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15,277 results for “GENETICS”
F I G U R E 2 A in A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales
F I G U R E 2 A priori discriminant analysis of principal components (DAPC) of trout genotypes from rivers flowing into Mount's Bay, Cornwall. Individuals are represented by individual points, with centroids for each river labelled. Discriminant function 1 (DF1) is represented by the x axis, and discriminant function 2 (DF2) by the y-axis
Fig. 3 in Prevalence and genetic diversity of haematozoa in South American waterfowl and evidence for intercontinental redistribution of parasites by migratory birds
Fig. 3. Bayesian phylogenetic tree of haematozoa mitochondrial DNA cytochrome b haplotypes obtained from infected waterfowl. Trees were rooted with mammalian Plasmodium outgroups. Node tips are labeled with parasite genus (Haem = Haemoproteus, Leuc = Leucocytozoon, and Plas = Plasmodium), followed by the lineage name, GenBank accession number for each sequence, host order (passerine/waterfowl), and the country/state from which the samples were collected. All haplotypes identified in this study are highlighted in red. Numbers on branches represent posterior probabilities from the analysis. Asterisks after node tip labels indicate sequences from our study that were identical to lineages previously found in non-waterfowl hosts. All reference sequences were obtained from the National Center for Biotechnology Information website.
Fig. 2. Minimum spanning network for haematozoa mitochondrial DNA cytochrome b in Prevalence and genetic diversity of haematozoa in South American waterfowl and evidence for intercontinental redistribution of parasites by migratory birds
Fig. 2. Minimum spanning network for haematozoa mitochondrial DNA cytochrome b haplotypes detected in South American waterfowl. Shaded circles represent unsampled nodes. All circles are drawn proportional to the frequency at which haplotypes were observed. Lines separating nodes are drawn to scale based on the number of nucleotide mutations, unless otherwise indicated by hash marks. Only haplotypes with a length of 358 bp or greater were included. Haplotype name abbreviations are as follows: Haem = Haemoproteus, Leuc = Leucocytozoon, and Plas = Plasmodium.
Fig. 1 in Prevalence and genetic diversity of haematozoa in South American waterfowl and evidence for intercontinental redistribution of parasites by migratory birds
Fig. 1. Map of sampling locations in Peru and Argentina. The number of waterfowl blood samples collected at each site is provided in parentheses.
Figure 6 in Description of a new species of the genus Rana (Anura: Ranidae) from western Guizhou, China, integrating morphological and molecular genetic data
Figure 6. Variation of the live adult male paratype GZNU20220705001 of Rana zhijinensis Luo, Xiao & Zhou, sp. nov. A. Dorsolateral view; B. Dorsal view; C. Ventral view.
Figure 1 in Description of a new species of the genus Rana (Anura: Ranidae) from western Guizhou, China, integrating morphological and molecular genetic data
Figure 1. Sampling localities of Rana zhijinensis Luo, Xiao & Zhou, sp. nov., R. culaiensis, R. hanluica, and R. omeimontis in Guizhou Province, China. A. Guiguo Town, Zhijin County; B. Supu Town, Qianxi County; C. Zhujianshan Nature Reserve, Huangping County; D. Leigongshan National Nature Reserve, Leishan County.
Figure 2 in Description of a new species of the genus Rana (Anura: Ranidae) from western Guizhou, China, integrating morphological and molecular genetic data
Figure 2. Phylogenetic tree based on three mitochondrial genes and six nuclear genes. A. Maternal tree; B. Nuclear gene tree. In both phylogenetic tree, ultrafast bootstrap support (UFB) values from ML analyses/Bayesian posterior probabilities (BPP) from BI analyses are given beside nodes. Scale bars denote nucleotide substitutions per sites for mitochondrial and nuclear genes.
Figure 5 in Description of a new species of the genus Rana (Anura: Ranidae) from western Guizhou, China, integrating morphological and molecular genetic data
Figure 5. Morphological features of the live adult male holotype GZNU2018081606 of Rana zhijinensis Luo, Xiao & Zhou, sp. nov. A. Dorsolateral view; B. Dorsal view; C. Ventral view; D. Egg cluster; E. Ventral view of hand and dark gray-blackish nuptial pad; F. Ventral view of foot.
Figure 4 in Description of a new species of the genus Rana (Anura: Ranidae) from western Guizhou, China, integrating morphological and molecular genetic data
Figure 4. Haplotype networks of Rana zhijinensis Luo, Xiao & Zhou, sp. nov. and its related species constructed based on the nuclear gene sequences. Different species of the R. japonica group are shown as different colors.
Figure 3 in Description of a new species of the genus Rana (Anura: Ranidae) from western Guizhou, China, integrating morphological and molecular genetic data
Figure 3. Phylogenetic tree based on four mitochondrial genes and six nuclear genes. In this phylogenetic tree, UFB from ML analyses/ BPP from BI analyses are given beside nodes. The scale bar represents 0.03 nucleotide substitutions per site. Red lines represent species delimitation results of bPTP and BPP.
F I G U R E 4 in A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales
F I G U R E 4 Correlation between geographic distance (km) against genetic distance (linear FST) for the trout samples from the River Camel. The red points represent those between the De Lank and all other sites, the black points for all pair-wise comparisons excluding the De Lank. Linear regression for all sites including the De Lank is given by the red line (r2 = 0.321, P = 0.231), and linear regression for all pair-wise sites excluding the De Lank is given by the black line (r2 = 0.658, P = 0.0671)
Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts
<p><span>Genetic variations are instrumental for unraveling phage evolution and deciphering their functional implications. Here we explore the underlying fine-scale genetic variations in the gut phageome, especially structural variations (SVs). By employing virome-enriched long-read metagenomics sequencing across 91 individuals, we identified a total of 14,438 non-redundant phage SVs, and revealed their prevalence within the human gut phageome. These SVs are mainly enriched in genes involved in recombination, DNA methylation, and antibiotic resistance. Strikingly, a substantial fraction of phage SV sequences share close homology with bacterial fragments, with most SVs enriched for horizontal gene transfer (HGT) mechanism. Further investigations showed that these SV sequences were genetic exchanged between specific phage-bacteria pairs, particularly between phages and their respective bacterial hosts. Temperate phages exhibits a higher frequency of genetic exchange with bacterial chromosomes then virulent phages. Collectively, our findings provide novel insights into the genetic landscape of the human gut phageome.</span></p>
Supplementary materials for Phylogenomics and genetic analysis of solvent-producing Clostridium species
<p>The genus <em>Clostridium</em> is a large and diverse group within the Bacillota (formerly Firmicutes), whose members can encode useful complex traits such as solvent production, gas-fermentation, and lignocellulose breakdown. We describe 270 genome sequences of solventogenic clostridia from a comprehensive industrial strain collection assembled by Professor David Jones that includes 194 <em>C. beijerenckiI, </em>57 <em>C. saccharobutylicum</em>, 4 <em>C. saccharoperbutylacetonicum</em>, 5 <em>C. butyricum</em>, 7 <em>C. acetobutylicum</em>, and 3 <em>C. tetanomorphum </em>genomes. We report methods, analyses and characterization for phylogeny, key attributes, core biosynthetic genes, secondary metabolites, plasmids, prophage/CRISPR diversity, cellulosomes and quorum sensing for the 6 species. The expanded genomic data described here will facilitate engineering of solvent-producing clostridia as well as non-model microorganisms with innately desirable traits. Sequences could be applied in conventional platform biocatalysts such as yeast or <em>Escherichia coli </em>for enhanced chemical production. Recently, gene sequences from this collection were used to engineer <em>Clostridium autoethanogenum</em>, a gas-fermenting autotrophic acetogen, for continuous acetone or isopropanol production<em>, </em>as well as butanol, butanoic acid, hexanol and hexanoic acid production. </p>
Dataset from Castel et al. 'Genetic sex determination in three closely related hydrothermal vent gastropods, including one species with intersex individuals'
<p>This is the dataset used in "Genetic sex determination in three closely related hydrothermal vent gastropods, including one species with intersex individuals"<br>Castel J, Pradillon F, Cueff V, Leger G, Daguin-Thiébaut C, Ruault S, Mary J, Hourdez S, Jollivet D, and Broquet T</p>
Fig. 1 in Spore Dimorphism in Nosema pyrausta (Microsporidia, Nosematidae): from Morphological Evidence to Molecular Genetic Verification
Fig. 1. DAPI fluorescence (A, С) and Nomarski contrast (B, D) of monokaryotic (A, B) and diplokaryotic (C, D) spores of microsporidia detected in Ostrinia nubilalis larvae. Arrows and double arrows indicate single nuclei and diplokarya, respectively. Scale bar = 4 µm.
Genetically identical mice express alternative reproductive tactics depending on social conditions in the field
<p>In many species, establishing and maintaining a territory is critical to survival and reproduction, and an animal's ability to do so is strongly influenced by the presence and density of competitors. Here we manipulate social conditions to study the alternative reproductive tactics displayed by genetically identical, age-matched laboratory mice competing for territories under ecologically realistic social environmental conditions. We introduced adult males and females of the laboratory mouse strain (C57BL/6J) into a large, outdoor field enclosure containing defendable resource zones under one of two social conditions. We first created a low-density social environment, such that the number of available territories exceeded the number of males. After males established stable territories, we introduced a pulse of intruder males and observed the resulting defensive and invasive tactics employed. In response to this change in social environment, males with large territories invested more in patrolling but were less effective at excluding intruder males as compared to males with small territories. Intruding males failed to establish territories and displayed an alternative tactic featuring greater exploration as compared to genetically identical territorial males. Alternative tactics did not lead to equal reproductive success—males that acquired territories experienced greater survival and had greater access to females.</p>
High genetic gains in wood volume and fecundity can be both achieved by direct selection in half-sib families of Pinus yunnanensis Franch.
<p><strong><span>Experiment background</span></strong></p> <p><span>This study focused on characterizing phenotypic variation among and within provenances of <em>Pinus yunnanensis</em><span> Franch. aged 16 years in </span></span><span>a common garden</span><span>, with an emphasis on key traits such as cone production, trunk straightness, and crown health, as well as their relationships with traditional growth traits like tree height, diameter at breast height, and wood volume. Specifically, the objectives were to (1) characterize the variation of each trait within and among provenances; (2) assess inter-trait relationships, exploring patterns of co-variation and potential trade-offs; and (3) evaluate the feasibility of multi-trait selection strategies that aim for simultaneous improvements in growth, trunk straightness, and fecundity, contributing valuable insights for advancing <em>P. yunnanensis</em><span> </span>breeding efforts.</span></p> <p><strong><span>Experimental Design</span></strong></p> <p><span>This study was conducted in a common garden for <em>P. yunnanensis</em> located in Lufeng County, central Yunnan Province (102°12' E, 25°13' N) at an altitude of 1860 meters. The site lies in the transition zone between the subtropical humid climate of eastern Yunnan and the sub-humid climate of southwest Yunnan. The climate is characterized by warm and dry winters, humid and hot summers, with a mean annual temperature of 15.5°C and annual precipitation ranging between 900–1000 mm. The dry season extends from November to April, accounting for 6%-17% of the total annual precipitation.</span></p> <p><span>The common garden was established in 2006, with progeny from 179 superior trees selected from six provenance regions, including Anning County (AN), Qujing City (QJ), Yongren County (YR), Yulong County (YL), Tengchong County (TC), and Ninglang County (NL). Each provenance includes 30 families, except for one provenance with 29 families. </span></p> <p><span>The common garden has an area of about 3 ha, with a random block design, and a planting scheme of 2 m × 3 m</span><span>. </span><a name="_Hlk181695359"></a><span>To minimize environmental variation across the study site, a horizontal banding method was used for land preparation prior to planting.</span><span> </span><span>To reduce environmental variation across the study site, a horizontal banding method was used during land preparation. In each block, six provenances were randomly arranged, and families were randomly assigned within each provenance. Five plants from each family were planted in rows, and the design was replicated four times. A total of 3467 progeny from 179 superior trees across six provenances were included in the trial.</span></p> <p><strong><span>Experimental Variables</span></strong></p> <p><span>The study measured nine phenotypic traits, which included both quantitative and qualitative traits, as outlined below:</span></p> <p><span>Tree Height (H): Measured directly with a Vertex Laser instrument (DZH-30, Harbin, China) in meters (m).</span></p> <p><span>Diameter at Breast Height (D): Measured using a circumference tape in centimeters (cm).</span></p> <p><span>Crown Diameter (LCD, SCD): Long crown diameter (LCD) and short crown diameter (SCD), representing the maximum and minimum tree crown diameter, respectively, measured in meters (m) using a tower ruler.</span></p> <p><span>Height Under the Branch (TH): Measured in meters (m) using a tower ruler.</span></p> <p><span>Wood Volume (V): Estimated using the formula based on the forestry industry standard for <em>P. yunnanensis</em> (Agriculture and Forestry Ministry of China, 1977), with units in cubic meters (m³).</span></p> <p><span>Cone Production (CP): The number of open and closed cones in the canopy, including both serotinous and non-serotinous cones, recorded in counts to assess fecundity.</span></p> <p><span>Trunk Straightness (ST): A subjective visual assessment using a classification system: 1 for a highly twisted stem, 5 for a perfectly straight stem.</span></p> <p><span>Crown Health (CH): Visual assessment of the tree's crown, considering damage from abiotic and biotic stresses, with a grading scale from 1 (severely damaged) to 5 (perfectly healthy).</span></p> <p><strong><span>Data Analysis Methods</span></strong></p> <p><span>Data analysis was performed using R (version 3.6.3). The following statistical methods were employed:</span></p> <p><span>Variance Analysis: Nested variance analysis was used to evaluate the significance of differences and partition phenotypic variation among and within provenances. </span></p> <p><span>Principal Component Analysis (PCA): PCA was performed on the standardized matrix of nine phenotypic traits to reveal the dimensional structure and patterns of the data.</span></p> <p><span>Structural Equation Modeling (SEM): SEM was used to examine the direct and indirect relationships among traits, such as growth (H, D, V), crown size (LCD, SCD, TH), fecundity (CP), trunk straightness (ST), and crown health (CH). This analysis helped identify the causal pathways between the traits.</span></p> <p><span>Random Forest Analysis (RF): RF analysis was conducted to assess the importance of specific traits in predicting fecundity (CP) and trunk straightness (ST). Regression and classification methods were used for these analyses, with 1000 decision trees to ensure stable importance measures.</span></p> <p><strong><span>Dataset Description</span></strong></p> <p><span>The excel file (Raw Data) includes the following sheets: 1- Variables: Details on all the variables. 2- </span><span>Values of phenotypic traits</span><span>. 3- </span><span>Variance components </span><span>of phenotypic traits among and within provenances</span><span>. 4-</span><span> </span><span>Coefficient of variance</span><span> for phenotypic traits</span><span>. 5-</span><span> <span>The</span> <span>average membership function values (SFM) and </span>comprehensive weight of each principal component (PCA)<span> of </span></span><span>phenotypic traits</span><span>.</span></p>
Figure 1 in Why we should develop guidelines and quantitative standards for using genetic data to delimit subspecies for data-poor organisms like cetaceans
Figure 1. Depiction of the divergence of lineages with four times (T1–T4) chosen to illustrate different levels of biological organization. At T1 the yellow lineage is found across the distribution and although there are likely Demographically Independent Populations (DIPs) that differ in frequencies of the blue, yellow, and red lineages, there are no discontinuities. At T2 some lineages may be diagnosable but likely do not yet appear to be separate lineages. At T3 three groups (the blue/green, yellow, and orange/red lineages) meet the subspecies definition (they are diagnosable and appear to be diverging separately). The divergence level is not sufficient that reconvergence can be ruled out. Between T3 and T4, barriers to gene flow change such that the yellow lineage comes into contact with the blue/green and red-dominated lineages. Blue has diverged in a manner by which gene flow does not resume and the green/yellow lineage dies out. The yellow lineage reconverges and persists alongside the red lineage with a small level of gene flow (orange). At T4 the blue lineage is a species evolving separately from the yellow/red species. The yellow/red species has two subspecies that are both diagnosable and partially diverged.
Figure 2 in Examining metrics and magnitudes of molecular genetic differentiation used to delimit cetacean subspecies based on mitochondrial DNA control region sequences
Figure 2. Relationship between ΦST and Nei's estimate of net divergence (dA) among cetacean population, subspecies, and species pairs estimated using mitochondrial DNA control region sequence data. Specific values mentioned in the text are numbered: 1 = Neophocaena species; 2 = killer whale populations. The three green squares in the left-hand side of the figure (ΦST <0.07) represent, from bottom to top, the subspecies comparisons for S. attenuata, S. longirostris, and L. obscurus, respectively.
Figure 1 in Examining metrics and magnitudes of molecular genetic differentiation used to delimit cetacean subspecies based on mitochondrial DNA control region sequences
Figure 1. Box and whisker plots showing median and 1st and 3rd quartiles, and minimum and maximum values for six metrics of genetic divergence among cetacean population, subspecies, and species pairs estimated using mitochondrial DNA control region sequence data.
ScienceDex guides
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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.