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FIGURE 2. A in A naturalized diploid Fragaria sp. (Rosaceae) found in southern Chile as revealed by morphological, ploidy and cytogenetic analyses
FIGURE 2. A Fragaria-MEN specimen collected in Menetue, Araucania Region, Chile (Latitude 39º19'49'' S; Longitude 71º43'17'' W, 370 m.a.s.l.) maintained in the herbarium of the University of Talca (UTAL N° 6312). Scale = 1 cm.
Genetic structure and evolution of diploid Cochlearia in Iceland
<p>Within the northern European <em>Cochlearia</em> (Brassicaceae), considerable chromosome variation has taken place without corresponding morphological differentiation, which has resulted in an intricate species complex including two base chromosome numbers and several ploidy levels. Here, we dig into the<em> </em>situation in Iceland. The distribution, genetic structure, taxonomy and origin of the two <em>Cochlearia</em> cytotypes (2<em>n</em> = 12 and 2<em>n</em> = 14) present in Iceland are discussed. Chromosome counts indicate that the 2<em>n</em> = 12 populations are dominating along the coast, whereas only 2<em>n</em> = 14 has been reported for inland alpine populations. RADseq data support geographically structured genetic variation along the Icelandic coast, as well as environmentally structured genetic differentiation between coastal and alpine populations. The alpine populations show genetic and morphological affiliation with <em>C. groenlandica </em>(2<em>n</em> = 14), which is widely distributed in the Arctic, but more comprehensive sampling is needed to conclude on the taxonomical status of the Icelandic coastal plants. To uncover the origin of and phylogenomic relationship among the two chromosome variants, comparative whole-genome sequencing should be performed.</p> <div></div>
FIGURE 4 in Physical mapping of 45S and 5S rDNA and telomeric repeat loci in eight diploid hyacinth cultivars
FIGURE 4. Dendrogram of eight hyacinths species using between-groups linkge At the Euclidean distance of 20, the eight were clustered into group I, II and III.
FIGURE. FISH karyotype pattern diagram of 8 diploid hyacinth cultivars a.'Gypsy Queen'; b.'Purple sensation' c.'Pink pearl' d.'Gypsy princess' e.'Blue pearl' f.'Odysseus' g.'Yellowstone' h.'Red pearl' Red point: 45S rDNA loci; Green point: 45S rDNA loci; Yellow point: ITR sites in Physical mapping of 45S and 5S rDNA and telomeric repeat loci in eight diploid hyacinth cultivars
FIGURE. FISH karyotype pattern diagram of 8 diploid hyacinth cultivars a.'Gypsy Queen'; b.'Purple sensation' c.'Pink pearl' d.'Gypsy princess' e.'Blue pearl' f.'Odysseus' g.'Yellowstone' h.'Red pearl' Red point: 45S rDNA loci; Green point: 45S rDNA loci; Yellow point: ITR sites
FIGURE. Results of FISH physical mapping on metaphase chromosomes of hyacinth 1. The distribution of 45S rDNA (red arrow) and 5S rDNA (green arrow) signals on the chromosomes; 2. The distribution of telomeric repeats signals on the chromosomes; 3. Chromosome karyotype with 45S rDNA and 5S rDNA; 4. Chromosome karyotype with telomeric repeats. A. 'Gypsy Queen' B.'Purple sensation' C.'Pink pearl' D.'Gypsy princess' E.'Blue pearl' F.'Odysseus' G.'Yellow stone' H.'Red pearl' in Physical mapping of 45S and 5S rDNA and telomeric repeat loci in eight diploid hyacinth cultivars
FIGURE. Results of FISH physical mapping on metaphase chromosomes of hyacinth 1. The distribution of 45S rDNA (red arrow) and 5S rDNA (green arrow) signals on the chromosomes; 2. The distribution of telomeric repeats signals on the chromosomes; 3. Chromosome karyotype with 45S rDNA and 5S rDNA; 4. Chromosome karyotype with telomeric repeats. A. 'Gypsy Queen' B.'Purple sensation' C.'Pink pearl' D.'Gypsy princess' E.'Blue pearl' F.'Odysseus' G.'Yellow stone' H.'Red pearl'
FIGURE. Eight diploid hyacinth cultivars a in Physical mapping of 45S and 5S rDNA and telomeric repeat loci in eight diploid hyacinth cultivars
FIGURE. Eight diploid hyacinth cultivars a.'Gypsy Queen'; b.'Purple Sensation' c.'Pink Pearl' d.'Gypsy Princess' e.'Blue Pearl' f.'Odysseus' g.'Yellow Stone' h.'Red Pearl'
FIGURE 9 in A new diploid species belonging to the Odontophrynus americanus species group (Anura: Odontophrynidae) from the Espinhaço range, Brazil
FIGURE 9. Geographic distribution in Brazil of Odontophrynus juquinha sp. nov. related to the altitude. MG = Minas Gerais State, ES = Espírito Santo State, BA = Bahia State, GO = Goiás State.
FIGURE 4 in A new diploid species belonging to the Odontophrynus americanus species group (Anura: Odontophrynidae) from the Espinhaço range, Brazil
FIGURE 4. Odontophrynus juquinha sp. nov. dorsal color variation. Paratypes UFMG (A) 5518 (female), (B) 419, (C) 420, (D) 11118, (E) 5598, (F) 5597, (G) 5512, (H) 5511, (I) 11172, (J) 13901, (K) 5596 (female), (L) 13904.
FIGURE 2 in A new diploid species belonging to the Odontophrynus americanus species group (Anura: Odontophrynidae) from the Espinhaço range, Brazil
FIGURE 2. Odontophrynus juquinha sp. nov., UFMG 5516 (holotype), adult male in (A) dorsal and (B) ventral view.
FIGURE 5 in A new diploid species belonging to the Odontophrynus americanus species group (Anura: Odontophrynidae) from the Espinhaço range, Brazil
FIGURE 5. Live specimens of (A) Odontophrynus americanus, (B) O. lavillai, (C) O. cordobae, and (D) O. maisuma.
FIGURE 3 in A new diploid species belonging to the Odontophrynus americanus species group (Anura: Odontophrynidae) from the Espinhaço range, Brazil
FIGURE 3. Odontophrynus juquinha sp. nov., UFMG 5516 (holotype), adult male. (A) Left hand, (B) left foot, (C) lateral and (D) dorsal views of head.
FIGURE 8 in A new diploid species belonging to the Odontophrynus americanus species group (Anura: Odontophrynidae) from the Espinhaço range, Brazil
FIGURE 8. Tadpole of Odontophrynus juquinha sp. nov. collected at Serra do Cabral, lot UFMG 1581, stage 34: (A) Lateral view, (B) dorsal and ventral view of body, (C) oral disc.
FIGURE 1 in A new diploid species belonging to the Odontophrynus americanus species group (Anura: Odontophrynidae) from the Espinhaço range, Brazil
FIGURE 1. Odontophrynus juquinha sp. nov. (paratype UFMG 13903; SVL = 46.2 mm); live adult male. Parque Nacional da Serra do Cipó, Municipality of Santana do Riacho, Minas Gerais State, Brazil. Photo by F. Leal.
FIGURE 7 in A new diploid species belonging to the Odontophrynus americanus species group (Anura: Odontophrynidae) from the Espinhaço range, Brazil
FIGURE 7. (A) Advertisement call of Odontophrynus juquinha sp. nov. and (B) call including a suffix, unvouchered male from Serra do Cipó, municipality of Morro do Pilar, MG, 1 November 2010, air temperature 19.2°C. (C) Call including a prefix, unvouchered male from Serra do Cabral, municipality of Buenópolis, MG, 27 November 2012, air temperature 19.2°C.
FIGURE 6 in A new diploid species belonging to the Odontophrynus americanus species group (Anura: Odontophrynidae) from the Espinhaço range, Brazil
FIGURE 6. (A) Karyotype of a male Odontophrynus juquinha sp. nov. (2n = 2x = 22; FN = 44) after conventional Giemsa staining. Meiotic stages: (B) Diakinesis, (C) Metaphase I, (D) Metaphase II.
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>
Supplementary material 1 from: Morin DP, Alexander PJ, Beck JB, Windham MD, Bailey CD (2018) Deciphering the sexual diploid members of the Boechera suffrutescens complex (Brassicaceae, Boechereae). PhytoKeys 98: 15-50. https://doi.org/10.3897/phytokeys.98.24296
Representative pollen morphologies : Explanation note: A. S2X pollen of B. rollei (Morin 13, NMC). B. Potentially functional pollen from an A3X individual (Morin 8, NMC). C. Representative malformed non-functional pollen from A2X and some A3X individuals (Christ 20051, OSC).
Supplementary material 2 from: Morin DP, Alexander PJ, Beck JB, Windham MD, Bailey CD (2018) Deciphering the sexual diploid members of the Boechera suffrutescens complex (Brassicaceae, Boechereae). PhytoKeys 98: 15-50. https://doi.org/10.3897/phytokeys.98.24296
Analysis 1 : Explanation note: A. STRUCTURE bar plots with the highest likelihood for K = 5, 6, and 8 respectively. Instability was consistently noted across iterations at all values of K. B. An MDS plot demonstrates distinctness in TL-ro in three dimensions and TL-su in two dimensions. Calculations for optimal K were ambiguous and inconsistent, as were clustering patterns with regard to the B. constancei clusters (TL-co, PLSI-co and CD-co), particularly with regard to TL-co. MDS plots do not represent analyses, but are a visual interpretation of the dataset. TL-su and TL-ro are the most distinct and coherent clusters based on allele sharing distance.
Training material for Calling variants in non-diploid systems
<p>The majority of life on Earth is non-diploid and represented by prokaryotes, viruses and their derivatives such as our own mitochondria or plant’s chloroplasts. In non-diploid systems allele frequencies can range anywhere between 0 and 100% and there could be multiple (not just two) alleles per locus. The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between sequencing noise (abundant in all NGS platforms) and true low frequency variants. </p>
FIGURE 2. Limonium ophioides A. Habitat. B. Habit. C. Leaves and stems. D in Limonium ophioides and L. nichoriense (Plumbaginaceae), two new diploid species from Peloponnisos, Greece
FIGURE 2. Limonium ophioides A. Habitat. B. Habit. C. Leaves and stems. D. Detail of the inflorescence.
ScienceDex guides
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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.