CiteULike: indigoviolet's watchlist

Genomic Analysis of Adaptive Differentiation in Drosophila melanogaster

Thomas Turner — 2008-05-21T03:39:32-00:00

Genetics, Vol. 179, No. 1. (1 May 2008), pp. 455-473.

Drosophila melanogaster shows clinal variation along latitudinal transects on multiple continents for several phenotypes, allozyme variants, sequence variants, and chromosome inversions. Previous investigation suggests that many such clines are due to spatially varying selection rather than demographic history, but the genomic extent of such selection is unknown. To map differentiation throughout the genome, we hybridized DNA from temperate and subtropical populations to Affymetrix tiling arrays. The dense genomic sampling of variants and low level of linkage disequilibrium in D. melanogaster enabled identification of many small, differentiated regions. Many regions are differentiated in parallel in the United States and Australia, strongly supporting the idea that they are influenced by spatially varying selection. Genomic differentiation is distributed nonrandomly with respect to gene function, even in regions differentiated on only one continent, providing further evidence for the role of selection. These data provide candidate genes for phenotypes known to vary clinally and implicate interesting new processes in genotype-by-environment interactions, including chorion proteins, proteins regulating meiotic recombination and segregation, gustatory and olfactory receptors, and proteins affecting synaptic function and behavior. This portrait of differentiation provides a genomic perspective on adaptation and the maintenance of variation through spatially varying selection. 10.1534/genetics.107.083659

Levers and fulcrums: progress in cis-regulatory motif models

Ewan Birney — 2008-03-28T16:35:47-00:00

Nature Methods, Vol. 5, No. 4., pp. 297-298.

Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome

Peter Andolfatto — 2007-11-10T18:10:48-00:00

Genome Res. (7 November 2007), gr.6691007.

Several recent studies have estimated that a large fraction of amino acid divergence between species of Drosophila was fixed by positive selection, using statistical approaches based on the McDonald-Kreitman test. However, little is known about associated selection coefficients of beneficial amino acid mutations. Recurrent selective sweeps associated with adaptive substitutions should leave a characteristic signature in genome variability data that contains information about the frequency and strength of selection. Here, I document a significant negative correlation between the level and the frequency of synonymous site polymorphism and the rate of protein evolution in highly recombining regions of the X chromosome of D. melanogaster. This pattern is predicted by recurrent adaptive protein evolution and suggests that adaptation is an important determinant of patterns of neutral variation genome-wide. Using a maximum likelihood approach, I estimate the product of the rate and strength of selection under a recurrent genetic hitchhiking model, [IMG]f1.gif" ALT="Formula" BORDER="0">2Nes [~] 3 x 108. Using an approach based on the McDonald-Kreitman test, I estimate that [~]50% of divergent amino acids were driven to fixation by positive selection, implying that beneficial amino acid substitutions are of weak effect on average, on the order of 105 (i.e., 2Nes [~] 40). Two implications of these results are that most adaptive substitutions will be difficult to detect in genome scans of selection and that population size (and genetic drift) may be an important determinant of the evolutionary dynamics of protein adaptation. 10.1101/gr.6691007

Gene Network Inference via Structural Equation Modeling in Genetical Genomics Experiments.

Bing Liu — 2008-02-06T11:38:22-00:00

Genetics (3 February 2008)

Our goal is gene network inference in Genetical Genomics or Systems Genetics experiments. For species where sequence information is available, we first perform expression QTL mapping by jointly utilizing cis, cistrans and trans regulation. After using local structural models to identify regulator-target pairs for each eQTL, we construct an encompassing directed network (EDN) by assembling all retained regulator-target relationships. The EDN has nodes corresponding to expressed genes and eQTLs, and directed edges from eQTLs to cis-regulated target genes, from cis-regulated genes to cistrans regulated target genes, from trans-regulator genes to target genes and from trans-eQTLs to target genes. For network inference within the strongly constrained search space defined by the EDN, we propose Structural Equation Modeling (SEM), because it can model cyclic networks and the EDN indeed contains feedback relationships. Based on a factorization of the likelihood and the constrained search space, our SEM algorithm infers networks involving several hundred genes and eQTL. Structure inference is based on a penalized likelihood ratio and an adaptation of Occam's Window model selection. The SEM algorithm was evaluated using data simulated with nonlinear ordinary differential equations and known cyclic network topologies and was applied to a real yeast data set.

Independent effects of cis- and trans-regulatory variation on gene expression in Drosophila melanogaster

Patricia Wittkopp — 2008-02-04T08:12:21-00:00

Genetics (3 February 2008), genetics.107.082032.

Biochemical interactions between cis-regulatory DNA sequences and trans-regulatory gene products suggest that cis- and trans-acting polymorphisms may interact genetically. Here we present a strategy to test this hypothesis by comparing the relative cis-regulatory activity of two alleles in different genetic backgrounds. Of the eight genes surveyed in this study, five were affected by trans-acting variation that altered total transcript levels, two of which were also affected by differences in cis-regulation. The presence of trans-acting variation had no effect on relative cis-regulatory activity, showing that cis-regulatory polymorphisms can function independently of trans-regulatory variation. The frequency of such independent interactions on a genomic scale is yet to be determined. 10.1534/genetics.107.082032

Multi-scale correlations in continuous genomic data.

RE Thurman — 2008-02-01T07:04:32-00:00

Pac Symp Biocomput (2008), pp. 201-215.

Functional genomic quantities such as histone modifications, chromatin accessibility, and evolutionary constraint can now be measured in a nearly continuous fashion across the genome. The genome is highly heterogeneous, and the relationships between different functional annotations may be fluid. Here we present an approach for visualizing, quantifying, and determining the statistical significance of local and regional correlations between high-density continuous genomic datasets. We use wavelets to generate a multi-scale view of each component data set and calculate correlations between data types as a function of genome position over a continuous range of scales in sliding window fashion. We determine the statistical significance of correlations using a non-parametric sampling approach. We apply the wavelet correlation method to histone modification and chromatin accessibility (DNasel sensitivity) data from the NHGRI ENCODE project. We show that DNaseI sensitivity is broadly correlated (though to differing degrees) with a number of different activating histone modifications. We examine the continuous relationship between the repressive histone modification H3K27me3 and the activating mark H3K4me2, and find these modifications to display significant duality, with both significant positively and negatively correlated genomic territories. While the former appear to recapitulate in definitive cells the so-called "bi-valent" pattern originally proposed as a signature of pluripotency, the presence of negatively correlated regions suggests that the regulatory events that underlie the observed modification patterns are complex and highly regionalized in the genome.

Using DNA duplex stability information for transcription factor binding site discovery.

R Gordân — 2008-02-01T06:20:50-00:00

Pac Symp Biocomput (2008), pp. 453-464.

Transcription factor (TF) binding site discovery is an important step in understanding transcriptional regulation. Many computational tools have already been developed, but their success in detecting TF motifs is still limited. We believe one of the main reasons for the low accuracy of current methods is that they do not take into account the structural aspects of TF-DNA interaction. We have previously shown that knowledge about the structural class of the TF and information about nucleosome occupancy can be used to improve motif discovery. Here, we demonstrate the benefits of using information about the DNA double-helical stability for motif discovery. We notice that, in general, the energy needed to destabilize the DNA double helix is higher at TF binding sites than at random DNA sites. We use this information to derive informative positional priors that we incorporate into a motif finding algorithm. When applied to yeast ChIP-chip data, the new informative priors improve the performance of the motif finder significantly when compared to priors that do not use the energetic stability information.

Use of an evolutionary model to provide evidence for a wide heterogeneity of required affinities between transcription factors and their binding sites in yeast.

RW Lusk — 2008-02-01T06:17:57-00:00

Pac Symp Biocomput (2008), pp. 489-500.

The identification of transcription factor binding sites commonly relies on the interpretation of scores generated by a position weight matrix. These scores are presumed to reflect on the affinity of the transcription factor for the bound sequence. In almost all applications, a cutoff score is chosen to distinguish between functional and non-functional binding sites. This cutoff is generally based on statistical rather than biological criteria. Furthermore, given the variety of transcription factors, it is unlikely that the use of a common statistical threshold for all transcription factors is appropriate. In order to incorporate biological information into the choice of cutoff score, we developed a simple evolutionary model that assumes that transcription factor binding sites evolve to maintain an affinity greater than some factor-specific threshold. We then compared patterns of substitution in binding sites predicted by this model at different thresholds to patterns of substitution observed at sites bound in vivo by transcription factors in S. cerevisiae. Assuming that the cutoff value that gives the best fit between the observed and predicted values will optimally distinguish functional and non-functional sites, we discovered substantial heterogeneity for appropriate cutoff values among factors. While commonly used thresholds seem appropriate for many factors, some factors appear to function at cutoffs satisfied commonly in the genome. This evidence was corroborated by local patterns of rate variation for examples of stringent and lenient p-value cutoffs. Our analysis further highlights the necessity of taking a factor-specific approach to binding site identification.

Alignment Uncertainty and Genomic Analysis

Karen Wong — 2008-01-25T07:09:02-00:00

Science, Vol. 319, No. 5862. (25 January 2008), pp. 473-476.

The statistical methods applied to the analysis of genomic data do not account for uncertainty in the sequence alignment. Indeed, the alignment is treated as an observation, and all of the subsequent inferences depend on the alignment being correct. This may not have been too problematic for many phylogenetic studies, in which the gene is carefully chosen for, among other things, ease of alignment. However, in a comparative genomics study, the same statistical methods are applied repeatedly on thousands of genes, many of which will be difficult to align. Using genomic data from seven yeast species, we show that uncertainty in the alignment can lead to several problems, including different alignment methods resulting in different conclusions. 10.1126/science.1151532

The effect of the guide tree on multiple sequence alignments and subsequent phylogenetic analyses.

S Nelesen — 2008-02-01T06:13:52-00:00

Pac Symp Biocomput (2008), pp. 25-36.

Many multiple sequence alignment methods (MSAs) use guide trees in conjunction with a progressive alignment technique to generate a multiple sequence alignment but use differing techniques to produce the guide tree and to perform the progressive alignment. In this paper we explore the consequences of changing the guide tree used for the alignment routine. We evaluate four leading MSA methods (ProbCons, MAFFT, Muscle, and ClustalW) as well as a new MSA method (FTA, for "Fixed Tree Alignment") which we have developed, on a wide range of simulated datasets. Although improvements in alignment accuracy can be obtained by providing better guide trees, in general there is little effect on the "accuracy" (measured using the SP-score) of the alignment by improving the guide tree. However, RAxML-based phylogenetic analyses of alignments based upon better guide trees tend to be much more accurate. This impact is particularly significant for ProbCons, one of the best MSA methods currently available, and our method, FTA. Finally, for very good guide trees, phylogenies based upon FTA alignments are more accurate than phylogenies based upon ProbCons alignments, suggesting that further improvements in phylogenetic accuracy may be obtained through algorithms of this type.

Multiple RTK pathways downregulate Groucho-mediated repression in Drosophila embryogenesis.

Einat Cinnamon — 2008-02-01T06:08:43-00:00

Development (23 January 2008)

RTK pathways establish cell fates in a wide range of developmental processes. However, how the pathway effector MAPK coordinately regulates the expression of multiple target genes is not fully understood. We have previously shown that the EGFR RTK pathway causes phosphorylation and downregulation of Groucho, a global co-repressor that is widely used by many developmentally important repressors for silencing their various targets. Here, we use specific antibodies that reveal the dynamics of Groucho phosphorylation by MAPK, and show that Groucho is phosphorylated in response to several RTK pathways during Drosophila embryogenesis. Focusing on the regulation of terminal patterning by the Torso RTK pathway, we demonstrate that attenuation of Groucho's repressor function via phosphorylation is essential for the transcriptional output of the pathway and for terminal cell specification. Importantly, Groucho is phosphorylated by an efficient mechanism that does not alter its subcellular localisation or decrease its stability; rather, modified Groucho endures long after MAPK activation has terminated. We propose that phosphorylation of Groucho provides a widespread, long-term mechanism by which RTK signals control target gene expression.

Delimiting the conserved features of hunchback function for the trunk organization of insects.

Henrique Marques-Souza — 2008-02-01T06:04:23-00:00

Development (23 January 2008)

The gap gene hunchback in Drosophila acts during syncytial blastoderm stage via a short-range gradient and concentration-dependent activation or repression of target genes. Orthologues of hunchback can be easily found in other insects, but it has been unclear how well its functions are conserved. The segmentation process in most insect embryos occurs under cellular conditions, which should not allow the formation of diffusion-controlled transcription factor gradients. We have studied here in detail the function of hunchback in the short germ embryo of Tribolium using parental RNAi and interaction with possible target genes. We find that hunchback is a major regulator of the trunk gap genes and Hox genes in Tribolium, but may only indirectly be required to regulate other segmentation genes. The core function of hunchback appears to be the setting of the Ultrabithorax expression border via a repression effect, and the activation of the Krüppel expression domain. These regulatory effects are likely to be direct and are conserved between Drosophila and Tribolium. We find no evidence for a classical gap phenotype in the form of loss of segments in the region of expression of hunchback. However, the phenotypic effects in Tribolium are highly comparable with those found for other short germ embryos, i.e. the core functions of hunchback in Tribolium appear to be the same in these other insects, although they are evolutionarily more distant to Tribolium, than Tribolium is to Drosophila. These results allow the disentanglement of the conserved role of hunchback in insects from the derived features that have been acquired in the lineage towards Drosophila. Given that the gap phenotype appears to occur only in long germ embryos and that the main role of hunchback appears to be the regionalization of the embryo, it may be appropriate to revive an alternative name for the class of gap genes, namely 'cardinal genes'.

Evigan: A Hidden Variable Model for Integrating Gene Evidence for Eukaryotic Gene Prediction.

Qian Liu — 2008-01-13T21:11:52-00:00

Bioinformatics (10 January 2008)

MOTIVATION: The increasing diversity and variable quality of evidence relevant to gene annotation argues for a probabilistic framework that automatically integrates such evidence to yield candidate gene models. RESULTS: Evigan is an automated gene annotation program for eukaryotic genomes, employing probabilistic inference to integrate multiple sources of gene evidence. The probabilistic model is a dynamic Bayes network whose parameters are adjusted to maximize the probability of observed evidence. Consensus gene predictions are then derived bymaximum likelihood decoding, yielding n-best models (with probabilities for each). Evigan is capable of accommodating a variety of different types of evidence, including (but not limited to) gene models computed by diverse gene nders, BLAST hits, EST matches, and splice site predictions; learned parameters encode the relative quality of evidence sources. Because separate training data is not required (apart from the training sets used by individual gene nders), Evigan is particularly attractive for newly sequenced genomes where little or no reliable manually-curated annotation is available. The ability to produce a ranked list of alternative gene models may facilitate identi cation of alternatively spliced transcripts. Experimental application to ENCODE regions of the human genome, and the genomes of Plasmodium vivax and Arabidopsis thaliana show that Evigan achieves better performance than any of the individual data sources used as evidence. AVAILABILITY: The source code is available at http://www.seas.upenn.edu/~strctlrn/evigan/evigan.html. CONTACT: qianliu@seas.upenn.edu.

Fungal CSL transcription factors

Martin Prevorovsky — 2007-07-14T06:29:03-00:00

BMC Genomics, Vol. 8 (13 July 2007), 233.

Contrasting the Efficacy of Selection on the X and Autosomes in Drosophila.

Nadia D Singh — 2008-01-11T18:02:01-00:00

Mol Biol Evol (13 December 2007)

To investigate the relative efficacy of both positive and purifying natural selection on the X chromosome and the autosomes in Drosophila, we compared rates and patterns of molecular evolution between these chromosome sets using the newly available alignments of orthologous genes from twelve species. Parameters that may influence the relative X vs. autosomal substitution rates include the relative effective population sizes, the male and female germline mutation rates, the distribution of allelic effects on fitness, and the degree of dominance of novel mutations. Our analysis reveals that codon usage bias is consistently greater for X-linked genes, suggesting that purifying selection consistently has greater efficacy on the X chromosome than on the autosomes across the Drosophila phylogeny. However, our results are less consistent with respect to the efficacy of positive selection, with only some lineages showing a higher substitution rate on the X chromosome. This suggests that either the distribution of selective effects of mutations or other relevant parameters are sufficiently variable across species to tip the balance in different ways in individual lineages. These data suggest that rates of substitution are not solely governed by adaptive evolution. This genome-wide analysis provides a clear picture that the efficacy of selection varies intragenomically, and that this effect is markedly more consistent across the phylogeny in the case of purifying selection. Our results also suggest that simple models that predict systematic differences in rates of evolution between the X and the autosomes can only be made to be compatible with these Drosophila data if the relevant population genetic parameters that drive substitution rates differ among species and chromosomal contexts.

CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction

Samuel Gross — 2007-12-21T22:53:56-00:00

Genome Biology, Vol. 8 (20 December 2007), R269.

Distinguishing protein-coding and noncoding genes in the human genome

Michele Clamp — 2007-11-26T23:07:17-00:00

Proceedings of the National Academy of Sciences (26 November 2007), 0709013104.

Although the Human Genome Project was completed 4 years ago, the catalog of human protein-coding genes remains a matter of controversy. Current catalogs list a total of approx24,500 putative protein-coding genes. It is broadly suspected that a large fraction of these entries are functionally meaningless ORFs present by chance in RNA transcripts, because they show no evidence of evolutionary conservation with mouse or dog. However, there is currently no scientific justification for excluding ORFs simply because they fail to show evolutionary conservation: the alternative hypothesis is that most of these ORFs are actually valid human genes that reflect gene innovation in the primate lineage or gene loss in the other lineages. Here, we reject this hypothesis by carefully analyzing the nonconserved ORFsspecifically, their properties in other primates. We show that the vast majority of these ORFs are random occurrences. The analysis yields, as a by-product, a major revision of the current human catalogs, cutting the number of protein-coding genes to approx20,500. Specifically, it suggests that nonconserved ORFs should be added to the human gene catalog only if there is clear evidence of an encoded protein. It also provides a principled methodology for evaluating future proposed additions to the human gene catalog. Finally, the results indicate that there has been relatively little true innovation in mammalian protein-coding genes. 10.1073/pnas.0709013104

Characterization of the Duffy gene promoter: evidence for tissue-specific abolishment of expression in Fy(a-b-) of black individuals.

S Iwamoto — 2007-12-05T23:01:43-00:00

Biochem Biophys Res Commun, Vol. 222, No. 3. (24 May 1996), pp. 852-859.

We have previously identified a novel first exon of Duffy gene and two inverse GATA motifs in the 600 bp 5' flanking region. The proximal GATA is positioned downstream from the start position of endothelium and upstream from that of erythroid. One base substitution (-365T --> C) was found in the proximal GATA motif from three black Fy(a-b-) individuals, and was regarded as a common polymorphic mutation in black Fy(a-b-) individuals. The upstream sequence of the novel first exon was inserted in the upstream of chloramphenicol acetyltransferase (CAT) gene and transfected in human erythroleukemia cell line (HEL) and human microvascular endothelial cells (HMvEC). The black type mutation abolished the CAT transcription in HEL cells but not in HMvEC. Deletion mutagenesis study revealed that the proximal GATA motif represent the erythroid regulatory core region for Duffy gene. Gel shift assay showed that the proximal GATA motif is the target sequence of GATA-1. These studies indicate that the black type mutation abolishes Duffy gene expression in erythroid but not in postcapillary venule endothelium, which is compatible with the Northern blot and immunohistochemical observation in black Fy(a-b-) individuals.

Detection of the signature of natural selection in humans: evidence from the Duffy blood group locus.

MT Hamblin — 2007-12-05T22:52:50-00:00

Am J Hum Genet, Vol. 66, No. 5. (May 2000), pp. 1669-1679.

The Duffy blood group locus, which encodes a chemokine receptor, is characterized by three alleles-FY*A, FY*B, and FY*O. The frequency of the FY*O allele, which corresponds to the absence of Fy antigen on red blood cells, is at or near fixation in most sub-Saharan African populations but is very rare outside Africa. The FST value for the FY*O allele is the highest observed for any allele in humans, providing strong evidence for the action of natural selection at this locus. Homozygosity for the FY*O allele confers complete resistance to vivax malaria, suggesting that this allele has been the target of selection by Plasmodium vivax or some other infectious agent. To characterize the signature of directional selection at this locus, we surveyed DNA sequence variation, both in a 1.9-kb region centered on the FY*O mutation site and in a 1-kb region 5-6 kb away from it, in 17 Italians and in a total of 24 individuals from five sub-Saharan African populations. The level of variation across both regions is two- to threefold lower in the Africans than in the Italians. As a result, the pooled African sample shows a significant departure from the neutral expectation for the number of segregating sites, whereas the Italian sample does not. The FY*O allele occurs on two major haplotypes in three of the five African populations. This finding could be due to recombination, recurrent mutation, population structure, and/or mutation accumulation and drift. Although we are unable to distinguish among these alternative hypotheses, it is likely that the two major haplotypes originated prior to selection on the FY*O mutation.

Disruption of a GATA motif in the Duffy gene promoter abolishes erythroid gene expression in Duffy-negative individuals.

C Tournamille — 2007-12-05T22:50:02-00:00

Nat Genet, Vol. 10, No. 2. (June 1995), pp. 224-228.

The mRNA for the Duffy blood group antigen, the erythrocyte receptor for the Plasmodium vivax malaria parasite, has recently been cloned and shown to encode a widely expressed chemokine receptor. Here, we show that the Duffy antigen/chemokine receptor gene (DARC) is composed of a single exon and that most Duffy-negative blacks carry a silent FY*B allele with a single T to C substitution at nucleotide -46. This mutation impairs the promoter activity in erythroid cells by disrupting a binding site for the GATA1 erythroid transcription factor. With the recent characterization of the FY*A and FY*B alleles, these findings provide the molecular basis of the Duffy blood group system and an explanation for the erythroid-specific repression of the DARC gene in Duffy-negative individuals.

Transcriptional regulation of a pair-rule stripe in Drosophila.

S Small — 2007-12-05T19:30:34-00:00

Genes Dev, Vol. 5, No. 5. (May 1991), pp. 827-839.

The periodic, seven-stripe pattern of the primary pair-rule gene even-skipped (eve) is initiated by crude, overlapping gradients of maternal and gap gene proteins in the early Drosophila embryo. Previous genetic studies suggest that one of the stripes, stripe 2, is initiated by the maternal morphogen bicoid (bcd) and the gap protein hunchback (hb), while the borders of the stripe are formed by selective repression, involving the gap protein giant (gt) in anterior regions and the Krüppel (Kr) protein in posterior regions. Here, we present several lines of evidence that are consistent with this model for stripe 2 expression, including in vitro DNA-binding experiments and transient cotransfection assays in cultured cells. These experiments suggest that repression involves a competition or short-range quenching mechanism, whereby the binding of gt and Kr interferes with the binding or activity of bcd and hb activators at overlapping or neighboring sites within the eve stripe 2 promoter element. Such short-range repression could reflect a general property of promoters composed of multiple, but autonomous regulatory elements.

Transcriptional regulatory code of a eukaryotic genome

Christopher Harbison — 2006-01-16T14:50:46-00:00

Nature, Vol. 431, No. 7004. (2004), pp. 99-104.

CONTRAST: de novo gene prediction using a semi-Markov conditional random field. Biomedical Computation at Stanford Symposium Proceedings (BCATS)

SS Gross — 2007-12-03T10:26:37-00:00

(2005)

Computational identification of evolutionarily conserved exons

A Siepel — 2007-12-03T10:23:23-00:00

Proceedings of the eighth annual international conference on Research in computational molecular biology (2004), pp. 177-186.

Dominant gain-of-function mutations that lead to misregulation of the C. elegans heterochronic gene lin-14, and the evolutionary implications of dominant mutations in pattern-formation genes.

G Ruvkun — 2007-11-26T00:35:21-00:00

Dev Suppl, Vol. 1 (1991), pp. 47-54.

The heterochronic gene lin-14 controls the temporal sequence of developmental events in the C. elegans postembryonic cell lineage. It encodes a nuclear protein that is normally present in most somatic cells of late embryos and L1 larvae but not in later larval stages or adults. Two lin-14 gain-of-function mutations cause an inappropriately high level of the lin-14 nuclear protein late in development. These mutations delete 3' untranslated sequences from the lin-14 mRNAs and identify a negative regulatory element that controls the formation of the lin-14 protein temporal gradient. The 21 kb lin-14 gene contains 13 exons that are differentially spliced to generate two lin-14 protein products with variable N-terminal regions and a constant C-terminal region. No protein sequence similarity to any proteins in various databases was found. The temporal and cellular expression patterns of lin-14 protein accumulation is altered by mutations in the heterochronic genes lin-4 and lin-28. The lin-4 gene is required to down-regulate lin-14 protein levels during the mid-L1 stage. The lin-4 gene product could be the trans-acting factor that binds to the negative regulatory element in the lin-14 3' untranslated region. In contrast, the lin-28 gene activity positively regulates lin-14 protein levels during early L1. Thus, these genes act antagonistically to regulate the lin-14 temporal switch. The normal down-regulation of lin-14 within 10 h of hatching is not determined by the passage of time per se, but rather is triggered when feeding induces post-embryonic development.(ABSTRACT TRUNCATED AT 250 WORDS)

Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter.

D Pribnow — 2007-11-26T00:26:11-00:00

Proc Natl Acad Sci U S A, Vol. 72, No. 3. (March 1975), pp. 784-788.

Escherichia coli RNA polymerase (EC 2.7.7.6), bound in a tight complex at an early T7 promoter, protects 41 to 43 base pairs of DNA from digestion by DNase. I. The protected DNA fragment contains both the binding site for RNA polymerase and the mRNA initiation point for the promoter. The sequence of the DNA fragment and the sequence of the mRNA that it codes for are presented here. A seven-base-pair sequence, apparently common to all promoters, is implicated in the formation of a tight binary complex with RNA polymerase.

Accounting for Bias from Sequencing Error in Population Genetic Estimates.

Philip L F Johnson — 2007-11-06T15:08:05-00:00

Mol Biol Evol (2 November 2007)

Sequencing error presents a significant challenge to population genetic analyses using low-coverage sequence in general and single-pass reads in particular. Bias in parameter estimates becomes severe when the level of polymorphism ("signal") is low relative to the amount of error ("noise"). Choosing an arbitrary quality score cutoff yields biased estimates, particularly with newer, non-Sanger sequencing technologies that have different quality score distributions. We propose a rule of thumb to judge when a given threshold will lead to significant bias and suggest alternative approaches that reduce bias.

Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes

Matthew Rasmussen — 2007-11-12T17:38:22-00:00

Genome Res. (7 November 2007), gr.7105007.

Comparative genomics provides a general methodology for discovering functional DNA elements and understanding their evolution. The availability of many related genomes enables more powerful analyses, but requires rigorous phylogenetic methods to resolve orthologous genes and regions. Here, we use 12 recently sequenced Drosophila genomes and nine fungal genomes to address the problem of accurate gene-tree reconstruction across many complete genomes. We show that existing phylogenetic methods that treat each gene tree in isolation show large-scale inaccuracies, largely due to insufficient phylogenetic information in individual genes. However, we find that gene trees exhibit common properties that can be exploited for evolutionary studies and accurate phylogenetic reconstruction. Evolutionary rates can be decoupled into gene-specific and species-specific components, which can be learned across complete genomes. We develop a phylogenetic reconstruction methodology that exploits these properties and achieves significantly higher accuracy, addressing the species-level heterotachy and enabling studies of gene evolution in the context of species evolution. 10.1101/gr.7105007

Dynamics and function of intron sequences of the wingless gene during the evolution of the Drosophila genus.

J Costas — 2007-11-21T01:23:08-00:00

Evol Dev, Vol. 6, No. 5. (t 2004), pp. 325-335.

To understand the function and evolution of genes with complex patterns of expression, such as the Drosophila wingless gene, it is essential to know how their transcription is regulated. However, extracting the relevant regulatory information from a genome is still a complex task. We used a combination of comparative genomics and functional approaches to identify putative regulatory sequences in two introns (1 and 3) of the wingless gene and to infer their evolution. Comparison of the sequences obtained from several Drosophila species revealed colinear and well-conserved sequence blocks in both introns. Drosophila willistoni showed a rate of evolution, in both introns, faster than expected from its phylogenetic position. Intron 3 appeared to be composed of two separate modules, one of them lost in the willistoni group. We tested whether sequence conservation in noncoding regions is a reliable indicator of regulatory function and, if this function is conserved, by analyzing D. melanogaster transgenic reporter lines harboring intron 3 sequences from D. melanogaster (Sophophora subgenus) and the species from the Drosophila subgenus presenting the most divergent sequence, D. americana. The analysis indicated that intron 3 contains pupal enhancers conserved during the evolution of the genus, despite the fact that only 30% of the D. melanogaster intron 3 sequences lie in conserved blocks. Additional analysis of D. melanogaster transgenic reporter lines harboring intron 3 sequences from D. willistoni revealed the absence of an abdomen-specific expression pattern, probably due to the above-mentioned loss of a regulatory module in this species.

Turnover of binding sites for transcription factors involved in early Drosophila development.

J Costas — 2007-10-16T21:11:16-00:00

Gene, Vol. 310 (22 May 2003), pp. 215-220.

Despite the importance of cis-regulatory regions in evolution, little is know about their evolutionary dynamics. In this report, we analyze the process of evolution of binding sites for transcription factors using as a model a well characterized system, the Drosophila early developmental enhancers. We compare the sequences of eight enhancer regions for early developmental genes between Drosophila melanogaster and other two species, Drosophila virilis and Drosophila pseudoobscura, searching for the presence/absence of 104 biochemically verified binding sites from D. melanogaster. We also modeled the binding specificity of each binding site by the use of well-defined positional weight matrices (PWMs). The comparisons showed that turnover of binding sites seems to fit a molecular clock, at an approximate rate of 0.94% of gain/loss of binding sites per million years. This intense turnover affects both high and low affinity binding sites at the same extent. Furthermore, the subset of overlapping binding sites is also subjected to this high turnover. Conserved binding sites seem to be constrained to maintain not only location but also the exact sequence at each particular position. Finally, we detected a significant decrease in mean PWM scores for the D. virilis binding sites in the case of Hunchback. Possible explanations for this fact are discussed.

Natural selection on protein-coding genes in the human genome

Carlos Bustamante — 2005-10-20T02:51:21-00:00

Nature, Vol. 437, No. 7062., pp. 1153-1157.

The cost of inbreeding in Arabidopsis.

CD Bustamante — 2006-08-03T22:26:32-00:00

Nature, Vol. 416, No. 6880. (4 April 2002), pp. 531-534.

Population geneticists have long sought to estimate the distribution of selection intensities among genes of diverse function across the genome. Only recently have DNA sequencing and analytical techniques converged to make this possible. Important advances have come from comparing genetic variation within species (polymorphism) with fixed differences between species (divergence). These approaches have been used to examine individual genes for evidence of selection. Here we use the fact that the time since species divergence allows combination of data across genes. In a comparison of amino-acid replacements among species of the mustard weed Arabidopsis with those among species of the fruitfly Drosophila, we find evidence for predominantly beneficial gene substitutions in Drosophila but predominantly detrimental substitutions in Arabidopsis. We attribute this difference to the Arabidopsis mating system of partial self-fertilization, which corroborates a prediction of population genetics theory that species with a high frequency of inbreeding are less efficient in eliminating deleterious mutations owing to their reduced effective population size.

Polymorphism and divergence for island-model species.

J Wakeley — 2007-11-19T02:45:15-00:00

Genetics, Vol. 163, No. 1. (January 2003), pp. 411-420.

Estimates of the scaled selection coefficient, gamma of Sawyer and Hartl, are shown to be remarkably robust to population subdivision. Estimates of mutation parameters and divergence times, in contrast, are very sensitive to subdivision. These results follow from an analysis of natural selection and genetic drift in the island model of subdivision in the limit of a very large number of subpopulations, or demes. In particular, a diffusion process is shown to hold for the average allele frequency among demes in which the level of subdivision sets the timescale of drift and selection and determines the dynamic equilibrium of allele frequencies among demes. This provides a framework for inference about mutation, selection, divergence, and migration when data are available from a number of unlinked nucleotide sites. The effects of subdivision on parameter estimates depend on the distribution of samples among demes. If samples are taken singly from different demes, the only effect of subdivision is in the rescaling of mutation and divergence-time parameters. If multiple samples are taken from one or more demes, high levels of within-deme relatedness lead to low levels of intraspecies polymorphism and increase the number of fixed differences between samples from two species. If subdivision is ignored, mutation parameters are underestimated and the species divergence time is overestimated, sometimes quite drastically. Estimates of the strength of selection are much less strongly affected and always in a conservative direction.

Unmasking Activation of the Zygotic Genome Using Chromosomal Deletions in the Drosophila Embryo

Stefano De Renzis — 2007-08-22T19:11:28-00:00

PLoS Biology, Vol. 5, No. 5. (1 May 2007), e117.

During the maternal-to-zygotic transition, a developing embryo integrates post-transcriptional regulation of maternal mRNAs with transcriptional activation of its own genome. By combining chromosomal ablation in Drosophila with microarray analysis, we characterized the basis of this integration. We show that the expression profile for at least one third of zygotically active genes is coupled to the concomitant degradation of the corresponding maternal mRNAs. The embryo uses transcription and degradation to generate localized patterns of expression, and zygotic transcription to degrade distinct classes of maternal transcripts. Although degradation does not appear to involve a simple regulatory code, the activation of the zygotic genome starts from intronless genes sharing a common cis-element. This cis-element interacts with a single protein, the Bicoid stability factor, and acts as a potent enhancer capable of timing the activity of an exogenous transactivator. We propose that this regulatory mode links morphogen gradients with temporal regulation during the maternal-to-zygotic transition.

Global analysis of patterns of gene expression during Drosophila embryogenesis

Pavel Tomancak — 2007-07-25T03:21:47-00:00

Genome Biology, Vol. 8 (23 July 2007), R145.

Reliable prediction of regulator targets using 12 Drosophila genomes.

Alexander Stark — 2007-11-16T23:59:59-00:00

Genome Res (7 November 2007)

Gene expression is regulated pre- and post-transcriptionally via cis-regulatory DNA and RNA motifs. Identification of individual functional instances of such motifs in genome sequences is a major goal for inferring regulatory networks yet has been hampered due to the motifs' short lengths that lead to many chance matches and poor signal-to-noise ratios. In this paper, we develop a general methodology for the comparative identification of functional motif instances across many related species, using a phylogenetic framework that accounts for the evolutionary relationships between species, allows for motif movements, and is robust against missing data due to artifacts in sequencing, assembly, or alignment. We also provide a robust statistical framework for evaluating motif confidence, which enables us to translate evolutionary conservation into a confidence measure for each motif instance, correcting for varying motif length, composition, and background conservation of the target regions. We predict targets of fly transcription factors and miRNAs in alignments of 12 recently sequenced Drosophila species. When compared to extensive genome-wide experimental data, predicted targets are of high quality, matching and surpassing ChIP-chip microarrays and recovering miRNA targets with high sensitivity. The resulting regulatory network suggests significant redundancy between pre- and post-transcriptional regulation of gene expression.

Programming gene expression with combinatorial promoters

Robert Cox — 2007-11-13T20:47:10-00:00

Mol Syst Biol, Vol. 3 (13 November 2007)

Dissecting Timing Variability in Yeast Meiosis

Iftach Nachman — 2007-11-07T17:35:40-00:00

Cell, Vol. 131, No. 3. (2 November 2007), pp. 544-556.

Summary Cell-to-cell variability in the timing of cell-fate changes can be advantageous for a population of single-celled organisms growing in a fluctuating environment. We study timing variability during meiosis in Saccharomyces cerevisiae, initiated upon nutritional starvation. We use time-lapse fluorescence microscopy to measure the timing of meiotic events in single cells and find that the duration of meiosis is highly variable between cells. This variability is concentrated between the beginning of starvation and the onset of early meiosis genes. Cell-cycle variability and nutritional history have little effect on this timing variability. Rather, variation in the production rate of the meiotic master regulator Ime1 and its gradual increase over time govern this variability, and cell size effects are channeled through Ime1. These results tie phenotypic variability with expression dynamics of a transcriptional regulator and provide a general framework for the study of temporal developmental processes.

MORPH: Probabilistic Alignment Combined with Hidden Markov Models of cis-Regulatory Modules

Saurabh Sinha — 2007-11-10T02:00:31-00:00

PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e216.

The discovery and analysis of cis-regulatory modules (CRMs) in metazoan genomes is crucial for understanding the transcriptional control of development and many other biological processes. Cross-species sequence comparison holds much promise for improving computational prediction of CRMs, for elucidating their binding site composition, and for understanding how they evolve. Current methods for analyzing orthologous CRMs from multiple species rely upon sequence alignments produced by off-the-shelf alignment algorithms, which do not exploit the presence of binding sites in the sequences. We present here a unified probabilistic framework, called MORPH, that integrates the alignment task with binding site predictions, allowing more robust CRM analysis in two species. The framework sums over all possible alignments of two sequences, thus accounting for alignment ambiguities in a natural way. We perform extensive tests on orthologous CRMs from two moderately diverged species Drosophila melanogaster and D. mojavensis, to demonstrate the advantages of the new approach. We show that it can overcome certain computational artifacts of traditional alignment tools and provide a different, likely more accurate, picture of cis-regulatory evolution than that obtained from existing methods. The burgeoning field of cis-regulatory evolution, which is amply supported by the availability of many related genomes, is currently thwarted by the lack of accurate alignments of regulatory regions. Our work will fill in this void and enable more reliable analysis of CRM evolution.

Contamination of the genome by very slightly deleterious mutations: why have we not died 100 times over?

AS Kondrashov — 2007-11-16T03:44:13-00:00

J Theor Biol, Vol. 175, No. 4. (21 August 1995), pp. 583-594.

It is well known that when s, the selection coefficient against a deleterious mutation, is below approximately 1/4Ne, where Ne is the effective population size, the expected frequency of this mutation is approximately 0.5, if forward and backward mutation rates are similar. Thus, if the genome size, G, in nucleotides substantially exceeds the Ne of the whole species, there is a dangerous range of selection coefficients, 1/G < s < 1/4Ne. Mutations with s within this range are neutral enough to accumulate almost freely, but are still deleterious enough to make an impact at the level of the whole genome. In many vertebrates Ne approximately 10(4), while G approximately 10(9), so that the dangerous range includes more than four orders of magnitude. If substitutions at 10% of all nucleotide sites have selection coefficients within this range with the mean 10(-6), an average individual carries approximately 100 lethal equivalents. Some data suggest that a substantial fraction of nucleotides typical to a species may, indeed, be suboptimal. When selection acts on different mutations independently, this implies too high a mutation load. This paradox cannot be resolved by invoking beneficial mutations or environmental fluctuations. Several possible resolutions are considered, including soft selection and synergistic epistasis among very slightly deleterious mutations.

The regulatory content of intergenic DNA shapes genome architecture.

CE Nelson — 2006-07-20T14:14:26-00:00

Genome Biol, Vol. 5, No. 4. (2004)

BACKGROUND: Factors affecting the organization and spacing of functionally unrelated genes in metazoan genomes are not well understood. Because of the vast size of a typical metazoan genome compared to known regulatory and protein-coding regions, functional DNA is generally considered to have a negligible impact on gene spacing and genome organization. In particular, it has been impossible to estimate the global impact, if any, of regulatory elements on genome architecture. RESULTS: To investigate this, we examined the relationship between regulatory complexity and gene spacing in Caenorhabditis elegans and Drosophila melanogaster. We found that gene density directly reflects local regulatory complexity, such that the amount of noncoding DNA between a gene and its nearest neighbors correlates positively with that gene's regulatory complexity. Genes with complex functions are flanked by significantly more noncoding DNA than genes with simple or housekeeping functions. Genes of low regulatory complexity are associated with approximately the same amount of noncoding DNA in D. melanogaster and C. elegans, while loci of high regulatory complexity are significantly larger in the more complex animal. Complex genes in C. elegans have larger 5' than 3' noncoding intervals, whereas those in D. melanogaster have roughly equivalent 5' and 3' noncoding intervals. CONCLUSIONS: Intergenic distance, and hence genome architecture, is highly nonrandom. Rather, it is shaped by regulatory information contained in noncoding DNA. Our findings suggest that in compact genomes, the species-specific loss of nonfunctional DNA reveals a landscape of regulatory information by leaving a profile of functional DNA in its wake.

Principles of Genome Evolution in the Drosophila melanogaster Species Group

José Ranz — 2007-06-14T01:02:58-00:00

PLoS Biology, Vol. 5, No. 6. (1 June 2007), e152.

That closely related species often differ by chromosomal inversions was discovered by Sturtevant and Plunkett in 1926. Our knowledge of how these inversions originate is still very limited, although a prevailing view is that they are facilitated by ectopic recombination events between inverted repetitive sequences. The availability of genome sequences of related species now allows us to study in detail the mechanisms that generate interspecific inversions. We have analyzed the breakpoint regions of the 29 inversions that differentiate the chromosomes of Drosophila melanogaster and two closely related species, D. simulans and D. yakuba, and reconstructed the molecular events that underlie their origin. Experimental and computational analysis revealed that the breakpoint regions of 59% of the inversions (17/29) are associated with inverted duplications of genes or other nonrepetitive sequences. In only two cases do we find evidence for inverted repetitive sequences in inversion breakpoints. We propose that the presence of inverted duplications associated with inversion breakpoint regions is the result of staggered breaks, either isochromatid or chromatid, and that this, rather than ectopic exchange between inverted repetitive sequences, is the prevalent mechanism for the generation of inversions in the melanogaster species group. Outgroup analysis also revealed evidence for widespread breakpoint recycling. Lastly, we have found that expression domains in D. melanogaster may be disrupted in D. yakuba, bringing into question their potential adaptive significance.

Rapid sequence turnover at an intergenic locus in Drosophila.

ND Singh — 2007-11-14T21:13:05-00:00

Mol Biol Evol, Vol. 21, No. 4. (April 2004), pp. 670-680.

Closely related species of Drosophila tend to have similar genome sizes. The strong imbalance in favor of small deletions relative to insertions implies that the unconstrained DNA in Drosophila is unlikely to be passively inherited from even closely related ancestors, and yet most DNA in Drosophila genomes is intergenic and potentially unconstrained. In an attempt to investigate the maintenance of this intergenic DNA, we studied the evolution of an intergenic locus on the fourth chromosome of the Drosophila melanogaster genome. This 1.2-kb locus is marked by two distinct, large insertion events: a nuclear transposition of a mitochondrial sequence and a transposition of a nonautonomous DNA transposon DNAREP1_DM. Because we could trace the evolutionary histories of these sequences, we were able to reconstruct the length evolution of this region in some detail. We sequenced this locus in all four species of the D. melanogaster species complex: D. melanogaster, D. simulans, D. sechellia, and D. mauritiana. Although this locus is similar in size in these four species, less than 10% of the sequence from the most recent common ancestor remains in D. melanogaster and all of its sister species. This region appears to have increased in size through several distinct insertions in the ancestor of the D. melanogaster species complex and has been shrinking since the split of these lineages. In addition, we found no evidence suggesting that the size of this locus has been maintained over evolutionary time; these results are consistent with the model of a dynamic equilibrium between persistent DNA loss through small deletions and more sporadic DNA gain through less frequent but longer insertions. The apparent stability of genome size in Drosophila may belie very rapid sequence turnover at intergenic loci.

Pseudogene evolution in Drosophila suggests a high rate of DNA loss.

DA Petrov — 2007-11-14T21:12:26-00:00

Mol Biol Evol, Vol. 15, No. 11. (November 1998), pp. 1562-1567.

How intron splicing affects the deletion and insertion profile in Drosophila melanogaster.

SE Ptak — 2007-11-14T21:11:28-00:00

Genetics, Vol. 162, No. 3. (November 2002), pp. 1233-1244.

Studies of "dead-on-arrival" transposable elements in Drosophila melanogaster found that deletions outnumber insertions approximately 8:1 with a median size for deletions of approximately 10 bp. These results are consistent with the deletion and insertion profiles found in most other Drosophila pseudogenes. In contrast, a recent study of D. melanogaster introns found a deletion/insertion ratio of 1.35:1, with 84% of deletions being shorter than 10 bp. This discrepancy could be explained if deletions, especially long deletions, are more frequently strongly deleterious than insertions and are eliminated disproportionately from intron sequences. To test this possibility, we use analysis and simulations to examine how deletions and insertions of different lengths affect different components of splicing and determine the distribution of deletions and insertions that preserve the original exons. We find that, consistent with our predictions, longer deletions affect splicing at a much higher rate compared to insertions and short deletions. We also explore other potential constraints in introns and show that most of these also disproportionately affect large deletions. Altogether we demonstrate that constraints in introns may explain much of the difference in the pattern of deletions and insertions observed in Drosophila introns and pseudogenes.

DNA loss and evolution of genome size in Drosophila.

DA Petrov — 2007-09-10T12:32:15-00:00

Genetica, Vol. 115, No. 1. (May 2002), pp. 81-91.

Mutation is often said to be random. Although it must be true that mutation is ignorant about the adaptive needs of the organism and thus is random relative to them as a rule, mutation is not truly random in other respects. Nucleotide substitutions, deletions, insertions, inversions, duplications and other types of mutation occur at different rates and are effected by different mechanisms. Moreover the rates of different mutations vary from organism to organism. Differences in mutational biases, along with natural selection, could impact gene and genome evolution in important ways. For instance, several recent studies have suggested that differences in insertion/deletion biases lead to profound differences in the rate of DNA loss in animals and that this difference per se can lead to significant changes in genome size. In particular, Drosophila melanogaster appears to have a very high rate of deletions and the correspondingly high rate of DNA loss and a very compact genome. To assess the validity of these studies we must first assess the validity of the measurements of indel biases themselves. Here I demonstrate the robustness of indel bias measurements in Drosophila, by comparing indel patterns in different types of nonfunctional sequences. The indel pattern and the high rate of DNA loss appears to be shared by all known nonfunctional sequences, both euchromatic and heterochromatic, transposable and non-transposable, repetitive and unique. Unfortunately all available nonfunctional sequences are untranscribed and thus effects of transcription on indel bias cannot be assessed. I also discuss in detail why it is unlikely that natural selection for or against DNA loss significantly affects current estimates of indel biases.

Mutational equilibrium model of genome size evolution.

DA Petrov — 2007-02-07T13:45:10-00:00

Theor Popul Biol, Vol. 61, No. 4. (June 2002), pp. 531-544.

The paper describes a mutational equilibrium model of genome size evolution. This model is different from both adaptive and junk DNA models of genome size evolution in that it does not assume that genome size is maintained either by positive or stabilizing selection for the optimum genome size (as in adaptive theories) or by purifying selection against too much junk DNA (as in junk DNA theories). Instead the genome size is suggested to evolve until the loss of DNA through more frequent small deletions is equal to the rate of DNA gain through more frequent long insertions. The empirical basis for this theory is the finding of a strong correlation and of a clear power-function relationship between the rate of mutational DNA loss (per bp) through small deletions and genome size in animals. Genome size scales as a negative 1.3 power function of the deletion rate per nucleotide. Such a relationship is not predicted by either adaptive or junk DNA theories. However, if genome size is maintained at equilibrium by the balance of mutational forces, this empirilical relationship can be readily accommodated. Within this framework, this finding would imply that the rate of DNA gain through large insertions scales up a quarter-power function of genome size. On this view, as genome size grows, the rate of growth through large insertions is increasing as a quarter power function of genome size and the rate of DNA loss through small deletions increases linearly, until eventually, at the stable equilibrium genome size value, rates of growth and loss equal each other. The current data also suggest that the long-term variation is genome size in animals is brought about to a significant extent by changes in the intrinsic rates of DNA loss through small deletions. Both the origin of mutational biases and the adaptive consequences of such a mode of evolution of genome size are discussed.

Pseudogene evolution and natural selection for a compact genome.

DA Petrov — 2007-11-14T20:59:40-00:00

J Hered, Vol. 91, No. 3. (n 2000), pp. 221-227.

Pseudogenes are nonfunctional copies of protein-coding genes that are presumed to evolve without selective constraints on their coding function. They are of considerable utility in evolutionary genetics because, in the absence of selection, different types of mutations in pseudogenes should have equal probabilities of fixation. This theoretical inference justifies the estimation of patterns of spontaneous mutation from the analysis of patterns of substitutions in pseudogenes. Although it is possible to test whether pseudogene sequences evolve without constraints for their protein-coding function, it is much more difficult to ascertain whether pseudogenes may affect fitness in ways unrelated to their nucleotide sequence. Consider the possibility that a pseudogene affects fitness merely by increasing genome size. If a larger genome is deleterious--for example, because of increased energetic costs associated with genome replication and maintenance--then deletions, which decrease the length of a pseudogene, should be selectively advantageous relative to insertions or nucleotide substitutions. In this article we examine the implications of selection for genome size relative to small (1-400 bp) deletions, in light of empirical evidence pertaining to the size distribution of deletions observed in Drosophila and mammalian pseudogenes. There is a large difference in the deletion spectra between these organisms. We argue that this difference cannot easily be attributed to selection for overall genome size, since the magnitude of selection is unlikely to be strong enough to significantly affect the probability of fixation of small deletions in Drosophila.

Evidence for DNA loss as a determinant of genome size.

DA Petrov — 2006-06-11T03:58:52-00:00

Science, Vol. 287, No. 5455. (11 February 2000), pp. 1060-1062.

Eukaryotic genome sizes range over five orders of magnitude. This variation cannot be explained by differences in organismic complexity (the C value paradox). To test the hypothesis that some variation in genome size can be attributed to differences in the patterns of insertion and deletion (indel) mutations among organisms, this study examines the indel spectrum in Laupala crickets, which have a genome size 11 times larger than that of Drosophila. Consistent with the hypothesis, DNA loss is more than 40 times slower in Laupala than in Drosophila.

High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups.

DA Petrov — 2007-11-14T20:58:05-00:00

Mol Biol Evol, Vol. 15, No. 3. (March 1998), pp. 293-302.

We recently proposed that patterns of evolution of non-LTR retrotransposable elements can be used to study patterns of spontaneous mutation. Transposition of non-LTR retrotransposable elements commonly results in creation of 5' truncated, "dead-on-arrival" copies. These inactive copies are effectively pseudogenes and, according to the neutral theory, their molecular evolution ought to reflect rates and patterns of spontaneous mutation. Maximum parsimony can be used to separate the evolution of active lineages of a non-LTR element from the fate of the "dead-on-arrival" insertions and to directly assess the relative frequencies of different types of spontaneous mutations. We applied this approach using a non-LTR element, Helena, in the Drosophila virilis group and have demonstrated a surprisingly high incidence of large deletions and the virtual absence of insertions. Based on these results, we suggested that Drosophila in general may exhibit a high rate of spontaneous large deletions and have hypothesized that such a high rate of DNA loss may help to explain the puzzling dearth of bona fide pseudogenes in Drosophila. We also speculated that variation in the rate of spontaneous deletion may contribute to the divergence of genome size in different taxa by affecting the amount of superfluous "junk" DNA such as, for example, pseudogenes or long introns. In this paper, we extend our analysis to the D. melanogaster subgroup, which last shared a common ancestor with the D. virilis group approximately 40 MYA. In a different region of the same transposable element, Helena, we demonstrate that inactive copies accumulate deletions in species of the D. melanogaster subgroup at a rate very similar to that of the D. virilis group. These results strongly suggest that the high rate of DNA loss is a general feature of Drosophila and not a peculiar property of a particular stretch of DNA in a particular species group.