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Text-fig. 9. Lusitanispermum choffatii gen. et sp. nov. seeds from the Early Cretaceous Famalicão locality (sample 025), Portugal; Synchrotron radiation X-ray tomographic microscopy (SRXTM, orthoslices). a) Longitudinal orthoslice (yz0769) through the median plane of the seed (S174345) showing expanded exotestal cells (ex, arrow head) in the hilar region and well-preserved cellular nutritive tissue with an embedded tiny embryo (asterisk markes the margin of the embryo); note well-developed mesotesta (me) on the raphal side of seed. b) Longitudinal orthoslice (yz0750) in the median plane showing detail of micropylar part of seed with well-preserved exotesta (ex) and mesotesta (me) and tiny embryo with two rudimentary cotyledons (asterisks mark the margin of the cotyledons); note numerous granular bodies in the cellular nutritive tissue that are probably the remains of protein and lipid bodies. c) Transverse orthoslice (xy0311) through seed below hilum showing the bulging exotesta (arrow heads) (S174472); note that the exotestal cells in this region have thinner walls (arrows). d) Transverse orthoslice (xy0900) through the middle of a seed showing the uneven thickening of the anticlinal walls of the exotestal cells (ex), which are thicker towards the outside and very thin towards the inside; note also mesotesta (me) and the well-preserved cellular nutritive tissue (S174472). Scale bars = 500 µm (a, d); 250 µm (b, c). in Extinct Taxa Of Exotestal Seeds Close To Austrobaileyales And Nymphaeales From The Early Cretaceous Of Portugal
Text-fig. 9. Lusitanispermum choffatii gen. et sp. nov. seeds from the Early Cretaceous Famalicão locality (sample 025), Portugal; Synchrotron radiation X-ray tomographic microscopy (SRXTM, orthoslices). a) Longitudinal orthoslice (yz0769) through the median plane of the seed (S174345) showing expanded exotestal cells (ex, arrow head) in the hilar region and well-preserved cellular nutritive tissue with an embedded tiny embryo (asterisk markes the margin of the embryo); note well-developed mesotesta (me) on the raphal side of seed. b) Longitudinal orthoslice (yz0750) in the median plane showing detail of micropylar part of seed with well-preserved exotesta (ex) and mesotesta (me) and tiny embryo with two rudimentary cotyledons (asterisks mark the margin of the cotyledons); note numerous granular bodies in the cellular nutritive tissue that are probably the remains of protein and lipid bodies. c) Transverse orthoslice (xy0311) through seed below hilum showing the bulging exotesta (arrow heads) (S174472); note that the exotestal cells in this region have thinner walls (arrows). d) Transverse orthoslice (xy0900) through the middle of a seed showing the uneven thickening of the anticlinal walls of the exotestal cells (ex), which are thicker towards the outside and very thin towards the inside; note also mesotesta (me) and the well-preserved cellular nutritive tissue (S174472). Scale bars = 500 µm (a, d); 250 µm (b, c).
Text-fig. 4. Pazlia hilaris gen. et sp. nov. (a, b) from the Early Cretaceous Famalicão locality (sample 025), Portugal (holotype, S175096) and Pazliopsis reyi gen. et sp. nov. (c, d) from the Early Cretaceous Torres Vedras locality (sample 038), Portugal (S174614); Synchrotron radiation X-ray tomographic microscopy (SRXTM, orthoslices). a) Longitudinal orthoslice (xy0984) through the median plane of the seed showing the strongly thickened sclerenchyma under the hilar scar (hi), micropylar slit (mi) and the raphe (ra); note cells of exotesta are almost equally tall on both raphal and anti-raphal sides of the seed and gradually become shorter towards the micropyle. b) Transverse orthoslice (xy0984) through middle of seed showing the thickened cells of the exotesta; note that cells of the exotesta are almost equally tall on both raphal and anti-raphal sides. c) Longitudinal orthoslice (yz0812) through apical part of seed in the median plane showing embryo with two rudimentary cotyledons (asterisks) and surrounding nutritive tissue; note the tiny cells of embryo with central structures we interpret as the fossilized remains of nuclei. d) Detail of (4c) showing tiny embryo with two rudimentary cotyledons (asterisks); nutritive tissue immediately surrounding the embryo is interpreted as endosperm (endo); whether there is any delimitation between this inner endosperm and the outer part of the nutritive tissues is not clear. Scale bars = 250 µm (a–c); 125 µm (d). in Extinct Taxa Of Exotestal Seeds Close To Austrobaileyales And Nymphaeales From The Early Cretaceous Of Portugal
Text-fig. 4. Pazlia hilaris gen. et sp. nov. (a, b) from the Early Cretaceous Famalicão locality (sample 025), Portugal (holotype, S175096) and Pazliopsis reyi gen. et sp. nov. (c, d) from the Early Cretaceous Torres Vedras locality (sample 038), Portugal (S174614); Synchrotron radiation X-ray tomographic microscopy (SRXTM, orthoslices). a) Longitudinal orthoslice (xy0984) through the median plane of the seed showing the strongly thickened sclerenchyma under the hilar scar (hi), micropylar slit (mi) and the raphe (ra); note cells of exotesta are almost equally tall on both raphal and anti-raphal sides of the seed and gradually become shorter towards the micropyle. b) Transverse orthoslice (xy0984) through middle of seed showing the thickened cells of the exotesta; note that cells of the exotesta are almost equally tall on both raphal and anti-raphal sides. c) Longitudinal orthoslice (yz0812) through apical part of seed in the median plane showing embryo with two rudimentary cotyledons (asterisks) and surrounding nutritive tissue; note the tiny cells of embryo with central structures we interpret as the fossilized remains of nuclei. d) Detail of (4c) showing tiny embryo with two rudimentary cotyledons (asterisks); nutritive tissue immediately surrounding the embryo is interpreted as endosperm (endo); whether there is any delimitation between this inner endosperm and the outer part of the nutritive tissues is not clear. Scale bars = 250 µm (a–c); 125 µm (d).
Text-fig. 7. Lusitanispermum choffatii gen. et sp. nov. seeds from the Early Cretaceous Famalicão locality (sample 025), Portugal; Synchrotron radiation X-ray tomographic microscopy (SRXTM, volume renderings). a) Holotype; seed in lateral view showing seed shape; note that the seed is broken near the lower surface of the hilum (S174345). b) Oblique apical view of micropylar-hilar region of holotype showing slightly ruptured micropylar slit (mi) in the outer integument and two bulging and abraded areas (arrow heads) close to hilum. c) Seed in oblique lateral-raphal view showing the two bulging structures (arrow heads) immediately adjacent to the lower edge of the hilum (S174472). d) Tangential, longitudinal cut (cut at yz0131) through the seed coat of seed in (7c) showing the undulate anticlinal cell walls of the exotesta cells that are thickest towards the outside and thinner towards the inside. Scale bars = 500 µm (a–c); 250 µm (d). in Extinct Taxa Of Exotestal Seeds Close To Austrobaileyales And Nymphaeales From The Early Cretaceous Of Portugal
Text-fig. 7. Lusitanispermum choffatii gen. et sp. nov. seeds from the Early Cretaceous Famalicão locality (sample 025), Portugal; Synchrotron radiation X-ray tomographic microscopy (SRXTM, volume renderings). a) Holotype; seed in lateral view showing seed shape; note that the seed is broken near the lower surface of the hilum (S174345). b) Oblique apical view of micropylar-hilar region of holotype showing slightly ruptured micropylar slit (mi) in the outer integument and two bulging and abraded areas (arrow heads) close to hilum. c) Seed in oblique lateral-raphal view showing the two bulging structures (arrow heads) immediately adjacent to the lower edge of the hilum (S174472). d) Tangential, longitudinal cut (cut at yz0131) through the seed coat of seed in (7c) showing the undulate anticlinal cell walls of the exotesta cells that are thickest towards the outside and thinner towards the inside. Scale bars = 500 µm (a–c); 250 µm (d).
Text-fig. 8. Lusitanispermum choffatii gen. et sp. nov. seeds from the Early Cretaceous Famalicão locality (sample 025) (a, b, d, e), and the Vale de Água locality (sample 333) (c, f, g), Portugal; Synchrotron radiation X-ray tomographic microscopy (SRXTM, volume renderings). a) Smaller seed in lateral view showing the bulging region (arrow head) close to hilum (S174467). b) Cut volume rending (cut at yz1032) of seed in (8a) showing the expanded cells of exotesta immediately adjacent to the lower edge of the hilum (hi), micropyle (mi) and the well preserved nutritive tissue. c) Small seed in lateral view showing the bulging exotesta (arrow head) close to hilum (S175046). d, e) Larger seed in lateral (d) and raphal (e) view (S174035). f) Detail of seed in (8c) showing the micropylar slit (mi) above the hilum (hi) and bulging exotestal tissue (arrow head) in which the walls of the exotestal cells have straight anticlinal walls. g) Surface of seed in (8c) showing the raised undulate anticlinal walls of the exotestal cells. Scale bars = 500 µm (a–e); 250 µm (f); 125 µm (g). in Extinct Taxa Of Exotestal Seeds Close To Austrobaileyales And Nymphaeales From The Early Cretaceous Of Portugal
Text-fig. 8. Lusitanispermum choffatii gen. et sp. nov. seeds from the Early Cretaceous Famalicão locality (sample 025) (a, b, d, e), and the Vale de Água locality (sample 333) (c, f, g), Portugal; Synchrotron radiation X-ray tomographic microscopy (SRXTM, volume renderings). a) Smaller seed in lateral view showing the bulging region (arrow head) close to hilum (S174467). b) Cut volume rending (cut at yz1032) of seed in (8a) showing the expanded cells of exotesta immediately adjacent to the lower edge of the hilum (hi), micropyle (mi) and the well preserved nutritive tissue. c) Small seed in lateral view showing the bulging exotesta (arrow head) close to hilum (S175046). d, e) Larger seed in lateral (d) and raphal (e) view (S174035). f) Detail of seed in (8c) showing the micropylar slit (mi) above the hilum (hi) and bulging exotestal tissue (arrow head) in which the walls of the exotestal cells have straight anticlinal walls. g) Surface of seed in (8c) showing the raised undulate anticlinal walls of the exotestal cells. Scale bars = 500 µm (a–e); 250 µm (f); 125 µm (g).
Fig. 2 in Genetic variability in four samples of Neoplecostomus yapo (Teleostei: Loricariidae) from the rio Paranapanema basin, Brazil
Fig. 2. Lateral view of four specimens of Neoplecostomus yapo from the following localities: A, ribeirão Atlântico, 85.9 mm SL; B) ribeirão Uraí, 93.3 mm SL; C) rio Verde, 96.0 mm SL; and D) rio Fortaleza, 97.4 mm SL (type locality of N. yapo).
Fig. 1 in Genetic variability in four samples of Neoplecostomus yapo (Teleostei: Loricariidae) from the rio Paranapanema basin, Brazil
Fig. 1. Partial map of South America showing the collecting sites of Neoplecostomus yapo. Circle = ribeirão Atlântico, município de Mandaguaçu; triangle = ribeirão Uraí, mun. Londrina; lozenge = rio Fortaleza, mun. Tibagi; and star = rio Verde, mun. Ponta Grossa, Paraná State.
Fig. 1. Sample places location. Points number 1, 3, 7, 12, 14, 18 and 20 in Reproductive biology of Rhaphiodon vulpinus (Ostariophysi: Cynodontidae) in the Tocantins River Basin, Brazil
Fig. 1. Sample places location. Points number 1, 3, 7, 12, 14, 18 and 20 = Tocantins river; 2 = Sono river; 4 = Lajeadinho river; 5 = Santa Luzia river; 6 = Mangues river; 8 = Areias river; 9 = Crixás river; 10 = Capivara Lagoon; 11 = Manuel Alves river; 13 = São Valério river; 15 = Santa Tereza river; 16 = Dionízio Lagoon; 17 = Água Branca Lagoon; 19 = Paranã river and 21 = Bonita Lagoon.
Fig. 5 in Size composition, monthly condition factor and morphometrics for fishery-dependent samples of Rioraja agassizi (Chondrichthyes: Rajidae), off Santos, Southeast Brazil
Fig. 5. Relationships between total (black symbols) and gutted weight (g) (grey symbols) for male (above) and females (below) of Rioraja agassizi.
Fig. 2 in Size composition, monthly condition factor and morphometrics for fishery-dependent samples of Rioraja agassizi (Chondrichthyes: Rajidae), off Santos, Southeast Brazil
Fig. 2. Maps of Southeast Brazil, showing the fishing hauls by month, conducted by a total of eight fishing vessels. Symbols represent the fishing hauls from where samples of Rioraja agassizi were collected (dotted circles), or when this information was not available, the total hauls recorded by the skippers (crosses).
Fig. 6 in Size composition, monthly condition factor and morphometrics for fishery-dependent samples of Rioraja agassizi (Chondrichthyes: Rajidae), off Santos, Southeast Brazil
Fig. 6. Median condition factor by month (from March, 2005 to March, 2006) considering total (black line) and gutted weight (g) (grey line) for males (above) and females (below) of Rioraja agassizi. Vertical bars represent the data interval.
Fig. 4 in Size composition, monthly condition factor and morphometrics for fishery-dependent samples of Rioraja agassizi (Chondrichthyes: Rajidae), off Santos, Southeast Brazil
Fig. 4. Relationship of disc width (cm) as a dependent variable of total length (cm) for males (black symbols) and females (grey symbols) of Rioraja agassizi.
Fig. 1 in Size composition, monthly condition factor and morphometrics for fishery-dependent samples of Rioraja agassizi (Chondrichthyes: Rajidae), off Santos, Southeast Brazil
Fig. 1. Map of the study area, southeast Brazil, south-western Atlantic Ocean. Symbols represent all the fishing hauls from where samples of Rioraja agassizi were collected.
Fig. 1 in Sampling effort and fish species richness in small terra firme forest streams of central Amazonia, Brazil
Fig. 1. Fish species accumulation curves estimated from samples obtained in 1st, 2nd, and 3rd order streams reaches located in the study areas of Biological Dynamics of Forest Fragments Project, Manaus, Amazonas State. The curves represent extrapolations from five reaches sampled in each stream segment.
Fig. 2 in Cytogenetical and morphological features reveal significant differences among Venezuelan and Brazilian samples of Mugil curema (Teleostei: Mugilidae)
Fig. 2. Karyotypes of Mugil curema and metaphase plates after C-banding (b and d) and Ag-NOR (c and f) in samples from Brazil (a-c) and Venezuela (d-f). An enlargement of the NOR-carrying chromosome pair is shown in the inset in c and f.
Data from: Fractal triads efficiently sample ecological diversity and processes across spatial scales
<p>The relative influence of ecological assembly processes, such as environmental filtering, competition, and dispersal, vary across spatial scales. Changes in phylogenetic and taxonomic diversity across environments provide insight into these processes, however, it is challenging to assess the effect of spatial scale on these metrics. Here, we outline a nested sampling design that fractally spaces sampling locations to concentrate statistical power across spatial scales in a study area. We test this design in northeast Utah, at a study site with distinct vegetation types (including sagebrush steppe and mixed conifer forest), that vary across environmental gradients. We demonstrate the power of this design to detect changes in community phylogenetic diversity across environmental gradients and assess the spatial scale at which the sampling design captures the most variation in empirical data. We find clear evidence of broad-scale changes in multiple features of phylogenetic and taxonomic diversity across aspect. At finer scales, we find additional variation in phylodiversity, highlighting the power of our fractal sampling design to efficiently detect patterns across multiple spatial scales. Thus, our fractal sampling design and analysis effectively identify important environmental gradients and spatial scales that drive community phylogenetic structure. We discuss the insights this gives us into the ecological assembly processes that differentiate plant communities found in northeast Utah.</p>
A unified genealogy of modern and ancient genomes: Unified, inferred tree sequences of 1000 Genomes, Human Genome Diversity, and Simons Genome Diversity Projects with ancient samples
<p>Unified, inferred tree sequences built from the 1000 Genomes phase 3, Human Genome Diversity, and Simons Genome Diversity Projects with high coverage sequenced ancient samples. The ancient samples are the Altai, Chagyrskaya, and Vindija Neanderthals, the Denisovan, and a high-coverage family of four from the Afanasievo Culture.</p> <p>Each tree sequence is the arm of an autosome (the short arm of acrocentric chromosomes are not included). Tree sequences were inferred with <a href="https://tsinfer.readthedocs.io/">tsinfer</a> version 0.2.1 and <a href="https://tsdate.readthedocs.io/en/latest/">tsdate</a> version 0.1.4, as described in <a href="http://www.biorxiv.org/content/10.1101/2021.02.16.431497v2">Wohns et al. (2021)</a>. The files were compressed using <a href="https://tszip.readthedocs.io/en/stable/">tszip</a>. All data is in GRCh38.</p> <p>The full data pipeline used to generate these tree sequences and associated metadata is available on <a href="https://github.com/awohns/unified_genealogy_paper">GitHub</a>. A description can be found in the Supplementary Material of <a href="https://www.biorxiv.org/content/10.1101/2021.02.16.431497v2">Wohns et al. (2021)</a>.</p> <p>Tree sequences can be decompressed as follows:</p> <pre><code>$ tsunzip hgdp_tgp_sgdp_high_cov_ancients_chr1_p.dated.trees.tsz</code></pre> <p>Once decompressed, trees files can be loaded and processed in Python using <a href="https://tskit.readthedocs.io/">tskit</a>. </p> <pre><code>import tskit ts = tskit.load("hgdp_tgp_sgdp_high_cov_ancients_chr1_p.dated.trees") # ts is an instance of tskit.TreeSequence print("The short arm of chromosome 1 contains {} trees".format(ts.num_trees))</code></pre> <p>Accessing variant sites in the tree sequence provides the position and id of variants:</p> <pre><code>import json site = ts.site(1000) site_metadata = json.loads(site.metadata) print("The position of site 1000 is {} and its ID is {}.".format(site.position, site_metadata["ID"]))</code></pre> <p>Metadata associated with individuals and populations was derived from the original sources (<a href="http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20130606_sample_info/20130606_g1k.ped">TGP</a>, <a>HGDP</a>, and <a href="https://sharehost.hms.harvard.edu/genetics/reich_lab/sgdp/SGDP_metadata.279public.21signedLetter.samples.txt">SGDP</a>) and converted to JSON form. For example, to access individual metadata we can use:</p> <pre><code>ind = ts.individual(0) metadata_dict = json.loads(ind.metadata)</code></pre> <p>The metadata_dict variable will now contain all the metadata for the individual with ID 0 as a dictionary. Metadata associated with populations can be found in a similar way. Population IDs are associated with individuals via their constituent nodes. For example,</p> <pre><code>pop_metadata = [json.loads(pop.metadata) for pop in ts.populations()] ind_node = ts.node(ind.nodes[0]) ind_pop_metadata = pop_metadata[ind_node.population]</code></pre> <p>After this, the ind_pop_metadata variable will contain the population level metadata for individual ID 0.</p>
What you sample is what you get: ecomorphological variation in Trithemis (Odonata, Libellulidae) dragonfly wings reconsidered
Abstract Background The phylogenetic ecology of the Afro-Asian dragonfly genus Trithemis has been investigated previously by Damm et al. (in Mol Phylogenet Evol 54:870–882, 2010) and wing ecomorphology by Outomuro et al. (in J Evol Biol 26:1866–1874, 2013). However, the latter investigation employed a somewhat coarse sampling of forewing and hindwing outlines and reported results that were at odds in some ways with expectations given the mapping of landscape and water-body preference over the Trithemis cladogram produced by Damm et al. (in Mol Phylogenet Evol 54:870–882, 2010). To further explore the link between species-specific wing shape variation and habitat we studied a new sample of 27 Trithemis species employing a more robust statistical test for phylogenetic covariation, more comprehensive representations of Trithemis wing morphology and a wider range of morphometric data-analysis procedures. Results Contrary to the Outomuro et al. (in J Evol Biol 26:1866–1874, 2013) report, our results indicate that no statistically significant pattern of phylogenetic covariation exists in our Trithemis forewing and hindwing data and that both male and female wing datasets exhibit substantial shape differences between species that inhabit open and forested landscapes and species that hunt over temporary/standing or running water bodies. Among the morphometric analyses performed, landmark data and geometric morphometric data-analysis methods yielded the worst performance in identifying ecomorphometric shape distinctions between Trithemis habitat guilds. Direct analysis of wing images using an embedded convolution (deep learning) neural network delivered the best performance. Bootstrap and jackknife tests of group separations and discriminant-function stability confirm that our results are not artifacts of overtrained discriminant systems or the "curse of dimensionality" despite the modest size of our sample. Conclusion Our results suggest that Trithemis wing morphology reflects the environment's "push" to a much greater extent than phylogeny's "pull". In addition, they indicate that close attention should be paid to the manner in which morphologies are sampled for morphometric analysis and, if no prior information is available to guide sampling strategy, the sample that most comprehensively represents the morphologies of interest should be obtained. In many cases this will be digital images (2D) or scans (3D) of the entire morphology or morphological feature rather than sparse sets of landmark/semilandmark point locations.
A new sampling capability for uncertainty quantification in the Ice-sheet and Sea-level System Model v4.19 using Gaussian Markov random fields -- Datasets and results
<p>Data archives for test experiments (Section 3) and Pine Island Glacier application (Section 4) from the manuscript "Kevin Bulthuis and Eric Larour, A new sampling capability for uncertainty quantification in the Ice-sheet and Sea-Level System Model v4.19 using Gaussian Markov random fields"</p> <p>Source code is available at https://doi.org/10.5281/zenodo.5532775.</p>
Sample Dataset for an Interactive Demonstration of Eidein
<p>The "dataset.hdf5" HDF5 file contains a sample of astronomical spectra for an interactive demonstration of Eidein. Eidein is an interactive visualisation tool for Bayesian active deep learning. The demonstration is available online at <a href="https://bit.ly/eidein">bit.ly/eidein</a>.</p> <p>The sample consists of 2048 spectra from the Sloan Digital Sky Survey (SDSS) superset of catalogue of quasars (<a href="https://www.sdss.org/dr16/algorithms/qso_catalog/">https://www.sdss.org/dr16/algorithms/qso_catalog/</a>). The spectra are normalised to pseudo-continuum (each continuum is subtracted from a corresponding spectrum).</p>
UPLC-QTOF data from a river sample extracted with various solid phase extraction phases - mz5 files with scans in centroid spectrum format
<p>This dataset has been acquired from a river sample (Marne River, France) collected as part of the Screenatm'eau project (Observatoire des Sciences de l’Univers - Enveloppes FLUides de la Ville à l’Exobiologie - OSU-EFLUVE, Université Paris-Est Créteil). The sample was processed by solid-phase extraction using multiple cartridges and phases, in triplicates (see the list of samples in the samplemetadata.csv file).</p> <p>Data was acquired with a SYNAPT HDMS QTOF (Waters) coupled with a Nano ACQUITY UPLC System (Waters), in ESI positive mode. Raw data was converted using Proteowizard MSConvert version 3.0.21288, using zlib compression, with the CWT peakpicking algorithm (snr=0, peakSpace=0) to transform profile to centroid data, and the zeroSamples option (removeExtra 1-). The chosen output formats were .mzML and .mz5.</p> <p>A list of markers was obtained after peak picking and alignment across all samples using the PatRoon R package with the OpenMS algorithm, and exported as a markertable.csv file. Each detected marker has m/z and retention time values (see the variablemetadata.csv file), and intensity values in all samples (markertable.csv).</p> <p>For file naming explanation and details about each SPE phase, see the readme.txt file.</p>
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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.