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Data from: Genomic and phenotypic architecture of a spruce hybrid zone (Picea sitchensis x P. glauca)
Interspecific hybridization may enhance the capacity of populations to adapt to changing environments, and has practical implications for reforestation. We use genomewide estimates of admixture and phenotypic traits for trees in a common garden to examine the extent and direction of gene flow across a Picea hybrid zone, testing assumptions of the bounded hybrid superiority and tension zone models of hybrid zone maintenance. Seeds were collected from the ecological transition zone spanning from maritime to continental climates across the Picea sitchensis-P. glauca contact zone, and 721 trees were planted in a common garden experiment within the hybrid zone. Individuals were genotyped using a panel of 384 candidate-gene single nucleotide polymorphisms (SNPs) putatively associated with adaptive traits in Picea, and phenotyped at age ten for height and autumn cold hardiness. Low interspecific heterozygosity in hybrids indicated intrinsic reproductive barriers were too weak to prevent widespread recombination, although introgression appeared asymmetric with P. sitchensis dominating the zone. While marker-based hybrid index was strongly correlated with climate and geography, phenotypic traits exhibited weak or no significant clines. Our results indicated that exogenous selection appeared to play a strong role in the distribution and structure of this hybrid zone, indicative of an environmentally determined bounded hybrid superiority model of hybrid zone maintenance, although endogenous mechanisms could not be ruled out. This study provides insight into the mechanisms underlying adaptation across ecologically transitional hybrid zones that will ultimately provide an additional tool in managing these economically important tree species.
Data from: Morphological, molecular, and ecological divergence in Pinus douglasiana and P. maximinoi
Pinus douglasiana and P. maximinoi (Pinus subsection Ponderosae) are closely-related New World pines with vague taxonomic boundaries where their natural ranges overlap in western Mexico. They are distinguished from each other by the width of their leaves and thickness of their cone scale apophyses. They are also sometimes confused with two other close relatives, Pinus pseudostrobus and P. yecorensis. We integrated morphological, molecular, and ecological data to clarify the taxonomic limits among these four species. Following previous studies, we evaluated 16 quantitative leaf and seed cone characters. Pinus douglasiana, P. maximinoi, and P. pseudostrobus formed non-discrete groups in multivariate space. The absence of leaf hypodermal intrusions, a persistent peduncle, and the shape of the seed cone are useful for differentiating P. pseudostrobus and P. yecorensis from P. douglasiana or P. maximinoi, and the latter two can usually be distinguished by needle width or cone scale apophysis thickness. Most individuals identified as P. douglasiana, and P. maximinoi shared haplotypes for a plastid ycf1 fragment that is relatively variable for the genus, while P. yecorensis has a closely related, exclusive haplotype. A distinct haplogroup included all individuals of P. pseudostrobus and the remaining individuals of P. douglasiana and P. maximinoi. Leaf width and cone scale thickness of P. douglasiana and P. maximinoi are correlated with elevation. According to potential distribution models, P. yecorensis is distributed in drier areas than P. douglasiana or P. maximinoi, while P. pseudostrobus occurs in more temperate areas, commonly at higher elevations. Pinus douglasiana and P. maximinoi can be considered as incipient species undergoing divergent evolution characterized by incomplete morphological, molecular, and ecological divergence.
Data from: Description of a new species of Petrolisthes in the Indo-West Pacific with a redefinition of P. hastatus Stimpson, 1858 and resurrection of P. inermis (Heller, 1862) (Crustacea, Anomura, Porcellanidae)
The porcellanid crab Petrolisthes hastatus Stimpson, 1858, has been traditionally viewed as a highly variable species with a wide distribution in the West Pacific. For more than a century there has been taxonomic confusion of this species with morphologically similar taxa, some of which were synonymized with Stimpson's taxon. We redefine P. hastatus, resurrect P. inermis as a valid species, discuss the status of P. tenkatei De Man, 1893, and describe a new species as P. elegantissimus from Indonesia.
Data from: The impact of climate change on the potential distribution of agricultural pests: the case of the coffee white stem borer (Monochamus leuconotus P.) in Zimbabwe
The production of agricultural commodities faces increased risk of pests, diseases and other stresses due to climate change and variability. This study assesses the potential distribution of agricultural pests under projected climatic scenarios using evidence from the African coffee white stem borer (CWB), Monochamus leuconotus (Pascoe) (Coleoptera: Cerambycidae), an important pest of coffee in Zimbabwe. A species distribution modeling approach utilising Boosted Regression Trees (BRT) and Generalized Linear Models (GLM) was applied on current and projected climate data obtained from the WorldClim database and occurrence data (presence and absence) collected through on-farm biological surveys in Chipinge, Chimanimani, Mutare and Mutasa districts in Zimbabwe. Results from both the BRT and GLM indicate that precipitation-related variables are more important in determining species range for the CWB than temperature related variables. The CWB has extensive potential habitats in all coffee areas with Mutasa district having the largest model average area suitable for CWB under current and projected climatic conditions. Habitat ranges for CWB will increase under future climate scenarios for Chipinge, Chimanimani and Mutare districts while it will decrease in Mutasa district. The highest percentage change in area suitable for the CWB was for Chimanimani district with a model average of 49.1% (3 906 ha) increase in CWB range by 2080. The BRT and GLM predictions gave similar predicted ranges for Chipinge, Chimanimani and Mutasa districts compared to the high variation in current and projected habitat area for CWB in Mutare district. The study concludes that suitable area for CWB will increase significantly in Zimbabwe due to climate change and there is need to develop adaptation mechanisms.
Data from: SNP genotyping identifies new signatures of selection in a deep sample of West African P. falciparum malaria parasites
We used a high density SNP array to genotype 75 P. falciparum isolates recently collected from Senegal and The Gambia in order to search for signals of selection in this malaria endemic region. We found little geographic or temporal stratification of the genetic diversity among the sampled parasites. Through application of the iHS and REHH haplotype-based tests for positive selection, we found evidence of recent selective sweeps at a known drug resistance locus, at several known antigenic loci, and at several genomic regions not previously identified as sites of recent selection. We discuss the value of deep population-specific genomic analyses for identifying selection signals within sampled endemic populations of parasites, which may correspond to local selection pressures such as distinctive therapeutic regimes or mosquito vectors.
Data from: NetView P: a network visualization tool to unravel complex population structure using genome-wide SNPs
Network-based approaches are emerging as valuable tools for the analysis of complex genetic structure in both wild and captive populations. NetView P combines data quality control with the construction of population networks based on mutual k-nearest-neighbours thresholds applied to genome-wide SNPs. The program is cross-platform compatible, open-source and efficiently operates on data ranging from hundreds to hundreds of thousands of SNPs through multiprocessing in Python. We used the pipeline for the analysis of pedigree data from simulated (n = 750, SNPs = 1279) and captive Silver-lipped Pearl Oysters (n = 415, SNPs = 1107), wild populations of the European Hake from the Atlantic and Mediterranean (n = 834, SNPs = 380) and Gray Wolves from North America (n = 239, SNPs = 86,103). The population networks effectively visualize large- and fine-scale genetic structure within and between populations, including family-level structure and relationships. NetView P comprises a network-based addition to other population analysis tools and provides user-friendly access to a complex network analysis pipeline through implementation in Python.
Data from: Reproductive ecology and isolation of Psittacanthus calyculatus and P. auriculatus mistletoes (Loranthaceae)
Background: Relationships between floral biology and pollinator behavior are important to understanding species diversity of hemiparasitic Psittacanthus mistletoes (c. 120 species). We aimed to investigate trait divergence linked to pollinator attraction and reproductive isolation (RI) in two hummingbird-pollinated and bird-dispersed Psittacanthus species with range overlap. Methods: We investigated the phylogenetic relationships, floral biology, pollinator assemblages, seed dispersers and host usage, and the breeding system and female reproductive success of two sympatric populations of P. calyculatus and P. auriculatus, and one allopatric population of P. calyculatus. Flowers in sympatry were also reciprocally pollinated to assess a post-mating component of RI. Results: Hummingbird assemblages differed between calyculatus populations, while allopatric plants of calyculatus opened more but smaller flowers with longer lifespans and produced less nectar than those in sympatry. Bayesian-based phylogenetic analysis indicated monophyly for calyculatus populations (i.e. both populations belong to the same species). In sympatry, calyculatus plants opened more and larger flowers with longer lifespans and produced same nectar volume than those of auriculatus; populations shared pollinators but seed dispersers and host usage differed between species. Nectar standing crops differed between sympatric populations, with lower visitation in calyculatus. Hand pollination experiments indicated a predominant outcrossing breeding system, with fruit set after interspecific pollination two times higher from calyculatus to auriculatus than in the opposite direction. Conclusions: Given the low genetic differentiation between calyculatus populations, observed trait divergence could have resulted from changes regarding the local communities of pollinators and, therefore, expected divergence for peripheral, allopatric populations. Using RI estimates, there were fewer heterospecific matings than expected by chance in P. calyculatus (RI4A = 0.629) as compared to P. auriculatus (RI4A = 0.20). When considering other factors of ecological isolation that affect co-occurrence, the RI4C values indicate that isolation by hummingbird pollinators was less effective (0.20) than isolation by host tree species and seed dispersers (0.80 and 0.60, respectively), suggesting that host usage is the most important ecological isolation factor between the two species. Accordingly, the absolute and relative cumulative strength values indicated that the host tree species' barrier is currently contributing the most to maintaining these species in sympatry.
Data from: Testing hypotheses of mitochondrial gene-tree paraphyly: unraveling mitochondrial capture of the Streak-breasted Scimitar Babbler (Pomatorhinus ruficollis) by the Taiwan Scimitar Babbler (P. musicus)
Species-level paraphyly inferred from mitochondrial gene trees is a prevalent phenomenon in taxonomy and systematics, but there are several potential causes that are not easily explained by currently used methods. The present study aims to test the underlying causes behind the observed paraphyly of Streak-breasted Scimitar Babbler (Pomatorhinus ruficollis) via statistical analyses of four mitochondrial (mtDNA) and nine nuclear (nuDNA) genes. Mitochondrial gene trees show paraphyly of P. ruficollis with respect to the Taiwan Scimitar Babbler (P. musicus), but nuclear genealogies support a sister-group relationship. Predictive coalescent simulations imply several hypothetical explanations, the most likely being mitochondrial capture of P. ruficollis by P. musicus for the observed cyto-nuclear incongruence. Further Approximate Bayesian Computation suggests a unidirectional introgression model with substantial level of gene flow from P. ruficollis to P. musicus during their initial divergence during the Late Pleistocene. This specific observation frames several potential causes for incongruent outcomes of mitochondrial and nuclear introgression in general, and on the whole, our results underscore the strength of multiple independent loci for species delimitation and importance of testing hypotheses that explain disparate causes of mitochondrial gene-tree paraphyly.
Data from: Soil carbon, nitrogen and phosphorus stoichiometry (C:N:P) in relation to conifer species productivity and nutrition across British Columbia perhumid rainforests
<p>Temperate rainforest soils of the Pacific Northwest are often carbon (C) rich and encompass a wide range in fertility reflecting varying nitrogen (N) and phosphorus (P) availability. Soil resource stoichiometry (C:N:P) may provide an effective measure of site nutrient status and help refine species-dependent patterns in forest productivity across edaphic gradients. We described the nature of soil organic matter for mineral soil and forest floor substrates across very wet (perhumid) rainforest sites of southwestern Vancouver Island (Canada), and employed soil element ratios as covariates in a long-term planting density trial to test their utility in defining basal area growth response of four conifer species. There were strong positive correlations in mineral soil C, N and organic P (P<sub>o</sub>) concentrations, and close alignment in C:N and C:P<sub>o</sub> both among and between substrates. Stand basal area after five decades was best reflected by soil C:N but included a significant species-soil interaction. The conifers with ectomycorrhizal fungi had diverging growth responses displaying either competitive (<i>Picea sitchensis</i>) or stress-tolerant (<i>Tsuga heterophylla</i>, <i>Pseudotsuga menziesii</i>) attributes, in contrast to a more generalist response by an arbuscular mycorrhizal tree (<i>Thuja plicata</i>). Despite the consistent patterns in organic matter quality we found no evidence via foliar nutrition for increased P availability with declining element ratios as we did for N. The often high C:P<sub>o</sub> ratios (as much as 3000) of these soils may reflect a stronger immobilization sink for P than N, which, along with ongoing sorption of PO<sub>4</sub><sup>-</sup>, could limit the utility of C:P<sub>o</sub> or N:P<sub>o</sub> to adequately reflect P supply. The dynamics and availability of soil P to trees, particularly as P<sub>o</sub>, deserves greater attention as many perhumid rainforests were co-limited by N and P, or, in some stands, possibly P alone. </p>
Data from: The Parmotrema acid test: a look at species delineation in the P. perforatum group 40 y later
Parmotrema perforatum and its relatives form a morphologically distinctive group of species, most of which are common and endemic to eastern North America. Species delimitation in this ecologically important group was the subject of extensive inquiry before the advent of molecular systematics and computationally intensive niche modeling. As part of a large-scale lichen biodiversity inventory of the Mid-Atlantic Coastal Plain, we used ITS sequence data to examine the utility of characters (morphological, chemical, reproductive, ecological) in circumscribing four species in this group (P. hypoleucinum, P. hypotropum, P. perforatum, P. subrigidum). We found that P. hypoleucinum and P. subrigidum as currently circumscribed are monophyletic and the latter comprises two chemotypes differing in the presence or absence of norstictic acid in addition to alectoronic acid. The sequences of P. hypotropum and P. perforatum, which are chemically identical species and differ only in reproductive mode, were intermixed in a single, well-supported clade. The two chemotypes of P. subrigidum are partially allopatric and their sequences are > 99% identical. Nonetheless, niche modeling suggests they occupy significantly different ecological niches. These results provide a new perspective on much-debated questions on species circumscription in lichens and suggest new avenues for genetic, ecological and systematic research.
Paternally inherited P-element copy number affects the magnitude of hybrid dysgenesis in Drosophila simulans and D. melanogaster
<p class="CxSpFirst">Transposable elements (TEs) are repetitive regions of DNA that are able to self-replicate and reinsert themselves throughout host genomes. Since the discovery of TEs, a prevalent question has been whether increasing TE copy number has an effect on the fitness of their hosts. <i>P</i>-elements (PEs) in <i>Drosophila</i> are a well-studied TE that has strong phenotypic effects. When a female without PEs (M) is crossed to a male with them (P), the resulting females are often sterile, a phenomenon called hybrid dysgenesis (HD). Here, we used short and long-read sequenced to infer the number of PEs in the genomes of dozens of isofemale lines from two <i>Drosophila</i> species and measured whether the magnitude of HD was correlated with the number of PEs in the paternal genome. Consistent with previous reports, we find evidence for a positive correlation between the paternal PE copy number and the magnitude of HD in progeny from ♀M ´ ♂ P crosses for both species. Other crosses are not affected by the number of PE copies. We also find that the correlation between the strength of HD and PE copy number differs between species which suggest there are genetic differences that might make some genomes more resilient to the potentially deleterious effects of TEs. Our results suggest that PE copy number interacts with other factors in the genome and the environment to cause HD and that the importance of these interactions is species-specific.</p>
Data from: Genomic and functional approaches reveal a case of adaptive introgression from Populus balsamifera (balsam poplar) in P. trichocarpa (black cottonwood)
Natural hybrid zones in forest trees provide systems to study the transfer of adaptive genetic variation by introgression. Previous landscape genomic studies in Populus trichocarpa, a keystone tree species, indicated genomic footprints of admixture with its sister species P. balsamifera and identified candidate genes for local adaptation. Here, we explored patterns of introgression and signals of local adaptation in P. trichocarpa and P. balsamifera, employing genome resequencing data from three chromosomes in pure species and admixed individuals from wild populations. Local ancestry analysis in admixed P. trichocarpa revealed a telomeric region in chromosome 15 with P. balsamifera ancestry, containing several candidate genes for local adaptation. Genomic analyses revealed signals of selection in certain genes in this region (e.g. PRR5, COMT1), and functional analyses based on gene expression variation and correlations with adaptive phenotypes suggest distinct functions of the introgressed alleles. In contrast, a block of genes in chromosome 12 paralogous to the introgressed region showed no signs of introgression or signatures of selection. We hypothesize that the introgressed region in chromosome 15 has introduced modular, or cassette-like variation into P. trichocarpa. These linked adaptive mutations are associated with a block of genes in chromosome 15 that appear to have undergone neo- or sub-functionalization relative to paralogs in a duplicated region on chromosome 12 that show no signatures of adaptive variation. The association between P. balsamifera introgressed alleles with the expression of adaptive traits in P. trichocarpa supports the hypothesis that this is a case of adaptive introgression in an ecologically important foundation species.
Data from: Ontogeny of the Furongian (late Cambrian) trilobite Proceratopyge cf. P. Lata Whitehouse from northern Victoria Land, Antarctica, and the evolution of metamorphosis in trilobites
There were multiple origins of metamorphosis-undergoing protaspides in trilobite evolution: within the superfamilies Remopleuridioidea, Trinucleoidea, and within the Order Asaphida. Recent studies have revealed that the protaspides of the Cambrian representatives of the Remopleuridioidea and the Trinucleoidea did not undergo metamorphosis. However, ontogeny of the Cambrian members of the Order Asaphida has remained unknown. This study documents the ontogeny of the Furongian asaphoidean ceratopygid trilobite, Proceratopyge cf. P. lata Whitehouse, from northern Victoria Land, Antarctica. Two stages for the protaspid phase, five developmental stages for the post-protaspid cranidia, and ten stages for the post-protaspid pygidia have been identified. Interestingly, the protaspis directly developed into a meraspis without metamorphosis. A new cladistic analysis resulted in a single most parsimonious tree, according to which the presence of the bulbous commutavi protaspis turns out to be a synapomorphy for Asaphidae + Cyclopygoidea, not a synapomorphy for the Order Asaphida as previously suggested. In addition, it is inferred that there was convergent evolution of indirectly-developing commutavi protaspides during the Furongian and Early Ordovician. Metamorphosis-entailing planktonic larvae evolved in many different metazoan lineages near the Cambrian–Ordovician transition, due to the escalating ecological pressure of the Great Ordovician Biodiversification Event. Since the bulbous commutavi protaspid morphology is thought to be an adaptation for a planktonic life mode, the convergent evolution of the indirect development in the three trilobite lineages at this period might have been a result of adaptation to the early phase of the Great Ordovician Biodiversification Event.
Data from: Recurrent hybridisation events between Primula vulgaris, P. veris and P. elatior (Primulaceae, Ericales) challenge the species boundaries: Using molecular markers to re‐evaluate morphological identifications
Three Primula species, Primula vulgaris, P. veris and P. elatior, have been objects of fascination for gardeners and botanists over several centuries. The species are able to hybridise, and where they co-occur, hybrids are commonly found. In Denmark, Møns Klint on the island of Møn and Købelev Skov on Lolland are examples of localities where all three species occur and where the hybrids P. ×digenea, the hybrid between P. vulgaris and P. elatior, and P. ×polyantha, the hybrid between P. veris and P. vulgaris, can also be found. To investigate relations between the species and their hybrids, 168 specimens from 10 geographical locations were sampled for genetic analysis using DNA markers and identified based on morphological traits, primarily inflorescense structure, the size, shape, colour and markings of corolla and leaf basis, leaf blade texture and hairiness. After identifying species-specific SNPs in the internal transcribed spacer sequence, these were used to resolve species and hybrid boundaries and status through a cleaved amplified polymorphic sequence assay. Polymorphisms in the chloroplast trnL sequence were used as a high-throughput marker and used to determine the maternal parent of hybrids. Ten simple sequence repeat markers were applied to obtain further insight into the genetic makeup of the accessions using Structure and Introgress, providing information of genetic variability within and between populations. Data analyses indicated that backcrossing of P. ×digenea hybrids with parental species has occurred, and that many of the P. ×digenea found in the study were later-generation hybrids rather than F1s. Analyses of P. ×polyantha specimens show mostly the expected pattern for primary hybrids but indications of P. veris ancestry of a P. vulgaris plant was discovered. Our results further indicate that some of the specimens initially identified as P. elatior include P. vulgaris among their progenitors and thus challenge currently accepted species boundaries.
Data from: Global database of matched Plasmodium falciparum and P. vivax incidence and prevalence records from 1985–2013
Measures of clinical incidence are necessary to help estimate the burden of a disease. Incidence is a metric not commonly measured in malariology because the longitudinal surveys required are costly and labour intensive. This database is an effort to collate published incidence records obtained using active case detection for Plasmodium falciparum and Plasmodium vivax malaria. The literature search methods, data abstraction procedures and data processing procedures are described here. A total of 1,680 spatio-temporally unique incidence records were collected for the database: 1,187 for P. falciparum and 493 for P. vivax. These data were gathered to model the relationship between clinical incidence and prevalence of infection and can be used for a variety of modelling exercises including the assessment of change in disease burden in relation to age and control interventions. The subset of data that have been used for such modelling exercises are described and identified.
1888 Harrison and Morton Top Hat - P
For more information about this item visit: https://bhpsite.org/ Source: Objaverse 1.0 / Sketchfab
P-8
vent pulmon 37 imágenes Source: Objaverse 1.0 / Sketchfab
Protein stable isotope fingerprinting (P-SIF): Pure culture samples, under various growth substrates
<p>Carbon stable isotope data for proteins extracted from a variety of pure culture samples.</p>
EOS-DATA-2016-01: Monte Carlo Pseudo Events for the Decays Bbar -> P mu X_nubar, P = D,pi
<p>This archive EOS-DATA-2016-01 contains pseudo events of the decays</p> <p> Bbar -> P mu X_nubar</p> <p>where X_nubar is either nubar or (nubar nu nubar), and P = D or pi. The archive<br /> complements the publication EOS-2016-01. The events are stored as binary files<br /> in the HDF5 format.</p>
Lepidium campestre, Fig in Häfliger & Wolf, Documenta Ciba Geigy, Dicot Weeds 1, p. 179
<p>uploaded by Plazi</p>
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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.