Evolution of introns and exons of class II major histocompatibility complex genes of vertebrates

 The phylogenetic relationships and patterns of nucleotide substitution were compared for introns and exons of class II major histocompatibility complex (MHC) genes in three datasets: human DRB1, human DQA1, and cyprinid fish DAB1. In both human DRB1 and cyprinid DAB1, there was strong evidence that recombination events between alleles have occurred in such a way that intron and exon sequences of a given allele do not necessarily share the same evolutionary history. In the case of human DRB1, recombination was found to have homogenized intron 1 and intron 2 sequences relative to exon 2 sequences within lineages of alleles but not between lineages. As a result, mean divergence times of intron sequences are much more recent than those of exonic sequences. Thus, the divergence time of DRB1 introns cannot be used to date that of exons in the same alleles, and the hypothesis that most human DRB1 polymorphism is of very recent origin is not supported. Received: 5 September 1999 / Revised: 30 December 1999     

The fate of duplicated genes: loss or new function?

Gene duplication events are important sources of novel gene functions. However, more often than not, a duplicate gene may lose its function and become a pseudogene. What is the relative frequency of these two scenarios: functional divergence versus gene loss? Given that most non-neutral mutations are deleterious, gene loss should be far more frequent than divergence. However, a recent empirical study suggests that about 50% of all gene duplications will lead to functional divergence. The study infers the frequency of functional divergence from the size distribution of gene families produced by two successive genome duplications early in vertebrate evolution. Reasons for this unexpectedly high frequency of functional divergence are discussed.     

Dissecting the correlation structure of a bivariate phenotype: Common genes or shared environment?

High correlations between two quantitative traits may be either due to common genetic factors or common environmental factors or a combination of both. In this study, we develop statistical methods to extract the genetic contribution to the total correlation between the components of a bivariate phenotype. Using data on bivariate phenotypes and marker genotypes for sib-pairs, we propose a test for linkage between a common QTL and a marker locus based on the conditional cross-sib trait correlations (trait 1 of sib 1—trait 2 of sib 2 and conversely) given the identity-by-descent (i.b.d.) sharing at the marker locus. We use Monte-Carlo simulations to evaluate the performance of the proposed test under different trait parameters and quantitative trait distributions. An application of the method is illustrated using data on two alcohol-related phenotypes from a project on the collaborative study on the genetics of alcoholism.     

Weird genetics? Evolution and nonmendelian genes

It is the simplicity of traditional genetics that has endowed it with such power. Its generalisations do describe most genetic phenomena in most organisms, most of the time … the great challenge [is] to explore the implications of the exceptions and to find new sets of even more potent rules, if any exist.     

Evolution of biodiversity: Hyperbola or exponent?

Two models of the evolution of biodiversity during the Phanerozoic are critically analyzed.     

The identification of a DNA polymorphism of the α fibrinogen gene,and the regional assignment of the human fibrinogen genes to 4q26-qter

Summary We have identified a common restriction fragment length polymorphism of the fibrinogen gene with the enzyme TaqI. This polymorphism is probably due to a single base change that creates or destroys a TaqI recognition site about 1000 basepairs from the 3 end of the fibrinogen géne. The frequency of the rare allele in 83 unrelated healthy individuals is 0.33. We have used in situ hybridisation of the fibrinogen cDNA to localise the gene on chromosome 4q29–31. We have confirmed this regional localisation by restriction fragment detection in a human x Chinese hamster somatic cell hybrid which contains a translocated human chromosome 4 with a breakpoint at 4q26. The , , and fibrinogen genes are all present on human chromosome 4q26-qter.     

Origin of the bacterial SET domain genes: vertical or horizontal?

The presence of Supressor of variegation-Enhanser of zeste-Trithorax (SET) domain genes in bacteria is a current paradigm for lateral genetic exchange between eukaryotes and prokaryotes. Because a major function of SET domain proteins is the chemical modification of chromatin and bacteria do not have chromatin, there is no apparent functional requirement for the existence of bacterial SET domain genes. Consequently, their finding in only a small fraction of pathogenic and symbiotic bacteria was taken as evidence that bacteria have obtained the SET domain genes from their hosts. Furthermore, it was proposed that the products of the genes would, most likely, be involved in bacteria-host interactions. The broadened scope of sequenced bacterial genomes to include also free-living and environmental species provided a larger sample to analyze the bacterial SET domain genes. By phylogenetic analysis, examination of individual chromosomal regions for signs of insertion, and evaluating the chromosomal versus SET domain genes' GC contents, we provide evidence that SET domain genes have existed in the bacterial domain of life independently of eukaryotes. The bacterial genes have undergone an evolution of their own unconnected to the evolution of the eukaryotic SET domain genes. Initial finding of SET domain genes in predominantly pathogenic and symbiotic bacteria resulted, most probably, from a biased sample. However, a lateral transfer of SET domain genes may have occurred between some bacteria and a family of Archaea. A model for the evolution and distribution of SET domain genes in bacteria is proposed.     

Evolution of caprine and ovine β-defensin genes

Defensins comprise an important family of anti-microbial peptides. Among vertebrates, numerous defensin genes have been detected, but their evolutionary background is still discussed. We investigated the molecular evolution and variability of β-defensins of Caprini via sequence analyses of defensin introns. Screening of several domestic and wild species of Caprini revealed a total of 13 discrete β-defensin coding sequences, with three of them described before this study. Phylogenetic analyses revealed that the array of newly described defensin genes is of monophyletic origin and has arisen in numerous independent duplication events after separation of the ancestral defensins. As a result of that scenario, recent defensin genes are distributed in a species-specific manner. Values of synonymous and non-synonymous substitutions demonstrated that both modes of evolutionary pressure, positive as well as negative selection, have acted. In addition, conservation of some β-defensin exons is demonstrated. Discrimination of certain β-defensin genes was possible only due to intron-specific differences. Therefore, sequence analyses restricted to the exons would result in underestimation of the number of β-defensin genes. Our study shows that for reconstruction of the phylogenetic history data of defensin introns are more appropriated. Comparisons among the amino acid sequences show moderate substitutions without changing the net charge of the mature peptides. Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.     

Evolution of the rabbit immunoglobulin κ chain genes

We have analyzed the organization and the structure of rabbit chain genes encoding b allotypes in wild rabbits. The 1 gene of the b95 allotype was cloned and its structure determined. The J region is composed of five segments but only J2 appears to be functional and is identical to the J2 segment of the b4 allotype. The J region is highly conserved among the various b allotypes, whereas the constant region exon displays a high level of differences when compared with other allotypes (9%–30% of different amino acids). The b95 J region is closer to that of b4^var and the constant region to b5 allotype constant region. Alignment of nucleotide sequences revealed that the constant region exon displays segmental similarities with b4 and bas constant regions. The mosaic structure of b95 allotype gene indicates that complex allotypes of 1 genes may result from genetic exchanges of gene conversion between the different genes.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide database and have been assigned the accession number M22542. Address correspondence and offprint requests to: P.-A. Cazenave.     

Does the evolutionary history of aminoacyl-tRNA synthetases explain the loss of mitochondrial tRNA genes?

The importation of cytosolic tRNAs is required for protein synthesis in the mitochondria of the wide variety of eukaryotes that lack a complete set of mitochondrial tRNA genes. The evolutionary history of the process, however, is still enigmatic. The analysis presented here suggests that the loss of distinct mitochondrial tRNA genes was not random and that it might be explained by the differential capabilities of mitochondrial aminoacyl-tRNA synthetases to charge imported eukaryotic-type tRNAs with amino acid.     

The origin of adaptive mutants: Random or nonrandom?

Several recent reports have claimed that adaptive mutants in bacteria and yeast are induced by selective conditions. The results of these reports suggest that mutants can arise nonrandomly with respect to fitness, contrary to what has been widely accepted. In several cases that have received careful experimental reexamination, however, the detection of seemingly nonrandom mutation has been explained as an experimental artifact. In the remaining cases, there is no evidence to suggest that cells have the capacity to direct or choose which genetic variants will arise. Instead, current models propose processes by which genetic variants persist as mutations only if they enable cell growth and DNA replication. Most of these models are apparently contradicted by experimental data. One model, the hypermutable state model, has recently received limited circumstantial support. However, in this model the origin of adaptive mutants is random; the apparent nonrandomness of mutation is merely a consequence of natural selection. The critical distinction between the origin of genetic variation (mutation) and the possible consequence of that variation (selection) has been neglected by proponents of directed mutation.     

The origin of recent introns: transposons?

The long-standing question of how genes acquire introns has provoked much debate. A recent study makes considerable progress by identifying numerous recently gained introns in nematodes - although it remains difficult to distinguish definitively between models of intron gain.     

Kasha or state selective behavior in the photochemistry of ortho-nitrobenzaldehyde?

The photochemistry of ortho-nitrobenzaldehyde dissolved in tetrahydrofuran was studied by means of femtosecond UV/Vis and IR spectroscopy. Comparison was made of the spectral and temporal signatures for ~400 nm and ~260 nm excitation. The 400 nm excitation promotes NBA to its lowest excited singlet state of nπ* character whereas for 260 nm an upper excited state of ππ* character is addressed. On the picosecond time scale, the molecule undergoes hydrogen transfer, yielding a ketene intermediate, internal conversion recovering the starting material, and intersystem crossing. Time constants and yields of these processes are virtually not affected by the excitation wavelength. For 400 nm excitation a ~100 fs decay component seen in the 260 nm experiment is absent, indicating that this component is due to a ππ* → nπ* internal conversion. In contrast to its formation, the decay of the ketene intermediate is influenced by the excitation wavelength. This can be attributed to different amounts of vibrational excitation.     

The role of floods in the lives of fish-eating birds: predator loss or benefit?

Floods accompanied by high flow and high water turbidity are usually believed to cause problems to fish-eating birds and mammals searching visually for their prey. In the present study the diets of breeding kingfishers were studied during the normal river situation and during a long-lasting flood event with respect to diet composition, size of fish prey and food diversity index. During the normal situation (flow 1.75 m³ s^?1, Secchi disc depth 0.5–1 m), the diet of a kingfisher was dominated by benthic fish species (52.9% by numbers, 63.9% by weight), the average size of fish taken was 6.5 cm L _T and 3.0 g and the food diversity index reached its lowest value (1.57). In contrast, during the long-lasting flood event (flow 5–28 m³ s^?1, Secchi disc depth 0.03–0.4 m) the diet of the kingfisher was dominated by sub-surface fish species (72.4% by numbers, 76.1% by weight) and both the average size of fish taken (7.4 cm L _T and 3.7 g) and the food diversity index (1.83) increased significantly. The birds provided their nestlings with lower numbers of fish of larger sizes, which resulted in very similar weights of the young birds prior to fledging when the flood and normal situations were compared. This study provides evidence that in different foraging conditions the kingfishers adopt different foraging strategies to maintain their high breeding success.