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Phylogeographical autocorrelation of phenotypic evolution in honey bees (Apis mellifera L.).

The analysis of phenotypic divergence among local populations within a species has been traditionally performed in a spatial context, although advances in genetic analysis using mtDNA have permitted a simultaneous evaluation of geographical and historical patterns of variation, so-called phylogeographical analysis. In this paper, we combine these two dimensions of variation (geographical space and phylogenetic history) to evaluate patterns of phenotypic evolution in honey bees (Apis mellifera L.). Data on 39 phenotypic traits, derived from 417 colonies grouped into 14 subspecies, were analysed using autocorrelation methods. Mantel tests indicated that the relationship between phenotypic divergence, estimated by Euclidean distances among subspecies' morphological centroids, was significant both when compared to geographical distance (r=0.371; P < 0.01) and to genetic distance (estimated as sequence divergence (%) in a mtDNA region encompassing part of the NADH dehydrogenase subunit 2 and isoleucine transfer RNA (r=0.329; P < 0.01)). For the analysis of each trait, the effects of the geographical co-ordinates (latitude and longitude of subspecies geographical range) and of the phylogenetic patterns (defined by eigenvectors of the genetic distance matrix) on phenotypic variation were simultaneously analysed using an extension of a recently developed model, called Phylogenetic Eigenvector Regression (PVR). In general terms, the partial regression slopes indicated that the variation in the characters traditionally associated with adaptive processes, such as body and wing size, were better explained by geographical position. However, characters usually thought to be neutral, such as wing venation angle, were more associated with phylogeny. This is expected because PVR can be interpreted as a partition model, in which adaptive variation tends to be independent of phylogeny (and, in this case, associated with geography). In addition, the first principal component derived from the expected values of the model for each trait, which can be interpreted as the phenotypic variation predicted by phylogeny, is more structured in a north-south cline than are the original data, supporting an adaptive interpretation. The phylogeographical autocorrelation analyses performed in this study show that different traits are more related to one of the two dimensions of variation (geography and phylogeny), and these patterns can furnish insights into the nature of phenotypic evolution in these organisms.

Animals↗

Involvement of the R2R3-MYB, AtMYB61, in the ectopic lignification and dark-photomorphogenic components of the det3 mutant phenotype.

Overexpression of a pine MYB, PtMYB4, in Arabidopsis caused ectopic lignin deposition and allowed the plants to undergo photomorphogenesis even when they were grown in the dark. The phenotype caused by PtMYB4 overexpression was reminiscent of the previously characterised dark-photomorphogenic mutant, de-etiolated 3 (det3); consequently, we tested the hypothesis that MYB misexpression may explain aspects of the det3 phenotype. We show here that AtMYB61, a member of the Arabidopsis R2R3-MYB family, is misexpressed in the det3 mutant. Semi-quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) experiments suggested that AtMYB61 was misexpressed in a det3 background relative to wild-type plants. Examination of AtMYB61 promoter activity in a det3 background showed that the spatial control of AtMYB61 expression was lost. In order to determine if such misexpression could explain the mutant phenotype, AtMYB61 was overexpressed in wild-type Arabidopsis plants. Transgenic plants that overexpressed AtMYB61 had the same ectopic lignification and dark-photomorphogenic phenotype as that of the det3 mutant. In order to test if AtMYB61 was necessary for these aspects of the det3 phenotype, AtMYB61 expression was downregulated in det3 plants in both antisense and sense suppression experiments. Suppression of AtMYB61 in a det3 mutant background restored all mutant phenotypes of the det3 mutant associated with development in the dark. Taken together, these results suggest that AtMYB61 misexpression was both sufficient and necessary to explain the ectopic lignification and dark-photomorphogenic phenotypes of the det3 mutant.

Arabidopsis↗

Phenotypic and genotypic markers of Staphylococcus epidermidis virulence.

OBJECTIVES: To analyze Staphylococcus epidermidis strains, previously tested for their virulence in a mouse model of subcutaneous infection, for various phenotypic traits (biofilm density, extracellular polysaccharide, slime-associated antigen (SAA)) and for the presence of the ica gene cluster, to determine which of these phenotypic and genotypic methods best correlates with virulence in the mouse model. METHODS: The quantitative biofilm assay was performed on 10 strains of S. epidermidis, comprising (1) RP62A (ATCC 35984), (2) the strongest and weakest biofilm producers in our collection, (3) a pair of phenotypic variants, and (4) a strain whose biofilm density was enhanced in iron-limited media. Biofilm density was measured after growth at 37 degrees C and at ambient temperature, in trypticase soy broth (TSB) with and without glucose supplementation and using both chemical and heat fixation. Strains were assayed for SAA using a double immunodiffusion method. Extracellular polysaccharide was detected by transmission electron microscopy (TEM). A 546-base-pair segment of the ica gene cluster was amplified by PCR. RESULTS: Biofilm formation in TSB, glucose-enriched TSB, extracellular polysaccharide (observed by TEM), expression of SAA and presence of the ica gene predicted virulence of nine, nine, nine, eight and eight of 10 strains, respectively. The phenotypic expression of biofilm and related properties was medium and temperature dependent. We encountered one ica-positive strain that failed to express biofilm in standard TSB at 37 degrees C, but was virulent in a mouse model, and another strain that lacked ica, produced biofilm and was virulent in the model. CONCLUSIONS: Mouse virulence in our model can be predicted by any of the phenotypic or genotypic methods examined for > or = 80% of strains. Medium and incubation conditions affect the expression of phenotypic markers by some strains. For the remaining strains, possible reasons for inconsistencies between the presence of the ica gene, phenotypic markers and mouse virulence include (1) dependence of biofilm on genes other than ica, (2) sequence differences in ica, (3) dependence of biofilm expression in vivo on strain characteristics and media used to prepare inocula for in vivo studies.

Animals↗

A family showing inheritance of the Inab phenotype.

An 86-year-old white American woman was found to have a very rare red cell phenotype, the Inab phenotype. Her cells were Cr(a-), Tc(a-b-c-), Dr(a-), Es(a-), WES(a-b-), and IFC-. Unlike the two other Inab phenotype patients, she has no history of protein-losing enteropathy or any similar intestinal disorder. One of her four siblings also has the Inab phenotype, providing the first evidence that this phenotype may be inherited. Serum inhibitions showed that anit-Cra, -TCa, -Dra, -WESb, and -IFC are partially inhibited by sera from three siblings with the common red cell phenotype but not by serum from the Inab phenotype sibling. The serum of the proposita contained an antibody to a high-frequency antigen that showed characteristics of being a Cromer-related antibody.

Aged↗

RHD genotyping in weak D phenotypes by multiple polymerase chain reactions.

BACKGROUND: Weak D phenotypes involve a quantitative variation of D. The genomic basis in weak D has been disputed, however. STUDY DESIGN AND METHODS: Five sequence-specific polymerase chain reactions (SSP-PCRs) on exons 2, 5, and 7 of the RHD gene were evaluated in 248 white and 98 Japanese blood donors and compared with the results obtained by amplification of intron 4 and serology. All methods and SSP-PCR testing on the 3' non-coding region of the RHD gene were applied to the genotyping of 94 DNA samples derived from individuals expressing weak D phenotypes. RESULTS: Concordant results were obtained with all genotyping and phenotyping methods in testing 201 D-positive and 145 D-negative donors. Four of 94 weak D samples were typed as D-negative by amplification of intron 4 and SSP-PCR on exon 5. Phenotyping with monoclonal antibodies revealed a DVI category in one of these cases and DFR phenotype in three of these cases. One weak D sample, which reacted like normal D-positive cells with all applied monoclonal antibodies, was typed falsely negative by SSP-PCR on exon 5 because of a point mutation at nucleotide 667 (T-->G) that resulted in a Phe223Val amino acid substitution. In this individual, heterozygosity was found at two other amino acid positions (Glu233Gln and Val238Met) by restriction fragment length polymorphism analysis. CONCLUSION: Genetic diversity in weak D phenotypes is rare. Only 1 of 90 true weak D phenotypes (1.1%) had a genetic variation in testing on seven gene regions of the RHD gene.

Asian People↗

Acquired and transient RBC CD55 deficiency (Inab phenotype) and anti-IFC.

BACKGROUND: Antigens of the Cromer blood group system reside on the glycoprotein CD55 (decay-accelerating factor). The Inab phenotype is the null phenotype of this system. So far, only five propositi have been described who exhibit this phenotype, and single-nucleotide substitutions in the CD55 gene have been found in three of them. This report describes the first example of a patient with an acquired and transient form of the Inab phenotype. CASE REPORT: A 54-year-old black patient was admitted to the hospital because of abdominal pain. Multiple splenic infarctions were visualized in the abdominal computerized tomography scan, and a prophylactic splenectomy was performed. The patient's serum reacted by an IAT with all donor RBCs tested. RESULTS: Serologic analysis showed that the patient had the rare Inab phenotype and that his serum contained anti-IFC. Flow cytometry demonstrated the absence of CD55 on his RBCs, whereas lymphocytes, monocytes, granulocytes, and platelets expressed CD55, albeit at a weaker level than cells of common phenotypes. cDNA revealed no differences from the published sequences. Flow cytometry performed 12 months after splenectomy showed reappearance of the CD55 antigen; serologic tests performed after 17 months revealed that the anti-IFC had almost disappeared and that the RBCs were again agglutinated by various Cromer antibodies. CONCLUSION: A patient with an acquired and transient form of the Inab phenotype is described, in whom the CD55 deficiency is limited to the RBCs and is associated with splenic infarctions.

Abdominal Pain↗

Tubular phenotypic change in progressive tubulointerstitial fibrosis in human glomerulonephritis.

There is much debate over the origins of fibroblast-type cells that accumulate in interstitial fibrosis. A controversial hypothesis, supported by data from animal and cell-culture studies, is that fibroblast-type cells can derive from tubular epithelial cells by a process of epithelial-mesenchymal transdifferentiation. However, to date, no evidence supports this postulate in human glomerulonephritis. This study sought to provide evidence that tubular epithelial cells can undergo phenotypic change toward a fibroblast-like cell in human glomerulonephritis. One hundred twenty-seven open renal biopsy specimens from patients with minimal change disease (MCD), immunoglobulin A (IgA) nephropathy, and rapidly progressive glomerulonephritis (RPGN) were examined for tubular phenotypic change by two-color immunohistochemistry using the criteria of de novo expression of alpha-smooth muscle actin (alpha-SMA), a myofibroblast marker; loss of the epithelial marker cytokeratin; and collagen production. In normal human kidney and MCD, tubular epithelial cells expressed cytokeratin with no evidence of alpha-SMA staining. However, in 36 of 90 cases of IgA nephropathy and 9 of 18 cases of RPGN, small numbers of tubular epithelial cells in areas of fibrosis showed de novo alpha-SMA expression, accounting for 0.4% +/- 0.2% (IgA nephropathy) and 3.8% +/- 1.5% (RPGN) of cortical tubules. An intermediate stage of phenotypic change was observed in some cuboidal epithelial cells that expressed both cytokeratin and alpha-SMA. Tubules containing alpha-SMA-positive (alpha-SMA(+)) cells also stained for collagen types I and III, suggesting that tubular cells undergoing phenotypic change have an active role in the fibrotic process. There also was a marked increase in transforming growth factor-beta1 (TGF-beta1) tubular expression in areas with interstitial fibrosis, including tubules with phenotypic change. There was a highly significant correlation between tubular alpha-SMA expression and interstitial fibrosis, interstitial alpha-SMA(+) myofibroblast accumulation, deposition of collagen types I and III, tubular TGF-beta1 expression, and renal dysfunction. In conclusion, this study provides evidence that tubular epithelial cells can undergo phenotypic change toward a myofibroblast-like phenotype on the basis of de novo alpha-SMA expression, loss of cytokeratin, and de novo collagen staining. These data, although not conclusive, provide the first support for the hypothesis that transdifferentiation of tubular epithelial cells has a role in progressive renal fibrosis in human glomerulonephritis.

Actins↗

Distinction of scrapie phenotypes in sheep by lesion profiling.

Major determinants of the pathological phenotype of natural scrapie are considered to be the agent strain and host prion protein (PrP) genotype, but the relationship between these is far from clear. Little is known about the strains that produce natural scrapie. A method of brain vacuolation profiling was developed which enables this aspect of disease phenotype to be characterized in detail. This method distinguished at least two distinct pathological phenotypes in sheep of a single genotype (ARQ/ARQ) from different flocks in the UK. Great similarity was also demonstrated between one of these phenotypes and the phenotype of sheep from a flock in Sardinia. The profile of four sheep of the same ARQ/ARQ genotype experimentally infected with bovine spongiform encephalopathy (BSE) was determined for comparison. It would appear from these preliminary observations that the application of lesion profiling techniques to ovine transmissible spongiform encephalopathy (TSE) may contribute to the definition of a particular scrapie phenotype within a flock. It may, therefore, have potential for improving our understanding of current TSE phenotypes in sheep, with regard to the possibility of identifying those of bovine origin.

Animals↗

Metabolic specialization associated with phenotypic switching in Candidaalbicans.

Phase and antigenic variation are mechanisms used by microbial pathogens to stochastically change their cell surface composition. A related property, referred to as phenotypic switching, has been described for some pathogenic fungi. This phenomenon is best studied in Candida albicans, where switch phenotypes vary in morphology, physiology, and pathogenicity in experimental models. In this study, we report an application of a custom Affymetrix GeneChip representative of the entire C. albicans genome and assay the global expression profiles of white and opaque switch phenotypes of the WO-1 strain. Of 13,025 probe sets examined, 373 ORFs demonstrated a greater than twofold difference in expression level between switch phenotypes. Among these, 221 were expressed at a level higher in opaque cells than in white cells; conversely, 152 were more highly expressed in white cells. Affected genes represent functions as diverse as metabolism, adhesion, cell surface composition, stress response, signaling, mating type, and virulence. Approximately one-third of the differences between cell types are related to metabolic pathways, opaque cells expressing a transcriptional profile consistent with oxidative metabolism and white cells expressing a fermentative one. This bias was obtained regardless of carbon source, suggesting a connection between phenotypic switching and metabolic flexibility, where metabolic specialization of switch phenotypes enhances selection in relation to the nutrients available at different anatomical sites. These results extend our understanding of strategies used in microbial phase variation and pathogenesis and further characterize the unanticipated diversity of genes expressed in phenotypic switching.

Base Sequence↗

Use of the Cre/lox recombination system to develop a non-lethal knock-in murine model for osteogenesis imperfecta with an alpha1(I) G349C substitution. Variability in phenotype in BrtlIV mice.

We utilized the Cre/lox recombination system to develop the first knock-in murine model for osteogenesis imperfecta (OI). The moderately severe OI phenotype was obtained from an alpha1(I) Gly(349) --> Cys substitution in type I collagen, reproducing the mutation in a type IV OI child. We introduced four single nucleotide (nt) changes into murine col1a1 exon 23: the disease causing G-->T transversion (nt 1546), an adjacent G-->T change (nt 1551) to generate a GUC ribozyme cleavage site, and two transversions (nt 1567 C-->A and nt 1569 C-->G) to cause a Leu --> Met substitution. We also introduced a 3.2-kilobase pair transcription/translation stop cassette in intron 22, flanked by directly repeating lox recombination sites. After homologous recombination in ES cells, two male chimeras were obtained. Chimeras were mated with transgenic females expressing Cre recombinase to remove the stop cassette from a portion of the progeny's cells. To generate mice with full expression of the Gly(349) --> Cys mutation, these offspring were then mated with wild-type females. Skeletal staining and bone histology of the F2 revealed a classical OI phenotype with deformity, fragility, osteoporosis and disorganized trabecular structure. We designate these mice BrtlIV (Brittle IV). BrtlIV mice have phenotypic variability ranging from perinatal lethality to long term survival with reproductive success. The phenotypic variability is not associated with differences in expression levels of the mutant allele in total RNA derived from tissue extracts. Expression of the mutant protein is also equivalent in different phenotypes. Thus, these mice are an excellent model for delineation of the modifying factors postulated to affect human OI phenotypes. In addition, we generated knock-in mice carrying an "intronic" inclusion by mating chimeras with wild-type females. Alternative splicing involving the stop cassette results in retention of non-collagenous sequences. These mice reproduce the lethal phenotype of similar human mutations and are designated BrtlII.

Alternative Splicing↗

T cell genetic background determines default T helper phenotype development in vitro.

A host's ability to resist certain pathogens such as Leishmania major can depend upon the phenotype of T helper (Th) subset that develops. Different murine genetic backgrounds are known to significantly alter the direction of Th subset development, although the cellular basis of this influence is poorly understood. To examine the basis of this effect we used an in vitro alpha/beta-T cell receptor (TCR) transgenic system for analysis of Th phenotype development. To control for TCR usage, we derived the DO11.10 alpha/beta-TCR transgene in several genetic backgrounds. Our findings suggest that the effects of genetic background on Th phenotype development reside within the T cell, and not the antigen-presenting cell compartment. Transgenic T cells from both the B10.D2 and BALB/c backgrounds showed development toward either the Th1 or Th2 phenotype under the strong directing influence of interleukin (IL) 12 and IL4, respectively. However, when T cells were activated in vitro under neutral conditions in which exogenous cytokines were not added, B10.D2-derived T cells acquired a significantly stronger Th1 phenotype than T cells from the BALB/c background, correspondent with in vivo Th responses to Leishmania in these strains. Importantly, these cytokine differences resulted in distinct functional properties, because B10.D2- but not BALB/c-derived T cells could induce macrophage production of nitric oxide, an important antimicrobial factor. Thus, the genetically determined default Th phenotype development observed in vitro may correspond to in vivo Th subset responses for pathogens such as Leishmania which do not initiate strong Th phenotype-directing signals.

Animals↗

Mutations in novel peroxin gene PEX26 that cause peroxisome-biogenesis disorders of complementation group 8 provide a genotype-phenotype correlation.

The human disorders of peroxisome biogenesis (PBDs) are subdivided into 12 complementation groups (CGs). CG8 is one of the more common of these and is associated with varying phenotypes, ranging from the most severe, Zellweger syndrome (ZS), to the milder neonatal adrenoleukodystrophy (NALD) and infantile Refsum disease (IRD). PEX26, encoding the 305-amino-acid membrane peroxin, has been shown to be deficient in CG8. We studied the PEX26 genotype in fibroblasts of eight CG8 patients--four with the ZS phenotype, two with NALD, and two with IRD. Catalase was mostly cytosolic in all these cell lines, but import of the proteins that contained PTS1, the SKL peroxisome targeting sequence, was normal. Expression of PEX26 reestablished peroxisomes in all eight cell lines, confirming that PEX26 defects are pathogenic in CG8 patients. When cells were cultured at 30 degrees C, catalase import was restored in the cell lines from patients with the NALD and IRD phenotypes, but to a much lesser extent in those with the ZS phenotype, indicating that temperature sensitivity varied inversely with the severity of the clinical phenotype. Several types of mutations were identified, including homozygous G89R mutations in two patients with ZS. Expression of these PEX26 mutations in pex26 Chinese hamster ovary cells resulted in cell phenotypes similar to those in the human cell lines. These findings confirm that the degree of temperature sensitivity in pex26 cell lines is predictive of the clinical phenotype in patients with PEX26 deficiency.

Amino Acid Sequence↗

Pneumococcal resistance to macrolides, lincosamides, ketolides, and streptogramin B agents: molecular mechanisms and resistance phenotypes.

The macrolides, lincosamides, ketolides, and streptogramin B agents (the MLKS(B) antimicrobial agents) have related chemical structures and share similar molecular targets on the 50S ribosomal subunit of Streptococcus pneumoniae. Mutations in rRNA or ribosomal proteins generate a variety of resistance phenotypes. The M phenotype of S. pneumoniae, which predominates in North America, affords low-level resistance to macrolides only (excluding macrolides with 16-member rings) by means of an efflux pump encoded by the mefA gene. The MLS(B) phenotype, which predominates in Europe, affords high-level resistance to macrolides, lincosamides, and streptogramin B agents and arises, in most cases, from dimethylation of adenine 2058 in the 23S rRNA of the 50S ribosomal subunit. Other, less common, phenotypes arise from other 23S rRNA modifications (ML and K phenotypes) or from amino acid substitution (MS(B) phenotype) or insertion (MKS(B) phenotype) into the 50S subunit ribosomal protein L4. In all cases, the decrease in susceptibility to ketolides (for example, telithromycin) is less than the decrease in susceptibility for other MLKS(B) agents.

Amino Acid Substitution↗

Temporal relationship between elongation of the HIV type 1 glycoprotein 120 V2 domain and the conversion toward a syncytium-inducing phenotype.

The second and third variable domains (V2 and V3) of the human immunodeficiency virus type 1 (HIV-1) gp120 envelope molecule have been shown to be determinants of syncytium-inducing (SI) capacity. Previously we have reported evidence that increased length of the V2 domain and duplication or relocation of potential N-linked glycosylation sites in V2 might be used as prognostic markers for evolution toward an SI phenotype. Here, we used a PCR assay that discriminates a 6-nucleotide difference in the length of the V2 domain, with a sensitivity of 1 elongated V2 domain when present in a background of 125 to 625 short V2 domains. Analysis of DNA isolated directly from PBMCs from 11 HIV-1-infected individuals prior to SI phenotype conversion revealed, however, that the usefulness of this PCR for V2 length polymorphism as predictive marker for SI phenotype evolution is limited. The strong association as observed in our previous study between elongation of the V2 domain and an SI phenotype prompted us to expand our first analysis. An extremely significant correlation was observed between V2 length and virus phenotype for samples obtained at about the moment of SI conversion, but not for samples obtained 3 to 35 months after SI phenotype conversion, suggesting that changes in V2 may be only transiently required to allow SI phenotype evolution. This possibly only transient nature of V2 elongation may explain the discrepancy between results by our group and others.

Amino Acid Sequence↗

Positioning of positively charged residues in the V3 loop correlates with HIV type 1 syncytium-inducing phenotype.

Although the V3 loop of the envelope glycoprotein (gp120) plays a role in determining the phenotype, pathogenesis, and tropism of human immunodeficiency virus-1 (HIV-1), there has not been any consistent correlation between structure and phenotype. Theoretically determined structures of the V3 loop of gp120, from 20 different viral strains, 10 syncytium-inducing (SI) and 10 non-syncytium-inducing (NSI) phenotype, revealed that all V3 loops from SI phenotypic strains had at least two positively charged residues in close proximity, on the same face of the loop. All of the SI phenotypic V3 loop structures were capable of forming strong divalent electrostatic interactions with disulfated sugars. The ability to form this interaction may be a determinant of the phenotype, tropism, and pathogenicity of HIV-1 viral strains. This structural motif was absent in all V3 loops from viral strains with the NSI phenotype.

Amino Acid Sequence↗

Phenotypic plasticity and integration in response to flooded conditions in natural accessions of Arabidopsis thaliana (L.) Heynh (Brassicaceae).

Flood response is a crucial component of the life strategy of many plants, but it is seldom studied in non-flooded tolerant species, even though they may be subjected to stressful environmental conditions. Phenotypic plasticity in reaction to environmental stress affects the whole plant phenotype and can alter the character correlations that constitute the phenotypic architecture of the individual, yet few studies have investigated the lability of phenotypic integration to water regime. Moreover, little has been done to date to quantify the sort of selective pressures that different components of a plant's phenotype may be experiencing under contrasting water regimes. Genetic differentiation and phenotypic plasticity at the single-trait and multivariate levels were investigated in 47 accessions of the weedy plant Arabidopsis thaliana, and the relationship of plastic characters to reproductive fitness was quantified. Results indicate that these plants tend to be highly genetically differentiated for all traits, in agreement with predictions made on the basis of environmental variation and mating system. Varied patterns of apparent selection under flooded and non-flooded conditions were also uncovered, suggesting trade-offs in allocation between roots and above-ground biomass, as well as between leaves and reproductive structures. While the major components of the plants' multivariate phenotypic architecture were not significantly affected by environmental changes, many of the details were different under flooded and non-flooded conditions.

Acclimatization↗

ReverseGWAS identifies combined phenotypes associated with a genotype in GWA studies.

MOTIVATION: Traditional genome-wide association studies (GWAS) aim to uncover the genetic variants associated with a single phenotype of interest (typically a disease), and to elucidate its genotypic architecture. However, many of today's GWAS simultaneously measure multiple related phenotypes, leading to the possibility of pursuing the reverse aim of elucidating the "phenotypic architecture" of a single genetic variant. In other words, we may ask what combination of measured phenotypes is associated with a given genotypic variant. ReverseGWAS is an algorithmic platform for answering such questions in the context of large-scale multi-phenotype GWAS. RESULTS: We demonstrate the effectiveness of ReverseGWAS on simulated data, showing its ability to identify logical combinations of phenotypes with a reasonable amount of noise. We then apply it to a selection of combined phenotypes from the UK Biobank, obtaining 719 candidate associations using autoimmune diseases and 205 using common ICD10 codes. We find that the majority of these associations (546/719 and 111/205, respectively) successfully replicate in an independent cohort, FinnGen. AVAILABILITY AND IMPLEMENTATION: The source code of ReverseGWAS is freely available to non-commercial users as an installable R package at https://github.com/Leonardini/rgwas.

Phenotype↗

A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. I. Basic theory and an analysis of alcohol dehydrogenase activity in Drosophila.

Because some genes have been cloned that have a known biochemical or physiological function, genetic variation can be measured in a population at loci that may directly influence a phenotype of interest. With this measured genotype approach, specific alleles or haplotypes in the probed DNA region can be assigned phenotypic effects. In this paper we address several problems encountered in implementing the measured genotype approach with restriction site data. A number of analytical problems arise in part as a consequence of the linkage disequilibrium that is commonly encountered when dealing with small DNA regions: 1) different restriction site polymorphisms are not statistically independent, 2) the sites being measured are not likely to be the direct cause of the associated phenotypic effects, 3) haplotype classes may be phenotypically heterogeneous, and 4) the sites that are most strongly associated with phenotypic effects are not necessarily the most closely linked to the actual genetic cause of the effects. When recombination and gene conversion are rare, the primary cause of linkage disequilibrium is history (mutational origin, genetic drift, hitchhiking, etc.). We deal with historical association directly by producing a cladogram that partially reconstructs the evolutionary history of the present-day haplotype variability. The cladogram defines a nested analysis of variance that simultaneously detects phenotypic effects, localizes the effects within the cladogram, and identifies haplotypes that are potentially heterogeneous in their phenotypic associations. The power of this approach is illustrated by an analysis of the associations between alcohol dehydrogenase (ADH) activity and restriction site variability in a 13-kb fragment surrounding the ADH locus in Drosophila melanogaster.

Alcohol Dehydrogenase↗