Molecular Biology and Evolution - recent issues

Lack of Evolutionary Conservation at Positions Important for Thermal Stability in the Yeast ODCase Protein

Jakubowska, A., Korona, R. — 2009-06-09

Mutations destabilizing the spatial structure of proteins can persist in populations if they are fixed by drift or compensated by other mutations. The prevalence and dynamics of these processes remain largely unrecognized. A suitable target to screen for both deleterious and compensatory mutations is the URA3 gene in yeast. We identified 13 positions in which a single missense substitution causes substantially strong thermal sensitivity. We then applied mild mutagenesis resulting in roughly one base substitution per gene and found that only reversions to an original amino acid can compensate for the thermal instability. However, the 13 positions are not visibly conserved across 53 species of Ascomycota, despite that the gene product is an enzyme of stable function and high efficiency. This shows how much fitness penalties for amino acid substitutions are background dependent, underscoring the role of complex intragenic interactions in the evolution of proteins.

Can Indirect Tests Detect a Known Recombination Event in Human mtDNA?

White, D. J., Gemmell, N. J. — 2009-06-09

Whether human mitochondrial DNA (mtDNA) recombines sufficiently to influence its evolution, evolutionary analysis, and disease etiology, remains equivocal. Overall, evidence from indirect studies of population genetic data suggests that recombination is not occurring at detectable levels. This may be explained by no, or low, recombination or, alternatively, current indirect tests may be incapable of detecting recombination in human mtDNA. To investigate the latter, we have tested whether six well-established indirect tests of recombination could detect recombination in a human mtDNA data set, in which its occurrence had been empirically confirmed. Three showed statistical evidence for recombination (r² vs. distance, the Homoplasy test, Neighborhood Similarity Score), and three did not (D' vs. distance, Max Chi Squared, Pairwise Homoplasy Index). Possible reasons for detection failure are discussed. Further, evidence from earlier studies suggesting a lack of recombination in mtDNA in humans is reconsidered, taking into account the appropriateness of the tests used, based on our new findings.

Is Interlineage Recombination Responsible for Low Divergence of Mitochondrial nad3 Genes in Mytilus galloprovincialis?

Burzynski, A., Smietanka, B. — 2009-06-09

The existence of mtDNA recombination in animals has been confirmed by several case studies. Still, for Mytilus mussels possessing two divergent mitochondrial genomes (M and F), which can recombine, no recombination between coding sequences of highly diverged M and F genomes has been shown. Based on the full sequences of both genomes, it has been suggested that particularly low divergence observed within the mitochondrial nad3 gene of the Mytilus galloprovincialis mussel may be caused by its exceptionally low evolutionary rate. Here, we contribute a new pair of mitochondrial genomes typical for M. galloprovincialis and show that this low divergence is not a sign of evolutionary conservation but is rather caused by the acquisition of an F-related sequence by the published M genome of M. galloprovincialis. The most likely scenario for this apparent mtDNA-coding region recombination case is an assembly artifact.

Molecular Evolution and Functional Diversification of Fatty Acid Desaturases after Recurrent Gene Duplication in Drosophila

Fang, S., Ting, C.-T., Lee, C.-R., Chu, K.-H., Wang, C.-C., Tsaur, S.-C. — 2009-06-09

Frequent gene duplications in the genome incessantly supply new genetic materials for functional innovation presumably driven by positive Darwinian selection. This mechanism in the desaturase gene family has been proposed to be important in triggering the pheromonal diversification in insects. With the recent completion of a dozen Drosophila genomes, a genome-wide perspective is possible. In this study, we first identified homologs of desaturase genes in 12 Drosophila species and noted that while gene duplication events are relatively frequent, gene losses are not scarce, especially in the desat1–desat2–desatF clade. By reconciling the gene tree with species phylogeny and the chromosomal synteny of the sequenced Drosophila genomes, at least one gene loss in desat2 and a minimum of six gene gains (resulting in seven desatF homologs, -), three gene losses and one relocation in desatF were inferred. Upon branching off the ancestral desat1 lineage, both desat2 and desatF gained novel functions through accelerating protein evolution. The amino acid residues under positive selection located near the catalytic sites and the C-terminal region might be responsible for altered substrate selectivity between closely related species. The association between the expression pattern of desatF- and the chemical composition of cuticular hydrocarbons implies that the ancestral function of desatF- is the second desaturation at the four carbons after the first double bond in diene synthesis, and the shift from bisexual to female-specific expression in desatF- occurred in the ancestral lineage of Drosophila melanogaster subgroup. A relationship between the number of expressed desatF homologs and the diene diversification has also been observed. These results suggest that the molecular diversification of fatty acid desaturases after recurrent gene duplication plays an important role in pheromonal diversity in Drosophila.

A Permutation Test of Host-Parasite Cospeciation

Hommola, K., Smith, J. E., Qiu, Y., Gilks, W. R. — 2009-06-09

We introduce a statistical method that explores host–parasite coevolution by testing the null hypothesis that hosts and their associated parasites evolved independently. This test is simple and intuitive and involves only suitable randomization of the observed data. It is not even necessary to construct host and parasite phylogenetic trees, as the test can be performed directly on distance matrices. Statistical power of the test was evaluated using simulated data consistent with the alternative hypothesis of cospeciation. Results were compared with the method of Mantel (1967) and the ParaFit method of Legendre et al. (2002). We observed that our method has greater power overall and thus a higher ability to detect cospeciation in closely related host–parasite systems. Our test was also successful when applied to the pocket gopher and chewing lice system.

Origin and Ascendancy of a Chimeric Fusion Gene: The {beta}/{delta}-Globin Gene of Paenungulate Mammals

Opazo, J. C., Sloan, A. M., Campbell, K. L., Storz, J. F. — 2009-06-09

The -globin gene (HBD) of eutherian mammals exhibits a propensity for recombinational exchange with the closely linked β-globin gene (HBB) and has been independently converted by the HBB gene in multiple lineages. Here we report the presence of a chimeric β/ fusion gene in the African elephant (Loxodonta africana) that was created by unequal crossing-over between misaligned HBD and HBB paralogs. The recombinant chromosome that harbors the β/ fusion gene in elephants is structurally similar to the "anti-Lepore" duplication mutant of humans (the reciprocal exchange product of the hemoglobin Lepore deletion mutant). However, the situation in the African elephant is unique in that the chimeric β/ fusion gene supplanted the parental HBB gene and is therefore solely responsible for synthesizing the β-chain subunits of adult hemoglobin. A phylogenetic survey of β-like globin genes in afrotherian and xenarthran mammals revealed that the origin of the chimeric β/ fusion gene and the concomitant inactivation of the HBB gene predated the radiation of "Paenungulata," a clade of afrotherian mammals that includes three orders: Proboscidea (elephants), Sirenia (dugongs and manatees), and Hyracoidea (hyraxes). The reduced fitness of the human Hb Lepore deletion mutant helps to explain why independently derived β/ fusion genes (which occur on an anti-Lepore chromosome) have been fixed in a number of mammalian lineages, whereas the reciprocal /β fusion gene (which occurs on a Lepore chromosome) has yet to be documented in any nonhuman mammal. This illustrates how the evolutionary fates of chimeric fusion genes can be strongly influenced by their recombinational mode of origin.

Inferring Population Mutation Rate and Sequencing Error Rate Using the SNP Frequency Spectrum in a Sample of DNA Sequences

Liu, X., Maxwell, T. J., Boerwinkle, E., Fu, Y.-X. — 2009-06-09

One challenge of analyzing samples of DNA sequences is to account for the nonnegligible polymorphisms produced by error when the sequencing error rate is high or the sample size is large. Specifically, those artificial sequence variations will bias the observed single nucleotide polymorphism (SNP) frequency spectrum, which in turn may further bias the estimators of the population mutation rate $$\theta =4N\mu $$ for diploids. In this paper, we propose a new approach based on the generalized least squares (GLS) method to estimate , given a SNP frequency spectrum in a random sample of DNA sequences from a population. With this approach, error rate can be either known or unknown. In the latter case, can be estimated given an estimation of . Using coalescent simulation, we compared our estimators with other estimators of . The results showed that the GLS estimators are more efficient than other estimators with error, and the estimation of is usable in practice when the per bp is small. We demonstrate the application of the estimators with 10-kb noncoding region sequence sampled from a human population and provide suggestions for choosing estimators with error.

Evolution of the Vertebrate Gene Regulatory Network Controlled by the Transcriptional Repressor REST

Johnson, R., Samuel, J., Ng, C. K. L., Jauch, R., Stanton, L. W., Wood, I. C. — 2009-06-09

Specific wiring of gene-regulatory networks is likely to underlie much of the phenotypic difference between species, but the extent of lineage-specific regulatory architecture remains poorly understood. The essential vertebrate transcriptional repressor REST (RE1-Silencing Transcription Factor) targets many neural genes during development of the preimplantation embryo and the central nervous system, through its cognate DNA motif, the RE1 (Repressor Element 1). Here we present a comparative genomic analysis of REST recruitment in multiple species by integrating both sequence and experimental data. We use an accurate, experimentally validated Position-Specific Scoring Matrix method to identify REST binding sites in multiply aligned vertebrate genomes, allowing us to infer the evolutionary origin of each of 1,298 human RE1 elements. We validate these findings using experimental data of REST binding across the whole genomes of human and mouse. We show that one-third of human RE1s are unique to primates: These sites recruit REST in vivo, target neural genes, and are under purifying evolutionary selection. We observe a consistent and significant trend for more ancient RE1s to have higher affinity for REST than lineage-specific sites and to be more proximal to target genes. Our results lead us to propose a model where new transcription factor binding sites are constantly generated throughout the genome; thereafter, refinement of their sequence and location consolidates this remodeling of networks governing neural gene regulation.

Calcium-Activated Potassium (BK) Channels Are Encoded by Duplicate slo1 Genes in Teleost Fishes

Rohmann, K. N., Deitcher, D. L., Bass, A. H. — 2009-06-09

Calcium-activated, large conductance potassium (BK) channels in tetrapods are encoded by a single slo1 gene, which undergoes extensive alternative splicing. Alternative splicing generates a high level of functional diversity in BK channels that contributes to the wide range of frequencies electrically tuned by the inner ear hair cells of many tetrapods. To date, the role of BK channels in hearing among teleost fishes has not been investigated at the molecular level, although teleosts account for approximately half of all extant vertebrate species. We identified slo1 genes in teleost and nonteleost fishes using polymerase chain reaction and genetic sequence databases. In contrast to tetrapods, all teleosts examined were found to express duplicate slo1 genes in the central nervous system, whereas nonteleosts that diverged prior to the teleost whole-genome duplication event express a single slo1 gene. Phylogenetic analyses further revealed that whereas other slo1 duplicates were the result of a single duplication event, an independent duplication occurred in a basal teleost (Anguilla rostrata) following the slo1 duplication in teleosts. A third, independent slo1 duplication (autotetraploidization) occurred in salmonids. Comparison of teleost slo1 genomic sequences to their tetrapod orthologue revealed a reduced number of alternative splice sites in both slo1 co-orthologues. For the teleost Porichthys notatus, a focal study species that vocalizes with maximal spectral energy in the range electrically tuned by BK channels in the inner ear, peripheral tissues show the expression of either one (e.g., vocal muscle) or both (e.g., inner ear) slo1 paralogues with important implications for both auditory and vocal physiology. Additional loss of expression of one slo1 paralogue in nonneural tissues in P. notatus suggests that slo1 duplicates were retained via subfunctionalization. Together, the results predict that teleost fish achieve a diversity of BK channel subfunction via gene duplication, rather than increased alternative splicing as witnessed for the tetrapod and invertebrate orthologue.

Variation in the Ratio of Nucleotide Substitution and Indel Rates across Genomes in Mammals and Bacteria

Chen, J.-Q., Wu, Y., Yang, H., Bergelson, J., Kreitman, M., Tian, D. — 2009-06-09

Rates of nucleotide substitution and insertion/deletion (indel) are known to vary across the functional components of a genome. Little attention has been paid, however, to the quantitative relationship between the two. Here we investigate the ratio of nucleotide substitutions to indels (S/I) in different regions of 4 primates, 70 bacteria, and 8 other genomes. We find that the ratio differs at 5.4-times between coding and noncoding, 3.3-times between conserved and less conserved coding sequences, and 1.46-times between nonrepeat and repeat regions. The S/I ratio is also positively correlated with the level of divergence between the genomes compared. Our results suggest that the S/I ratio may reflect differences in the efficacy of selection against indels. Due to the sensitivity of indel density in different regions, this ratio varies over a much larger range. With the recent discovery suggesting that indels act as local enhancers of mutation in surrounding sequences, nucleotide substitution rates are expected to be accelerated in regions of low constraint, where indels tend to accumulate, but will otherwise be modulated in proportion to the level of a sequence's functional constraint. Indels, therefore, may play a nontrivial role in controlling differences in genetic variation and divergence across functional regions of a genome.

A Proteomic Survey of Chlamydomonas reinhardtii Mitochondria Sheds New Light on the Metabolic Plasticity of the Organelle and on the Nature of the {alpha}-Proteobacterial Mitochondrial Ancestor

2009-06-09

Mitochondria play a key role in the life and death of eukaryotic cells, yet the full spectrum of mitochondrial functions is far from being fully understood, especially in photosynthetic organisms. To advance our understanding of mitochondrial functions in a photosynthetic cell, an extensive proteomic survey of Percoll-purified mitochondria from the metabolically versatile, hydrogen-producing green alga Chlamydomonas reinhardtii was performed. Different fractions of purified mitochondria from Chlamydomonas cells grown under aerobic conditions were analyzed by nano-liquid chromatography–electrospray ionization–mass spectrometry after protein separation on sodium dodecyl sulfate polyacrylamide gel electrophoresis or on blue-native polyacrylamide gel electrophoresis. Of the 496 nonredundant proteins identified, 149 are known or predicted to reside in other cellular compartments and were thus excluded from the molecular and evolutionary analyses of the Chlamydomonas proteome. The mitochondrial proteome of the photosynthetic alga reveals important lineage-specific differences with other mitochondrial proteomes, reflecting the high metabolic diversity of the organelle. Some mitochondrial metabolic pathways in Chlamydomonas appear to combine typical mitochondrial enzymes and bacterial-type ones, whereas others are unknown among mitochondriate eukaryotes. The comparison of the Chlamydomonas proteins to their identifiable homologs predicted from 354 sequenced genomes indicated that Arabidopsis is the most closely related nonalgal eukaryote. Furthermore, this phylogenomic analysis shows that free-living -proteobacteria from the metabolically versatile orders Rhizobiales and Rhodobacterales better reflect the gene content of the ancestor of the chlorophyte mitochondria than parasitic -proteobacteria with reduced and specialized genomes.

Recent Strong Positive Selection on Drosophila melanogaster HDAC6, a Gene Encoding a Stress Surveillance Factor, as Revealed by Population Genomic Analysis

Svetec, N., Pavlidis, P., Stephan, W. — 2009-06-09

Based on nearly complete genome sequences from a variety of organisms, data on naturally occurring genetic variation on the scale of hundreds of loci to entire genomes have been collected in recent years. In parallel, new statistical approaches (such as the composite likelihood ratio and "SweepFinder" tests) have been developed to infer evidence of recent positive selection from these data and to localize the target of selection. Here, we apply these methods to the X chromosome of Drosophila melanogaster in an effort to map genes involved in ecological adaptation. Using slight modifications of these tests that increase their robustness against past demographic changes, we detected evidence that recent strongly positive selection has been acting on a 2.7-kb region in an ancestral African population. This region overlaps with the 3' end of HDAC6, a gene that encodes a newly characterized stress surveillance factor. HDAC6 is an unusual histone deacetylase being localized in the cytoplasm. Its ubiquitin-binding and tubulin-deacetylase activities suggest that HDAC6 is very different from other histone deacetylases. Indeed, recent discoveries have shown that HDAC6 is a key regulator of cytotoxic stress resistance.

The Fruitless Gene in Nasonia Displays Complex Sex-Specific Splicing and Contains New Zinc Finger Domains

Bertossa, R. C., van de Zande, L., Beukeboom, L. W. — 2009-06-09

The transcription factor Fruitless exerts a broad range of functions during Drosophila development, the most apparent of which is the determination of sexual behavior in males. Although fruitless sequences are found in other insect orders, little is known about fruitless structure and function outside Diptera. We have performed a thorough analysis of fruitless transcripts in the haplo-diploid wasp Nasonia vitripennis and found both sex-specific and non–sex-specific transcripts similar to those found in Drosophila. In Nasonia, however, a novel, large fruitless transcript is present in females only. Putative binding sites for sex-specific splicing factors found in Nasonia fruitless and doublesex as well as Apis mellifera doublesex transcripts were sufficient to identify a corresponding female-specific fruitless exon in A. mellifera, suggesting that similar factors in both hymenopteran species could be responsible for sex-specific splicing of both genes. Furthermore, new C₂H₂ zinc finger domains found in Nasonia fruitless transcripts were also identified in the fruitless locus of major holometabolous insect species but not in drosophilids. Conservation of important domains and sex-specific splicing in Diptera and Hymenoptera support the hypothesis that fruitless is an ancient gene and has conserved functions in insects. Considerable divergences in other parts of the gene are expected to underlie species-specific differences and may help to explain diversity observed in insect sexual behaviors.

Translationally Optimal Codons Associate with Structurally Sensitive Sites in Proteins

Zhou, T., Weems, M., Wilke, C. O. — 2009-06-09

The mistranslation-induced protein misfolding hypothesis predicts that selection should prefer high-fidelity codons at sites at which translation errors are structurally disruptive and lead to protein misfolding and aggregation. To test this hypothesis, we analyzed the relationship between codon usage bias and protein structure in the genomes of four model organisms, Escherichia coli, yeast, fly, and mouse. Using both the Mantel–Haenszel procedure, which applies to categorical data, and a newly developed association test for continuous variables, we find that translationally optimal codons associate with buried residues and also with residues at sites where mutations lead to large changes in free energy (G). In each species, only a subset of all amino acids show this signal, but most amino acids show the signal in at least one species. By repeating the analysis on a reduced data set that excludes interdomain linkers, we show that our results are not caused by an association of rare codons with solvent-accessible linker regions. Finally, we find that our results depend weakly on expression level; the association between optimal codons and buried sites exists at all expression levels, but increases in strength as expression level increases.

Genetic and Demographic Implications of the Bantu Expansion: Insights from Human Paternal Lineages

2009-06-09

The expansion of Bantu languages, which started around 5,000 years before present in west/central Africa and spread all throughout sub-Saharan Africa, may represent one of the major and most rapid demographic movements in the history of the human species. Although the genetic footprints of this expansion have been unmasked through the analyses of the maternally inherited mitochondrial DNA lineages, information on the genetic impact of this massive movement and on the genetic composition of pre-Bantu populations is still scarce.

Here, we analyze an extensive collection of Y-chromosome markers—41 single nucleotide polymorphisms and 18 short tandem repeats—in 883 individuals from 22 Bantu-speaking agriculturalist populations and 3 Pygmy hunter-gatherer populations from Gabon and Cameroon. Our data reveal a recent origin for most paternal lineages in west Central African populations most likely resulting from the expansion of Bantu-speaking farmers that erased the more ancient Y-chromosome diversity found in this area. However, some traces of ancient paternal lineages are observed in these populations, mainly among hunter-gatherers. These results are at odds with those obtained from mtDNA analyses, where high frequencies of ancient maternal lineages are observed, and substantial maternal gene flow from hunter-gatherers to Bantu farmers has been suggested. These differences are most likely explained by sociocultural factors such as patrilocality. We also find the intriguing presence of paternal lineages belonging to Eurasian haplogroup R1b1*, which might represent footprints of demographic expansions in central Africa not directly related to the Bantu expansion.

Strong Evidence for Lineage and Sequence Specificity of Substitution Rates and Patterns in Drosophila

Singh, N. D., Arndt, P. F., Clark, A. G., Aquadro, C. F. — 2009-06-09

Rates of single nucleotide substitution in Drosophila are highly variable within the genome, and several examples illustrate that evolutionary rates differ among Drosophila species as well. Here, we use a maximum likelihood method to quantify lineage-specific substitutional patterns and apply this method to 4-fold degenerate synonymous sites and introns from more than 8,000 genes aligned in the Drosophila melanogaster group. We find that within species, different classes of sequence evolve at different rates, with long introns evolving most slowly and short introns evolving most rapidly. Relative rates of individual single nucleotide substitutions vary ~3-fold among lineages, yielding patterns of substitution that are comparatively less GC-biased in the melanogaster species complex relative to Drosophila yakuba and Drosophila erecta. These results are consistent with a model coupling a mutational shift toward reduced GC content, or a shift in mutation–selection balance, in the D. melanogaster species complex, with variation in selective constraint among different classes of DNA sequence. Finally, base composition of coding and intronic sequences is not at equilibrium with respect to substitutional patterns, which primarily reflects the slow rate of the substitutional process. These results thus support the view that mutational and/or selective processes are labile on an evolutionary timescale and that if the process is indeed selection driven, then the distribution of selective constraint is variable across the genome.

Characterization of 67 Mitochondrial tRNA Gene Rearrangements in the Hymenoptera Suggests That Mitochondrial tRNA Gene Position Is Selectively Neutral

Dowton, M., Cameron, S. L., Dowavic, J. I., Austin, A. D., Whiting, M. F. — 2009-06-09

We present entire sequences of two hymenopteran mitochondrial genomes and the major portion of three others. We combined these data with nine previously sequenced hymenopteran mitochondrial genomes. This allowed us to infer and analyze the evolution of the 67 mitochondrial gene rearrangements so far found in this order. All of these involve tRNA genes, whereas four also involve larger (protein-coding or ribosomal RNA) genes. We find that the vast majority of mitochondrial gene rearrangements are independently derived. A maximum of four of these rearrangements represent shared, derived organizations, whereas three are convergently derived. The remaining mitochondrial gene rearrangements represent new mitochondrial genome organizations. These data are consistent with the proposal that there are an enormous number of alternative mitochondrial genome organizations possible and that mitochondrial genome organization is, for the most part, selectively neutral. Nevertheless, some mitochondrial genes appear less mobile than others. Genes close to the noncoding region are generally more mobile but only marginally so. Some mitochondrial genes rearrange in a pattern consistent with the duplication/random loss model, but more mitochondrial genes move in a pattern inconsistent with this model. An increased rate of mitochondrial gene rearrangement is not tightly associated with the evolution of parasitism. Although parasitic lineages tend to have more mitochondrial gene rearrangements than nonparasitic lineages, there are exceptions (e.g., Orussus and Schlettererius). It is likely that only a small proportion of the total number of mitochondrial gene rearrangements that have occurred during the evolution of the Hymenoptera have been sampled in the present study.

The Evolutionarily Dynamic IFN-Inducible GTPase Proteins Play Conserved Immune Functions in Vertebrates and Cephalochordates

Li, G., Zhang, J., Sun, Y., Wang, H., Wang, Y. — 2009-06-09

Interferon (IFN)-inducible GTPases currently include four families of proteins: myxovirus resistant proteins (Mxs), guanylate-binding proteins (GBPs), immunity-related GTPase proteins (IRGs), and very large inducible GTPase proteins (VLIGs). They are all under conserved regulation by IFNs in humans and mice and play a critical role in preventing microbial infections. However, differences between vertebrates are poorly characterized, and their evolutionary origins have not been studied in detail. In this study, we performed comparative genomic analysis of the four families in 18 representative animals that yielded several unexpected results. Firstly, we found that Mx, GBP, and IRG protein families arose before the divergence of chordate subphyla, but VLIG emerged solely in vertebrates. Secondly, IRG, GBP, and VLIG families have experienced a high rate of gene gain and loss during the evolution, with the GBP family being lost entirely in two pufferfish and VLIG family lost in primates and carnivores. Thirdly, the regulation of these genes by IFNs is highly conserved throughout vertebrates although the VLIG protein sequences in fish have lost the first 870 amino acid residues. Finally, amphioxus IFN-inducible GTPase genes are all highly expressed in immune-related organs such as gill, liver, and intestine and are upregulated after challenge with PolyI:C and pathogens, although no IFNs or their receptors were detected in the current amphioxus genome database. These results suggest that IFN-inducible GTPase genes play conserved immune functions both in vertebrates and in cephalochordates.

Evolutionary Scenarios of Notch Proteins

Theodosiou, A., Arhondakis, S., Baumann, M., Kossida, S. — 2009-06-09

Notch is a highly conserved family of transmembrane receptors and transcription factors that are key players in several developmental processes. In this study, we identified novel Notch sequences from various species covering from worm to human and conducted a comprehensive phylogenetic analysis in order to confirm and extend the evolutionary history of Notch. Our findings confirm an independent duplication event in Caenorhabditis elegans resulting in two Notch genes and show that the vertebrate Notch genes resulted from two duplication events, both of which occurred before the divergence of teleosts and tetrapoda. Furthermore, we demonstrate that the vertebrate Notch2 group is phylogenetically closer to Notch3 and that Notch2 appeared at the first round of vertebrate duplication events. Moreover, there is evidence that the two Notch1 genes in fish, appeared by a recent duplication of Notch1 in teleost after the divergence of teleost and tetrapoda. Whether this is from ancient whole genome duplication (WGD) or gene duplication remains to be elucidated. The fourth group of Notch (Notch4) was found only in mammals. We suggest two possible scenarios for the origin of the Notch4 subfamily: 1) Notch4 appeared at the time of the two WGDs in the early chordate but has been maintained only in the mammalian lineage and was lost in the other lineages, 2) a recent independent duplication event took place in the mammalian lineage. The increase of the sequencing data from Xenopus tropicalis, Gallus gallus genome projects and of other avian and reptile genomes will shed more light on this event. Nevertheless, the great divergence of Notch4, from the other three Notch genes, suggests a rapid divergence raising questions about the functional implication of this event. In addition, comparison of the organization of Notch syntenic genes among species supports the coordinated rearrangements during evolution for Notch, PBX, and BRD families that may lead to possible functional relationships.

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

Price, M. N., Dehal, P. S., Arkin, A. P. — 2009-06-09

Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement Neighbor-Joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N²) space and O(N²L) time, but FastTree requires just O(NLa + N ) memory and O(N log (N)La) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 h and 2.4 GB of memory. Just computing pairwise Jukes–Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 h and 50 GB of memory. In simulations, FastTree was slightly more accurate than Neighbor-Joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

Sixty Million Years in Evolution of Soft Grain Trait in Grasses: Emergence of the Softness Locus in the Common Ancestor of Pooideae and Ehrhartoideae, after their Divergence from Panicoideae

Charles, M., Tang, H., Belcram, H., Paterson, A., Gornicki, P., Chalhoub, B. — 2009-06-09

Together maize, Sorghum, rice, and wheat grass (Poaceae) species are the most important cereal crops in the world and exhibit different "grain endosperm texture." This trait has been studied extensively in wheat because of its pivotal role in determining quality of products obtained from wheat grain. Grain softness protein-1 and Puroindolines A and B (grain storage proteins), encoded by Ha-like genes: Gsp-1, Pina, and Pinb, of the Hardness (Ha) locus, are the main determinants of the grain softness/hardness trait in wheat. The origin and evolution of grain endosperm texture in grasses was addressed by comparing genomic sequences of the Ha orthologous region of wheat, Brachypodium, rice, and Sorghum. Results show that the Ha-like genes are present in wheat and Brachypodium but are absent from Sorghum bicolor. A truncated remnant of an Ha-like gene is present in rice. Synteny analysis of the genomes of these grass species shows that only one of the paralogous Ha regions, created 70 My by whole-genome duplication, contained Ha-like genes. The comparative genome analysis and evolutionary comparison with genes encoding grain reserve proteins of grasses suggest that an ancestral Ha-like gene emerged, as a new member of the prolamin gene family, in a common ancestor of the Pooideae (Triticeae and Brachypoidieae tribes) and Ehrhartoideae (rice), between 60 and 50 My, after their divergence from Panicoideae (Sorghum). It was subsequently lost in Ehrhartoideae. Recurring duplications, deletions, and/or truncations occurred independently and appear to characterize Ha-like gene evolution in the grass species. The Ha-like genes gained a new function in Triticeae, such as wheat, underlying the soft grain phenotype. Loss of these genes in some wheat species leads, in turn, to hard endosperm seeds.

Computational Methods for Evaluating Phylogenetic Models of Coding Sequence Evolution with Dependence between Codons

Rodrigue, N., Kleinman, C. L., Philippe, H., Lartillot, N. — 2009-06-09

In recent years, molecular evolutionary models formulated as site-interdependent Markovian codon substitution processes have been proposed as means of mechanistically accounting for selective features over long-range evolutionary scales. Under such models, site interdependencies are reflected in the use of a simplified protein tertiary structure representation and predefined statistical potential, which, along with mutational parameters, mediate nonsynonymous rates of substitution; rates of synonymous events are solely mediated by mutational parameters. Although theoretically attractive, the models are computationally challenging, and the methods used to manipulate them still do not allow for quantitative model evaluations in a multiple-sequence context. Here, we describe Markov chain Monte Carlo computational methodologies for sampling parameters from their posterior distribution under site-interdependent codon substitution models within a phylogenetic context and allowing for Bayesian model assessment and ranking. Specifically, the techniques we expound here can form the basis of posterior predictive checking under these models and can be embedded within thermodynamic integration algorithms for computing Bayes factors. We illustrate the methods using two data sets and find that although current forms of site-interdependent models of codon substitution provide an improved fit, they are outperformed by the extended site-independent versions. Altogether, the methodologies described here should enable a quantified contrasting of alternative ways of modeling structural constraints, or other site-interdependent criteria, and establish if such formulations can match (or supplant) site-independent model extensions.

Evolution of the vertebrate twist family and synfunctionalization: a mechanism for differential gene loss through merging of expression domains

2009-06-09

Comparative Analysis of Structural Diversity and Sequence Evolution in Plant Mitochondrial Genes Transferred to the Nucleus

Liu, S.-L., Zhuang, Y., Zhang, P., Adams, K. L. — 2009-06-09

Lowly Expressed Human MicroRNA Genes Evolve Rapidly

Liang, H., Li, W.-H. — 2009-05-12

To study the evolution of human microRNAs (miRNAs), we examined nucleotide variation in humans, sequence divergence between species, and genomic clustering patterns for miRNAs with different expression levels. We found that expression level is a major indicator of the rate of evolution and that ~30% of currently annotated human miRNA genes are almost free of selective pressure.

Evolution of the Caenorhabditis elegans Genome

Cutter, A. D., Dey, A., Murray, R. L. — 2009-05-12

A fundamental problem in genome biology is to elucidate the evolutionary forces responsible for generating nonrandom patterns of genome organization. As the first metazoan to benefit from full-genome sequencing, Caenorhabditis elegans has been at the forefront of research in this area. Studies of genomic patterns, and their evolutionary underpinnings, continue to be augmented by the recent push to obtain additional full-genome sequences of related Caenorhabditis taxa. In the near future, we expect to see major advances with the onset of whole-genome resequencing of multiple wild individuals of the same species. In this review, we synthesize many of the important insights to date in our understanding of genome organization and function that derive from the evolutionary principles made explicit by theoretical population genetics and molecular evolution and highlight fertile areas for future research on unanswered questions in C. elegans genome evolution. We call attention to the need for C. elegans researchers to generate and critically assess nonadaptive hypotheses for genomic and developmental patterns, in addition to adaptive scenarios. We also emphasize the potential importance of evolution in the gonochoristic (female and male) ancestors of the androdioecious (hermaphrodite and male) C. elegans as the source for many of its genomic and developmental patterns.

Environmental Genomics: A Tale of Two Fishes

2009-05-12

The influence of the environment on two congeneric fishes, Gillichthys mirabilis and Gillichthys seta, that live in the Gulf of California at temperatures of 10–25 °C, and up to 42–44 °C, respectively, was addressed by analyzing their genomes. Compared with G. mirabilis, G. seta showed some striking features. Substitution rates in the mitochondrial genes were found to be extremely fast, in fact faster than in noncoding control regions (D-loops), from which a divergence time of less than 0.66–0.75 Mya could be estimated. In the nuclear genome, 1) both AT -> GC/GC -> AT and transversion: transition ratios in coding sequences (CDSs) were relatively high; moreover, the ratios of nonsynonymous/synonymous changes (Ka/Ks) suggested that some genes were under positive selection; 2) DNA methylation showed a very significant decrease; and 3) a GC-rich minisatellite underwent a 4-fold amplification in the gene-rich regions. All these observations clearly indicate that the environment (temperature and the accompanying hypoxia) can rapidly mold the nuclear as well as the mitochondrial genome. The stabilization of gene-rich regions by the amplification of the GC-rich minisatellite and by the GC increase in nuclear CDSs is of special interest because it provides a model for the formation of the GC-rich and gene-rich isochores of the genomes of mammals and birds.

Duplications and Expression of DIVARICATA-Like Genes in Dipsacales

Howarth, D. G., Donoghue, M. J. — 2009-05-12

The genetics underlying flower symmetry shifts between radial and bilateral symmetry has been intensively studied in the model Antirrhinum majus. Understanding the conservation or diversification of this genetic pathway in other plants is of special interest in understanding angiosperm evolution and ecology. Evidence from Antirrhinum indicates that TCP and MYB transcription factors, especially CYCLOIDEA (CYC), DICHOTOMA (DICH), DIVARICATA (DIV), and RADIALIS (RAD) play a role in specifying dorsal identity (CYC, DICH, and RAD) and ventral identity (DIV) in the corolla and androecium of monosymmetric (bilateral) flowers. Previous data indicate that the ECE clade of TCP genes (including CYC and DICH) underwent two duplication events around the diversification of the core eudicots. In this study, we examined the duplication events within Dipsacales, which contains both radially and bilaterally symmetrical flowered species. Additionally, we report here the phylogenetic relationships of the DIV-like genes across core eudicots. Like TCP genes, we found three core eudicot clades of DIV-like genes, with duplications occurring around the diversification of the core eudicots, which we name DIV1, DIV2, and DIV3. The Antirrhinum genes, DIVARICATA and its sister DVL1, fall into the DIV1 clade. We also found additional duplications within these clades in Dipsacales. Specifically, the Caprifoliaceae (bilaterally symmetrical clade) duplicated independently in each of the three core eudicot DIV clades. Using reverse transcription polymerase chain reaction (rtPCR), we showed that most of these copies are expressed across floral tissues in the Dipsacales species Heptacodium miconioides. One copy, DipsDIV1A (orthologous to DIV and DVL1), was expressed in a dorsal–ventral pattern. DipsDIV1A was expressed only in petal tissue, in both dorsal and ventral regions but was lacking from lateral petals. We argue that this suggests that DipsDIV1A may be expressed in a similar pattern to DIV in Antirrhinum, suggesting a broad conservation of this pathway. Finally, DIV contains a large intron near the beginning of the second MYB domain, which shows promise as a highly variable molecular marker for phylogenetic studies.

Support Patterns from Different Outgroups Provide a Strong Phylogenetic Signal

Schneider, A., Cannarozzi, G. M. — 2009-05-12

It is known that the accuracy of phylogenetic reconstruction decreases when more distant outgroups are used. We quantify this phenomenon with a novel scoring method, the outgroup score pOG. This score expresses if the support for a particular branch of a tree decreases with increasingly distant outgroups. Large-scale simulations confirmed that the outgroup support follows this expectation and that the pOG score captures this pattern. The score often identifies the correct topology even when the primary reconstruction methods fail, particularly in the presence of model violations. In simulations of problematic phylogenetic scenarios such as rate variation among lineages (which can lead to long-branch attraction artifacts) and quartet-based reconstruction, the pOG analysis outperformed the primary reconstruction methods. Because the pOG method does not make any assumptions about the evolutionary model (besides the decreasing support from increasingly distant outgroups), it can detect cases of violations not treated by a specific model or too strong to be fully corrected. When used as an optimization criterion in the construction of a tree of 23 mammals, the outgroup signal confirmed many well-accepted mammalian orders and superorders. It supports Atlantogenata, a clade of Afrotheria and Xenarthra, and suggests an Artiodactyla–Chiroptera clade.

Molecular Evolution of the Drosophila Retinome: Exceptional Gene Gain in the Higher Diptera

Bao, R., Friedrich, M. — 2009-05-12

Using genomic information from mosquito, red flour beetle, honeybee, mouse, and sea anemone, we have studied the molecular evolution of 91 Drosophila genes involved in eye primordium determination, retinal differentiation, and phototransduction. Our results show that the majority of these gene sequences predate the diversification of endopterygote insects. However, all three functional groups contain a conspicuous fraction of evolutionarily younger genes, which originated by tandem duplication in the lineage leading to Drosophila, whereas gene duplications are rare in other insect lineages. We conclude that the retention of duplicated genes spiked during the early diversification of the higher Diptera possibly due to an extended period of exceptional population size reduction. Genetic data suggest that gene duplication played an important role in the evolution of visual performance in the fast flying higher Diptera by spatial or intracellular subfunctionalization. Developmental gene duplications, by contrast, predominantly retained overlapping expression patterns and preserved partial to complete redundancy consistent with a role in boosting developmental robustness.

Layers of Evolvability in a Bacteriophage Life History Trait

Heineman, R. H., Bull, J. J., Molineux, I. J. — 2009-05-12

Functional redundancy in genomes arises from genes with overlapping functions, allowing phenotypes to persist after gene knockouts. Evolutionary redundancy or evolvability of a genome is one step removed, in that functional redundancy is absent but the genome has the potential to evolve to restore a lost phenotype. Exploring the extent to which this recovery alters gene networks can illuminate how functional gene interactions change through time. Here, the evolvability of lysis was studied in bacteriophage T7, revealing hidden functional interactions. Lysis is the destruction of host cell wall and membranes that releases progeny and is therefore essential for phage propagation. In most phages, lysis is mediated by a two-component genetic module: a muralytic enzyme that degrades the bacterial cell wall (endolysin) and a holin that permeabilizes the inner membrane to allow the endolysin access to the cell wall. T7 carries one known holin, one endolysin, and a second muralytic enzyme that plays little role in lysis by wild-type phage. If the primary endolysin is deleted, the second muralytic enzyme evolves to restore normal lysis after selection for faster growth. Here, a second level of evolutionary redundancy was revealed. When the second muralytic enzyme was prevented from adapting in a genome lacking the primary endolysin, the phage reevolved lysis de novo in the absence of any known muralytic enzymes by changes in multiple genes outside the original lysis module. This second level of redundancy proved to be evolutionarily inferior to the first, and both result in a lower fitness and slower lysis than wild-type T7. Deletion of the holin gene delayed lysis time modestly; fitness was restored by compensatory substitutions in genes that lack known roles in lysis of the wild type.

Evolutionary Forces Act on Promoter Length: Identification of Enriched Cis-Regulatory Elements

Kristiansson, E., Thorsen, M., Tamas, M. J., Nerman, O. — 2009-05-12

Transcription factors govern gene expression by binding to short DNA sequences called cis-regulatory elements. These sequences are typically located in promoters, which are regions of variable length upstream of the open reading frames of genes. Here, we report that promoter length and gene function are related in yeast, fungi, and plants. In particular, the promoters for stress-responsive genes are in general longer than those of other genes. Essential genes have, on the other hand, relatively short promoters. We utilize these findings in a novel method for identifying relevant cis-regulatory elements in a set of coexpressed genes. The method is shown to generate more accurate results and fewer false positives compared with other common procedures. Our results suggest that genes with complex transcriptional regulation tend to have longer promoters than genes responding to few signals. This phenomenon is present in all investigated species, indicating that evolution adjust promoter length according to gene function. Identification of cis-regulatory elements in Saccharomyces cerevisiae can be done with the web service located at http://enricher.zool.gu.se.

Phylogenetically Close Group I Introns with Different Positions among Paramecium bursaria Photobionts Imply a Primitive Stage of Intron Diversification

Hoshina, R., Imamura, N. — 2009-05-12

Group I introns are a distinct RNA group that catalyze their excision from precursor RNA transcripts and ligate the exons. Group I introns have a sporadic and highly biased distribution due to the two intron transfer mechanisms of homing and reverse splicing. These transfer pathways recognize assigned sequences even when introns are transferred beyond the species level. Consequently, introns at homologous gene sites between different host organisms are more related than those at heterologous sites within an organism. We describe the subgroup IE introns of two Chlorella species that are symbiotic green algae (photobionts) of a ciliate, Paramecium bursaria. One strain Chlorella sp. SW1-ZK (Csw.) had two IE introns at S651 and L2449, and the other strain Chlorella sp. OK1-ZK (Cok.) had four IE introns at S943, L1688, L1926, and L2184 (numbering reflects their homologous position in Escherichia coli rRNA gene: S = small subunit rRNA, L = large subunit rRNA). Despite locating on six heterologous sites, the introns formed a monophyletic clade independent of other groups. Phylogenetic and structural analyses of the introns indicated that Csw.L2449 has an archaic state, and the other introns are assumed to be originated from this intron. Some of the introns shared common internal guide sequences, which are necessary for misdirected transfer (i.e., transposition) via reverse splicing. Other introns, however, shared similar sequence fragments further upstream, after the insertions. We propose a hypothetical model to explain how these intron transpositions may have occurred in these photobionts; they transposed by a combination of homing-like event requiring relaxed sequence homology of recognition sequences and reverse splicing. This case study may represent a key to describe how group I intron explores new insertion sites.

The NBPF1 Promoter Has Been Recruited from the Unrelated EVI5 Gene Before Simian Radiation

Vandepoele, K., Andries, V., van Roy, F. — 2009-05-12

Most new genes arise through the duplication of existing genes. In most cases, the duplication is not limited to the coding sequence but encompasses the regulatory region as well. The NBPF gene family has expanded during recent primate evolution, and it has no known mouse ortholog. One of its members, NBPF1, was found to be disrupted by a constitutional translocation in a neuroblastoma patient. Here, we show that the ancestral NBPF gene copied the regulatory region from an unrelated gene, EVI5, after the split between simians and prosimians but before simian radiation. Phylogenetic analysis points to the possible involvement of positive selection acting on the NBPF1 promoter in the simian lineage. We previously showed decreased NBPF1 expression in certain neuroblastoma cell lines. Here, we show that this expression pattern is mimicked by the EVI5 gene, but partly by different mechanisms. Epigenetic regulation of the EVI5 promoter is common in neuroblastoma cell lines, but it is not for the NBPF promoters. Here, we describe the recent acquisition of the NBPF1 promoter from an unrelated gene, and remarkably, both the donor (EVI5) and acceptor (NBPF1) genes are disrupted by constitutional translocations in patients with neuroblastoma, suggesting a functional link between these genes and the disease.

Multiple Dicer Genes in the Early-Diverging Metazoa

2009-05-12

Dicer proteins are highly conserved, are present in organisms ranging from plants to metazoans, and are essential components of the RNA interference pathway. Although the complement of Dicer proteins has been investigated in many "higher" metazoans, there has been no corresponding characterization of Dicer proteins in any early-branching metazoan. We cloned partial cDNAs of genes belonging to the Dicer family from the anthozoan cnidarian Nematostella vectensis and two distantly related haplotypes (species lineages) of the Placozoa (Trichoplax adhaerens 16S haplotype 1 [H1] and Placozoa sp. [H2]). We also identified Dicer genes in the hydrozoan Hydra magnipapillata and the demosponge Amphimedon queenslandica with the use of publicly available sequence databases. Two Dicer genes are present in each cnidarian species, whereas five Dicer genes each are found in the Porifera and Placozoa. Phylogenetic analyses comparing these and other metazoan Dicers suggest an ancient duplication event of a "Proto-Dicer" gene. We show that the Placozoa is the only known metazoan phylum which contains both representatives of this duplication event and that the multiple Dicer genes of the "basal" metazoan phyla represent lineage-specific duplications. There is a striking diversity of Dicer genes in basal metazoans, in stark contrast to the single Dicer gene found in most higher metazoans. This new data has allowed us to formulate new hypotheses regarding the evolution of metazoan Dicer proteins and their possible functions in the early diverging metazoan phyla. We theorize that the multiple placozoan Dicer genes fulfill a specific biological requirement, such as an immune defense strategy against viruses.

Genomic Patterns of Adaptive Divergence between Chromosomally Differentiated Sunflower Species

Strasburg, J. L., Scotti-Saintagne, C., Scotti, I., Lai, Z., Rieseberg, L. H. — 2009-05-12

Understanding the genetic mechanisms of speciation and basis of species differences is among the most important challenges in evolutionary biology. Two questions of particular interest are what roles divergent selection and chromosomal differentiation play in these processes. A number of recently proposed theories argue that chromosomal rearrangements can facilitate the development and maintenance of reproductive isolation and species differences by suppressing recombination within rearranged regions. Reduced recombination permits the accumulation of alleles contributing to isolation and adaptive differentiation and protects existing differences from the homogenizing effects of introgression between incipient species. Here, we examine patterns of genetic diversity and divergence in rearranged versus collinear regions in two widespread, extensively hybridizing sunflower species, Helianthus annuus and Helianthus petiolaris, using sequence data from 77 loci distributed throughout the genomes of the two species. We find weak evidence for increased genetic divergence near chromosomal break points but not within rearranged regions overall. We find no evidence for increased rates of adaptive divergence on rearranged chromosomes; in fact, collinear chromosomes show a far greater excess of fixed amino acid differences between the two species. A comparison with a third sunflower species indicates that much of the nonsynonymous divergence between H. annuus and H. petiolaris probably occurred during or soon after their formation. Our results suggest a limited role for chromosomal rearrangements in genetic divergence, but they do document substantial adaptive divergence and provide further evidence of how species integrity and genetic identity can be maintained at many loci in the face of extensive hybridization and gene flow.

Population Genomic Analysis of ALMS1 in Humans Reveals a Surprisingly Complex Evolutionary History

2009-05-12

Mutations in the human gene ALMS1 result in Alström Syndrome, which presents with early childhood obesity and insulin resistance leading to Type 2 diabetes. Previous genomewide scans for selection in the HapMap data based on linkage disequilibrium and population structure suggest that ALMS1 was subject to recent positive selection. Through a detailed population genomic analysis of existing genomewide data sets and new resequencing data obtained in geographically diverse populations, we find that the signature of selection at ALMS1 is considerably more complex than what would be expected for an idealized model of a selective sweep acting on a newly arisen advantageous mutation. Specifically, we observed three highly divergent and globally dispersed haplogroups, two of which carry a set of seven derived nonsynonymous single nucleotide polymorphisms that are nearly fixed in Asian populations. Our data suggest that the interaction of human demographic history and positive selection on standing variation in Eurasian populations approximately 15 thousand years ago parsimoniously explains the spectrum of extant ALMS1 variation. These results provide new insights into the evolutionary history of ALMS1 in humans and suggest that selective events identified in genomewide scans may be more complex than currently appreciated.

A Genomewide Comparison of Population Structure at STRPs and Nearby SNPs in Humans

Payseur, B. A., Jing, P. — 2009-05-12

Patterns of population structure provide insights into evolutionary processes and help identify groups of individuals for genotype–phenotype association studies. With increasing availability of polymorphic molecular markers across genomes, the examination of population structure using large numbers of unlinked loci has become a common practice in evolutionary biology and human genetics. The two classes of molecular variation most widely used for this purpose, short tandem repeat polymorphisms (STRPs) and single-nucleotide polymorphisms (SNPs), differ in mutational properties expected to affect population structure. To measure the relative ability of these loci to describe population structure, we compared diversity at neighboring STRPs and SNPs from 720 genomic regions in the four populations that comprise the Human HapMap. Comparing loci from the same genomic regions allowed us to focus on the contribution of mutational differences (rather than variation in genealogical history) to disparities in population structure between STRPs and SNPs. Relative to average values for SNPs from the same regions, STRPs had lower F_st, but higher G_st' and I_n values. STRP–SNP correlations in population structure across genomic regions were statistically significant but weak in magnitude. Separate analyses by repeat type showed that these correlations were driven primarily by tetranucleotide and trinucleotide STRPs; measures of population structure at dinucleotides and SNPs were not significantly correlated. Pairwise comparisons among populations revealed effects of divergence time on differences in population structure between STRPs and SNPs. Collectively, these results confirm that individual STRPs can provide more information about population structure than individual SNPs, but suggest that the difference in structure at STRPs and SNPs depends on local genealogical history. Our study motivates theoretical comparisons of population structure at loci with different mutational properties.

Differences in DNA Methylation Patterns and Expression of the CCRK Gene in Human and Nonhuman Primate Cortices

2009-05-12

Changes in DNA methylation patterns during embryo development and differentiation processes are linked to the transcriptional plasticity of our genome. However, little is known about the evolutionary conservation of DNA methylation patterns and the evolutionary impact of epigenetic differences between closely related species. Here we compared the methylation patterns of CpG islands (CGIs) in the promoter regions of seven genes in humans and chimpanzees. We identified a block of CpGs in the cell cycle–related kinase (CCRK) gene that is more methylated in the adult human cortex than in the chimpanzee cortex and, in addition, it exhibits considerable intraspecific variation both in humans and chimpanzees. The species-specifically methylated region (SMR) lies between the almost completely methylated 5' region and the completely demethylated 3' region of the presumed CCRK CGI promoter. It is part of an Alu-Sg1 repeat that has been integrated into the promoter region in a common ancestor of humans and New World monkeys. This SMR is relatively hypomethylated in the rhesus monkey cortex and more or less completely methylated in the baboon cortex, indicating extraordinary methylation dynamics during primate evolution. The mRNA expression level of CCRK has also changed during the course of primate evolution. CCRK is expressed at much higher levels in human and baboon cortices, which display an average SMR methylation of 70% and 100%, respectively, than in chimpanzee and rhesus macaque cortices with an average SMR methylation of 35% and 40%, respectively. The observed evolutionary dynamics suggests a possibility that CCRK has been important for evolution of the primate brain.

Evidence for Homologous Recombination in Intracellular Chemosynthetic Clam Symbionts

Stewart, F. J., Young, C. R., Cavanaugh, C. M. — 2009-05-12

Homologous recombination is a fundamental mechanism for the genetic diversification of free-living bacteria. However, recombination may be limited in endosymbiotic bacteria, as these taxa are locked into an intracellular niche and may rarely encounter sources of foreign DNA. This study tested the hypothesis that vertically transmitted endosymbionts of deep-sea clams (Bivalvia: Vesicomyidae) show little or no evidence of recombination. Phylogenetic analysis of 13 loci distributed across the genomes of 14 vesicomyid symbionts revealed multiple, well-supported inconsistencies among gene tree topologies, and maximum likelihood–based tests rejected a hypothesis of shared evolutionary history (linkage) among loci. Further, multiple statistical methods confirmed the presence of recombination by detecting intragenic breakpoints in two symbiont loci. Recombination may be confined to a subset of vesicomyid symbionts, as some clades showed high levels of genomic stability, whereas others showed clear patterns of homologous exchange. Notably, a mosaic genome is present in symB, a symbiont lineage shown to have been acquired laterally (i.e., nonvertically) by Vesicomya sp. JdF clams. The majority of loci analyzed here supported a tight sister clustering of symB with the symbiont of a host species from the Mid-Atlantic Ridge, whereas others placed symB in a clade with symA, the dominant phylotype of V. sp. JdF clams. This result raises the hypothesis that lateral symbiont transfer between hosts may facilitate recombination by bringing divergent symbiont lineages into contact. Together, the data show that homologous recombination contributes to the diversification of vesicomyid clam symbionts, despite the intracellular lifestyle of these bacteria.

mRNA Retrotransposition Coupled with 5' Inversion as a Possible Source of New Genes

Kojima, K. K., Okada, N. — 2009-05-12

Human long interspersed nuclear element-1 (L1) occupies one-sixth of our genome and has contributed to genome evolution in various ways. Approximately 10% of human L1 copies are composed of two L1 segments; the 5' segment and 3' segment are in head-to-head (i.e., 5'-inverted) orientation. Besides mediating their own retrotransposition, L1 has the ability to mobilize mRNA "in trans," and the number of retrotransposed mRNA sequences (retrocopies) is estimated to be >6,000. In this study, we identified 48 human-specific retrocopies and 95 chimpanzee-specific retrocopies by comparing the human and chimpanzee genomes. Among these retrocopies, 12 were 5'-inverted. The characteristics of these 5'-inverted retrocopies were similar to those of 5'-inverted L1 copies, indicating that the 5' inversion is generated by the same mechanism. With these findings, we examined the possibility that 5' inversion of the retrocopy generates a new gene that codes for a peptide with a different N terminus. We identified several potential 5'-inverted retrogenes, including those of thymopoietin beta (TMPO) and eukaryotic translation initiation factor 3 subunit 5 (EIF3F). The most interesting candidate was the 5'-inverted retrocopy of small nuclear ribonucleoprotein polypeptide N (SNRPN). This retrocopy was transcribed in the reverse orientation in several organs, had multiple transcript variants, and encoded a protein containing a peptide fragment derived from the N-terminal portion of SNRPN. Our results suggest that mRNA retrotransposition coupled with 5' inversion may be a mechanism to generate new genes distinct from parental genes.

Deletion Rate Evolution and Its Effect on Genome Size and Coding Density

Pettersson, M. E., Kurland, C. G., Berg, O. G. — 2009-05-12

Deletion rates are thought to be important factors in determining the genome size of organisms in nature. Although it is indisputable that deletions, and thus deletion rates, affect genome size, it is unclear how, or indeed if, genome size is regulated via the deletion rate. Here, we employ a mathematical model to determine the evolutionary fate of deletion rate mutants. Simulations are employed to explore the interactions between deletions, deletion rate mutants, and genome size. The results show that, in this model, the fate of deletion rate mutants will depend on the fraction of essential genomic material, on the frequency of sexual recombination, as well as on the population size of the organism.

We find that there is no optimal deletion rate in any state. However, at one critical coding density, all changes in deletion rate are neutral and the rate may drift either up or down. As a consequence, the coding density of the genome is expected to fluctuate around this critical density. Characteristic differences in the impact of deletion rate mutations on prokaryote and eukaryote genomes are described.

Ecological Nitrogen Limitation Shapes the DNA Composition of Plant Genomes

Acquisti, C., Elser, J. J., Kumar, S. — 2009-04-14

Phenotypes and behaviors respond to resource constraints via adaptation, but the influence of ecological limitations on the composition of eukaryotic genomes is still unclear. We trace connections between plant ecology and genomes through their elemental composition. Inorganic sources of nitrogen (N) are severely limiting to plants in natural ecosystems. This constraint would favor the use of N-poor nucleotides in plant genomes. We show that the transcribed segments of undomesticated plant genomes are the most N poor, with genomes and proteomes bearing signatures of N limitation. Consistent with the predictions of natural selection for N conservation, the precursors of transcriptome show the greatest deviations from Chargaff's second parity rule. Furthermore, crops show higher N contents than undomesticated plants, likely due to the relaxation of natural selection owing to the use of N-rich fertilizers. These findings indicate a fundamental role of N limitation in the evolution of plant genomes, and they link the genomes with the ecosystem context within which biota evolve.

Gene Cluster Statistics with Gene Families

Raghupathy, N., Durand, D. — 2009-04-14

Identifying genomic regions that descended from a common ancestor is important for understanding the function and evolution of genomes. In distantly related genomes, clusters of homologous gene pairs are evidence of candidate homologous regions. Demonstrating the statistical significance of such "gene clusters" is an essential component of comparative genomic analyses. However, currently there are no practical statistical tests for gene clusters that model the influence of the number of homologs in each gene family on cluster significance. In this work, we demonstrate empirically that failure to incorporate gene family size in gene cluster statistics results in overestimation of significance, leading to incorrect conclusions. We further present novel analytical methods for estimating gene cluster significance that take gene family size into account. Our methods do not require complete genome data and are suitable for testing individual clusters found in local regions, such as contigs in an unfinished assembly. We consider pairs of regions drawn from the same genome (paralogous clusters), as well as regions drawn from two different genomes (orthologous clusters).

Determining cluster significance under general models of gene family size is computationally intractable. By assuming that all gene families are of equal size, we obtain analytical expressions that allow fast approximation of cluster probabilities. We evaluate the accuracy of this approximation by comparing the resulting gene cluster probabilities with cluster probabilities obtained by simulating a realistic, power-law distributed model of gene family size, with parameters inferred from genomic data. Surprisingly, despite the simplicity of the underlying assumption, our method accurately approximates the true cluster probabilities. It slightly overestimates these probabilities, yielding a conservative test. We present additional simulation results indicating the best choice of parameter values for data analysis in genomes of various sizes and illustrate the utility of our methods by applying them to gene clusters recently reported in the literature. Mathematica code to compute cluster probabilities using our methods is available as supplementary material.

Phylogenetic Relationships and Molecular Adaptation Dynamics of Human Rhinoviruses

Lewis-Rogers, N., Bendall, M. L., Crandall, K. A. — 2009-04-14

Human rhinoviruses (HRVs) are responsible for nearly 50% of all common cold infections. Ordinarily, HRV infections are mild and self-limiting; nonetheless, every year they result in significant loss of economic productivity and substantial inappropriate antibiotic use. Development of effective vaccine and antiviral prophylaxis against HRV has been hampered by the extensive antigenic diversity present among the nearly 100 serotypes. To gain new insights into the evolutionary processes that create the genetic diversity present among HRVs, we tested for recombination and selection for individual genes and the coding genome for 45 HRV serotypes using estimated phylogenetic relationships. Although the structural capsid genes and nonstructural genes recovered incongruent tree topologies, no recombination was detected using substitution methods. Therefore, the coding genome was determined to be appropriate for phylogenetic tests. Results of the Shimodaira–Hasegawa (SH) test support the hypothesis that the capsid genes recover a different evolutionary history than the nonstructural genes. Our best phylogenetic estimate based on the coding genome suggests that HRV-B is more closely related to enterovirus than to HRV-A; however, several alternative phylogenetic hypotheses were not rejected by the SH test. Positive selection was examined by using two different approaches; d_N/d_S rate ratio and the physicochemical phenotypes for 31 amino acid properties. Analyses using d_N/d_S failed to detect positive selection. However, protein phenotypic expression appears to be a more sensitive approach. There was extensive stabilizing and destabilizing positive selection in HRV-A major and HRV-B serotypes for all proteins, except in 3A in HRV-B, which overlapped with functional, structural, and to a greater extent in uncharacterized genomic regions. In contrast, the evolution of HRV-A minor serotypes appears to be driven primarily by destabilizing selection. Our results demonstrate that HRV-A major, HRV-A minor, and HRV-B serotypes have not been similarly influenced by purifying selection.

New Superfamilies of Eukaryotic DNA Transposons and Their Internal Divisions

Bao, W., Jurka, M. G., Kapitonov, V. V., Jurka, J. — 2009-04-14

Despite their enormous diversity and abundance, all currently known eukaryotic DNA transposons belong to only 15 superfamilies. Here, we report two new superfamilies of DNA transposons, named Sola and Zator. Sola transposons encode DDD-transposases (transposase, TPase) and are flanked by 4-bp target site duplications (TSD). Elements from the Sola superfamily are distributed in a variety of species including bacteria, protists, plants, and metazoans. They can be divided into three distinct groups of elements named Sola1, Sola2, and Sola3. The elements from each group have extremely low sequence identity to each other, different termini, and different target site preferences. However, all three groups belong to a single superfamily based on significant PSI-Blast identities between their TPases. The DDD TPase sequences encoded by Sola transposons are not similar to any known TPases. The second superfamily named Zator is characterized by 3-bp TSD. The Zator superfamily is relatively rare in eukaryotic species, and it evolved from a bacterial transposon encoding a TPase belonging to the "transposase 36" family (Pfam07592). These transposons are named TP36 elements (abbreviated from transposase 36).

Haplotypic Background of a Private Allele at High Frequency in the Americas

2009-04-14

Recently, the observation of a high-frequency private allele, the 9-repeat allele at microsatellite D9S1120, in all sampled Native American and Western Beringian populations has been interpreted as evidence that all modern Native Americans descend primarily from a single founding population. However, this inference assumed that all copies of the 9-repeat allele were identical by descent and that the geographic distribution of this allele had not been influenced by natural selection. To investigate whether these assumptions are satisfied, we genotyped 34 single nucleotide polymorphisms across ~500 kilobases (kb) around D9S1120 in 21 Native American and Western Beringian populations and 54 other worldwide populations. All chromosomes with the 9-repeat allele share the same haplotypic background in the vicinity of D9S1120, suggesting that all sampled copies of the 9-repeat allele are identical by descent. Ninety-one percent of these chromosomes share the same 76.26 kb haplotype, which we call the "American Modal Haplotype" (AMH). Three observations lead us to conclude that the high frequency and widespread distribution of the 9-repeat allele are unlikely to be the result of positive selection: 1) aside from its association with the 9-repeat allele, the AMH does not have a high frequency in the Americas, 2) the AMH is not unusually long for its frequency compared with other haplotypes in the Americas, and 3) in Latin American mestizo populations, the proportion of Native American ancestry at D9S1120 is not unusual compared with that observed at other genomewide microsatellites. Using a new method for estimating the time to the most recent common ancestor (MRCA) of all sampled copies of an allele on the basis of an estimate of the length of the genealogy descended from the MRCA, we calculate the mean time to the MRCA of the 9-repeat allele to be between 7,325 and 39,900 years, depending on the demographic model used. The results support the hypothesis that all modern Native Americans and Western Beringians trace a large portion of their ancestry to a single founding population that may have been isolated from other Asian populations prior to expanding into the Americas.

Microsatellites Are Molecular Clocks That Support Accurate Inferences about History

Sun, J. X., Mullikin, J. C., Patterson, N., Reich, D. E. — 2009-04-14

Microsatellite length mutations are often modeled using the generalized stepwise mutation process, which is a type of random walk. If this model is sufficiently accurate, one can estimate the coalescence time between alleles of a locus after a mathematical transformation of the allele lengths. When large-scale microsatellite genotyping first became possible, there was substantial interest in using this approach to make inferences about time and demography, but that interest has waned because it has not been possible to empirically validate the clock by comparing it with data in which the mutation process is well understood. We analyzed data from 783 microsatellite loci in human populations and 292 loci in chimpanzee populations, and compared them with up to one gigabase of aligned sequence data, where the molecular clock based upon nucleotide substitutions is believed to be reliable. We empirically demonstrate a remarkable linearity (r² > 0.95) between the microsatellite average square distance statistic and sequence divergence. We demonstrate that microsatellites are accurate molecular clocks for coalescent times of at least 2 million years (My). We apply this insight to confirm that the African populations San, Biaka Pygmy, and Mbuti Pygmy have the deepest coalescent times among populations in the Human Genome Diversity Project. Furthermore, we show that microsatellites support unbiased estimates of population differentiation (F_ST) that are less subject to ascertainment bias than single nucleotide polymorphism (SNP) F_ST. These results raise the prospect of using microsatellite data sets to determine parameters of population history. When genotyped along with SNPs, microsatellite data can also be used to correct for SNP ascertainment bias.

Genomic and Proteomic Analyses Reveal Non-Neofunctionalized Vitellogenins in a Basal Clupeocephalan, the Atlantic Herring, and Point to the Origin of Maturational Yolk Proteolysis in Marine Teleosts

Kristoffersen, B. A., Nerland, A., Nilsen, F., Kolarevic, J., Finn, R. N. — 2009-04-14

Oocyte hydration is a unique event in oviparous marine teleosts that provides the single-celled egg with an essential pool of water for survival during early development in the saline oceanic environment. A conserved mechanism of maturational yolk proteolysis of a neofunctionalized vitellogenin (VtgAa) has been shown to underlie the hydration event in all teleosts that spawn pelagic eggs (pelagophils), and is argued to be a key adaptation for teleost radiation in the oceanic environment 55 Ma. We have recently shown that a small pool of free amino acids (FAAs) significantly contributes to the osmolarity of the ovulated egg in an ancestral marine teleost, the Atlantic herring that spawns benthic eggs (benthophil). To determine whether multiple forms of vtg exist and whether neofunctionalization of the gene products are related to the egg FAA pool in this species, genomic sequences conserved between the exons of Atlantic herring and zebrafish were amplified. This approach identified a small polymorphic intron between exons 9 and 10 in Atlantic herring and demonstrated that two closely related major vtg transcripts (chvtgAc1 and chvtgAc2) are expressed during oogenesis. A separate polymerase chain reaction–based approach identified a more ancestral phosvitinless transcript (chvtgC). Proteomic analyses of the translated products of the major vtg forms demonstrated that the yolk proteins are similarly processed during deposition, and oocyte maturation and reveal that vtgs have duplicated but not neofunctionalized in this species. Phylogenetic analyses consistently clustered the transcripts and proteins as the basal sister group to the Ostariophysi in full congruence with the Clupeocephalan rank, and suggest that expansion of ostariophysan vtgAo1 and vtgAo2 genes occurred in a lineage-specific manner after separation from the Clupeiformes. Three-dimensional modeling of the ChvtgAc1 sequence against the resolved lamprey lipovitellin module revealed that the tertiary structure is highly conserved, with most substitutions occurring on the outside of the molecule. The data indicate that the phosvitin domain, the smallest yet reported for teleosts, and an N-terminal fragment of the lipovitellin light chain contribute to the FAA pool. The present findings thus show that yolk proteolysis and the generation of an organic osmolyte pool of FAAs was an adaptive response to spawning in seawater also for the Clupeiformes, but that this process was not evolutionarily successful in terms of biodiversity until vtg gene neofunctionalization occurred in the Acanthomorpha.

The Correlation of Evolutionary Rate with Pathway Position in Plant Terpenoid Biosynthesis

Ramsay, H., Rieseberg, L. H., Ritland, K. — 2009-04-14

Genes are expected to face stronger selective constraint and to evolve more slowly if they encode enzymes upstream as opposed to downstream in metabolic pathways, because upstream genes are more pleiotropic, being required for a wider range of end products. However, few clear examples of this trend in evolutionary rate variation exist. We examined whether genes involved in plant terpenoid biosynthesis exhibit such a pattern, using data for 40 genes from five fully sequenced angiosperms, Oryza, Vitis, Arabidopsis, Populus, and Ricinus. Our results show that d_N/d_S does in fact correlate with pathway position along pathways converting glucose to the terpenoid phytohormones abscissic acid, gibberellic acid (GA), and brassinosteroids. Upstream versus downstream rate variation is particularly strong in the GA pathway. In contrast, we found no or little apparent variation in d_N/d_S with gene copy number. We also introduce a new measure of pathway position, the Pathway Pleiotropy Index (PPI), which counts groups of enzymes between pathway branch points. We found that this measure is superior to pathway position in explaining variation in d_N/d_S along each pathway. Although at least 8 of the 40 genes showed evidence of positive selection, correlations of d_N/d_S with PPI remain significant when these genes are removed. Therefore, our results are consistent with the prediction that selective constraint is progressively relaxed along metabolic pathways.

The Effect of Sequence Evolution on Protein Structural Divergence

Williams, S. G., Lovell, S. C. — 2009-04-14

The complex constraints imposed by protein structure and function result in varied rates of sequence and structural divergence in proteins. Analysis of sequence differences between homologous proteins can advance our understanding of structural divergence and some of the constraints that govern the evolution of these molecules. Here, we assess the relationship between amino acid sequence and structural divergence. Firstly, we demonstrate that the relationship between protein sequence and structural divergence is governed by a variety of evolutionary constraints, including solvent exposure and secondary structure. Secondly, although compensatory substitutions are widespread, we find many radical size-changing mutations that are not compensated by neighboring complementary changes. Instead, these noncompensated substitutions are mitigated by alteration of protein structure. These results suggest a combined mechanism of accommodating substitutions in proteins, involving both coevolution and structural accommodation. Such a mechanism can explain previously observed correlated substitutions of residues that are distant both in sequence and structure, allowing an integrated view of sequence and structural divergence of proteins.

Differential Retention of Metabolic Genes Following Whole-Genome Duplication

Gout, J.-F., Duret, L., Kahn, D. — 2009-04-14

Classical studies in Metabolic Control Theory have shown that metabolic fluxes usually exhibit little sensitivity to changes in individual enzyme activity, yet remain sensitive to global changes of all enzymes in a pathway. Therefore, little selective pressure is expected on the dosage or expression of individual metabolic genes, yet entire pathways should still be constrained. However, a direct estimate of this selective pressure had not been evaluated. Whole-genome duplications (WGDs) offer a good opportunity to address this question by analyzing the fates of metabolic genes during the massive gene losses that follow. Here, we take advantage of the successive rounds of WGD that occurred in the Paramecium lineage. We show that metabolic genes exhibit different gene retention patterns than nonmetabolic genes. Contrary to what was expected for individual genes, metabolic genes appeared more retained than other genes after the recent WGD, which was best explained by selection for gene expression operating on entire pathways. Metabolic genes also tend to be less retained when present at high copy number before WGD, contrary to other genes that show a positive correlation between gene retention and preduplication copy number. This is rationalized on the basis of the classical concave relationship relating metabolic fluxes with enzyme expression.

Quantification of Adaptive Evolution of Genes Expressed in Avian Brain and the Population Size Effect on the Efficacy of Selection

Axelsson, E., Ellegren, H. — 2009-04-14

Whether protein evolution is mainly due to fixation of beneficial alleles by positive selection or to random genetic drift has remained a contentious issue over the years. Here, we use two genomewide polymorphism data sets collected from chicken populations, together with divergence data from >5,000 chicken–zebra finch gene orthologs expressed in brain, to assess the amount of adaptive evolution in protein-coding genes of birds. First, we show that estimates of the fixation index (FI, the ratio of fixed nonsynonymous-to-synonymous changes over the ratio of the corresponding polymorphisms) are highly dependent on the character of the underlying data sets. Second, by using polymorphism data from high-frequency alleles, to avoid the confounding effect of slightly deleterious mutations segregating at low frequency, we estimate that about 20% of amino acid changes have been brought to fixation through positive selection during avian evolution. This estimate is intermediate to that obtained in humans (lower) and flies as well as bacteria (higher), and is consistent with population genetics theory that stipulates a positive relationship between the efficiency of selection and the effective population size. Further, by comparing the FIs for common and all alleles, we estimate that 20% of nonsynonymous variation segregating in chicken populations represent slightly deleterious mutations, which is less than in Drosophila. Overall, these results highlight the link between the effective population size and positive as well as negative selection.

Molecular Determinants and Evolutionary Dynamics of Wobble Splicing

Lv, J., Yang, Y., Yin, H., Chu, F., Wang, H., Zhang, W., Zhang, Y., Jin, Y. — 2009-04-14

Alternative splicing at tandem splice sites (wobble splicing) is widespread in many species, but the mechanisms specifying the tandem sites remain poorly understood. Here, we used synaptotagmin I as a model to analyze the phylogeny of wobble splicing spanning more than 300 My of insect evolution. Phylogenetic analysis indicated that the occurrence of species-specific wobble splicing was related to synonymous variation at tandem splice sites. Further mutagenesis experiments demonstrated that wobble splicing could be lost by artificially induced synonymous point mutations due to destruction of splice acceptor sites. In contrast, wobble splicing could not be correctly restored through mimicking an ancestral tandem acceptor by artificial synonymous mutation in in vivo splicing assays, which suggests that artificial tandem splice sites might be incompatible with normal wobble splicing. Moreover, combining comparative genomics with hybrid minigene analysis revealed that alternative splicing has evolved from the 3' tandem donor to the 5' tandem acceptor in Culex pipiens, as a result of an evolutionary shift of cis element sequences from 3' to 5' splice sites. These data collectively suggest that the selection of tandem splice sites might not simply be an accident of history but rather in large part the result of coevolution between splice site and cis element sequences as a basis for wobble splicing. An evolutionary model of wobble splicing is proposed.

Founders, Drift, and Infidelity: The Relationship between Y Chromosome Diversity and Patrilineal Surnames

King, T. E., Jobling, M. A. — 2009-04-14

Most heritable surnames, like Y chromosomes, are passed from father to son. These unique cultural markers of coancestry might therefore have a genetic correlate in shared Y chromosome types among men sharing surnames, although the link could be affected by mutation, multiple foundation for names, nonpaternity, and genetic drift. Here, we demonstrate through an analysis of 1,678 Y-chromosomal haplotypes within 40 British surnames a remarkably high degree of coancestry that generally increases as surnames become rarer. On average, the proportion of haplotypes lying within descent clusters is 62% but ranges from 0% to 87%. The shallow time depth of many descent clusters within names, the lack of a detectable effect of surname derivation on diversity, and simulations of surname descent suggest that genetic drift through variation in reproductive success is important in structuring haplotype diversity. Modern patterns therefore provide little reliable information about the original founders of surnames some 700 years ago. A comparative analysis of published data on Y diversity within Irish surnames demonstrates a relative lack of surname frequency dependence of coancestry, a difference probably mediated through distinct Irish and British demographic histories including even more marked genetic drift in Ireland.

Molecular Evolution of the Testis TAFs of Drosophila

Li, V. C., Davis, J. C., Lenkov, K., Bolival, B., Fuller, M. T., Petrov, D. A. — 2009-04-14

The basal transcription machinery is responsible for initiating transcription at core promoters. During metazoan evolution, its components have expanded in number and diversified to increase the complexity of transcriptional regulation in tissues and developmental stages. To explore the evolutionary events and forces underlying this diversification, we analyzed the evolution of the Drosophila testis TAFs (TBP-associated factors), paralogs of TAFs from the basal transcription factor TFIID that are essential for normal transcription during spermatogenesis of a large set of specific genes involved in terminal differentiation of male gametes. There are five testis-specific TAFs in Drosophila, each expressed only in primary spermatocytes and each a paralog of a different generally expressed TFIID subunit. An examination of the presence of paralogs across taxa as well as molecular clock dating indicates that all five testis TAFs likely arose within a span of ~38 My 63–250 Ma by independent duplication events from their generally expressed paralogs. Furthermore, the evolution of the testis TAFs has been rapid, with apparent further accelerations in multiple Drosophila lineages. Analysis of between-species divergence and intraspecies polymorphism indicates that the major forces of evolution on these genes have been reduced purifying selection, pervasive positive selection, and coevolution. Other genes that exhibit similar patterns of evolution in the Drosophila lineages are also characterized by enriched expression in the testis, suggesting that the pervasive positive selection acting on the tTAFs is likely to be related to their expression in the testis.

Genomic Organization and Evolution of the Vomeronasal Type 2 Receptor-Like (OlfC) Gene Clusters in Atlantic Salmon, Salmo salar

2009-04-14

There are three major multigene superfamilies of olfactory receptors (OR, V1R, and V2R) in mammals. The ORs are expressed in the main olfactory organ, whereas the V1Rs and V2Rs are located in the vomeronasal organ. Fish only possess one olfactory organ in each nasal cavity, the olfactory rosette; therefore, it has been proposed that their V2R-like genes be classified as olfactory C family G protein-coupled receptors (OlfC). There are large variations in the sizes of OR gene repertoires. Previous studies have shown that fish have between 12 and 46 functional V2R-like genes, whereas humans have lost all functional V2Rs, and frog sp. have more than 240. Pseudogenization of V2R genes is a prevalent event across species. In the mouse and frog genomes, there are approximately double the number of pseudogenes compared with functional genes. An oligonucleotide probe was designed from a conserved sequence from four Atlantic salmon OlfC genes and used to screen the Atlantic salmon bacterial artificial chromosome (BAC) library. Hybridization-positive BACs were matched to fingerprint contigs, and representative BACs were shotgun cloned and sequenced. We identified 55 OlfC genes. Twenty-nine of the OlfC genes are classified as putatively functional genes and 26 as pseudogenes. The OlfC genes are found in two genomic clusters on chromosomes 9 and 20. Phylogenetic analysis revealed that the OlfC genes could be divided into 10 subfamilies, with nine of these subfamilies corresponding to subfamilies found in other teleosts and one being salmon specific. There is also a large expansion in the number of OlfC genes in one subfamily in Atlantic salmon. Subfamily gene expansions have been identified in other teleosts, and these differences in gene number reflect species-specific evolutionary requirements for olfaction. Total RNA was isolated from the olfactory epithelium and other tissues from a presmolt to examine the expression of the odorant genes. Several of the putative OlfC genes that we identified are expressed only in the olfactory epithelium, consistent with these genes encoding odorant receptors.

Molecular Evolution of the {beta}{gamma} Lens Crystallin Superfamily: Evidence for a Retained Ancestral Function in {gamma}N Crystallins?

Weadick, C. J., Chang, B. S.W. — 2009-04-14

Within the vertebrate eye, β crystallins are extremely stable lens proteins that are uniquely adapted to increase refractory power while maintaining transparency. Unlike crystallins, which are well-characterized, multifunctional proteins that have important functions both in and out of the lens, β lens crystallins are a diverse group of proteins with no clear ancestral or contemporary nonlens role. We carried out phylogenetic and molecular evolutionary analyses of the β-crystallin superfamily in order to study the evolutionary history of the N crystallins, a recently discovered, biochemically atypical family suggested to possess a divergent or ancestral function. By including nonlens, β-motif-containing sequences in our analysis as outgroups, we confirmed the phylogenetic position of the N family as sister to other crystallins. Using maximum likelihood codon models to estimate lineage-specific nonsynonymous-to-synonymous rate ratios revealed strong positive selection in all of the early lineages within the β family, with the striking exception of the lineage leading to the N crystallins which was characterized by strong purifying selection. Branch-site analysis, used to identify candidate sites involved in functional divergence between N crystallins and its sister clade containing all other crystallins, identified several positively selected changes at sites of known functional importance in the β crystallin protein structure. Further analyses of a fish-specific N crystallin gene duplication revealed a more recent episode of positive selection in only one of the two descendant lineages (N2). Finally, from the guppy, Poecilia reticulata, we isolated complete N1 and N2 coding sequence data from cDNA and partial coding sequence data from genomic DNA in order to confirm the presence of a novel N2 intron, discovered through data mining of two pufferfish genomes. We conclude that the function of the N family likely resembles the ancestral vertebrate β crystallin more than other β families. Furthermore, owing to the presence of an additional intron in some fish N2 crystallins, and the inferred action of positive selection following the fish-specific N duplication, we suggest that further study of fish N crystallins will be critical in further elucidating possible ancestral functions of N crystallins and any nonstructural role they may have.

Evolution of Mutation Rates: Phylogenomic Analysis of the Photolyase/Cryptochrome Family

Lucas-Lledo, J. I., Lynch, M. — 2009-04-14

Photoreactivation, one of the first DNA repair pathways to evolve, is the direct reversal of premutagenic lesions caused by ultraviolet (UV) irradiation, catalyzed by photolyases in a light-dependent, single-enzyme reaction. It has been experimentally shown that photoreactivation prevents UV mutagenesis in a broad range of species. In the absence of photoreactivation, UV-induced photolesions are repaired by the more complex and much less efficient nucleotide excision repair pathway. Despite their obvious beneficial effects, several lineages, including placental mammals, lost photolyase genes during evolution. In this study, we ask why photolyase genes have been lost in those lineages and discuss the significance of these losses in the context of the evolution of the genomic mutation rates. We first perform an extensive phylogenomic analysis of the photolyase/cryptochrome family, to assess what species lack each kind of photolyase gene. Then, we estimate the ratio of nonsynonymous to synonymous substitution rates in several groups of photolyase genes, as a proxy of the strength of purifying natural selection, and we ask whether less evolutionarily constrained photolyase genes are more likely lost. We also review functional data and compare the efficiency of different kinds of photolyases. We find that eukaryotic photolyases are, on average, less evolutionarily constrained than eubacterial ones and that the strength of natural selection is correlated with the affinity of photolyases for their substrates. We propose that the loss of photolyase genes in eukaryotic species may be due to weak natural selection and may result in a deleterious increase of their genomic mutation rates. In contrast, the loss of photolyase genes in prokaryotes may not cause an increase in the mutation rate and be neutral in most cases.

Solvent Exposure Imparts Similar Selective Pressures across a Range of Yeast Proteins

Conant, G. C., Stadler, P. F. — 2009-04-14

We study how an amino acid residue's solvent exposure influences its propensity for substitution by analyzing multiple alignments of 61 yeast genes for which the crystal structure is known. We find that the selective constraint on the interior residues is on average 10 times that of residues on the surface. Surprisingly, there is no correlation between the overall selective constraint observed for a protein alignment and the ratio of constraints on interior and surface residues. By modeling the selective constraint on several amino acid properties, we show that although residue volume and hydropathy are strongly conserved across most alignments, there is little variation in interior versus surface conservation for these two properties. By contrast, residue charge (isoelectric point) is less generally conserved when considering the protein as a whole but shows a strong constraint against the introduction of charged residues into the protein interior.

Phylogenetic Signals in DNA Composition: Limitations and Prospects

Mrazek, J. — 2009-04-14

The concept of genome signature allows sequence comparisons without alignment. It relies on the premise that oligonucleotide compositions of DNA segments from the same or closely related genomes tend to be more similar than those from distantly related genomes. This concept has been used in detection of lateral gene transfer, phylogenetic classification of metagenome sequences (binning), and in studies of evolution of viruses and plasmids. The goal of this work is to explore limitations of genome signature in phylogenetic classification of DNA sequences and to identify formal representations of genome signature that expose best the phylogenetic relationships among prokaryotes. We found that genome signatures that best represent phylogenetic relationships are those normalized to factor out differences in G + C content and utilizing the standard A-C-G-T alphabet or the degenerate R-Y (purine–pyrimidine) alphabet. The main limitation of all genome signature representations tested is lack of divergence among some distantly related species. "Crowding" of the genome signature space and absence of molecular clock likely contribute to this phenomenon. We introduce "periodicity signatures"—formal representations of periodic sequence patterns related to DNA curvature—which can discriminate between bacterial and archaeal DNA sequences. Interestingly, archaea of the order Halobacteriaceae have periodic signatures similar to bacteria, possibly due to their early divergence from other archaea, extensive lateral gene transfer, or due to their adaptation to high salt environments. Our results have practical implications for development and application of genome signature–based methods for analysis and classification of DNA sequences.

Gene Sampling Can Bias Multi-Gene Phylogenetic Inferences: The Relationship between Red Algae and Green Plants as a Case Study

Inagaki, Y., Nakajima, Y., Sato, M., Sakaguchi, M., Hashimoto, T. — 2009-04-14

The monophyly of Plantae including glaucophytes, red algae, and green plants (green algae plus land plants) has been recovered in recent phylogenetic analyses of large multi-gene data sets (e.g., those including >30,000 amino acid [aa] positions). On the other hand, Plantae monophyly has not been stably reconstructed in inferences from multi-gene data sets with fewer than 10,000 aa positions. An analysis of 5,216 aa positions in Nozaki et al. (Nozaki H, Iseki M, Hasegawa M, Misawa K, Nakada T, Sasaki N, Watanabe M. 2007. Phylogeny of primary photosynthetic eukaryotes as deduced from slowly evolving nuclear genes. Mol Biol Evol. 24:1592–1595.) strongly rejected the monophyly of Plantae, whereas Hackett et al. (Hackett JD, Yoon HS, Li S, Reyes-Prieto A, Rummele SE, Bhattacharya D. 2007. Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates. Mol Biol Evol. 24:1702–1713.) robustly recovered the Plantae clade in an analysis of 6,735 aa positions. We suspected that the significant incongruity observed between the two studies was attributable to a bias generally overlooked in multi-gene phylogenetic estimation, rather than data size, taxon sampling, or methods for tree reconstruction. Although glaucophytes were excluded from our analyses due to a shortage of sequence data, we found that the recovery of a sister–group relationship between red algae and green plants primarily depends on gene sampling in phylogenetic inferences from <10,000 aa positions. Phylogenetic analyses of data sets with fewer than 10,000 aa positions, which can be prepared without large-scale sequencing (e.g., expressed sequence tag analyses), are practical in challenging various unresolved issues in eukaryotic evolution. However, our results indicate that severe biases can arise from gene sampling in multi-gene inferences from <10,000 aa positions. We also address the validity of fast-evolving gene exclusion in multi-gene phylogenetic analyses, in light of this gene sampling bias.

Evolutionary Origin and Genomic Organization of Micro-RNA Genes in Immunoglobulin Lambda Variable Region Gene Family

Das, S. — 2009-04-14

The genomic organizations and functions of many miRNA genes have been described in recent years, but the origin and evolution of miRNAs in the exons of protein-coding genes are not well understood. The overlap of miR-650 genes with the protein-coding region of immunoglobulin lambda variable (IGVL) region genes has given a unique opportunity to witness a birth of miRNA gene. Both sequence comparisons and structure predictions indicate that the miR-650 genes are present in multiple copies and overlap in the same transcription orientation with the leader exon of primate IGVL genes of a specific phylogenetic clan (clan II). By reconstructing the phylogeny of the clan II IGVL genes, the stages in which the mutations accumulated in the leader exon and gave rise to a stable hairpin structure of miR-650 could be documented. The copy number variation of miR-650 genes among different species is the result of the duplication or deletion of the IGVL genes. To my knowledge, this is the first report of a genomic association between miRNA and the protein-coding genes of a multigene family. Analysis of the upstream region of the leader exon suggests that the IGVL and the mir-650 genes use the same promoter region for their transcription. However, in contrast to the general expectation about the expression of miRNAs that overlap with other genes in the same transcriptional orientation, this analysis provides evidence that the miR-650 gene is apparently transcribed independently of the IGVL gene with which it overlaps because they are expressed in different cell types.

Parallel Evolution between Aromatase and Androgen Receptor in the Animal Kingdom

Tiwary, B. K., Li, W.-H. — 2009-04-14

Environmental Sequence Data from the Sargasso Sea Reveal That the Characteristics of Genome Reduction in Prochlorococcus Are Not a Harbinger for an Escalation in Genetic Drift

Hu, J., Blanchard, J. L. — 2009-04-14

About the Cover: 1859 and All That

Graur, D. — 2009-04-14