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356 results for “heritability”
Accurate and Efficient Estimation of Local Heritability using Summary Statistics and LD Matrix -- Demo datasets for the HEELS tutorials
<p>We introduced a new estimator for local heritability, "HEELS", which attains comparable statistical efficiency as the REML estimator (such as those produced by GCTA and BOLT-REML) but only requires summary-level statistics – Z-scores from marginal association tests and the empirical LD. Our method has been implemented into an open-source Python-based command line tool. </p> <p>The datasets released here can be downloaded to test the two main functions of our software package: 1) estimating local heritability; 2) computing the low-dimensional representation of the LD matrix. They are meant to accompany the HEELS tutorials we have posted onto the wiki pages of our github repository: https://github.com/huilisabrina/HEELS/wiki.</p> <p> </p>
The heritability of inducible defenses in tadpoles.
The evolution of plastic traits requires phenotypic trade-offs and heritable traits, yet the latter requirement has received little attention, especially for predatorinduced traits. Using a half-sib design, I examined the narrow-sense heritability of predator-induced behaviour, morphology, and life history in larval wood frogs (Rana sylvatica). Many of the traits had significant additive genetic variation in predator (caged Anax longipes) and no-predator environments. Whereas most traits had moderate to high heritability across environments, tail depth exhibited high heritability with predators but low heritability without predators. In addition, several traits had significant heritability for plasticity, suggesting a potential for selection to act on plasticity per se. Genetic correlations confirmed known phenotypic relationships across environments and identified novel relationships within each environment. This appears to be the first investigation of narrow-sense heritabilities for predator-induced traits and confirms that inducible traits previously shown to be under selection also have a genetic basis and should be capable of exhibiting evolutionary responses.
Summary statistics data for "Genetic Analyses Support the Contribution of mRNA N6-methyladenosine (m6A) Modification to Human Diseases Heritability"
<p>We included the summary statistics data associated with our manuscript "<strong>Genetic Analyses Support the Contribution of mRNA <em>N</em><sup>6</sup>-methyladenosine (m<sup>6</sup>A) Modification to Human Diseases Heritability". </strong></p> <p>We also included the newly imputed genotype data for the 60 YRI individuals involved in our study, the joint m<sup>6</sup>A peaks tested (locations of the molecular phetnotype in BED12 format) and normalized log odds ratio (enrichment) of these joint peaks (molecular phenotype data). </p>
Data from: Telomere heritability and parental age at conception effects in a wild avian population
<p>Individual variation in telomere length is predictive of health and mortality risk across a range of species. However, the relative influence of environmental and genetic variation on individual telomere length in wild populations remains poorly understood. Heritability of telomere length has primarily been calculated using parent–offspring regression which can be confounded by shared environments. To control for confounding variables, quantitative genetic 'animal models' can be used, but few studies have applied animal models in wild populations. Furthermore, parental age at conception may also influence offspring telomere length, but most studies have been cross-sectional. We investigated within- and between- parental age at conception effects and heritability of telomere length in the Seychelles warbler using measures from birds caught over 20 years and a multi-generational pedigree. We found a weak negative within-paternal age at conception effect (as fathers aged, their offspring had shorter telomeres) and a weak positive between-maternal age at conception effect (females that survived to older ages had offspring with longer telomeres). Animal models provided evidence that heritability and evolvability of telomere length was low in this population, and that variation in telomere length was not driven by early-life effects of hatch period or parental identities. qPCR plate had a large influence on telomere length variation and not accounting for it in the models would have underestimated heritability. Our study illustrates the need to include and account for technical variation in order to accurately estimate heritability, as well as other environmental effects, on telomere length in natural populations. </p>
Low-frequency somatic mutations are heritable in tropical trees Dicorynia guianensis and Sextonia rubra
<p>Somatic mutations potentially play a role in plant evolution, but common expectations pertaining to plant somatic mutation remain insufficiently tested. Unlike in most animals, the plant germline is assumed to be set aside late in development, leading to the expectation that plants accumulate somatic mutations along growth. Therefore, several predictions were made on the fate of somatic mutations: mutations have generally low frequency in plant tissues; mutations at high frequency have a higher chance of intergenerational transmission; branching topology of the tree dictates mutation distribution; and, exposure to UV radiation increases mutagenesis. To provide new insights into mutation accumulation and transmission in plants, we produced two high-quality reference genomes and a unique dataset of 60 high-coverage whole-genome sequences of two tropical tree species, <i>Dicorynia guianensis</i> (Fabaceae) and <i>Sextonia rubra </i>(Lauraceae). We identified 15,066 <i>de novo</i> somatic mutations in <i>D. guianensis</i> and 3,208 in <i>S. rubra</i>, surprisingly almost all found at low frequency. We demonstrate that: 1) low-frequency mutations can be transmitted to the next generation; 2) mutation phylogenies deviate from the branching topology of the tree; and 3) mutation rates and mutation spectra are not demonstrably affected by differences in UV exposure. Altogether, our results suggest far more complex links between plant growth, ageing, UV exposure, and mutation rates than commonly thought.</p>
Processed data to accompany "Clonally heritable gene expression imparts a layer of diversity within cell types"
<p>This is the processed data underlying the paper "Clonally heritable gene expression imparts a layer of diversity within cell types" by Mold, Weissman, et al. Data has been gone through preprocessing steps, using the Python Notebooks found at <a href="https://github.com/MartyWeissman/ClonalOmics/tree/main/Data">https://github.com/MartyWeissman/ClonalOmics/tree/main/Data</a>. </p> <p>Smaller files are provided in .csv (comma-separated-value) format and larger files such as expression matrices are provided in .loom format (<a href="https://anndata.readthedocs.io/en/latest/">using the AnnData package</a>).</p> <p> </p> <p> </p>
Heritability of cognitive performance in wild Western Australian magpies
<p>Individual differences in cognitive performance can have genetic, social and environmental components. Most research on the heritability of cognitive traits comes from humans or captive non-human animals, whilst less attention has been given to wild populations. Western Australian magpies (<em>Gymnorhina tibicen dorsalis</em>, hereafter magpies) show phenotypic variation in cognitive performance, which affects reproductive success. Despite high levels of individual repeatability, we do not know whether cognitive performance is heritable in this species. Here, we quantify broad-sense heritability of associative learning ability in a wild population of Western Australian magpies. Specifically, we explore whether offspring associative learning performance is predicted by maternal associative learning performance, or by the social environment (group size) when tested at three time points during the first year of life. We found no significant relationship between maternal and offspring associative learning performance, with an estimated broad-sense heritability of just -0.004 ± 0.024 (CI: -0.050/0.044). However, complementing previous findings, we find that at 300 days post-fledging, individuals raised in larger groups passed the test in fewer trials compared to individuals from small groups. Our results highlight the pivotal influence of the social environment on cognitive development.</p>
Vitamin D status is heritable and under environment-dependent selection in the wild
<p>Vitamin D has a well-established role in skeletal health and is increasingly linked to chronic disease and mortality in humans and companion animals. Despite the clear significance of vitamin D for health and obvious implications for fitness under natural conditions, no longitudinal study has tested whether the circulating concentration of vitamin D is under natural selection in the wild. Here, we show that concentrations of dietary-derived vitamin D and endogenously-produced vitamin D metabolites are heritable and largely polygenic in a wild population of Soay sheep (<em>Ovis aries</em>). Vitamin D status was positively associated with female adult survival, and vitamin D status predicted female fecundity in particular, good environment years when sheep density and competition for resources was low. Our study provides evidence that vitamin D status has the potential to respond to selection, as well as new insights into how vitamin D metabolism is associated with fitness in the wild. </p>
Heritable variation in host quality as measured through an ectoparasite's performance
<p>Obligate parasites need one or more hosts to complete their life cycle. However, hosts might show intraspecific variation in quality with respect to the parasites themselves, thus affecting on-host and off-host parasite performance. High heritability in host quality for the parasite may therefore exert long-lasting selective pressures on the parasite<br> and influence host–parasite coevolution. However, the amount of variation and heritability in host quality are unknown for most parasite species, especially in wild populations of hosts. Both measures were estimated in a wild-caught bird Parus major that was experimentally infested by two developmental stages (larva and nymph) of a ectoparasite (the tick Ixodes arboricola). We examined variation in host quality through variation in tick performance, namely the on-host performance (attachment success, feeding time, engorgement weight and feeding success) and the off-host performance (moulting time, moulting success and overall survival). Herein we also investigated the influence on tick performance of host traits linked with the bird's life history and physiology such as body condition, sex, age and haematocrit. By correlating tick performance variables between larvae and nymphs feeding on the same bird at different times, we found a significant correlation in attachment success, suggesting consistent among-host variation for this performance measure, but no significant larva-nymph correlations for the other tick variables. Animal models relating tick performance variables to the host pedigree showed a strong heritable signal for host quality as measured through tick feeding time, and lower but substantial estimates in other performance variables. With regard to the host traits, feeding success and survival of tick larvae were lower on female birds, and nymphal survival was higher on older birds. Larval feeding time was negatively correlated with host haematocrit. This is one of the first studies showing consistent intraspecific variation and heritability of host quality for a multistage ectoparasite.</p>
Further evidence from common garden rearing experiments of heritable traits separating lean and siscowet lake charr (Salvelinus namaycush) ecotypes
<p>Genetic evidence of selection for complex and polygenically regulated phenotypes can easily become masked by neutral population genetic structure and phenotypic plasticity. Without direct evidence of genotype-phenotype associations, it can be difficult to conclude to what degree a phenotype is heritable or a product of environment. Common garden laboratory studies control for environmental stochasticity and help to determine the mechanism that regulates traits. Here we assess lipid content, growth, weight, and length variation in full and hybrid F<sub>1</sub> crosses of deep and shallow water sympatric lake charr ecotypes reared for nine years in a common garden experiment. Redundancy analysis (RDA) and quantitative-trait-loci (QTL) genomic scans are used to identify associations between genotypes at 19,714 single nucleotide polymorphisms (SNPs) aligned to the lake charr genome and individual phenotypes to determine the role that genetic inheritance plays in ecotype phenotypic diversity. Lipid content, growth, length, and weight differed significantly among lake charr crosses throughout the experiment suggesting that pedigree plays a large role in lake charr development. Polygenic scores of 15 SNPs putatively associated with lipid content and/or condition factor indicated that ecotype distinguishing traits are polygenically regulated and additive. A QTL identified on chromosome 38 contained >200 genes, some of which were associated with lipid metabolism and growth, demonstrating the complex nature of ecotype diversity. The results of our common garden study further indicate that lake charr ecotypes observed in nature are pre-determined at birth and that ecotypes differ fundamentally in lipid metabolism and growth.</p>
Rhesus macaque cone ratio heritability
<p><span>A defining feature of catarrhine primates is uniform trichromacy – the ability to distinguish red (long; L), green (medium; M), and blue (short; S) wavelengths of light. While the tuning of photoreceptors is conserved, the ratio of L:M cones in the retina is variable within and between species, with human cone ratios differing from other catarrhines. Yet, the sources and structure of variation in cone ratios are poorly understood, precluding a broader understanding of color vision variability. Here, we report a large-scale study of a pedigreed population of macaques. We collected foveal RNA and analysed opsin gene expression using cDNA. We estimated the additive genetic variance of cone ratios. The average L:M ratio and standard error was 1.03:1± 0.02. There was no age effect, and genetic contribution to variation was negligible. We found marginal sex effects with females having larger ratios than males. S cone ratios (0.143: 1± 0.002) had significant genetic variance with a heritability estimate of 43% but did not differ between sexes or age groups. Our results contextualize the derived human condition of L-cone dominance and provide new information about the heritability of cone ratios and variation in primate color vision.</span></p>
Novel host plant unmasks heritable variation in plant preference within an insect population
<p>Introductions of novel plant species can disturb the historical resource environment of herbivorous insects, resulting in strong selection to either adopt or exclude the novel host. However, an adaptive response depends on heritable genetic variation for preference or performance within the targeted herbivore population, and it is unclear how heritability of host-use preference may differ between novel and historical hosts. <em>Pieris macdunnoughii</em> butterflies in the Rocky Mountains lay eggs on the nonnative mustard <em>Thlaspi arvense</em>, which is lethal to their offspring. Heritability analyses revealed considerable sex-linked additive genetic variation in host preference within a population of this butterfly. This was contrary to general predictions about the genetic basis of preference variation, which are hypothesized to be sex-linked between populations but autosomal within populations. Evidence of sex-linkage disappeared when butterflies were tested on methanol-based chemical extracts, suggesting these chemicals in isolation may not be the primary driver of female choice among available host plants. Although unexpected, evidence for within-population sex-linked genetic variation in preference for <em>T. arvense</em> over native hosts indicates that persistent maladaptive oviposition on this lethal plant must be maintained by alternative evolutionary dynamics such as migration- or drift-selection balance or pleiotropic constraints.</p>
Integrative genetic analyses illuminates ALS heritability and identifies novel risk genes
<p>Amyotrophic lateral sclerosis (ALS), the major adult onset motor neuron disease, has substantial heritability, in part shared with fronto-temporal dementia (FTD). We show here that ALS heritability is enriched in splicing variants and in binding sites of 6 RNA binding proteins including TDP-43 and FUS. A discovery and replication transcriptome wide association study (TWAS) identified 6 loci associated with ALS, 3 in known ALS loci (<em>C9ORF72, SCFD1, SLC9A8</em>) and 3 novel loci including <em>NUP50 </em>encoding for the nucleopore basket protein NUP50 In our meta-analysis of TWAS cohorts, <em>NUP50 </em>common variant was associated with ALS and to decreased expression of <em>NUP50 </em>in the central nervous system. Independently, we further show association of rare variants in <em>NUP50</em> with ALS risk (<em>P</em> = 3.71.10<sup>-03</sup>; odds ratio = 3.29; 95%CI, 1.37 to 7.87) in a cohort of 9,390 ALS/FTD patients and 4,594 controls. Cells from one patient carrying a <em>NUP50 </em>frameshift mutation displayed a decreased levels of NUP50. Loss of NUP50 leads to neuronal death in cultured neurons, and motor defects in <em>Drosophila </em>and zebrafish models. Thus, our study identifies alterations in splicing in neurons as a critical pathogenic process in ALS, uncovers several new loci potentially contributing to ALS, and provides genetic evidence linking nuclear pore defects to ALS.</p>
Gene-environment interaction explains a part of missing heritability in human body mass index
<p>Gene-environment (G×E) interaction could partially explain missing heritability in traits; however, the magnitudes of G×E interaction effects remain unclear. Here, we estimate the heritability of G×E interaction for body mass index (BMI) by subjecting genome-wide interaction study data of 331,282 participants in the UK Biobank to linkage disequilibrium score regression (LDSC) and linkage disequilibrium adjusted kinships–software for estimating SNP heritability from summary statistics (LDAK-SumHer) analyses. Among 14 obesity-related lifestyle factors, MET score, pack years of smoking, and alcohol intake frequency significantly interact with genetic factors in both analyses, accounting for the partial variance of BMI. The G×E interaction heritability (%) and standard error of these factors by LDSC and LDAK-SumHer are as follows: MET score, 0.45% (0.12) and 0.65% (0.24); pack years of smoking, 0.52% (0.13) and 0.93% (0.26); and alcohol intake frequency, 0.32% (0.10) and 0.80% (0.17), respectively. Moreover, these three factors are partially validated for their interactions with genetic factors in other obesity-related traits, including waist circumference, hip circumference, waist-to-hip ratio adjusted with BMI, and body fat percentage. Our results suggest that G×E interaction may partly explain the missing heritability in BMI, and two G×E interaction loci identified could help in understanding the genetic architecture of obesity.</p>
Data to support: Moving beyond heritability in the search for coral adaptive potential
<p><span>Global environmental change is happening at unprecedented rates. Coral reefs are among the ecosystems most threatened by global change. For wild populations to persist, they must adapt. Knowledge shortfalls about corals' complex ecological and evolutionary dynamics, however, stymie predictions about potential adaptation to future conditions. Here, we review adaptation through the lens of quantitative genetics. We argue that coral adaptation studies can benefit greatly from "wild" quantitative genetic methods, where traits are studied in wild populations undergoing natural selection, genomic relationship matrices can replace breeding experiments, and analyses can be extended to examine genetic constraints among traits. Individuals with advantageous genotypes for anticipated future conditions can be identified. Finally, genomic genotyping supports simultaneous consideration of how genetic diversity is arrayed across geographic and environmental distances, providing greater context for predictions of phenotypic evolution at a metapopulation scale.</span></p>
Data for: Position in the plant size hierarchy is not heritable
<p><span>The rate of fitness evolution is largely determined by the amount of genetic variation for fitness in the population. In many plant populations, a few large individuals often occur alongside many more, smaller individuals. In annual plants, size is highly correlated with fitness. The contribution of genetic variation to position in the plant size hierarchy has not been investigated. We genotyped individuals at opposing positions in the plant size distribution in a natural population of the annual plant <em>Impatiens</em> <em>capensis</em> (Jewelweed). No significant genetic variation for position in the size hierarchy was detected when population structure was accounted for. This result suggests that the rate of evolution for increased plant fitness is constrained by low levels of standing genetic variation.</span></p>
Data used in: Heritability and variance components of seed size in wild species: influences of breeding design and the number of genotypes tested
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Heritable variation in host quality as measured through an ectoparasite's performance
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Novel host plant unmasks heritable variation in plant preference within an insect population
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Heritability of cognitive performance in wild Western Australian magpies
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