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opencc-by-4.0Jun 2020View details →

The Cassandra retrotransposon landscape in sugar beet (Beta vulgaris): Recombination and re-shuffling leads to a high structural variability

Here we provide supplementary data for our study of non-autonomous Cassandra terminal-repeat retrotransposons in miniature (TRIMs) in sugar beet and related genomes. Cassandra sequences are distributed across the plant kingdom and share a unique feature: conserved 5S rDNA promoter motifs within their long terminal repeats (LTRs). This dataset contains two multiple sequence alignments and a sequence list of tandemly-arranged (TA) Cassandra sequences in FASTA format. Alignments cover LTR and internal regions of all Amaranthaceae Cassandra (Ama-Cassandra) from our study. This includes Cassandra full-length sequences from B. vulgaris (Ama_Cassandra_Beet_full-length) and C. quinoa (Ama_Cassandra_Quinoa_full-length). Sequence names include information on host plant, subfamily classification, localisation (scaffold), start and stop position, a Lab-unique TE identifier and sequence orientation. For the tandemly-arranged Cassandra sequences from sugar beet, we provide a sequence list of twelve sequences (Ama_Cassandra_TA_Beet_list). Here, sequence names refer to TA copy number, host, localisation (scaffold), start and stop position, a Lab-unique TE identifier and sequence orientation. All sequences were identified in the recent genome assemblys of B. vulgaris (RefBeet1.2; Dohm et al. 2014) and C. quinoa (ASM168347v1; Jarvis et al., 2017).

openother-openJan 2022View details →

19th Century United States Newspaper images predicted as Photographs with labels for "human", "animal", "human-structure" and "landscape"

The Dataset contains images derived from the Newspaper Navigator (news-navigator.labs.loc.gov/), a dataset of images drawn from the Library of Congress Chronicling America collection (<a href="https://chroniclingamerica.loc.gov/">chroniclingamerica.loc.gov/</a>).  <blockquote> [The Newspaper Navigator dataset] consists of extracted visual content for 16,358,041 historic newspaper pages in Chronicling America. The visual content was identified using an object detection model trained on annotations of World War 1-era Chronicling America pages, including annotations made by volunteers as part of the <a href="https://labs.loc.gov/work/experiments/beyond-words/">Beyond Words</a> crowdsourcing project. source:<a href="https://news-navigator.labs.loc.gov/"> https://news-navigator.labs.loc.gov/</a> </blockquote> One of these categories is 'photographs'. This dataset contains a sample of these images with additional labels indicating if the photograph has one or more of the following labels: "human", "animal", "human-structure" and "landscape" The data is organised as follows: <ul> <li>The images themselves can be found in `images.zip`</li> <li>`newspaper-navigator-sample-metadata.csv` contains metadata about each image drawn from the Newspaper Navigator Dataset.</li> <li>`multi_label.csv` contains the labels for the images as a CSV file</li> <li>`annotations.csv` conains the labels for the images with additional metadata</li> </ul> This dataset was created for use in an under-review Programming Historian tutorial (<a href="http://programminghistorian.github.io/ph-submissions/lessons/computer-vision-deep-learning-pt2">http://programminghistorian.github.io/ph-submissions/lessons/computer-vision-deep-learning-pt2</a>) The primary aim of the data was to provide a realistic example dataset for teaching computer vision for working with digitised heritage material. The data is shared here since it may be useful for others. This data documentation is a work in progress and will be updated when the Programming Historian tutorial is released publicly. The metadata CSV file contains the following columns: - filepath - pub_date - page_seq_num - edition_seq_num - batch - lccn - box - score - ocr - place_of_publication - geographic_coverage - name - publisher - url - page_url - month - year - iiif_url

opencc-by-4.0Jan 2023View details →

Supplementary material for "Surface frustration re-patterning underlies the structural landscape and evolvability of fungal orphan candidate effectors"

Tables Table S1. List of fungal genomes analyzed in this work, associated references and properties. Table S2. List of all secreted proteins less than 300 amino-acids from the 20 fungal genomes. The table includes Signalp4.0 output, mature sequence, Espritz % disorder, pfam domains, AlphaFold top prediction pLDDT and the associated pdb file in Dataset S1. Table S3. Top Hits to pdb database for all OCE structures. 'network_node_name' corresponds to the portein identifier in the OCE structure similarity network provided in Dataset S3. 'Hidef_raw_community' corresponds to groups of structural OCE analogs identified by HiDEF community detection performed on the network provided in Dataset S3. Table S4. Table S4. List of the 62 major OCE folds with associated statistics. Columns I to AB provide the number of occurrences per species. Note that the actual number of members per species might be underestimated due to the stringent pipeline used for OCE identification (excluding proteins larger than 300 amino acids or containing PFAMs for instance).   Table S5. Relative surface exposure, conformational flexibility and conservation data mapped on residues of members of the Alt-A1 and BoNT families. RMSD, root mean square deviation for all aligned atoms; Conservation, percentage conservation in multiple structure alignment. Table S6. Assignment of NCBI accessions to MMseqs clusters and assignment of MMseqs clusters to HMM matching-based super-clusters. Table S7. Co-mutation occurrences and associated p-values in two OCE clades from the Alt-A1 and KP6 families. Table S8. Amino acid properties inferred from mutation scans and frustration analyses in Alt-A1 cluster yellow1 and KP6 cluster 43. 'Number of aa variants' corresponds to the number of different amino acids found at each position (deletion counts as 1). 'Alanine scan ∆Z' and 'Deletion scan ∆Z' correspond to the difference between Z-score for the native protein agains itself and Z-score for the native protein against mutant at each position (either Alanine replacement or 5-aa deletion). 'Destabilization factor' is the average of column E and F. 'Stabilization factor' corresponds to the difference between expected structural variation due to destabilization factor and the observed structural variation in multiple mutants. 'netEffect' is difference between column G and H. 'Max co-mutation %' is the highest frequency of co-mutation observed with other residues in natural variants, with 'Min co-mutation p-value (Bonferroni corrected)' the associated p-value.Table S9.  Sequence and delta Z of natural variants and mutants from AA1_cl25 Table S9. List of natural variants and in silico mutants from the Alt-A1 cluster 25 analyzed in this work, including protein sequence and structure comparison scores (comparison with the reconstructed clade ancestor n0). Table S10. List of natural variants and in silico mutants from the KP6 cluster 43 analyzed in this work, including protein sequence and structure comparison scores (comparison with the reconstructed clade ancestor n0). Table S11. Summary statistics for the phylogenetic trees of 15 OCE clades analyzed for structure and frustration evolution. Table S12. Mapping of structural and frustration data onto phylogenetic trees for 15 OCE clades. The corresponding trees and protein structures are provided in Dataset S7. Datasets Dataset S1. AlphaFold rank1 models for 3 927 OCEs (.pdb format). Dataset S2. Pairwise structure comparison for 3 911 OCE. DALI matrix output containing pairwise Z-scores. Dataset S3. Network file including 2 561 OCEs with 3 or more vertices of Z-score weight 5.2 or more, in .sif and .xgmml formats. Dataset S4. Videos illustrating the mapping of relative surface exposure and structural variability in Alt-A1 and BoNT groups, amino-acids conservation, co-selected mutation patches and residue net stabilization effects on Alt-A1 clade 25 ancestor and KP6 cluster 43 ancestor. Color scales are as in Figure 2 and 3 respectively (.mp4 format). Dataset S5. Phylogenetic trees (.nwk), ancestral (.fasta) and modern variant (.faa) sequences, and AlphaFold best protein models (.pdb) for members of KP6 cluster 43 and Alt-A1 cluster 25. The archive includes 140 Alt-A1 protein structure and 128 KP6 protein structures. Dataset S6. Best predicted structures for 917 natural variants and mutants of AA1_cl25 and 801 natural variants and mutants of KP6_cl43 (.pdb format). Dataset S7. Phylogenetic trees (.nwk) and AlphaFold best protein models (.pdb) for 15 OCE clades. The file includes 2 598 protein structures distributed from clades AA1_s (139), AA1_t (135), AA1_y1 (140), AA1_y2 (90), AA1_y3 (128), BoNT_s (291), CIP_s (167), CIP_t (231), crystallin (233), GNK2 (189), KP6_cl3 (203), KP6_cl26 (111), KP6_cl43 (123), KP6_cl96 (231), KP6_cl242 (187). Text and Figures Text S1. Contains supplementary methods, results and figures S1 to S13.

opencc-by-4.0Apr 2023View details →

Dataset (81 forest parcels) supplementing the publication "Owner attitudes and landscape parameters drive stand structure and valuable habitats in small-scale private forests of Lower Saxony (Germany)"

The dataset about 81 small-scale private forest parcels contains the answer variables and predictors used in the publication "Owner attitudes and landscape parameters drive stand structure and valuable habitats in small-scale private forests of Lower Saxony (Germany)".

opencc-by-4.0Jul 2023View details →

ScRAPv20230731: Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae

Saccharomyces cerevisiae Reference Assembly Panel (ScRAP) v20230731 > The haplotype-resolved and/or collapsed T2T genome assemblies for 142 S. cerevisiae strains isolated from diverse geographical and ecological niches.

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Landscape structure and farming management interacts to modulate pollination supply and crop production in blueberries

Pollination services are affected by landscape context, farming management, and pollinator community structure, all of which impact flower visitation rates, pollen deposition and final production. We studied these processes in Argentina for Highbush Blueberry crops which depend on pollinators to produce marketable yields. We studied how land cover and honeybee stocking influence the abundance of wild and managed pollinators in blueberry crops, using structural equation modeling to disentangle the cascading effects through which pollinators contribute to blueberry fruit number, size, nutritional content and overall yield. All pollinator functional groups responded to landscape changes at a spatial scale under 1000 m, and the significance or direction of the effects were modulated by the field-level deployment of honeybee hives. Fruit diameter increased with pollen deposited, but decreased with honeybee abundance, which, had indirect effects on fruit acidity and sugar content. Honeybees had a positive effect on the number of fruit produced by the plants and also benefited the overall yield (kg plant-1) through independent effects on both the quality and quantity components of fruit production. Synthesis and applications: Deployment of beehives in blueberry fields can buffer, but not compensate for the negative effects on honeybee abundance produced by surrounding large scale none-flowering crops. Such compensation would require high-quality beehives by monitoring their health and strength. The contribution of honeybees to crop production is not equal across production metrics. That is, higher abundance of honeybees increases the number of berries produced, but at the cost of smaller and more acidic fruits, potentially reducing market value. Growers must consider this trade-off between fruit quantity and quality when actively managing honeybee abundance.

opencc-zeroNov 2023View details →

opencc-by-4.0Mar 2020View details →

Рис. 2. Изменение виΑового богатства и таксономической структуры зонаΛьных фаун прямокрыΛых северо-востока Русской равнины. Fig. 2. Changes in species richness and taxonomic structure of Orthoptera fauna of the Russian Plain. in Fauna and landscape-zonal distribution of Orthoptera in the Komi Republic (Russia)

Рис. 2. Изменение виΑового богатства и таксономической структуры зонаΛьных фаун прямокрыΛых северо-востока Русской равнины. Fig. 2. Changes in species richness and taxonomic structure of Orthoptera fauna of the Russian Plain.

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Data from: Context matters: the landscape matrix determines the population genetic structure of temperate forest herbs across Europe

Context. Plant populations in agricultural landscapes are mostly fragmented and their functional connectivity often depends on seed and pollen dispersal by animals. However, little is known about how the interactions of seed and pollen dispersers with the agricultural matrix translate into gene flow among plant populations. Objectives. We aimed to identify effects of the landscape structure on the genetic diversity within, and the genetic differentiation among, spatially isolated populations of three temperate forest herbs. We asked, whether different arable crops have different effects, and whether the orientation of linear landscape elements relative to the gene dispersal direction matters. Methods. We analysed the species' population genetic structures in seven agricultural landscapes across temperate Europe using microsatellite markers. These were modelled as a function of landscape composition and configuration, which we quantified in buffer zones around, and in rectangular landscape strips between, plant populations. Results. Landscape effects were diverse and often contrasting between species, reflecting their association with different pollen- or seed dispersal vectors. Differentiating crop types rather than lumping them together yielded higher proportions of explained variation. Some linear landscape elements had both a channelling and hampering effect on gene flow, depending on their orientation. Conclusions. Landscape structure is a more important determinant of the species' population genetic structure than habitat loss and fragmentation per se. Landscape planning with the aim to enhance the functional connectivity among spatially isolated plant populations should consider that even species of the same ecological guild might show distinct responses to the landscape structure.

opencc-zeroDec 2021View details →

opencc-by-4.0Jan 2022View details →

Riparian buffers maintain aquatic trophic structure in agricultural landscapes

Supporting data and R code for the publication entitled "Riparian buffers maintain aquatic trophic structure in agricultural landscapes".

opencc-by-4.0Feb 2022View details →

Tree size, microhabitat diversity and landscape structure determine the value of isolated trees for bats in farmland

Isolated trees are increasingly recognised as playing a vital role in supporting biodiversity in agricultural landscapes, yet their occurrence has declined substantially in recent decades. Most bats in Europe are tree-dependent species that rely on woody elements in order to persist in farmlands. However, isolated trees are rarely considered in conservation programs and landscape planning. Further investigations are therefore urgently required to identify which trees – based on both their intrinsic characteristics and their location in the landscape – are particularly important for bats. We acoustically surveyed 57 isolated trees for bats to determine the relative and interactive effects of size, tree-related microhabitat (TreM) diversity and surrounding landscape context on bat activity. Tall trees with large diameter at breast height and crown area positively influenced the activity of Pipistrellus pipistrellus and small Myotis bats (Myotis spp.) while smaller and thinner trees favoured M. myotis activity. The diversity of TreMs that can be used as roosts had a positive effect on (i) Barbastella barbastellus activity only when trees were relatively close (10% within 100 radius scale). The potential benefits of isolated trees for bats result from ecological mechanisms operating at both tree and landscape scales, underlining the crucial need for implementing a multi-scale approach in conservation programs. Maintaining the largest and most TreM-diversified trees located in the most heterogeneous agricultural landscapes will provide the greatest benefits.

opencc-by-4.0Dec 2023View details →

Figure 5 in Landscape biogeography and population structuring of a facultatively amphidromous galaxiid fish, Galaxias brevipinnis

Figure 5. – Bar plots showing density of Galaxias brevipinnis larvae per m3 of water in plume, near shore, and off shore sites in large river (left) and small river (right) sites. The Dart River, Reese River, Greenstone River, and Buckler Burn are tributaries of Lake Wakatipu while Makarora River, Matukituki River, Boundary Creek, and Albert Burn are tributaries of Lake Wānaka. No larvae were collected in near shore and off shore samples from Greenstone River.

opencc-by-4.0Dec 2023View details →

Figure 3. – Average STRUCTURE results aggregated using CLUMPAK for populations 2–6 and 9. K in Landscape biogeography and population structuring of a facultatively amphidromous galaxiid fish, Galaxias brevipinnis

Figure 3. – Average STRUCTURE results aggregated using CLUMPAK for populations 2–6 and 9. K = 6 was selected as the most likely population estimate using Evanno's method. STRUCTURE initially separated the lakes draining to the east coast (L. Wānaka and L. Wakatipu) from all other sites at K = 2. The West Coast lakes were split away next (K = 3), with L. Moeraki and L. Paringa splitting at K = 4 and L. Cristabel at K = 5. East coast L. Wānaka and L. Wakatipu were split at K = 6. L. Paringa and L. Moeraki are split form each other at K = 9.

Figure 1 in 'Mainland-island' population structure of a terrestrial salamander in a forest-bocage landscape with little evidence for in situ ecological speciation

Figure 1. ContinentalFrancewiththedepartmentMayennehighlighted (A) andhabitatmodelforthe Fire salamander indepartment Mayenne (B). Themap representsthe habitat suitability model Ps = (1/ (1 + exp(−0.0303*percent_forest_cover-0.00562*altitude-0.0299*percent_hedgerow_cover + 1.769))) and was visualized with ILWIS 3.6 software58, available at https://52north.org/software/software-projects/ilwis/. Habitat suitability increases from deep blue with a probability of occurrence of zero to deep red with a probability of occurrence at unity (see colour bar). Prime fire salamander habitats are found at higher altitudes and are forested (in black) or with a dense hedgerow cover. Populations genetically investigated are located in and around the largely deciduous forests Forêt de Bourgon (FB) and Bois de Hermet (BH) and listed in Table 1.The outer geographicalcoordinates of the department are 1.239–0.049W and 47.733–48.568N.

Figure 3 in 'Mainland-island' population structure of a terrestrial salamander in a forest-bocage landscape with little evidence for in situ ecological speciation

Figure 3. (A) Clustering of pairwise Fst-values of Kottenforstfire salamanderpopulations (localities K01-K47) with the UPGMA-method. Numbers K01-K27 represent populations in the western section of the forest and K28-K47 represent populationsin the eastern section of the forest. The basal cluster at Fst <0.04 is composed of two groups (shaded) composed of mostly eastern (14/16 = 88%) or mostlywestern localities (14/15 = 93%). Populations breeding in streams are shown by the letter S. Note that populations that join the dendrogram at higher Fst-values are characterized by mostlysmall effectivepopulation sizes (Ňe ≤ 10, indicated by small open dots; X – Ňe not determined). B top panel - Populationsplotted along the firstand second axis of a principal component analysis. Middle panel - Ellipses represent means ± standarddeviation for sevenstream populations (left ellipse) and 40 non-streampopulations (right ellipse). Lower panel - Ellipsesrepresent means ± standard deviation forthe western (left) and eastern (right) sectionof the Kottenforst, forsmall populations (Ňe ≤ 10) shown by interruptedlines andfor larger populations (Ňe> 10) shown by uninterrupted lines. Notethat for the larger populations the ellipses for western and eastern localities do not overlap.

Figure 4. MicrosatellitepopulationgeneticdataforthefiresalamanderintheKottenforst, Germany21,24 in 'Mainland-island' population structure of a terrestrial salamander in a forest-bocage landscape with little evidence for in situ ecological speciation

Figure 4. MicrosatellitepopulationgeneticdataforthefiresalamanderintheKottenforst, Germany21,24 analyzed in the framework of allopatric speciation, i.e. a secondary spatial contact of a western pond-breeding lineage and an eastern stream-breeding lineage. The 95% credible cline regions are shown by grey shading. Solid and open round symbolsrepresent larger (Ňe> 10) andsmall populations (Ňe ≤ 10), respectively. Note that the stream-breeding populations that gave the composite genotype its name are all located in the eastern section of the Kottenforst (six data points indicated with a forward slash (/). One 'intermittent stream' in the western section is indicated by a backward slash. Also note the paucity of data at and around the steepest part of the clines. A – loadings on the first PC axis versus geographical distance. The clinecentre is at km 365.3 of the Universal Transverse Mercator (UTM) grid. Cline width is 3952 m. B – frequency of the stream-breeding genotype versus distance (after21). Thecline centre is at UTM km 365.1 and the cline widthis 1108 m. For model details see Supplementary Information VI.

Figure 2 in 'Mainland-island' population structure of a terrestrial salamander in a forest-bocage landscape with little evidence for in situ ecological speciation

Figure 2. (A) Clustering of pairwise Fst-values of firesalamander populations (Mayenne localities 1–41) with the UPGMA-method. The basal cluster at Fst <0.010 is mostly composed of forest populations (F, 17/21 = 81%) whereas populationsthat jointhe dendrogramat higher Fst-values are mostly fromthe bocage (B, 14/20 = 70%). At Fst> 0.025 the contribution of the bocage populations is eightout of eight. Notethat populations thatjoin the dendrogram at the highest Fst-values are characterizedby mostly small effective population sizes (Ňe ≤ 10, indicated by small open dots). (B) Populations plotted along the first and second axis of a principal component analysis. The 23 forest populations are shown by small solid round symbols and the solid ellipse represents the mean ± standard deviation. Eighteenpopulations from the bocageare shown by large open round symbols, with the mean ± standard deviation shown bythe widerellipse with the interrupted line.

opencc-by-4.0Dec 2020View details →

Bauder Et Al. - Landscape features fail to explain spatial genetic structure

RMarkdown script and data in an Excel sheet to evaluate spatial genetic structure in white-tailed deer across Ohio and compare the support for isolation by distance (IBD) and isolation by landscape resistance (IBR) models in explaining this structure. We used genetic data from 619 individual deer from 24 counties across Ohio tested at 11 microsatellites and haplotypes from a 547-bp fragment of the mitochondrial DNA control region. We used spatial and non-spatial genetic clustering tests to evaluate genetic structure in both types of genetic data and empirically optimized landscape resistance surfaces to compare IBD and IBR using microsatellite data. v2 (BauderEtAl_Files_for_archiving2.zip) includes additional and updated files not in v1.