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PubMed1990

[Genetic and evolutionary analysis of cases of Darier's disease].

In the past 10 years the authors have observed 27 people (13 men and 14 women) suffering from Darier's disease in Somogy county. Out of these 22 cases were familiar and 5 isolated. The praevalence of dysceratosis follicularis vegetans was found 1 to 16,000 in the area. In the 3 familiar cases the dysceratotic papules of Darier's disease followed the naevus-lines, drawing out the Arnosan-triangle in the meantime. In the case of one of the nonfamiliar occurrences the Darier's diseased papules running stripelike also wrote out the naevus-lines, strictly localized to one side of the body. The stripes composed by the dysceratotic papules ran bipolarly in these cases too; heading from a point of the lumbosacral part of the median line of the back towards the navel. According to the authors the direction of the development of the epidermal elements of the skin is expressed in the early phase of embryonic life by the dysceratotic papules running bipolarly and following naevus-lines as embryological rudiments.

Adult↗
PubMed1995

Intestinal methanogenesis in primates--a genetic and evolutionary approach.

The presence of significant numbers of intestinal methanogens among vertebrates does neither depend on elaborated morphological structures nor on predominantly plant-based diets. Phylogenetic rather than dietary restrictions limit the occurrence of methanogenic bacteria also in the hindguts of primates. The Old-World monkeys are methanogenic--with the only exceptions of Cheirogaleid lemurs and bush-babies. In contrast, among New World monkeys the lack of intestinal methanogens is observed frequently in capuchins and marmosets. Since the absence of methanogens does not parallel distinct morphological, physiological, or ethological characteristics, it is likely that methanogenesis depends on a hereditary predisposition. In humans, methane-producers account for approximately 50% of the European populations. In this study, 56 individuals belonging to 5 families were studied for the occurrence of methane in the breath. The results of this screen are compatible with the assumption that the trait "methane emission" segregates as an autosomal, dominant character. Our findings suggest a high specificity of the symbiosis between primates and methanogenic bacteria. Therefore, the persistence of significant numbers of methanogens in the hindgut might be facilitated by a specific receptor for methanogenic bacteria.

Animals↗
PubMed1996

Human red blood cell Wright antigens: a genetic and evolutionary perspective on glycophorin A-band 3 interaction.

The Wright (Wra/Wrb) blood group polymorphism is defined by an allelic change (Lys658Glu) in the band 3 protein; nevertheless, the Wrb antigen apparently requires glycophorin A (GPA) for surface presentation. To gain insight into the structural basis for this protein-protein interaction and delineate its relationship with Wrb antigen expression, we investigated GPA and band 3 sequence polymorphisms occurring in rare humans and nonhuman primates. The lack of GPA or amino acid residues 59 through 71 of GPA results in the absence of Wrb from human red blood cells (RBCs) exhibiting the MkMk, En(a-), or MiV phenotype. However, the SAT homozygous cells carried a Glu658 form of band 3 and a hybrid glycophorin with the entire GPA extramembrane domain from residues 1 through 71, yet expressed no Wrb antigen. This finding suggests that formation of the Wrb antigenic structure is dependent on protein folding and that the transmembrane junction of GPA is important in maintaining the required conformation. Comparative analyses of GPA and band 3 homologues led to the identification in the interacting regions of conserved and dispensable amino acid residues that correlated with the Wrb positive or negative status on nonhuman primates. In particular, the chimpanzee RBCs cells expressed Wrb and the Glu658 form of band 3, which is identical to humans, but their GPA contained the Gly rather than Arg residue at position 61. Taken together, the results suggest that (1) Arg61 of GPA and the proposed Arg61-Glu658 charge pair are not crucial for Wrb antigen exhibition and (2) the role of GPA for interaction with band 3, including Glu658, probably involves a number of amino acid residues located in the alpha-helical region and transmembrane junction.

Amino Acid Sequence↗
PubMed2005

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Molecular genetics of natural populations.

Significant progress in evolutionary genetics has been made by studying, on the one hand, patterns of DNA sequence polymorphism and, on the other, genetic architecture of complex adaptive traits. However, connections between nucleotide variants under selection and adaptively relevant phenotypes are missing. Such connections can be established using precise gene replacement. We review the recent successful introduction of this technique to the analysis of two evolutionarily interesting loci--Odysseus and desaturase2. Both genes have subtle phenotypes that nevertheless could be identified using gene replacement, demonstrating that effects of naturally occurring alleles can be measured in the laboratory. This is an important first step in connecting statistical signatures of selection with adaptation in nature. More candidate genes involved in adaptation, for example, through cloning of genes responsible for reproductive isolation, now need to be identified. Molecular genetic manipulation, DNA polymorphism analysis, and field studies then have to be integrated to provide fresh insights into the mechanisms of evolutionary change.

Alleles↗
PubMed1999

Partial nucleotide sequencing and molecular evolution of epidemic causing Dengue 2 strains.

To study the genetic variability and to detect evolutionary changes and movement of dengue 2 (DEN-2) strains, nucleotide sequencing of the envelope protein gene and the nonstructural protein 1 gene junction was performed for 9 isolates from the 1996 Delhi epidemic and 1 isolate from the 1967 Delhi epidemic. The epidemic strains had a divergence of 10%-11% from the 1967 strains, but were quite similar to DEN-2 isolates from Seychelles, Somalia, and Torres Strait. In addition, the sequence data were compared to the prototype DEN-2 strain, New Guinea C, and other published DEN-2 sequences from different parts of the world. The phylogenetic analysis by the Molecular Evolutionary Genetics Analysis program suggests that the 1996 Delhi isolates of DEN-2 were genotype IV. The 1967 isolate was similar to a 1957 isolate of DEN-2, P9-122, from India, and was classified as genotype V. This study indicates that earlier DEN-2 strains of genotype V have been replaced by genotype IV.

Base Sequence↗
PubMed2001

Population genomics: a bridge from evolutionary history to genetic medicine.

Studies of human genetic variation are making contributions in several key areas. Evolutionary genetic studies yield critical clues about the histories of human populations, and they provide substantial support for an African origin of modern humans. The analysis of genetic variation has formed a foundation for DNA-based forensic applications. And, as attention is focused on locating genes underlying complex diseases, it is becoming clear that a better understanding of genetic variation will help to guide gene-mapping efforts. Population genomics, the large-scale comparison of DNA sequences, is now beginning to provide new insights in these areas. We review some of the general patterns of human genetic variation, and we show how our knowledge of these patterns can aid in the mapping and cloning of disease-causing genes.

Evolution, Molecular↗
PubMed2005

Genetic variability under mutation selection balance.

A fundamental problem in evolutionary genetics is understanding how high levels of genetic variation in quantitative traits are maintained in natural populations. Variation is removed by the natural selection of individuals with optimal phenotypes and is recovered by mutation; however, previous analyses had indicated that a mutation-selection balance was insufficient to maintain observed levels of genetic variation in these traits. Using more general models, however, it has recently been shown that it is indeed a sufficient mechanism. These models can be used to explore other phenomena in evolutionary biology.

Journal Article↗
PubMed2004

Genetic codes as evolutionary filters: subtle differences in the structure of genetic codes result in significant differences in patterns of nucleotide substitution.

The codon-degeneracy model (CDM) predicts that patterns of nucleotide substitution in protein-coding genes are largely determined by the relative frequencies of four-fold (4f), two-fold, and non-degenerate sites, the attributes of which are determined by the structure of the governing genetic code. The CDM thus further predicts that genetic codes with alternative structures will "filter" molecular evolution differentially. A method, therefore, is presented by which the CDM may be applied to the unique structure of any genetic code. The mathematical relationship between the proportion of transitions at 4f degenerate nucleotide sites and the transition-to-transversion ratio is described. Predictions for five individual genetic codes, relative to the relationship between code structure and expected patterns of nucleotide substitution, are clearly defined. To test this "filter" hypothesis of genetic codes, simulated DNA sequence data sets were generated with a variety of input parameter values to estimate the relationship between patterns of nucleotide substitution and best-fit estimates of transition bias at 4f degenerate sites for both the universal genetic code and the vertebrate mitochondrial genetic code. These analyses confirm the prediction of the CDM that, all else being equal, even small differences in the structure of alternative genetic codes may result in significant shifts in the overall pattern of nucleotide substitution.

Codon↗
PubMed2025

Chromosome-level genome assembly of Triplophysa scleroptera.

Triplophysa scleroptera is an endemic fish species in Qinghai Lake and the upper reaches of the Yellow River. However, studies on conservation and evolutionary genetics were seriously impeded by the absence of a reference genome. Here, by using PacBio HiFi sequencing and Hi-C assembly technology, we assembled a chromosome-level genome of T. scleroptera, with a total length of 660.22 Mb and 99.82% of the sequence anchored to 25 chromosomes. The contig N50 and scaffold N50 were 9.09 Mb and 24.38 Mb, respectively. The evaluation using BUSCO indicated the genome assembly to be 96.40% complete. About 33.41% of the genome consists of repeat elements. We predicted 26,168 protein-coding genes in the genome, and 99.02% of them were functionally annotated. This high-quality reference genome would serve as a valuable genomic resource for advancing evolutionary conservation genetics studies in this species.

Animals↗
PubMed2001

Ecotoxicology and population genetics: the emergence of "phylogeographic and evolutionary ecotoxicology".

Genetics of ecotoxicology has recently emerged as a priority research field. The advent of polymerase chain reaction and molecular population genetics has made it possible to examine the genetics in even the smallest individuals. Although a potentially powerful technique, current approaches oversimplify the relationship of change in gene frequency to contaminant exposure. Many of these approaches cannot control for random correlation or accessory abiotic factors that impinge on the system tested. Indeed, the gestalt approaches of laboratory exposure or natural field experiments may ignore significant genome-level interactions that are important within a given system. At the very least, these approaches would benefit by a biogeographic survey of genetic variation to understand geographic microevolutionary patterns, or phylogeography, within a species to reduce spurious correlations and erroneous conclusions. Other single locus approaches can be chosen to enhance this approach if genetic/environmental interactions have been characterized for laboratory populations or for other model systems.

Animals↗
PubMed1997

Evolutionary dynamics of genetic variation in Epstein-Barr virus isolates of diverse geographical origins: evidence for immune pressure-independent genetic drift.

The question whether immune pressure exerted by cytotoxic T lymphocytes (CTLs) can influence the long-term evolution of genetically stable viruses such as Epstein-Barr virus (EBV) has generated considerable scientific interest, primarily due to its important implications for the overall biology of the virus. While arguing for a role of CTLs in the evolution of viruses, it is important to differentiate between genetic variation in virus and immune recognition of these variant virus by CTLs. To assess the role of genetic selection in the long-term evolution of EBV, we have analyzed a large panel of type 1 EBV isolates from African, Southeast Asian, Papua-New Guinean (PNG), and Australian Caucasian individuals. Seven different regions of the EBV genome, which include nine CTL epitopes restricted through a range of HLA class I alleles, were sequenced and compared. Although numerous nucleotide changes were identified within these isolates, comparison of synonymous and nonsynonymous substitutions in the CTL epitope indicated that the genetic variation was generated mostly independently of immune selection pressure. Surprisingly, an inverse correlation between genetic variation within certain CTL epitopes and the frequency distribution of HLA alleles that present the CTL epitopes was seen, suggesting that the evolutionary pressures on the CTL epitopes of the virus may be toward their conservation rather than their inactivation. Furthermore, molecular evolutionary genetic analysis of nucleotide sequences revealed that viral isolates from PNG are evolving as a lineage distinct from isolates from African, Southeast Asian, and Australian Caucasian individuals.

Amino Acid Sequence↗
PubMed1998

The molecular evolution of development.

Morphological differences between species, from simple single-character differences to large-scale variation in body plans, can be traced to changes in the timing and location of developmental events. This has led to a growing interest in understanding the genetic basis behind the evolution of developmental systems. Molecular evolutionary genetics provides one of several approaches to dissecting the evolution of developmental systems, by allowing us to reconstruct the history of developmental genetic pathways, infer the origin and diversification of developmental gene functions, and assess the relative contributions of various evolutionary forces in shaping regulatory gene evolution.

Animal Population Groups↗