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PubMed2000

Evolution of vertebrate immunoglobulin variable gene segments.

Evolution of Ig V gene segments are generally characterized by (a) evolution by "the birth and death process" and (b) diversifying selection. However, the detailed evolutionary pattern of V gene segments varies among species due to the fact that the humoral immune system itself has changed during vertebrate evolution. The change in somatic diversification system coupled with the change in lymphocyte development has imposed a significant impact on the evolution of Ig genes. In order to understand the evolution of immunological genes it is important to view it in the context of the evolution of the entire immune system itself.

Animals↗
PubMed2000

Roles of selection intensity, major genes, and minor genes in evolution of insecticide resistance.

A prominent hypothesis about insecticide resistance is that genes of major effect play a key role in field-evolved resistance because the intensity of selection is extremely high in the field. A corollary hypothesis is that the lower intensity of selection in laboratory selection experiments favors polygenic control of insecticide resistance. Contrary to these hypotheses, a literature review revealed that the intensity of selection for insecticide resistance in the field varies widely and overlaps broadly with selection intensities in the laboratory. Also contrary to these hypotheses, results from simulations of population genetic models suggest that selection intensities typical of laboratory selection experiments favor resistance that is conferred by major genes. Major genes dominated responses to selection for resistance across a wide range of simulated selection intensities, with and without fitness costs and refuges. The simulation results also suggest that the intensity of selection, rather than the number of loci conferring resistance, is central in determining rates of resistance evolution and effectiveness of refuges.

Animals↗
PubMed1995

The beta-tubulin gene family evolution in the Drosophila montium subgroup of the melanogaster species group.

The beta 1-, beta 2-, and beta 3-tubulin genes have been mapped by in situ hybridization on the polytene chromosomes of 11 selected species (15 strains) belonging to the Drosophila montium subgroup. Although the hybridization pattern among the strains of the same species does not differ, this pattern is significantly different among the species. The beta-tubulin genes in the montium subgroup seem to be organized in a cluster, or in a semicluster or are completely dispersed. The clustered arrangements is found in the North-Oriental sibling species D. auraria, D. triauraria, and D. quadraria. The semiclustered arrangement, wherein the beta 1 and beta 2 genes are located at the same locus while beta 3 is at a different one, appears in the South-Oriental species D. bicornuta, D. serrata, and D. birchii, as well as in the Afrotropical species D. diplacantha and D. seguyi. The complete separation of the genes is observed in the Indian species D. kikkawai and D. jambulina and in the Afrotropical species D. vulcana. Based on the above results, a possible mode of evolution of the beta-tubulin genes in the montium subgroup is attempted. In addition, phylogenetic relationships among the montium species are discussed.

Animals↗
PubMed2004

The evolution of gene expression in mouse hippocampus in response to selective breeding for increased locomotor activity.

The evolution of behavior has been notoriously difficult to study at the molecular level, but mouse genetic technology offers new promise. We applied selective breeding to increase voluntary wheel running in four replicate lines of Mus domesticus (S mice) while maintaining four additional lines through random breeding to serve as controls (C mice). The goal of the study was to identify the gene expression profile of the hippocampus that may have evolved to facilitate the increased voluntary running. The hippocampus was of interest because it is known to display marked physiological responses in association with wheel running itself. We used high-density oligonucleotide arrays representing 11,904 genes. To control for the confounding influence of physical activity itself on gene expression, animals were housed individually without access to running wheels, and were sampled during the day when they are normally inactive. Two-month-old female mice in estrus were used (n = 16 total; two per line; 8 S and 8 C). After correcting for an acceptable false discovery rate (10%), 30 genes, primarily involved in transcription and translation, significantly increased expression whereas 23 genes, distributed among many categories including immune function and neuronal signaling, decreased expression in S versus C mice. These changes were relatively small in magnitude relative to the changes in gene expression that occur in the hippocampus in response to wheel running itself. A priori tests of dopamine receptor expression levels demonstrated an increase of approximately 20% in the expression of D2 and D4 receptors. These results suggest that relatively small changes in the expression patterns of hippocampal genes underlie large changes in phenotypic response to selection, and that the genetic architecture of running motivation likely involves the dopaminergic system as well as CNS signaling machinery.

Analysis of Variance↗
PubMed2002

Gene order evolution and paleopolyploidy in hemiascomycete yeasts.

The wealth of comparative genomics data from yeast species allows the molecular evolution of these eukaryotes to be studied in great detail. We used "proximity plots" to visually compare chromosomal gene order information from 14 hemiascomycetes, including the recent Génolevures survey, to Saccharomyces cerevisiae. Contrary to the original reports, we find that the Génolevures data strongly support the hypothesis that S. cerevisiae is a degenerate polyploid. Using gene order information alone, 70% of the S. cerevisiae genome can be mapped into "sister" regions that tile together with almost no overlap. This map confirms and extends the map of sister regions that we constructed previously by using duplicated genes, an independent source of information. Combining gene order and gene duplication data assigns essentially the whole genome into sister regions, the largest gap being only 36 genes long. The 16 centromere regions of S. cerevisiae form eight pairs, indicating that an ancestor with eight chromosomes underwent complete doubling; alternatives such as segmental duplications can be ruled out. Gene arrangements in Kluyveromyces lactis and four other species agree quantitatively with what would be expected if they diverged from S. cerevisiae before its polyploidization. In contrast, Saccharomyces exiguus, Saccharomyces servazzii, and Candida glabrata show higher levels of gene adjacency conservation, and more cases of imperfect conservation, suggesting that they split from the S. cerevisiae lineage after polyploidization. This finding is confirmed by sequences around the C. glabrata TRP1 and IPP1 loci, which show that it contains sister regions derived from the same duplication event as that of S. cerevisiae.

Ascomycota↗
PubMed2003

Bayesian gene/species tree reconciliation and orthology analysis using MCMC.

MOTIVATION: Comparative genomics in general and orthology analysis in particular are becoming increasingly important parts of gene function prediction. Previously, orthology analysis and reconciliation has been performed only with respect to the parsimony model. This discards many plausible solutions and sometimes precludes finding the correct one. In many other areas in bioinformatics probabilistic models have proven to be both more realistic and powerful than parsimony models. For instance, they allow for assessing solution reliability and consideration of alternative solutions in a uniform way. There is also an added benefit in making model assumptions explicit and therefore making model comparisons possible. For orthology analysis, uncertainty has recently been addressed using parsimonious reconciliation combined with bootstrap techniques. However, until now no probabilistic methods have been available. RESULTS: We introduce a probabilistic gene evolution model based on a birth-death process in which a gene tree evolves 'inside' a species tree. Based on this model, we develop a tool with the capacity to perform practical orthology analysis, based on Fitch's original definition, and more generally for reconciling pairs of gene and species trees. Our gene evolution model is biologically sound (Nei et al., 1997) and intuitively attractive. We develop a Bayesian analysis based on MCMC which facilitates approximation of an a posteriori distribution for reconciliations. That is, we can find the most probable reconciliations and estimate the probability of any reconciliation, given the observed gene tree. This also gives a way to estimate the probability that a pair of genes are orthologs. The main algorithmic contribution presented here consists of an algorithm for computing the likelihood of a given reconciliation. To the best of our knowledge, this is the first successful introduction of this type of probabilistic methods, which flourish in phylogeny analysis, into reconciliation and orthology analysis. The MCMC algorithm has been implemented and, although not yet being in its final form, tests show that it performs very well on synthetic as well as biological data. Using standard correspondences, our results carry over to allele trees as well as biogeography.

Algorithms↗
PubMed1991

Sex chromosome evolution: platypus gene mapping suggests that part of the human X chromosome was originally autosomal.

To investigate the evolution of the mammalian sex chromosomes, we have compared the gene content of the X chromosomes in the mammalian groups most distantly related to man (marsupials and monotremes). Previous work established that genes on the long arm of the human X chromosome are conserved on the X chromosomes in all mammals, revealing that this region was part of an ancient mammalian X chromosome. However, we now report that several genes located on the short arm of the human X chromosome are absent from the platypus X chromosome, as well as from the marsupial X chromosome. Because monotremes and marsupials diverged independently from eutherian mammals, this finding implies that the whole human X short arm region is a relatively recent addition to the X chromosome in eutherian mammals.

Animals↗
PubMed1986

The prothrombin gene and serine proteinase evolution.

The gene coding for human prothrombin has been isolated from two human genomic DNA libraries using a human prothrombin cDNA. Present evidence indicates that the gene is approximately 24 kb in length with about 90% of the DNA representing intervening sequence. Thirteen intervening sequences were found to interrupt the region coding for the mRNA into 14 exons. These intervening sequences vary greatly in size and contain at least 11 copies of Alu repetitive DNA. The positions where several of the intervening sequences interrupt the coding region appear to separate functional and structural domains of the protein. A similar placement of intervening sequences in genes coding for proteins homologous to prothrombin has been observed and provides additional evidence that these proteins have evolved from a common ancestor.

Amino Acid Sequence↗
PubMed1996

Identification of interdomain sequences promoting the intronless evolution of a bacterial protein family.

In the evolution of eukaryotic genes, introns are believed to have played a major role in increasing the probability of favorable duplication events, chance recombinations, and exon shuffling resulting in functional hybrid proteins. As a rule, prokaryotic genes lack introns, and the examples of prokaryotic introns described do not seem to have contributed to gene evolution by exon shuffling. Still, certain protein families in modern bacteria evolve rapidly by recombination of genes, duplication of functional domains, and as shown for protein PAB of the anaerobic bacterial species Peptostreptococcus magnus, by the shuffling of an albumin-binding protein module from group C and G streptococci. Characterization of a protein PAB-related gene in a P. magnus strain with less albumin-binding activity revealed that the shuffled module was missing. Based on this fact and observations made when comparing gene sequences of this family of bacterial surface proteins interacting with albumin and/or immunoglobulin, a model is presented that can explain how this rapid intronless evolution takes place. A new kind of genetic element is introduced: the recer sequence promoting interdomain, in frame recombination and acting as a structure-less flexibility-promoting spacer in the corresponding protein. The data presented also suggest that antibiotics could represent the selective pressure behind the shuffling of protein modules in P. magnus, a member of the indigenous bacterial flora.

Albumins↗
PubMed1983

DNA sequence adjacent to flagellar genes and evolution of flagellar-phase variation.

A variety of factors, including phase variation, are involved in the regulation of flagellin gene expression in Salmonella sp. Flagellar-phase variation refers to the alternate expression of two different flagellin genes, H1 and H2. Site-specific inversion of a DNA segment adjacent to the H2 gene is responsible for switching expression. The segment includes the H2 promoter as well as the hin gene, which is required to mediate the inversion. Sequences in this region have homology with the corresponding sequences adjacent to the H1 flagellin gene in Salmonella sp. and the hag flagellin gene in Escherichia coli. The hin gene has also been shown to be homologous to the gin gene, which is found on bacteriophage Mu. To understand gene expression and the origin of these relationships, we have compared the DNA sequence adjacent to all three flagellin genes. The sequence data suggest a mechanism for the evolution of the hin-H2 locus.

Amino Acid Sequence↗
PubMed2003

Parallel evolution by gene duplication in the genomes of two unicellular fungi.

Phylogenetic analysis of conserved gene families in fission yeast Schizosaccharomyces pombe and brewer's yeast Saccharomyces cerevisiae showed that gene duplications have occurred independently in the same families in each of these two lineages to a far greater extent than expected by chance. These species represent distinct lineages of the phylum Ascomycota that independently evolved a "yeast" life cycle with a unicellular thallus that reproduces by budding, and many of the genes that have duplicated independently in the two lineages are known to be involved in crucial aspects of this life cycle. Parallel gene duplication thus appears to have played a role in the independent origin of similar adaptations in the two species. The results indicate that using phylogenetic analysis to test for parallel gene duplication in different species may help in identifying genes responsible for similar but independently evolved adaptations.

Evolution, Molecular↗
PubMed2003

Parallel evolution by gene duplication in the genomes of two unicellular fungi.

Phylogenetic analysis of conserved gene families in fission yeast Schizosaccharomyces pombe and brewer's yeast Saccharomyces cerevisiae showed that gene duplications have occurred independently in the same families in each of these two lineages to a far greater extent than expected by chance. These species represent distinct lineages of the phylum Ascomycota that independently evolved a "yeast" life cycle with a unicellular thallus that reproduces by budding, and many of the genes that have duplicated independently in the two lineages are known to be involved in crucial aspects of this life cycle. Parallel gene duplication thus appears to have played a role in the independent origin of similar adaptations in the two species. The results indicate that using phylogenetic analysis to test for parallel gene duplication in different species may help in identifying genes responsible for similar but independently evolved adaptations

Evolution, Molecular↗
PubMed2006

Codon-usage bias versus gene conversion in the evolution of yeast duplicate genes.

Many Saccharomyces cerevisiae duplicate genes that were derived from an ancient whole-genome duplication (WGD) unexpectedly show a small synonymous divergence (K(S)), a higher sequence similarity to each other than to orthologues in Saccharomyces bayanus, or slow evolution compared with the orthologue in Kluyveromyces waltii, a non-WGD species. This decelerated evolution was attributed to gene conversion between duplicates. Using approximately 300 WGD gene pairs in four species and their orthologues in non-WGD species, we show that codon-usage bias and protein-sequence conservation are two important causes for decelerated evolution of duplicate genes, whereas gene conversion is effective only in the presence of strong codon-usage bias or protein-sequence conservation. Furthermore, we find that change in mutation pattern or in tDNA copy number changed codon-usage bias and increased the K(S) distance between K. waltii and S. cerevisiae. Intriguingly, some proteins showed fast evolution before the radiation of WGD species but little or no sequence divergence between orthologues and paralogues thereafter, indicating that functional conservation after the radiation may also be responsible for decelerated evolution in duplicates.

Codon↗
PubMed2001

Aspartyl proteinase genes from apicomplexan parasites: evidence for evolution of the gene structure.

Aspartyl proteinases are a widely distributed family of enzymes. All vertebrate aspartyl proteinases share a conserved nine-exon gene structure, but in other organisms the structure of aspartyl proteinase genes varies considerably. The exon-intron patterns generally reflect phylogeny based on amino acid sequences. However, close comparison of these gene structures reveals some striking features, such as the conservation of intron positions and intron phases between aspartyl proteinases from nematodes and apicomplexans. Here, we discuss the implications of gene structure for the possible evolution of the aspartyl proteinase family, with particular reference to the plasmepsins of Plasmodium falciparum and eimepsin from Eimeria tenella.

Amino Acid Sequence↗