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Figure 1 in A review of molecular genetic markers and analytical approaches that have been used for delimiting marine mammal subspecies and species
Figure 1. Sample sizes used in publications of molecular genetic studies of marine mammals at different taxonomic levels. Graphs present the proportion of studies at each taxonomic level that fall into each sample size category. (A) minimum total sample size per focal taxon; (B) maximum sample size per single sampling locality. Papers were categorized as examining taxonomic questions at: species = subspecies/species boundary; subspecies = population/subspecies boundary; uncertain = taxonomic boundary uncertain (see text).
Figure 2 in A review of molecular genetic markers and analytical approaches that have been used for delimiting marine mammal subspecies and species
Figure 2. Types of molecular genetic data used in published studies examining questions at the species-level, subspecies-level, or undefined taxonomic level for marine mammals. Note that studies may have used more than one data type. Mitochondrial DNA sequence data (MtDNASeq), nuclear DNA sequence data (NuSeq), microsatellites (Msats), morphological data (Morph).
Data from: Pitfalls and pointers: an accessible guide to marker gene amplicon sequencing in ecological applications
<p>Next Generation Sequencing (NGS) is a powerful tool that has been rapidly adopted by many ecologists studying microbial communities. Despite the exciting demonstration of NGS technology as a tool for ecological research, cryptic pitfalls inherent to its use can obscure correct interpretation of NGS data. Here, we provide an accessible overview of a NGS process that uses marker gene amplicon sequences (MGAS) that will allow scientists, particularly community ecologists, to make appropriate methodological choices and understand limits on inference about community composition and diversity that can be drawn from MGAS data.</p> <p>We describe the MGAS pipeline, focusing specifically on cryptic sources of variation that have received less emphasis in the ecological literature, but which may substantially impact inference about microbial community diversity and composition. By simulating communities from published microbiome data, we demonstrate how these sources of variation can generate inaccurate or misleading patterns.</p> <p>We specifically highlight sample dilution without researcher awareness and lane-to-lane variability, two cryptic sources of variation arising during the MGAS pipeline. These sources of variation affect estimates of species presence and relative abundance, particularly for species with moderate to low abundances. Each of these sources of bias can lead to errors in the estimation of both absolute and relative abundance within, and turnover among, microbial communities.</p> <p>Awareness and understanding of what happens and, specifically, why it happens during MGAS generation is key to generating a strong data set and building a robust community matrix. Requesting sample dilution information from the sequencing center, including technical replicates across sequencing lanes, and understanding how sampling intensity and community taxa distribution patterns shape the measurement of community richness, evenness, and diversity are critical for drawing correct ecological inferences using MGAS data.</p>
Sensing Echoes: Temporal misalignment as the Earliest Marker of Neurodevelopmental Derail
<p>FROM THE PREPRINT:</p> <p>Sensory transduction and transmission delays operate and propagate along different time scales. From microseconds in the auditory domain, to hundreds of milliseconds in the visual, and kinesthetic domains, the brain must successfully align disparate delays arising from endogenously self-generated streams of motor and visceral sensorial information, with exogenous sensory inputs. To produce a cohesive response to environmental goals, constantly explore, adapt, and develop a sense of simultaneity, the brain must resolve this major feat and compensate for excessive delays in any sensory modality. Disruption in these processes may lead to altered perception of the self and others, and inadvertently affect social interactions. But how early such issues may emerge and be reliably detectable, remains a challenge. Here we assess in neonates, the transmission latencies of a sound wave that travels from the cochlear nerve to the brainstem on its way to the primary auditory cortex. Already at birth, we find systematic and cumulative delays in the propagation of this wave in neonates that later received a diagnosis of autism. Furthermore, we discover that the distributions of such temporal delays have far narrower bandwidth than those from neonates who did not receive the autism diagnosis. We identify associated codependent genes’ networks and define a reliable marker of neurodevelopment derail, detectable at birth. Under the precision autism model, we propose that the brainstem contains an endogenous clock anchoring and aligning disparate timescales critical for the emergence and maintenance of congruent percepts of the self and others.</p>
Fig. 4 in Redescription And New Host Record Of Diplostamenides Sciaenae (Monogenea, Microcotylidae) And Its Phylogenetic Status Using Molecular Markers
Fig. 4. Phylogenetic tree topology of partial 18S rRNA nucleotide sequence data for different microcotylids and outgroup as diclidophorids through NJ and ME methods. The bootstrap values for 1000 replicates are shown as in the phylogram and branch length is genetic distance between taxa.
Fig. 3 in Redescription And New Host Record Of Diplostamenides Sciaenae (Monogenea, Microcotylidae) And Its Phylogenetic Status Using Molecular Markers
Fig. 3. Phylogenetic tree topology of parital 28S rRNA nucleotide sequence data for the members of microcotytlidae and outgroup of members of diclidophoridae through NJ and ME methods. The bootstrap values for 1000 replicates are shown as in the phylogram and branch length is genetic distance between taxa.
Fig. 1 in Redescription And New Host Record Of Diplostamenides Sciaenae (Monogenea, Microcotylidae) And Its Phylogenetic Status Using Molecular Markers
Fig. 1. Diplostamenides sciaenae: A — whole mount (ventral view): OS, oral sucker; P, pharyn×; OE, oesophagus; GA, genital atrium; IC, intestinal caecum; VI, vitellarium; H, haptor; C, clamp B — reproductive system: V, vas deferens; VD, vitelline duct; O, ovary; CVD, common vitelline duct; GIC, genitointestinal canal; OD, oviduct; OT, ootype; T, testes C — genital atrium and spines: AS, atrial spines; D — clamp and associated sclerites: SMD, scleritum marginal dorsale; SMV, scleritum marginal ventrale; SM, Scleritum median; SOB, scleritum obliqum basale; ETD, extreme terminal dorsale; ETV, extreme terminal ventrale.
Fig. 2 in Redescription And New Host Record Of Diplostamenides Sciaenae (Monogenea, Microcotylidae) And Its Phylogenetic Status Using Molecular Markers
Fig. 2. Diplostamenides sciaenae digital phototmicrographs (present study): A — whole mount; B — clamp and associated sclerites; C — gential atrium and spines; D — anterior region with oral suckers, pharyn× and oesophagus. Abbreviations are provided in figure 1.
Fig. 1 in Molecular Characterization Of Lates Niloticus (Perciformes, Latidae) Populations From Three Nigerian Waterbodies Using Random Amplified Polymorphic Dna And Microsatellite Markers
Fig. 1. Map showing the sample locations of L. niloticus (Linnaeus, 1758). Population 1 — Kainji lake, Population 2 — River Benue, Makurdi and Population 3 — Ikere-Gorge reservoir, Iseyin, Oyo state.
Validating marker-less pose estimation with 3D x-ray radiography
<p class="MsoNormal"><span>These data were generated to evaluate the accuracy of DeepLabCut (DLC), a deep learning marker-less motion capture approach, by comparing it to a 3D x-ray video radiography system that tracks markers placed under the skin (XROMM). We recorded behavioral data simultaneously with XROMM and RGB video as marmosets foraged and reconstructed three-dimensional kinematics in a common coordinate system. We used XMALab to track 11 XROMM markers, and we used the toolkit Anipose to filter and triangulate DLC trajectories of 11 corresponding markers on the forelimb and torso. We performed a parameter sweep of relevant Anipose and post-processing parameters to characterize their effect on tracking quality. We compared the median error of DLC+Anipose to human labeling performance and placed this error in the context of the animal's range of motion. </span></p>
Standardized nuclear markers improve and homogenize species delimitation in Metazoa
<p><span>Species are the fundamental units of life and evolution. Their recognition is essential for science and society. Molecular methods have been increasingly employed for the identification of animal species, despite several challenges. </span></p> <p><span>Here, we explore with genomic data from nine animal lineages a set of nuclear</span><span> </span><span>markers, namely metazoan-level universal single-copy orthologs (metazoan USCOs), for their use in species delimitation. Our data sets include arthropods and vertebrates. We use various data assembly strategies and employ coalescent-based species inference as well as population admixture analyses and phenetic methods.</span></p> <p><span>We demonstrate that metazoan USCOs well distinguish closely related morphospecies and consistently outperform classical mitochondrial DNA barcoding in discriminating closely related species in different animal taxa. USCOs overcome the general shortcomings of mitochondrial DNA barcodes, and due to standardization across Metazoa, also those of other approaches. They accurately assign samples not only to lower but also to higher taxonomic levels. </span></p> <p><span>Metazoan USCOs provide a powerful and unifying framework for DNA-based species delimitation and taxonomy in animals and their employment could result in a more efficient use of research data and resources.</span></p>
FIG. 3 in Gaming and divination pieces, markers of ownership, or all three? Zooarchaeology and the interpretation of knuckle bones found in tombs of the Iberian necropolis of El Poblado (Coimbra del Barranco Ancho, Murcia, Spain)
FIG. 3. — Minimum number of individuals (MNI) calculated from the astragali assemblage of Sheep (Ovis Aries Linnaeus, 1758), Goat (Capra hircus Linnaeus, 1758), Roe deer (Capreolus capreolus Linnaeus, 1758), Red deer (Cervus ela- phus Linnaeus, 1758) and Pig (Sus scrofa Linnaeus, 1758).
FIG. 6 in Gaming and divination pieces, markers of ownership, or all three? Zooarchaeology and the interpretation of knuckle bones found in tombs of the Iberian necropolis of El Poblado (Coimbra del Barranco Ancho, Murcia, Spain)
FIG. 6. — Some examples of modified bone or ivory objects from Tomb 43. A, B, two imitation astragali in "plantar" and "lateral" view; C, different faces of the ivory dice recovered (according to Blasco Martín 2016: 249). Scale bar: 1 cm. Photo credit: J. Gómez Carrasco.
FIG. 4. — Tomb 116 in Gaming and divination pieces, markers of ownership, or all three? Zooarchaeology and the interpretation of knuckle bones found in tombs of the Iberian necropolis of El Poblado (Coimbra del Barranco Ancho, Murcia, Spain)
FIG. 4. — Tomb 116, "Triangular pyramid" shaped knuckle bones (caprines). Scale bar: 1 cm. Photo credit: J. Gómez Carrasco.
Model output and PTt marker data for van Agtmaal et al., 2022 (in review), Frontiers in Earth Science
<p>Model output for reproduction of key figures in the manuscript van Agtmaal et al. titled "Quantifying continental collision dynamics for Alpine-style orogens" currently under revision in Frontiers in Earth Science</p>
Lithogenesis of a phosphatized tephra marker horizon in the Eocene Messel maar lake
<p>Diffractograms of the Messel pit marker horizon M - messelite bands and a band consisting of messelite, montgomeryite, and mantienneite</p>
Figure 3 in Genome-wide characterization of microsatellites and development of polymorphic markers shared between two weevils of Eucryptorrhynchus (Coleoptera: Curculionidae)
Figure 3. Genetic structure of Eucryptorrhynchus brandti (a) and E. scrobiculatus (b) populations based on 14 microsatellite markers inferred using the software STRUCTURE. Each bin indicates an individual. Different colors show the identified clusters. The best number of clusters (K) is 3. Abbreviations: BJHD—Haidian District, Beijing; NXZW—Zhongwei, Ningxia; SDTA—Tai'an, Shandong; SXYL—Yangling, Shaanxi.
Figure 2 in Genome-wide characterization of microsatellites and development of polymorphic markers shared between two weevils of Eucryptorrhynchus (Coleoptera: Curculionidae)
Figure 2. Frequency distribution of microsatellites among different motifs in the Eucryptorrhynchus brandti and E. scrobiculatus. The "others" category represents summed motifs with counts below 100.
Figure 1 in Genome-wide characterization of microsatellites and development of polymorphic markers shared between two weevils of Eucryptorrhynchus (Coleoptera: Curculionidae)
Figure 1. Collection sites for specimens of Eucryptorrhynchus brandti (red) and E. scrobiculatus (green). Abbreviations: BJHD— Haidian District, Beijing (116.22°E, 40.04°N); NXZW—Zhongwei, Ningxia (105.12°E, 37.50°N); SDTA—Tai'an, Shandong (116.72°E, 36.27°N); SXYL—Yangling, Shaanxi (108.07°E, 34.26°N).
Dataset for the comparison of accelerometry-based and self-reported physical activity and their association with cardiovascular risk markers in children from South Africa
<p>Dataset used to evaluate and compare self-reported with accelerometry-based physical activity measurements as well as their associations with cardiovascular risk markers among South African school-aged children from disadvantaged communities.</p> <p>It encompasses anonymized, unique, identification numbers, demographic and body-mass-index, blood pressure, lipid panel and blood glucose measures.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.