D Penny

..In this study we have conducted a genome-scale survey of medium-length ncRNAs from the protozoan parasites Giardia intestinalis and Trichomonas vaginalis...

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..To date there is no phylogenetic model that allows for change in the proportion of variable sites, and the degree to which this affects phylogenetic reconstruction is unknown...

..With six new bird mitochondrial genomes (hummingbird, swift, kagu, rail, flamingo and grebe) we test the proposed Metaves/Coronaves division within Neoaves and the parallel radiations in this primary avian clade...

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..The uniqueness (or not) of the origin of life, though still difficult, is similarly amenable to the testing of alternative hypotheses...

..Implications arising from these early divergences are discussed, particularly the possibility of competition between the small dinosaurs and the new mammal clades...

..e. well established in LECA), and regardless of which is ultimately correct, it pays to separate out various questions and to focus on testing the predictions of sub-theories...

..The accurate reconstruction of older divergences from sequence data is still a major problem, and molecular evolution still requires mathematical models that also have a sound biochemical basis...

..The last universal common ancestor may have been mesophilic and could have had many features of the eukaryote genome, but its cytology is unknown...

..It seems that eukaryotic ancestors had relatively large intron numbers and 'weak' 5'ss, a pattern associated with frequent alternative splicing in modern organisms...

..In addition, passerines form a relatively old group in Neoaves, and many modern avian lineages diverged during the Cretaceous. Although many aspects of the avian tree are stable, additional taxon sampling is required...

..Consequently, many published studies may need to be reexamined...

..The later derivation of prokaryote RNA metabolism and genome structure can be accounted for by the two complementary mechanisms of r-selection and thermoreduction...

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..In order to estimate divergence dates it may eventually be advantageous to use the nucleotide interchanges that show little rate change...

..HDV is a satellite viroid-like RNA virus that requires HBV for replication. It can either co-infect with, or super-infect upon HBV infection resulting in acute infection and/or chronic infection respectively...

..Incomplete taxon sampling was also a problem for Neoaves, and although some resolution is now available there are still problems because current phylogenetic methods still fail to account for real features of DNA sequence evolution...

..In addition, we report that within the birds of prey and allies, we did not find evidence pairing New World vultures with storks or accipitrids (hawks, eagles, and osprey) with Falconids...

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..This work has implications not only for the dispersal of the Polynesian bottle gourd but also for the domestication and dispersal of the species as a whole...

..The general approach has considerable potential, especially when combined with indexed sequencing of different groups of genomes...

..For all the cases tested here, tree estimation using a two taxon outgroup was more accurate than when using a single-taxon outgroup. However, the ingroup was most accurately recovered when no outgroup was used...

..The finding that pigeons and sandgrouse may be more closely related to falcons than to previous candidates such as shorebirds or parrots invites further investigation...

..Molecular dating mt genomes support a major diversification of at least 12 neoavian lineages in the Late Cretaceous. Our results form a basis for further testing with both nuclear-coding sequences and rare genomic changes...

..The general and ancestral nature of most basic RNA-processing steps places a new focus on the generality of the spatial and temporal steps in RNA processing...

..Thus, the eukaryote genome may be uniquely informative about the transition from an earlier RNA genome world to the modern DNA genome world...

..ABSTRACT: Correction to Shavit Grievink L, Penny D, Hendy MD, Holland BR: LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites. BMC Evol Biol 2008, 8(1):317...

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..Overall, including ancestral sequences in searches with BLAST and/or HMMER was the most successful approach in the recovery of potential RNase P protein gene homologues, making this a useful technique in early homologue identification...

..However, a short therian stem lineage is inferred, which is at variance with the traditionally deep placement of monotremes on morphological data...

..In higher copy-fidelity experiments, six-letter alphabets outperform the four-letter alphabets, suggesting that the canonical alphabet is indeed a relic of the RNA world...

..On the basis of our quantitative results, we expect the evolutionary tree for mammals to be resolved quickly, and this will allow other problems to be solved...

..Although the last common ancestor of extant eukaryotes appears to show much of the molecular complexity seen today, we do not, from this work, infer anything of the properties of the earlier "first eukaryote."..

..Multicellular organisms evolve largely through morphological changes, not through extensive changes to cellular biochemistry...

..Comparing nucleotide compositions may identify taxa that differ in aspects of their DNA repair mechanisms...

..Namely, a pair of Australian lineages comes deeper in the tree (in agreement with archaeological data), and the non-African part of the tree shows greater agreement with the geographical distribution of lineages...

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..By contrast, Cryptosporidium introns are less evolutionary conserved with Toxoplasma than are introns from other apicomplexans; thus the few remaining introns are not simply indispensable ancestral introns...

..These results also provide evidence that multiple intron insertion into the same site is rare, further supporting the notion that early eukaryotic ancestors were very intron rich...

..The rate of signal loss (or signal retention) varies with the gene and/or the method of analysis...

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..Any engineer would have replaced cytosine, but evolution is a tinkerer not an engineer. By keeping cytosine and replacing uracil the problem was never eliminated, returning once again with the advent of DNA methylation...

..Further, RY coding was found to nullify AGCT coding nucleotide composition bias...

..These results focus attention on the functional roles of eukaryotic UTRs and deepen the mystery of UTR intron splicing...

..Subsequent computational analysis has revealed additional putative C/D-box snoRNAs. Our results will lead towards a future understanding of RNA metabolism in the deep-branching eukaryote Giardia, as more ncRNAs are characterized...

..Our findings reinforce the conclusion that spliceosomal small-nuclear RNAs existed in the last common ancestor of eukaryotes...

..Statistical reanalysis of the data suggests, instead, that intron losses have outnumbered intron gains in paralogous gene families...

..We suggest that intron loss/gain in some eukaryotic lineages may be concentrated in relatively short episodes coincident with occasional TE invasions...

..This pattern implies that rates of intron creation were higher during earlier periods of evolution and further focuses attention on the causes of initial intron proliferation...

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..85~2.7 billion years ago, leads to an unexpected prediction of a long period (approximately 1-3 billion years) with no phagocytotes -- a veritable Garden of Eden...

..Finally, we demonstrate an inverse relationship between AS and gene duplication, suggesting that the latter may be primarily responsible for the emergence of new functional transcripts in nematodes...

..From genomic context, we identify three strong H/ACA snoRNA candidates. These together with a further 47 candidates obtained by our analysis are being experimentally screened...

..Intronization is more common than the reverse process, loss of splicing of retained introns. Finally, these findings link alternative splicing with modern intron creation...

..In this article, we discuss the growing evidence that these differences are subject to selection acting on introns depending on the biology of the organism and the gene involved...

..The three best supported positions of the root were passerine, but the traditional rooting position between paleognaths and neognaths could not be excluded...

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..We recommend that network programs be incorporated into best practice analysis, along with ML and Bayesian trees...

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..Significantly, the absence of ancestrally amitochondriate eukaryotes (archezoa) among extant eukaryotes is neither evidence for an archaeal host for the ancestor of mitochondria, nor evidence against a eukaryotic host...

..Thus, a comprehensive exploration of potential systematic biases is still required, even though genome-scale data sets greatly reduce sampling error...

..The package is highly interactive and available for PCs...

..This strategy depends on detecting and excluding (or accounting for) major sources of non-historical signal, such as from compositional non-stationarity. [Base composition; combined data; marsupial; mitochondrial genome; phylogeny.]...

..Among eubacteria and archaebacteria, proteobacterial and methanogen genomes, respectively, shared more similarity with the yeast genome than other prokaryotic genomes surveyed...

..Including the additional species paints a very different picture, with 13 remaining characters consistent with Ecdysozoa versus only 1 consistent with Coelomata...

..5 billion years. Nine other predicted introns are due to annotation errors reflecting apparent mistakes in the E. histolytica genome assembly. These results underscore the massive differences in intron gain rates through evolution...

..The mutation rate calculated for the RSV B G gene was significantly higher than for RSV A. Together, these data reveal that RSV subgroups exhibit different patterns of evolution, with subgroup B viruses evolving faster than A...