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FIGURE 7 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)
FIGURE 7. Austinixa cuestai sp. nov.; A–C, male paratype, cw 8.3 mm (ULLZ 5566); D–F ovigerous female paratype, cw 8.3 mm (ULLZ 5566); both from Nagualapa, Pacific coast of Nicaragua. A, male pleon; B, left first gonopod, sternal surface; C, left first gonopod tip, pleonal surface; D, right cheliped, internal; E, right cheliped, external; F, female pleon. Scale bars = 1.0 mm (A, B, D–F), 0.5 mm (C).
FIGURE 11 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)
FIGURE 11. Austinixa felipensis; A–C, male, cw 12.3 mm (ULLZ 5556); D–F, female cw 10.6 mm, both from San Felipe, Baja California, Mexico. A, male pleon; B, right first gonopod, sternal surface; C, right first gonopod tip, pleonal surface; D, left chela, external; E, left chela, internal. Scale bars = 1.0 mm (A, B, D–F), 0.5 mm (C).
FIGURE 9 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)
FIGURE 9. Austinixa roblesi sp. nov.; A–D, ovigerous female paratype, cw 9.8 mm (USNM 1558340); E, ovigerous female paratype, cw 9.4 mm (ULLZ 12115); F, female paratype, cw 6.6 mm (ULLZ 13143); all from Dangriga, Belize. A, carapace, dorsal; B, enlarged right side of carapace, dorsal; C, carapace frontal region, from anterior; D, right chela, internal; E, left chela, dorsal, F, female pleon. Scale bars = 1.5 mm (A), 1.0 mm (B–F).
FIGURE 5 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)
FIGURE 5. Austinixa artankeri sp. nov.; A, male paratype, cw 7.3 mm (UF 18916); B, male paratype, cw 8.5 mm (ULLZ 13732); C, D, male paratype, cw 6.2 mm (ULLZ 13731); E, ovigerous female paratype, cw 8.5 mm (UF 18928); F, female paratype, cw 8.8 mm (UF 18950); G, ovigerous female paratype, cw 9.0 mm (USNM 1558331); H, ovigerous female paratype, cw 5.8 mm (ULLZ 13644), all from Bocas del Toro, Caribbean coast of Panama. A, right chela, internal, setae not shown; B, male pleon; C, D, left first gonopod, pleonal surface, entire and enlarged tip; E, right chela, internal, setae not shown; left chela, internal, setae not shown. Scale bars = 1.0 mm (A, B, E–H), 0.5 mm (C), 0.25 mm (D).
FIGURE 3 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)
FIGURE 3. Distribution of the species of Austinixa Heard & Manning, 1997. In most cases, latitudinal ranges are shown. For A. cristata, the latitudinal range shown corresponds to the distribution on the Atlantic coast only. Specific locations are shown for records of A. cristata in the Gulf of Mexico, as well as for A. bragantina and three undescribed species (symbols as shown in legend). Only A. bragantina and A. leptodactyla were not included in the present phylogenetic analyses.
FIGURE 2 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)
FIGURE 2. Phylogeny of Pinnotheroidea, with emphasis on Austinixa Heard & Manning, 1997, inferred from Maximum Likelihood analysis of concatenated 1415 bp sequence of mitochondrial 16S/tRNA-Leu/NADH1 complex (705 bp), the mitochondrial 12S rRNA gene (293 bp) and nuclear histone 3 subunit (328 bp). Maximum Likelihood (ML) bootstrap, Bayesian (BAY) posterior probabilities and maximum parsimony (MP) bootstrap values are shown, in order ML/BAY/MP. "–" indicates a value lower than 50%. When all three values are the same, only one number is shown. If values are lower than 50% for all three, no number is shown. Letters and collection accession numbers follow the species name, to distinguish geographic origin and samples (see Material and methods for abbreviations). Modified from Palacios Theil et al. (2016) and generic assignments of some species of Pinnixa updated according to Palacios Theil & Felder (2020)
FIGURE 1 in Phylogeny of the genus Austinixa Heard & Manning, 1997, inferred from mitochondrial and nuclear molecular markers, with descriptions of three new species and redescription of Austinixa felipensis (Glassell, 1935) (Decapoda: Brachyura: Pinnotheridae)
FIGURE 1. Consensus tree for Austinixa Heard & Manning, 1997, inferred from Maximum Likelihood analysis of 821 bp sequence of mitochondrial 16S/tRNA-Leu/NADH1 gene complex. Bootstrap values higher than 50% indicated at internal nodes. Letters and collection accession numbers follow the species name, to distinguish geographic origin and samples (see Material and methods for abbreviations).
Time Course of Recovery for Performance Attributes and Circulating Markers of Muscle Damage Following a Rugby Union Match in Amateur Athletes
<p>Supplemental file 1 - Raw data associated with article titled "Time Course of Recovery for Performance Attributes and Circulating Markers of Muscle Damage Following a Rugby Union Match in Amateur Athletes" in MDPI's journal <em>Sports</em></p>
CLDF dataset derived from Tang and Her's "Quantitative typological data on classifiers and plural markers" from 2019
<p>Cite the source of the dataset as:</p> <blockquote> <p>Tang, Marc and One-Soon Her. 2019. Insights on the Greenberg-Sanches-Slobin Generalization: Quantitative typological data on classifiers and plural markers. Folia Linguistica, 53(2): 297-331. https://doi.org/10.1515/flin-2019-2013</p> </blockquote>
Data from: Friends and Family: a software program for identification of unrelated individuals from molecular marker data. And from: Genetic diversity, relatedness and inbreeding of ranched and fragmented Cape buffalo populations in southern Africa
The identification of related and unrelated individuals from molecular marker data is often difficult, particularly when no pedigree information is available and the data set is large. High levels of relatedness or inbreeding can influence genotype frequencies and thus genetic marker evaluation, as well as the accurate inference of hidden genetic structure. Identification of related and unrelated individuals is also important in breeding programmes, to inform decisions about breeding pairs and translocations. We present Friends and Family, a Windows executable program with a graphical user interface that identifies unrelated individuals from a pairwise relatedness matrix or table generated in programs such as COANCESTRY and GenAlEx. Friends and Family outputs a list of samples that are all unrelated to each other, based on a user-defined relatedness cut-off value. This unrelated data set can be used in downstream analyses, such as marker evaluation or inference of genetic structure. The results can be compared to that of the full data set to determine the effect related individuals have on the analyses. We demonstrate one of the applications of the program: how the removal of related individuals altered the Hardy-Weinberg equilibrium test outcome for microsatellite markers in an empirical data set. Friends and Family can be obtained from https://github.com/DeondeJager/Friends-and-Family.
Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers
<p>Introduction: Antimicrobial resistant (AMR) genes in bacteria are often carried on plasmids. Since these plasmids can spread the AMR genes between bacteria, it is important to know if the genes are located on highly transferable plasmids or in the more stable chromosomes. Whole genome sequence (WGS) analysis makes it easy to determine if a strain contains a resistance gene, however, it is not easy to determine if the gene is located on the chromosome or on a plasmid as genome sequence assembly generally results in 50-300 DNA fragments (contigs). With our newly developed prediction tool, we analyze the composition of these contigs to predict their likely source, plasmid or chromosomal. This information can be used to determine if a resistant gene is chromosomally located or on a plasmid. The tool is optimized for 19 different bacterial species, including Campylobacter, E. coli, and Salmonella, and can also be used for metagenomic assemblies.</p> <p>Methods: The tool identifies the number of chromosomal marker genes, plasmid replication genes and plasmid typing genes using CheckM and DIAMOND Blast, and determines pentamer frequencies and contig sizes per contig. A prediction model was trained using Random Forest on an extensive set of plasmids and chromosomes from 19 different bacterial species and validated on separate test sets of known chromosomal and plasmid contigs of the different bacteria. Results: Prediction of plasmid contigs was nearly perfect when calculated based on number of correctly predicted bases, with up to 99% specificity and 99% sensitivity. Prediction of small contigs remains difficult, since these contigs consists primarily of repeated sequences present in both plasmid and chromosome, e.g. transposases.</p> <p>Conclusion: The newly developed tool is able to determine if contigs are chromosomal or plasmid with a very high specificity and sensitivity (up to 99%) and can be very useful to analyze WGS data of bacterial genomes and their antimicrobial resistance genes.</p> <p>Plasmid databases can be downloaded from: http://klif.uu.nl/download/plasmid_db/</p> <p>Data used for training can be downloaded here: http://klif.uu.nl/download/plasmid_db/trainingsets2/</p>
QTL mapping and marker development for tolerance to sulfur phytotoxicity in melon (Cucumis Melo)
<p><span>Elemental sulfur is an effective, inexpensive fungicide for many foliar pathogens, but severe phytotoxicity prohibits its use on many melon varieties. Sulfur phytotoxicity causes chlorosis and necrosis of leaf tissue, leading to plant death in the most sensitive lines, while other varieties have little to no damage. A high-density, genotyping-by-sequencing (GBS)-based genetic map of a recombinant inbred line (RIL) population segregating for sulfur tolerance was used for a quantitative trait loci (QTL) mapping study of sulfur phytotoxicity in melon. One major (qSulf-1) and two minor (qSulf-8 and qSulf-12) QTL were associated with sulfur tolerance in the population. <a name="_Hlk40443716">The development of Kompetitive Allele-Specific PCR (KASP) markers developed across qSulf-1 decreased the QTL interval from 239 kb (cotyledons) and 157 kb (leaves) to 97 kb (both tissues). </a>The markers were validated for linkage to sulfur tolerance in a set of melon cultivars. These KASP markers can be incorporated into melon breeding programs for introgression of sulfur tolerance into elite melon germplasm.</span></p> <p> </p> <p> </p>
Data from: Predominant east to west colonisations across major oceanic barriers: insights into the phylogeographic history of the hydroid superfamily Plumularioidea, suggested by a mitochondrial DNA barcoding marker
We provide preliminary insights into the global phylogeographic and evolutionary patterns across species of the hydrozoan superfamily Plumularioidea (Cnidaria: Hydrozoa). We analysed 1114 16S sequences of 198 putative species of Plumularioidea collected worldwide. We investigated genetic connections and divergence in relation to present-day and ancient biogeographic barriers, climate changes and oceanic circulation. Geographical distributions of most species are generally more constrained than previously assumed. Some species able to raft are dispersed widely. Human-mediated dispersal explains some wide geographical ranges. Trans-Atlantic genetic connections are presently unlikely for most of the tropical-temperate species, but were probably more frequent until the Miocene-Pliocene transition, before restriction of the Tethys Sea and the Central American Seaway. Trans-Atlantic colonisations were predominantly directed westwards through (sub)tropical waters. The Azores were colonized multiple times and through different routes, mainly from the east Atlantic, at least since the Pliocene. Extant geminate clades separated by the Isthmus of Panama have predominantly Atlantic origin. Various ancient colonisations mainly directed from the Indian Ocean to the Atlantic, occurred through the Tethys Sea and around South Africa in periods of lower intensity of the Benguela upwelling. Thermal tolerance, population sizes, dispersal strategies, oceanic currents, substrate preference and land barriers are important factors for dispersal and speciation of marine hydroids.
Data from: Population genetic structures of two ecologically distinct species Betula platyphylla and B. ermanii inferred based on nuclear and chloroplast DNA markers
Climatic oscillations during the last glacial maximum (LGM) significantly affected the distribution patterns and genetic structure of extant plants. Northeast China (NEC) is a major biodiversity center in East Asia, and the influence of historical climate change on NEC populations is critical for understanding species responses to future climate change. However, only a few phylogeographic studies of cool-temperate deciduous tree species have been conducted in the area, and results are inconsistent for species with different niches or distribution areas. We employed multiple chloroplast and nuclear markers to investigate the genetic structure of two ecologically contrasting species, Betula platyphylla and B. ermanii, in NEC. Rare haplotypes were identified in the chloroplast genome of these species, and both exhibited high levels of nucleotide diversity based on a fragment of the nuclear gene G3PDH and microsatellites. Moreover, significant phylogeographic structure was detected for B. platyphylla, suggesting that these populations had recolonized from independent glacial refuges, whereas no genetic structure was found for B. ermanii.
Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in silico whole genome subtraction
<p>Background: Homologous sex chromosomes can differentiate over time because recombination is suppressed in the region of the sex determining locus, leading to the accumulation of repeats, progressive loss of genes that lack differential influence on the sexes and sequence divergence on the hemizygous homolog. Divergence in the non-recombining regions leads to the accumulation of Y or W specific sequence useful for developing sex-linked markers. Here we use <i>in silico</i> whole-genome subtraction to identify putative sex-linked sequences in the scincid lizard <i>Bassiana duperreyi</i> which has heteromorphic XY sex chromosomes.</p> <p>Results: We generated 96.7 x 10<sup>9</sup> 150 bp paired-end genomic sequence reads from a XY male and 81.4 x 10<sup>9</sup> paired-end reads from an XX female for <i>in silico</i> whole genome subtraction to yield Y enriched contigs. We identified 7 reliable markers which were validated as Y chromosome specific by polymerase chain reaction (PCR) against a panel of 20 males and 20 females.</p> <p>Conclusions: The sex of <i>B. duperreyi</i> can be reversed by low temperatures (XX genotype reversed to a male phenotype). We have developed sex-specific markers to identify the underlying genotypic sex and its concordance or discordance with phenotypic sex in wild populations of <i>B. duperreyi</i>. Our pipeline can be applied to isolate Y or W chromosome-specific sequences of any organism and is not restricted to sequence residing within single-copy genes. This study greatly improves our knowledge of the Y chromosome in <i>B. duperreyi</i> and will enhance future studies of reptile sex determination and sex chromosome evolution.</p>
Assigning the sex-specific markers via genotyping-by-sequencing onto the Y chromosome for a torrent frog Amolops mantzorum
<p><span>We use a genotyping-by-sequencing (GBS) approach to identify sex-linked markers in a torrent frog (<i>Amolops mantzorum</i>) using wild-caught individuals of 21 males and 19 females from the same population. A total of 141 putatively sex-linked markers were screened from 1,015,964 GBS tags through three approaches, respectively based on sex differences in allele frequencies, sex difference in heterozygosity, and sex-limited occurrence. With validations, 69 sex-linked markers were confirmed, all of which point to male heterogamety. The male specificity of eight sex markers was further verified by PCR amplifications with a large number of additional individuals covering the whole geographic distribution of the species. Y chromosome (No. 5) was microdissected under a light microscope, amplified by whole-genome amplification, and assembled a draft Y genome. 55 out of 69 sex-linked markers could be mapped to the Y chromosome assembly (i.e 79.7 %). Thus the chromosome 5 could be added as candidate chromosomes that particularly favored to recruit for sex determination than others among frogs. Three sex-linked markers that mapped on Y chromosome were aligned to three different promoter regions of <i>Rana rugosa</i> CYP19A1 gene, which might be considered as a candidate gene to trigger sex determination in <i>A</i>.<i> mantzorum</i>.</span></p>
Data from: Genetic variation and phylogeographic structure of Laodelphax striatellus in China based on microsatellite markers
<p>The small brown planthopper (SBPH)<i><span>, </span></i><i><span>Laodelphax striatellus</span></i> (Fallén) (Hemiptera: Delphacidae), is an important agricultural pest that has caused serious economic losses in the major rice-producing areas of China. To effectively manage this insect pest, we analyzed its genetic variation, genetic structure and population demographic history. We used nine nuclear microsatellite loci to investigate the genetic diversity and population genetic structure of SBPH at 43 sampling sites in China. High levels of genetic diversity and genetic differentiation among most populations were detected. Overall, neighbour-joining dendrograms, STRUCTURE and principal coordinate analysis (PCoA) revealed no genetically distinct groups and exhibited an admixed phylogeographic structure in China. Isolation by distance (IBD) and spatial autocorrelation analyses demonstrated no correlation between genetic distance and geographic distance. On the other hand, bottleneck analysis indicated that SBPH populations had not undergone severe bottleneck effects in these regions. This study provides useful data for resolving the genetic relationships and migration patterns of SBPH and thus contribute to developing effective management strategies for this pest.</p>
Data from: Population genetic structure and intraspecific genetic distance of Periplaneta americana (Blattodea: Blattidae) based on mitochondrial and nuclear DNA markers
<p>The American cockroach (<i>Periplaneta americana</i>) is a globally invasive pest that can cause significant economic loss and threaten human health. Although it is abundant and lives in close proximity to humans, few studies have investigated the genetic diversity of <i>P. americana</i>. Our study analyzed 1053 <i>P. americana</i> and other <i>Periplaneta</i> species' samples from different locations in China and the USA. A traditional tree-based method using 17 unique mitochondrial COI haplotypes of <i>P. americana</i> and 20 haplotypes of the other <i>Periplaneta</i> species accurately identified <i>P. americana</i> with a barcoding threshold of 5.1%. To identify the population genetic structure of <i>P. americana,</i> we investigated <i>wingless</i> gene and pooled them with obtained mtDNA data for a combined analysis. Although the genetic diversity of the USA group was relatively higher than the China group, the number of haplotypes and alleles of both groups was small. Molecular variance (AMOVA), intraspecific phylogeny, and haplotype networks indicated that <i>P. americana</i> had very little global genetic differentiation. The weak geographic genetic structure might reflect the human-mediated dispersal of <i>P. americana</i>. Despite no apparent phylogeographic assignment of mtDNA and nuclear lineages was observed in both BI trees, the integrated COI sequence data identified four distinct <i>P. americana</i> haplotype groups, showing four ancient maternal lineages of <i>P. americana</i> in China and the USA.</p>
SNPs markers of Trypoxylus dichotomus developed by using specific‐locus amplified fragment sequencing (SLAF‐seq) techniques
<p>The Japanese rhinoceros beetle Trypoxylus dichotomus is one of the largest beetle species in the world and is commonly used in traditional chinese medicine. Ten subspecies of T. dichotomus and a related Trypoxylus species (T. kanamorii) have been described throughout Asia, but their taxonomic delimitations remain problematic. To clarify issues such as taxonomy, and the degree of genetic differentiation of Trypoxylus populations, we investigated the genetic structure, genetic variability and phylogeography of 53 specimens of Trypoxylus species from 44 locations in five Asian countries (China, Japan, Korea, Thailand, and Myanmar). Using specific‐locus amplified fragment sequencing (SLAF‐seq) techniques, we developed 330,799 SLAFs over 114.16M reads, in turn yielding 46,939 high-resolution single nucleotide polymorphisms (SNPs) for genotyping.</p>
................................................................................................................................................. Fig. 3. SDSPAGE analysis of total bacterial protein extracts of the four roe deer isolates as well as other Bartonella species. Extracts of total bacterial protein were separated by SDSPAGE and stained with Coomassie brilliant blue. Lanes: M, molecular mass markers; 1, R1T; 2, R3; 3, R4; 4, R6; 5, Bartonella henselae; 6, Bartonella quintana; 7, Bartonella bacilliformis; 8, Bartonella elizabethae; 9, Bartonella clarridgeiae; 10, Bartonella alsatica; 11, Bartonella tribocorum; 12, Bartonella grahamii. in Bartonella schoenbuchii sp. nov., isolated from the blood of wild roe deer.
................................................................................................................................................. Fig. 3. SDSPAGE analysis of total bacterial protein extracts of the four roe deer isolates as well as other Bartonella species. Extracts of total bacterial protein were separated by SDSPAGE and stained with Coomassie brilliant blue. Lanes: M, molecular mass markers; 1, R1T; 2, R3; 3, R4; 4, R6; 5, Bartonella henselae; 6, Bartonella quintana; 7, Bartonella bacilliformis; 8, Bartonella elizabethae; 9, Bartonella clarridgeiae; 10, Bartonella alsatica; 11, Bartonella tribocorum; 12, Bartonella grahamii.
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.