Resampling the pool of genotypic possibilities: an adaptive function of sexual reproduction.

Background: Natural populations harbor significant levels of genetic variability. Because of this standing genetic variation, the number of possible genotypic combinations is many orders of magnitude greater than the population size. This means that any given population contains only a tiny fraction of all possible genotypic combinations.

Sex solves Haldane's dilemma.

The cumulative reproductive cost of multi-locus selection has been considered to be a potentially limiting factor on the rate of adaptive evolution. In this paper, we show that Haldane's arguments for the accumulation of reproductive costs over multiple loci are valid only for a clonally reproducing population of asexual genotypes. We show that a sexually reproducing population avoids this accumulation of costs.

The advantage of recombination when selection is acting at many genetic Loci.

Natural selection can act at many loci across the genome. But as the number of polymorphic loci increases linearly, the number of possible genotypic combinations increases exponentially. Consequently, a finite population - even a very large population - contains only a small sample of all possible multi-locus genotypes.

The evolution of genomic GC content undergoes a rapid reversal within the genus Plasmodium.

The genome of the malarial parasite Plasmodium falciparum is extremely AT rich. This bias toward a low GC content is a characteristic of several, but not all, species within the genus Plasmodium. We compared 4283 orthologous pairs of protein-coding sequences between Plasmodium falciparum and the less AT-biased Plasmodium vivax.

The DNA Barcode Linker.

DNA barcoding is based on the use of short DNA sequences to provide taxonomic tags for rapid, efficient identification of biological specimens. Currently, reference databases are being compiled. In the future, it will be important to facilitate access to these databases, especially for nonspecialist users.

Finite populations, finite resources, and the evolutionary maintenance of genetic recombination.

Most previous models for the evolution of sex implicitly assume infinite population sizes and limitless resources. However, because favorable mutations are very rare and eukaryotic populations are finite, it has already been shown that multiple favorable mutants virtually never occur by chance. Therefore, sex is required to combine different favorable mutations into a single lineage.

Nucleotide substitution bias within the genus Drosophila affects the pattern of proteome evolution.

The availability of complete genome sequences for 12 Drosophila species provides an unprecedented resource for large-scale studies of genome evolution. In this study, we looked for correlated shifts in the patterns of genome and proteome evolution within the genus Drosophila. Specifically, we asked if the nucleotide composition of the Drosophila willistoni genome--which is significantly less GC rich than the other 11 sequenced Drosophila genomes--is reflected in an altered pattern of amino acid substitutions in the encoded proteins.

Uncorrected nucleotide bias in mtDNA can mimic the effects of positive Darwinian selection.

The relative rates of nucleotide substitution at synonymous and nonsynonymous sites within protein-coding regions have been widely used to infer the action of natural selection from comparative sequence data. It is known, however, that mutational and repair biases can affect rates of evolution at both synonymous and nonsynonymous sites. More importantly, it is also known that synonymous sites are particularly prone to the effects of nucleotide bias.

An evolutionary footprint of age-related natural selection in mitochondrial DNA.

By comparing mtDNA sequences between different orders of mammals, we show that both longevity and generation time are significantly correlated with the nucleotide content of the mtDNA. Specifically, there is a positive correlation between generation time and mt GC content. This correlation is repeated, at a finer evolutionary scale, within the primates.

Assessing the effect of varying sequence length on DNA barcoding of fungi.

DNA barcoding shows enormous promise for the rapid identification of organisms at the species level. There has been much recent debate, however, about the need for longer barcode sequences, especially when these sequences are used to construct molecular phylogenies. Here, we have analysed a set of fungal mitochondrial sequences - of various lengths - and we have monitored the effect of reducing sequence length on the utility of the data for both species identification and phylogenetic reconstruction.

Joint stationary moments of a two-island diffusion model of population subdivision.

An expression for joint stationary moments of a diffusion approximation to a generalized Wright-Fisher model, corresponding to two finite populations of equal sizes, with migration and mutation, is derived. This gives a complete description of the stationary distribution of allele frequencies in the balance between migration, mutation and genetic drift. We derive the sampling formula in terms of the joint stationary moments, and we also prove that the diffusion process corresponding to this model of population division is not reversible.

A universal DNA mini-barcode for biodiversity analysis.

Background: The goal of DNA barcoding is to develop a species-specific sequence library for all eukaryotes. A 650 bp fragment of the cytochrome c oxidase 1 (CO1) gene has been used successfully for species-level identification in several animal groups. It may be difficult in practice, however, to retrieve a 650 bp fragment from archival specimens, (because of DNA degradation) or from environmental samples (where universal primers are needed).

Highly similar noncoding genomic DNA sequences: ultraconserved, or merely widespread?

In this note, I propose an explanation for the seeming contradiction between bioinformatics-based predictions of an essential function for ultraconserved DNA sequences, and the lack of an experimental demonstration of such function.

DNA asymmetric strand bias affects the amino acid composition of mitochondrial proteins.

Variations in GC content between genomes have been extensively documented. Genomes with comparable GC contents can, however, still differ in the apportionment of the G and C nucleotides between the two DNA strands. This asymmetric strand bias is known as GC skew.

DNA barcodes provide a quick preview of mitochondrial genome composition.

DNA barcodes have achieved prominence as a tool for species-level identifications. Consequently, there is a rapidly growing database of these short sequences from a wide variety of taxa. In this study, we have analyzed the correlation between the nucleotide content of the short DNA barcode sequences and the genomes from which they are derived.

DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics.

DNA barcoding aims to provide an efficient method for species-level identifications and, as such, will contribute powerfully to taxonomic and biodiversity research. As the number of DNA barcode sequences accumulates, however, these data will also provide a unique 'horizontal' genomics perspective with broad implications. For example, here we compare the goals and methods of DNA barcoding with those of molecular phylogenetics and population genetics, and suggest that DNA barcoding can complement current research in these areas by providing background information that will be helpful in the selection of taxa for further analyses.

Rapid divergence of codon usage patterns within the rice genome.

Background: Synonymous codon usage varies widely between genomes, and also between genes within genomes. Although there is now a large body of data on variations in codon usage, it is still not clear if the observed patterns reflect the effects of positive Darwinian selection acting at the level of translational efficiency or whether these patterns are due simply to the effects of mutational bias. In this study, we have included both intra-genomic and inter-genomic comparisons of codon usage.

Benchmarking DNA barcodes: An assessment using available primate sequences.

DNA barcoding has been recently promoted as a method for both assigning specimens to known species and for discovering new and cryptic species. Here we test both the potential and the limitations of DNA barcodes by analysing a group of well-studied organisms--the primates. Our results show that DNA barcodes provide enough information to efficiently identify and delineate primate species, but that they cannot reliably uncover many of the deeper phylogenetic relationships.

Thermal adaptation of the small subunit ribosomal RNA gene: a comparative study.

We carried out a comprehensive survey of small subunit ribosomal RNA sequences from archaeal, bacterial, and eukaryotic lineages in order to understand the general patterns of thermal adaptation in the rRNA genes. Within each lineage, we compared sequences from mesophilic, moderately thermophilic, and hyperthermophilic species. We carried out a more detailed study of the archaea, because of the wide range of growth temperatures within this group.

Cytosine usage modulates the correlation between CDS length and CG content in prokaryotic genomes.

Previous studies have argued that, given the AT-rich nature of stop codons, the length and CG% of coding sequences (CDSs) should be positively correlated. This prediction is generally supported empirically by prokaryotic genomes. However, the correlation is weak for a number of species, with 4 species showing a negative correlation.

Structural organization and chromosomal location of the chicken alpha-amylase gene family.

Characterization of the Gallus gallus alpha-amylase gene family revealed that the chicken genome contains two distinct amy loci. One of the two loci is expressed in the chicken pancreas while cDNA clones for the second locus were detected in a library constructed from liver mRNA. Fluorescent in situ hybridization to chromosome spreads showed that the two loci are both located on chromosome 8 within the chicken genome.

Characterization of the bovine ampkgamma1 gene.

AMP-activated protein kinase (AMPK) represents the mammalian form of the core component of a kinase cascade that is conserved between fungi, plants, and animals. AMPK plays a major role in protecting mammalian cells from metabolic stress by switching off biosynthetic pathways that require ATP and switching on ATP-regenerating pathways. In this report, we describe the isolation and characterization of the gene for the noncatalytic bovine gamma1 subunit of AMPK.

Genomic and proteomic adaptations to growth at high temperature.

Most positively selected mutations cause changes in metabolism, resulting in a better-adapted phenotype. But as well as acting on the information content of genes, natural selection may also act directly on nucleic acid and protein molecules. We review the evidence for direct temperature-dependent natural selection acting on genomes, transcriptomes and proteomes.

Phylogenetic position of species in the genera Anoplophrya, Plagiotoma, and Nyctotheroides (Phylum Ciliophora), endosymbiotic ciliates of annelids and anurans.

We have used small subunit rRNA gene sequences to determine the phylogenetic relationships of species in three genera of endosymbiotic ciliates. We have confirmed that the astome Anoplophrya marylandensis is related to ciliates in the Class Oligohymenophorea, supporting the view that astomes are derived from hymenostome-like ancestors. We confirmed that Plaglotoma lumbrici, formerly considered to be a heterotrich, is a stichotrich spirotrich ciliate most closely related to Paraurostyla weissei in this analysis.