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ICECAP-2 consortium bed elevation model for Princess Elizabeth Land, East Antarctica
<p>We present a new topographic digital elevation model (DEM) for Princess Elizabeth Land (PEL) – the last remaining region in Antarctica to be surveyed. The DEM covers an area of 899,730 km2 and was established from new aero geophysical data collected by the ICECAP-2 consortium, led by the Polar Research Institute of China, from four different surveys since 2015. Two products are available; (1) 500 m bed elevation model; and (2) 500 m ice thickness model. The mass conservation (MC) method is used to infer ice thickness DEM across faster-flowing (>30 m yr-1) regions of the ice sheet, and streamline diffusion at slower-flowing areas. The ice thickness DEM is then integrated with the ice surface DEM from the Reference Elevation Model of Antarctica (Howat, et al., 2019) to generate the bed elevation model. Together with BedMachine Antarctica, and Bedmap2, this new bed DEM for PEL completes the first-order measurement of subglacial Antarctica – an international mission that began 70 years ago. </p>
Data from: A strong east-west Mediterranean divergence supports a new phylogeographic history of the carob tree (Ceratonia siliqua, Leguminosae) and multiple domestications from native populations
Aim: Phylogeography of fruit trees is challenging due to the recurrent exchanges between domesticated and wild populations. Here we tested the eastern refugium hypothesis (ERH) for the carob tree, Ceratonia siliqua, which supports its natural and domestication origins in the Eastern Mediterranean and a feral origin in the West. Location: Mediterranean basin Taxon: Ceratonia siliqua L., Leguminosae Methods: Divergence time of the divergence between the carob tree and its sister species (C. oreothauma) was estimated based on two nuclear and one plastid sequences. Variation from four plastid regions and 17 nuclear microsatellite loci were used to decipher genetic structure in the carob tree and to test coalescent-based models by an Approximate Bayesian Computation (ABC) approach. We assessed our hypotheses by examining palaeobotanical records and hindcasting the past distribution of the carob tree at the Mid-Holocene, Last Glacial Maximum (LGM) and Last Interglacial (LIG) using species distribution modelling (SDM). Results: The split between C. oreothauma and C. siliqua was estimated at 6.4 Ma, and a first divergence within C. siliqua at 1.3 Ma. After a presence since the Oligocene, Ceratonia was found in the Western and the Eastern Mediterranean in the fossil records during the Pleistocene. Plastid and nuclear markers, characterized by low allelic richness, revealed a strong west-east genetic structuring. Approximate Bayesian computation (ABC) analyses rejected the ERH. Main conclusions: Our study supports a severe population decline during LIG. The strong west-east divergence and the occurrence of four lineages within C. siliqua provided support for a new hypothesis of multiple domestications of the carob tree from native populations throughout the Mediterranean basin.
ICECAP-2 consortium processed airborne ice thickness data from the Princess Elizabeth Land, East Antarctica
<p>Airborne ice thickness data from the Princess Elizabeth Land (PEL), East Antarctica was collected in four separate seasons. During the first ICECAP2 season (2015/16), a survey acquiring exploratory ‘fan-shaped’ radial profiles to maximize range and data return on each flight was completed across the broadly unknown region of PEL. These flight lines extend from the coastal Progress Station to the interior ice-sheet divide at Ridge B. In the second and third seasons (2016/17 and 2017/18), a survey ‘grid’ was completed, targeting enhanced resolution over a proposed subglacial lake and a series of basal canyons (Jamieson et al., 2016). In the fourth season (2018/19), a few additional transects were completed to fill the largest data gaps within aircraft range. Field data acquisition was achieved using the “Snow Eagle 601” aero geophysical platform; a BT-67 airplane operated by the Polar Research Institute of China for the Chinese National Antarctic Research Expedition (CHINARE) program. The suite of instruments configured on the airplane include a phase-coherent radio-echo sounder system, operating at a central frequency of 60 MHz and a peak power of 8 kW, making it capable of penetrating deep (>3 km) ice in Antarctica. After applying coherent integration and pulse compression at a bandwidth of 15 MHz, which gave an along-track spatial sampling rate and a vertical resolution of ~10 m and ~5.6 m, respectively.</p>
SCINDA GPS and UHF data supporting analysis in "On the Generation of an Unseasonal EPB Over South East Asia"
<p>This dataset contains ground-based GPS ionospheric scintillation data collected from Bandung, Indonesia during July 2014. This GPS receiver is part of the Scintillation Network Decision Aid (SCINDA) network (Groves et al., 1997). This particular dataset supports the analysis conducted in Currie et al. (2020).</p> <p><br> Currie, J. L., B. A. Carter, J. Retterer, T. Dao, R. Pradipta, R. Caton, K. Groves, Y. Otsuka, T. Yokoyama, K. Hozumi, T Le Truong, M. Terkildsen (2020), On the Generation of an Unseasonal EPB Over South East Asia, Submitted to JGR: Space Physics, Sept 2020.</p> <p>Groves, K.M., S. Basu, E. J. Weber, M. Smitham, H. Kuenzler, C.E. Valladares, R. Sheehan, E. MacKenzie, J.A. Secan, P. Ning, W.J. McNeill, D.W. Moonan, and M.J. Kendra (1997), Equatorial scintillation and systems support, Radio Science, 32, 2047-2064, doi:10.1029/97RS00836.</p>
Whole genome sequence analysis of porcine astroviruses reveals novel genetically diverse genotypes circulating in East African smallholder pig farms
<p>Supplementary materials for the porcine astrovirus study in East Africa.</p> <p><strong>Table S1</strong>: Pairwise comparison of nucleotide sequence identities of the complete (near complete, U460) genomes of the seven (7) astrovirus field strains (bold) and with sequences of other astroviruses available in GenBank </p> <p><strong>Table S2</strong>. Summary of nucleotide sequence identity matrix of the capsid protein (ORF2) among the seven (7) astroviruses field strains (bold) and the known reference strains in the GenBank using Clustal Omega</p> <p><strong>Table S3</strong>. Summary of amino acid sequence identity matrix of the capsid protein (ORF2) among the 7 astroviruses field strains (bold) and the known reference strains in the GenBank using Clustal Omega</p> <p><strong>Table S4</strong>: Estimates of evolutionary divergence between the East African PoAstVs and selected known AstV in the GenBank based on the amino acid sequences of complete ORF2 protein. The number of amino acid differences per site from between sequences is shown. Standard error estimate(s) are shown above the diagonal for our strains.</p> <p><strong>Table S5</strong>. Recommended potential linear antigenic epitopes predicted inside capsid protein (ORF2) of our field strains by SVMTriP web-based tool and corresponding antigenicity predicted by VaxiJen software</p>
House mouse Mus musculus dispersal in East Eurasia inferred from 98 newly determined complete mitochondrial genome sequences
<div> <p><span><span><span><span><span><span><span><span><span><span><span>The Eurasianhouse mouse <i>Mus musculus</i>is useful for tracing prehistorical human movement related to the spread of farming. We determined whole mitochondrial DNA (mtDNA) sequences (ca. 16,000 bp) of 98 wild-derived individuals of two subspecies, <i>M</i>. <i>m</i>. <i>musculus </i>(MUS) and <i>M</i>. <i>m</i>. <i>castaneus </i>(CAS). We revealed directional dispersals reaching as far asthe Japanese Archipelagofrom their homelands. Our phylogenetic analysis indicated that the eastward movement of MUS was characterised by five step-wise regional extension events: 1) broad spatial expansion into eastern Europe and the western part of western China, 2) dispersal to the eastern part of western China, 3) dispersal tonorthern China, 4) dispersal to the Korean Peninsula and 5) colonisation and expansion in the Japanese Archipelago. These events were estimated to have occurred during the last 2,000–18,000 years. The dispersal of CAS was characterised by three events: initial divergences(ca. 7,000–9,000 years ago) of haplogroups in northern most China and the eastern coast of India, followed by two population expansion events that likely originated from the Yangtze River basinto broad areas of South and Southeast Asia, including Sri Lanka, Bangladesh and Indonesia (ca. 4,000–6,000 years ago) and to Yunnan, southern China and the Japanese Archipelago (ca. 2,000–3,500). This study provides a solid framework for the spatiotemporal movementof the human-associated organisms in Holocene Eastern Eurasia using whole mtDNA sequences, reliable evolutionary rates and accurate branching patterns. The information obtained here contributes to the analysis of a variety of animals and plants associated with prehistoric human migration.</span></span></span></span></span></span></span></span></span></span></span></p> </div>
Data from: New taxa of Rhododendron tschonoskii alliance (Ericaceae) from East Asia
Three new taxa, Rhododendron sohayakiense Y. Watan. & T. Yukawa (Ericaceae), and its two varieties, var. kiusianum Y. Watan., T. Yukawa & T. Minamitani and var. koreanum Y. Watan. & T. Yukawa are described and illustrated from Japan and South Korea. They can be distinguished each other and from the other members of the R. tschonoskii alliance, i.e. R. tschonoskii, R. tetramerum, R. trinerve and R. tsusiophyllum, by the combination of leaf size, leaf morphologies including lateral nerves on abaxial leaf surface, corolla morphologies including number of corolla lobes, style length and anther form. Phylogenetic inferences based on chloroplast DNA and genome-wide sequences revealed that each of the three new taxa is monophyletic and they further form a clade. Distributions of the three taxa are also clearly separated each other and also from the other members of the R. tschonoskii alliance.
Supplementary material 1 from: Parapar J, Capa M, Nygren A, Moreira J (2020) To name but a few: descriptions of five new species of Terebellides (Annelida, Trichobranchidae) from the North East Atlantic. ZooKeys 992: 1-58. https://doi.org/10.3897/zookeys.992.55977
Table S1. Locality and collecting data, museum registration numbers and references to figures of Terebellides specimens
Supplementary material 2 from: Parapar J, Capa M, Nygren A, Moreira J (2020) To name but a few: descriptions of five new species of Terebellides (Annelida, Trichobranchidae) from the North East Atlantic. ZooKeys 992: 1-58. https://doi.org/10.3897/zookeys.992.55977
Table S2. List of COI sequences considered in present study (Group A), museum vouchers and GenBank accession numbers
FIGURE 42 in Integrative taxonomic review of the genus Synopsia Hübner, 1825 in the Middle East (Lepidoptera: Geometridae: Ennominae)
FIGURE 42. Map of Synopsia phasidaria phasidaria comb. nov., Synopsia phasidaria afghana comb. nov. and Synopsia centralis bona sp. showing the distribution of these taxa. Different symbols illustrated in the rectangle indicating on the type localities of the subspecies of Synopsia phasidaria phasidaria comb. nov..
FIGURES 37–40 in Integrative taxonomic review of the genus Synopsia Hübner, 1825 in the Middle East (Lepidoptera: Geometridae: Ennominae)
FIGURES 37–40. Female genitalia and details characters of Synopsia species. 37: Synopsia sociaria (Italy, Naturns, g.prep. 0497/2019 D. Wanke; a: genitalia; b: signum; c: lamella antevaginalis); 38: Paratype of Synopsia phasidaria mirabica syn. nov. of Synopsia phasidaria phasidaria (Iran, Kuh i Mirabi, g.prep. 0502/2020 D. Wanke); 39: Synopsia phasidaria phasidaria comb. nov. (Iran, Azerbaijan-e-Gharbi, g.prep. 0299/2019 D. Wanke); 40a-d: signum of Synopsia phasidaria phasidaria comb. nov. showing the intraspecific variation (a: Turkey, Hakkari, g.prep. 0468/2019 D. Wanke; b: Iran, Lorestan, g.prep. 0478/2019 D. Wanke; c: Iran, Zanjan, g.prep. 0477/2019 D. Wanke; d: Iran, Yasuj, g.prep. 0486/2019 D. Wanke); 40e: lamella antevaginalis of Synopsia phasidaria phasidaria comb. nov. (Iran, Kendevan, g.prep. 0474/2019 D. Wanke). 37b-c and 40 out of scale. Scale-bar 1mm
FIGURE 41 in Integrative taxonomic review of the genus Synopsia Hübner, 1825 in the Middle East (Lepidoptera: Geometridae: Ennominae)
FIGURE 41. Maximum likelihood analysis of the two Synopsia species and 4 closely related genera (Chariaspilates, Angerona, Hypoxystis, Siona) based on COI 5' sequences (built with MEGA X; Kimura 2-parameter model; bootstrap method, 1000 replications). Symbols in S. phasidaria: Stars indicating on females with strongly bipectinate antennae; diamonds indicating on females with shortly bipectinate antennae.
FIGURE 36 in Integrative taxonomic review of the genus Synopsia Hübner, 1825 in the Middle East (Lepidoptera: Geometridae: Ennominae)
FIGURE 36. Details of the male genitalia capsule and the aedeagus of Synopsia phasidaria phasidaria comb. nov., showing the intraspecific variation. A: distal margin of the harpe; B1: gnathos from posterior view; B2-3: gnathos from ventral view, C1-6: cornuti on the vesica.
FIGURES 30–32 in Integrative taxonomic review of the genus Synopsia Hübner, 1825 in the Middle East (Lepidoptera: Geometridae: Ennominae)
FIGURES 30–32. Male genitalia of Synopsia species. 30: Holotype of Synopsia phasidaria alvandi syn. nov. of Synopsia phasidaria phasidaria (Iran, Alvand, g.prep. EP Wiltshire 1470, NHMUK 010920110); 31: Holotype of Synopsia phasidaria mirabica syn. nov. of Synopsia phasidaria phasidaria (Iran, Kuh i Mirabi, g.prep. 0501/2020 D. Wanke); 32: Synopsia phasidaria phasidaria comb. nov. (Iran, Zanjan, g.prep. 0106/2018 D. Wanke); a = genitalia capsule; b = aedeagus. Scale-bar 1 mm.
FIGURES 5–26 in Integrative taxonomic review of the genus Synopsia Hübner, 1825 in the Middle East (Lepidoptera: Geometridae: Ennominae)
FIGURES 5–26. Wing pattern of Synopsia species. 5-7: S. sociaria (5: France, Le Meés; 6: Armenia, Syunik, g.prep. 0230/2019 D. Wanke; 7: Italy, Naturns, g.prep. 0497/2019 D. Wanke); 8-22: Nominotypical subspecies; 8: Paratype of Synopsia phasidaria ardschira syn. nov. of Synopsia phasidaria phasidaria (Iran, Fars, g.prep. 11026); 9: Holotype of Synopsia phasidaria alvandi syn. nov. of Synopsia phasidaria phasidaria (Iran, Alvand, g.prep. EP Wiltshire 1470, NHMUK 010920110); 10: Holotype of Synopsia phasidaria jodes syn. nov. of Synopsia phasidaria phasidaria (Iran, Demawend, g.prep. 7100, NHMUK 014172449); 11: Holotype of Synopsia phasidaria mirabica syn. nov. of Synopsia phasidaria phasidaria (Iran, Kuh i Mirabi, g.prep. 0501/2020 D. Wanke); 12: Paratype of Synopsia phasidaria mirabica syn. nov. of Synopsia phasidaria phasidaria (Iran, Kuh i Mirabi, g.prep. 0502/2020 D. Wanke); 13-22: Synopsia phasidaria phasidaria comb. nov. (13: Turkey, Hakkari, g.prep. 0466/2019 D. Wanke; 14: Armenia, Yeranos, g.prep. 0381/2019 D. Wanke; 15: Iran, Zanjan, g.prep. 0106/2018 D. Wanke; 16: Iran, Zanjan, g.prep. 0477/2019 D. Wanke; 17: Iran, Zanjan, g.prep. 0105/2018 D. Wanke; 18: Iran, Tehran, g.prep. 0472/2019 D. Wanke; 19: Iran, Fars, Sine Sefid, g.prep. 11027 [no type specimen of Synopsidia phasidaria chiraza was traced in the collection of Brandt, except this specimen labeled as Synopsidia phasidaria chiraza by Brandt]; 20: Iran, Yasuj, g.prep. 0485/2019 D. Wanke; 21: Iran, Golestan, g.prep. 0483/2019 D. Wanke; 22: Iran, Lorestan, g.prep. 0478/2019 D. Wanke); 23: Holotype of Synopsia phasidaria afghana comb. nov. (Afghanistan, Kabul); 24: Paratype of Synopsia phasidaria afghana comb. nov. (Afghanistan, Kabul, g.prep. WW216); 25: Holotype of Synopsia centralis bona sp. (Iran, Fars, g.prep. EP Wiltshire 1467, NHMUK 010920114); 26: Synopsia centralis bona sp. (Iran, Fars, NHMUK 014172450); a = upperside; b = underside. Scale-bar 1cm.
FIGURES 27–29 in Integrative taxonomic review of the genus Synopsia Hübner, 1825 in the Middle East (Lepidoptera: Geometridae: Ennominae)
FIGURES 27–29. Male genitalia of Synopsia species. 27: Synopsia sociaria (Kazakhstan, NE Rudnichnyy, g.prep. 0103/2018 D. Wanke); 28: Synopsia sociaria (Armenia, Syunik, g.prep. 0230/2019 D. Wanke); 29: Paratype of Synopsia phasidaria ardschira syn. nov. of Synopsia phasidaria phasidaria (Iran, Fars, g.prep. 11026); a = genitalia capsule; b = aedeagus. Scale-bar 1 mm.
FIGURE 4 in Integrative taxonomic review of the genus Synopsia Hübner, 1825 in the Middle East (Lepidoptera: Geometridae: Ennominae)
FIGURE 4. Comparison of the forewing venation of Synopsia and related genera. (Species taken for drawing: A: Synopsia sociaria; B: Chariaspilates formosaria; C: Phthonandria atrilineata indica; D: Angerona prunaria; E: Hypoxystis pluviaria; F: Siona lineata).
FIGURE 3 in Integrative taxonomic review of the genus Synopsia Hübner, 1825 in the Middle East (Lepidoptera: Geometridae: Ennominae)
FIGURE 3. Wing venation of male specimens of A: Synopsia (S. sociaria type species for the genus) and B: Synopsidia (S. phasidaria) syn. nov. of Synopsia. Note that both wing venations do not show significant differences.
FIGURES 33–35 in Integrative taxonomic review of the genus Synopsia Hübner, 1825 in the Middle East (Lepidoptera: Geometridae: Ennominae)
FIGURES 33–35. Male genitalia of Synopsia species. 33: Synopsia phasidaria phasidaria comb. nov. (Turkey, Hakkari, g.prep. 0466/2019 D. Wanke); 34: Paratype of Synopsia phasidaria afghana comb. nov. (Afghanistan, Kabul, g.prep. WW216); 35: Holotype of Synopsia centralis bona sp. (Iran, Fars, g.prep. EP Wiltshire 1467); a = genitalia capsule; b = aedeagus. Scale-bar 1mm
FIGURE 2 in Integrative taxonomic review of the genus Synopsia Hübner, 1825 in the Middle East (Lepidoptera: Geometridae: Ennominae)
FIGURE 2. SEM close-up photos of the two different forms of bipectinate antennae in female of Synopsia phasidaria comb. nov.. Photos A strongly bipectinate (A1 lateral, A2 ventral); B weakly bipectinate (B1 lateral, B2 ventral). Scale-bar 100 µm.
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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.