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Fig. 1 in Notes on and Corrections to the Recent "A Revision of the North American Species of Euconnus (Napochus) Thomson, North of Mexico (Coleoptera: Staphylinidae: Scydmaeninae)" by K. H. Stephan, D. S. Chandler, S. T. O'Keefe, and E. G. Riley
Fig. 1. Correct version of Map 60 for Stephan et al. (2021).
[Data] Recent consumer OLED monitors can be suitable for vision science
<p>Monitor data collected using X-Rite i1Display Colorimeter and X-Rite i1Pro3 Spectrophotometer. 4 datasets for 2 OLED monitors (Asus, Samsung), 1 LED projector (VPixx PROPixx), and 1 LCD monitor (LG UltraGear).</p> <p>Each dataset contains luminance measurements of R, G, B channels and grayscale, pixel signal responses and waveforms that were recorded using OSRTT PRO CS (photodiodes). Luminance measurements include ramps, two channels saturated (OCS), filling factor (Average Pixel Level), and uniformity measurements.</p>
Data from: Russian wheat aphids (Diuraphis noxia) in China: native range expansion or recent introduction?
In this study, we explore the population genetics of the Russian wheat aphid (RWA) (Diuraphis noxia), one of the world's most invasive agricultural pests, in north-western China. We have analysed the data of 10 microsatellite loci and mitochondrial sequences from 27 populations sampled over 2 years in China. The results confirm that the RWAs are holocyclic in China with high genetic diversity indicating widespread sexual reproduction. Distinct differences in microsatellite genetic diversity and distribution revealed clear geographic isolation between RWA populations in northern and southern Xinjiang, China, with gene flow interrupted across extensive desert regions. Despite frequent grain transportation from north to south in this region, little evidence for RWA translocation as a result of human agricultural activities was found. Consequently, frequent gene flow among northern populations most likely resulted from natural dispersal, potentially facilitated by wind currents. We also found evidence for the long-term existence and expansion of RWAs in China, despite local opinion that it is an exotic species only present in China since 1975. Our estimated date of RWA expansion throughout China coincides with the debut of wheat domestication and cultivation practices in western Asia in the Holocene. We conclude that western China represents the limit of the far eastern native range of this species. This study is the most comprehensive molecular genetic investigation of the RWA in its native range undertaken to date and provides valuable insights into the history of the association of this aphid with domesticated cereals and wild grasses.
Data from: Integrating genomic and phenotypic data to evaluate alternative phylogenetic and species delimitation hypotheses in a recent evolutionary radiation of grasshoppers
Although resolving phylogenetic relationships and establishing species limits is a primary goal of systematics, these tasks remain challenging at both conceptual and analytical levels. Here, we integrated genomic and phenotypic data and employed a comprehensive suite of coalescent-based analyses to develop and evaluate competing phylogenetic and species delimitation hypotheses in a recent evolutionary radiation of grasshoppers (Chorthippus binotatus group) composed of two species and eight putative subspecies. To resolve the evolutionary relationships within this complex, we first evaluated alternative phylogenetic hypotheses arising from multiple schemes of genomic data processing and contrasted genetic-based inferences with different sources of phenotypic information. Second, we examined the importance of number of loci, demographic priors, number and kind of phenotypic characters, and sex-based trait variation for developing alternative species delimitation hypotheses. The best-supported topology was largely compatible with phenotypic data and showed the presence of two clades corresponding to the nominative species groups, one including three well-resolved lineages and the other comprising a four-lineage polytomy and a well-differentiated sister taxon. Integrative species delimitation analyses indicated that the number of employed loci had little impact on the obtained inferences but revealed the higher power provided by an increasing number of phenotypic characters and the usefulness of assessing their phylogenetic information-content and differences between sexes in among-taxa trait variation. Overall, our study highlights the importance of integrating multiple sources of information to test competing phylogenetic hypotheses and elucidate the evolutionary history of species complexes representing early-stages of divergence where conflicting inferences are more prone to appear.
Data from: A recently transferred cluster of bacterial genes in Trichomonas vaginalis –lateral gene transfer and the fate of acquired genes.
Background: Lateral Gene Transfer (LGT) has recently gained recognition as an important contributor to some eukaryote proteomes, but the mechanisms of acquisition and fixation in eukaryotic genomes are still uncertain. A previously defined norm for LGTs in microbial eukaryotes states that the majority are genes involved in metabolism, the LGTs are typically localized one by one, surrounded by vertically inherited genes on the chromosome, and phylogenetics shows that a broad collection of bacterial lineages have contributed to the transferome. Results: A unique 34 kbp long fragment with 27 clustered genes (TvLF) of prokaryote origin was identified in the sequenced genome of the protozoan parasite Trichomonas vaginalis. Using a PCR based approach we confirmed the presence of the orthologous fragment in four additional T. vaginalis strains. Detailed sequence analyses unambiguously suggest that TvLF is the result of one single, recent LGT event. The proposed donor is a close relative to the firmicute bacterium Peptoniphilus harei. High nucleotide sequence similarity between T. vaginalis strains, as well as to P. harei, and the absence of homologs in other Trichomonas species, suggests that the transfer event took place after the radiation of the genus Trichomonas. Some genes have undergone pseudogenization and degradation, indicating that they may not be retained in the future. Functional annotations reveal that genes involved in informational processes are particularly prone to degradation. Conclusions: We conclude that, although the majority of eukaryote LGTs are single gene occurrences, they may be acquired in clusters of several genes that are subsequently cleansed of evolutionarily less advantageous genes.
Data From: Genetic structure of recently fragmented suburban populations of European stag beetle
<p>Habitat loss and fragmentation due to urbanisation can negatively affect metapopulation persistence when gene flow among populations is reduced and population sizes decrease. Inference of patterns and processes of population connectivity derived from spatial genetic analysis has proven invaluable for conservation and management. However, a more complete account of population dynamics may be obtained by combining spatial and temporal sampling. We, therefore, performed a genetic study on European stag beetle (<i>Lucanus cervus</i> L.) populations in a suburban context using samples collected in three locations and during the period 2002-2016. The sampling area has seen recent landscape changes which resulted in population declines. Through the use of a suite of FST, clustering analysis, individual assignment, and relatedness analysis we assessed fine scale spatiotemporal genetic variation within and among habitat patches using 283 individuals successfully genotyped at 17 microsatellites. Our findings suggested the three locations to hold demographically independent populations, at least over time scales of relevance to conservation, though with higher levels of gene flow in the past. Contrary to expectation from tagging studies, dispersal appeared to be mainly female-biased. Although the life cycle of stag beetle suggests its generations to be discrete, no clear temporal structure was identified, which could be attributed to the varying duration of larval development. Since population bottlenecks were detected and estimates of effective number of breeders were low, conservation actions are eminent which should include the establishment of suitable dead wood for oviposition on both local and regional scales to increase (re)colonisation success and connectivity among current populations.</p>
Data from: Detecting recent selective sweeps while controlling for mutation rate and background selection
A composite likelihood ratio test implemented in the program SweepFinder is a commonly used method for scanning a genome for recent selective sweeps. SweepFinder uses information on the spatial pattern (along the chromosome) of the site frequency spectrum (SFS) around the selected locus. To avoid confounding effects of background selection and variation in the mutation process along the genome, the method is typically applied only to sites that are variable within species. However, the power to detect and localize selective sweeps can be greatly improved if invariable sites are also included in the analysis. In the spirit of a Hudson-Kreitman-Aguadé test, we suggest adding fixed differences relative to an outgroup to account for variation in mutation rate, thereby facilitating more robust and powerful analyses. We also develop a method for including background selection, modeled as a local reduction in the effective population size. Using simulations we show that these advances lead to a gain in power while maintaining robustness to mutation rate variation. Furthermore, the new method also provides more precise localization of the causative mutation than methods using the spatial pattern of segregating sites alone.
Data from: Fine-scale spatial genetic structure across the species range reflects recent colonization of high elevation habitats in silver fir (Abies alba Mill.)
<p class="western"><span>Variation in genetic diversity across species ranges has long been recognized as highly informative for assessing populations' resilience and adaptive potential. The spatial distribution of genetic diversity within populations, referred to as fine-scale spatial genetic structure (FSGS), also carries information about recent demographic changes, yet it has rarely been connected to range scale processes. We studied eight silver fir (<i>Abies alba </i>Mill.<i>)</i> population pairs (sites), growing at high and low elevations, representative of the main genetic lineages of the species. A total of 1368 adult trees and 540 seedlings were genotyped using 137 and 116 single nucleotide polymorphisms (SNPs), respectively. Sites revealed a clear east-west isolation-by-distance pattern consistent with the post-glacial colonization history of the species. Genetic differentiation among sites (<i>F</i><sub>CT</sub>=0.148) was an order of magnitude greater than between elevations within sites (<i>F</i><sub>SC</sub>=0.031), nevertheless high elevation populations consistently exhibited a stronger FSGS. Structural equation modeling revealed that elevation and, to a lesser extent, post-glacial colonization history, but not climatic and habitat variables, were the best predictors of FSGS across populations. These results suggest that high elevation habitats have been colonized more recently across the species range. Additionally, paternity analysis revealed a high reproductive skew among adults and a stronger FSGS in seedlings than in adults, suggesting that FSGS may conserve the signature of demographic changes for several generations. Our results emphasize that spatial patterns of genetic diversity within populations provide information about demographic history complementary to non-spatial statistics, and could be used for genetic diversity monitoring, especially in forest trees.</span></p>
FIGURE 15 in Resurrection of Salvia species (Lamiaceae) recently synonymized in Flora Mesoamericana
FIGURE 15. Salvia unicostata, inflorescence. (picture taken by J.G. González-Gallegos)
FIGURE 1 in Synopsis and annotated checklist of Recent marine Bryozoa from Brazil
FIGURE 1. Political map of the Brazilian coast indicating regions, states, and oceanic islands.
FIGURE 4 in New data on the recently described Xiphion heracleanum (Iridaceae), endemic to Morocco
FIGURE 4. Bulb (left) and bulbil (right) of Xiphion heracleanum. Scale bar: 1 cm.
FIG. 6. – Pycnogonum staplesi n in Deep-water Pycnogonida from recent cruises to Papua New Guinea and Melanesia, with an appendix of new records from Polynesia and descriptions of five new species
FIG. 6. – Pycnogonum staplesi n. sp., holotype (Py 922): A, habitus, lateral (note, mid-dorsal tubercle on trunk segment 2 broken); B, habitus, dorsal; C, distal articles of third leg, with detail of split spinule. Scale bar: A, B, 3 mm; C, 0.4 mm.
Figure 1 in Genetic and morphometric variation of the Blackcap (Sylvia atricapilla) on the Azores Archipelago reveals a recent range expansion
Figure 1. Location of the Azores Archipelago and islands isotopic ages.
Figures 18-24 from: Czaja A, Gladstone NS, Becerra-López JL, Estrada-Rodríguez JL, Sáenz‑Mata J, Hernández-Terán F (2021) A remarkable new genus and species of subterranean freshwater snail from a recently dried-up spring of Viesca, Coahuila, Northern Mexico. Subterranean Biology 39: 129-141. https://doi.org/10.3897/subtbiol.39.67799
Figures 18-24 SEM images of Phreatoviesca spinosa gen. nov. et sp. nov. 18 shell apex with protoconch, UJMC 508 19 paratype 3, shell apex with protoconch, UJMC 503 20 shell apex with protoconch, UJMC 510 21 paratype 1, apex with protoconch, UJMC 501 22 smooth specimen with body whorl shows irregular, strong marked growth lines, UJMC 508 23 paratype 1, body whorl shows irregular, strong marked growth lines, UJMC 501 24 paratype 2, body whorl shows regularly spaced shovel-shaped spines, UJMC 502.
Figures 14-17 from: Czaja A, Gladstone NS, Becerra-López JL, Estrada-Rodríguez JL, Sáenz‑Mata J, Hernández-Terán F (2021) A remarkable new genus and species of subterranean freshwater snail from a recently dried-up spring of Viesca, Coahuila, Northern Mexico. Subterranean Biology 39: 129-141. https://doi.org/10.3897/subtbiol.39.67799
Figures 14-17 SEM images of Phreatoviesca spinosa gen. nov. et sp. nov. 14 specimen with strong spines, UJMC 506 15 specimen with ribs, UJMC 507 16 specimen with smooth whorls, UJMC 508 17 specimen with smooth whorls, UJMC 509. Scale bar: 1 mm.
Figure 1 from: Czaja A, Gladstone NS, Becerra-López JL, Estrada-Rodríguez JL, Sáenz‑Mata J, Hernández-Terán F (2021) A remarkable new genus and species of subterranean freshwater snail from a recently dried-up spring of Viesca, Coahuila, Northern Mexico. Subterranean Biology 39: 129-141. https://doi.org/10.3897/subtbiol.39.67799
Figure 1 Map of the study area with localization of the sampling site near the town of Viesca, Coahuila, Mexico.
Figures 2-13 from: Czaja A, Gladstone NS, Becerra-López JL, Estrada-Rodríguez JL, Sáenz‑Mata J, Hernández-Terán F (2021) A remarkable new genus and species of subterranean freshwater snail from a recently dried-up spring of Viesca, Coahuila, Northern Mexico. Subterranean Biology 39: 129-141. https://doi.org/10.3897/subtbiol.39.67799
Figures 2-13 Shells of Phreatoviesca spinosa gen. nov. et sp. nov. 2, 3 holotype, specimen from both sides, UJMC 500 4, 5 paratype 1, specimen from both sides, UJMC 501 6 paratype 2, specimen with a 'corkscrew'-like morphology, UJMC 502 7, 8 paratype 3, specimen from both sides, UJMC 503 9 paratype 4, specimen with smooth whorls and a trumpet-like aperture, UJMC 504 10, 11 paratype 5, specimen with smooth whorls, UJMC 505. Opercula 12, 13 paratype 5, specimen with smooth whorls, UJMC 505. Scale bar: 1 mm.
Genotype and individual data for genetic structure in Louisiana Iris species reveals patterns of recent and historical admixture
<p><b><span>Premise: </span></b><span>When divergent lineages come into secondary contact reproductive isolation may be incomplete, thus providing an opportunity to investigate how speciation is manifested in the genome. The Louisiana Irises (<i>Iris</i>, series <i>Hexagonae</i>) comprise a group of three or more ecologically and reproductively divergent lineages that can produce hybrids where they come into contact. In this study we sought to estimate standing genetic variation to understand the current distribution of population structure in the Louisiana Irises.</span></p> <p><b><span>Methods:</span></b><span> We used genotyping-by-sequencing techniques to sample the genomes of Louisiana Iris species across their ranges. Twenty populations were sampled (total n=632) across 11,249 loci. Population genetic data were assessed using ENTROPY and PCA models. </span></p> <p><b><span>Results: </span></b><span>We discovered evidence for interspecific gene flow in parts of the range and revealed patterns of population structure at odds with widely accepted nominal taxonomy. Undescribed hybrid populations were discovered that were designated as belonging to the <i>I. brevicaulis</i> lineage. <i>Iris nelsonii </i>shared significant ancestry with only one of the purported parent species, <i>I. fulva, </i>evidence inconsistent with a hybrid origin.</span></p> <p><b><span>Conclusions: </span></b><span>This study provides several key findings important to the investigation of standing genetic variation in the Louisiana Iris species complex. <i>Iris brevicaulis</i> has a large amount of genetic diversity within it relative to the other nominal species. In addition, this study has discovered a previously unknown hybrid zone between <i>I. brevicaulis </i>and <i>I. hexagona</i> along the Texas coast. Finally, <i>I. nelsonii</i> does not appear to have mixed ancestry from three parental taxa as has been the longstanding hypothesis. </span></p>
FIG. 34. Limatula demiradiata. Sta. z398 in The Recent species of the genera Limatula and Limea (Bivalvia, Limacea) present in the Atlantic, with particular reference to those in deep water
FIG. 34. Limatula demiradiata. Sta. z398, dorsal view of shell. Scale bar: 1 mm.
FIG. 29. Limatula laminifera. Sta. 118 in The Recent species of the genera Limatula and Limea (Bivalvia, Limacea) present in the Atlantic, with particular reference to those in deep water
FIG. 29. Limatula laminifera. Sta. 118, lateral view of shell from the left side. Scale bar: 1 mm.
ScienceDex guides
Understand access before you commit
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.