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134 results for “association test”
Data from: Testing the association of phenotypes with polyploidy: An example using herbaceous and woody eudicots
Although numerous studies have surveyed the frequency with which different plant characters are associated with polyploidy, few statistical tools are available to identify the factors that potentially facilitate polyploidy. We describe a new probabilistic model, BiChroM, designed to associate the frequency of polyploidy and chromosomal change with a binary phenotypic character in a phylogeny. BiChroM provides a robust statistical framework for testing differences in rates of polyploidy associated with phenotypic characters along a phylogeny while simultaneously allowing for evolutionary transitions between character states. We used BiChroM to test whether polyploidy is more frequent in woody or herbaceous plants, based on tree with 4,711 eudicot species. Although polyploidy occurs in woody species, rates of chromosome doubling were over six times higher in herbaceous species. Rates of single chromosome increases or decreases were also far higher in herbaceous than woody species. Simulation experiments indicate that BiChroM performs well with little to no bias and relatively little variance at a wide range of tree depths when trees have at least 500 taxa. Thus, BiChroM provides a first step towards a rigorous statistical framework for assessing the traits that facilitate polyploidy.
Data from: A chromosome 5q31.1 locus associates with tuberculin skin test reactivity in HIV-positive individuals from tuberculosis hyper-endemic regions in east Africa
One in three people has been infected with Mycobacterium tuberculosis (MTB), and the risk for MTB infection in HIV-infected individuals is even higher. We hypothesized that HIV-positive individuals living in tuberculosis-endemic regions who do not get infected by Mycobacterium tuberculosis are genetically resistant. Using an "experiment of nature" design that proved successful in our previous work, we performed a genome-wide association study of tuberculin skin test positivity using 469 HIV-positive patients from prospective study cohorts of tuberculosis from Tanzania and Uganda to identify genetic loci associated with MTB infection in the context of HIV-infection. Among these individuals, 244 tested were tuberculin skin test (TST) positive either at enrollment or during the >8 year follow up, while 225 were not. We identified a genome-wide significant association between the dominant model of rs877356 and binary TST status in the combined cohort (OR=0.2671, p=1.22x10-8). Association was replicated with similar significance when examining TST induration as a continuous trait. The variant lies in the 5q31.1 region, 57kb downstream from IL9. Two-locus analyses of association of variants near rs877356 showed a haplotype comprised of rs877356 and an IL9 missense variant rs2069885 had the most significant association (p=1.59x10-12). We also replicated previously linked loci on chromosomes 2, 5, and 11. IL9 is a cytokine produced by mast cells and T¬H2 cells during inflammatory responses, providing a possible link between airway inflammation and protection from MTB infection. Our results indicate that studying uninfected participants with extensive exposure increases the power to detect associations in complex infectious disease.
Data from: Space use and social association in a gregarious ungulate: testing the conspecific attraction and resource dispersion hypotheses
Animals use a variety of proximate cues to assess habitat quality when resources vary spatiotemporally. Two nonmutually exclusive strategies to assess habitat quality involve either direct assessment of landscape features or observation of social cues from conspecifics as a form of information transfer about forage resources. The conspecific attraction hypothesis proposes that individual space use is dependent on the distribution of conspecifics rather than the location of resource patches, whereas the resource dispersion hypothesis proposes that individual space use and social association are driven by the abundance and distribution of resources. We tested the conspecific attraction and the resource dispersion hypotheses as two nonmutually exclusive hypotheses explaining social association and of adult female caribou (Rangifer tarandus). We used location data from GPS collars to estimate interannual site fidelity and networks representing home range overlap and social associations among individual caribou. We found that home range overlap and social associations were correlated with resource distribution in summer and conspecific attraction in winter. In summer, when resources were distributed relatively homogeneously, interannual site fidelity was high and home range overlap and social associations were low. Conversely, in winter when resources were distributed relatively heterogeneously, interannual site fidelity was low and home range overlap and social associations were high. As access to resources changes across seasons, caribou appear to alter social behavior and space use. In summer, caribou may use cues associated with the distribution of forage, and in winter caribou may use cues from conspecifics to access forage. Our results have broad implications for our understanding of caribou socioecology, suggesting that caribou use season‐specific strategies to locate forage. Caribou populations continue to decline globally, and our finding that conspecific attraction is likely related to access to forage suggests that further fragmentation of caribou habitat could limit social association among caribou, particularly in winter when access to resources may be limited.
Data from: Assessing thermal adaptation using family-based association and FST-outlier tests in a threatened trout
Discovering genetic markers associated with phenotypic or ecological characteristics can improve our understanding of adaptation and guide conservation of key evolutionary traits. The Lahontan cutthroat trout (Oncorhynchus clarkii henshawi) of the northern Great Basin Desert, USA, demonstrated exceptional tolerance to high temperatures in the desert lakes where it resided historically. This trait is central to a conservation hatchery effort to protect the genetic legacy of the nearly extinct lake ecotype. We genotyped full‐sibling families from this conservation broodstock and samples from the only two remaining, thermally distinct, native lake populations at 4,644 new single nucleotide polymorphisms (SNPs). Family‐based genome‐wide association testing of the broodstock identified nine and 26 SNPs associated with thermal tolerance (p < 0.05 and p < 0.1), measured in a previous thermal challenge experiment. Genes near the associated SNPs had complex functions related to immunity, growth, metabolism and ion homeostasis. Principal component analysis using the thermotolerance‐related SNPs showed unexpected divergence between the conservation broodstock and the native lake populations at these loci. FST outlier tests on the native lake populations identified 18 loci shared between two or more of the tests, with two SNPs identified by all three tests (p < 0.01); none overlapped with loci identified by association testing in the broodstock. A recent history of isolation and the complex genetic and demographic backgrounds of Lahontan cutthroat trout probably limited our ability to find shared thermal tolerance loci. Our study extends the still relatively rare application of genomic tools testing for markers associated with important phenotypic or environmental characteristics in species of conservation concern.
Data from: Evidence for contemporary and historical gene flow between guppy populations in different watersheds, with a test for associations with adaptive traits
In dendritic river systems, gene flow is expected to occur primarily within watersheds. Yet, rare cross‐watershed transfers can also occur, whether mediated by (often historical) geological events or (often contemporary) human activities. We explored these events and their potential evolutionary consequences by analyzing patterns of neutral genetic variation (microsatellites) and adaptive phenotypic variation (male color) in wild guppies (Poecilia reticulata) distributed across two watersheds in northern Trinidad. We found the expected signatures of within‐watershed gene flow; yet we also inferred at least two instances of cross‐watershed gene flow—one in the upstream reaches and one further downstream. The upstream cross‐watershed event appears to be very recent (41 ± 13 years), suggesting dispersal via recent flooding or undocumented human‐mediated transport. The downstream cross‐watershed event appears to be considerably older (577 ± 265 years), suggesting a role for rare geological or climatological events. Alongside these strong signatures of both contemporary and historical gene flow, we found little evidence of impacts on presumably adaptive phenotypic differentiation, except perhaps in the one instance of very recent cross‐watershed gene flow. Selection in this system seems to overpower gene flow—at least on the spatiotemporal scales investigated here.
Risk for excessive anticoagulation during hemodialysis is associated with type of vascular access and bedside coagulation testing: Results of a cross-sectional study
<p>Anonymized dataset of the cross-sectional study assessing (i) heparin dosing within a prevalent hemodialysis cohort, (ii) the anticoagulant effects of the heparinization strategy and (iii) identifying predictive factors of the heparin dosing regimen.</p>
Shear wave velocities and associated CPT data for S-PCPT testing in the North Sea
<p>This dataset combines shear wave velocity measurements and associated CPT for offshore wind farm sites in The Netherlands and Germany. The data has been collected by RVO in The Netherlands and BSH in Germany and is available in the public domain. The author has processed the data as part of his PhD research at Vrije Universiteit Brussel.</p>
A test of the role of associative learning in originating sexual preferences in the guppy
<p><span>How do female sexual preferences for male ornamental traits arise? The developmental origins of female preferences are still an understudied area, with most explanations pointing to genetic mechanisms. One intriguing, little-explored, alternative focuses on the role of associative learning in driving this process. According to this hypothesis, a preference learned in an ecological context can be transferred into a sexual context, resulting in changes in mating preferences as a by-product. I tested this hypothesis by first training female guppies to associate either orange or black colour with food delivery; I then presented videos of males with computer-manipulated coloured spots and measured female preference towards them. I also allowed females from both treatments to mate with males differing in their ratio of orange-to-black spots and measured the males' reproductive success. After training, female sexual preferences significantly diverged among treatments in the expected direction. In addition, orange males sired a greater proportion of offspring with females food-conditioned on orange compared to those conditioned on black. These results show that mating preferences can arise as a by-product of associative learning, which, via translation into variation in male fitness, can become associated with indirect genetic benefits, potentially leading to further evolution.</span></p>
Data from: Genetic basis of adult migration timing in anadromous steelhead discovered through multivariate association testing
Migration traits are presumed to be complex and to involve interaction among multiple genes, thus we employed both univariate analyses and multivariate Random Forest (RF) machine learning algorithm to conduct association mapping of 15,239 single nucleotide polymorphisms (SNPs) for adult migration-timing phenotype in steelhead (Oncorhynchus mykiss). Our study focused on a model natural population of steelhead that exhibits two distinct migration-timing life histories with high levels of admixture in nature. Neutral divergence was limited between fish exhibiting summer- and winter-run migration owing to high levels of interbreeding, but a univariate mixed linear model found three SNPs from a major effect gene to be significantly associated with migration-timing (p < 0.000005) that explained 46% of trait variation. Alignment to the annotated S. salar genome provided evidence that all three SNPs localize within a 46 kb region overlapping GREB1-like (an estrogen target gene) on chromosome Ssa03. Additionally, multivariate analyses with RF identified that these 3 SNPs plus 15 additional SNPs explained up to 60% of trait variation. These candidate SNPs may provide the ability to predict adult migration-timing of steelhead to facilitate conservation management of this species and this study demonstrates the benefit of multivariate analyses for association studies.
Figures 96–104. Gnathos and associated characters. 96–101 in Phylogeny of Neotropical Castniinae (Lepidoptera: Cossoidea: Castniidae): testing the hypothesis of the mimics as a monophyletic group and implications for the arrangement of the genera
Figures 96–104. Gnathos and associated characters. 96–101, lateral view: 96, Imara therapon (Kollar, 1839) comb. nov.; 97, Geyeria galinthias (Hopffer, 1856) comb. nov.; 98, Yagra fonscolombe (Godart, [1824]); 99, Telchin licus (Drury, 1773); 100, Corybantes pylades (Stoll, 1782); 101, Prometheus cochrus (Fabricius, 1787). 102–104, posterior view: 102, Telchin syphax (Fabricius, 1775); 103, Synpalamides phalaris (Fabricius, 1793); 104, Corybantes pylades (Stoll, 1872). Scale bars: 1 mm.
Testing the potential contribution of Wolbachia to speciation when cytoplasmic incompatibility becomes associated with host‐related reproductive isolation
<p>Endosymbiont induced cytoplasmic incompatibility (CI) may play an important role in arthropod speciation. However, whether CI consistently becomes associated or coupled with other host-related forms of reproductive isolation (RI) to impede the transfer of endosymbionts between hybridizing populations and further the divergence process remains an open question. Here, we show varying degrees of pre- and post-mating RI exist among allopatric populations of two interbreeding cherry-infesting tephritid fruit flies (<i>Rhagoletis cingulata</i> and <i>R. indifferens</i>) across North America. These flies display allochronic and sexual isolation among populations, as well as unidirectional reductions in egg hatch in hybrid crosses involving southwestern USA males. All populations are infected by a <i>Wolbachia </i>strain, <i>w</i>Cin2, whereas a second strain, <i>w</i>Cin3, only coinfects flies from the Southwest USA and Mexico. Strain <i>w</i>Cin3 is associated with a unique mtDNA haplotype and unidirectional postmating RI, implicating the strain as the cause of CI. When coupled with non-endosymbiont RI barriers, we estimate the strength of CI associated with <i>w</i>Cin3 would not prevent the strain from introgressing from infected Southwestern to uninfected populations elsewhere in the USA if populations were to come into secondary contact and hybridize. In contrast, cytoplasmic-nuclear coupling may be sufficient to impede the transfer of <i>w</i>Cin3 if Mexican and USA populations were to come into contact. We discuss our results in the context of the general paucity of examples demonstrating stable <i>Wolbachia</i> hybrid zones and whether the spread of <i>Wolbachia</i> among taxa can be constrained in natural hybrid zones long enough for the endosymbiont to participate in speciation.</p>
Genome-wide association study of polygenic risk score-defined phenotype suffers from inflated test-statistics
<p>Simulation results from running the following script 100 times: https://github.com/euffelmann/paper-ad_prs_extremes/blob/main/scripts/ad_prs_extremes_simulation.R.</p> <p>These files can be used to reproduce tables and figures in: https://github.com/euffelmann/paper-ad_prs_extremes</p>
Association of Wolbachia with gene expression in Drosophila testes
<div> <em>Wolbachia</em> is a genus of intracellular symbiotic bacteria that are widely distributed in arthropods and nematodes. These maternally inherited bacteria regulate host reproductive systems in various ways to facilitate their vertical transmission. Since the identification of <em>Wolbachia</em> in many insects, the relationship between <em>Wolbachia</em> and the host has attracted great interest. Numerous studies have indicated that <em>Wolbachia</em> modifies a variety of biological processes in the host. Previous studies in <em>Drosophila melanogaster</em> (<em>D. melanogaster</em>) have demonstrated that <em>Wolbachia</em> can affect spermatid differentiation, chromosome deposition, and sperm activity in the early stages of spermatogenesis, leading to sperm dysfunction. Here, we explored the putative effect of <em>Wolbachia</em> in sperm maturation using transcriptomic approaches to compare gene expression in <em>Wolbachia-</em>infected and <em>Wolbachia</em>-free <em>D. melanogaster</em> adult testes. Our findings show that <em>Wolbachia</em> affects many biological processes in <em>D. melanogaster</em> adult testes, and most of the differentially expressed genes involved in carbohydrate metabolism, lysosomal degradation, proteolysis, lipid metabolism, and immune response were upregulated in the presence of <em>Wolbachia</em>. In contrast, some genes that are putatively associated with cutin and wax biosynthesis and peroxisome pathways were downregulated. We did not find any differentially expressed genes that are predicted to be related to spermatogenesis in the datasets. This work provides additional information for understanding the <em>Wolbachia</em>-host intracellular relationships.</div>
FIGURE 17 in Using DNA barcodes to test the association of sexes and morphs in Calodesma spp (Lepidoptera, Erebidae, Arctiinae, Arctiini, Pericopina) of Trinidad, West Indies with an overview of the genus, taxonomic changes and a new species
FIGURE 17. Mimicry ring of diurnal black moths with white or transparent spots in Trinidad, W.I. in which the white morphs of the two Calodesma spp. in Trinidad fit; all captured at flowers of Austroeupatorium inulaefolium; A-C, dorsal view above, ventral view below; D–E, dorsal view left, ventral view right. A, Ctenucha andrei Rothschild ♀ Cat's Hill, 24.ix.2017 (J. Morrall). B, Autochloris almon (Cramer) ♀, data as #A. C, Calonotus tripunctatus Druce ♀, data as #A. D, Melanchroia atera (Stoll) ♁, Parrylands, x.2017 (S. Alston-Smith). F, M. atera ♀, data as #A. Life size.
FIGURE 16 in Using DNA barcodes to test the association of sexes and morphs in Calodesma spp (Lepidoptera, Erebidae, Arctiinae, Arctiini, Pericopina) of Trinidad, West Indies with an overview of the genus, taxonomic changes and a new species
FIGURE 16 Views of the head and anterior thorax of Calodesma pseudocollaris new species. A–C paratype male. D–F allotype female.
FIGURE 14 in Using DNA barcodes to test the association of sexes and morphs in Calodesma spp (Lepidoptera, Erebidae, Arctiinae, Arctiini, Pericopina) of Trinidad, West Indies with an overview of the genus, taxonomic changes and a new species
FIGURE 14. Habitus and male genitalia of Seileria eucyaniformis Dognin, type species of the genus Seileria. Specimen in MNHU.
FIGURE 6 in Using DNA barcodes to test the association of sexes and morphs in Calodesma spp (Lepidoptera, Erebidae, Arctiinae, Arctiini, Pericopina) of Trinidad, West Indies with an overview of the genus, taxonomic changes and a new species
FIGURE 6. Calodesma militta BOLD:AAK1660 females white morph from Trinidad, W.I., captured at flowers of Austroeupatorium inulaefolium; dorsal view above, ventral view below. A, Cat's Hill, 24.ix.2017, J. Morrall, DNA 136. B, Parrylands, x.2017, S. Alston-Smith, DNA 166. C, as #A, DNA 140. D, as #A, DNA 141. E, as #B, DNA 174. F, as #A, DNA 142. G, as #B, DNA 170. H, as #B, DNA 167; this specimen is an almost exact match in dorsal view to the type of Centronia plorator Kaye. I, Calodesma sp. unresolved BIN, West Trinity, x.2017, DNA 182 (failed, no barcode available). Life size.
FIGURE 13 in Using DNA barcodes to test the association of sexes and morphs in Calodesma spp (Lepidoptera, Erebidae, Arctiinae, Arctiini, Pericopina) of Trinidad, West Indies with an overview of the genus, taxonomic changes and a new species
FIGURE 13. Life history of Calodesma militta, collaris morph, collected as penultimate instar on Malpighia glabra, Trinidad, Mt. Hope, 10.646 -61.420 (Gosula 2021); penultimate instar found 24.iv.2021; pupated 1.v.2021; adult 11.v.2021. Top row, penultimate instar caterpillar; second row, final instar caterpillar; third row, cast final instar caterpillar skin and pupa; bottom row, adult male.
FIGURE 12 in Using DNA barcodes to test the association of sexes and morphs in Calodesma spp (Lepidoptera, Erebidae, Arctiinae, Arctiini, Pericopina) of Trinidad, West Indies with an overview of the genus, taxonomic changes and a new species
FIGURE 12. Similarity relationships of Calodesma spp. based on this work, barcodes from the ML collection, and selected public sequences in BOLD. Many duplicate DNA barcodes available for C. maculifrons from Costa Rica and some for C. militta from Trinidad are omitted so as to facilitate presentation. The taxonomy used is that developed in this work, and where relevant the names used here for the various morphs are included in parentheses after the scientific name. Bootstrap values are shown only if>70% and distances only if>0.002. The evolutionary history was inferred using the Neighbor-Joining method (Saitou and Nei 1987). The optimal tree with the sum of branch length = 0.15482979 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches (Felsenstein 1985). The tree is drawn to scale, with branch lengths (next to the branches) in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Kimura 2-parameter method (Tamura et al. 2004) and are in the units of the number of base substitutions per site. The analysis involved 73 nucleotide sequences. Codon positions included were 1st+2nd+3rd+Noncoding. All ambiguous positions were removed for each sequence pair. There was a total of 689 positions in the final dataset. Evolutionary analyses were conducted in MEGAX (Kumar et al. 2018).
FIGURE 7 in Using DNA barcodes to test the association of sexes and morphs in Calodesma spp (Lepidoptera, Erebidae, Arctiinae, Arctiini, Pericopina) of Trinidad, West Indies with an overview of the genus, taxonomic changes and a new species
FIGURE 7. Calodesma militta BOLD:AAK1660 females orange morph from Trinidad, W.I.; dorsal view above, ventral view below. A, Lalaja Ridge, 23.xii.2019 J. Morrall, DNA 377. B, Hololo Mountain Road, 3.x.2017 J. Morrall, DNA 145. C, Arima valley, Simla, xii.2020, S. Alston-Smith, DNA 475. D, Arima valley, Simla, xii.2020, S. Alston-Smith, DNA 474. E, East of Point Fortin, 30.ix.1982, M.J.W. Cock, DNA 315. F, Rio Claro–Guayaguayare Road, milestones 4–5, 17.ix.1978, M.J.W. Cock, DNA 316. Life size.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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OpenNeuro
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