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Genetic datasets, climatic conditions at sampled localities, and occurrence data to: Ice age-driven range shifts of diploids and expanding autotetraploids within a conserved niche (Grünig, Patsiou & Parisod, 2024, New Phytologist)
<div> <h3><strong>This repository includes</strong></h3> - An overview of the raw sequencing reads deposited in the European Nucleotide Archive (ENA) for the 370 individuals sampled in 17 diploid and 19 tetraploid field populations <div>- Scripts used to genotype diploids and autotetraploids samples of <em>Biscutella laevigata</em> from ddRADseq data</div> <div>- Input data (as vcf format) used in population genetic analyses</div> <div>- Scripts used to run the different genetic analyses</div> <div>- Dataset of extracted climatic conditions at sampled localities</div> <div>- Occurrence dataset used for the climatic niche modelling</div> <br> <h3><strong>Description of the data and file structure</strong></h3> <strong>00.ENA_samples_correspondance.txt: </strong>provides ENA project ID, run ID (i.e. raw fastq files), sample ID, and alias for each sample included in the study.<br> <div> </div> <div><strong>1.scripts_reads_to_vcf.zip:</strong> consists of the following:</div> - <strong>1.reads_to_vcf.md: </strong>md file with scripts documenting the read quality check, demultiplexing, mapping, SNP calling using GATK4, and filtering steps<br> <div>- Additional scripts called within <strong>1.reads_to_vcf.md</strong>:</div> <div>-- 1.3. Mapping: <strong>02_run_mapping_XXX.py</strong> and <strong>BWA-mem_bisc1_sg.py</strong> scripts</div> <div>-- 1.4.a. HaplotypeCaller: <strong>03_V1_gvcf.py</strong></div> <div>-- 1.4.b. GDBI + genotypeGVCF: <strong>03_V3_gdbi_genotype_per100scaf.py</strong></div> <br> <div><strong>2.datasets_genetics.tar.gz</strong> consists of the following</div> <br> <div>- <strong>bisc_all370_diminDP15_tetraminDP30.vcf.gz</strong>: "Initial SNPs dataset" = biallelic SNPs fulfilling GATK quality hard filtering recommendations, present in at least 50% of samples. Genotypes with DP<15 for diploids and DP<30 for tetraploids are set to no-call. This vcf was used as basis for fastsimcoal dataset preparation, and as basis for subsequent selection of loci fulfilling requirements of each analysis. It includes 2246701 biallelic SNPs for 370 samples</div> <br> <div>- <strong>bisc_all370_diminDP15_tetraminDP30_MD05_pruned.vcf.gz:</strong> subset of the "Initial SNPs dataset" retaining SNPs called in at least 50% of samples, and pruned for Linkage disequilibrium. This vcf includes 107574 biallelic SNPs for 370 samples and was used in the analysis of the proportion of diploids diagnostic alleles shared by tetraploids.</div> <br> <div>- <strong>bisc_all370_diminDP15_tetraminDP30_MD01_pruned.vcf.gz: </strong>subset of the "Initial SNPs dataset", retaining SNPs called in at least 90% of samples, and pruned for Linkage disequilibrium. This vcf includes 4444 biallelic SNPs for 370 samples and was used in the analyses of Population diversity and differentiation (SpaGeDi, GenoDive, PCA), and f3-statistics.</div> <br> <div>- <strong>bisc_all370_diminDP15_tetraminDP30_MD0.1_pruned_MAC3rm.vcf.gz:</strong> subset of the "Initial SNPs dataset", retaining SNPs called in at least 90% of samples, pruned for Linkage disequilibrium, and with a minor allele count of 3. This vcf includes 2593 biallelic SNPs for 370 samples and was used in STRUCTURE analysis</div> <br><br> <div><strong>3.pres_2x.txt:</strong> list of the 128 diploid occurrences used in climatic niche modelling</div> <br> <div><strong>3.pres_4x_strat_reg.txt:</strong> list of the 924 tetraploid occurrences used in climatic niche modelling</div> <br> <div><strong>biscall_chelsa_ordered_noDEM.txt:</strong> climatic data extracted from the CHELSA dataset at sampled localities</div> <br> <div><strong>4.plot_GTfreqs.md:</strong> markdown file including scripts to plot allele and genotype frequencies</div> <br> <div> </div> <h3><strong>Sharing/Access information</strong></h3> Raw sequencing reads have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under the accession number PRJEB48869:<a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB48869"> https://www.ebi.ac.uk/ena/browser/view/PRJEB48869</a></div>
Fig. 2 in Old museum samples and recent taxonomy: A taxonomic, biogeographic and conservation perspective of the Niphargus tatrensis species complex (Crustacea: Amphipoda)
Fig. 2 Most parsimonious tree based on morphological characters; except for branch-length differences, identical topology was obtained regardless of the weighting scheme
Fig. 1 in Old museum samples and recent taxonomy: A taxonomic, biogeographic and conservation perspective of the Niphargus tatrensis species complex (Crustacea: Amphipoda)
Fig. 1 Morphological characters included in the analysis. (a–c) Inner lobe of maxilliped, showing flattened spines; a Niphargus aggtelekiensis "f. lurensis", b N. tatrensis "f. schneebergensis", c N.. aggtelekiensis, topotype. (d, e) Dactylus with (d) and without (e) additional spiniform seta. (f–h) Niphargus tatrensis, telson narrowed and concave in apical part (f = "forma schneebergensis", g = topotype, h = "forma reyersdorfensis"). (i–l) Niphargus aggtelekiensis, telson broad convex (i = topotype, j = "forma oethscerensis", k = "forma lunzensis", l = "forma salzburgensis")
Supplementary material 1 from: Unterweger PA, Klammer J, Unger M, Betz O (2018) Insect hibernation on urban green land: a winter-adapted mowing regime as a management tool for insect conservation. BioRisk 13: 1-29. https://doi.org/10.3897/biorisk.13.22316
Table with all captured species / morphotypes sorted by order, family and species / morphotype. : Explanation note: Collection: University of Tübingen, Evolutionary Biology of Invertebrates, Auf der Morgenstelle 28, 72076 Tübingen, Germany. Individuals with scientific species name that were checked by a taxonomic expert were counted as taxonomic species (s); all the other determinations were counted as morphotypes (m). Morphotypes are defined by the lowest practical taxonomic level (e.g. Hanula et al. 2009; Kutschbach-Brohl et al. 2010). In some cases, the family or the morphometric body length (in mm, numbers in column C, Mini: smaller than 1 mm) was counted as a morphotype (Daly 1985). In cases for which the determination was not validated by a taxonomic expert, our species determination was checked for plausibility in terms of its geographical occurrence via the Entomofauna Germanica (http://www.colkat.de, 2017.11.06). Alternatively (if no taxonomic name could be found), a classification letter / number was assigned for a morphotype. The provided author name refers to the lowest practical taxonomic level (e.g. Hanula et al. 2009; Kutschbach-Brohl et al. 2010). Validation: name of scientific expert who checked the taxonomic determination. Management type of meadow in autumn: mown /unmown. Plant compartment: flower head, stem, tuft, leaves. All numbers represent total sums of all sample sites over the entire study period. Brown-labelled species names are thought to have hibernated in the soil. Green-labelled species names could only be found in flower heads and stems. Black-labelled species occurred in all plant compartments without any preference for a specific plant compartment.
FIGURE 7 in Overview of Niphargidae (Crustacea: Amphipoda) in Belgium: distribution, taxonomic notes and conservation issues
FIGURE 7. Illustrations of some distinct body parts of population herein referred to as Niphargus sp. 1.
FIGURE 6 in Overview of Niphargidae (Crustacea: Amphipoda) in Belgium: distribution, taxonomic notes and conservation issues
FIGURE 6. Distribution of Niphargus sp. 1 (red circles) and unidentified species of Niphargus sp. (green circles) in Belgium. Data come from new records published for the first time in this study, while some records of Niphargus sp. come from published data (see text for details).
FIGURE 4 in Overview of Niphargidae (Crustacea: Amphipoda) in Belgium: distribution, taxonomic notes and conservation issues
FIGURE 4. Distribution of N.pachypus (left) and N.puteanus (right) in Belgium. Blue circles refer to data from published sources, while red circles refer to new records published for the first time in this study.
FIGURE 5 in Overview of Niphargidae (Crustacea: Amphipoda) in Belgium: distribution, taxonomic notes and conservation issues
FIGURE 5. Distribution of N.schellenbergi (left) and N.virei (right) in Belgium. Blue circles refer to data from published sources, while red circles refer to new records published for the first time in this study.
FIGURE 3 in Overview of Niphargidae (Crustacea: Amphipoda) in Belgium: distribution, taxonomic notes and conservation issues
FIGURE 3. Distribution of N. dimorphopus (left) and N. fontanus (right) in Belgium. Blue circles refer to data from published sources, while red circles refer to new records published for the first time in this study.
FIGURE 2 in Overview of Niphargidae (Crustacea: Amphipoda) in Belgium: distribution, taxonomic notes and conservation issues
FIGURE 2. Distribution of M. leruthi (left) and N. aquilex (right) in Belgium. Blue circles refer to data from published sources, while red circles refer to new records published for the first time in this study.
FIGURE 1 in Overview of Niphargidae (Crustacea: Amphipoda) in Belgium: distribution, taxonomic notes and conservation issues
FIGURE 1. Localities with Niphargidae in Belgium. Blue circles refer to data from published sources, while red circles refer to new records published for the first time in this study.
FIGURE 8 in Overview of Niphargidae (Crustacea: Amphipoda) in Belgium: distribution, taxonomic notes and conservation issues
FIGURE 8. Number of Niphargidae species per locality (left) and per 10x10 km quadrants (right) in Belgium.
FIGURE 5 in Lost species in Cameroon: rediscovery of the endangered freshwater crab, Louisea balssi (Bott, 1959) (Brachyura: Potamonautidae), with notes on its ecology and conservation
FIGURE 5. Louisea balssi (Bott, 1959), adult male CW 16.2 mm from Man's Crater Lake Manengouba, Cameroon (ZMB Crust. 30319). a, G1 ventral view; b, G1 dorsal view; c, G2 ventral view. Scale bar equals 1 mm (a,b), 2 mm (c).
FIGURE 6 in Lost species in Cameroon: rediscovery of the endangered freshwater crab, Louisea balssi (Bott, 1959) (Brachyura: Potamonautidae), with notes on its ecology and conservation
FIGURE 6. View of Man's Crater Lake Manengouba, Cameroon, showing the steep forested slopes that include the stream habitat of Louisea balssi (Bott, 1959).
FIGURE 3 in Lost species in Cameroon: rediscovery of the endangered freshwater crab, Louisea balssi (Bott, 1959) (Brachyura: Potamonautidae), with notes on its ecology and conservation
FIGURE 3. Louisea balssi (Bott, 1959), adult male CW 16.2 mm from Man's Crater Lake Manengouba, Cameroon (ZMB Crust. 30319). a, right chela frontal view; b, left chela frontal view; c, right cheliped carpus showing the first (distal) and second (proximal) carpal teeth; d, right cheliped merus showing the inferior margin with the large and prominent distal tooth and the toothed margin. Scale bar equals 5 mm (a, b), 2 mm (c, d).
FIGURE 4 in Lost species in Cameroon: rediscovery of the endangered freshwater crab, Louisea balssi (Bott, 1959) (Brachyura: Potamonautidae), with notes on its ecology and conservation
FIGURE 4. Louisea balssi (Bott, 1959), adult male CW 16.2 mm from Man's Crater Lake Manengouba, Cameroon (ZMB Crust. 30319). a, third maxilliped showing the faint vertical groove on the ischium, and the absence of a flagellum on the exopod; a, frontal view of right mandible showing small hard setose process at the junction between the palp segments; b, ventral view of the right mandible. Scale bar equals 2 mm (a), 1 mm (c, d).
FIGURE 2 in Lost species in Cameroon: rediscovery of the endangered freshwater crab, Louisea balssi (Bott, 1959) (Brachyura: Potamonautidae), with notes on its ecology and conservation
FIGURE 2. Louisea balssi (Bott, 1959), adult male CW 16.2 mm from Man's Crater Lake Manengouba, Cameroon (ZMB Crust. 30319). a, carapace dorsal view; b, carapace, frontal view; c, thoracic sternite. Scale bar equals 5 mm (a,b,c).
FIGURE 1 in Lost species in Cameroon: rediscovery of the endangered freshwater crab, Louisea balssi (Bott, 1959) (Brachyura: Potamonautidae), with notes on its ecology and conservation
FIGURE 1. Louisea balssi (Bott, 1959), adult male CW 16.2 mm from Man's Crater Lake Manengouba, Cameroon (ZMB Crust. 30319) (missing left periopod 5). Dorsal view of whole animal showing color when freshly collected. Scale bar equals 8 mm.
Supplementary material 1 from: Assmann T, Boutaud E, Buse J, Gebert J, Drees C, Friedman A-L-L, Khoury F, Marcus T, Orbach E, Renan I, Schmidt C, Zumstein P (2018) The tiger beetles (Coleoptera, Cicindelidae) of the southern Levant: from cybertaxonomy to conservation biolog. ZooKeys 734: 43-103. https://doi.org/10.3897/zookeys.734.21989
TIGER BEETLE ID : Disclaimer of warranties. You expressly understand and agree that your use of the app "TIGER BEETLES ID" is at your sole risk and that the app is provided "as is" and "as available" without warranty of any kind from the authors.
Supplementary material 3 from: Mandić R, Adžemović M, Marjanović Ž (2018) Conservation and trade of wild edible mushrooms of Serbia – history, state of art and perspectives. Nature Conservation 25: 31-53. https://doi.org/10.3897/natureconservation.25.21919
Annual amounts of mushrooms allowed to harvest (in kg, according to INCS) : Explanation note: The document provides table with official data on mushroom and truffle amounts that have been allowed to harvest since 1993, according to INCS.
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