An evaluation of elongation factor 1 alpha as a phylogenetic marker for eukaryotes.
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Elongation factor 1 alpha (EF-1 alpha) is a highly conserved ubiquitous protein involved in translation that has been suggested to have desirable properties for phylogenetic inference. To examine the utility of EF-1 alpha as a phylogenetic marker for eukaryotes, we studied three properties of EF-1 alpha trees: congruency with other phyogenetic markers, the impact of species sampling, and the degree of substitutional saturation occurring between taxa. Our analyses indicate that the EF-1 alpha tree is congruent with some other molecular phylogenies in identifying both the deepest branches and some recent relationships in the eukaryotic line of descent. However, the topology of the intermediate portion of the EF-1 alpha tree, occupied by most of the protist lineages, differs for different phylogenetic methods, and bootstrap values for branches are low. Most problematic in this region is the failure of all phylogenetic methods to resolve the monophyly of two higher-order protistan taxa, the Ciliophora and the Alveolata. JACKMONO analyses indicated that the impact of species sampling on bootstrap support for most internal nodes of the eukaryotic EF-1 alpha tree is extreme. Furthermore, a comparison of observed versus inferred numbers of substitutions indicates that multiple overlapping substitutions have occurred, especially on the branch separating the Eukaryota from the Archaebacteria, suggesting that the rooting of the eukaryotic tree on the diplomonad lineage should be treated with caution. Overall, these results suggest that the phylogenies obtained from EF-1 alpha are congruent with other molecular phylogenies in recovering the monophyly of groups such as the Metazoa, Fungi, Magnoliophyta, and Euglenozoa. However, the interrelationships between these and other protist lineages are not well resolved. This lack of resolution may result from the combined effects of poor taxonomic sampling, relatively few informative positions, large numbers of overlapping substitutions that obscure phylogenetic signal, and lineage-specific rate increases in the EF-1 alpha data set. It is also consistent with the nearly simultaneous diversification of major eukaryotic lineages implied by the "big-bang" hypothesis of eukaryote evolution. (+info)
Unusually high evolutionary rate of the elongation factor 1 alpha genes from the Ciliophora and its impact on the phylogeny of eukaryotes.
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The elongation factor 1 alpha (EF-1 alpha) has become widely employed as a phylogenetic marker for studying eukaryotic evolution. However, a disturbing problem, the artifactual polyphyly of ciliates, is always observed. It has been suggested that the addition of new sequences will help to circumvent this problem. Thus, we have determined 15 new ciliate EF-1 alpha sequences, providing for a more comprehensive taxonomic sampling of this phylum. These sequences have been analyzed together with a representation of eukaryotic sequences using distance-, parsimony-, and likelihood-based phylogenetic methods. Such analyses again failed to recover the monophyly of Ciliophora. A study of the substitution rate showed that ciliate EF-1 alpha genes exhibit a high evolutionary rate, produced in part by an increased number of variable positions. This acceleration could be related to alterations of the accessory functions acquired by this protein, likely to those involving interactions with the cytoskeleton, which is very modified in the Ciliophora. The high evolutionary rate of these sequences leads to an artificial basal emergence of some ciliates in the eukaryotic tree by effecting a long-branch attraction artifact that produces an asymmetric topology for the basal region of the tree. The use of a maximum-likelihood phylogenetic method (which is less sensitive to long-branch attraction) and the addition of sequences to break long branches allow retrieval of more symmetric topologies, which suggests that the asymmetric part of the tree is most likely artifactual. Therefore, the sole reliable part of the tree appears to correspond to the apical symmetric region. These kinds of observations suggest that the general eukaryotic evolution might have consisted of a massive radiation followed by an increase in the evolutionary rates of certain groups that emerge artificially as early branches in the asymmetric base of the tree. Ciliates in the case of the EF-1 alpha genes would offer clear evidence for this hypothesis. (+info)
Interaction of process partitions in phylogenetic analysis: an example from the swallowtail butterfly genus Papilio.
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In this study, we explored how the concept of the process partition may be applied to phylogenetic analysis. Sequence data were gathered from 23 species and subspecies of the swallowtail butterfly genus Papilio, as well as from two outgroup species from the genera Eurytides and Pachliopta. Sequence data consisted of 1,010 bp of the nuclear protein-coding gene elongation factor-1 alpha (EF-1 alpha) as well as the entire sequences (a total of 2,211 bp) of the mitochondrial protein-coding genes cytochrome oxidase I and cytochrome oxidase II (COI and COII). In order to examine the interaction between the nuclear and mitochondrial partitions in a combined analysis, we used a method of visualizing branch support as a function of partition weight ratios. We demonstrated how this method may be used to diagnose error at different levels of a tree in a combined maximum-parsimony analysis. Further, we assessed patterns of evolution within and between subsets of the data by implementing a multipartition maximum-likelihood model to estimate evolutionary parameters for various putative process partitions. COI third positions have an estimated average substitution rate more than 15 times that of EF-1 alpha, while COII third positions have an estimated average substitution rate more than 22 times that of EF-1 alpha. Ultimately, we found that although the mitochondrial and nuclear data were not significantly incongruent, homoplasy in the fast-evolving mitochondrial data confounded the resolution of basal relationships in the combined unweighted parsimony analysis despite the fact that there was relatively strong support for the relationships in the nuclear data. We conclude that there may be shortcomings to the methods of "total evidence" and "conditional combination" because they may fail to detect or accommodate the type of confounding bias we found in our data. (+info)
Diagnosing anaemia in pregnancy in rural clinics: assessing the potential of the Haemoglobin Colour Scale.
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Anaemia in pregnancy is a common and severe problem in many developing countries. Because of lack of resources and staff motivation, screening for anaemia is often solely by clinical examination of the conjunctiva or is not carried out at all. A new colour scale for the estimation of haemoglobin concentration has been developed by WHO. The present study compares the results obtained using the new colour scale on 729 women visiting rural antenatal clinics in Malawi with those obtained by HemoCue haemoglobinometer and electronic Coulter Counter and with the assessment of anaemia by clinical examination of the conjunctiva. Sensitivity using the colour scale was consistently better than for conjunctival inspection alone and interobserver agreement and agreement with Coulter Counter measurements was good. The Haemoglobin Colour Scale is simple to use, well accepted, cheap and gives immediate results. It shows considerable potential for use in screening for anaemia in antenatal clinics in settings where resources are limited. (+info)
Laboratory assay reproducibility of serum estrogens in umbilical cord blood samples.
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We evaluated the reproducibility of laboratory assays for umbilical cord blood estrogen levels and its implications on sample size estimation. Specifically, we examined correlation between duplicate measurements of the same blood samples and estimated the relative contribution of variability due to study subject and assay batch to the overall variation in measured hormone levels. Cord blood was collected from a total of 25 female babies (15 Caucasian and 10 Chinese-American) from full-term deliveries at two study sites between March and December 1997. Two serum aliquots per blood sample were assayed, either at the same time or 4 months apart, for estrone, total estradiol, weakly bound estradiol, and sex hormone-binding globulin (SHBG). Correlation coefficients (Pearson's r) between duplicate measurements were calculated. We also estimated the components of variance for each hormone or protein associated with variation among subjects and variation between assay batches. Pearson's correlation coefficients were >0.90 for all of the compounds except for total estradiol when all of the subjects were included. The intraclass correlation coefficient, defined as a proportion of the total variance due to between-subject variation, for estrone, total estradiol, weakly bound estradiol, and SHBG were 92, 80, 85, and 97%, respectively. The magnitude of measurement error found in this study would increase the sample size required for detecting a difference between two populations for total estradiol and SHBG by 25 and 3%, respectively. (+info)
Maximum-likelihood generalized heritability estimate for blood pressure in Nigerian families.
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Elevated blood pressure (BP) is more common in relatives of hypertensives than in relatives of normotensives, indicating familial resemblance of the BP phenotypes. Most published studies have been conducted in westernized societies. To assess the ability to generalize these estimates, we examined familial patterns of BP in a population-based sample of 510 nuclear families, including 1552 individuals (320 fathers, 370 mothers, 475 sons, and 387 daughters) from Ibadan, Nigeria. The prevalence of obesity in this community is low (body mass index: fathers, 21.6; mothers, 23.6; sons, 19.2; and daughters=21.0 kg/m2). The BP phenotype used in all analyses was created from the best regression model by standardizing the age-adjusted systolic blood pressure (SBP) and diastolic blood pressure (DBP) to 0 mean and unit variance. Heritability was estimated by use of the computer program SEGPATH from the most parsimonious model of "no spouse and neither gender nor generation difference" as 45% for SBP and 43% for DBP. The lack of a significant spouse correlation is consistent with little or no influence of the common familial environment. However, the heritability estimate of <50% for both SBP and DBPs reinforces the importance of the nonshared environmental effect. (+info)
A gene for X-linked idiopathic congenital nystagmus (NYS1) maps to chromosome Xp11.4-p11.3.
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Congenital nystagmus (CN) is a common oculomotor disorder (frequency of 1/1,500 live births) characterized by bilateral uncontrollable ocular oscillations, with onset typically at birth or within the first few months of life. This condition is regarded as idiopathic, after exclusion of nervous and ocular diseases. X-linked, autosomal dominant, and autosomal recessive modes of inheritance have been reported, but X-linked inheritance is probably the most common. In this article, we report the mapping of a gene for X-linked dominant CN (NYS1) to the short arm of chromosome X, by showing close linkage of NYS1 to polymorphic markers on chromosome Xp11.4-p11.3 (maximum LOD score of 3.20, over locus DXS993). Because no candidate gene, by virtue of its function, has been found in this region of chromosome Xp, further studies are required, to reduce the genetic interval encompassing the NYS1 gene. It is hoped that the complete gene characterization will address the complex pathophysiology of CN. (+info)
A note on power approximations for the transmission/disequilibrium test.
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The transmission/disequilibrium test (TDT) is a popular method for detection of the genetic basis of a disease. Investigators planning such studies require computation of sample size and power, allowing for a general genetic model. Here, a rigorous method is presented for obtaining the power approximations of the TDT for samples consisting of families with either a single affected child or affected sib pairs. Power calculations based on simulation show that these approximations are quite precise. By this method, it is also shown that a previously published power approximation of the TDT is erroneous. (+info)