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PubMed2004

Evolution of 4-coumarate:coenzyme A ligase (4CL) gene and divergence of Larix (Pinaceae).

The evolutionary dynamics of the 4CL gene encoding 4-coumarate:coenzyme A ligase was investigated in the genus Larix (Pinaceae) by comparing copy number, GC content and codon usage, sequence divergence, and phylogenetic analysis. All 4CL clones of Larix formed a strongly supported monophyletic group, in which two robust clades (4clA and 4clB) derived from an ancient gene duplication event in the common ancestor of Larix were identified. Further gene duplication in the 4clA clade gave rise to two subclades 4clA(1) and 4clA(2). Frequent duplication/deletion appears to be a common evolutionary phenomenon in the 4CL gene family and paralogous genes differ greatly in their evolution rate. The existence of L. speciosa in subclades 4clA(1) and 4clA(2) suggests that this species may represent a primitive form of Larix or the closest relative of the common ancestor of the Eurasian Sect. Multiserialis. In addition, cpDNA and nrDNA ITS analyses support the hypothesis of an early separation of Larix into a North American and a Eurasian clade, which is congruent with the results of previous allozyme and very recent AFLP analyses. The unexpected close relationship between North American larches and the short-bracted species L. gmelinii in East Asia, based on the 4CL gene tree, may stem from lineage sorting.

Base Composition↗
PubMed2005

Recently evolved genes identified from Drosophila yakuba and D. erecta accessory gland expressed sequence tags.

The fraction of the genome associated with male reproduction in Drosophila may be unusually dynamic. For example, male reproduction-related genes show higher-than-average rates of protein divergence and gene expression evolution compared to most Drosophila genes. Drosophila male reproduction may also be enriched for novel genetic functions. Our earlier work, based on accessory gland protein genes (Acp's) in D. simulans and D. melanogaster, suggested that the melanogaster subgroup Acp's may be lost and/or gained on a relatively rapid timescale. Here we investigate this possibility more thoroughly through description of the accessory gland transcriptome in two melanogaster subgroup species, D. yakuba and D. erecta. A genomic analysis of previously unknown genes isolated from cDNA libraries of these species revealed several cases of genes present in one or both species, yet absent from ingroup and outgroup species. We found no evidence that these novel genes are attributable primarily to duplication and divergence, which suggests the possibility that Acp's or other genes coding for small proteins may originate from ancestrally noncoding DNA.

Animals↗
PubMed2003

The enigma of ribonuclease P evolution.

The 5'-end maturation of tRNAs is catalyzed by the ribonucleoprotein enzyme ribonuclease P (RNase P) in all organisms. Here we provide, for the first time, a comprehensive overview on the representation of individual RNase P protein homologs within the Eukarya and Archaea. Most eukaryotes have homologs for all four protein subunits (Pop4, Rpp1, Pop5 and Rpr2) present in the majority of Archaea. Pop4 is the only RNase P protein subunit identifiable in all Eukarya and Archaea with available genome sequences. Remarkably, there is no structural homology between bacterial and archaeal-eukaryotic RNase P proteins. The simplest interpretation is that RNase P has an 'RNA-alone' origin and progenitors of Bacteria and Archaea diverged very early in evolution and then pursued completely different strategies in the recruitment of protein subunits during the transition from the 'RNA-alone' to the 'RNA-protein' state of the enzyme.

Animals↗
PubMed2005

Evolution by recombination and transspecies polymorphism in the MHC class I gene of Xenopus laevis.

The patterns of major histocompatibility complex (MHC) evolution involve duplications, deletions, and independent divergence of loci during episodes punctuated by natural selection. Major differences in MHC evolution among taxa have previously been attributed to variation in linkage patterns of class I and class II MHC genes. Here we characterize patterns of evolution in the MHC class Ia gene of Xenopus laevis in terms of polymorphism, recombination, and extent of transspecies polymorphism. We also compare these patterns to see if a correlation exists with linkage or separation of the MHC class I and class II regions as seen in amphibians and teleost fishes. In X. laevis, we find high levels of polymorphism. Also, genetic exchange is relatively frequent and occurs in intron II, reshuffling allelic forms of exons 2 and 3. Evolutionary relationships among class I alleles show an intermingling of alleles from divergent Xenopus species rather than a species-specific clustering. Results indicate that the patterns of evolution are similar to those found in salmonid fishes and are different from the mode of evolution seen in primates. Similar patterns of class Ia evolution in salmonid fishes and X. laevis suggest that nonlinkage of class I and class II regions alone is insufficient to explain some patterns of MHC evolution in salmonids.

Animals↗
PubMed2005

Molecular evolution in the Drosophila melanogaster species subgroup: frequent parameter fluctuations on the timescale of molecular divergence.

Although mutation, genetic drift, and natural selection are well established as determinants of genome evolution, the importance (frequency and magnitude) of parameter fluctuations in molecular evolution is less understood. DNA sequence comparisons among closely related species allow specific substitutions to be assigned to lineages on a phylogenetic tree. In this study, we compare patterns of codon usage and protein evolution in 22 genes (>11,000 codons) among Drosophila melanogaster and five relatives within the D. melanogaster subgroup. We assign changes to eight lineages using a maximum-likelihood approach to infer ancestral states. Uncertainty in ancestral reconstructions is taken into account, at least to some extent, by weighting reconstructions by their posterior probabilities. Four of the eight lineages show potentially genomewide departures from equilibrium synonymous codon usage; three are decreasing and one is increasing in major codon usage. Several of these departures are consistent with lineage-specific changes in selection intensity (selection coefficients scaled to effective population size) at silent sites. Intron base composition and rates and patterns of protein evolution are also heterogeneous among these lineages. The magnitude of forces governing silent, intron, and protein evolution appears to have varied frequently, and in a lineage-specific manner, within the D. melanogaster subgroup.

Amino Acid Substitution↗
PubMed2003

Structure of the bc1 complex from Seculamonas ecuadoriensis, a jakobid flagellate with an ancestral mitochondrial genome.

In eubacteria, the respiratory bc(1) complex (complex III) consists of three or four different subunits, whereas that of mitochondria, which have descended from an alpha-proteobacterial endosymbiont, contains about seven additional subunits. To understand better how mitochondrial protein complexes evolved from their simpler bacterial predecessors, we purified complex III of Seculamonas ecuadoriensis, a member of the jakobid protists, which possess the most bacteria-like mitochondrial genomes known. The S. ecuadoriensis complex III has an apparent molecular mass of 460 kDa and exhibits antimycin-sensitive quinol:cytochrome c oxidoreductase activity. It is composed of at least eight subunits between 6 and 46 kDa in size, including two large "core" subunits and the three "respiratory" subunits. The molecular mass of the S. ecuadoriensis bc(1) complex is slightly lower than that reported for other eukaryotes, but about 2x as large as complex III in bacteria. This indicates that the departure from the small bacteria-like complex III took place at an early stage in mitochondrial evolution, prior to the divergence of jakobids. We posit that the recruitment of additional subunits in mitochondrial respiratory complexes is a consequence of the migration of originally alpha-proteobacterial genes to the nucleus.

Amino Acid Sequence↗
PubMed2006

Evidence for an early gene duplication event in the evolution of the mitochondrial transcription factor B family and maintenance of rRNA methyltransferase activity in human mtTFB1 and mtTFB2.

Most metazoans have two nuclear genes encoding orthologues of the well-characterized Saccharomyces cerevisiae mitochondrial transcription factor B (sc-mtTFB). This class of transcription factors is homologous to the bacterial KsgA family of rRNA methyltransferases, which in Escherichia coli dimethylates adjacent adenine residues in a stem-loop of the 16S rRNA. This posttranscriptional modification is conserved in most metazoan cytoplasmic and mitochondrial rRNAs. Homo sapiens mitochondrial transcription factor B1 (h-mtTFB1) possesses this enzymatic activity, implicating it as a dual-function protein involved in mitochondrial transcription and translation. Here we demonstrate that h-mtTFB2 also has rRNA methyltransferase activity but is a less efficient enzyme than h-mtTFB1. In contrast, sc-mtTFB has no detectable rRNA methyltransferase activity, correlating with the lack of the corresponding modification in the mitochondrial rRNA of budding yeast. Based on these results, and reports that Drosophila melanogaster mtTFB1 and mtTFB2 do not have completely overlapping functions, we propose a model for human mtDNA regulation that takes into account h-mtTFB1 and h-mtTFB2 likely having partially redundant transcription factor and rRNA methyltransferase functions. Finally, phylogenetic analyses of this family of proteins strongly suggest that the presence of two mtTFB homologues in metazoans is the result of a gene duplication event that occurred early in eukaryotic evolution prior to the divergence of fungi and metazoans. This model suggests that, after the gene duplication event, differential selective pressures on the rRNA methyltransferase and transcription factor activities of mtTFB genes occurred, with extreme cases culminating in the loss of one of the paralogous genes in certain species.

Animals↗
PubMed2005

Plant conserved non-coding sequences and paralogue evolution.

Genome duplication is a powerful evolutionary force and is arguably most prominent in plants, where several ancient whole-genome duplication events have been documented. Models of gene evolution predict that functional divergence between duplicates (subfunctionalization) is caused by the loss of regulatory elements. Studies of conserved non-coding sequences (CNSs), which are putative regulatory elements, indicate that plants have far fewer CNSs per gene than mammals, suggesting that plants have less complex regulatory mechanisms. Furthermore, a recent study of a duplicated gene pair in maize suggests that CNSs are lost in a complementary fashion, perhaps driving subfunctionalization. If subfunctionalization is common, one expects duplicate genes to diverge in expression; recent microarray analyses in Arabidopsis thalinia suggest that this is the case. Plant genomes are relatively complex on a genomic level because of the prevalence of whole-genome duplication and, paradoxically, subfunctionalization after duplication can lead to relatively simple regulatory regions on a per gene basis.

Base Sequence↗
PubMed1993

Pattern of nucleotide substitutions in growth hormone-prolactin gene family: a paradigm for evolution by gene duplication.

The growth hormone-prolactin gene family in mammals is an interesting example of evolution by gene duplication. Divergence among members of duplicated gene families and among species was examined by using reported gene sequences of growth hormone, prolactin and their receptors. Sequence divergence among species was found to show a general tendency in which a generation-time effect is pronounced for synonymous substitutions but not so for nonsynonymous substitutions. Divergence among duplicated genes is characterized by the relatively high rate of nonsynonymous substitutions, i.e., the rate is close to that of synonymous ones. In view of the stage- and tissue-specific expression of duplicated genes, some of the amino acid substitutions among duplicated genes is likely to be caused by positive Darwinian selection.

Amino Acid Sequence↗
PubMed2002

Proposal for an allele nomenclature system based on the evolutionary divergence of haplotypes.

The classical view of what constitutes an "allele" has been challenged by recent findings of a great deal of human genetic variability, i.e., we can expect, on average, one variant site every 100-250 bases of our haploid genome. The haplotype is defined as "the patterns of co-occurrence of variant sites on the same chromosome" (and therefore within each particular gene). Sufficient evidence exists for the divergence of haplotypes during evolution of Homo sapiens sapiens, and the total number of haplotypes per gene will reflect the amount of time any particular ethnic group has existed on the planet, e.g., greatest in Africans, fewer in East Asians, and still fewer in Caucasians. If the average gene spans 30 kb, we can expect approximately 170 polymorphic variant sites per gene in the world population. We do not see 2(170) haplotypes, however; we might find only 10 to 200 haplotypes (depending on the gene's size and degree of conservation of the gene product). This finite number allows for a reasonable haplotype nomenclature system for each gene, based on evolutionary divergence. For polymorphic variants (i.e., frequency > or = 0.01), I propose using Arabic numerals for the major clades (e.g., *1, *2, em leader *20, *21), capital letters for sublineages (e.g., *2A, *2B, *2C), and Arabic numerals for sub-sublineages (e.g., *22G12, *22G13); additional subcategories may be added, in an alternating number/letter/number/letter sequence, depending on the complexity of present-day haplotypes of a particular gene. Web sites with a web master and external advisory committee should be set up for each gene superfamily, family, or individual gene (depending on complexity), and an international haplotype nomenclature committee, perhaps comprised of several dozen of these web masters, should oversee haplotype nomenclature for the entire human genome. The higher heterozygosity and multiallelic nature makes haplotypes more informative than biallelic SNPs. Ultimately, our knowledge of haplotype patterns, rather than single variant sites, of perhaps several hundred genes will likely be helpful in finding associations between genotype and any multiplex phenotype (e.g., complex diseases including cancer, and/or toxicity of pharmaceutical agents or environmental pollutants).

Alleles↗
PubMed2000

Genomic exploration of the hemiascomycetous yeasts: 19. Ascomycetes-specific genes.

Comparisons of the 6213 predicted Saccharomyces cerevisiae open reading frame (ORF) products with sequences from organisms of other biological phyla differentiate genes commonly conserved in evolution from 'maverick' genes which have no homologue in phyla other than the Ascomycetes. We show that a majority of the 'maverick' genes have homologues among other yeast species and thus define a set of 1892 genes that, from sequence comparisons, appear 'Ascomycetes-specific'. We estimate, retrospectively, that the S. cerevisiae genome contains 5651 actual protein-coding genes, 50 of which were identified for the first time in this work, and that the present public databases contain 612 predicted ORFs that are not real genes. Interestingly, the sequences of the 'Ascomycetes-specific' genes tend to diverge more rapidly in evolution than that of other genes. Half of the 'Ascomycetes-specific' genes are functionally characterized in S. cerevisiae, and a few functional categories are over-represented in them.

Ascomycota↗
PubMed2002

'Superfast' or masticatory myosin and the evolution of jaw-closing muscles of vertebrates.

There are four fibre types in mammalian limb muscles, each expressing a different myosin isoform that finely tunes fibre mechanics and energetics for locomotion. Functional demands on jaw-closer muscles are complex and varied, and jaw muscles show considerable phylogenetic plasticity, with a repertoire for myosin expression that includes limb, developmental, alpha-cardiac and masticatory myosins. Masticatory myosin is a phylogenetically ancient motor with distinct light chains and heavy chains. It confers high maximal muscle force and power. It is highly jaw-specific in expression and is found in several orders of eutherian and marsupial mammals including carnivores, chiropterans, primates, dasyurids and diprotodonts. In exceptional species among these orders, masticatory myosin is replaced by some other isoform. Masticatory myosin is also found in reptiles and fish. It is postulated that masticatory myosin diverged early during gnathostome evolution and is expressed in primitive mammals. During mammalian evolution, mastication of food became important, and in some taxa jaw closers replaced masticatory myosin with alpha-cardiac, developmental, slow or fast limb myosins to adapt to the variety of diets and eating habits. This occurred early in some taxa (rodents, ungulates) and later in others (macropods, lesser panda, humans). The cellular basis for the uniqueness of jaw-closing muscles lies in their developmental origin.

Animals↗
PubMed2002

Phylogeography of Lake Malawi cichlids of the genus Pseudotropheus: significance of allopatric colour variation.

One of the most compelling features of the cichlid fishes of the African Great Lakes is the seemingly endless diversity of male coloration. Colour diversification has been implicated as an important factor driving cichlid speciation. Colour has also been central to cichlid taxonomy and, thus, to our concept of species diversity. We undertook a phylogeographical examination of several allopatric populations of the Lake Malawi cichlid Pseudotropheus zebra in order to reconstruct the evolutionary history of the populations, which exhibit one of two dorsal fin colours. We present evidence that populations with red dorsal fins (RT) are not monophyletic. The RT population defining the northern limit of the distribution has evidently originated independently of the southern RT populations, which share a common ancestry. This evidence of species-level colour convergence is an important discovery in our understanding of cichlid evolution. It implies that divergence in coloration may accompany speciation, and that allopatric populations with similar coloration cannot be assumed to be conspecific. In addition to this finding, we have observed evidence for introgression, contributing to current evidence that this phenomenon may be extremely widespread. Thus, in species-level phylogenetic reconstructions, including our own, consideration must be given to the potential effects of introgression.

Alleles↗
PubMed1992

The evolution of mouse and human complement C3-binding proteins: divergence of form but conservation of function.

Despite the fact that the early components of the mouse and human complement cascades are very similar, there are marked differences between the two species in the structure of C3 receptors and the molecules that control homologous lysis. Here, Michael Holers, Taroh Kinoshita and Hector Molina compare and contrast the mouse and human RCA region products and conclude that the receptor and regulatory roles are conserved despite the structural variation.

Animals↗
PubMed2006

A resistance-like gene identified by EST mapping and its association with a QTL controlling Fusarium head blight infection on wheat chromosome 3BS.

Fusarium head blight (FHB) is a major disease in the wheat growing regions of the world. A quantitative trait locus (QTL) on the short arm of chromosome 3B controls much of the variation for resistance. The cloning of candidate disease-resistance genes for FHB QTLs on chromosome 3B can provide further elucidation of the mechanisms that control resistance. However, rearrangements and divergence during plant genome evolution often hampers the identification of sequences with similarity to known disease-resistance genes. This study focuses on the use of wheat expressed sequence tags (ESTs) that map to the region on chromosome 3B containing the QTL for FHB resistance and low-stringency BLAST searching to identify sequences with similarity to known disease-resistance genes. One EST rich with leucine repeats and low similarity to a protein kinase domain of the barley Rpg1 gene was identified. Genetic mapping using a Ning894037 x Alondra recombinant inbred (RI) population showed that this EST mapped to the QTL on the short arm of chromosome 3B and may represent a portion of a newly diverged gene contributing to FHB resistance. The EST is a new marker suitable for marker-assisted selection and provides a starting point to begin map-based cloning for chromosome walking and investigate new diverged genes at this locus.

Amino Acid Sequence↗
PubMed2004

Individual colour patches as multicomponent signals.

Colour patches are complex traits, the components of which may evolve independently through a variety of mechanisms. Although usually treated as simple, two-dimensional characters and classified as either structural or pigmentary, in reality colour patches are complicated, three-dimensional structures that often contain multiple pigment types and structural features. The basic dermal chromatophore unit of fishes, reptiles and amphibians consists of three contiguous cell layers. Xanthophores and erythrophores in the outermost layer contain carotenoid and pteridine pigments that absorb short-wave light; iridophores in the middle layer contain crystalline platelets that reflect light back through the xanthophores; and melanophores in the basal layer contain melanins that absorb light across the spectrum. Changes in any one component of a chromatophore unit can drastically alter the reflectance spectrum produced, and for any given adaptive outcome (e.g. an increase in visibility), there may be multiple biochemical or cellular routes that evolution could take, allowing for divergent responses by different populations or species to similar selection regimes. All of the mechanisms of signal evolution that previously have been applied to single ornaments (including whole colour patches) could potentially be applied to the individual components of colour patches. To reach a complete understanding of colour patch evolution, however, it may be necessary to take an explicitly multi-trait approach. Here, we review multiple trait evolution theory and the basic mechanisms of colour production in fishes, reptiles and amphibians, and use a combination of computer simulations and empirical examples to show how multiple trait evolution theory can be applied to the components of single colour patches. This integrative perspective on animal colouration opens up a host of new questions and hypotheses. We offer specific, testable functional hypotheses for the most common pigmentary (carotenoid, pteridine and melanin) and structural components of vertebrate colour patches.

Animals↗
PubMed1999

Ligands and receptors: common theme in insect storage protein transport.

The passage of macromolecules through biological membranes is an essential process for all multicellular organisms. Insects have developed a mechanism different from that known for all other eukaryotes investigated so far. This review discusses the function and evolution of this mechanism. Insect pupae do not feed during metamorphosis. Therefore they depend on material that has been accumulated during the larval life. At the end of this period, shortly before pupariation, a rise in titer of ecdysteroid hormones induces the incorporation of a large fraction of storage proteins (hexamerins) from the body fluid into the fat body cells. The transport of hexamerins across the cell-membrane is mediated by a specific ecdysteroid-controlled receptor. It is synthesized as a precursor protein that is subsequently processed into the active receptor. This receptor protein is very unusual because it is closely related to its own hexamerin ligand. Sequence comparison shows that the hexamerins and hexamerin receptors diverged early in insect evolution and derive from a common hemocyanin ancestor.

Amino Acid Sequence↗
PubMed1996

Phenylalanine ammonia-lyase gene structure, expression, and evolution in Nicotiana.

Phenylalanine ammonia-lyase (PAL) catalyzes the first reaction in the general phenylpropanoid pathway leading to the production of phenolic compounds with a significant range of biological function. A PAL gene we designated gPAL1, cloned from tobacco, consists of two exons separated by an intron of 1932 bp. Exon I, 398 bp, and exon II, 1747 bp, together encode a polypeptide of 715 amino acids. A putative TATA box and polyadenylation signal are found 144 bp upstream of the initiation codon and 193 bp downstream from the stop codon, respectively. Using various parts of gPAL1 as probes, genomic Southern blots indicated the presence of a small family of PAL genes in the tobacco genome that can be divided into two distinct subfamilies, one consisting of pal1 and pal2 and another of pal3 and pal4. Comparative genomic blot analysis of progenitor species (Nicotiana tomentosiformis and N. sylvestris) indicated that each species contains one PAL gene from each of the subfamilies, suggesting that pal1 and pal3 (or pal2 and pal4) diverged prior to the evolution of N. tabacum. Expression of the PAL gene family was examined using RNA gel blots. PAL transcript levels were significantly higher in flowers and roots than in leaves and stems of mature plants. PAL transcripts accumulate differentially during flower and leaf maturation in that mRNA levels decline during flower maturation but increase during leaf maturation. In leaves, PAL transcripts rapidly accumulated afer wounding.

Amino Acid Sequence↗