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opennotspecifiedMar 2020View details →

FIGS. 100–104. Ovaskella ovaskae and Vancouvereuma shawi. Figs. 100, 101. Ovaskella sinuosa. Fig. 100. Anterior gonopods, posterior view. Fig. 101. Right posterior gonopod coxite, posterior view. Figs. 102–104. Vancouvereuma shawi. Fig. 102. Anterior gonopods, posterior view. Fig. 103. Right posterior gonopod coxite, posterior view. Fig. 104 in The millipede family Conotylidae in northwestern North America, with a complete bibliography of the family (Diplopoda, Chordeumatida, Heterochordeumatidea, Conotyloidea)

FIGS. 100–104. Ovaskella ovaskae and Vancouvereuma shawi. Figs. 100, 101. Ovaskella sinuosa. Fig. 100. Anterior gonopods, posterior view. Fig. 101. Right posterior gonopod coxite, posterior view. Figs. 102–104. Vancouvereuma shawi. Fig. 102. Anterior gonopods, posterior view. Fig. 103. Right posterior gonopod coxite, posterior view. Fig. 104. Posterior gonopods, posterior view.

opencc-zeroAug 2020View details →

Data from: Spatiotemporal variation in completeness of the early cynodont fossil record and its implications for mammalian evolutionary history

Mammals are the only surviving group of Cynodontia, a synapsid clade that first appears in the fossil record in the late Permian, ~260 million years ago. Here, using three metrics that capture skeletal completeness, we quantify the quality of the early cynodont fossil record in time and space to evaluate the impact of sampling and preservational biases on our understanding of the group's evolutionary history. There is no consistent global sampling signal for early cynodonts. Completeness of the cynodont fossil record increases across the Permian/Triassic boundary, peaking in the Early–early Late Triassic. This peak is dominated by specimens from southern Africa and South America, where a highly seasonal climate likely favoured preservation. Completeness is generally lower thereafter, correlated with a shift from a Gondwanan to a predominantly Laurasian fossil record. Phylogenetic and stratigraphic congruence in early cynodonts is high, although their fossil record exhibits less skeletal completeness overall than other tetrapod clades, including the contemporaneous anomodont synapsids. This discrepancy could be due to differences in the diagnosability of their fossils, especially for small-bodied species. Establishing the timing and assembly of derived ('mammalian') anatomical features in Cynodontia is obscured by sampling. Two of the major nodes at which acquisition of mammalian features is concentrated (Cynodontia and Mammaliamorpha) suffer from lengthy intervals of poor sampling prior to becoming abundant parts of tetrapod faunas. Low completeness in these intervals limits our ability to determine when certain 'key' mammalian characteristics evolved, or to identify the selective pressures that might have driven their origins.

opencc-by-4.0Sep 2020View details →

Database of partially and completely buried craters in the northern smooth plains of Mercury

This table is the database of all the partially and completely buried craters identified in the northern smooth plains of Mercury. Crater classes: A: rim-completely-exposed craters in smooth plains; B: rim-completely-exposed craters on smooth-plains/cratered-terrain boundaries; C: rim-partially-exposed craters in smooth plains; D: rim-partially-exposed craters on smooth-plains/cratered-terrain boundaries;  E: rim-completely-buried craters in smooth plains.

opencc-zeroAug 2020View details →

House mouse Mus musculus dispersal in East Eurasia inferred from 98 newly determined complete mitochondrial genome sequences

<div> The Eurasianhouse mouse Mus musculusis 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, M. m. musculus (MUS) and M. m. castaneus (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. </div>

opencc-zeroSep 2020View details →

Data from: The first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (Testudines: Geoemydidae): characterization and comparative analysis

Characterization of complete mitogenome is a widely used genomics study for species delineation and evolutionary research. However, the sequences and structural motifs contained within the mitogenome have been rarely examined to understand the phylogeny and evolutionary history among Testudines. Hence, the mitogenomic features of several Testudines taxa are still anonymous to the scientific communities. The present study decodes the first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (16,657 bp) by using next-generation sequencing. This denovo assembly encodes 37 genes: 13 protein coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA (rRNAs), and one control region (CR). The mitogenome contained 19 intergenic spacer and six overlapping regions. Most of the genes were encoded on majority strand, except for one PCG (NADH dehydrogenase subunit 6) and eight tRNAs. Most of the PCGs were started with an ATG initiation codon, except for cytochrome oxidase subunit 1 with 'GTG' and NADH dehydrogenase subunit 5 with 'ATA'. The termination codons, 'TAA' and 'AGA' were observed in NADH dehydrogenase subunit 4l and NADH dehydrogenase subunit 6 respectively. The Relative Synonymous Codon Usage analysis revealed the maximum abundance of Alanine, Isoleucine, Leucine, and Threonine. The non-synonymous/synonymous ratios were <1 in all PCGs, which indicates strong negative selection among all Geoemydid species. The study also found the typical cloverleaf secondary structure in most of the tRNA genes, except for Serine (trnS1) with lack of the conventional DHU arm. The Wobble base pairing was observed in the different stems (DHU, acceptor, and anticodon) of 11 tRNAs. The comparative study of Geoemydid mitogenomes revealed the occurrence of tandem repeats was frequent in the 3´ end of CR. Further, two copies of a unique tandem repeat 'TTCTCTTT' were identified in P. tentoria. The Bayesian and Maximum Likelihood phylogenetic trees using concatenation of 13 PCGs revealed the close relationships of P. tentoria with Batagur trivittata in the studied dataset. All the Geoemydid species showed distinct clustering with high bootstrap support congruent with previous evolutionary hypotheses. We suggest that the generations of more mitogenomes of Geoemydid species, especially for Batagurinae subfamily, are required to improve our understanding their in-depth phylogenetic and evolutionary relationships.

FIG. 4 in The complete mitochondrial genome of the Eurasian wryneck Jynx torquilla (Aves Piciformes: Picidae) and its phylogenetic inference

FIG. 4. Phylogenetic trees of 17 piciform species based on the amino acid dataset. The numbers abutting branches refer to Bayesian posterior probabilities (left) and ML bootstraps (right), ‾ not recovered. Branch lengths and topology are from the BI analysis. Halcyon pileata (Coraciiformes) was used to root the trees as an outgroup.

FIG. 2 in The complete mitochondrial genome of the Eurasian wryneck Jynx torquilla (Aves Piciformes: Picidae) and its phylogenetic inference

FIG. 2. Genetic distance within subfamily, between subfamily and family. Each boxplot represents the P distance based on the nucleotide and the amino acid datasets from 13 mitochondrial PCGs. Lower horizontal bar represents smallest observation, lower edge of rectangle represents 25 percentile, central bar within rectangle represents median, upper edge of rectangle represents 75 percentile, upper horizontal bar represents largest observation.

FIG. 1 in The complete mitochondrial genome of the Eurasian wryneck Jynx torquilla (Aves Piciformes: Picidae) and its phylogenetic inference

FIG. 1. Circular map of the J. torquilla mitogenome. The inner circle shows the GC content, which is calculated based on a window-sliding method. The outer circle shows the gene features, orange for rRNA, red for tRNA, and blue for CDS. Genes inside the circle (on the J strand) are transcribed clockwise, while the outsides (on the N strand) are transcribed counterclockwise.

FIG. 3 in The complete mitochondrial genome of the Eurasian wryneck Jynx torquilla (Aves Piciformes: Picidae) and its phylogenetic inference

FIG. 3. Phylogenetic trees of 17 piciform species based on the nucleotide dataset inferred from Bayesian inference (a) and maximum likelihood (b). The numbers abutting branches refer to Bayesian posterior probabilities (BPP) and bootstrap support (BS). Halcyon pileata (Coraciiformes) was used to root the trees as an outgroup.

opencc-zeroNov 2020View details →

Near-complete sequence of a novel reovirus genome identified from Callinectes sapidus

The Atlantic blue crab, Callinectes sapidus, is an estuarine keystone species that functions as both predator and prey in food webs and supports a multi-million dollar fishery along the western Atlantic coast from the US mid-Atlantic to southern Brazil. Throughout their range, blue crabs are host to viral, bacterial, fungal, protozoan, and metazoan pathogens. Reoviruses are non-enveloped icosahedral viruses with genomes comprised of 9 to 12 segments of linear double-stranded RNA (dsRNA). They have been found in diverse host species including brachyuran crustaceans. This work describes the sequence of a novel reovirus genome, discovered in Callinectes sapidus. The double-stranded RNA genome of CsRV2 consists of 12 segments that encode 13 putative proteins. High nucleotide sequence identity with Eriocheir sinensis Reovirus 905 revealed this virus belongs to Cardoreovirus within the Reoviridae family.

opencc-by-4.0Nov 2020View details →

Temporal Knowledge Base Completion: New Algorithms and Evaluation Protocols

This project contains datasets used for Temporal Knowledge Base Completion (TKBC) paper [1]. Find more details here: https://github.com/dair-iitd/tkbi [1] "<a href="https://arxiv.org/abs/2005.05035">Temporal Knowledge Base Completion: New Algorithms and Evaluation Protocols</a>" Jain, Prachi*, Sushant Rathi*, Mausam and Soumen Chakrabarti. EMNLP 2020.

opencc-by-4.0Dec 2020View details →

Complete set of raw and processed datasets, as well as associated Jupyter notebooks for analysis, associated with manuscript entitled: "The MOUSE project: a practical approach for obtaining traceable, wide-range X-ray scattering information"

This dataset is a complete set of raw, processed and analyzed data, complete with Jupiter notebooks, associated with the manuscript mentioned in the title.  In the manuscript, we provide a ``systems architecture''-like overview and detailed discussions of the methodological and instrumental components that, together, comprise the "MOUSE" project (Methodology Optimization for Ultrafine Structure Exploration). Through this project, we aim to provide a comprehensive methodology for obtaining the highest quality X-ray scattering information (at small and wide angles) from measurements on materials science samples.

FIGURE 6 in Towards completion of the species inventory of small-sized leaf-tailed geckos: two new species of Uroplatus from northern Madagascar

FIGURE 6. Individuals of Uroplatus fivehy sp. nov. from the type locality (Sorata) photographed in life. A, B and E, males (attribution to voucher number uncertain); C, D, G, females (attribution to voucher number uncertain); F, female paratype (ZSM 1722/2012) from Sorata; H, male holotype (ZSM 1721/2012) from Sorata showing shape and size of the tail.

FIGURE 8 in Towards completion of the species inventory of small-sized leaf-tailed geckos: two new species of Uroplatus from northern Madagascar

FIGURE 8. Preserved holotypes of Uroplatus fangorn sp. nov. (ZSM 79/2005) and U. fivehy sp. nov. (ZSM 1721/2012).

FIGURE 5 in Towards completion of the species inventory of small-sized leaf-tailed geckos: two new species of Uroplatus from northern Madagascar

FIGURE 5. Individuals of Uroplatus fangorn sp. nov. photographed in life. A, Male holotype (ZSM 79/2005) from Marojejy. B, C, D, male paratype (ZSM 644/2014) from Andrevorevo. E, F, G, female paratype (UADBA-R 70054 / DRV 6281), from Andrevorevo.

FIGURE 2 in Towards completion of the species inventory of small-sized leaf-tailed geckos: two new species of Uroplatus from northern Madagascar

FIGURE 2. Haplotype networks of nuclear genes. Colors correspond to species; circles are scaled according to the number of samples per haplotype; inferred intermediate steps between haplotypes are represented by small black circles.

FIGURE 4 in Towards completion of the species inventory of small-sized leaf-tailed geckos: two new species of Uroplatus from northern Madagascar

FIGURE 4. Morphological differentiation between Uroplatus fangorn sp. nov., U. fivehy sp. nov., and their closest relative, U. finiavana. The upper panel shows boxplots (median, quartiles, minimum/maximum and outliers) for selected meristic and morphometric variables and ratios; asterisks mark comparisons between U. fivehy and U. finiavana that were significant in Mann-Whitney U tests (* P <0.05; ** P <0.01). No statistical comparisons were performed for U. fangorn due to low sample size (N = 3). For original values of measurements, see Table 1. The lower panel shows intact (not regenerated) tails of individuals of the three species, illustrating differences in size and shape between species and sexes (all tails from males except where indicated as females).

FIGURE 1 in Towards completion of the species inventory of small-sized leaf-tailed geckos: two new species of Uroplatus from northern Madagascar

FIGURE 1. Bayesian inference phylogenetic tree of the Uroplatus ebenaui group based on a 2686 bp alignment of five concatenated mitochondrial and nuclear gene fragments (ND4, 12S rRNA, 16S rRNA, COX1, CMOS). Posterior probability values are shown on the nodes (omitted for most shallow nodes). Uroplatus alluaudi was used as the outgroup (not shown).

FIGURE 7 in Towards completion of the species inventory of small-sized leaf-tailed geckos: two new species of Uroplatus from northern Madagascar

FIGURE 7. Individuals of Uroplatus fivehy sp. nov. photographed in life. A, male paratype ZSM 634/2009 from Angozongahy Campsite, Makira. B, additional individual from Angozongahy (attribution to voucher number uncertain). C, D, female from Angozongahy (attribution to voucher number uncertain). E, male from Marotandrano (attribution to voucher number uncertain); note unpigmented oral mucosa in F.

FIGURE 3 in Towards completion of the species inventory of small-sized leaf-tailed geckos: two new species of Uroplatus from northern Madagascar

FIGURE 3. Map of northern Madagascar showing reliable locality records of Uroplatus fangorn sp. nov., U. fivehy sp. nov., and their closest relative, U. finiavana. Colors in map show remaining primary vegetation following the Madagascar Vegetation Mapping Project carried out from 2003–2006 (Moat & Smith 2007); green is humid forest (rainforest), reddish tones are deciduous forest and spiny forest-thicket.