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Figure 3 from: Santos D, Saraiva RVC, Ferraz TM, Arruda ECP, Buril MT (2020) A threatened new species of Ipomoea (Convolvulaceae) from the Brazilian Cerrado revealed by morpho-anatomical analysis. PhytoKeys 151: 93-106. https://doi.org/10.3897/phytokeys.151.49833
Figure 3 A, BIpomoea maranhensisA arrangement of vascular bundles in U; prominent/concave main rib shape B dorsiventral mesophyll C–FI. burchelliiC arrangement of vascular bundles in V; convex/flat main rib shape D mesophyll isobilateral E glandular trichomes restricted to the abaxial surface of the leaf (red arrow) F parenchymatous tissue with isodiametric cells (Photos by E. Pereira Arruda). AD: adaxial epidermis; AB: abaxial epidermis; Is: isodiametric cells; Pa: Parenchymatous tissue; Pp: palisade parenchyma; Sp: spongy parenchyma; Vb: vascular bundle; Tr: trichome.
Figure 1 from: Santos D, Saraiva RVC, Ferraz TM, Arruda ECP, Buril MT (2020) A threatened new species of Ipomoea (Convolvulaceae) from the Brazilian Cerrado revealed by morpho-anatomical analysis. PhytoKeys 151: 93-106. https://doi.org/10.3897/phytokeys.151.49833
Figure 1 A–FIpomoea maranhensisA branch with leaves (abaxial surface) and flowers B branch with leaves (adaxial surface) and floral buds C leaf in abaxial view presenting sericeous aspect D floral bud E sepals F ovary (Photos by F. Santos and Flora do Brasil 2019).
Figure 2 from: Santos D, Saraiva RVC, Ferraz TM, Arruda ECP, Buril MT (2020) A threatened new species of Ipomoea (Convolvulaceae) from the Brazilian Cerrado revealed by morpho-anatomical analysis. PhytoKeys 151: 93-106. https://doi.org/10.3897/phytokeys.151.49833
Figure 2 A–HIpomoea maranhensisA twining habit B primary and secondary veins on the abaxial surface C floral bud D sepals with apex long acuminate E flower F open corolla G stamen H gynoecium. Drawn by Regina Carvalho from Félix et al. 8136.
Genotype count for all coding variants in type I IFN genes investigated in 659 life-threatening COVID-19 patients and 534 asymptomatic/mild infected controls
<p>Clinical outcome upon infection with SARS-CoV-2 ranges from silent infection to lethal COVID-19. We have found an enrichment in rare variants predicted to be loss-of-function (LOF) at the 13 human loci known to govern TLR3- and IRF7-dependent type I interferon (IFN) immunity to influenza virus, in 659 patients with life-threatening COVID-19 pneumonia, relative to 534 subjects with asymptomatic or benign infection. By testing these and other rare variants at these 13 loci, we experimentally define LOF variants in 23 patients (3.5%), aged 17 to 77 years, underlying autosomal recessive or dominant deficiencies. We show that human fibroblasts with mutations affecting this pathway are vulnerable to SARS-CoV-2. Inborn errors of TLR3- and IRF7-dependent type I IFN immunity can underlie life-threatening COVID-19 pneumonia in patients with no prior severe infection.</p>
Figure 9 from: Samain M-S, Granados Mendoza C, Martínez Salas EM (2021) On Hydrangea peruviana, an endangered species from Ecuador, and Hydrangea oerstedii, very common in Costa Rica and Panama, and seven threatened Central and South American Hydrangeas, which have been confounded with these. PhytoKeys 171: 91-153. https://doi.org/10.3897/phytokeys.171.56351
Figure 9 Hydrangea panamensisA plant growing along the stem of a CecropiaB infructescence with young and mature fruits, and enlarged marginal flowers. Hydrangea peruvianaC stolons with adventitious roots and decussate leaves. A, B field images of collection Samain & Martínez 2012-063C field image of collection Granados Mendoza et al. 2012-112.
Figure 5 from: Samain M-S, Granados Mendoza C, Martínez Salas EM (2021) On Hydrangea peruviana, an endangered species from Ecuador, and Hydrangea oerstedii, very common in Costa Rica and Panama, and seven threatened Central and South American Hydrangeas, which have been confounded with these. PhytoKeys 171: 91-153. https://doi.org/10.3897/phytokeys.171.56351
Figure 5 Hydrangea goudotiiA branch with leaves seen abaxially, old inflorescence axes and the vegetative portion of the flowering branch B inflorescence bud with cucullate inflorescence bracts and densely pubescent inflorescence axis C inflorescence of functionally male plant, with enlarged marginal flowers and a few flowers that still show stamens A field image of collection Granados Mendoza et al. 2012-105B, C field images of collection Granados Mendoza et al. 2012-43.
Figure 16 from: Samain M-S, Granados Mendoza C, Martínez Salas EM (2021) On Hydrangea peruviana, an endangered species from Ecuador, and Hydrangea oerstedii, very common in Costa Rica and Panama, and seven threatened Central and South American Hydrangeas, which have been confounded with these. PhytoKeys 171: 91-153. https://doi.org/10.3897/phytokeys.171.56351
Figure 16 Hydrangea weberbaueriA branch with inflorescences with enlarged marginal flowers B functionally male inflorescence with enlarged marginal flowers, and reduced flowers with large stamens C functionally female inflorescence with enlarged marginal flowers D close-up of functionally male flowers with large stamens and reduced pistils E close-up of functionally female flowers with reduced stamens and large pistils. A, B field images of collection Granados Mendoza et al. 2012-16C field image of collection Granados Mendoza et al. 2012-21D field image of collection Samain et al. 2011-068.
Figure 11 from: Samain M-S, Granados Mendoza C, Martínez Salas EM (2021) On Hydrangea peruviana, an endangered species from Ecuador, and Hydrangea oerstedii, very common in Costa Rica and Panama, and seven threatened Central and South American Hydrangeas, which have been confounded with these. PhytoKeys 171: 91-153. https://doi.org/10.3897/phytokeys.171.56351
Figure 11 Hydrangea peruviana. Infructescence with young fruits and densely pubescent apex of the inflorescence axis. Field image of collection Granados Mendoza et al. 2012-112.
Figure 13 from: Samain M-S, Granados Mendoza C, Martínez Salas EM (2021) On Hydrangea peruviana, an endangered species from Ecuador, and Hydrangea oerstedii, very common in Costa Rica and Panama, and seven threatened Central and South American Hydrangeas, which have been confounded with these. PhytoKeys 171: 91-153. https://doi.org/10.3897/phytokeys.171.56351
Figure 13 Hydrangea trianaeA branch with leaves seen abaxially and inflorescence buds B functionally female inflorescence with enlarged marginal flowers C basal portion of functionally male inflorescence with densely pubescent apex of the inflorescence axis, and a few open male flowers with large stamens D close-up of functionally female flowers with petals, reduced stamens and large pistils. A, C field images of collection Samain et al. 2011-064B, D field images of collection Samain et al. 2011-067.
Figure 12 from: Samain M-S, Granados Mendoza C, Martínez Salas EM (2021) On Hydrangea peruviana, an endangered species from Ecuador, and Hydrangea oerstedii, very common in Costa Rica and Panama, and seven threatened Central and South American Hydrangeas, which have been confounded with these. PhytoKeys 171: 91-153. https://doi.org/10.3897/phytokeys.171.56351
Figure 12 Hydrangea schlimii. Branch with inflorescences with many enlarged flowers. Image of specimen Linden 1139 (BR).
Figure 1 from: Samain M-S, Granados Mendoza C, Martínez Salas EM (2021) On Hydrangea peruviana, an endangered species from Ecuador, and Hydrangea oerstedii, very common in Costa Rica and Panama, and seven threatened Central and South American Hydrangeas, which have been confounded with these. PhytoKeys 171: 91-153. https://doi.org/10.3897/phytokeys.171.56351
Figure 1 Hydrangea caucana. Branch with infructescences with mature fruits and enlarged marginal flowers. Image of specimen A. Cogollo et al. 2669 (MO).
Figure 15 from: Samain M-S, Granados Mendoza C, Martínez Salas EM (2021) On Hydrangea peruviana, an endangered species from Ecuador, and Hydrangea oerstedii, very common in Costa Rica and Panama, and seven threatened Central and South American Hydrangeas, which have been confounded with these. PhytoKeys 171: 91-153. https://doi.org/10.3897/phytokeys.171.56351
Figure 15 Hydrangea weberbaueriA apical portion of a branch with young leaves where the characteristic leaf venation and margin can be observed B adaxial leaf side showing the typical leaf venation of this species C glabrous apex of the inflorescence axis of a functionally female inflorescence. A field image of collection Granados Mendoza et al. 2012-23B field image of collection Samain et al. 2011-056C field image of collection Samain et al. 2011-068.
Figure 10 from: Samain M-S, Granados Mendoza C, Martínez Salas EM (2021) On Hydrangea peruviana, an endangered species from Ecuador, and Hydrangea oerstedii, very common in Costa Rica and Panama, and seven threatened Central and South American Hydrangeas, which have been confounded with these. PhytoKeys 171: 91-153. https://doi.org/10.3897/phytokeys.171.56351
Figure 10 Hydrangea peruvianaA branch with inflorescence B branch with leaves seen abaxially and inflorescence C close up of infructescence with maturing fruits and enlarged marginal flowers. A, B field images of collection Granados Mendoza et al. 2012-111C field image of collection Granados Mendoza et al. 2012-112.
Figure 4 from: Samain M-S, Granados Mendoza C, Martínez Salas EM (2021) On Hydrangea peruviana, an endangered species from Ecuador, and Hydrangea oerstedii, very common in Costa Rica and Panama, and seven threatened Central and South American Hydrangeas, which have been confounded with these. PhytoKeys 171: 91-153. https://doi.org/10.3897/phytokeys.171.56351
Figure 4 Hydrangea durifolia. Branch with inflorescence buds and inflorescences. Image of specimen E.P. Killip & A.C. Smith 18366 (US).
Figure 7 from: Samain M-S, Granados Mendoza C, Martínez Salas EM (2021) On Hydrangea peruviana, an endangered species from Ecuador, and Hydrangea oerstedii, very common in Costa Rica and Panama, and seven threatened Central and South American Hydrangeas, which have been confounded with these. PhytoKeys 171: 91-153. https://doi.org/10.3897/phytokeys.171.56351
Figure 7 Hydrangea oerstediiA branch with leaves seen abaxially B flowering branch of functionally male plant with three inflorescences with enlarged marginal flowers and many flowers with large stamens C inflorescence of functionally male plant with enlarged marginal flowers, most flowers in bud with petals visible, and a few open flowers with long stamens D close-up of functionally male inflorescence E close-up of functionally male flowers with reduced pistils F close-up of functionally female flowers with reduced stamens and large pistils. A field image of collection Samain & Martínez 2012-044B field image of collection Samain & Martínez 2013-025C field image of collection Samain & Martínez 2012-044D field image of collection Samain et al. 2019-003E field image of collection Samain & Martínez 2013-025F field image of collection Samain & Martínez 2013-021.
Figure 3 from: Samain M-S, Granados Mendoza C, Martínez Salas EM (2021) On Hydrangea peruviana, an endangered species from Ecuador, and Hydrangea oerstedii, very common in Costa Rica and Panama, and seven threatened Central and South American Hydrangeas, which have been confounded with these. PhytoKeys 171: 91-153. https://doi.org/10.3897/phytokeys.171.56351
Figure 3 Hydrangea durifolia. Branch with distinct "vegetative" leaves, floral axes with leaves and inflorescence buds. Image of specimen E.P. Killip & A.C. Smith 18366 (GH).
Data from: Can physiographic regions substitute for genetically-determined conservation units? A case study with the threatened plant, Silene spaldingii
Protecting genetic diversity throughout the range of a species is important for conservation, as doing so provides for long-term evolutionary potential and persistence under a changing environment. Conservation of diversity at the intraspecific level requires identification of all genetically distinct population segments within species; i.e., conservation units (CUs). Silene spaldingii occurs in grasslands of the Columbia Plateau region of western North America and is listed as threatened under the Federal Endangered Species Act. The recovery plan identified five physiographic regions across the range of the species to use as surrogates for genetic CUs. We collected leaf samples from an average of 26 plants from each of 19 of the largest populations across all five physiographic regions and used variable microsatellite and chloroplast DNA markers to determine how genetic variation is distributed across the range of the species and how well physiographic regions reflect population structure within this species. Results of several multivariate analyses clustered our samples into four genetic groups which did not correspond well with the physiographic regions. We observed little genetic differentiation among populations in the main range of the species which encompasses nearly all of four contiguous physiographic regions. However, three other distinct genetic groups were identified: two in the disjunct northeast corner and one at the southeast edge of the main range. Modification of the CUs to reflect the genetic groups rather than the physiographic regions would result in CUs which better reflect historical patterns of population structure. Moreover, use of the genetic units to inform translocation and genetic rescue efforts could improve our ability to mimic natural patterns of gene flow. Our results suggest that physiographic regions may not always be an accurate reflection of population structure for threatened or endangered species.
Data from: Interacting livestock and fire may both threaten and increase viability of a fire-adapted Mediterranean carnivorous plant
1. Quantifying interactive effects of environmental drivers on population dynamics can be critical for a robust analysis of population viability. Fire regimes, among the most widespread disturbances driving population dynamics, are increasingly modified by and interact with human activities. However, viability of fire-adapted species is typically assessed overlooking disturbance interactions, potentially resulting in suboptimal management actions. 2. We investigated whether increasing human disturbances in fire-prone ecosystems may pose a threat or an opportunity to improve population viability, using demographic data of the carnivorous, post-fire recruiting plant Drosophyllum lusitanicum, endemic to heathlands in the southwestern Mediterranean Basin. We built integral projection models and simulated population dynamics under different combinations of two key disturbance types affecting populations: fire and livestock browsing and trampling. We used perturbation analyses to determine potential long-term consequences of maintaining fundamentally different disturbance types. 3. Despite most populations inhabiting browsed habitats, simulations showed a greater extinction risk in populations under high livestock pressure compared with ones under low or moderate pressures. Extinction risk decreased when fire return intervals shortened in populations under low or moderate livestock pressure; however, the opposite pattern emerged in heavily browsed populations, where short intervals between fires increased extinction. 4. Elasticity analyses showed that decreases in viability under frequent disturbance interactions (heavy browsing and frequent fire) may be explained by selection against seed dormancy in populations with frequent browsing and trampling. This may potentially cause populations to collapse when fires kill above-ground plants without populations being able to recover from a seed bank. 5. Synthesis and applications: Incorporating disturbance interactions can result in a different assessment of viability of a fire-adapted species than considering fire regimes alone. In Mediterranean ecosystems, fire management may be more effective when integrating moderate human activities. However, replacing fires by human disturbances, a currently widespread strategy in many fire-prone ecosystems, is not recommended since it may fundamentally alter population dynamics and selection pressures and decrease viability of fire-adapted species.
Data from: Mining microsatellite markers from public expressed sequence tags databases for the study of threatened plants
Background: Simple Sequence Repeats (SSRs) are widely used in population genetic studies but their classical development is costly and time-consuming. The ever-increasing available DNA datasets generated by high-throughput techniques offer an inexpensive alternative for SSRs discovery. Expressed Sequence Tags (ESTs) have been widely used as SSR source for plants of economic relevance but their application to non-model species is still modest. Methods: Here, we explored the use of publicly available ESTs (GenBank at the National Center for Biotechnology Information-NCBI) for SSRs development in non-model plants, focusing on genera listed by the International Union for the Conservation of Nature (IUCN). We also search two model genera with fully annotated genomes for EST-SSRs, Arabidopsis and Oryza, and used them as controls for genome distribution analyses. Overall, we downloaded 16 031 555 sequences for 258 plant genera which were mined for SSRsand their primers with the help of QDD1. Genome distribution analyses in Oryza and Arabidopsis were done by blasting the sequences with SSR against the Oryza sativa and Arabidopsis thaliana reference genomes implemented in the Basal Local Alignment Tool (BLAST) of the NCBI website. Finally, we performed an empirical test to determine the performance of our EST-SSRs in a few individuals from four species of two eudicot genera, Trifolium and Centaurea. Results: We explored a total of 14 498 726 EST sequences from the dbEST database (NCBI) in 257 plant genera from the IUCN Red List. We identify a very large number (17 102) of ready-to-test EST-SSRs in most plant genera (193) at no cost. Overall, dinucleotide and trinucleotide repeats were the prevalent types but the abundance of the various types of repeat differed between taxonomic groups. Control genomes revealed that trinucleotide repeats were mostly located in coding regions while dinucleotide repeats were largely associated with untranslated regions. Our results from the empirical test revealed considerable amplification success and transferability between congenerics. Conclusions: The present work represents the first large-scale study developing SSRs by utilizing publicly accessible EST databases in threatened plants. Here we provide a very large number of ready-to-test EST-SSR (17 102) for 193 genera. The cross-species transferability suggests that the number of possible target species would be large. Since trinucleotide repeats are abundant and mainly linked to exons they might be useful in evolutionary and conservation studies. Altogether, our study highly supports the use of EST databases as an extremely affordable and fast alternative for SSR developing in threatened plants.
Data from: Monarch butterfly population decline in North America: identifying the threatening processes
The monarch butterfly (Danaus plexippus) population in North America has sharply declined over the last two decades. Despite rising concern over the monarch butterfly's status, no comprehensive study of the factors driving this decline has been conducted. Using partial least-squares regressions and time-series analysis, we investigated climatic and habitat-related factors influencing monarch population size from 1993 to 2014. Potential threats included climatic factors, habitat loss (milkweed and overwinter forest), disease and agricultural insecticide use (neonicotinoids). While climatic factors, principally breeding season temperature, were important determinants of annual variation in abundance, our results indicated strong negative relationships between population size and habitat loss variables, principally glyphosate use, but also weaker negative effects from the loss of overwinter forest and breeding season use of neonicotinoids. Further declines in population size because of glyphosate application are not expected. Thus, if remaining threats to habitat are mitigated we expect climate-induced stochastic variation of the eastern migratory population of monarch butterfly around a relatively stationary population size.
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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.