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28 results for “Genome Phenotypic variations”
Data From: Evaluating the correlation between genome-wide diversity and the release of plastic phenotypic variation in experimental translocations to novel natural environments
<p>Phenotypic reaction norms are often shaped and constrained by selection and are important for allowing organisms to respond to environmental change. However, selection cannot constrain reaction norms for environmental conditions that populations have not experienced. This may allow cryptic neutral genetic variation for the reaction norm to accumulate such that a release of phenotypic variation occurs when it is exposed to novel conditions. Most genomic diversity behaves as if functionally neutral. Genome-wide diversity metrics may therefore correlate with levels of cryptic genetic variation and, as a result, could exhibit a positive relationship with a release of phenotypic variation in novel environments. To test this hypothesis, we conducted translocations of juvenile brook trout (Salvelinus fontinalis) from 12 populations to novel uninhabited ponds that represented a gradient of environmental conditions. We assessed reaction norms for morphological traits (body size and four morphometric relative warps) across pond environmental gradients and evaluated the effect of genome-wide heterozygosity on phenotypic variability. All traits displayed plastic reaction norms. Overall, we found some evidence that a release of phenotypic variation consistent with cryptic genetic variation can occur in novel environmental conditions. However, the extent to which this release was correlated with average genome-wide diversity was limited to only one of five morphological traits examined. Our results suggest that the link between genomic diversity and the accumulation of cryptic genetic variation in reaction norms may be limited. Similarly, reaction norms were constrained for many of the morphological traits examined. Past conditions may have constrained reaction norms in the putatively novel environments despite significant deviations from contemporary source population habitat. Additionally, as a generalist colonizing species brook trout may exhibit plastic phenotypes across a wide range of environmental conditions.</p>
Consilience across multiple, independent genomic data sets reveals species in a complex with limited phenotypic variation
<p>Species delimitation in the genomic era has focused predominantly on the application of multiple analytical methodologies to a single massive parallel sequencing (MPS) data set, rather than leveraging the unique but complementary insights provided by different classes of MPS data. In this study we demonstrate how the use of two independent MPS data sets, a sequence capture data set and a single nucleotide polymorphism (SNP) data set generated via genotyping-by-sequencing, enables the resolution of species in three complexes belonging to the grass genus <em>Ehrharta, </em>whose strong population structure and subtle morphological variation limit the effectiveness of traditional species delimitation approaches. Sequence capture data are used to construct a comprehensive phylogenetic tree of <em>Ehrharta </em>and to resolve population relationships within the focal clades, while SNP data are used to detect patterns of gene pool sharing across populations, using a novel approach that visualises multiple values of K. Given that the two genomic data sets are fully independent, the strong congruence in the clusters they resolve provides powerful ratification of species boundaries in all three complexes studied. Our approach is also able to resolve a number of single-population species and a probable hybrid species, both which would be difficult to detect and characterize using a single MPS data set. Overall, the data reveal the existence of 11 and five species in the <em>E. setacea</em> and <em>E. rehmannii </em>complexes, with the <em>E. ramosa</em> complex requiring further sampling before species limits are finalized. Despite phenotypic differentiation being generally subtle, true crypsis is limited to just a few species pairs and triplets. We conclude that, in the absence of strong morphological differentiation, the use of multiple, independent genomic data sets is necessary in order to provide the cross-data set corroboration that is foundational to an integrative taxonomic approach.</p>
Data From: Evaluating the correlation between genome-wide diversity and the release of plastic phenotypic variation in experimental translocations to novel natural environments
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Variation in the resource environment affects patterns of seasonal adaptation at phenotypic and genomic levels in <em>Drosophila melanogaster</em>
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Consilience across multiple, independent genomic data sets reveals species in a complex with limited phenotypic variation
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Data from: Host-induced genome instability rapidly generates phenotypic variation across Candida albicans strains and ploidy states
<p>Candida albicans is an opportunistic fungal pathogen of humans that is typically diploid yet has a highly labile genome tolerant of large-scale perturbations including chromosomal aneuploidy and loss-of-heterozygosity events. The ability to rapidly generate genetic variation is crucial for C. albicans to adapt to changing or stressful environments, like those encountered in the host. Genetic variation occurs via stress-induced mutagenesis or can be generated through its parasexual cycle, in which tetraploids arise via diploid mating or stress-induced mitotic defects and undergo nonmeiotic ploidy reduction. However, it remains largely unknown how genetic background contributes to C. albicans genome instability in vitro or in the host environment. Here, we tested how genetic background, ploidy, and the host environment impacts C. albicans genome stability. We found that host association induced both loss-of-heterozygosity events and genome size changes, regardless of genetic background or ploidy. However, the magnitude and types of genome changes varied across C. albicans strain background and ploidy state. We then assessed if host-induced genomic changes resulted in fitness consequences on growth rate and nonlethal virulence phenotypes and found that many host-derived isolates significantly changed relative to their parental strain. Interestingly, diploid host-associated C. albicans predominantly decreased host reproductive fitness, whereas tetraploid host-associated C. albicans increased host reproductive fitness. Together, these results are important for understanding how host-induced genomic changes in C. albicans alter its relationship with the host.</p> <p>IMPORTANCE Candida albicans is an opportunistic fungal pathogen of humans. The ability to generate genetic variation is essential for adaptation and is a strategy that C. albicans and other fungal pathogens use to change their genome size. Stressful environments, including the host, induce C. albicans genome instability. Here, we investigated how C. albicans genetic background and ploidy state impact genome instability, both in vitro and in a host environment. We show that the host environment induces genome instability, but the magnitude depends on C. albicans genetic background. Furthermore, we show that tetraploid C. albicans is highly unstable in host environments and rapidly reduces in genome size. These reductions in genome size often resulted in reduced virulence. In contrast, diploid C. albicans displayed modest host-induced genome size changes, yet these frequently resulted in increased virulence. Such studies are essential for understanding how opportunistic pathogens respond and potentially adapt to the host environment.</p> <p> </p>
Data from: Phenotypic, ecological and genomic variation in common bully (Gobiomorphus cotidianus) populations along depth gradients in New Zealand's Southern Great Lakes
<p>Depth gradients in lakes are often key drivers of population divergence and speciation in fishes. New Zealand has many deep lakes but no known profundal specialist fishes or cases of intralacustrine speciation. We sampled a native benthic fish, the common bully, from 5–90 m depth in four South Island lakes, to test for morphological, ecological, or genetic differentiation associated with depth. Deeper fish consistently had narrower bodies, while other morphological traits showed variable relationships with depth. Carbon and nitrogen stable isotope values of fish increased with depth, largely tracking isotopic trends with depth of benthic invertebrate prey. Genotyping-by-sequencing showed some genome-wide differentiation between two of the lakes, but no evidence for within-lake genetic structuring along depth gradients. These results indicate that individual bullies associate with shallower or deeper habitats within their lifetimes, but we found no evidence of progress toward genetic divergence within lakes. The apparent lack of intralacustrine genetic divergence in New Zealand's fishes may be explained by a combination of environmental factors and constraints intrinsic to its marine-derived freshwater fish fauna.</p>
Duck pan-genome reveals two transposon-derived structural variations caused bodyweight enlarging and white plumage phenotype formation during evolution
<p><span>Structural variations (SVs) are a major source of domestication and improvement traits. We present the first duck pan-genome constructed using five genome assemblies capturing ~40.98 Mb new sequences. This pan-genome together with high-depth sequencing data (>46.5X) identified 101,041 SVs, of which substantial proportions were derived from transposable element (TE) activity. Many TE-derived SVs anchored in a gene body or regulatory region are linked to domestication and improvement. By combining quantitative genetics with molecular experiments, we dissect how TE-derived SVs change gene expression of <em>IGF2BP1</em> and generate novel transcripts of <em>MITF</em>, shaping body weight and plumage color. In the <em>IGF2BP1</em> locus, the TE-derived SV explains the largest effect on body weight among avian species (27.61% of phenotypic variation). Our findings highlight the </span><span>importance of using a pan-genome as a reference in genomics studies</span><span> and explore the roles of TE-derived SVs in trait formation and in livestock breeding.</span></p>
Phenotypic variation and genome-wide association studies of main culm panicle node number, maximum node production rate, and degree-days to heading in rice
<p>To understand the genetic basis of main culm panicle node number, maximum node production rate, and degree-days to heading in rice (Oryza sativa), we conducted genome-wide association studies using a diversity panel of 220 rice accessions and 854,832 SNP markers generated using genotyping-by-sequencing (GBS), with 1X coverage. The raw genotype data was filtered, selecting single nucleotide polymorphisms (SNPs) having less than 50% missing data and minimum allele frequency (MAF) >5%. After initial filtering, imputation was conducted using BEAGLE V4.0 in 1,075,302 SNP markers. After imputation, the dataset was filtered a second time by removing SNPs with less than 5% MAF and more than 5% missing data. A total of 854,832 SNPs were used in the genome-wide association analyses. The dataset representing the genotype data of 854,832 SNP markers by 220 rice accessions is presented here.</p>
Figure 6 in Subspecies at crossroads: the evolutionary significance of genomic and phenotypic variation in a wide-ranging Australian lizard (Ctenotus pantherinus)
Figure 6. Genotypic clustering and admixture in Ctenotus pantherinus. Bars depict the relative proportion of alleles in each individual corresponding to the inferred genotypic clusters (i.e. ancestry proportions of individuals). Pie charts on the map indicate the average ancestry proportions corresponding to each cluster at each site (based on all individuals at that site). The clusters closely match the sample composition and geographical distribution of major clades from the nuclear phylogenetic analysis (Fig. 5). Multicoloured pies indicate admixture among clusters.
Figure 2 in Subspecies at crossroads: the evolutionary significance of genomic and phenotypic variation in a wide-ranging Australian lizard (Ctenotus pantherinus)
Figure 2. Selected phenotypic characters examined in museum specimens of Ctenotus pantherinus and their variation. A, dorsal coloration (from left to right): typical ocellated pattern, vertebral stripe, longitudinal lines, hiatus of ocelli on the vertebral region and ocelli with thick dark borders. B, condition of the plantar scales: smooth, pyramidal and with a spiny projection. C, condition of the subdigital lamellae (yellow arrows): single broad keel, single fine keel and fine medial keel flanked by two smaller parallel keels. Variation among the character states shown was often near-continuous and difficult to categorize.
Figure 1. A in Subspecies at crossroads: the evolutionary significance of genomic and phenotypic variation in a wide-ranging Australian lizard (Ctenotus pantherinus)
Figure 1. A, Illustrative picture of C. pantherinus in life (subspecies C. p. ocellifer), courtesy of Eric Vanderduys. B, C, distributions of currently recognized Ctenotus pantherinus subspecies. B, presumed distributions of C. pantherinus subspecies as typically presented in field guides and taxonomic compendiums (based on Ehmann & Strahan, 1992; Storr et al., 1999). Subspecies are as follows: C. p. acripes (a), C. p. calx (c), C. p. ocellifer (o) and C. p. pantherinus (p). Note the disjunct distribution of C. p. acripes, whose type locality is on a Western Australian island (Barrow Island; arrow). C, sampling localities of 1464 voucher specimens split by subspecies assignment as in the original museum records (for details on how we compiled these data, see the Material and methods section). Note that subspecies ranges as commonly understood (B) often disagree with those suggested by museum records.
Human Genomic Population Structure and Phenotype-genotype Variation in ADME Genes in Four Populations
ClinicalTrials.gov study NCT02789527. IPD Sharing: UNDECIDED. Countries: 4. Publications: 1.
Data from: Phenotypic, ecological and genomic variation in common bully (Gobiomorphus cotidianus) populations along depth gradients in New Zealand's Southern Great Lakes
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Phenotypic variation and genome-wide association studies of main culm panicle node number, maximum node production rate, and degree-days to heading in rice
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Data from: Host-induced genome instability rapidly generates phenotypic variation across Candida albicans strains and ploidy states
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Duck pan-genome reveals two transposon-derived structural variations caused bodyweight enlarging and white plumage phenotype formation during evolution
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Spatial predictors of genomic and phenotypic variation differ in a lowland Middle American bird (Icterus gularis)
<p>Spatial patterns of intraspecific variation are shaped by factors such as geographic distance among populations, historical changes in gene flow and interactions with local environments. Although these factors are not mutually exclusive and operate on both genomic and phenotypic variation, it is unclear how they affect these two axes of variation. We address this question by exploring the predictors of genomic and phenotypic divergence in Icterus gularis, a broadly distributed Middle American bird that exhibits marked geographic variation in body size across its range. We combined a comprehensive SNP and phenotypic dataset to test whether genome-wide genetic and phenotypic differentiation are best explained by (a) isolation by distance, (b) isolation by history, or (c) isolation by environment. We find that the pronounced genetic and phenotypic variation in I. gularis are only partially correlated and differ regarding spatial predictors. Whereas genomic variation is largely explained by historical barriers to gene flow, phenotypic diversity can be best predicted by contemporary environmental heterogeneity. Our genomic analyses reveal strong phylogeographic structure coinciding with the Chivela Pass at the Isthmus of Tehuantepec and was formed in the Pleistocene, when populations were isolated in north-south refugia. In contrast, we found a strong association between body size and environmental variables, such as temperature and precipitation. The relationship between body size and local climate is consistent with a pattern produced by either natural selection or environmental plasticity. Overall, these results provide empirical evidence for why phenotypic and genomic data are often in conflict in taxonomic and phylogeographic studies.</p>
Spatial predictors of genomic and phenotypic variation differ in a lowland Middle American bird (Icterus gularis)
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Data from: Genome-wide association mapping in a wild avian population identifies a link between genetic and phenotypic variation in a life-history trait
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International Brain Laboratory public data
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OpenNeuro
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