MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Molecular Biology and Evolution' source. Thu, 09 Feb 2012 16:56:50 +0100 http://www.medworm.com/index.php?rid=5593008&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F873%3Frss%3D1 Several reports from mammals indicate that an increase in the mutation rate in late-replicating regions may, in part, be responsible for the observed genomic heterogeneity in neutral substitution rates and levels of diversity, although the mechanisms for this remain poorly understood. Recent evidence also suggests that late replication is associated with high mutability in yeast. This then raises the question as to whether a similar effect is operating across all eukaryotes. Limited evidence from one chromosome arm in Drosophila melanogaster suggests the opposite pattern, with regions overlapping early-firing origins showing increased levels of diversity and divergence. Given the availability of genome-wide replication timing profiles for D. melanogaster, we now return to this issue. Consi... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5593008 Fri, 13 Jan 2012 05:00:00 +0100 5593008 http://www.medworm.com/index.php?rid=5593007&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F861%3Frss%3D1 A salient feature of genomes of higher organisms is the birth and death of gene copies. An example is the alpha prolamin genes, which encode seed storage proteins in grasses (Poaceae) and represent a medium-size gene family. To better understand the mechanism, extent, and pace of gene amplification, we compared prolamin gene copies in the genomes of two different tribes in the Panicoideae, the Paniceae and the Andropogoneae. We identified alpha prolamin (setarin) gene copies in the diploid foxtail millet (Paniceae) genome (490 Mb) and compared them with orthologous regions in diploid sorghum (730 Mb) and ancient allotetraploid maize (2,300 Mb) (Andropogoneae). Because sequenced genomes of other subfamilies of Poaceae like rice (389 Mb) (Ehrhartoideae) and Brachypodium (272 Mb) (Pooideae) d... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5593007 Fri, 13 Jan 2012 05:00:00 +0100 5593007 http://www.medworm.com/index.php?rid=5593006&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F849%3Frss%3D1 The number of introns varies considerably among different organisms. This can be explained by the differences in the rates of intron gain and loss. Two factors that are likely to influence these rates are selection for or against introns and the mutation rate that generates the novel intron or the intronless copy. Although it has been speculated that stronger selection for a compact genome might result in a higher rate of intron loss and a lower rate of intron gain, clear evidence is lacking, and the role of selection in determining these rates has not been established. Here, we studied the gain and loss of introns in the two closely related species Arabidopsis thaliana and A. lyrata as it was recently shown that A. thaliana has been undergoing a faster genome reduction driven by selection... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5593006 Fri, 13 Jan 2012 05:00:00 +0100 5593006 http://www.medworm.com/index.php?rid=5593005&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F837%3Frss%3D1 Sex chromosomes play a role in many important biological processes, including sex determination, genomic conflicts, imprinting, and speciation. In particular, they exhibit several unusual properties such as inheritance pattern, hemizygosity, and reduced recombination, which influence their response to evolutionary factors (e.g., drift, selection, and demography). Here, we examine the evolutionary forces driving X chromosome evolution in aphids, an XO system where females are homozygous (XX) and males are hemizygous (X0) at sex chromosomes. We show by simulations that the unusual mode of transmission of the X chromosome in aphids, coupled with cyclical parthenogenesis, results in similar effective population sizes and predicted levels of genetic diversity for X chromosomes and autosomes und... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5593005 Fri, 13 Jan 2012 05:00:00 +0100 5593005 http://www.medworm.com/index.php?rid=5593004&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F825%3Frss%3D1 Thermophily is thought to be a primitive trait, characteristic of early forms of life on Earth, that has been gradually lost over evolutionary time. The genus Bacillus provides an ideal model for studying the evolution of thermophily as it is an ancient taxon and its contemporary species inhabit a range of thermal environments. The thermostability of reconstructed ancestral proteins has been used as a proxy for ancient thermal adaptation. The reconstruction of ancestral "enzymes" has the added advantages of demonstrable activity, which acts as an internal control for accurate inference, and providing insights into the evolution of enzymatic catalysis. Here, we report the reconstruction of the structurally complex core metabolic enzyme LeuB (3-isopropylmalate dehydrogenase, E. C. 1.1.1.85) ... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5593004 Fri, 13 Jan 2012 05:00:00 +0100 5593004 http://www.medworm.com/index.php?rid=5593003&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F811%3Frss%3D1 CD5 is a lymphocyte surface coreceptor of still incompletely understood function. Currently available information indicates that CD5 participates not only in cell-to-cell immune interactions through still poorly defined endogenous ligands expressed on hemopoietic and nonhemopoietic cells but also in recognition of exogenous and highly conserved microbial structures such as fungal β-glucans. Preceding single nucleotide polymorphism (SNP) data analysis provided evidence for a recent selective sweep in East Asia and suggested a nonsynonymous substitution at position 471 (A471V; rs2229177) of the cytoplasmatic region of the CD5 receptor as the most plausible target of selection. The present report further investigates the role of natural selection in the CD5 gene by a resequencing approac... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5593003 Fri, 13 Jan 2012 05:00:00 +0100 5593003 http://www.medworm.com/index.php?rid=5593002&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F797%3Frss%3D1 We analyzed the genome-wide pattern of single nucleotide polymorphisms (SNPs) in a sample with 12 strains of Staphylococcus aureus. Population structure of S. aureus seems to be complex, and the 12 strains were divided into five groups, named A, B, C, D, and E. We conducted a detailed analysis of the topologies of gene genealogies across the genomes and observed a high rate and frequency of tree-shape switching, indicating extensive homologous recombination. Most of the detected recombination occurred in the ancestral population of A, B, and C, whereas there are a number of small regions that exhibit evidence for homologous recombination with a distinct related species. As such regions would contain a number of novel mutations, it is suggested that homologous recombination would play a cru... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5593002 Fri, 13 Jan 2012 05:00:00 +0100 5593002 http://www.medworm.com/index.php?rid=5593001&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F787%3Frss%3D1 The wealth of available genomic data presents an unrivaled opportunity to study the molecular basis of evolution. Studies on gene family expansions and site-dependent analyses have already helped establish important insights into how proteins facilitate adaptation. However, efforts to conduct full-scale cross-genomic comparisons between species are challenged by both growing amounts of data and the inherent difficulty in accurately inferring homology between deeply rooted species. Proteins, in comparison, evolve by means of domain rearrangements, a process more amenable to study given the strength of profile-based homology inference and the lower rates with which rearrangements occur. However, adapting to a constantly changing environment can require molecular modulations beyond reach of r... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5593001 Fri, 13 Jan 2012 05:00:00 +0100 5593001 http://www.medworm.com/index.php?rid=5593000&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F771%3Frss%3D1 Males and females share the same genome, thus, phenotypic divergence requires differential gene expression and sex-specific regulation. Accordingly, the analysis of expression patterns is pivotal to the understanding of sex determination mechanisms. Many bivalves are stable gonochoric species, but the mechanism of gonad sexualization and the genes involved are still unknown. Moreover, during the period of sexual rest, a gonad is not present and sex cannot be determined. A mechanism associated with germ line differentiation in some bivalves, including the Manila clam Ruditapes philippinarum, is the doubly uniparental inheritance (DUI) of mitochondria, a variation of strict maternal inheritance. Two mitochondrial lineages are present, one transmitted through eggs and the other through sperm,... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5593000 Fri, 13 Jan 2012 05:00:00 +0100 5593000 http://www.medworm.com/index.php?rid=5592999&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F763%3Frss%3D1 In this study, we directly estimate the mtDNA mutation rate and spectrum using Daphnia pulex mutation-accumulation (MA) lines derived from sexual (cyclically parthenogenetic) and asexual (obligately parthenogenetic) lineages. The nearly complete mitochondrial genome sequences of 82 sexual and 47 asexual MA lines reveal high mtDNA mutation rate of 1.37 x 10–7 and 1.73 x 10–7 per nucleotide per generation, respectively. The Daphnia mtDNA mutation rate is among the highest in eukaryotes, and its spectrum is dominated by insertions and deletions (70%), largely due to the presence of mutational hotspots at homopolymeric nucleotide stretches. Maximum likelihood estimates of the Daphnia mitochondrial effective population size reveal that between five and ten copies of mitochondrial ge... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5592999 Fri, 13 Jan 2012 05:00:00 +0100 5592999 http://www.medworm.com/index.php?rid=5592998&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F751%3Frss%3D1 We describe a procedure for model averaging of relaxed molecular clock models in Bayesian phylogenetics. Our approach allows us to model the distribution of rates of substitution across branches, averaged over a set of models, rather than conditioned on a single model. We implement this procedure and test it on simulated data to show that our method can accurately recover the true underlying distribution of rates. We applied the method to a set of alignments taken from a data set of 12 mammalian species and uncovered evidence that lognormally distributed rates better describe this data set than do exponentially distributed rates. Additionally, our implementation of model averaging permits accurate calculation of the Bayes factor(s) between two or more relaxed molecular clock models. Finall... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5592998 Fri, 13 Jan 2012 05:00:00 +0100 5592998 http://www.medworm.com/index.php?rid=5592997&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F737%3Frss%3D1 Although many phylogenetic studies have focused on developing hypotheses about relationships, advances in data collection and computation have increased the feasibility of collecting large independent data sets to rigorously test controversial hypotheses or carefully assess artifacts that may be misleading. One such relationship in need of independent evaluation is the position of Passeriformes (perching birds) in avian phylogeny. This order comprises more than half of all extant birds, and it includes one of the most important avian model systems (the zebra finch). Recent large-scale studies using morphology, mitochondrial, and nuclear sequence data have generated very different hypotheses about the sister group of Passeriformes, and all conflict with an older hypothesis generated using D... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5592997 Fri, 13 Jan 2012 05:00:00 +0100 5592997 http://www.medworm.com/index.php?rid=5592996&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F721%3Frss%3D1 Various nucleotide substitution models have been developed to accommodate among lineage rate heterogeneity, thereby relaxing the assumptions of the strict molecular clock. Recently developed "uncorrelated relaxed clock" and "random local clock" (RLC) models allow decoupling of nucleotide substitution rates between descendant lineages and are thus predicted to perform better in the presence of lineage-specific rate heterogeneity. However, it is uncertain how these models perform in the presence of punctuated shifts in substitution rate, especially between closely related clades. Using cetaceans (whales and dolphins) as a case study, we test the performance of these two substitution models in estimating both molecular rates and divergence times in the presence of substantial lineage-specific... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5592996 Fri, 13 Jan 2012 05:00:00 +0100 5592996 http://www.medworm.com/index.php?rid=5592995&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F707%3Frss%3D1 The rate of change in DNA is an important parameter for understanding molecular evolution and hence for inferences drawn from studies of phylogeography and phylogenetics. Most rate calibrations for mitochondrial coding regions in marine species have been made from divergence dating for fossils and vicariant events older than 1–2 My and are typically 0.5–2% per lineage per million years. Recently, calibrations made with ancient DNA (aDNA) from younger dates have yielded faster rates, suggesting that estimates of the molecular rate of change depend on the time of calibration, decaying from the instantaneous mutation rate to the phylogenetic substitution rate. aDNA methods for recent calibrations are not available for most marine taxa so instead we use radiometric dates for sea-le... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5592995 Fri, 13 Jan 2012 05:00:00 +0100 5592995 http://www.medworm.com/index.php?rid=5592994&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F689%3Frss%3D1 Although the possibility of gene evolution by domain rearrangements has long been appreciated, current methods for reconstructing and systematically analyzing gene family evolution are limited to events such as duplication, loss, and sometimes, horizontal transfer. However, within the Drosophila clade, we find domain rearrangements occur in 35.9% of gene families, and thus, any comprehensive study of gene evolution in these species will need to account for such events. Here, we present a new computational model and algorithm for reconstructing gene evolution at the domain level. We develop a method for detecting homologous domains between genes and present a phylogenetic algorithm for reconstructing maximum parsimony evolutionary histories that include domain generation, duplication, loss,... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5592994 Fri, 13 Jan 2012 05:00:00 +0100 5592994 http://www.medworm.com/index.php?rid=5592993&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F675%3Frss%3D1 Levels of nucleotide variability are frequently positively correlated with recombination rate and negatively associated with gene density due to the effects of selection on linked variation. These relationships are determined by properties that frequently differ among species, including the mating system, and aspects of genome organization such as how genes are distributed along chromosomes. In rice, genes are found at highest density in regions with frequent crossing-over. This association between gene density and recombination rate provides an opportunity to evaluate the effects of selection in a genomic context that differs from other model organisms. Using single-nucleotide polymorphism data from Asian domesticated rice Oryza sativa ssp. japonica and ssp. indica and their progenitor sp... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5592993 Fri, 13 Jan 2012 05:00:00 +0100 5592993 http://www.medworm.com/index.php?rid=5592992&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F663%3Frss%3D1 Among the criteria to evaluate the performance of a phylogenetic method, robustness to model violation is of particular practical importance as complete a priori knowledge of evolutionary processes is typically unavailable. For studies of robustness in phylogenetic inference, a utility to add well-defined model violations to the simulated data would be helpful. We therefore introduce ImOSM, a tool to imbed intermittent evolution as model violation into an alignment. Intermittent evolution refers to extra substitutions occurring randomly on branches of a tree, thus changing alignment site patterns. This means that the extra substitutions are placed on the tree after the typical process of sequence evolution is completed. We then study the robustness of widely used phylogenetic methods: maxi... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5592992 Fri, 13 Jan 2012 05:00:00 +0100 5592992 http://www.medworm.com/index.php?rid=5592991&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F647%3Frss%3D1 β-Catenin is a multifunctional scaffolding protein with roles in Wnt signaling, cell adhesion, and centrosome separation. Here, we report on independent duplications of the insect β-Catenin ortholog armadillo (arm) in the red flour beetle Tribolium castaneum and the pea aphid Acyrthosiphon pisum. Detailed sequence analysis shows that in both species, one paralog lost critical residues of the α-Catenin binding domain, which is essential for cell adhesion, and accumulated a dramatically higher number of amino acid substitutions in the central Arm repeat domain. Residues associated with aspects of Wnt signaling, however, are conserved in both paralogs. Consistent with these molecular signatures, the effects of specific and combinatorial knockdown experiments in the Tribolium e... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5592991 Fri, 13 Jan 2012 05:00:00 +0100 5592991 http://www.medworm.com/index.php?rid=5592990&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F631%3Frss%3D1 Transposable elements are widespread mobile DNA sequences able to integrate into new locations within genomes. Through transposition and recombination, they significantly contribute to genome plasticity and evolution. They can also regulate gene expression and provide regulatory and coding sequences (CDSs) for the evolution of novel gene functions. We have identified a new superfamily of DNA transposon on the Y chromosome of the platyfish Xiphophorus maculatus. This element is 11 kb in length and carries a single CDS of 24 exons. The N-terminal part of the putative protein, which is expressed in all adult tissues tested, contains several nucleic acid– and protein-binding domains and might correspond to a novel type of transposase/integrase not described so far in any transposon. In a... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5592990 Fri, 13 Jan 2012 05:00:00 +0100 5592990 http://www.medworm.com/index.php?rid=5592989&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F617%3Frss%3D1 Sub-Saharan Africa has consistently been shown to be the most genetically diverse region in the world. Despite the fact that a substantial portion of this variation is partitioned between groups practicing a variety of subsistence strategies and speaking diverse languages, there is currently no consensus on the genetic relationships of sub-Saharan African populations. San (a subgroup of KhoeSan) and many Pygmy groups maintain hunter-gatherer lifestyles and cluster together in autosomal-based analysis, whereas non-Pygmy Niger-Kordofanian speakers (non-Pygmy NKs) predominantly practice agriculture and show substantial genetic homogeneity despite their wide geographic range throughout sub-Saharan Africa. However, KhoeSan, who speak a set of relatively unique click-based languages, have long b... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5592989 Fri, 13 Jan 2012 05:00:00 +0100 5592989 http://www.medworm.com/index.php?rid=5592988&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F599%3Frss%3D1 The SAR11 clade, here represented by Candidatus Pelagibacter ubique, is the most successful group of bacteria in the upper surface waters of the oceans. In contrast to previous studies that have associated the 1.3 Mb genome of Ca. Pelagibacter ubique with the less than 1.5 Mb genomes of the Rickettsiales, our phylogenetic analysis suggests that Ca. Pelagibacter ubique is most closely related to soil and aquatic Alphaproteobacteria with large genomes. This implies that the SAR11 clade and the Rickettsiales have undergone genome reduction independently. A gene flux analysis of 46 representative alphaproteobacterial genomes indicates the loss of more than 800 genes in each of Ca. Pelagibacter ubique and the Rickettsiales. Consistent with their different phylogenetic affiliations, the pattern ... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5592988 Fri, 13 Jan 2012 05:00:00 +0100 5592988 http://www.medworm.com/index.php?rid=5592987&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F579%3Frss%3D1 Whole-genome or multiple gene phylogenetic analysis is of interest since single gene analysis often results in poorly resolved trees. Here, the use of spectral techniques for analyzing multigene data sets is explored. The protein sequences are treated as categorical time series, and a measure of similarity between a pair of sequences, the spectral covariance, is based on the common periodicity between these two sequences. Unlike the other methods, the spectral covariance method focuses on the relationship between the sites of genetic sequences. By properly scaling the dissimilarity measures derived from different genes between a pair of species, we can use the mean of these scaled dissimilarity measures as a summary statistic to measure the taxonomic distances across multiple genes. The me... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5592987 Fri, 13 Jan 2012 05:00:00 +0100 5592987 http://www.medworm.com/index.php?rid=5592986&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F565%3Frss%3D1 Drosophila melanogaster has long been used as a model for the molecular genetics of innate immunity. Such work has uncovered several immune receptors that recognize bacterial and fungal pathogens by binding unique components of their cell walls and membranes. Drosophila also act as hosts to metazoan pathogens such as parasitic wasps, which can infect a majority of individuals in natural populations, but many aspects of their immune responses against these more closely related pathogens are poorly understood. Here, we present data describing the transcriptional induction and molecular evolution of a candidate Drosophila anti-wasp immunity gene, lectin-24A. Lectin-24A has a secretion signal sequence and its lectin domain suggests a function in sugar group binding. Transcript levels of lectin... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5592986 Fri, 13 Jan 2012 05:00:00 +0100 5592986 http://www.medworm.com/index.php?rid=5592985&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F545%3Frss%3D1 Although genetic studies have contributed greatly to our understanding of the colonization of Near and Remote Oceania, important gaps still exist. One such gap is the Solomon Islands, which extend between Bougainville and Vanuatu, thereby bridging Near and Remote Oceania, and include both Austronesian-speaking and Papuan-speaking groups. Here, we describe patterns of mitochondrial DNA (mtDNA) and nonrecombining Y chromosome (NRY) variation in over 700 individuals from 18 populations in the Solomons, including 11 Austronesian-speaking groups, 3 Papuan-speaking groups, and 4 Polynesian Outliers (descended via back migration from Polynesia). We find evidence for ancient (pre-Lapita) colonization of the Solomons in old NRY paragroups as well as from M2-M353, which probably arose in the Solomon... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5592985 Fri, 13 Jan 2012 05:00:00 +0100 5592985 http://www.medworm.com/index.php?rid=5592984&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F531%3Frss%3D1 Many of the eukaryotic phylogenomic analyses published to date were based on alignments of hundreds to thousands of genes. Frequently, in such analyses, the most realistic evolutionary models currently available are often used to minimize the impact of systematic error. However, controversy remains over whether or not idiosyncratic gene family dynamics (i.e., gene duplications and losses) and incorrect orthology assignments are always appropriately taken into account. In this paper, we present an innovative strategy for overcoming orthology assignment problems. Rather than identifying and eliminating genes with paralogy problems, we have constructed a data set comprised exclusively of conserved single-copy protein domains that, unlike most of the commonly used phylogenomic data sets, shoul... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5592984 Fri, 13 Jan 2012 05:00:00 +0100 5592984 http://www.medworm.com/index.php?rid=5592983&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F517%3Frss%3D1 Chimeric genes form through the combination of portions of existing coding sequences to create a new open reading frame. These new genes can create novel protein structures that are likely to serve as a strong source of novelty upon which selection can act. We have identified 14 chimeric genes that formed through DNA-level mutations in Drosophila melanogaster, and we investigate expression profiles, domain structures, and population genetics for each of these genes to examine their potential to effect adaptive evolution. We find that chimeric gene formation commonly produces mid-domain breaks and unites portions of wholly unrelated peptides, creating novel protein structures that are entirely distinct from other constructs in the genome. These new genes are often involved in selective swee... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5592983 Fri, 13 Jan 2012 05:00:00 +0100 5592983 http://www.medworm.com/index.php?rid=5592982&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F503%3Frss%3D1 Transposable elements (TEs) are highly abundant in the genome and capable of mobility, two properties that make them particularly prone to transfer horizontally between organisms. Although the impact of horizontal transfer (HT) of TEs is well recognized in prokaryotes, the frequency of this phenomenon and its contribution to genome evolution in eukaryotes remain poorly appreciated. Here, we provide evidence that a DNA transposon called SPIN has colonized the genome of 17 species of reptiles representing nearly every major lineage of squamates, including 14 families of lizards, snakes, and amphisbaenians. Slot blot analyses indicate that SPIN has amplified to high copy numbers in most of these species, ranging from 2,000–28,000 copies per haploid genome. In contrast, we could not dete... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5592982 Fri, 13 Jan 2012 05:00:00 +0100 5592982 http://www.medworm.com/index.php?rid=5592981&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F487%3Frss%3D1 Proliferative and endoreduplicative cell cycles are used to variable extents during the ontogeny of individual organisms and in different evolutionary lineages. Chordate growth and development is typically dominated by proliferative cycles, but the urochordate, Oikopleura dioica, has systemically elaborated a number of endocycling modes to support rapid development and growth in an extraordinarily short chordate life cycle. Here, we identify the O. dioica cyclin and cyclin-dependent kinase (CDK) complements and assess their deployment with respect to mitotic, meiotic, and endoreduplicative life cycle phases. Oikopleura dioica’s "transcriptional" cyclin and CDK complements are similar to other complex invertebrates, whereas both the "cell cycle" cyclin and CDK complements display asto... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5592981 Fri, 13 Jan 2012 05:00:00 +0100 5592981 http://www.medworm.com/index.php?rid=5592980&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F473%3Frss%3D1 We report analysis of several data sets, demonstrating that IBD is more common than expected by naïve models of population genetics. We show that the frequency of IBD pairs is population dependent and can be used to cluster individuals into populations, detect a homogeneous subpopulation within a larger cohort, and infer bottleneck events in such a subpopulation. Specifically, we show that Ashkenazi Jewish individuals are all connected through transitive remote family ties evident by sharing of 50 cM IBD to a publicly available data set of less than 400 individuals. We further expose regions where long-range haplotypes are shared significantly more often than elsewhere in the genome, observed across multiple populations, and enriched for common long structural variation. These are inc... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5592980 Fri, 13 Jan 2012 05:00:00 +0100 5592980 http://www.medworm.com/index.php?rid=5592979&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F457%3Frss%3D1 Phylogenomics refers to the inference of historical relationships among species using genome-scale sequence data and to the use of phylogenetic analysis to infer protein function in multigene families. With rapidly decreasing sequencing costs, phylogenomics is becoming synonymous with evolutionary analysis of genome-scale and taxonomically densely sampled data sets. In phylogenetic inference applications, this translates into very large data sets that yield evolutionary and functional inferences with extremely small variances and high statistical confidence (P value). However, reports of highly significant P values are increasing even for contrasting phylogenetic hypotheses depending on the evolutionary model and inference method used, making it difficult to establish true relationships. W... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5592979 Fri, 13 Jan 2012 05:00:00 +0100 5592979 http://www.medworm.com/index.php?rid=5592978&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F451%3Frss%3D1 Rate heterogeneity among lineages is a common feature of molecular evolution, and it has long impeded our ability to accurately estimate the age of evolutionary divergence events. The development of relaxed molecular clocks, which model variable substitution rates among lineages, was intended to rectify this problem. Major subtypes of pandemic HIV-1 group M are thought to exemplify closely related lineages with different substitution rates. Here, we report that inferring the time of most recent common ancestor of all these subtypes in a single phylogeny under a single (relaxed) molecular clock produces significantly different dates for many of the subtypes than does analysis of each subtype on its own. We explore various methods to ameliorate this problem. We conclude that current molecula... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5592978 Fri, 13 Jan 2012 05:00:00 +0100 5592978 http://www.medworm.com/index.php?rid=5592977&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2F445%3Frss%3D1 The DARC (Duffy antigen/receptor for chemokines) gene, also called Duffy or FY, encodes a membrane-bound chemokine receptor. Two malaria parasites, Plasmodium vivax and Plasmodium knowlesi, use DARC to trigger internalization into red blood cells. Although much has been reported on the evolution of DARC null alleles, little is known about the evolution of the coding portion of this gene or the role that protein sequence divergence in this receptor may play in disease susceptibility or zoonosis. Here, we show that the Plasmodium interaction domain of DARC is nearly invariant in the human population, suggesting that coding polymorphism there is unlikely to play a role in differential susceptibility to infection. However, an analysis of DARC orthologs from 35 simian primate species reveals hi... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5592977 Fri, 13 Jan 2012 05:00:00 +0100 5592977 http://www.medworm.com/index.php?rid=5592976&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2FNP-b%3Frss%3D1 (Source: Molecular Biology and Evolution) Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5592976 Fri, 13 Jan 2012 05:00:00 +0100 5592976 http://www.medworm.com/index.php?rid=5592975&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2FNP-a%3Frss%3D1 (Source: Molecular Biology and Evolution) Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5592975 Fri, 13 Jan 2012 05:00:00 +0100 5592975 http://www.medworm.com/index.php?rid=5592974&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F2%2FNP%3Frss%3D1 (Source: Molecular Biology and Evolution) Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5592974 Fri, 13 Jan 2012 05:00:00 +0100 5592974 http://www.medworm.com/index.php?rid=5533409&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F443%3Frss%3D1 (Source: Molecular Biology and Evolution) Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533409 Thu, 22 Dec 2011 05:00:00 +0100 5533409 http://www.medworm.com/index.php?rid=5533408&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F441%3Frss%3D1 (Source: Molecular Biology and Evolution) Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533408 Thu, 22 Dec 2011 05:00:00 +0100 5533408 http://www.medworm.com/index.php?rid=5533407&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F429%3Frss%3D1 The reconstruction of an ancient polyploidization history is often challenging, although it is a crucial step in clarifying the mechanisms underlying the contemporary success and diversity of polyploids. Phylogenetic relationships of duplicated gene pairs of polyploids, with respect to their orthologs in related diploids, have been used to address this problem, but they often result in conflicting topologies among different genes. Asimitellaria is an East Asian endemic tetraploid lineage of perennials (genus Mitella; Saxifragaceae) that has diversified in riparian habitats. Phylogenetic analyses of four nuclear-encoded, single-copy (per haploid) genes GBSSI-A, GBSSI-B, GS-II, and PepCK all supported a single allopolyploid origin of Asimitellaria, but they did not lead to a consensus about ... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533407 Thu, 22 Dec 2011 05:00:00 +0100 5533407 http://www.medworm.com/index.php?rid=5533406&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F421%3Frss%3D1 The distribution in the human genome of the largest family of mobile elements, the Alu sequences, has been investigated for the past 30 years, and the vast majority of Alu sequences were shown to have the highest density in GC-rich isochores. Ten years ago, it was discovered, however, that the small "youngest" (most recently transposed) Alu families had a strikingly different distribution compared with the "old" families. This raised the question as to how this change took place in evolution. We solved what was considered to be a "mystery" by 1) revisiting our previous results on the integration and stability of retroviral sequences, and 2) assessing the densities of acceptor sites TTTT/AA in isochore families. We could conclude 1) that the open state of chromatin structure plays a crucial... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533406 Thu, 22 Dec 2011 05:00:00 +0100 5533406 http://www.medworm.com/index.php?rid=5533405&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F409%3Frss%3D1 Botanical fruits derive from ovaries and their most important function is to favor seed dispersal. Fleshy fruits do so by attracting frugivorous animals that disperse seeds together with their own excrements (endozoochory). Gymnosperms make seeds but have no ovaries to be transformed into fruits. Many species surround their seeds with fleshy structures and use endozoochory to disperse them. Such structures are functionally fruits and can derive from different anatomical parts. Ginkgo biloba and Taxus baccata fruit-like structures differ in their anatomical origin since the outer seed integument becomes fleshy in Ginkgo, whereas in Taxus, the fleshy aril is formed de novo. The ripening characteristics are different, with Ginkgo more rudimentary and Taxus more similar to angiosperm fruits. M... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533405 Thu, 22 Dec 2011 05:00:00 +0100 5533405 http://www.medworm.com/index.php?rid=5533404&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F401%3Frss%3D1 Sexual reproduction is extremely widespread in spite of its presumed costs relative to asexual reproduction, indicating that it must provide significant advantages. One postulated benefit of sex and recombination is that they facilitate the purging of mildly deleterious mutations, which would accumulate in asexual lineages and contribute to their short evolutionary life span. To test this prediction, we estimated the accumulation rate of coding (nonsynonymous) mutations, which are expected to be deleterious, in parts of one mitochondrial (COI) and two nuclear (Actin and Hsp70) genes in six independently derived asexual lineages and related sexual species of Timema stick insects. We found signatures of increased coding mutation accumulation in all six asexual Timema and for each of the thre... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533404 Thu, 22 Dec 2011 05:00:00 +0100 5533404 http://www.medworm.com/index.php?rid=5533403&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F391%3Frss%3D1 Anaplasma phagocytophilum is an obligately intracellular tick-transmitted bacterial pathogen of humans and other animals. During the course of infection, A. phagocytophilum utilizes gene conversion to shuffle ~100 functional pseudogenes into a single expression cassette of the msp2(p44) gene, which codes for the major surface antigen and major surface protein 2 (MSP2). The role and extent of msp2(p44) recombination, particularly in hosts that only experience acute infections, is not clear. In the present study, we explored patterns of recombination and expression of the msp2(p44) gene of A. phagocytophilum in a serially infected mouse model. Even though the bacterium was passed rapidly among mice, minimizing the opportunities for the host to develop adaptive immunity, we detected the emerg... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533403 Thu, 22 Dec 2011 05:00:00 +0100 5533403 http://www.medworm.com/index.php?rid=5533402&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F381%3Frss%3D1 Retroelements represent a considerable fraction of many eukaryotic genomes and are considered major drives for adaptive genetic innovations. Recent discoveries showed that despite not normally using DNA intermediates like retroviruses do, Mononegaviruses (i.e., viruses with nonsegmented, negative-sense RNA genomes) can integrate gene fragments into the genomes of their hosts. This was shown for Bornaviridae and Filoviridae, the sequences of which have been found integrated into the germ line cells of many vertebrate hosts. Here, we show that Rhabdoviridae sequences, the major Mononegavirales family, have integrated only into the genomes of arthropod species. We identified 185 integrated rhabdoviral elements (IREs) coding for nucleoproteins, glycoproteins, or RNA-dependent RNA polymerases; ... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533402 Thu, 22 Dec 2011 05:00:00 +0100 5533402 http://www.medworm.com/index.php?rid=5533401&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F367%3Frss%3D1 Diatoms and other chlorophyll-c containing, or chromalveolate, algae are among the most productive and diverse phytoplankton in the ocean. Evolutionarily, chlorophyll-c algae are linked through common, although not necessarily monophyletic, acquisition of plastid endosymbionts of red as well as most likely green algal origin. There is also strong evidence for a relatively high level of lineage-specific bacterial gene acquisition within chromalveolates. Therefore, analyses of gene content and derivation in chromalveolate taxa have indicated particularly diverse origins of their overall gene repertoire. As a single group of functionally related enzymes spanning two distinct gene families, fructose 1,6-bisphosphate aldolases (FBAs) illustrate the influence on core biochemical pathways of spec... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533401 Thu, 22 Dec 2011 05:00:00 +0100 5533401 http://www.medworm.com/index.php?rid=5533400&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F359%3Frss%3D1 We report a synthesis of autosomal, Y chromosome, and mitochondrial DNA (mtDNA) variation in populations from all major subregions and linguistic phyla of the area. Autosomal genome variation in the Caucasus reveals significant genetic uniformity among its ethnically and linguistically diverse populations and is consistent with predominantly Near/Middle Eastern origin of the Caucasians, with minor external impacts. In contrast to autosomal and mtDNA variation, signals of regional Y chromosome founder effects distinguish the eastern from western North Caucasians. Genetic discontinuity between the North Caucasus and the East European Plain contrasts with continuity through Anatolia and the Balkans, suggesting major routes of ancient gene flows and admixture. (Source: Molecular Biology and Ev... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533400 Thu, 22 Dec 2011 05:00:00 +0100 5533400 http://www.medworm.com/index.php?rid=5533399&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F347%3Frss%3D1 Epidemiological processes leave a fingerprint in the pattern of genetic structure of virus populations. Here, we provide a new method to infer epidemiological parameters directly from viral sequence data. The method is based on phylogenetic analysis using a birth–death model (BDM) rather than the commonly used coalescent as the model for the epidemiological transmission of the pathogen. Using the BDM has the advantage that transmission and death rates are estimated independently and therefore enables for the first time the estimation of the basic reproductive number of the pathogen using only sequence data, without further assumptions like the average duration of infection. We apply the method to genetic data of the HIV-1 epidemic in Switzerland. (Source: Molecular Biology and Evolut... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533399 Thu, 22 Dec 2011 05:00:00 +0100 5533399 http://www.medworm.com/index.php?rid=5533398&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F337%3Frss%3D1 Accelerated rates of mitochondrial protein evolution have been proposed to reflect Darwinian coadaptation for efficient energy production for mammalian flight and brain activity. However, several features of mammalian mtDNA (absence of recombination, small effective population size, and high mutation rate) promote genome degradation through the accumulation of weakly deleterious mutations. Here, we present evidence for "compensatory" adaptive substitutions in nuclear DNA- (nDNA) encoded mitochondrial proteins to prevent fitness decline in primate mitochondrial protein complexes. We show that high mutation rate and small effective population size, key features of primate mitochondrial genomes, can accelerate compensatory adaptive evolution in nDNA-encoded genes. We combine phylogenetic info... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533398 Thu, 22 Dec 2011 05:00:00 +0100 5533398 http://www.medworm.com/index.php?rid=5533397&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F325%3Frss%3D1 Recent studies have observed that Bayesian analyses of sequence data sets using the program MrBayes sometimes generate extremely large branch lengths, with posterior credibility intervals for the tree length (sum of branch lengths) excluding the maximum likelihood estimates. Suggested explanations for this phenomenon include the existence of multiple local peaks in the posterior, lack of convergence of the chain in the tail of the posterior, mixing problems, and misspecified priors on branch lengths. Here, we analyze the behavior of Bayesian Markov chain Monte Carlo algorithms when the chain is in the tail of the posterior distribution and note that all these phenomena can occur. In Bayesian phylogenetics, the likelihood function approaches a constant instead of zero when the branch length... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533397 Thu, 22 Dec 2011 05:00:00 +0100 5533397 http://www.medworm.com/index.php?rid=5533396&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F313%3Frss%3D1 The pea aphid genome was recently found to harbor genes for carotenoid biosynthesis, reflecting an ancestral transfer from a fungus. To explore the evolution of the carotene desaturase gene family within aphids, sequences were retrieved from a set of 34 aphid species representing numerous deeply diverging lineages of aphids and analyzed together with fungal sequences retrieved from databases. All aphids have at least one copy of this gene and some aphid species have up to seven, whereas fungal genomes consistently have a single copy. The closest relatives of aphids, adelgids, also have carotene desaturase; these sequences are most closely related to those from aphids, supporting a shared origin from a fungal to insect transfer predating the divergence of adelgids and aphids. Likewise, all ... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533396 Thu, 22 Dec 2011 05:00:00 +0100 5533396 http://www.medworm.com/index.php?rid=5533395&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F303%3Frss%3D1 It has been hypothesized that two successive rounds of whole-genome duplication (WGD) in the stem lineage of vertebrates provided genetic raw materials for the evolutionary innovation of many vertebrate-specific features. However, it has seldom been possible to trace such innovations to specific functional differences between paralogous gene products that derive from a WGD event. Here, we report genomic evidence for a direct link between WGD and key physiological innovations in the vertebrate oxygen transport system. Specifically, we demonstrate that key globin proteins that evolved specialized functions in different aspects of oxidative metabolism (hemoglobin, myoglobin, and cytoglobin) represent paralogous products of two WGD events in the vertebrate common ancestor. Analysis of conserve... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533395 Thu, 22 Dec 2011 05:00:00 +0100 5533395 http://www.medworm.com/index.php?rid=5533394&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F293%3Frss%3D1 Land plants have a remarkable life cycle that alternates between a diploid sporophytic and a haploid gametophytic generation, both of which are multicellular and changed drastically during evolution. Classical MIKC MADS-domain (MIKCC) transcription factors are famous for their role in sporophytic development and are considered crucial for its evolution. About the regulation of gametophyte development, in contrast, little is known. Recent evidence indicated that the closely related MIKC* MADS-domain proteins are important for the functioning of the Arabidopsis thaliana male gametophyte (pollen). Furthermore, also in bryophytes, several MIKC* genes are expressed in the haploid generation. Therefore, that MIKC* genes have a similar role in the evolution of the gametophytic phase as MIKCC gene... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533394 Thu, 22 Dec 2011 05:00:00 +0100 5533394 http://www.medworm.com/index.php?rid=5533393&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F279%3Frss%3D1 Anopheles gambiae sensu stricto exists as two often-sympatric races termed the M and S molecular forms, characterized by fixed differences at an X-linked marker. Extreme divergence between M and S forms at pericentromeric "genomic islands" suggested that selection on variants therein could be driving interform divergence in the presence of ongoing gene flow, but recent work has detected much more widespread genomic differentiation. Whether such genomic islands are important in reproductive isolation or represent ancestral differentiation preserved by low recombination is currently unclear. A critical test of these competing hypotheses could be provided by comparing genomic divergence when rates of recent introgression vary. We genotyped 871 single nucleotide polymorphisms (SNPs) in A. gamb... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533393 Thu, 22 Dec 2011 05:00:00 +0100 5533393 http://www.medworm.com/index.php?rid=5533392&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F271%3Frss%3D1 Codon substitution models have traditionally been parametric Markov models, but recently, empirical and semiempirical models also have been proposed. Parametric codon models are typically based on 61x61 rate matrices that are derived from a small number of parameters. These parameters are rooted in experience and theoretical considerations and generally show good performance but are still relatively arbitrary. We have previously used principal component analysis (PCA) on data obtained from mammalian sequence alignments to empirically identify the most relevant parameters for codon substitution models, thereby confirming some commonly used parameters but also suggesting new ones. Here, we present a new semiempirical codon substitution model that is directly based on those PCA results. The s... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533392 Thu, 22 Dec 2011 05:00:00 +0100 5533392 http://www.medworm.com/index.php?rid=5533391&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F261%3Frss%3D1 This study establishes that deuterostomes share a remarkable conserved physiological process that involves a splicing factor and expression of tissue-specific isoforms of a target gene that expedites a highly conserved signaling pathway. (Source: Molecular Biology and Evolution) Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533391 Thu, 22 Dec 2011 05:00:00 +0100 5533391 http://www.medworm.com/index.php?rid=5533390&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F249%3Frss%3D1 Milk consumption and lactose digestion after weaning are exclusively human traits made possible by the continued production of the enzyme lactase in adulthood. Multiple independent mutations in a 100-bp region—part of an enhancer—approximately 14-kb upstream of the LCT gene are associated with this trait in Europeans and pastoralists from Saudi Arabia and Africa. However, a single mutation of purported western Eurasian origin accounts for much of observed lactase persistence outside Africa. Given the high levels of present-day milk consumption in India, together with archaeological and genetic evidence for the independent domestication of cattle in the Indus valley roughly 7,000 years ago, we sought to determine whether lactase persistence has evolved independently in the subco... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533390 Thu, 22 Dec 2011 05:00:00 +0100 5533390 http://www.medworm.com/index.php?rid=5533389&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F239%3Frss%3D1 Prolactin (PRL) is a multifunctional signaling molecule best known for its role in regulating lactation in mammals. Systemic PRL is produced by the anterior pituitary, but extrapituitary PRL has also been detected in many tissues including the human endometrium. Prolactin is essential for pregnancy in rodents and one of the most dramatically induced genes in the endometrium during human pregnancy. The promoter for human endometrial Prl is located about 5.8 kb upstream of the pituitary promoter and is derived from a transposable element called MER39. Although it has been shown that prolactin is expressed in the pregnant endometrium of a few mammals other than humans, MER39 has been described as primate specific. Thus, in an effort to understand mechanisms of prolactin regulatory evolution, ... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533389 Thu, 22 Dec 2011 05:00:00 +0100 5533389 http://www.medworm.com/index.php?rid=5533388&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F229%3Frss%3D1 In order to gain further insight into the processes underlying rapid reproductive protein evolution, we have conducted a population genetic survey of 44 reproductive tract–expressed proteases, protease inhibitors, and targets of proteolysis in Drosophila melanogaster and Drosophila simulans. Our findings suggest that positive selection on this group of genes is temporally heterogeneous, with different patterns of selection inferred using tests sensitive at different time scales. Such variation in the strength and targets of selection through time may be expected under models of sexual conflict and/or host–pathogen interaction. Moreover, available functional information concerning the genes that show evidence of selection suggests that both sexual selection and immune processes ... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533388 Thu, 22 Dec 2011 05:00:00 +0100 5533388 http://www.medworm.com/index.php?rid=5533387&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F219%3Frss%3D1 DNA methylation of coding regions, known as gene body methylation, is conserved across eukaryotic lineages. The function of body methylation is not known, but it may either prevent aberrant expression from intragenic promoters or enhance the accuracy of splicing. Given these putative functions, we hypothesized that body-methylated genes would be both longer and more functionally important than unmethylated genes. To test these hypotheses, we reanalyzed single-base resolution bisulfite sequence data from Arabidopsis thaliana to differentiate body-methylated genes from unmethylated genes using a probabilistic approach. Contrasting genic characteristics between the two groups, we found that body-methylated genes tend to be longer and to be more functionally important, as measured by phenotypi... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533387 Thu, 22 Dec 2011 05:00:00 +0100 5533387 http://www.medworm.com/index.php?rid=5533386&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F207%3Frss%3D1 Due to past and current climatic changes, range contractions and range shifts are essential stages in the history of a species. However, unlike range expansions, the molecular consequences of these processes have been little investigated. In order to fill this gap, we simulated patterns of molecular diversity within and between populations for various types of range contractions and range shifts. We show that range contractions tend to decrease genetic diversity as compared with population with stable ranges but quite counterintuitively fast range contractions preserve higher levels of diversity and induce lower levels of genetic differentiation among refuge areas than slow contractions. Contrastingly, fast range shifts lead to lower levels of diversity than slow range shifts. At odds with... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533386 Thu, 22 Dec 2011 05:00:00 +0100 5533386 http://www.medworm.com/index.php?rid=5533385&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F195%3Frss%3D1 Does hybridization play a broad innovative role in evolution? Many studies have shown hybrid origins of individual species, particularly in major adaptive radiations, but this may be a consequence, rather than a cause, of the existence of many closely related species. Cases of hybridization in the early stages of major adaptive radiations are comparatively rare. Here, we report phylogenetic evidence for ancient introgression between distinct lineages of the species-rich Lake Malawi haplochromine cichlid fishes. Mitochondrial DNA (mtDNA) sequences indicated surprisingly close relationships between the shallow-water rocky habitat "Mbuna" species and a group of dark-adapted "Deep-Benthic" species specialized for feeding in low-light conditions (dawn/dusk, under overhangs, and deep water). By ... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533385 Thu, 22 Dec 2011 05:00:00 +0100 5533385 http://www.medworm.com/index.php?rid=5533384&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F187%3Frss%3D1 Alternative splicing (AS) is known to significantly affect exon-level protein evolutionary rates in mammals. Particularly, alternatively spliced exons (ASEs) have a higher nonsynonymous-to-synonymous substitution rate (dN/dS) ratio than constitutively spliced exons (CSEs), possibly because the former are required only occasionally for normal biological functions. Meanwhile, intrinsically disordered regions (IDRs), the protein regions lacking fixed 3D structures, are also reported to have an increased evolutionary rate due to lack of structural constraint. Interestingly, IDRs tend to be located in alternative protein regions. Yet which of these two factors is the major determinant of the increased dN/dS in mammalian ASEs remains unclear. By comparing human–macaque and human–mous... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533384 Thu, 22 Dec 2011 05:00:00 +0100 5533384 http://www.medworm.com/index.php?rid=5533383&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F179%3Frss%3D1 Intron density is highly variable across eukaryotic species. It seems that different lineages have experienced considerably different levels of intron gain and loss events, but the reasons for this are not well known. A large number of mechanisms for intron loss and gain have been suggested, and most of them have at least some level of indirect support. We therefore figured out that the variability in intron density can be a reflection of the fact that different mechanisms are active in different lineages. Quite a number of these putative mechanisms, both for intron loss and for intron gain, postulate that the enzyme reverse transcriptase (RT) has a key role in the process. In this paper, we lay out three predictions whose approval or falsification gives indication for the involvement of R... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533383 Thu, 22 Dec 2011 05:00:00 +0100 5533383 http://www.medworm.com/index.php?rid=5533382&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F167%3Frss%3D1 Gene duplication followed by adaptive selection is believed to be the primary driver of venom evolution. However, to date, no studies have evaluated the importance of gene duplications for venom evolution using a genomic approach. The availability of a sequenced genome and a venom gland transcriptome for the enigmatic platypus provides a unique opportunity to explore the role that gene duplication plays in venom evolution. Here, we identify gene duplication events and correlate them with expressed transcripts in an in-season venom gland. Gene duplicates (1,508) were identified. These duplicated pairs (421), including genes that have undergone multiple rounds of gene duplications, were expressed in the venom gland. The majority of these genes are involved in metabolism and protein synthesis... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533382 Thu, 22 Dec 2011 05:00:00 +0100 5533382 http://www.medworm.com/index.php?rid=5533381&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F157%3Frss%3D1 Genes with the homeobox motif are crucial in developmental biology and widely implicated in the evolution of development. The Antennapedia (ANTP)-class is one of the two major classes of animal homeobox genes, and includes the Hox genes, renowned for their role in patterning the anterior–posterior axis of animals. The origin and evolution of the ANTP-class genes are a matter of some debate. A principal guiding hypothesis has been the existence of an ancient gene Mega-cluster deep in animal ancestry. This hypothesis was largely established from linkage data from chordates, and the Mega-cluster hypothesis remains to be seriously tested in protostomes. We have thus mapped ANTP-class homeobox genes to the chromosome level in a lophotrochozoan protostome. Our comparison of gene organizati... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533381 Thu, 22 Dec 2011 05:00:00 +0100 5533381 http://www.medworm.com/index.php?rid=5533380&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F145%3Frss%3D1 There have been conflicting arguments as to what happened in the human–chimpanzee speciation event. Patterson et al. (2006, Genetic evidence for complex speciation of humans and chimpanzees. Nature 441:1103–1108) proposed a hypothesis that the human–chimpanzee speciation event involved a complicated demographic process: that is, the ancestral lineages of humans and chimpanzees experienced temporal isolation followed by a hybridization event. This hypothesis stemmed from two major observations: a wide range of human–chimpanzee nucleotide divergence across the autosomal genome and very low divergence in the X chromosome. In contrast, Innan and Watanabe (2006, The effect of gene flow on the coalescent time in the human-chimpanzee ancestral population. Mol Biol Evol. 23... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533380 Thu, 22 Dec 2011 05:00:00 +0100 5533380 http://www.medworm.com/index.php?rid=5533379&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F133%3Frss%3D1 Although gene duplication plays a major role in organismal evolution, it may also lead to gene dosage imbalance, thereby having an immediate adverse effect on an organism’s fitness. Investigating the evolution of the expression patterns of genes that duplicated after the divergence of rodents and primates, we confirm that adaptive evolution has been involved in dosage rebalance after gene duplication. To understand mechanisms underlying this process, we examined 1) microRNA (miRNA)-mediated gene regulation, 2) cis-regulatory sequence modifications, and 3) DNA methylation. Neither miRNA-mediated regulation nor cis-regulatory changes was found to be associated with expression reduction of duplicate genes. By contrast, duplicate genes, especially lowly expressed copies, were heavily met... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533379 Thu, 22 Dec 2011 05:00:00 +0100 5533379 http://www.medworm.com/index.php?rid=5533378&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F123%3Frss%3D1 The IT—insulin/target of rapamycin (TOR)—signal transduction pathway is a relatively well-characterized pathway that plays a central role in fundamental biological processes. Network-level analyses of DNA divergence in Drosophila and vertebrates have revealed a clear gradient in the levels of purifying selection along this pathway, with the downstream genes being the most constrained. Remarkably, this feature does not result from factors known to affect selective constraint such as gene expression, codon bias, protein length, and connectivity. The present work aims to establish whether the selective constraint gradient detected along the IT pathway at the between-species level can also be observed at a shorter time scale. With this purpose, we have surveyed DNA polymorphism in ... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533378 Thu, 22 Dec 2011 05:00:00 +0100 5533378 http://www.medworm.com/index.php?rid=5533377&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F113%3Frss%3D1 The apicomplexan parasite Cryptosporidium parvum possesses a mitosome, a relict mitochondrion with a greatly reduced metabolic capability. This mitosome houses a mitochondrial-type protein import apparatus, but elements of the protein import pathway have been reduced, and even lost, through evolution. The small Tim protein family is a case in point. The genomes of C. parvum and related species of Cryptosporidium each encode just one small Tim protein, CpTimS. This observation challenged the tenet that small Tim proteins are always found in pairs as α3β3 hexamers. We show that the atypical CpTimS exists as a relatively unstable homohexamer, shedding light both on the early evolution of the small Tim protein family and on small Tim hexamer formation in contemporary eukaryotes. (So... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533377 Thu, 22 Dec 2011 05:00:00 +0100 5533377 http://www.medworm.com/index.php?rid=5533376&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F101%3Frss%3D1 Inflammatory bowel disease 5 (IBD5) is a 250 kb haplotype on chromosome 5 that is associated with an increased risk of Crohn’s disease in Europeans. The OCTN1 gene is centrally located on IBD5 and encodes a transporter of the antioxidant ergothioneine (ET). The 503F variant of OCTN1 is strongly associated with IBD5 and is a gain-of-function mutation that increases absorption of ET. Although 503F has been implicated as the variant potentially responsible for Crohn’s disease susceptibility at IBD5, there is little evidence beyond statistical association to support its role in disease causation. We hypothesize that 503F is a recent adaptation in Europeans that swept to relatively high frequency and that disease association at IBD5 results not from 503F itself, but from one or more... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533376 Thu, 22 Dec 2011 05:00:00 +0100 5533376 http://www.medworm.com/index.php?rid=5533375&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F91%3Frss%3D1 Animals and fungi diverged from a common unicellular ancestor of Opisthokonta, yet they exhibit significant differences in their components of Ca2+ signaling pathways. Many Ca2+ signaling molecules appear to be either animal-specific or fungal-specific, which is generally believed to result from lineage-specific adaptations to distinct physiological requirements. Here, by analyzing the genomic data from several close relatives of animals and fungi, we demonstrate that many components of animal and fungal Ca2+ signaling machineries are present in the apusozoan protist Thecamonas trahens, which belongs to the putative unicellular sister group to Opisthokonta. We also identify the conserved portion of Ca2+ signaling molecules in early evolution of animals and fungi following their divergence.... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533375 Thu, 22 Dec 2011 05:00:00 +0100 5533375 http://www.medworm.com/index.php?rid=5533374&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F81%3Frss%3D1 This study provides a new angle to understand the role of 5' UTR in gene expression regulation and evolution. (Source: Molecular Biology and Evolution) Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533374 Thu, 22 Dec 2011 05:00:00 +0100 5533374 http://www.medworm.com/index.php?rid=5533373&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F71%3Frss%3D1 A genome must locate its coding genes on the chromosomes in a meaningful manner with the help of natural selection, but the mechanism of gene order evolution is poorly understood. To explore the role of selection in shaping the current order of coding genes and their cis-regulatory elements, a comparative genomic approach was applied to the baker's yeast Saccharomyces cerevisiae and its close relatives. S. cerevisiae have experienced a whole-genome duplication followed by an extensive reorganization process of gene order, during which a number of new adjacent gene pairs appeared. We found that the proportion of new adjacent gene pairs in divergent orientation is significantly reduced, suggesting that such new divergent gene pairs may be disfavored most likely because their coregulation may... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533373 Thu, 22 Dec 2011 05:00:00 +0100 5533373 http://www.medworm.com/index.php?rid=5533372&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F61%3Frss%3D1 Over 3,000 human diseases are known to be linked to heritable genetic variation, mapping to over 1,700 unique genes. Dating of the evolutionary age of these disease-associated genes has suggested that they have a tendency to be ancient, specifically coming into existence with early metazoa. The approach taken by past studies, however, assumes that the age of a disease is the same as the age of its common ancestor, ignoring the fundamental contribution of duplication events in the evolution of new genes and function. Here, we date both the common ancestor and the duplication history of known human disease-associated genes. We find that the majority of disease genes (80%) are genes that have been duplicated in their evolutionary history. Periods for which there are more disease-associated ge... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533372 Thu, 22 Dec 2011 05:00:00 +0100 5533372 http://www.medworm.com/index.php?rid=5533371&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F51%3Frss%3D1 The proteins of the ammonium transporter/methylammonium permease/Rhesus factor family (AMT/MEP/Rh family) are responsible for the movement of ammonia or ammonium ions across the cell membrane. Although it has been established that the Rh proteins are distantly related to the other members of the family, the evolutionary history of the AMT/MEP/Rh family remains unclear. Here, we use phylogenetic analysis to infer the evolutionary history of this family of proteins across 191 genomes representing all main lineages of life and to provide a new classification of the proteins in this family. Our phylogenetic analysis suggests that what has heretofore been conceived of as a protein family with two clades (AMT/MEP and Rh) is instead a protein family with three clades (AMT, MEP, and Rh). We show t... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533371 Thu, 22 Dec 2011 05:00:00 +0100 5533371 http://www.medworm.com/index.php?rid=5533370&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F43%3Frss%3D1 Spliceosomal introns are hallmarks of eukaryotic genomes, dividing coding regions into separate exons, which are joined during mRNA intron removal catalyzed by the spliceosome. With few known exceptions, spliceosomal introns are cis-spliced, that is, removed from one contiguous pre-mRNA transcript. The protistan intestinal parasite Giardia lamblia exhibits one of the most reduced eukaryotic genomes known, with short intergenic regions and only four known spliceosomal introns. Our genome-wide search for additional introns revealed four unusual cases of spliceosomal intron fragmentation, with consecutive exons of conserved protein-coding genes being dispersed to distant genomic sites. Independent transcripts are trans-spliced to yield contiguous mature mRNAs. Most strikingly, a dynein heavy ... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533370 Thu, 22 Dec 2011 05:00:00 +0100 5533370 http://www.medworm.com/index.php?rid=5533369&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F39%3Frss%3D1 Iodamoeba is the last genus of obligately parasitic human protist whose phylogenetic position is unknown. Iodamoeba small subunit ribosomal DNA sequences were obtained using samples from three host species, and phylogenetic analyses convincingly placed Iodamoeba as a sister taxon to Endolimax. This clade in turn branches among free-living amoeboflagellates of the genus Mastigamoeba. Two Iodamoeba ribosomal lineages (RL1 and RL2) were detected whose sequences differ by 31%, each of which is found in both human and nonhuman hosts. (Source: Molecular Biology and Evolution) Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533369 Thu, 22 Dec 2011 05:00:00 +0100 5533369 http://www.medworm.com/index.php?rid=5533368&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F35%3Frss%3D1 Gloeobacter violaceus, the earliest diverging oxyphotobacterium (cyanobacterium) on the 16S ribosomal RNA tree, has five copies of the photosystem II psbA gene encoding the D1 reaction center protein subunit. These copies are widely distributed throughout the 4.6 Mbp genome with only one copy colocalizing with other PSII subunits, in marked contrast to all other psbA genes in all publicly available sequenced genomes. A clustering of two other psb genes around psbA3 (glr2322) is unique to Gloeobacter. We provide experimental proof for the transcription of a psbA3DC operon, encoding three of the five reaction center core subunits (D1, D2, and CP43). This is the first example of a transcribed gene cluster containing the D1/D2 or D1/D2/CP43 subunits of PSII in an oxygenic phototroph (prokaryot... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533368 Thu, 22 Dec 2011 05:00:00 +0100 5533368 http://www.medworm.com/index.php?rid=5533367&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F31%3Frss%3D1 Two recent high-profile studies offered empirical evidence for a "snowballing" accumulation of postzygotic incompatibilities in Drosophila and Solanum (tomatoes). Here we present a reanalysis of the Solanum data that is motivated by population genetic principles. Specifically, the high levels of intraspecific nucleotide polymorphism in wild tomato species and presumably large effective population size throughout the divergence history of this clade imply that ancestral polymorphism should be taken into account when evaluating sequence divergence between species. Based on our reanalyses of synonymous-site divergence between the four focal Solanum species and a wide range of ancestral polymorphism, we assessed under which conditions the reported accumulation of seed sterility factors support... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533367 Thu, 22 Dec 2011 05:00:00 +0100 5533367 http://www.medworm.com/index.php?rid=5533366&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F25%3Frss%3D1 The information left by recombination in our genomes can be used to make inferences on our recent evolutionary history. Specifically, the number of past recombination events in a population sample is a function of its effective population size (Ne). We have applied a method, Identifying Recombination in Sequences (IRiS), to detect specific past recombination events in 30 Old World populations to infer their Ne. We have found that sub-Saharan African populations have an Ne that is approximately four times greater than those of non-African populations and that outside of Africa, South Asian populations had the largest Ne. We also observe that the patterns of recombinational diversity of these populations correlate with distance out of Africa if that distance is measured along a path crossing... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533366 Thu, 22 Dec 2011 05:00:00 +0100 5533366 http://www.medworm.com/index.php?rid=5533365&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F21%3Frss%3D1 Understanding the function of noncoding regions in the genome, such as introns, is of central importance to evolutionary biology. One approach is to assay for the targets of natural selection. On one hand, the sequence of introns, especially short introns, appears to evolve in an almost neutral manner. Whereas on the other hand, a large proportion of intronic sequence is under selective constraint. This discrepancy is largely dependent on intron length and differences in the methods used to infer selection. We have used a method based on DNA strand asymmetery that does not require comparison with any putatively neutrally evolving sequence, nor sequence conservation between species, to detect selection within introns. The strongest signal we identify is associated with short introns. This s... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533365 Thu, 22 Dec 2011 05:00:00 +0100 5533365 http://www.medworm.com/index.php?rid=5533364&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F17%3Frss%3D1 Despite being silent with respect to protein sequence, synonymous nucleotide substitutions can be targeted by natural selection directly at the DNA or RNA level. However, there has been no systematic assessment of how frequent this type of selection is. Here, we have constructed 53 single random synonymous substitution mutants of the bacteriophages Qβ and X174 by site-directed mutagenesis and assayed their fitness. Analysis of this mutant collection and of previous studies undertaken with a variety of single-stranded (ss) viruses demonstrates that selection at synonymous sites is stronger in RNA viruses than in DNA viruses. We estimate that this type of selection contributes approximately 18% of the overall mutational fitness effects in ssRNA viruses under our assay conditions and tha... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533364 Thu, 22 Dec 2011 05:00:00 +0100 5533364 http://www.medworm.com/index.php?rid=5533363&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F13%3Frss%3D1 Whether higher-order chromatin organization is related to genome stability over evolutionary time remains elusive. We find that regions of conserved gene order across the genus Drosophila are larger if they harbor genes bound by B-type lamin (Lam) and Suppressor of Under-Replication (SUUR), two proteins located at the nuclear periphery. Low recombination rates and coexpression of genes in regions of conserved gene order do not explain the lower probability of disruption in these regions by genome rearrangements. Instead, we find a significant colocalization between evolutionarily stable genomic regions associated with Lam and sequences thought to regulate local gene expression, which have the potential to impose constraints on genome rearrangement. At least in the genus Drosophila, localiz... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533363 Thu, 22 Dec 2011 05:00:00 +0100 5533363 http://www.medworm.com/index.php?rid=5533362&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F7%3Frss%3D1 Concerted evolution leading to homogenization of tandemly repeated DNA arrays is widespread and important for genome evolution. We investigated the range and nature of the process at chromosomal and array levels using the 1.688 tandem repeats of Drosophila melanogaster where large arrays are present in the heterochromatin of chromosomes 2, 3, and X, and short arrays are found in the euchromatin of the same chromosomes. Analysis of 326 euchromatic and heterochromatic repeats from 52 arrays showed that the homogenization of 1.688 repeats occurred differentially for distinct genomic regions, from euchromatin to heterochromatin and from local arrays to chromosomes. We further found that most euchromatic arrays are either close to, or are within introns of, genes. The short size of euchromatic ... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533362 Thu, 22 Dec 2011 05:00:00 +0100 5533362 http://www.medworm.com/index.php?rid=5533361&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2F1%3Frss%3D1 Errors in the inferred multiple sequence alignment may lead to false prediction of positive selection. Recently, methods for detecting unreliable alignment regions were developed and were shown to accurately identify incorrectly aligned regions. While removing unreliable alignment regions is expected to increase the accuracy of positive selection inference, such filtering may also significantly decrease the power of the test, as positively selected regions are fast evolving, and those same regions are often those that are difficult to align. Here, we used realistic simulations that mimic sequence evolution of HIV-1 genes to test the hypothesis that the performance of positive selection inference using codon models can be improved by removing unreliable alignment regions. Our study shows th... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533361 Thu, 22 Dec 2011 05:00:00 +0100 5533361 http://www.medworm.com/index.php?rid=5533360&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2FNP-b%3Frss%3D1 (Source: Molecular Biology and Evolution) Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533360 Thu, 22 Dec 2011 05:00:00 +0100 5533360 http://www.medworm.com/index.php?rid=5533359&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2FNP-a%3Frss%3D1 (Source: Molecular Biology and Evolution) Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533359 Thu, 22 Dec 2011 05:00:00 +0100 5533359 http://www.medworm.com/index.php?rid=5533358&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F29%2F1%2FNP%3Frss%3D1 (Source: Molecular Biology and Evolution) Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5533358 Thu, 22 Dec 2011 05:00:00 +0100 5533358 http://www.medworm.com/index.php?rid=5417604&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F12%2F3405%3Frss%3D1 (Source: Molecular Biology and Evolution) Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5417604 Mon, 14 Nov 2011 05:00:00 +0100 5417604 http://www.medworm.com/index.php?rid=5417603&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F12%2F3395%3Frss%3D1 Many socially important fungi encode an elevated number of subtilisin-like serine proteases, which have been shown to be involved in fungal mutualisms with grasses and in parasitism of insects, nematodes, plants, other fungi, and mammalian skin. These proteins have endopeptidase activities and constitute a significant part of fungal secretomes. Here, we use comparative genomics to investigate the relationship between the quality and quantity of serine proteases and the ability of fungi to cause disease in invertebrate and vertebrate animals. Our screen of previously unexamined fungi allowed us to annotate and identify nearly 1000 subtilisin-containing proteins and to describe six new categories of serine proteases. Architectures of predicted proteases reveal novel combinations of subtilisi... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5417603 Mon, 14 Nov 2011 05:00:00 +0100 5417603 http://www.medworm.com/index.php?rid=5417602&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F12%2F3381%3Frss%3D1 This study constitutes the most comprehensive analysis to date of the biochemical and molecular causes of naturally occurring genetic variation in enzyme activity that covaries strongly with life history. (Source: Molecular Biology and Evolution) Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5417602 Mon, 14 Nov 2011 05:00:00 +0100 5417602 http://www.medworm.com/index.php?rid=5417601&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F12%2F3367%3Frss%3D1 Although many models have been proposed that could lead to the maintenance of gene duplicates, the ways in which interacting gene duplicates influence each other’s evolution and function remain poorly understood. Here, we focus on duplication and loss of the B class MADS box transcription factor genes in the euasterids I and the ramifications of such changes on paralog evolution and their encoded functions. In core eudicots, the B class genes belong to two paralogous lineages whose products form obligate heterodimers. Based on comparative genomic and phylogenetic analyses, we show that five stepwise B class MADS box gene gain or loss events occurred during the radiation of the euasterids I within core eudicots. Gene loss in one sublineage was correlated with a deficit of other sublin... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5417601 Mon, 14 Nov 2011 05:00:00 +0100 5417601 http://www.medworm.com/index.php?rid=5417600&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F12%2F3355%3Frss%3D1 Statistical methods for molecular dating of viral origins have been used extensively to infer the time of most common recent ancestor for many rapidly evolving pathogens. However, there are a number of cases, in which epidemiological, historical, or genomic evidence suggests much older viral origins than those obtained via molecular dating. We demonstrate how pervasive purifying selection can mask the ancient origins of recently sampled pathogens, in part due to the inability of nucleotide-based substitution models to properly account for complex patterns of spatial and temporal variability in selective pressures. We use codon-based substitution models to infer the length of branches in viral phylogenies; these models produce estimates that are often considerably longer than those obtained... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5417600 Mon, 14 Nov 2011 05:00:00 +0100 5417600 http://www.medworm.com/index.php?rid=5417599&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F12%2F3345%3Frss%3D1 The functional and evolutionary significance of DNA methylation in insect genomes remains to be resolved. Nasonia is well situated for comparative analyses of DNA methylation and genome evolution, since the genomes of a moderately distant outgroup species as well as closely related sibling species are available. Using direct sequencing of bisulfite-converted DNA, we uncovered a substantial level of DNA methylation in 17 of 18 Nasonia vitripennis genes and a strong correlation between methylation level and CpG depletion. Notably, in the sex-determining locus transformer, the exon that is alternatively spliced between the sexes is heavily methylated in both males and females, whereas other exons are only sparsely methylated. Orthologous genes of the honeybee and Nasonia show highly similar r... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5417599 Mon, 14 Nov 2011 05:00:00 +0100 5417599 http://www.medworm.com/index.php?rid=5417598&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F12%2F3331%3Frss%3D1 Evolution of new cellular functions can be achieved both by changes in protein coding sequences and by alteration of expression patterns. Variation of expression may lead to changes in cellular function with relatively little change in genomic sequence. We therefore hypothesize that one of the first signals of functional divergence should be evolution of transcription factor–binding sites (TFBSs). This adaptation should be detectable as substantial variation in the TFBSs of alleles. New data sets allow the first analyses of intraspecies variation from large number of whole-genome sequences. Using data from the Saccharomyces Genome Resequencing Project, we have analyzed variation in TFBSs. We find a large degree of variation both between these closely related strains and between pairs... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5417598 Mon, 14 Nov 2011 05:00:00 +0100 5417598 http://www.medworm.com/index.php?rid=5417597&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F12%2F3319%3Frss%3D1 The human RAC2 gene encodes a small GTP-binding protein with a pivotal role in immune activation and in the induction of peripheral immune tolerance through restimulation-induced cell death (RICD). Different human pathogens target the protein product of RAC2, suggesting that the gene may be subject to natural selection, and that variants in RAC2 may affect immunological phenotypes in humans. We scanned the genomic region encompassing the entire transcription unit for the presence of putative noncoding regulatory elements conserved across mammals. This information was used to select two RAC2 gene regions and analyze their intraspecific genetic diversity. Results suggest that a region covering the 3' untranslated region has been a target of multiallelic balancing selection (or diversifying s... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5417597 Mon, 14 Nov 2011 05:00:00 +0100 5417597 http://www.medworm.com/index.php?rid=5417596&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F12%2F3309%3Frss%3D1 Bacterial genes are commonly encoded in clusters, known as operons, which share transcriptional regulatory control and often encode functionally related proteins that take part in certain biological pathways. Operons that are coregulated are known to colocalize in the genome, suggesting that their spatial organization is under selection for efficient expression regulation. However, the internal order of genes within operons is believed to be poorly conserved, and hence expression requirements are claimed to be too weak to oppose gene rearrangements. In light of these opposing views, we set out to investigate whether the internal location of the regulatory genes within operons is under selection. Our analysis shows that transcription factors (TFs) are preferentially encoded as either first ... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5417596 Mon, 14 Nov 2011 05:00:00 +0100 5417596 http://www.medworm.com/index.php?rid=5417595&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F12%2F3297%3Frss%3D1 The selective forces acting on a protein-coding gene are commonly inferred using evolutionary codon models by contrasting the rate of nonsynonymous substitutions to the rate of synonymous substitutions. These models usually assume that the synonymous substitution rate, Ks, is homogenous across all sites, which is justified if synonymous sites are free from selection. However, a growing body of evidence indicates that the DNA and RNA levels of protein-coding genes are subject to varying degrees of selective constraints due to various biological functions encoded at these levels. In this paper, we develop evolutionary models that account for these layers of selection by allowing for both among-site variability of substitution rates at the DNA/RNA level (which leads to Ks variability among pr... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5417595 Mon, 14 Nov 2011 05:00:00 +0100 5417595 http://www.medworm.com/index.php?rid=5417594&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F12%2F3285%3Frss%3D1 The initiation of the intracellular symbiosis that would give rise to mitochondria and eukaryotes was a major event in the history of life on earth. Hypotheses to explain eukaryogenesis fall into two broad and competing categories: those proposing that the host was a phagocytotic proto-eukaryote that preyed upon the free-living mitochondrial ancestor (hereafter FMA), and those proposing that the host was an archaebacterium that engaged in syntrophy with the FMA. Of key importance to these hypotheses are whether the FMA was motile or nonmotile, and the atmospheric conditions under which the FMA thrived. Reconstructions of the FMA based on genome content of Rickettsiales representatives—generally considered to be the closest living relatives of mitochondria—indicate that it was n... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5417594 Mon, 14 Nov 2011 05:00:00 +0100 5417594 http://www.medworm.com/index.php?rid=5417593&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F12%2F3271%3Frss%3D1 Insertions or deletions (indels) of amino acids residues have been recognized as an important source of genetic and structural divergence between paralogous Bcl-2 family members. However, these signature sequences have not so far been extensively investigated amongst orthologous Bcl-2 family proteins. Bcl2l10 is an antiapoptotic member of the Bcl-2 family that has evolved rapidly throughout the vertebrate lineage and which shows conserved abundant expression in eggs and oocytes. In this paper, we have unraveled two major sites of divergence between human Bcl2l10 and its vertebrate homologs. The first one provides length variation at the N-terminus (before the BH4 domain) and the second one is located between the predicted α5–α6 pore-forming helices, providing an unprecede... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5417593 Mon, 14 Nov 2011 05:00:00 +0100 5417593 http://www.medworm.com/index.php?rid=5417592&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F12%2F3253%3Frss%3D1 In this study, we obtained the genome sequences of Simkania negevensis Z, Waddlia chondrophila 2032/99, and Parachlamydia acanthamoebae UV-7. This enabled us to perform the first comprehensive comparative and phylogenomic analysis of representative members of four major families of the Chlamydiae, including the Chlamydiaceae. We identified a surprisingly large core gene set present in all genomes and a high number of diverse accessory genes in those Chlamydiae that do not primarily infect humans or animals, including a chemosensory system in P. acanthamoebae and a type IV secretion system. In S. negevensis, the type IV secretion system is encoded on a large conjugative plasmid (pSn, 132 kb). Phylogenetic analyses suggested that a plasmid similar to the S. negevensis plasmid was originally ... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5417592 Mon, 14 Nov 2011 05:00:00 +0100 5417592 http://www.medworm.com/index.php?rid=5417591&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F12%2F3237%3Frss%3D1 In recent years, the increasing availability of genomic resources has provided an opportunity to develop phylogenetic markers for phylogenomics. Efficient methods to search for candidate markers from the huge number of genes within genomic data are particularly needed in the era of phylogenomics. Here, rather than using the traditional approach of comparing genomes of two distantly related taxa to develop conserved primers, we take advantage of the multiple genome alignment resources from the the University of California–San Cruz Genome Browser and present a simple and straightforward bioinformatic approach to automatically screen for candidate nuclear protein–coding locus (NPCL) markers. We tested our protocol in tetrapods and successfully obtained 21 new NPCL markers with hig... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5417591 Mon, 14 Nov 2011 05:00:00 +0100 5417591 http://www.medworm.com/index.php?rid=5417590&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F12%2F3225%3Frss%3D1 The Asteraceae (Compositae) is a large family of over 20,000 wild, weedy, and domesticated species that comprise approximately 10% of all angiosperms, including annual and perennial herbs, shrubs and trees, and species on every continent except Antarctica. As a result, the Asteraceae provide a unique opportunity to understand the evolutionary genomics of lineage radiation and diversification at numerous phylogenetic scales. Using publicly available expressed sequence tags from 22 species representing four of the major Asteraceae lineages, we assessed neutral and nonneutral evolutionary processes across this diverse plant family. We used bioinformatic tools to identify candidate genes under selection in each species. Evolution at silent and coding sites were assessed for different Gene Onto... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5417590 Mon, 14 Nov 2011 05:00:00 +0100 5417590 http://www.medworm.com/index.php?rid=5417589&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F12%2FNP-b%3Frss%3D1 (Source: Molecular Biology and Evolution) Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5417589 Mon, 14 Nov 2011 05:00:00 +0100 5417589 http://www.medworm.com/index.php?rid=5417588&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F12%2FNP-a%3Frss%3D1 (Source: Molecular Biology and Evolution) Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5417588 Mon, 14 Nov 2011 05:00:00 +0100 5417588 http://www.medworm.com/index.php?rid=5417587&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F12%2FNP%3Frss%3D1 (Source: Molecular Biology and Evolution) Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5417587 Mon, 14 Nov 2011 05:00:00 +0100 5417587 http://www.medworm.com/index.php?rid=5355386&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F11%2F3213%3Frss%3D1 We described 13 chimeric genes resulting from gene recombination with sympatric R. typhi. The transferred DNA sequences present different sizes and functions, suggesting that the horizontal transfer in R. felis is random and neutral within its specific host. Our study shows that the strict intracellular bacteria R. felis exhibits a mosaic genome. We therefore developed a new representation for the evolutionary history of R. felis showing its different putative ancestors in the form of a rhizome. (Source: Molecular Biology and Evolution) Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5355386 Sun, 23 Oct 2011 04:00:00 +0100 5355386 http://www.medworm.com/index.php?rid=5355385&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F11%2F3195%3Frss%3D1 Bacterial genome annotations contain a number of coding sequences (CDSs) that, in spite of reading frame disruptions, encode a single continuous polypeptide. Such disruptions have different origins: sequencing errors, frameshift, or stop codon mutations, as well as instances of utilization of nontriplet decoding. We have extracted over 1,000 CDSs with annotated disruptions and found that about 75% of them can be clustered into 64 groups based on sequence similarity. Analysis of the clusters revealed deep phylogenetic conservation of open reading frame organization as well as the presence of conserved sequence patterns that indicate likely utilization of the nonstandard decoding mechanisms: programmed ribosomal frameshifting (PRF) and programmed transcriptional realignment (PTR). Further en... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5355385 Sun, 23 Oct 2011 04:00:00 +0100 5355385 http://www.medworm.com/index.php?rid=5355384&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F11%2F3183%3Frss%3D1 We present evidence that links specific molecular changes in secretion mediating proteins of microbes to their ecological adaptations. (Source: Molecular Biology and Evolution) Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5355384 Sun, 23 Oct 2011 04:00:00 +0100 5355384 http://www.medworm.com/index.php?rid=5355383&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F11%2F3171%3Frss%3D1 The serial coalescent extends traditional coalescent theory to include genealogies in which not all individuals were sampled at the same time. Inference in this framework is powerful because population size and evolutionary rate may be estimated independently. However, when the sequences in question are affected by selection acting at many sites, the genealogies may differ significantly from their neutral expectation, and inference of demographic parameters may become inaccurate. I demonstrate that this inaccuracy is severe when the mutation rate and strength of selection are jointly large, and I develop a new likelihood calculation that, while approximate, improves the accuracy of population size estimates. When used in a Bayesian parameter estimation context, the new calculation allows f... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5355383 Sun, 23 Oct 2011 04:00:00 +0100 5355383 http://www.medworm.com/index.php?rid=5355382&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F11%2F3151%3Frss%3D1 The preovulatory hydration of teleost oocytes is a unique process among vertebrates. The hydration mechanism is most pronounced in marine acanthomorph teleosts that spawn pelagic (floating) eggs; however, the molecular pathway for water influx remains poorly understood. Recently, we revealed that whole-genome duplication (WGD) resulted in teleosts harboring the largest repertoire of molecular water channels in the vertebrate lineage and that a duplicated aquaporin-1 paralog is implicated in the oocyte hydration process. However, the origin and function of the aquaporin-1 paralogs remain equivocal. By integrating the molecular phylogeny with synteny and structural analyses, we show here that the teleost aqp1aa and -1ab paralogs (previously annotated as aqp1a and -1b, respectively) arose by ... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5355382 Sun, 23 Oct 2011 04:00:00 +0100 5355382 http://www.medworm.com/index.php?rid=5355381&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F11%2F3139%3Frss%3D1 Whole genome duplication (WGD) and subsequent evolution of gene pairs have been shown to have shaped the present day genomes of most, if not all, plants and to have played an essential role in the evolution of many eukaryotic genomes. Analysis of the rice (Oryza sativa ssp. japonica) genome sequence suggested an ancestral WGD ~50–70 Ma common to all cereals and a segmental duplication between chromosomes 11 and 12 as recently as 5 Ma. More recent studies based on coding sequences have demonstrated that gene conversion is responsible for the high sequence conservation which suggested such a recent duplication. We previously showed that gene conversion has been a recurrent process throughout the Oryza genus and in closely related species and that orthologous duplicated regions are also... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5355381 Sun, 23 Oct 2011 04:00:00 +0100 5355381 http://www.medworm.com/index.php?rid=5355380&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F11%2F3127%3Frss%3D1 There is a recent emergence of interest in the genes involved in gametic recognition as drivers of reproductive isolation. The recent population genomic sequencing of two species of sexually primitive yeasts (Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V et al. [23 co-authors]. 2009. Population genomics of domestic and wild yeasts. Nature 458:337–341.) has provided data for systematic study of the roles these genes play in the early evolution of sex and speciation. Here, we discovered that among genes encoding cell surface proteins, the sexual adhesin genes have evolved significantly more rapidly than others, both within and between Saccharomyces cerevisiae and its closest relative S. paradoxus. This result was supported by an... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5355380 Sun, 23 Oct 2011 04:00:00 +0100 5355380 http://www.medworm.com/index.php?rid=5355379&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F11%2F3113%3Frss%3D1 In insects, some of the most ecologically important symbioses are nutritional symbioses that provide hosts with novel traits and thereby facilitate exploitation of otherwise inaccessible niches. One such symbiosis is the ancient obligate intracellular symbiosis of aphids with the -proteobacteria, Buchnera aphidicola. Although the nutritional basis of the aphid/Buchnera symbiosis is well understood, the processes and structures that mediate the intimate interactions of symbiotic partners remain uncharacterized. Here, using a de novo approach, we characterize the complement of 40 amino acid polyamine organocation (APC) superfamily member amino acid transporters (AATs) encoded in the genome of the pea aphid, Acyrthosiphon pisum. We find that the A. pisum APC superfamily is characterized by ex... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5355379 Sun, 23 Oct 2011 04:00:00 +0100 5355379 http://www.medworm.com/index.php?rid=5355378&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F11%2F3099%3Frss%3D1 Major histocompatibility complex (MHC) class I molecules play a pivotal role in immune defense system, presenting the antigen peptides to cytotoxic CD8+ T lymphocytes. Most vertebrates possess multiple MHC class I loci, but the analysis of their evolutionary relationships between distantly related species has difficulties because genetic events such as gene duplication, deletion, recombination, and/or conversion have occurred frequently in these genes. Human MHC class I genes have been conserved only within the primates for up to 46–66 My. Here, we performed comprehensive analysis of the MHC class I genes of the medaka fish, Oryzias latipes, and found that they could be classified into four groups of ancient origin. In phylogenetic analysis using these genes and the classical and non... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5355378 Sun, 23 Oct 2011 04:00:00 +0100 5355378 http://www.medworm.com/index.php?rid=5355377&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F11%2F3087%3Frss%3D1 Natural selection is expected to act strongly on immune system genes as hosts adapt to novel, diverse, and coevolving pathogens. Population genetic studies of host defense genes with parallel functions in model organisms have revealed distinct evolutionary histories among the different components—receptors, adaptors, and effectors—of the innate immune system. In humans, however, detailed evolutionary studies have been mainly confined to the receptors and in particular to Toll-like receptors (TLRs). By virtue of a toll/interleukin-1 receptor (TIR) domain, TLRs activate distinct signaling pathways, which are mediated by the five TIR-containing adaptors: myeloid differentiation factor-88 (MyD88), myeloid differentiation factor-88 adaptor-like protein (MAL), toll/interleukin-1 rece... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5355377 Sun, 23 Oct 2011 04:00:00 +0100 5355377 http://www.medworm.com/index.php?rid=5355376&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F11%2F3069%3Frss%3D1 We report several lines of evidence for balancing selection acting on the regulatory regions, which may indicate that these HLA-G lineages may be related to the differential HLA-G expression profiles. (Source: Molecular Biology and Evolution) Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5355376 Sun, 23 Oct 2011 04:00:00 +0100 5355376 http://www.medworm.com/index.php?rid=5355375&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F11%2F3061%3Frss%3D1 Piwi-interacting RNAs (piRNAs) are a recently discovered class of 24- to 30-nt noncoding RNAs whose best-understood function is to repress transposable elements (TEs) in animal germ lines. In humans, TE-derived sequences comprise ~45% of the genome and there are several active TE families, including LINE-1 and Alu elements, which are a significant source of de novo mutations and intrapopulation variability. In the "ping-pong model," piRNAs are thought to alternatively cleave sense and antisense TE transcripts in a positive feedback loop. Because piRNAs are poorly conserved between closely related species, including human and chimpanzee, we took a population genomics approach to study piRNA function and evolution. We found strong statistical evidence that piRNA sequences are under selective... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5355375 Sun, 23 Oct 2011 04:00:00 +0100 5355375 http://www.medworm.com/index.php?rid=5355374&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F11%2F3045%3Frss%3D1 We present a novel heuristic that evaluates a small fraction of these complex models and identifies the optimal model. (Source: Molecular Biology and Evolution) Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5355374 Sun, 23 Oct 2011 04:00:00 +0100 5355374 http://www.medworm.com/index.php?rid=5355373&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F11%2F3033%3Frss%3D1 Adaptive evolution frequently occurs in episodic bursts, localized to a few sites in a gene, and to a small number of lineages in a phylogenetic tree. A popular class of "branch-site" evolutionary models provides a statistical framework to search for evidence of such episodic selection. For computational tractability, current branch-site models unrealistically assume that all branches in the tree can be partitioned a priori into two rigid classes—"foreground" branches that are allowed to undergo diversifying selective bursts and "background" branches that are negatively selected or neutral. We demonstrate that this assumption leads to unacceptably high rates of false positives or false negatives when the evolutionary process along background branches strongly deviates from modeling a... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5355373 Sun, 23 Oct 2011 04:00:00 +0100 5355373 http://www.medworm.com/index.php?rid=5355372&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F11%2F3019%3Frss%3D1 The emergence of photosynthetic eukaryotes has played a crucial role in evolution and has strongly modified earth's ecology. Several phylogenetic analyses have established that primary plastids arose from a cyanobacterium through endosymbiosis. However, the question of which present-day cyanobacterial lineage is most closely related to primary plastids has been unclear. Here, we have performed an extensive phylogenomic investigation on the origin of primary plastids based on the analysis of up to 191 protein markers and over 30,000 aligned amino acid sites from 22 primary photosynthetic eukaryotes and 61 cyanobacteria representing a wide taxonomic sampling of this phylum. By using a number of solutions to circumvent a large range of systematic errors, we have reconstructed a robust global ... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5355372 Sun, 23 Oct 2011 04:00:00 +0100 5355372 http://www.medworm.com/index.php?rid=5355371&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F11%2F3009%3Frss%3D1 Most plant phylogenetic inference has used DNA sequence data from the plastid genome. This genome represents a single genealogical sample with no recombination among genes, potentially limiting the resolution of evolutionary relationships in some contexts. In contrast, nuclear DNA is inherently more difficult to employ for phylogeny reconstruction because major mutational events in the genome, including polyploidization, gene duplication, and gene extinction can result in homologous gene copies that are difficult to identify as orthologs or paralogs. Gene tree parsimony (GTP) can be used to infer the rooted species tree by fitting gene genealogies to species trees while simultaneously minimizing the estimated number of duplications needed to reconcile conflicts among them. Here, we use GTP... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5355371 Sun, 23 Oct 2011 04:00:00 +0100 5355371 http://www.medworm.com/index.php?rid=5355370&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F11%2F3005%3Frss%3D1 The cis-regulatory element contributed to gaining humanness is of great interest in human evolutionary studies. A human-accelerated region exceeding neutral evolutionary rates, termed HACNS1, was recently reported as a positively selected sequence acquiring novel TF-binding sites responsible for human-specific gain of limb enhancer function. However, another possibility is loss of function in repressor element in HACNS1. Signature of the human substitutions in the 81-bp region infers that a GC-biased gene conversion (BGC) might create these seemingly excessive substitutions. To evaluate the 81-bp function, we performed transgenic mouse assay of the HACNS1 construct lacking the 81-bp region. The deleted construct showed similar enhancer activity to the intact human HACNS1, suggesting that t... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5355370 Sun, 23 Oct 2011 04:00:00 +0100 5355370 http://www.medworm.com/index.php?rid=5355369&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F11%2F2999%3Frss%3D1 In this study, we have performed a survey of the 5' flanking region of the B4galnt2 gene in several Mus musculus subspecies and Mus spretus. Our results reveal a clear pattern of trans-species polymorphism and indicate that allele classes conferring alternative tissue-specific expression patterns have been maintained for >2.8 My in the genus Mus. Furthermore, analysis of B4galnt2 expression patterns revealed the presence of an additional functional class of alleles, supporting a role for gastrointestinal phenotypes in the long-term maintenance of expression variation at this gene. (Source: Molecular Biology and Evolution) Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5355369 Sun, 23 Oct 2011 04:00:00 +0100 5355369 http://www.medworm.com/index.php?rid=5355368&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F11%2F2993%3Frss%3D1 The vast majority of extant birds possess highly differentiated Z and W sex chromosomes. Nucleotide sequence data from gametologs (homologs on opposite sex chromosomes) suggest that this divergence occurred throughout early bird evolution via stepwise cessation of recombination between identical sex chromosomal regions. Here, we investigated avian sex chromosome differentiation from a novel perspective, using retroposon insertions and random insertions/deletions for the reconstruction of gametologous gene trees. Our data confirm that the CHD1Z/CHD1W genes differentiated in the ancestor of the neognaths, whereas the NIPBLZ/NIPBLW genes diverged in the neoavian ancestor and independently within Galloanserae. The divergence of the ATP5A1Z/ATP5A1W genes in galloanserans occurred independently ... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5355368 Sun, 23 Oct 2011 04:00:00 +0100 5355368 http://www.medworm.com/index.php?rid=5355367&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F11%2F2987%3Frss%3D1 Phylogenomic analyses have revealed several important metazoan clades, such as the Ecdysozoa and the Lophotrochozoa. However, the phylogenetic positions of a few taxa, such as ctenophores, chaetognaths, acoelomorphs, and Xenoturbella, remain contentious. Thus, the findings of qualitative markers or "rare genomic changes" seem ideal to independently test previous phylogenetic hypotheses. We here describe a rare genomic change, the presence of the gene UDP-GlcNAc 2-epimerase/N-acetylmannosamine kinase (GNE). We show that GNE is encoded in the genomes of deuterostomes, acoelomorphs and Xenoturbella, whereas it is absent in protostomes and nonbilaterians. Moreover, the GNE has a complex evolutionary origin involving unique lateral gene transfer events and/or extensive hidden paralogy for each ... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5355367 Sun, 23 Oct 2011 04:00:00 +0100 5355367 http://www.medworm.com/index.php?rid=5355366&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F11%2F2983%3Frss%3D1 In the telomeres of the silkworm Bombyx mori, telomeric repeat–specific non-long terminal repeat (LTR) retrotransposon SARTBm1 is accumulated in the TTAGG telomeric repeats. Here, we identify novel telomeric repeat–specific non-LTR retrotransposons, SARTTc family, from the red flour beetle Tribolium castaneum in the unconventional TCAGG telomeric repeats. To compare the sequence specificity of SARTBm1 and SARTTc1, we developed a comparable ex vivo retrotransposition assay. Both SARTBm1 and SARTTc1 preferred the telomeric sequence of their hosts, suggesting that the target specificity of these retrotransposons coevolved with their host’s telomeric repeats. Swapping experiment indicated that the endonuclease domain is involved in recognizing the target sequence. Moreover, S... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5355366 Sun, 23 Oct 2011 04:00:00 +0100 5355366 http://www.medworm.com/index.php?rid=5355365&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F11%2F2973%3Frss%3D1 In contrast to the conventional use of genes to determine the evolution of phenotypes, we have functionally integrated epithelial–mesenchymal interactions that have facilitated lung phylogeny and ontogeny in response to major geologic epochs. As such, this model reveals the underlying principles of lung physiology based on the evolutionary interactions between internal and external selection pressures, providing a novel understanding of lung biology. As a result, it predicts how cell–molecular changes in this process can cause disease and offers counterintuitive insights to diagnosis and treatment based on evolutionary principles. (Source: Molecular Biology and Evolution) Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5355365 Sun, 23 Oct 2011 04:00:00 +0100 5355365 http://www.medworm.com/index.php?rid=5355364&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F11%2FNP-b%3Frss%3D1 (Source: Molecular Biology and Evolution) Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5355364 Sun, 23 Oct 2011 04:00:00 +0100 5355364 http://www.medworm.com/index.php?rid=5355363&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F11%2FNP-a%3Frss%3D1 (Source: Molecular Biology and Evolution) Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5355363 Sun, 23 Oct 2011 04:00:00 +0100 5355363 http://www.medworm.com/index.php?rid=5355362&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F11%2FNP%3Frss%3D1 (Source: Molecular Biology and Evolution) Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5355362 Sun, 23 Oct 2011 04:00:00 +0100 5355362 http://www.medworm.com/index.php?rid=5246317&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F10%2F2961%3Frss%3D1 The origin of metazoans required the evolution of mechanisms for maintaining differentiated cell types within a multicellular individual, in part through spatially differentiated patterns of gene transcription. The unicellular ancestor of metazoans was presumably capable of regulating gene expression temporally in response to changing environmental conditions, and spatial cell differentiation in metazoans may represent a co-option of preexisting regulatory mechanisms. Myc is a critical regulator of cell growth, proliferation, and death that is found in all metazoans but absent in other multicellular lineages, including fungi and plants. Homologs of Myc and its binding partner, Max, exist in two of the closest living relatives of animals, the choanoflagellate Monosiga brevicollis (Mb) and C... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5246317 Tue, 20 Sep 2011 04:00:00 +0100 5246317 http://www.medworm.com/index.php?rid=5246316&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F10%2F2949%3Frss%3D1 In conclusion, we demonstrate the value of detailed comparative annotation in generating a comprehensive set of AS transcripts, increasing our understanding of AS evolution in vertebrates. Our data supports a model whereby the acquisition of functional AS has occurred throughout vertebrate evolution and is considered alongside amino acid change as a key mechanism in gene evolution. (Source: Molecular Biology and Evolution) Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5246316 Tue, 20 Sep 2011 04:00:00 +0100 5246316 http://www.medworm.com/index.php?rid=5246315&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F10%2F2935%3Frss%3D1 Pentatricopeptide repeat (PPR) proteins are the largest known RNA-binding protein family, and are found in all eukaryotes, being particularly abundant in higher plants. PPR proteins localize mostly to mitochondria and chloroplasts, and many were shown to modulate organellar genome expression on the posttranscriptional level. Although the genomes of land plants encode hundreds of PPR proteins, only a few have been identified in Fungi and Metazoa. As the current PPR motif profiles are built mainly on the basis of the predominant plant sequences, they are unlikely to be optimal for detecting fungal and animal members of the family, and many putative PPR proteins in these genomes may remain undetected. In order to verify this hypothesis, we designed a hidden Markov model-based bioinformatic to... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5246315 Tue, 20 Sep 2011 04:00:00 +0100 5246315 http://www.medworm.com/index.php?rid=5246314&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F10%2F2921%3Frss%3D1 Vitamin B12 (cobalamin) is a dietary requirement for humans because it is an essential cofactor for two enzymes, methylmalonyl-CoA mutase and methionine synthase (METH). Land plants and fungi neither synthesize or require cobalamin because they do not contain methylmalonyl-CoA mutase, and have an alternative B12-independent methionine synthase (METE). Within the algal kingdom, approximately half of all microalgal species need the vitamin as a growth supplement, but there is no phylogenetic relationship between these species, suggesting that the auxotrophy arose multiple times through evolution. We set out to determine the underlying cellular mechanisms for this observation by investigating elements of B12 metabolism in the sequenced genomes of 15 different algal species, with representativ... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5246314 Tue, 20 Sep 2011 04:00:00 +0100 5246314 http://www.medworm.com/index.php?rid=5246313&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F10%2F2905%3Frss%3D1 We analyzed 40 single nucleotide polymorphism and 19 short tandem repeat Y-chromosomal markers in a large sample of 1,525 indigenous individuals from 14 populations in the Caucasus and 254 additional individuals representing potential source populations. We also employed a lexicostatistical approach to reconstruct the history of the languages of the North Caucasian family spoken by the Caucasus populations. We found a different major haplogroup to be prevalent in each of four sets of populations that occupy distinct geographic regions and belong to different linguistic branches. The haplogroup frequencies correlated with geography and, even more strongly, with language. Within haplogroups, a number of haplotype clusters were shown to be specific to individual populations and languages. The... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5246313 Tue, 20 Sep 2011 04:00:00 +0100 5246313 http://www.medworm.com/index.php?rid=5246312&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F10%2F2893%3Frss%3D1 TATA box, the core promoter element, exists in a broad range of eukaryotes, and the expression of TATA-containing genes usually responds to various environmental stresses. Hence, the evolution of TATA-box in duplicate genes may provide some clues for the interrelationship among environmental stress, expression differentiation, and duplicate gene preservation. In the present study, we observed that the TATA box is significantly overrepresented in duplicate genes compared with singletons in human, worm, Arabidopsis, and yeast genomes. We then conducted an extensive functional genomic analysis to investigate the evolution of TATA box along over 700 yeast gene family phylogenies. After reconstructing the ancestral TATA-box states (presence or absence), we found that significantly higher number... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5246312 Tue, 20 Sep 2011 04:00:00 +0100 5246312 http://www.medworm.com/index.php?rid=5246311&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F10%2F2883%3Frss%3D1 Concerted evolution describes the unusual evolutionary pattern exhibited by certain repetitive sequences, whereby all the repeats are maintained in the genome with very similar sequences but differ between related species. The pattern of concerted evolution is thought to result from continual turnover of repeats by recombination, a process known as homogenization. Approaches to studying concerted evolution have largely been observational because of difficulties investigating repeat evolution in an experimental setting with large arrays of identical repeats. Here, we establish an experimental evolution approach to look at the rate and dynamics of concerted evolution in the ribosomal DNA (rDNA) repeats. A small targeted mutation was made in the spacer of a single rDNA unit in Saccharomyces c... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5246311 Tue, 20 Sep 2011 04:00:00 +0100 5246311 http://www.medworm.com/index.php?rid=5246310&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F10%2F2873%3Frss%3D1 Mitochondrial genomes of onychophorans (velvet worms) present an interesting problem: Some previous studies reported them lacking several transfer RNA (tRNA) genes, whereas others found that all their tRNA genes were present but severely reduced. To resolve this discrepancy, we determined complete mitochondrial DNA (mtDNA) sequences of the onychophorans Oroperipatus sp. and Peripatoides sympatrica as well as cDNA sequences from 14 and 10 of their tRNAs, respectively. We show that tRNA genes in these genomes are indeed highly reduced and encode truncated molecules, which are restored to more conventional structures by extensive tRNA editing. During this editing process, up to 34 nucleotides are added to the tRNA sequences encoded in Oroperipatus sp. mtDNA, rebuilding the aminoacyl acceptor ... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5246310 Tue, 20 Sep 2011 04:00:00 +0100 5246310 http://www.medworm.com/index.php?rid=5246309&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F10%2F2855%3Frss%3D1 Whole-genome comparisons provide insight into genome evolution by informing on gene repertoires, gene gains/losses, and genome organization. Most of our knowledge about eukaryotic genome evolution is derived from studies of multicellular model organisms. The eukaryotic phylum Apicomplexa contains obligate intracellular protist parasites responsible for a wide range of human and veterinary diseases (e.g., malaria, toxoplasmosis, and theileriosis). We have developed an in silico protein-encoding gene based pipeline to investigate synteny across 12 apicomplexan species from six genera. Genome rearrangement between lineages is extensive. Syntenic regions (conserved gene content and order) are rare between lineages and appear to be totally absent across the phylum, with no group of three genes ... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5246309 Tue, 20 Sep 2011 04:00:00 +0100 5246309 http://www.medworm.com/index.php?rid=5246308&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F10%2F2843%3Frss%3D1 We used next generation sequencing to characterize and compare the genomes of the recently derived allotetraploid, Nicotiana tabacum (<200,000 years old), with its diploid progenitors, Nicotiana sylvestris (maternal, S-genome donor), and Nicotiana tomentosiformis (paternal, T-genome donor). Analysis of 14,634 repetitive DNA sequences in the genomes of the progenitor species and N. tabacum reveal all major types of retroelements found in angiosperms (genome proportions range between 17–22.5% and 2.3–3.5% for Ty3-gypsy elements and Ty1-copia elements, respectively). The diploid N. sylvestris genome exhibits evidence of recent bursts of sequence amplification and/or homogenization, whereas the genome of N. tomentosiformis lacks this signature and has considerably fewer homogeno... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5246308 Tue, 20 Sep 2011 04:00:00 +0100 5246308 http://www.medworm.com/index.php?rid=5246307&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F10%2F2833%3Frss%3D1 In this study, we analyzed DNA variation by pooling 71 genes from 85–100 individuals for DNA sequencing. For each of the two nearby S. alba populations, we obtained ~2,500 x coverage on the Illumina GA platform and for the Sanya population, an additional 5,400 x coverage on the AB SOLiD platform. For the Sanya sample, although each sequencing method called many putative single nucleotide polymorphisms, the two sets of calls did not overlap, suggesting platform-dependent errors. Conventional sequencing corroborated that each population is monomorphic. The two populations differ by 54 bp of 79,000 sites, but 90% of the variants are found in 10% of the genes. Strong local adaptation and high migration may help to explain the extensive monomorphism shared by the two populations in the pr... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5246307 Tue, 20 Sep 2011 04:00:00 +0100 5246307 http://www.medworm.com/index.php?rid=5246306&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F10%2F2823%3Frss%3D1 Inverted duplicates (IDs) are pervasive in genomes and have been reported to play functional roles in various biological processes. However, the general underlying evolutionary forces that maintain IDs in genomes remain largely elusive. Through a systematic screening of the Drosophila melanogaster genome, 20,223 IDs were detected in nonrepetitive intergenic regions, far more than expectation under the neutrality model. 3,846 of these IDs were identified to have stable hairpin structure (i.e., the structural IDs). Based on whole-genome transcriptome profiling data, we found 628 unannotated expressed structural IDs, which had significantly different genomic distributions and structural properties from the unexpressed IDs. Among the expressed structural IDs, 130 exhibited higher expression in... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5246306 Tue, 20 Sep 2011 04:00:00 +0100 5246306 http://www.medworm.com/index.php?rid=5246305&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F10%2F2811%3Frss%3D1 This study sought a better understanding of the evolutionary history of WFDC genes in humans and focused on exploring the adaptive selection signatures found in populations of European (Utah residents with ancestry from northern and western Europe [CEU]) and African (Yoruba from Ibadan, in Nigeria [YRI]) ancestry in a genome-wide scan for putative targets of recent adaptive selection. Our approach included resequencing coding and noncoding regions of WFDC6, EPPIN, and WFDC8 in 20 CEU and of SPINT4 in 20 YRI individuals. We generated 302 kb and 60 kb of high-quality sequence data from CEU and of YRI populations, respectively, enabling the identification of 72 single nucleotide polymorphisms. Using classic neutrality tests, empirical and haplotype-based analysis, we pinpointed WFDC8 and SPIN... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5246305 Tue, 20 Sep 2011 04:00:00 +0100 5246305 http://www.medworm.com/index.php?rid=5246304&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F10%2F2799%3Frss%3D1 This study shows that gene inactivation or loss can be involved in the origin of phenotypic differences between species, thereby restricting the possibility of reversion to the ancestral state. It also demonstrates that parallel evolution of red flowers in three different species occurs via a common developmental/regulatory change but by mutations in different genes. (Source: Molecular Biology and Evolution) Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5246304 Tue, 20 Sep 2011 04:00:00 +0100 5246304 http://www.medworm.com/index.php?rid=5246303&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F10%2F2787%3Frss%3D1 Pax genes encode evolutionarily conserved transcription factors that play critical roles in embryonic development and organogenesis. Pax proteins are subdivided into four subfamilies: group I (Pax1and 9), II (Pax2, 5, and 8), III (Pax3 and 7), and IV (Pax4 and 6), based on the presence of a paired domain, an octapeptide motif and part or all of the homeodomain. Studies of the evolution of this gene family are incomplete. Nevertheless, it is known that each family evolved via duplication from four corresponding ancestral genes. Pax gene functions have been shown to be conserved within subgroups. It remains unclear, however, whether any (early) conserved function is shared between subgroups. To investigate conserved functions between subfamily II and III, we replaced an allele of Pax3 with a... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5246303 Tue, 20 Sep 2011 04:00:00 +0100 5246303 http://www.medworm.com/index.php?rid=5246302&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F10%2F2773%3Frss%3D1 We present a congruence method that accommodates both very large numbers of genes and high degrees of incongruence. Our method uses clustering algorithms to identify subsets of genes based on similarity of phylogenetic signal. It involves only a single phylogenetic analysis per gene, and therefore, computation time scales nearly linearly with the number of genes in the data set. We show that our method performs very well with sets of sequence alignments simulated under a wide variety of conditions. In addition, we present an analysis of core genes of prokaryotes, often assumed to have been largely vertically inherited, in which we identify two highly incongruent classes of genes. This result is consistent with the complexity hypothesis. (Source: Molecular Biology and Evolution) Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5246302 Tue, 20 Sep 2011 04:00:00 +0100 5246302 http://www.medworm.com/index.php?rid=5246301&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F10%2F2761%3Frss%3D1 In this study, we examined the evolutionary histories of Wolbachia infections, known as wPip, in the common house mosquito Culex pipiens, which exhibits the greatest variation in CI crossing patterns observed in any insect. We first investigated a panel of 20 wPip strains for their genetic diversity through a multilocus scheme combining 13 Wolbachia genes. Because Wolbachia depend primarily on maternal transmission for spreading within arthropod populations, we also studied the variability in the coinherited Cx. pipiens mitochondria. In total, we identified 14 wPip haplotypes, which all share a monophyletic origin and clearly cluster into five distinct wPip groups. The diversity of Cx. pipiens mitochondria was extremely reduced, which is likely a consequence of cytoplasmic hitchhiking driv... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5246301 Tue, 20 Sep 2011 04:00:00 +0100 5246301 http://www.medworm.com/index.php?rid=5246300&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F10%2F2751%3Frss%3D1 Several isolates of the marine cyanobacterial genus Prochlorococcus have smaller genome sizes than those of the closely related genus Synechococcus. In order to test whether loss of protein-coding genes has contributed to genome size reduction in Prochlorococcus, we reconstructed events of gene family evolution over a strongly supported phylogeny of 12 Prochlorococcus genomes and 9 Synechococcus genomes. Significantly, more events both of loss of paralogs within gene families and of loss of entire gene families occurred in Prochlorococcus than in Synechococcus. The number of nonancestral gene families in genomes of both genera was positively correlated with the extent of genomic islands (GIs), consistent with the hypothesis that horizontal gene transfer (HGT) is associated with GIs. Howeve... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5246300 Tue, 20 Sep 2011 04:00:00 +0100 5246300 http://www.medworm.com/index.php?rid=5246299&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F10%2F2741%3Frss%3D1 Feather cloaks ("kakahu"), particularly those adorned with kiwi feathers, are treasured items or "taonga" to the Maori people of "Aotearoa"/New Zealand. They are considered iconic expression of Maori culture. Despite their status, much of our knowledge of the materials used to construct cloaks, the provenance of cloaks, and the origins of cloak making itself, has been lost. We used ancient DNA methods to recover mitochondrial DNA sequences from 849 feather samples taken from 109 cloaks. We show that almost all (>99%) of the cloaks were constructed using feathers from North Island brown kiwi. Molecular sexing of nuclear DNA recovered from 92 feather cloak samples also revealed that the sex ratio of birds deviated from a ratio of 1:1 observed in reference populations. Additionally, we con... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5246299 Tue, 20 Sep 2011 04:00:00 +0100 5246299 http://www.medworm.com/index.php?rid=5246298&cid=s_32018_67_f&fid=32018&url=http%3A%2F%2Fmbe.oxfordjournals.org%2Fcgi%2Fcontent%2Fshort%2F28%2F10%2F2731%3Frss%3D1 Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary... Molecular Biology and Evolution journals http://www.medworm.com/rss/comments.php?id=5246298 Tue, 20 Sep 2011 04:00:00 +0100 5246298