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Fig. 7 in Middle and late Eocene fish otoliths from the eastern and southern USA

Fig. 7. Measured section at the Pamunkey River, 1 km E of Eanes property, Virginia (after Strickland 1985, loc. 37).

Fig. 2 in Middle and late Eocene fish otoliths from the eastern and southern USA

Fig. 2. Stratigraphic position of otolith-bearing strata in the US Gulf Coast middle and upper Eocene. A. The studied formations are indicated in yellow (after Dockery 1980, 1986c). B. Detailed stratigraphic units and biostratigraphic zonations for the succession in Mississippi (after Dockery & Thompson 2016).

Fig. 1 in Middle and late Eocene fish otoliths from the eastern and southern USA

Fig. 1. Maps showing the sampling sites on the US Gulf and eastern Atlantic Coasts (Texas, Louisiana, Mississippi, Alabama, Virginia).A. Sites 1–23 from Texas. B. Sites 25–43 from Mississippi and Alabama. 1. Pin Oak Creek. 2. Hooker Creek. 3. Burleson Bluff. 4–10. Rocky Branch, 1.5 miles SW of Stone City Bluff, samples 0–6. 11. Stone City Bluff, Brazos River. 12. Little Brazos River, under Highway 21 bridge. 13. Little Brazos River, Stenzel loc. 14. Little Brazos River, 1.5 km S of Highway 21 bridge. 15. Little Brazos River, confluence with Brazos River. 16. Dunn's Ranch, NNE of Bryan. 17. Robbins, roadside. 18. Wall Farm 2. 19. Wall Farm 1. 20. Cedar Creek, E of Centerville. 21. Alabama Ferry, on Trinity River, North. 22. Crockett. 23. Nacogdoces Dam. 24. Copenhagen (after Nolf & Stringer 2003). 25. Cynthia, Mississippi Lite clay pit. 26. Midway, Techeva Creek. 27. Jackson, boring at the corner of Amite and Mill Streets. 28. Jackson, Town Creek. 29. Jackson, Riverside Park. 30. Newton, NE exit off Interstate 20. 31. Dobys Bluff. 32. Quitman, Archusa Water Park. 33. Chickasawhay River, Hunting Lodge. 34. Evansboro (SE of town). 35. Puss Cuss Creek. 36. Isney. 37. Melvin (SE of town). 38. Gilbertown. 39. Barrytown, County Road 21. 40. Coffeeville Landing, samples A–D. 41. Coffeeville Landing, sample S. 42. Little Stave Creek. 43. Claiborne Bluff, Gosport F. 44. Pamunkey River, Devil's Hole. 45. Pamunkey River, 1 km E of Eanes property. 46. Pamunkey River, Horseshoe, Old Church type locality. 47. Pamunkey River, SW of Pampatike Landing.

Fig. S1 in Middle and late Eocene fish otoliths from the eastern and southern USA

Fig. S1. Comparison of Claibornian and Jacksonian otolith assemblages from the middle and late Eocene of the eastern and southern USA. A cluster analysis (A) and a principal coordinate analysis, PCoA (B) with Bray-Curtis similarity index were performed based on the taxonomic composition (presence/ absence) of each assemblage. Bootstrap values are given at the roots of each cluster in (A).

Fig. 38 in Middle and late Eocene fish otoliths from the eastern and southern USA

Fig. 38 (opposite page). Fish otoliths from the US middle and upper Eocene. A. "Ophichthus" brevior (Koken, 1888), holotype (ZMB Ot. 26), "Jackson Beds", Mississippi (?). B. Gnathophis dissimilis (Frizzell & Lamber, 1962), Moodys Branch F., Town Creek, Jackson, Mississippi (IRSNB P 9038). C. Paraconger solidus Müller, 1999, holotype (coll. Institut für Geowissenschaften, University of Leipzig, Nr. 10/P67), Piney Point F., loc. 24 (Horseshoe) of Müller, 1999, Virginia. D–G. Paraconger yazooensis Nolf & Stringer, 2003, Yazoo Clay, Tullos M., Copenhagen, Louisiana. D. Holotype (IRSNB P 6962). E–G. Paratypes (IRSNB P 6963–6965). H. Muraenanguilla aff. thevenini (Priem, 1906), Yazoo Clay, Copenhagen, Louisiana (IRSNB P 6966). I. Signata nicoli Dante & Frizzell, 1965, Weches F., Pleasanto, Atascosa County, Texas, holotype (USNM 23370). J. Xenosirembo decipiens (Koken, 1888), lectotype (ZMB Ot. 135), middle Eocene, "Clayborne Group", southern USA. K. Brotula aquitanica Nolf, 1980, Yazoo Clay, Tullos M., Copenhagen, Louisiana (IRSNB P 7419). L–O. Aequalobythites aequaloides (Nolf & Stringer, 2003), Yazoo Clay, Copenhagen, Louisiana. L. Holotype (IRSNB P 6977). M–O. Paratypes (IRSNB P 6978–6980). 1 = ventral view; 2 = inner view. Scale bars = 1 mm.

opencc-by-4.0Sep 2016View details →

Plate 1 in Late Neogene And Pleistocene Porgy Fishes (Teleostei, Sparidae) Of The Eastern Paratethys, With Comments On Their Palaeoecology

Plate 1. Molariform teeth and their fragments assigned to Pagrus sp. (figs 1–6), Pagrus cinctus (figs 7–11) and Sparidae gen. et sp. indet. (figs 12–13): 1 — unnumbered, Shirokino 2; 2 — unnumbered, Shirokino 2; 3 — unnumbered, Shirokino 2; 4 — unnumbered, Shirokino 2; 5 — NMNHU-P 53/5117, Novopetrovka; 6 — NMN- HU-P 53/5118, Novopetrovka; 7 — NMNHU-P 29/229, Bezymiannoe; 8 — unnumbered, apical view, Mariupol'; 9 — NMNHU-P 53/5119, Trudomirovka; 10 — unnumbered, apical view, Mariupol'; 11 — unnumbered, apical view, Mariupol'; 12 — unnumbered, apical view, Mariupol'; 13 — NMNHU-P 29/228, Bezymiannoe. Apical view in a, basal in b, lateral in c.

IGM Population of HFF structures using Hi-C, laminB1 DamID, 3D HIPMAp FISH and single cell SPRITE data

This repository accompanies the manuscript "Integrative Genome Modeling Platform reveals essentiality of rare contact events in 3D genome organizations", to appear in Nat. Methods (2022), see also https://www.biorxiv.org/content/10.1101/2021.08.22.457288v1. It contains the preprocessed input data files (Hi-C, laminB1 DamID, 3D HIPMAp FISH and single cell SPRITE) for the HFF fibroblast cell line to be used in the Integrative Genome Modeling platform (IGM) developed in the Alber lab at UCLA (https://github.com/alberlab/igm). Also, we provide the configuration file to run IGM with those datasets, as we did in generating the HDSF population discussed in the accompanying manuscript. Such population is also provided as an "hss" file. Documentation and a simple demo/tutorial on how IGM can be run is given on the Alber lab Github @ https://github.com/alberlab/igm. All files can be read in using the h5py and alabtools (available @https://github.com/alberlab/alabtools) Python packages. More detailed information is provided in the manuscript and associated Supplementary Information file.   For any inquiry/suggestions/doubts please reach out to Lorenzo Boninsegna (bonimba@g.ucla.edu) or Dr. Frank Alber (falber@g.ucla.edu).

opencc-zeroMay 2022View details →

dryad40/100

Data from: Periodic environmental disturbance drives repeated ecomorphological diversification in an adaptive radiation of Antarctic fishes

The ecological theory of adaptive radiation has profoundly shaped our conceptualization of the rules that govern diversification. However, while many radiations follow classic early burst patterns of diversification as they fill ecological space, the longer-term fates of these radiations depend on many factors, such as climatic stability. In systems with periodic disturbances, species-rich clades can contain nested adaptive radiations of subclades with their own distinct diversification histories, and how adaptive radiation theory applies in these cases is less clear. Here, we investigated patterns of ecological and phenotypic diversification within two iterative adaptive radiations of cryonotothenioid fishes in Antarctica's Southern Ocean: crocodile icefishes and notoperches. For both clades, we observe evidence of repeated diversification into disparate regions of trait space between closely related taxa and into overlapping regions of trait space between distantly related taxa. We additionally find little evidence that patterns of ecological divergence are correlated with evolution of morphological disparity, suggesting that these axes of divergence may not be tightly linked. Finally, we reveal evidence of repeated convergence in sympatry that suggests niche complementarity. These findings reflect the dynamic history of Antarctic marine habitats, and may guide hypotheses of diversification dynamics in environments characterized by periodic disturbance.

Fig. 8 in Revision of the African cichlid fish genus Ctenochromis (Teleostei, Cichliformes), including a description of the new genus Shuja from Lake Tanganyika and the new species Ctenochromis scatebra from northern Tanzania

Fig. 8. Morphology of Ctenochromis Pfeffer, 1893, imaged using x-ray tomography micro CT. a. Ctenochomis pectoralis Pfeffer, 1893, paralectotype BMNH 1899.2.27.1 from Korogwe. b. C. pectoralis from the Ruvu River (part of BMNH 2021.7.15.1-3). c. C. scatebra Genner, Ngatunga &

Fig. 7 in Revision of the African cichlid fish genus Ctenochromis (Teleostei, Cichliformes), including a description of the new genus Shuja from Lake Tanganyika and the new species Ctenochromis scatebra from northern Tanzania

Fig. 7. Morphology of Ctenochromis Pfeffer, 1893.a, d, g. Oral teeth.b, e, h. Chest squamation illustrating scale-free patches. c, f, i. Cheek squamation illustrating the reduction in scale number towards the ventral section of the cheek. a–c. Ctenochomis pectoralis Pfeffer, 1893 from Korogwe (paralectotype BMNH 1899.2.27.1); d–f. C. pectoralis from the Ruvu River (part of BMNH 2021.7.15.1-3); g–i. C. scatebra Genner, Ngatunga & Turner sp. nov. from Chemka Springs (holotype BMNH 2021.7.15.4). Scale bars:

Fig. 6. a. Ctenochomis pectoralis Pfeffer, 1893, lectotype ZMH402 in Revision of the African cichlid fish genus Ctenochromis (Teleostei, Cichliformes), including a description of the new genus Shuja from Lake Tanganyika and the new species Ctenochromis scatebra from northern Tanzania

Fig. 6. a. Ctenochomis pectoralis Pfeffer, 1893, lectotype ZMH402 from Korogwe (imaged by Thilo Weddehage). b. C. pectoralis, paralectotype BMNH 1899.2.27.1 from Korogwe. c. C. pectoralis, ♂ from Ruvu River shortly after capture (part of BMNH 2021.7.15.1-3). d. C. pectoralis, ♂ from Ruvu River preserved state (part of BMNH 2021.7.15.1-3). e. C. scatebra Genner, Ngatunga & Turner sp. nov., ♂ from Chemka Springs shortly after capture (part of BMNH 2021.7.15.1-3). f. C. scatebra

Fig. 4 in Revision of the African cichlid fish genus Ctenochromis (Teleostei, Cichliformes), including a description of the new genus Shuja from Lake Tanganyika and the new species Ctenochromis scatebra from northern Tanzania

Fig. 4. Phylogenetic reconstructions of representatives of populations of Ctenochromis Pfeffer, 1893, as well as representatives of the Lake Malawi haplochromine radiation, and the Lake Tanganyika Tropheini Poll, 1986. a. Maximum Likelihood phylogenetic reconstruction based on 11 288 SNPs. b. Maximum Likelihood phylogenetic reconstruction based on 1047 basepairs of the entired NADH2 mtDNA gene. In both trees, numbers on branches indicate percentage bootstrap support, and branches with> 70% support are shown. The scale bars represent a measure of genetic distance. See Table 1 for sampling details. Collection localities are in parentheses. Samples from Nyumba ya Mungu have accessions

Fig. 5. Shuja horei gen. et comb. nov. a in Revision of the African cichlid fish genus Ctenochromis (Teleostei, Cichliformes), including a description of the new genus Shuja from Lake Tanganyika and the new species Ctenochromis scatebra from northern Tanzania

Fig. 5. Shuja horei gen. et comb. nov. a. Illustration from the original type specimen (Günther 1894). b. A freshly caught specimen collected in 2016 from the Malagarasi River, Ilagala (BMNH 2021.7.15.14). c. Radiographs of the type series (syntypes) from the Natural History Museum (BMNH 1889.1.30.13– 15). Note the prognathous jaw that distinguishes Shuja Genner, Ngatunga & Turner gen. nov. from other genera within the Tropheini Poll, 1986. Radiographs from the Natural History Museum, London

Fig. 3. Principal Component Axes 1 and 2 in Revision of the African cichlid fish genus Ctenochromis (Teleostei, Cichliformes), including a description of the new genus Shuja from Lake Tanganyika and the new species Ctenochromis scatebra from northern Tanzania

Fig. 3. Principal Component Axes 1 and 2 of morphological measurements of specimens of Ctenochromis pectoralis Pfeffer, 1893 of the type series from Korogwe, compared with specimens of C. pectoralis from the Ruvu River, and C. scatebra Genner, Ngatunga & Turner sp. nov. from Chemka Springs. The image of C. pectoralis from Korogwe is from the original description (Pfeffer 1893). Collection localities are in parentheses following the species names. In total, Principal Component Axes 1 and 2

Fig. 1 in Revision of the African cichlid fish genus Ctenochromis (Teleostei, Cichliformes), including a description of the new genus Shuja from Lake Tanganyika and the new species Ctenochromis scatebra from northern Tanzania

Fig. 1. The type locality of Ctenochromis pectoralis Pfeffer, 1893 is Korogwe, in the lower section of the Pangani River system. Collection sites of specimens of Ctenochromis for this study were Chemka Springs and the Ruvu River (which flows between Lake Jipe to the east, and Nyumba ya Mungu Reservoir to the west). A further population of Ctenochromis has been reported from Mzima Springs, in

Global nutrient cycling by commercially targeted marine fish (Le Mézo et al., 2022, Biogeosciences)

Model outputs and code used for the study "Global nutrient cycling by commercially targeted marine fish" published in Biogeosciences (Le Mézo et al., 2022).  <ul> <li>composite4b_cycling_MCV3_PotH_LME_2010_R2_2010_fNPP7_ks24_p50_c7_newFNPP_Online_nruns_31 = model outputs with <ul> <li>composite.maps contains the 2D fields</li> <li>y200 refers to fields at the pristine state and yglo to fields at the global peak catch.</li> <li>dfish is the fish biomass in wet weight per gram (size class)</li> <li>resp5 is the cycling rate that was used in the paper (defined in the Methods section)</li> </ul> </li> <li><a href="https://zenodo.org/api/files/72a2b98c-e4e5-4282-9ffa-0a7a1717e009/01_Mean_and_uncertainty_commercial_fish.mlx">Main_script.mlx</a> = main code used to compute the nutrient content and cycling of fish and the comparisons with other fields</li> <li><a href="https://zenodo.org/api/files/72a2b98c-e4e5-4282-9ffa-0a7a1717e009/size_bins_width.m">size_bins_width.m</a> = code used to compute the model size bin width</li> <li>data_annual.mat = NO3, PO4, NPP, C export fields</li> <li>composite_MCV3_PotH_LME_2010_R2_2010_fNPP7_ks24_p50_c7_newFNPP_Online_nruns_31.mat is the model outputs with <ul> <li>cyc.composite.maps.yglo.mean.harvest being the catch field at global peak catch</li> </ul> </li> <li>solublefraction_Mahowald2009_360x180.nc is the Fe deposition field</li> <li> Brahneyetal2015_nitrogenandphosphorus2x2annualdep_360x180.nc is the N deposition field</li> <li>mask_LME.mat is the mask of LME areas</li> <li>ocean_topaz_tracers.timmean.BOATS_grid_fed.nc is the modeled dissolved Fe concentrations in seawater by the TOPAZ model</li> <li>zeu_lee_modis_aqua_average_2002-2019.nc is the euphotic depth field used to compute the nutrient concentrations</li> <li><a href="https://zenodo.org/api/files/72a2b98c-e4e5-4282-9ffa-0a7a1717e009/woa05_nitrate_month.nc">woa05_nitrate_month.nc</a> is the NO3 field used to make the spatial interpolations of the Fe:C stoichiometric ratios.</li> <li><a href="https://zenodo.org/api/files/72a2b98c-e4e5-4282-9ffa-0a7a1717e009/mass_50sizes_boats.mat">mass_50sizes_boats.mat</a> is the mass of each size class of the BOATS model</li> <li><a href="https://zenodo.org/api/files/72a2b98c-e4e5-4282-9ffa-0a7a1717e009/Tables%20S2%20and%20S3.xlsx">Tables S2 and S3.xlsx</a> litterature compilation of values for N and P in fish and zooplankton</li> <li>Galbraith et al (2019) SI.pdf is the supplement to Galbraith et al. (2019) in which the data compilation for the Fe content of fish, zooplankton and phytoplankton can be found.</li> </ul>

Fig. 6. a. Ctenochomis pectoralis Pfeffer, 1893, lectotype ZMH402 in Revision of the African cichlid fish genus Ctenochromis (Teleostei, Cichliformes), including a description of the new genus Shuja from Lake Tanganyika and the new species Ctenochromis scatebra from northern Tanzania

Fig. 4 in Revision of the African cichlid fish genus Ctenochromis (Teleostei, Cichliformes), including a description of the new genus Shuja from Lake Tanganyika and the new species Ctenochromis scatebra from northern Tanzania

Fig. 1 in Revision of the African cichlid fish genus Ctenochromis (Teleostei, Cichliformes), including a description of the new genus Shuja from Lake Tanganyika and the new species Ctenochromis scatebra from northern Tanzania

Fig. 5. Shuja horei gen. et comb. nov. a in Revision of the African cichlid fish genus Ctenochromis (Teleostei, Cichliformes), including a description of the new genus Shuja from Lake Tanganyika and the new species Ctenochromis scatebra from northern Tanzania