California, Mexico (22°89’56N). Images and morphometric data are provided in 7 datasets: 1) boxed_full_images.zip: 1,256 full-lot (overview) images with boxed object identified by the segment module. 2) zstacks.zip: image stacks for each of the 1,256 sample lots processed by segment. These image stacks may potentially be used to generate individual 3D height maps. 3) 2d_edfs_labeled.zip: 12,035 individual extended-depth-of-focus (EDF) images produced by focus. A list of the individuals represented is provided in TableS1 in metadata.zip. 4) 2d_outlines.zip: 12,035 EDF images with 2D outline overlays for quality control. 5) 2d_coordinates.zip: 1,256 .csv files of the outline shape coordinates for all lots successfully processed with AutoMorph, including one file (all_coordinates_limpets.csv) with the coordinates for all 12,035 individuals extracted. 6) master_2d_measurements.csv: UCMP locality numbers, UCMP lot numbers, locality coordinates, object identification numbers output by AutoMorph, and morphometric data for all 12,035 individuals. Each individual has associated full-lot, individual EDF, 2D and outline images, as well as outline shape coordinates, all of which may be found in the .zip files listed above. Object identification numbers, which are used to link morphometric measurements with associated images, can be found in the column ‘object IDs’. Morphometric data provided includes major axis length, minor axis length, perimeter length, eccentricity, and rugosity, as well as aspect ratio and the height and width of the aspect rectangle. Locality coordinates are rounded to the nearest 0.1 degree to account for potential measurement uncertainty. 7) metadata.zip: A directory containing 5 tables in corresponding .xslx files. Table 1 provides UCMP specimen and locality numbers, site names, rounded coordinates, and the number of individuals per UCMP lot. Table 2 provides the number of species per site, with locality numbers and species names also provided. Table 3 provides information on the species’ range minima and maxima observed in the present dataset, as well as the number of individuals per species. Table 4 provides a comparison of hand measurements and AutoMorph outputs for 41 specimens, used for measurement validation. Table 5 provides locality information mismatches for three UCMP specimen lots. Table S1 provides a list of all objects included in the dataset, including an indication of which objects have known locality coordinates. The dataset provided accompanies the manuscript “Twelve thousand Recent limpets (Mollusca, Patellogastropoda) from a northeastern Pacific latitudinal gradient” submitted to Scientific Data. This manuscript describes methods of data collection and contains important usage notes, and should thus be consulted before attempting to use the data provided here. This work was funded by the American Chemical Society PRF Grant #55837-DNI8 and by support from Yale University.

Рис. 1. Филогенетические свЯЗи семейства отрЯда Patellogastropoda (по: Nakano, Ozawa [2011], с иЗменениЯми). in Erginidae fam. nov. (Patellogastropoda) - a new family of limpets

Рис. 1. Филогенетические свЯЗи семейства отрЯда Patellogastropoda (по: Nakano, Ozawa [2011], с иЗменениЯми).

Рис. 2. Особенности строение представителей Erginidae. A – Problacmaea sybaritica, велигеры иЗ выводковой сумки (в – велюм, м – трофические меШки, н – нога): фото К.Г. Колбина; B, C – провиЗорнаЯ радула Erginus galkini; D, E – Erginus galkini, раковина молодого ЭкЗемплЯра (длина 3.2 мм) (D); раковина ювенильной особи с протоконхом и телеоконхом (E); F – Problacmaea sybaritica, раковина молодого ЭкЗемплЯра (длина 1.2 мм); G – Problacmaea apicina, раковина ювенильной особи с протоконхом и телеоконхом. МасШтаб: A, G – 50 мкм, B, C – 3 мкм, E – 100 мкм. in Erginidae fam. nov. (Patellogastropoda) - a new family of limpets

Рис. 2. Особенности строение представителей Erginidae. A – Problacmaea sybaritica, велигеры иЗ выводковой сумки (в – велюм, м – трофические меШки, н – нога): фото К.Г. Колбина; B, C – провиЗорнаЯ радула Erginus galkini; D, E – Erginus galkini, раковина молодого ЭкЗемплЯра (длина 3.2 мм) (D); раковина ювенильной особи с протоконхом и телеоконхом (E); F – Problacmaea sybaritica, раковина молодого ЭкЗемплЯра (длина 1.2 мм); G – Problacmaea apicina, раковина ювенильной особи с протоконхом и телеоконхом. МасШтаб: A, G – 50 мкм, B, C – 3 мкм, E – 100 мкм.

Fig. 2 in Erginidae fam. nov. (Patellogastropoda) - a new family of limpets

Fig. 2. Morphology of some erginids. A – Problacmaea sybaritica, veligers from brooding sac (в – velum, м – trophical sacs, н – foot): photograph courtesy of K.G. Kolbin; B, C – provisional radula of Erginus galkini; D, E – Erginus galkini, shell of young specimen (length 3.2 mm) (D), juvenile shell with protoconch and teleoconch (E); F – Problacmaea sybaritica, shell of young specimen (length 1.2 mm); G – Problacmaea apicina, juvenile shell with protoconch and teleoconch. Scale: A, G – 50 μm, B, C – 3 μm, E – 100 μm.

opencc-by-4.0Dec 2020View details →

Fig. 3 in Diel movement patterns of Pacific sugar limpet, Patelloida saccharina (Gastropoda: Patellogastropoda: Lottiidae) in response to semi-diurnal tides of Samal Island, Philippines

Fig. 3. Movement patterns of Patelloida saccharina limpets in Catagman, Samal Island, during various lunar phases. A, New Moon, 27–28 March 2017; B, First Quarter, 4–5 April 2017; C, Full Moon, 9–10 April 2017; D, Last Quarter, 19–20 April 2017. The left and right y-axes correspond to the percentage of moving limpets and tidal height measurements in metres above chart datum (C.D.), respectively. Grey vertical bars represent the percentage of actively moving limpets during each lunar phase. The bar at the bottom corresponds to the day-night cycle: (from left to right) white = daytime, grey = transitioning to sunset, black = night-time, grey = sunrise. Note that the activity of P. saccharina limpets was observed during dark periods only, from sunset to night-time until before sunrise, as long as they were covered by the tide.

opencc-by-4.0Dec 2020View details →

Fig. 2 in Diel movement patterns of Pacific sugar limpet, Patelloida saccharina (Gastropoda: Patellogastropoda: Lottiidae) in response to semi-diurnal tides of Samal Island, Philippines

Fig. 2. Patelloida saccharina clamped on: A, bare rock face; B, rock covered with sand and turf algae. C, portion of the 5 × 5 cm grid quadrat laid on a reef patch with three P. saccharina individuals. Apices of limpet shells were painted with nail polish. Photographs by EY Zapanta and MA Fortaleza.

zenodo36/100

Fig. 1 in Erginidae fam. nov. (Patellogastropoda) - a new family of limpets

Fig. 1. Phylogenetic tree of the patellogastropod families (after Nakano, Ozawa [2011], modified).

FIGURE 5 in Molecular analysis reveals a new cryptic species in a limpet Lottia kogamogai (Patellogastropoda: Lottiidae) from Japan

FIGURE 5. The geographical distribution of three Lottia species with warm sea currents around Japan. The record of Lottia goshimai n.sp. from Russian coast is from Kristof et al. (2016).

FIGURE 2 in Molecular analysis reveals a new cryptic species in a limpet Lottia kogamogai (Patellogastropoda: Lottiidae) from Japan

FIGURE 2. Shell morphology of Lottia species. A–H. Lottia goshimai n. sp. A. Holotype, on rocks, UMUT-RM32483, Usujiri, Hakodate, Hokkaido (Loc. F); 10.8 x 8.4 x 3.7 mm. B. Paratype 1, on rocks, NSMT-Mo78956, Karakuwa, Kesennuma, Miyagi (Loc. R); 12.7 x 10.6 x 6.2 mm. C. Paratype 2, on rocks, NSMT-Mo78957, Usujiri, Hakodate, Hokkaido (Loc. F); 15.3 x 12.0 x 6.7 mm. D. Paratype 3, on rocks, UMUT-RM32492, Shirakami, Matsumae, Hokkaido (Loc. D); 14.4 x 11.6 x.7.4 mm. E. Paratype 4, on rocks, UMUT-RM32471, Takashima, Otaru, Hokkaido (Loc. B); 8.1 x 5.9 x 3.5 mm. F. Paratype 5, on rocks, UMUT-RM32496, Asamushi, Aomori, Aomori (Loc. I); 8.7 x 6.8 x 3.1 mm. G. Paratype 6, on Septifer virgatus, UMUT- RM32494, Shirakami, Matsumae, Hokkaido (Loc. D); 8.9 x 7.0 x 5.6 mm. H. Paratype 7, on Septifer virgatus, UMUT- RM32479, Esan, Hakodate, Hokkaido (Loc. G); 9.6 x 7.8 x 5.0 mm. I. Lottia luchuana, on rocks, UMUT-RM32514, Onna, Okinawa (Loc. r); 10.5 x 8.3 x 4.7 mm. J. Lottia kogamogai, on rocks, UMUT-RM32417, Banda, Tateyama, Chiba (Loc. Y); 11.8 x 9.5 x 4.0 mm. K. Lottia lindbergi, on rocks, UMUT-RM32509, Kaminokuni, Hiyama, Hokkaido (Loc. C); 14.3 x 11.0 x 5.6 mm. L. Lottia tenuisculpta, on rocks, UMUT-RM32506, Takashima, Otaru, Hokkaido (Loc. B); 11.6 x 9.2 x 5.1 mm. Scale bar = 1 cm.

FIGURE 6 in Molecular analysis reveals a new cryptic species in a limpet Lottia kogamogai (Patellogastropoda: Lottiidae) from Japan

FIGURE 6. Phylogenetic tree of Bayesian analysis based on COI data (661 bp). The numbers above each branch are NJ bootstrap/MP bootstrap/Bayesian posterior probabilities. Three species of Nipponacmea were used as outgroup.

FIGURE 1 in Molecular analysis reveals a new cryptic species in a limpet Lottia kogamogai (Patellogastropoda: Lottiidae) from Japan

FIGURE 1. Localities of specimens used in the present study. Letters correspond to localities in Table 1.

opennotspecifiedJul 2022View details →

Fig. 3 in The taxonomic position of brooding limpets of the genera Erginus and Rhodopetala (Patellogastropoda)

Fig. 3. Bayesian inference analysis of COI sequences for the genus Erginus. Numerals above or below the branches are Bayesian posterior probabilities and bootstrap values of the ML and NJ analysis, respectively. The species of the genus Erginus from the Russian Far East included in this analysis are highlighted in bold. Synapomorphies: a, brooding pouch; b, subcephalic tentacle ('penis').

opennotspecifiedJul 2022View details →

Fig. 2 in The taxonomic position of brooding limpets of the genera Erginus and Rhodopetala (Patellogastropoda)

Fig. 2. Bayesian phylogenetic tree of Patellogastropoda for combined molecular data (concatenated sequences from 12S, 16S, and COI mtDNA). Numerals at nodes are posterior probability values and bootstrap values (BS) of the ML analysis, respectively. Values of BS <70% are not shown.

opennotspecifiedJul 2022View details →

Fig. 1 in The taxonomic position of brooding limpets of the genera Erginus and Rhodopetala (Patellogastropoda)

Fig. 1. Limpet specimens used in this analysis. (A, B) Rhodopetala rosea, Simushir Island (shell length 6 mm); (C) Erginus sybariticus, Erineyskaya Inlet (shell length 19 mm); (D, I) Erginus moskalevi, Taui Bay, head with "penis" (arrow) (D) and shell (I) (shell length 9 mm); (E, F) Erginus puniceus, typical forms, Sea of Japan (shell length 5 mm); (G) Erginus puniceus, "sybariticus" form, Sea of Japan (shell length 6 mm); (H) Erginus apicinus, Simushir Island (shell length 7 mm).

Figure 11 in Systematic revision of Nacella (Patellogastropoda: Nacellidae) based on a complete phylogeny of the genus, with the description of a new species from the southern tip of South America

Figure 11. Nacella edgari, Kerguelen and Heard Islands, sub-Antarctic Indian Ocean. Scale bar = 1.0 cm for all unless specified otherwise. A = Port-aux-Français, Kerguelen Island, B = Îles du Prince-de-Monaco, Kerguelen Island, C = Atlas Cove, Heard Island. A–F, shell morphology and coloration of Nacella edgari. A–C, lateral view. D–F, dorsal view. G, mantle tentacles, cephalic tentacles and foot coloration patterns. H, radula. I, distribution.

Figure 7 in Systematic revision of Nacella (Patellogastropoda: Nacellidae) based on a complete phylogeny of the genus, with the description of a new species from the southern tip of South America

Figure 7. Nacella flammea, Patagonia, South America. Scale bar = 1.0 cm for all unless specified otherwise. A = Melimoyu, B = Port Famine, C = Falkland/Malvinas Islands. A–F, shell morphology and coloration of Nacella flammea. A–C, lateral view. D–F, dorsal view. G, mantle tentacles, cephalic tentacles and foot coloration patterns. H, radula. I, distribution.

Figure 10 in Systematic revision of Nacella (Patellogastropoda: Nacellidae) based on a complete phylogeny of the genus, with the description of a new species from the southern tip of South America

Figure 10. Nacella kerguelenensis, Kerguelen and Heard Islands, sub-Antarctic Indian Ocean. Scale bar = 1.0 cm for all unless specified otherwise. A = Port-aux-Français, Kerguelen Island, B = Baie des Cascades, Kerguelen Island, C = Atlas Cove, Heard Island. A–F, shell morphology and coloration of Nacella kerguelenensis. A–C, lateral view. D–F, dorsal view. G, mantle tentacles, cephalic tentacles and foot coloration patterns. H, radula. I, distribution.

Figure 6 in Systematic revision of Nacella (Patellogastropoda: Nacellidae) based on a complete phylogeny of the genus, with the description of a new species from the southern tip of South America

Figure 6. Nacella mytilina, Patagonia, South America. Scale bar = 1.0 cm for all unless specified otherwise. A = Port Famine, B = Navarino Island, C = Falkland/Malvinas Islands. A–F, shell morphology and coloration of Nacella mytilina. A–C, lateral view. D–F, dorsal view. G, mantle tentacles, cephalic tentacles and foot coloration patterns. H, radula. I, distribution.

Figure 4 in Systematic revision of Nacella (Patellogastropoda: Nacellidae) based on a complete phylogeny of the genus, with the description of a new species from the southern tip of South America

Figure 4. Nacella magellanica, Patagonia, South America. Scale bar = 1.0 cm for all unless specified otherwise. A = Chiloé, B = Port Famine, C = Falkland/Malvinas Islands. A–F, shell morphology and coloration of Nacella magellanica. A–C, lateral view. D–F, dorsal view. G, mantle tentacles, cephalic tentacles and foot coloration patterns. H, radula. I, distribution.

Figure 3 in Systematic revision of Nacella (Patellogastropoda: Nacellidae) based on a complete phylogeny of the genus, with the description of a new species from the southern tip of South America

Figure 3. Nacella clypeater, Central Chile, South America. Scale bar = 1.0 cm for all unless specified otherwise. A = La Misión, B = Tubul, C = Coquimbo. A–F, shell morphology and coloration of Nacella clypeater. A–C, lateral view. D–F, dorsal view. G, mantle tentacles, cephalic tentacles and foot coloration patterns. H, radula. I, distribution.