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288 results for “genetic polymorphisms”
Fig. 1 in A new polymorphic species of Leptochelia (Crustacea: Tanaidacea) from Guinea Bissau, West Africa, with comments on genetic variation within Leptochelia
Fig. 1. Leptochelia africana sp. n., female: (A, B) holotype: (A) dorsal view, (B) lateral view; (C–F) paratype: (C) antennule, (D) antenna, (E) pleopod, (F) uropod. Scale bars = 1.0 mm (A, B) and 0.5 mm (C–F).
Fig. 8. Protanais ligniamator Larsen, 2006 in A new polymorphic species of Leptochelia (Crustacea: Tanaidacea) from Guinea Bissau, West Africa, with comments on genetic variation within Leptochelia
Fig. 8. Protanais ligniamator Larsen, 2006, SEM: (A) pleopod 1; (B) same, exopod, higher magnification.
Fig. 5 in A new polymorphic species of Leptochelia (Crustacea: Tanaidacea) from Guinea Bissau, West Africa, with comments on genetic variation within Leptochelia
Fig. 5. Leptochelia africana sp. n., primary male, paratype: (A) cheliped; (B) pereopod 1; (C) pereopod 2; (D) pereopod 3; (E) pereopod 4; (F) pereopod 5; (G) pereopod 6; (H) uropod. Scale bar = 0.5 mm.
Fig. 4 in A new polymorphic species of Leptochelia (Crustacea: Tanaidacea) from Guinea Bissau, West Africa, with comments on genetic variation within Leptochelia
Fig. 4. Leptochelia africana sp. n., male paratypes: (A) secondary male, lateral view; (B–J) primary male: (B) dorsal view, (C) lateral view, (D) antennule, (E) antenna, (F) labrum, (G) maxillule palp, (H) maxilliped, (I) epignath, (J) pleopod. Scale bars = 1.0 mm (A–C), 0.5 mm (D, E, J) and 0.1 mm (F–H).
Data from: Association genetics of growth and adaptive traits in loblolly pine (Pinus taeda L.) using whole-exome-discovered polymorphisms
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Genetic polymorphisms in COMT and BDNF influence synchronization dynamics of human neuronal oscillations
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Data accompanying Polyphenisms and polymorphisms: genetic variation in plasticity and color variation within and among bluefin killifish populations
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Data from: A genetic polymorphism underlying alternative reproductive tactics in Eurycea salamanders
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Data from: Genetic polymorphism in Chondrilla (Asteraceae) in the South of European Russia and the nature of Chondrilla juncea L.
<p>We studied genetic diversity in 54 populations of nine species of the genus Chondrilla (C. acantholepis, C. ambigua, C. brevirostris, C. canescens, C. graminea, C. juncea, C. laticoronata, C. latifolia, and C. pauciflora) from SE European Russia and the neighboring territories of NW Kazakhstan. Analyses of the trnT–trnF region of plastid DNA and the internal transcribed spacer of ribosomal DNA (ITS1–5.8S–ITS2) using Statistical Parsimony, Maximum Likelihood and Neighbor Net methods revealed two major evolutionary lineages roughly corresponding to two subgenera traditionally recognized within Chondrilla in the region. Within the first evolutionary lineage (subgenus Brachyrhynchus) sexual diploid C. ambigua and its putatively hybrid apomictic derivatives C. brevirostris, C. laticoronata and C. pauciflora can be recognized. Their identity is confirmed by analyses of ISSR markers. The second evolutionary lineage (subgenus Chondrilla) is comprised comprises by C. juncea, C. acantholepis, C. canescens, C. graminea, and C. latifolia in European Russia. Analyses of morphological variability and the genealogy of plastid and nuclear markers genealogy favor their treatment as a single species C. juncea.</p> <div class="yj6qo"> </div> <div class="adL"> </div>
Data from: Ecology can inform genetics: disassortative mating contributes to MHC polymorphism in Leach's storm-petrels (Oceanodroma leucorhoa)
Studies of MHC-based mate choice in wild populations generally test hypotheses by assuming female choice and male-male competition, whether or not mate choice dynamics have been previously determined for the species under study. Here we examined mate choice patterns in a small burrow-nesting seabird, the Leach's storm-petrel (Oceanodroma leucorhoa), using the Major Histocompatibility Complex (MHC). The life history and ecology of this species is extreme: both partners work together to fledge a single chick during the breeding season, a task that requires regularly traveling hundreds of kilometers to and from foraging grounds over a six to eight-week provisioning period. Using a five-year dataset unprecedented for this species (n=1027 adults and 925 chicks), we found a positive relationship between variation in female reproductive quality and heterozygosity at Ocle-DAB2, a MHC class IIB locus. Contrary to previous reports rejecting disassortative mating as a mechanism for maintaining genetic polymorphism in this species, here we show that males make significant disassortative mate choice decisions. Variability in female reproductive success suggests that the most common homozygous females (Ocle-DAB201 / Ocle-DAB201) may be physiologically disadvantaged and, therefore, less preferred as lifelong partners for choosy males. The results from this study support the role of mate choice in maintaining high levels of MHC variability in a wild seabird species, and highlights the need to incorporate a broader ecological framework and sufficient sample sizes into studies of MHC-based mating patterns in wild populations in general.
Data from: Selection on a genetic polymorphism counteracts ecological speciation in a stick insect
The interplay between selection and aspects of the genetic architecture of traits (such as linkage, dominance, and epistasis) can either drive or constrain speciation. Despite accumulating evidence that speciation can progress to "intermediate" stages—with populations evolving only partial reproductive isolation—studies describing selective mechanisms that impose constraints on speciation are more rare than those describing drivers. The stick insect Timema cristinae provides an example of a system in which partial reproductive isolation has evolved between populations adapted to different host plant environments, in part due to divergent selection acting on a pattern polymorphism. Here, we demonstrate how selection on a green/melanistic color polymorphism counteracts speciation in this system. Specifically, divergent selection between hosts does not occur on color phenotypes because melanistic T. cristinae are cryptic on the stems of both host species, are resistant to a fungal pathogen, and have a mating advantage. Using genetic crosses and genome-wide association mapping, we quantify the genetic architecture of both the pattern and color polymorphism, illustrating their simple genetic control. We use these empirical results to develop an individual-based model that shows how the melanistic phenotype acts as a "genetic bridge" that increases gene flow between populations living on different hosts. Our results demonstrate how variation in the nature of selection acting on traits, and aspects of trait genetic architecture, can impose constraints on both local adaptation and speciation.
Data from: Evaluation of a single nucleotide polymorphism baseline for genetic stock identification of Chinook Salmon (Oncorhynchus tshawytscha) in the California Current Large Marine Ecosystem
Chinook Salmon is an economically and ecologically important species, and populations from the west coast of North America are a major component of fisheries in the North Pacific Ocean. The anadromous life history strategy of this species generates populations (or stocks) that typically are differentiated from neighboring populations. In many cases, it is desirable to discern the stock of origin of an individual fish or the stock composition of a mixed sample to monitor the stock-specific effects of anthropogenic impacts and alter management strategies accordingly. Genetic stock identification (GSI) provides such discrimination, and we describe here a novel GSI baseline composed of genotypes from more than 8000 individual fish from 69 distinct populations at 96 single nucleotide polymorphism (SNP) loci. The populations included in this baseline represent the likely sources for more than 99% of the salmon encountered in ocean fisheries of California and Oregon. This new genetic baseline permits GSI with the use of rapid and cost-effective SNP genotyping, and power analyses indicate that it provides very accurate identification of important stocks of Chinook Salmon. In an ocean fishery sample, GSI assignments of more than 1000 fish, with our baseline, were highly concordant (98.95%) at the reporting unit level with information from the physical tags recovered from the same fish. This SNP baseline represents an important advance in the technologies available to managers and researchers of this species.
Data from: Distances and their visualization in studies of spatial-temporal genetic variation using single nucleotide polymorphisms (SNPs)
<p>Distance measures are widely used for examining genetic structure in datasets that comprise many individuals scored for a very large number of attributes. Genotype datasets composed of single nucleotide polymorphisms (SNPs) typically contain bi-allelic scores for tens of thousands if not hundreds of thousands of loci.</p> <p>We examine the application of distance measures to SNP genotypes and sequence tag presence-absences (SilicoDArT) and use real datasets and simulated data to illustrate pitfalls in the application of genetic distances and their visualization.</p> <p>The datasets used to illustrate points in the associated review are provided here together with the R script used to analyse the data. Data are either simulated internal to this script or are SNP data generated as part of other studies and included as compressed binary files readily accessable by reading into R using R base function readRDS(). Refer to the analysis script for examples.</p>
Genome-wide single nucleotide polymorphisms reveal the genetic diversity and population structure of Creole goats from northern Peru
<p>Goat farming constitutes a significant source of income for farmers in northern Peru. There is currently an absence of information about the genetics of Peruvian Creole goats that would enable us to understand their origins and genetic spread. The objective of this study was to estimate the genetic diversity of Creole goats from northern Peru using SNP markers. This study involved the collection of 192 male Creole goats from three key goat production regions in northern Peru. These goat samples were genotyped using the GGPGoat70k SNP panel. To explore the genetic influence of other breeds on Peruvian Creole goats, our dataset was combined with previously published SNP genotypes. External data set includes multiple breeds genotypes sampled from Argentina, Brazil, Spain, and Alpine breed from Italy, France, and Switzerland. After quality control 52,832 autosomal SNPs were used to assess genetic diversity in the Peruvian goats. For the population structure analysis of the merged data 20,513 common SNPs were used. Estimations for expected heterozygosity (H<sub>e</sub>), observed heterozygosity (H<sub>o</sub>), and inbreeding coefficient (F<sub>IS</sub>) were computed for the Peruvian groups. AMOVA, principal component analysis and ADMIXTURE were conducted to evaluate the population structure in the two data sets, Peru and merged. The results revealed a considerable genetic diversity, with H<sub>o</sub> values ranging from 0.40 to 0.41 for the Peruvian sampling groups, and inbreeding coefficient was notably low for Peruvian goat. The population structure analysis demonstrated a distinction (p< 0.05) from other breeds. These findings suggest a level of genetic differentiation of the Peruvian goat population among other breeds, although further research is needed considering samples from other Peruvian areas. We expect this study will contribute to define genetic management strategies to prevent the loss of genetic diversity in Peruvian goat populations and for upcoming advancements in this field.</p>
RAD-seq generated single nucleotide polymorphisms resolve patterns of genetic diversity and structure of the freshwater mussel Ptychobranchus fasciolaris in glaciated and unglaciated regions of North America
<p>Included are the initial unfiltered SNP output from the STACKS pipeline, and the final filtered SNP dataset in VCF format used to do analysis in the manuscript titled "<span>RAD-seq generated single nucleotide polymorphisms resolve patterns of genetic diversity and structure of the freshwater mussel <em>Ptychobranchus fasciolaris </em>in glaciated and unglaciated regions of North America" which was submitted to <em>Hydrobiologia </em>in September 2024.</span></p>
Phenotypic architecture of sociality and its associated genetic polymorphisms in zebrafish
<p>Sociality is often seen as a single phenotypic trait, but it relies on motivational and cognitive components implemented by specific causal mechanisms. Hence, these components may have evolved independently, or may have been linked by phenotypic correlations driven by a shared selective pressure for increased social competence. Furthermore, these components may be domain-specific or of general domain across social and non-social contexts. Here we have characterized the phenotypic architecture of sociality in zebrafish, which has been increasingly used as a model organism in social neuroscience. For this purpose, we have behaviorally phenotyped zebrafish from different wild type lines in four tests: social tendency, social and non-social recognition, and open-field test. Our results indicate that: (1) sociality has two main components that are independent from each other (social tendency and social recognition), hence not supporting the occurrence of a sociality syndrome; (2) both social traits are phenotypically linked to non-social traits (non-social exploration and non-social memory, respectively), forming two general behavioral modules, general inspection and general recognition, and suggesting that sociality traits have been co-opted from general-domain motivational and cognitive traits. Moreover, the study of the association between genetic polymorphisms (i.e. single nucleotide polymorphisms, SNPs) and each behavioral module further supports this view, since several SNPs from a list of candidate "social" genes, are statistically associated with the general inspection (motivational), but not with a general recognition (cognitive), behavioral module. The SNPs associated with general inspection are widespread across different chromosomes and include neurotransmitters, neuromodulators, and synaptic plasticity genes, suggesting that this behavioral module is regulated by multiple genes, each of them with small effects. Together, these results support the occurrence of general domain motivational and cognitive behavioral modules in zebrafish, which have been co-opted for the social domain.</p>
Fig. 6 in Genetically Determined Colour Polymorphism In Larvae Of Ceriagrion Chaoi (Insecta: Odonata: Coenagrionidae)
Fig. 6. Ceriagrion chaoi male emerged from dark larva.
Fig. 5 in Genetically Determined Colour Polymorphism In Larvae Of Ceriagrion Chaoi (Insecta: Odonata: Coenagrionidae)
Fig. 5. Female Ceriagrion chaoi emerging from brown larva.
Fig. 1 in Genetically Determined Colour Polymorphism In Larvae Of Ceriagrion Chaoi (Insecta: Odonata: Coenagrionidae)
Fig. 1. Exuviae of brown (left) and dark (right) colour larvae of Ceriagrion chaoi.
Data and scripts from: Balanced polymorphism fuels rapid selection in an invasive crab despite high gene flow and low genetic diversity
<p><em>Carcinus maenas</em> is a globally invasive species which spreads and thrives across a range of temperate environments. In the northwestern Pacific, the species has spread across >12 degrees of latitude in 10 years from a single source, following its introduction <35 years ago. Using six locations spanning >1,500 km, we examined genetic structure and selection to temperature using 9,376 Single Nucleotide Polymorphisms (SNPs) derived from cardiac transcriptome sequencing.</p> <p>Data in this repository includes information on sequenced samples (*.csv, *.txt), a cleaned transcriptome assembly after expression filtering (*.fasta), transcriptome annotation from EnTAP (*.tsv), list of transcripts removed from analysis after mapping (*.txt), high-quality SNPs identified from the transcriptome sequencing with GATK (seven files representing different SNP sets used in the analysis; *.vcf), and four custom scripts used in processing SNP data (*.py and *.R).</p> <p>Raw sequence data is archived in GenBank's SRA. 2015-2016 samples: BioProject ID PRJNA690934 and BioSample IDs SAMN17267686–SAMN17267781. 2011 samples: BioProject ID PRJNA283611 and BioSample IDs SAMN03653390–SAMN03653413.</p>
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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.