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663 results for “mud”
Genome evolution and introgression in the New Zealand mud snails Potamopyrgus estuarinus and Potamopyrgus kaitunuparaoa
<p>We have sequenced, assembled, and analyzed the nuclear and mitochondrial genomes and transcriptomes of <i>Potamopyrgus estuarinus</i> and <i>Potamopyrgus kaitunuparaoa</i>, two prosobranch snail species native to New Zealand that together span the continuum from estuary to freshwater.<i> </i>These two species are the closest known relatives of the freshwater species <i>P. antipodarum—</i>a model for studying the evolution of sex, host-parasite coevolution, and biological invasiveness—and thus provide key evolutionary context for understanding its unusual biology. The <i>P. estuarinus</i> and <i>P. kaitunuparaoa </i>genomes are very similar in size and overall gene content. Comparative analyses of genome content indicate that these two species harbor a near-identical set of genes involved in meiosis and sperm functions, including seven genes with meiosis-specific functions. These results are consistent with obligate sexual reproduction in these two species and provide a framework for future analyses of <i>P. antipodarum—</i>a species comprising both obligately sexual and obligately asexual lineages, each separately derived from a sexual ancestor. Genome-wide multigene phylogenetic analyses indicate that <i>P. kaitunuparaoa</i> is likely the closest relative to <i>P. antipodarum. </i>We nevertheless show that there has been considerable introgression between <i>P. estuarinus</i> and <i>P. kaitunuparaoa.</i> That introgression does not extend to the mitochondrial genome, which appears to serve as a barrier to hybridization between <i>P. estuarinus </i>and <i>P. kaitunuparaoa.</i> Nuclear-encoded genes whose products function in joint mitochondrial-nuclear enzyme complexes exhibit similar patterns of non-introgression, indicating that incompatibilities between the mitochondrial and the nuclear genome may have prevented more extensive gene flow between these two species.<i> </i> </p>
Indicative distribution map for Ecosystem Functional Group M1.8 Subtidal mud plains
<p>This archive contains indicative distribution maps and profiles for <strong>M1.8 Subtidal mud plains</strong>, a ecosystem functional group (EFG, level 3) of the <a href="https://global-ecosystems.org/">IUCN Global Ecosystem Typology</a> (v2.0). Please refer to Keith <em>et al.</em> (2020) for details.</p> <p>The descriptive profiles provide brief summaries of key ecological traits and processes, maps are indicative of global distribution patterns, and are not intended to represent fine-scale patterns. The maps show areas of the world containing major (value of 1, coloured red) or minor occurrences (value of 2, coloured yellow) of each ecosystem functional group. Minor occurrences are areas where an ecosystem functional group is scattered in patches within matrices of other ecosystem functional groups or where they occur in substantial areas, but only within a segment of a larger region. Given bounds of resolution and accuracy of source data, the maps should be used to query which EFG are likely to occur within areas, rather than which occur at particular point locations. Detailed methods and references for the maps are included in the profile (xml format).</p>
Rates of consumption of marsh periwinkles (Littoraria irrorata) by mud crabs (Eurytium limosum and Panopeus obesus) between August and December in a Georgia salt marsh
Predatory mud crabs (Panopeus obesus and Eurytium limosum) are two of the main resident infaunal predators in southeastern US salt marshes.The relative importance of the two species in the trophic control of marsh periwinkles (snails; Littoraria irrorata) is likley to change across seasons. We therefore manipulated the these predator species (Panopeus obesus and Eurytium limosum) in experimental cages in the field (at Dean Creek, Sapelo Island, GA) and assessed monthly predation rates over four months, between 15th August to 15th December. We included 3 treatments, consisting of two treatments containing each species alone, and one containing both species together; all treatments had the same density. Specifically, 1) 4 x Panopeus individuals; 2) 4 x Eurytium individuals; 3) 2 x Panopeus individuals + 2 Eurytium individuals. Only adult crabs (33-40mm carapace diameter) were used. We maintained the treatments over 4 months (15th Aug - 15th Dec 2009), replacing any missing crabs every two weeks and counting the number of snails killed by predators each month.
Effects of the relative abundance of predatory mud crabs (Panopeus obesus and Eurytium limosum) on abundances of snails and fiddler crabs in a Georgia salt marsh
Predatory mud crabs (Panopeus obesus and Eurytium limosum) are two of the main resident infaunal predators in southeastern US salt marshes. Little is known, however, about their effects on important prey species. These influences are llikely to be dependent on the identity and relative abundances of the two predator species. We therefore manipulated the relative abundances of Panopeus and Eurytium in experimental cages in the field (at Airport Marsh, Sapelo Island, GA). We maintained the treatments over 4 months (July - October 2011), before assessing impacts on predator limb loss (an indicator of interspecific antagonism) and prey densitities (small and large mud fiddler crabs and marsh periwinkles).
Mud and organic content are strongly correlated with microplastic contamination in a meandering riverbed - Data sets
<p>This is the dataset relating to publication "Microplastics distribution in a meandering riverbed reveasl mud content as a universal normalizer for microplastic contamination in aquatic environments" by Van Daele, M., Van Bastelaere, B., de Clercq, J., Meyer, I., Vercauteren, M. and Asselman, J.</p> <p>It contains the microplastic and sedimentological data that support the findings of that publication, with a seperate file for data obtained from riberbed sediments and the water column. It further contains a file with all source data for the graphs in the figures of the main manuscript and the Supplementary Information<span><span>.</span></span></p>
Flow dynamics and pump kinematics in polychaete burrows constructed in a transparent mud analog
We used Particle Tracking Velocimetry (PTV) to measure fluid flow within burrows constructed by the polychaete Alitta succinea in a transparent mud analog. We also measured the kinematics of the undulatory pumping by the polychaete that drives flow through the burrow. The flow velocity data is presented in the spreadsheet worm_burrow_particle_tracking_data.csv and consists of the x and y coordinates (in mm) of each tracked particle, the time at which it was tracked (in seconds) and the velocity of the particle at that time (in mm per second). The ClipID is the reference of the video clip the data is from, and is a unique identifier. The SequenceID is retained between the pump dynamics data and the particle tracking data, because worm kinematics and flow dynamics were recorded simultaneously. Each tracked particle in a given sequence has a unique TrackID. The worm kinematics data consists of the track of the peak of the undulatory wave created as an individual polychaete ventilates its burrow and is presented in the spreadsheet worm_burrow_pump_dynamics_data.csv. The variables included are the x and y coordinates of the wave peak (in mm), the time at which the point was taken (in seconds) and the instantaneous velocity of the wave peak at that time (in mm per second). The ClipID is the reference of the video clip the data is from, and is a unique identifier. The SequenceID is retained between the pump dynamics data and the particle tracking data, because worm kinematics and flow dynamics were recorded simultaneously. Each tracked wave in a given sequence has a unique TrackID. The metadata, in the spreadsheet worm_burrow_metadata.csv, gives the polychaete Individual ID (a unique identifier for each specimen used) for each Clip ID and Sequence ID from the data spreadsheets, the location in the burrow at which the video was taken (between the head of the worm and the burrow entrance is "ahead", between the tail of the worm and the burrow exit is "behind", and a video of
Fig. 5 in Setaphyes elenae sp. nov., a new species of mud dragon (Kinorhyncha: Allomalorhagida) from Skagerrak (north-eastern Atlantic Ocean)
Fig. 5. Boxplots showing the ranges of different body measurements of Setaphyes elenae sp. nov., S. dentatus (Reinhard, 1881) and S. flaveolatus (Zelinka, 1928). A. Total trunk length. B. Standard sternal width. C. Lateral terminal spines' length.
Fig. 4 in Setaphyes elenae sp. nov., a new species of mud dragon (Kinorhyncha: Allomalorhagida) from Skagerrak (north-eastern Atlantic Ocean)
Fig. 4. Scanning electron micrographs showing general overview and details of the cuticular trunk morphology of a non-type specimen of Setaphyes elenae sp. nov. A. Dorsal overview. B. Middorsal elevation of segment 4. C. Cuticular ornamentation of anterior margin of segment 1. D. Detail of primary and secondary pectinate fringes of segment 5. E. Middorsal to paradorsal view of segment 2. F. Laterodorsal seta of segment 5. G. Middorsal process of segment 1. H. Ventral view of segments 4–5. I. Dorsal view of segment 10. J. Subdorsal sensory spots of segment 8. Abbreviations: mde = middorsal elevation; mdp = middorsal process; pdse = paradorsal seta; ppf = primary pectinate fringe; s = segment; vmse = ventromedial seta. Numbers after abbreviations indicate corresponding segment; sensory spots are marked as dashed circles. Scale bars: A = 100 µm; B, D, F–G, J = 1 µm; C, E, H–I = 10 µm.
Fig. 3 in Setaphyes elenae sp. nov., a new species of mud dragon (Kinorhyncha: Allomalorhagida) from Skagerrak (north-eastern Atlantic Ocean)
Fig. 3 (opposite page). Light micrographs showing trunk overviews and details of cuticular trunk characters of ♀, holotype (NHMD 655358) (A–L, N) and ♂, paratype (NHMD 655361) (M) of Setaphyes elenae sp. nov. A. Dorsal overview. B. Dorsal view on right half of segment 1. C. Ventral view on left half of segment 1. D. Dorsal view on right half of segment 2. E. Ventral view on left half of segment 2. F. Dorsal view on right half of segment 3. G. Ventral view on left half of segment 3. H. Ventral overview. I. Dorsal view on right half of segment 4. J. Ventral view on left half of segment 4. K. Dorsal view on right half of segment 8. L. Ventral view on left half of segment 8. M. Dorsal view on right half of segment 9. N. Ventral view on left half of segment 9. Abbreviations: ldse = laterodorsal seta; lts = lateral terminal spine; lvse = lateroventral seta; mde = middorsal elevation; mdp = middorsal process; pdse = paradorsal seta; vlse = ventrolateral seta; vmse = ventromedial seta. Numbers after abreviations indicate correspong segment; sensory spots are marked as dashed circles, and glandular cell outlets as continuous circles. Scale bars: A, H = 100 µm; B–G, I–N = 20 µm.
Fig. 2 in Setaphyes elenae sp. nov., a new species of mud dragon (Kinorhyncha: Allomalorhagida) from Skagerrak (north-eastern Atlantic Ocean)
Fig. 2 (opposite page). Line art illustrations of adult Setaphyes elenae sp. nov. A. ♀, ventral overview. B. ♀, dorsal overview. C. ♂, segments 10–11, ventral view. D. ♂, segments 1–2, ventral view. Abbreviations: bsj = ball-and-socket joint; dpl = dorsal placid; gcoI = type I glandular cell outlet; ldcr = laterodorsal cuticular ridge; ldse = laterodorsal seta; ldss = laterodorsal sensory spot; lts = lateral terminal spine; lvse = lateroventral seta; mde = middorsal elevation; mdp = middorsal process; ms = muscular scar; pdse = paradorsal seta; pdss = paradorsal sensory spot; ppf = primary pectinate fringe; ps = penil spine; pvap = paraventral apodeme; sdss = subdorsal sensory spot; spf = secondary pectinate fringe; vlcr = ventrolateral cuticular ridge; vlse = ventrolateral seta; vlss = ventrolateral sensory spot; vmse = ventromedial seta; vmss = ventromedial sensory spot; vmt = ventromedial tube; vpl = ventral placid. Scale bar = 100 µm
Stochastic Modelling of Thin Mud Drapes inside Point Bar Reservoirs with ALLUVSIM-GANSim
<p>Here is the dataset and code for the paper by Hu, X et al. (2023, under review). <span>Stochastic Modelling of Thin Mud Drapes inside Point Bar Reservoirs with ALLUVSIM-GANSim,</span> Water Resources Research.</p>
Figs. 7–9. Paraharmotrema karinganiense Dutton & Bullard n in Paraharmotrema karinganiense n. gen., n. sp. (Digenea: Liolopidae) infecting the intestine of serrated hinged terrapin (Pelusios sinuatus), east African black mud turtle (Pelusios subniger), and South African helmeted turtle (Pelomedusa galeata) and a phylogenetic hypothesis for liolopid genera
Figs. 7–9. Paraharmotrema karinganiense Dutton & Bullard n. sp. (Digenea: Liolopidae) from the intestine of the intestine of the serrated hinged terrapin, Pelusios sinuatus (Smith 1838) (Pleurodira: Pelomedusidae). (7) Tegumental scales in antero-dextral ventral body surface, ventral view, light micrograph. (8) Tegumental scales on ventral body surface posterior to oral sucker, ventral view, light micrograph. (9) Tegumental scales in same position as in Fig. 8 (showing exposed tips of scales only), ventral view, scanning electron micrograph.
Figs. 5–6. Paraharmotrema karinganiense Dutton & Bullard n in Paraharmotrema karinganiense n. gen., n. sp. (Digenea: Liolopidae) infecting the intestine of serrated hinged terrapin (Pelusios sinuatus), east African black mud turtle (Pelusios subniger), and South African helmeted turtle (Pelomedusa galeata) and a phylogenetic hypothesis for liolopid genera
Figs. 5–6. Paraharmotrema karinganiense Dutton & Bullard n. sp. (Digenea: Liolopidae) from intestine of serrated hinged terrapin, Pelusios sinuatus (Smith 1838) (Pleurodira: Pelomedusidae). (5) Ventral sucker, ventral view, scanning electron micrograph. (6) Ventral sucker, ventral view, light micrograph.
Figs. 1–2. Paraharmotrema karinganiense Dutton & Bullard n in Paraharmotrema karinganiense n. gen., n. sp. (Digenea: Liolopidae) infecting the intestine of serrated hinged terrapin (Pelusios sinuatus), east African black mud turtle (Pelusios subniger), and South African helmeted turtle (Pelomedusa galeata) and a phylogenetic hypothesis for liolopid genera
Figs. 1–2. Paraharmotrema karinganiense Dutton & Bullard n. sp. (Digenea: Liolopidae). (1) Body of adult (holotype, USNM No. 1659278) from intestine of serrated hinged terrapin, Pelusios sinuatus (Smith 1838) (Pleurodira: Pelomedusidae), ventral view. (2) Body of juvenile (paratype, USNM No. 1659285) from intestine of east African black mud turtle, Pelusios subniger (Bonnaterre, 1789) (Pleurodira: Pelomedusidae), dorsal view. Oral sucker (os), pharynx (ph), nerve commissure (nc), excretory system (es), sinistral caecum (sc), ventral sucker (vs), vitellarium (vr), cirrus sac (cs), metraterm (m), vas deferens (vd), anterior vas efferens (ave), anterior testis (at), uterus (u), posterior vas efferens (pve), ovary (o), posterior testis (pt), and excretory pore (ep).
Figs. 3–4. Paraharmotrema karinganiense Dutton & Bullard n in Paraharmotrema karinganiense n. gen., n. sp. (Digenea: Liolopidae) infecting the intestine of serrated hinged terrapin (Pelusios sinuatus), east African black mud turtle (Pelusios subniger), and South African helmeted turtle (Pelomedusa galeata) and a phylogenetic hypothesis for liolopid genera
Figs. 3–4. Paraharmotrema karinganiense Dutton & Bullard n. sp. (Digenea: Liolopidae) from intestine of serrated hinged terrapin, Pelusios sinuatus (Smith 1838) (Pleurodira: Pelomedusidae). (3) Female genitalia (holotype, USNM No. 1659278), ventral view. (4) Male genitalia (holotype, USNM No. 1659278), ventral view. Egg (e), ovary (o), oviduct (ov), ootype (oo), uterus (u), primary vitelline reservoir (pvr), dextral caecum (dc), transverse vitelline duct (tvd), sinistral caecum (sc), dextral excretory branch (deb), posterior vas efferens (pve), sinistral excretory branch (seb), posterior testis (pt), cirrus sac (cs), pars prostatica (pp), secondary bipartite internal seminal vesicle (sbisv), cirrus (c), initial bipartite internal seminal vesicle (ibisv), common genital pore (cgp), metraterm (m), vitellarium (vr), and vas deferens (vd).
Fig. 5 in A New Species of the Mud Shrimp Genus Axianassa (Crustacea: Decapoda: Gebiidea: Axianassidae) from Japan
Fig. 5. Axianassa japonica sp. nov., holotype, male (cl 3.8 mm), CBM-ZC 12479, left thoracic appendages. A, third maxilliped, lateral view; B, same, coxa to ischium, dorsal view; C, first pereopod, lateral view; D, same, dactylus, lateral view (setae omitted); E, third pereopod, lateral view; F, same, dactylus, lateral view; G, fourth pereopod, lateral view; H, same, dactylus, lateral view; I, fifth pereopod, lateral view; J, same, propodus and dactylus, flexor view; K, same, dactylus, extensor view. Scale bars: 0.5 mm.
Fig. 2 in A New Species of the Mud Shrimp Genus Axianassa (Crustacea: Decapoda: Gebiidea: Axianassidae) from Japan
Fig. 2. Axianassa japonica sp. nov., holotype, male (cl 3.8 mm), CBM-ZC 12479. A, carapace, dorsal view (setae omitted); B, anterior part of carapace and cephalic appendages, dorsal view; C, same, lateral view; D, telson, dorsal view; E, uropod, dorsal view (perpendicular) (marginal setae omitted). Scale bar: 1 mm for A; 0.5 mm for B–E.
Fig. 1 in A New Species of the Mud Shrimp Genus Axianassa (Crustacea: Decapoda: Gebiidea: Axianassidae) from Japan
Fig. 1. Axianassa japonica sp. nov., holotype, male (cl 3.8 mm), CBM-ZC 12479, entire animal in lateral view. Scale bar: 1 mm.
Fig. 3 in A New Species of the Mud Shrimp Genus Axianassa (Crustacea: Decapoda: Gebiidea: Axianassidae) from Japan
Fig. 3. Axianassa japonica sp. nov., holotype, male (cl 3.8 mm), CBM-ZC 12479, various parts from left side. A, mandible, inner view; B, same, outer view; C, maxillule, outer view; D, maxilla, outer view; E, first maxilliped, outer view; F, second maxilliped, outer view; G, epipod of third maxilliped, lateral view; H, epipod of first pereopod, lateral view; I, epipod of fourth pereopod, lateral view. Scale bars: 0.5 mm.
FIG. 5 in Mud lobster Thalassina Latreille, 1806 (Decapoda: Gebiidea: Thalassinidae), its Cenozoic occurrences in Italy and palaeobiogeography
FIG. 5. — Disputed fossil occurrences of Thalassina Latreille, 1806 (see the text for more details): A, Thalassina grandidactylus Robineau-Desvoidy, 1849 from the 'Neocomian' of France (refigured from Robineau-Desvoidy 1849: pl. 5, fig. 16); B, Thalassina sp. from the Pliocene of Italy (refigured from Ristori 1891: pl. 1, fig. 16); C, Thalassina sp. from the Pliocene of Italy (refigured from Ristori 1891: pl. 1, fig. 17).
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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.