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15,277 results for “GENETICS”
Genetic diversity and efficacy of natural selection in spiders with pre-copulatory sexual cannibalism
<p>Factors that increase reproductive variance among individuals act to reduce effective population size (Ne), which accelerates loss of genetic diversity and decreases efficacy of purifying selection. These factors include sexual cannibalism, offspring investment, and mating system. Pre-copulatory sexual cannibalism where the female consumes the male prior to mating exacerbates this effect. We performed comparative transcriptomics in two spider species, the cannibalistic Trechaleoides biocellata and the non-cannibalistic T. keyserlingi, to generate genomic evidence to support these predictions. First, we estimated heterozygosity and found that genetic diversity is relatively lower in the cannibalistic species. Second, we calculated dN/dS ratios as a measure of purifying selection, higher dN/dS ratio indicated relaxed purifying selection in the cannibalistic species. These results are consistent with the hypothesis that sexual cannibalism impacts operational sex ratio and demographic processes, which interact with evolutionary forces to shape the genetic structure of populations. However, other factors such as the mating system and life-history traits contribute to shape Ne. Comparative analyses across multiple contrasting species-pairs would be required to disentangle these effects. Our study highlights that extreme behaviours such as pre-copulatory cannibalism may have profound eco-evolutionary effects. </p>
Data and code from: Evaluating genomic offset predictions in a forest tree with high population genetic structure
<p>Predicting how tree populations will respond to climate change is an urgent societal concern. An increasingly popular way to make such predictions is the genomic offset (GO) approach, which aims to use genomic and climate data to identify populations that may experience climate maladaptation in the near future. More precisely, GO tries to represent the change in allele frequencies required to maintain the current gene-climate relationships under climate change. However, the GO approach has major limitations and, despite promising validation of its predictions using height data from common gardens, it still lacks broad empirical testing. In the present study, we evaluated the consistency and empirical validity of GO predictions in maritime pine (<em>Pinus pinaster</em> Ait.), a tree species from southwestern Europe and North Africa with a marked population genetic structure. First, gene-climate relationships were estimated using 9,817 SNPs genotyped in 454 trees from 34 populations; and candidate SNPs potentially involved in climate adaptation were identified. Second, GO was predicted using four methods, namely Gradient Forest (GF), Redundancy Analysis (RDA), latent factor mixed model (LFMM) and Generalised Dissimilarity Modeling (GDM), two sets of SNPs (candidate and control SNPs) and five climate general circulation models (GCMs) to account for uncertainty in future climate predictions. Last, the empirical validity of GO predictions was evaluated within a Bayesian framework by estimating the associations between GO predictions and two independent data sources: mortality data from National Forest Inventories (NFI), and mortality and height data from five common gardens in contrasting environments. We found high variability in GO predictions across methods, SNP sets and GCMs. Regarding validation, GO predictions with GDM and GF (and to a lesser extent RDA) based on the candidate SNPs showed the strongest and most consistent associations with mortality rates in common gardens and NFI plots. We found almost no association between GO predictions and tree height in common gardens, most likely due to the overwhelming effect of population genetic structure on tree height in this species. Our study demonstrates the imperative to validate GO predictions with a range of independent data sources before they can be used as informative and reliable metrics in conservation or management strategies.</p>
Fig. 2 in Genetic diversity of Egyptian populations of the African Common Toad (Sclerophrys regularis, Reuss 1833)
Fig. 2. Phylogenetic tree of African Common Toad, using COI haplotypes based on the Maximum Likelihood method. Numbers refer to localities mentioned in the text: 1. Sharm El-Shaikh; 2. Arish; 3. Ismailia; 4. Damietta; 5. Alexandria; 6. Matrouh; 7. Gharbiya; 8. Cairo; 9. SiwaOasis; 10. Bani Sweif; 11. Menia; 12. Sohag; 13. Qena; 14. Aswan.
Elution profiles and protein interaction data accompanying "Ancient eukaryotic protein interactions illuminate modern genetic disorders"
<div> <p> </p> <table> <tbody> <tr> <td> <h2><strong>DESCRIPTION</strong></h2> </td> <td> <h2><strong>FILENAME</strong></h2> </td> <td> <h2><strong>LOCATION</strong></h2> </td> </tr> <tr> <td> <p>LECA 10K OG set</p> </td> <td> <p>leca_ogs_annotated.xlsx</p> </td> <td> <p>Paper, Table S1</p> <p>Zenodo</p> </td> </tr> <tr> <td> <p>Summary of biological resources</p> </td> <td> <p>resource_summary.xlsx</p> </td> <td> <p>Paper, Table S2</p> <p>Zenodo</p> </td> </tr> <tr> <td> <p>LECA interactome (complexes)</p> </td> <td> <p>leca_ppis_fdr10_clustered_annotated.xlsx</p> </td> <td> <p>Paper, Table S3</p> <p>Zenodo</p> </td> </tr> <tr> <td> <p>CFMS - ref proteomes</p> </td> <td> <p>cfms_ref_proteomes.xlsx</p> </td> <td> <p>Paper, Table S4</p> <p>Zenodo</p> </td> </tr> <tr> <td> <p>ML - top algorithms</p> </td> <td> <p>tpot_top_algorithms.xlsx</p> </td> <td> <p>Paper, Table S5</p> <p>Zenodo</p> </td> </tr> <tr> <td> <p>LECA interactome (pairwise)</p> </td> <td> <p>leca_ppis_fdr10_pairwise.csv</p> </td> <td> <p>Zenodo</p> </td> </tr> <tr> <td> <p>UniProt Subcellular Localization IDs</p> </td> <td> <p>uniprot_localization_codes.xlsx</p> </td> <td> <p>Zenodo</p> </td> </tr> <tr> <td> <p>Dollo parsimony - ref proteomes</p> </td> <td> <p>dollo_parsimony_ref_proteomes.xlsx</p> </td> <td> <p>Zenodo</p> </td> </tr> <tr> <td> <p>Dollo parsimony - input trait matrix</p> </td> <td> <p>dollo_parsimony_count_matrix.tsv</p> </td> <td> <p>Zenodo</p> </td> </tr> <tr> <td> <p>CFMS - raw elution profiles</p> </td> <td> <p>amorphea_raw_elution_vectors.csv</p> <p>excavata_raw_elution_vectors.csv</p> <p>tsar_raw_elution_vectors.csv</p> <p>archaeplastida_raw_elution_vectors.csv</p> </td> <td> <p>Zenodo</p> </td> </tr> <tr> <td> <p>CFMS - normalized elution profiles</p> </td> <td> <p>amorphea_norm_elution_vectors.csv</p> <p>excavata_norm_elution_vectors.csv</p> <p>tsar_norm_elution_vectors.csv</p> <p>archaeplastida_norm_elution_vectors.csv</p> </td> <td> <p>Zenodo</p> </td> </tr> <tr> <td> <p>CFMS/APMS - complete feature matrix</p> </td> <td> <p>feature_matrix.csv</p> </td> <td> <p>Zenodo</p> </td> </tr> <tr> <td> <p>ML - top features</p> </td> <td> <p>linearsvc_top_100_features.xlsx</p> </td> <td> <p>Zenodo</p> </td> </tr> <tr> <td> <p>OMIM disease propagation, statistics</p> </td> <td> <p>omim_disease_propagation_stats.xlsx</p> </td> <td> <p>Zenodo</p> </td> </tr> <tr> <td> <p>OMIM disease propagation, top 20 hits per disease</p> </td> <td> <p>omim_disease_propagation_top20hits_per_disease.xlsx</p> </td> <td> <p>Zenodo</p> </td> </tr> <tr> <td> <p>Curated OMIM gene-disease relationships for LECA OGs</p> </td> <td> <p>omim_disease_network.tsv</p> </td> <td> <p>Zenodo</p> </td> </tr> <tr> <td>Curated OMIM gene-disease relationships for human UniProt IDs</td> <td>omim_disease_groups.csv</td> <td>Zenodo</td> </tr> </tbody> </table> </div> <p> </p>
Fig. 2 in Genetic characterization and description of Leishmania (Leishmania) ellisi sp. nov.: a new human-infecting species from the USA
Fig. 2 Phylogenetic tree demonstrating the relative position of Leishmania sp. strain 218-L139 based on a concatenated sequence comprising several nuclear loci. Phylogenetic tree demonstrating the relative position of Leishmania strain 218-L139 (brown star) based on alignment of a concatenated sequence comprising the 18S rDNA, 28S rDNA, CKIIα, GAPDH, and RPOIILS nuclear sequences. The alignment contains 6577 positions from 33 taxa. The tree was built using maximum likelihood (1000 bootstrap replicates) and Bayesian
Fig. 1 in Genetic characterization and description of Leishmania (Leishmania) ellisi sp. nov.: a new human-infecting species from the USA
Fig. 1 Morphology of Leishmania strain 218-L139 promastigotes and amastigotes. Cultured Leishmania strain 218-L139 promastigotes as observed under DIC microscopy following growth in complete RPMI culture medium without gentamicin (A). Giemsa-stained touch preparation made from a cutaneous lesion, showing Leishmania strain 218-L139 amastigotes inside a mononuclear phagocyte in addition to free amastigotes (B). Giemsastained smear of cultured promastigotes of Leishmania strain 218-L139 grown in gentamicin-free complete RPMI medium (C)
Fig. 3 in Genetic characterization and description of Leishmania (Leishmania) ellisi sp. nov.: a new human-infecting species from the USA
Fig. 3 Phylogenetic tree demonstrating the relative position of Leishmania strain 218-L139 based on partial maxicircle genome sequences. Phylogenetic tree demonstrating the relative position of Leishmania strain 218-L139 (brown star) based on alignment of partial maxicircle genome sequences. The alignment contains 9471 positions from 67 taxa. The tree was built using maximum likelihood (1000 bootstrap replicates) and the TVM + F + I + G4 model, and Bayesian inference using the GTR + I + G model where the proportion of invariable sites was set to 0.1. Posterior probability values and bootstrap support are reported for each node (pp/bs). The tree was rooted with the Strigomonas/Blechomonas/Herpetomonas clade. The relative position of each Leishmania subgenus is shown to the right of the corresponding clades (Leishmania, Sauroleishmania, Viannia, Mundinia). The scale bar represents the number of substitutions per site
Data from: Female-biased population sex ratios caused by genetic rather than ecological mechanisms in dwarf willow (Salix herbacea L.)
<p>Biased sex ratios among reproductive individuals are common in plants, but the underlying mechanisms, as well as the evolutionary consequences, are not well understood. The classical theory of Düsing and Fisher predicts an equal primary sex ratio at seed production, based on the selective advantage of the rare sex. Biased sex ratios among reproductive plants can arise from sexual dimorphism in survival and flowering. Sex ratio biases can also be present from the seed stage; in these cases, assumptions of Düsing's and Fisher's theory, for example, random mating or demographic equilibrium, are thought to be violated.</p> <p>We investigated mechanisms leading to female-biased sex ratios in the arctic-alpine dwarf willow <em>Salix herbacea</em> L. We studied sex ratios in three natural populations over three years as well as in 29 crosses (full-sib families) under controlled conditions over four growth periods. We tested whether sex ratio was associated with habitat parameters (elevation and snowmelt time), or with germination, survival or flowering, and whether females and males differed in size or flowering that may cause observation bias.</p> <p>We detected a strong and consistent female bias, both in natural populations (sex ratio [proportion of females]: 0.71-0.82) and in our controlled experiment (overall sex ratio: 0.70-0-72). Female bias became more pronounced with increasing elevation. Our data did not support sexual dimorphism in size or flowering. Family sex ratios varied largely (from 0.25 to 1), including many female-biased families, unbiased families and two male-biased families. Families with lower germination, seedling establishment, survival or flowering did not have stronger female bias, indicating that intrinsically higher survival or flowering in females does not explain overall female bias. </p> <p>Synthesis: Our results suggest that sex ratio bias in <em>S. herbacea</em> is already present in seeds and does not arise through intrinsic differences between sexes. Candidate mechanisms that can lead to both overall female bias and variation in sex ratio among families are meiotic drive or cyto-nuclear interactions. The pioneer habit of <em>Salix</em> may lead to non-equilibrium population dynamics that allow for the long-term persistence of variable genetic sex ratio distortion systems that arise from genetic conflict.</p>
Multinational evaluation of genetic diversity indicators for the Kunming-Montreal Global Biodiversity Framework
<p>Under the recently adopted Kunming-Montreal Global Biodiversity Framework, 196 Parties committed to report the status of genetic diversity for all species. To facilitate reporting, three genetic diversity indicators were developed, two of which focus on processes contributing to genetic diversity conservation: maintaining genetically distinct populations and ensuring populations are large enough to maintain genetic diversity. The major advantage of these indicators is that they can be estimated with or without DNA-based data. However, demonstrating their feasibility requires addressing the methodological challenges of using data gathered from diverse sources, across diverse taxonomic groups, and for countries of varying socioeconomic status and biodiversity levels. Here, we assess the genetic indicators for 919 taxa, representing 5,271 populations across nine countries, including megadiverse countries and developing economies. Eighty-three percent of taxa assessed had data available to calculate at least one indicator. Our results show that although the majority of species maintain most populations, 58% of species have populations too small to maintain genetic diversity. Moreover, genetic indicator values suggest that IUCN Red List status and other initiatives fail to assess genetic status, highlighting the critical importance of genetic indicators.</p>
The genetic basis of incipient sexual isolation in Drosophila melanogaster
<p>Speciation is a fundamental evolutionary process, but the genetic changes accompanying speciation are difficult to determine since true species do not produce viable and fertile offspring. Partially reproductively isolated incipient species are useful for assessing genetic changes that occur prior to speciation. Drosophila melanogaster from Zimbabwe, Africa are partially sexually isolated from other <em>D. melanogaster</em> populations whose males have poor mating success with Zimbabwe females. We used the North American <em>D. melanogaster</em> Genetic Reference Panel (DGRP) to show that there is significant genetic variation in the mating success of DGRP males with Zimbabwe females, to map genetic variants and genes associated with variation in mating success, and to determine whether mating success to Zimbabwe females is associated with other quantitative traits previously measured in the DGRP. Incipient sexual isolation is highly polygenic and associated with the common African inversion In(3R)K and the amount of the sex pheromone 5,9-heptacosadiene in DGRP females. We functionally validated the effect of eight candidate genes using RNA interference to provide testable hypotheses for future studies investigating the molecular genetic basis of incipient sexual isolation in <em>D. melanogaster</em>.</p>
Figure 2 in Variations in heterochromatin content reveal important polymorphisms for studies of genetic improvement in garlic (Allium sativum L.)
Figure 2. Idiograms of the accessions "Sussuapara - PI" (A), "Santo Antônio de Lisboa - PI" (B), "Catetinho do Paraná 1254" (C), "Branco Mineiro - PI" (D), "Cateto Roxo 99" (E), "Roxo de Minas" (F), and "Sergipe" (G). Yellow dash and circle represent the CMA+/DAPI- band. Chromosomal order (CO), chromosome morphology (CM), metacentric (M), submetacentric (SM), short arm (p), and long arm (q). Vertical bar in karyogram and ideogram = 10 µm.
Figure 1. Allium sativum L in Variations in heterochromatin content reveal important polymorphisms for studies of genetic improvement in garlic (Allium sativum L.)
Figure 1. Allium sativum L.cytological data obtained by conventional Giemsa staining.Prophase and interphase nucleus (A), prometaphase (B), and metaphase (C) obtained with the use of antimitotic. Mitotic cycle is shown in d-f: anaphase (D), end of anaphase (E), and telophase (F). Dots and red arrow indicate the distended nucleolar organiser region (NOR). Bar = 10 µm.
Fig. 3 in Assessing genetic diversity of three species of potato tuber moths (Gelechiidae, Lepidoptera) in the Ecuadorian highlands
Fig. 3. Distribution of 5 haplotypes and sequence identity between each pair of Symmetrischema tangolias haplotypes. St-H1 was present in all 4 provinces; St-H2 was present in 3 provinces; the other 3 haplotypes were present only in 1 province for each haplotype. Arrows point to province(s) instead of a specific sampling location.
Fig. 1 in Assessing genetic diversity of three species of potato tuber moths (Gelechiidae, Lepidoptera) in the Ecuadorian highlands
Fig. 1. Use of pheromone traps to collect potato tuber moths in Cacha, Chimborazo, and Tishinguirí, Bolívar: (A) potato crops are grown in mountainous regions of Ecuador where smallholder terrace farming is predominant; (B) low-cost pheromone traps were made of plastic bottles; a species-specific lure is fixed to the bottle cap using a string, and thumb-sized holes were carved to allow moths to fly into the bottle that was filled with soapy water; (C) 3 different traps were placed (pointed by arrows) in each field at least 100 m apart to catch different moths.
Fig. 5 in Assessing genetic diversity of three species of potato tuber moths (Gelechiidae, Lepidoptera) in the Ecuadorian highlands
Fig. 5. Distribution of 3 haplotypes and sequence identity between each pair of Phthorimaea operculella haplotypes. Po-H1 was present in all 4 provinces, Po-H3 was present only in Cotopaxi and Chimborazo; Po-H2 was limited to Tungurahua.
Fig. 2 in Assessing genetic diversity of three species of potato tuber moths (Gelechiidae, Lepidoptera) in the Ecuadorian highlands
Fig. 2. Alignment of 5 COI haplotype sequences of Symmetrischema tangolias samples. KX443104.1 is a reference sequence from GenBank. Sequences of these 5 haplotypes were deposited in GenBank with accession numbers MN223391 to MN223395.
Fig. 4 in Assessing genetic diversity of three species of potato tuber moths (Gelechiidae, Lepidoptera) in the Ecuadorian highlands
Fig. 4. Alignment of 3 unique COI haplotype sequences of Phthorimaea operculella. MF121882 is a reference sequence from GenBank. Sequences of these 3 haplotypes were deposited in GenBank with accession numbers MN205567 to MN205569.
A field study of the molecular response of brown macroalgae to heavy metal exposure: an (epi)genetic approach
<p>We used next-generation sequencing to study DNA methylation changes and DNA sequence variation (SNPs) in thalli from four populations of the brown macroalgae <em>Fucus vesiculosus</em> reciprocally transplanted between two polluted and two unpolluted sites. For this, we performed reduced representation bisulfite DNA sequencing.</p>
Figure 3 in Genetic variation within a species of parasitic nematode, Skrjabingylus chitwoodorum, in skunks
Figure 3: Maximum likelihood phylogenetic tree of 492 base pair fragment of the cytochrome oxidase I gene for 44 samples of Skrjabingylus. Maximum likelihood analysis was performed using the best-fitting model, Hasegawa-Kishino-Yano of DNA substitution with Gamma distribution. Bootstrap values are based on 1000 replicates and values ≥70 are shown on branches. Number with prefix ASK identifies the specific host from which the sample was collected. Prefix KP is a Genbank accession number.
Figure 4 in Genetic variation within a species of parasitic nematode, Skrjabingylus chitwoodorum, in skunks
Figure 4: Median joining network showing the relationships among haplotypes of 44 samples of Skrjabingylus chitwoodorum from hosts Mephitis mephitis and Spilogale putorius interrupta using COI mtDNA. Sizes of solid black circles correlate to shared haplotypes among multiple counties. Small open circles represent hypothetical haplotypes and ticks on branches represent number of mutational steps.
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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.