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15,277 results for “GENETICS”
Data from: The effects of inbreeding, genetic dissimilarity and phenotype on male reproductive success in a dioecious plant
Pollen fate can strongly affect the genetic structure of populations with restricted gene flow and significant inbreeding risk. We established an experimental population of inbred and outbred Silene latifolia plants to evaluate the effects of (i) inbreeding depression, (ii) phenotypic variation and (iii) relatedness between mates on male fitness under natural pollination. Paternity analysis revealed that outbred males sired significantly more offspring than inbred males. Independently of the effects of inbreeding, male fitness depended on several male traits, including a sexually dimorphic (flower number) and a gametophytic trait (in vitro pollen germination rate). In addition, full-sib matings were less frequent than randomly expected. Thus, inbreeding, phenotype and genetic dissimilarity simultaneously affect male fitness in this animal-pollinated plant. While inbreeding depression might threaten population persistence, the deficiency of effective matings between sibs and the higher fitness of outbred males will reduce its occurrence and counter genetic erosion.
Data from: Genome-wide genotyping uncovers genetic profiles and history of the Russian cattle breeds
One of the most economically important areas within the Russian agricultural sector is dairy and beef cattle farming contributing about $11 billion to the Russian economy annually. Trade connections, selection and breeding have resulted in the establishment of a number of breeds that are presumably adapted to local climatic conditions. Little however is known about the ancestry and history of Russian native cattle. To address this question, we genotyped 274 individuals from 18 breeds bred in Russia and compared them to 135 additional breeds from around the world that had been genotyped previously. Our results suggest a shared ancestry between most of the Russian cattle and European taurine breeds, apart from a few breeds that shared ancestry with the Asian taurines. The Yakut cattle, belonging to the latter group, was found to be the most diverged breed in the whole combined dataset according to structure results. Haplotype sharing further suggests that the Russian cattle can be divided into four major clusters reflecting ancestral relations with other breeds. Herein, we therefore shed light on to the history of Russian cattle and identified closely related breeds to those from Russia. Our results will facilitate future research on detecting signatures of selection in cattle genomes and eventually inform future genetics-assisted livestock breeding programs in Russia and in other countries.
Data from: Towards understanding the genetic basis of mouth asymmetry in the scale-eating cichlid Perissodus microlepis
How polymorphisms consisting in left–right asymmetries are produced and maintained in natural populations is a tantalizing question, which remains largely unanswered. The scale-eating cichlid fish Perissodus microlepis is a remarkable example of extreme ecological specialization achieved by morphological and behavioural laterality. Its asymmetric mouth is accompanied by a pronounced lateralized foraging behaviour, where a left-bending morph preferentially feeds on the scales of the right side of its prey, while the opposite is true for the right morph. This striking asymmetry made this fish a textbook example of the astounding degree of ecological specialization and negative frequency-dependent selection. Yet, the genetic basis underlying this spectacular laterality remains unknown. We addressed this question through analyses of wild-caught fish using high-throughput DNA sequencing data. A novel array of SNP markers was developed by ddRAD sequencing (ddRADseq) and the use of pooled DNA samples (PoolSeq). We obtained more than 155 000 SNPs using ddRADseq and 3 900 000 SNPs with PoolSeq. Among these, we identified one (ddRAD) SNP, and 38 or 378 (PoolSeq) windows that are differentiated between the left and right morphs accounting for spurious associations due to geographic structuring. This allowed us to uncover candidate genomic regions that potentially contain genes for this trait. Then, this interesting trait has a genetic basis that is likely to be influenced by multiple loci. This result contributes to a greater understanding of the genetic bases of left–right asymmetry and, ultimately, the evolutionary processes governing the maintenance of this striking case of laterality.
Data from: Genetic population structure of the round whitefish (Prosopium cylindraceum) in North America: multiple markers reveal glacial refugia and regional subdivision.
Round whitefish (Prosopium cylindraceum) have a broad, disjunct range across northern North America and Eurasia, and little is known about their genetic population structure. We performed genetic analyses of round whitefish from 17 sites across its range using nine microsatellites, two mitochondrial DNA (mtDNA) loci, and 4918 to 8835 single-nucleotide polymorphism (SNP) loci. Our analyses identified deep phylogenetic division between eastern and western portions of the range, likely indicative of origins from at least two separate Pleistocene glacial refugia. Regionally, microsatellites and SNPs identified congruent patterns in subdivision, and population structure was consistent with expectations based on hydrologic connectivity. Within the Laurentian Great Lakes, Lake Huron and Lake Ontario were identified as key areas of interest. Lake Huron appears to be a contemporary source population for several other Great Lakes, and Lake Ontario contains a genetically discrete group of round whitefish. In all cases, multiple genetic markers yielded similar patterns, but SNPs offered substantially enhanced resolution. We conclude that round whitefish have population subdivision on several scales important for understanding their evolutionary history and conservation planning.
Immunotherapy-mediated thyroid dysfunction: genetic risk and impact on outcomes with PD-1 blockade in non-small cell lung cancer
<p>Polygenic risk score weights derived using LDpred for hypothyroidism and thyroid medication use.</p>
Data from: Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)
The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1–89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6–6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential.
Mixed mating in a multi-origin population suggests high potential for genetic rescue in North Island brown kiwi, Apteryx mantelli
<p>Reinforcement translocations are increasingly utilised in conservation with the goal of achieving genetic rescue. However, concerns regarding undesirable results, such as genetic homogenisation or replacement, are widespread. One factor influencing translocation outcomes is the rate at which the resident and the introduced individuals interbreed. Consequently, post-release mate choice is a key behaviour to consider in conservation planning. Here we studied mating, and its consequences for genomic admixture, in the North Island brown kiwi <i>Apteryx mantelli</i> population on Ponui Island which was founded by two translocation events over 50 years ago. The two source populations used are now recognised as belonging to two separate management units between which birds differ in size and are genetically differentiated. We examined the correlation between male and female morphometrics for 17 known pairs and quantified the relatedness of 20 pairs from this admixed population. In addition, we compared the genetic similarity and makeup of 106 Ponui Island birds, including 23 known pairs, to birds representing the source populations for the original translocations. We found no evidence for size-assortative mating. On the contrary, genomic SNP data suggested that kiwi of one feather did not flock together, meaning that mate choice resulted in pairing between individuals that were less related than expected by random chance. Furthermore, the birds in the current Ponui Island population were found to fall along a gradient of genomic composition consistent with non-clustered representation of the two parental genomes. These findings indicate potential for successful genetic rescue in future <i>Apteryx</i> reinforcement translocations, a potential that is currently underutilised due to restrictive translocation policies. In light of our findings, we suggest that reconsideration of these policies could render great benefits for the future diversity of this iconic genus in New Zealand.</p>
Genetic structure and mating patterns in sessile oak (Quercus petraea (Matt.) Liebl.)
<p>Oaks (<em>Quercus</em>) are major components of temperate forest ecosystems in the Northern Hemisphere where they form intermediate or climax communities. Sessile oak (<em>Quercus petraea</em>) forests represent the climax vegetation in eastern Germany and western Poland. Here, sessile oak forms pure stands or occurs intermixed with Scots Pine (<em>Pinus sylvestris</em>). A large body of research is available on gene flow, reproduction dynamics, and genetic structure in fragmented landscapes and mixed populations. At the same time, our knowledge regarding large, contiguous and monospecific populations is considerably less well developed. Our study is an attempt to further develop our understanding of the reproduction ecology of sessile oak as an ecologically and economically important forest tree by analyzing mating patterns and genetic structure within adult trees and seedlings originating from one or two reproduction events in an extensive, naturally regenerating sessile oak forest. We detected positive spatial genetic structure up to 30 meters between adult trees and up to 40 meters between seedlings. Seed dispersal distances averaged 8.4 meters. Pollen dispersal distances averaged 22.6 meters. In both cases, the largest proportion of the dispersal occurred over short distances. Dispersal over longer distances was more common for pollen but also appeared regularly for seeds. The reproductive success of individual trees was highly skewed. Only 41 percent of all adult trees produced any offspring while the majority did not participate in reproduction. Among those trees that contributed to the analyzed seedling sample, 80 percent contributed 1-3 gametes. Only 20 percent of all parent trees contributed four or more gametes. However, these relatively few most fertile trees contributed 51 percent of all gametes within the seedling sample. Our study demonstrates that extensive, apparently homogenous oak forests are far from uniform on the genetic level. On the contrary, they form highly complex mosaics of remarkably small local neighborhoods. This counterbalances the levelling effect of long-distance dispersal and may increase the species' adaptive potential. Incorporating these dynamics in the management, conservation and restoration of oak forests can support the conservation of forest genetic diversity and assist those forests in coping with environmental change.</p>
Data from: Subspecies delineation amid phenotypic, geographic, and genetic discordance in a songbird
Understanding the processes that drive divergence within and among species is a long-standing goal in evolutionary biology. Traditional approaches to assessing differentiation rely on phenotypes to identify intra- and interspecific variation, but many species express subtle morphological gradients in which boundaries among forms are unclear. This intraspecific variation may be driven by differential adaptation to local conditions and may thereby reflect the evolutionary potential within a species. Here, we combine genetic and morphological data to evaluate intraspecific variation within the Nelson's (Ammodramus nelsoni) and saltmarsh (A. caudacutus) sparrow complex, a group with populations that span considerable geographic distributions and a habitat gradient. We evaluated genetic structure among and within five putative subspecies of A. nelsoni and A. caudacutus using a reduced-representation sequencing approach to generate a panel of 1,929 SNPs among 69 individuals. Although we detected morphological differences among some groups, individuals sorted along a continuous phenotypic gradient. In contrast, the genetic data identified three distinct clusters corresponding to populations that inhabit coastal salt marsh, interior freshwater marsh, and coastal brackish-water marsh habitats. These patterns support the current species-level recognition but do not match the subspecies-level taxonomy within each species– a finding which may have important conservation implications. We identified loci exhibiting patterns of elevated divergence among and within these species, indicating a role for local selective pressures in driving patterns of differentiation across the complex. We conclude that this evidence for adaptive variation among subspecies warrants the consideration of evolutionary potential and genetic novelty when identifying conservation units for this group.
Data from: Revisiting comparisons of genetic diversity in stable and declining species: assessing genome-wide polymorphism in North American bumble bees using RAD sequencing
Genetic variation is of key importance for a species' evolutionary potential, and its estimation is a major component of conservation studies. New DNA sequencing technologies have enabled the analysis of large portions of the genome in nonmodel species, promising highly accurate estimates of such population genetic parameters. Restriction site-associated DNA sequencing (RADseq) is used to analyse thousands of variants in the bumble bee species Bombus impatiens, which is common, and Bombus pensylvanicus, which is in decline. Previous microsatellite-based analyses have shown that gene diversity is lower in the declining B. pensylvanicus than in B. impatiens. RADseq nucleotide diversities appear much more similar in the two species. Both species exhibit allele frequencies consistent with historical population expansions. Differences in diversity observed at microsatellites thus do not appear to have arisen from long-term differences in population size and are either recent in origin or may result from mutational processes. Additional research is needed to explain these discrepancies and to investigate the best ways to integrate next-generation sequencing data and more traditional molecular markers in studies of genetic diversity.
Genetic and cellular/biochemical data for mouse Pycard gene differences altering mRNA turnover and IL-1b release
<p>Quantitative trait locus mapping for interleukin-1b release after inflammasome priming and activation was performed on bone marrow-derived macrophages (BMDM) from an AKRxDBA/2 strain intercross. The strongest associated locus mapped very close to the <i>Pycard</i> gene on chromosome 7, which codes for the inflammasome adaptor protein apoptosis-associated speck-like protein containing a CARD (ASC). The DBA/2 and AKR <i>Pycard</i> genes only differ at single nucleotide polymorphism (SNP) in their 3' untranslated region (UTR). DBA/2 vs. AKR BMDM had increased levels of <i>Pycard</i> mRNA expression and ASC protein, and increased inflammasome speck formation, which was associated with increased <i>Pycard</i> mRNA stability without an increased transcription rate. CRIPSR/Cas9 gene editing was performed on DBA/2 embryonic stem cells to change the <i>Pycard</i> 3'UTR SNP from the DBA/2 to the AKR allele. This single base change significantly reduced <i>Pycard</i> expression and inflammasome activity after cells were differentiated into macrophages due to reduced <i>Pycard</i> mRNA stability.</p>
FIGURE 4 in A redescription of the carinate pillsnail, Euchemotrema hubrichti (Pilsbry, 1940) (Pulmonata: Polygyridae), with notes on habitat and genetics
FIGURE 4. Line drawing of the reproductive tract. Abbreviations: AG = albumen gland, EP = epiphallus, FO = free oviduct, GA = genital atrium, HD = hermaphroditic duct, P = penis, PR = penial retractor, PS = prostate, UT = uterus, VD = vas deferens.
FIGURE 3 in A redescription of the carinate pillsnail, Euchemotrema hubrichti (Pilsbry, 1940) (Pulmonata: Polygyridae), with notes on habitat and genetics
FIGURE 3. The shell of E. hubrichti. Top row: Shell figures from Pilsbry, 1940 (fig. 423, p. 687). Bottom row: Shell figures from present study for comparison (shell measurements: 4.3 mm X 9.4 mm X 4.75 whorls). The black number 2 on the shell indicates that this shell was taken from one of the four specimens used for sequencing of the mitochondrial COI gene.
Data from: Genetic drift and selection in many-allele range expansions
We experimentally and numerically investigate the evolutionary dynamics of four competing strains of E. coli with differing expansion velocities in radially expanding colonies. We compare experimental measurements of the average fraction, correlation functions between strains, and the relative rates of genetic domain wall annihilations and coalescences to simulations modeling the population as a one-dimensional ring of annihilating and coalescing random walkers with deterministic biases due to selection. The simulations reveal that the evolutionary dynamics can be collapsed onto master curves governed by three essential parameters: (1) an expansion length beyond which selection dominates over genetic drift; (2) a characteristic angular correlation describing the size of genetic domains; and (3) a dimensionless constant quantifying the interplay between a colony's curvature at the frontier and its selection length scale. We measure these parameters with a new technique that precisely measures small selective differences between spatially competing strains and show that our simulations accurately predict the dynamics without additional fitting. Our results suggest that the random walk model can act as a useful predictive tool for describing the evolutionary dynamics of range expansions composed of an arbitrary number of genotypes with different fitnesses.
Data from: Genetic variation in the developmental regulation of cortical avpr1a among prairie voles
Early experiences can have enduring impacts on brain and behavior, but the strength of these effects can be influenced by genetic variation. In principle, polymorphic CpGs (polyCpGs) may contribute to gene-by-environment interactions (GxE) by altering DNA methylation. In this study, we investigate the influence of polyCpGs on the development of vasopressin receptor 1a abundance in the retrosplenial cortex (RSC-V1aR) of prairie voles (Microtus ochrogaster). Two alternative alleles (HI/LO) predict RSC avpr1a expression, V1aR abundance and sexual fidelity in adulthood; these alleles differ in the frequency of CpG sites and in methylation at a putative intron enhancer. We hypothesized that the elevated CpG abundance in LO alleles would make homozygous LO/LO voles more sensitive to developmental perturbations. We found that genotype differences in RSC-V1aR abundance emerged early in ontogeny and were accompanied by differences in methylation of the putative enhancer. As predicted, postnatal treatment with an oxytocin receptor antagonist (OTA) reduced RSC-V1aR abundance in LO/LO adults but not their HI/HI siblings. Similarly, methylation inhibition by zebularine increased RSC-V1aR in LO/LO adults, but not in HI/HI siblings. These data demonstrate a gene-by-environment interaction in RSC-V1aR. Surprisingly, however, neither OTA nor zebularine altered adult methylation of the intronic enhancer, suggesting that differences in sensitivity could not be explained by CpG density at the enhancer alone. Methylated DNA immunoprecipiation-sequencing (MeDIP-seq) revealed additional differentially methylated regions between HI/HI and LO/LO voles. Future research should examine the role of these regions and other regulatory elements in the ontogeny of RSC-V1aR and its developmentally induced changes.
Data from: Whole genome sequencing of two North American Drosophila melanogaster populations reveals genetic differentiation and positive selection
The prevailing demographic model for Drosophila melanogaster suggests that the colonization of North America occurred very recently from a subset of European flies that rapidly expanded across the continent. This model implies a sudden population growth and range expansion consistent with very low or no population subdivision. As flies adapt to new environments, local adaptation events may be expected. To describe demographic and selective events during North American colonization, we have generated a data set of 35 individual whole-genome sequences from inbred lines of D. melanogaster from a west coast US population (Winters, California, USA) and compared them with a public genome data set from Raleigh (Raleigh, North Carolina, USA). We analysed nuclear and mitochondrial genomes and described levels of variation and divergence within and between these two North American D. melanogaster populations. Both populations exhibit negative values of Tajima's D across the genome, a common signature of demographic expansion. We also detected a low but significant level of genome-wide differentiation between the two populations, as well as multiple allele surfing events, which can be the result of gene drift in local subpopulations on the edge of an expansion wave. In contrast to this genome-wide pattern, we uncovered a 50-kilobase segment in chromosome arm 3L that showed all the hallmarks of a soft selective sweep in both populations. A comparison of allele frequencies within this divergent region among six populations from three continents allowed us to cluster these populations in two differentiated groups, providing evidence for the action of natural selection on a global scale.
FIGURE 2 in On the morphological, biological and genetic heterogeneity of the genus Orchis (Orchidaceae, Orchidinae)
FIGURE 2. Principal component analysis showing distribution of samples with 95% confidence ellipses around the group means and correlation of characters with the first two axes. Symbols refer to Table 1.
FIGURE 5 in On the morphological, biological and genetic heterogeneity of the genus Orchis (Orchidaceae, Orchidinae)
FIGURE 5. Percentages of pollinator species by insect order for subgenera Masculae and Orchis (from various sources collected by Claessens & Kleynen, 2011).
FIGURE 1 in On the morphological, biological and genetic heterogeneity of the genus Orchis (Orchidaceae, Orchidinae)
FIGURE 1. Maximum clade credibility tree of ITS sequences of 26 Orchis species with Traunsteinera globosa as outgroup, inferred with Bayesian relaxed clock analysis. Original data were from Bateman et al. (2003). The uncorrelated lognormal clock model was used, and the root height was fixed at 1.0. Posterior distributions of parameters were approximated using two independent Markov chain Monte Carlo analyses of 2.0 × 107 generations followed by a discarded burn-in of 2.0 × 106 generations (10%).
FIGURE 4 in On the morphological, biological and genetic heterogeneity of the genus Orchis (Orchidaceae, Orchidinae)
FIGURE 4. Discriminant analysis showing distribution of individuals and correlation of characters, according to the first two canonical axes (78.2% and 21.8% of total variation, respectively). Ellipses incorporate 50% of individuals. Symbols refer to Table 1.
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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.