Protein evolution in different cellular environments: cytochrome b in sharks and mammals

DNA sequences for the mitochondrial cytochrome b gene were determined for 13 species of sharks. Rates and patterns of amino acid replacement are compared for sharks and mammals. Absolute rates of cytochrome b evolution are six times slower in sharks than in mammals. Bivariate plots of the number of nonsynonymous and silent transversions are indistinguishable in the two groups, however, suggesting that the differences in amino acid replacement rates are due primarily to differences in DNA substitution rates. Patterns of amino acid replacement are also similar in the two groups. Conserved and variable regions occur in the same parts of the cytochrome b gene, and there is little evidence that the types of amino acid changes are significantly different between the groups. Similarity in the relative rates and patterns of protein change between the two groups prevails despite dramatic differences in the cellular environments of sharks and mammals. Poor penetrance of physiological differences through to rates of protein evolution provides support for the neutral theory and suggests that, for cytochrome b, patterns of evolution have been relatively constant throughout much of vertebrate history.      

Estimation of age structure in anthropological demography.

The past decade has produced considerable debate over the feasibility of paleodemographic research, with much attention focusing on the question of reliability of age estimates. We show here that in cases where age is estimated rather than known, the traditional method of assigning individuals to age classes will produce biased estimates of age structure. We demonstrate the effect of this bias both mathematically and by computer simulation, and show how a more appropriate method from the fisheries literature (the "iterated age length key") can be used to estimate age structure. Because it is often the case that ages are also estimated for extant groups, we suggest that our results are relevant to the general field of anthropological demography, and that it is time for us to improve the statistical basis for age structure estimation. We further suggest that the oft noted paucity of older individuals in skeletal collections is a simple result of the use of inappropriate methods of age estimation, and that this problem can be rectified in the future by using maximum likelihood estimates of life table or hazard functions incorporating the uncertainty of age estimates.     

Heads up: evolution of exaggerated head length in the minute litter bug genus <Emphasis Type="Italic">Nannocoris</Emphasis> Reuter (Hemiptera: Schizopteridae)

Evolutionary biologists have long been intrigued by exaggerated morphologies tied to sexual or natural selection. In insects, relatively few studies have investigated the evolution of such traits at the genus level and above and have used comparative phylogenetic methods to do so. We here investigate the interspecific evolution of head length in the minute litter bug genus Nannocoris Reuter based on the first phylogenetic hypothesis of the group (25 ingroup species, five gene regions, 3409 bp) and ancestral state reconstruction. Head lengths in this speciose genus range from approximately one sixth of the total body length to more than a quarter of the body length, while the head and mouthpart (rostrum) lengths are correlated. Different species therefore possess a markedly different reach of the rostrum when extended. The analyses show that head length evolution in Nannocoris is plastic, with head length elongations and reductions occurring in several clades, derived from ancestors with moderately elongated heads. Evidence is provided that exaggerated head lengths evolved through elongation of either the genal (pricei group) or the tip (arimensis group) region of the head. The biology of species in the genus Nannocoris is unknown, but given the lack of sexual dimorphism of head lengths, we speculate that head evolution in this genus may be driven by natural selection, potentially in the context of prey capture.     

Two types of double-strand breaks in electron and photon tracks and their relation to exchange-type chromosome aberrations

Yields of DNA double-strand breaks (dsb), i. e. the average number of dsb, N–, per relative molar mass, M _r , and dose, D, produced by electrons and photons in the energy range 50 eV – 1 MeV were calculated. The experimental data of dsb induction by ultrasoft x-rays and by photons agree well with the calculated yields of dsb as a function of photon energy. The dsb are classified into simple and complex ones. Energy transfers of less than about 200 eV producing at least two ionizations generate mainly simple dsb, while low-energy electrons with an initial energy between 200 and 500 eV induce preferentially complex dsb. Assuming that dsb is the main DNA lesion leading to exchange-type chromosome aberrations (etca), three different mechanisms have to be considered: 1) complex dsb on its own; 2) interaction between two dsb induced by the same primary particle; and 3) interaction between two dsb induced by different primary particles. Mechanisms 1) and 2) produce a linear term, whereas mechanism 3) leads to a quadratic term for the yield of etca. The sum of contributions 1) and 2) to the yield of dicentrics describes fairly well the non-trivial structure of the experimental data. The results suggest that interaction between complex dsb does not contribute significantly to the formation of dicentrics via mechanism 3). Received: 30 July 1995 / Accepted in revised form: 28 March 1996     

Codon usage bias analysis of genes linked with esophagus cancer

Esophageal cancer involves multiple genetic alternations. A systematic codon usage bias analysis was completed to investigate the bias among the esophageal cancer responsive genes. GC-rich genes were low (average effective number of codon value was 49.28). CAG and GTA are over-represented and under-represented codons, respectively. Correspondence analysis, neutrality plot, and parity rule 2 plot analysis confirmed the dominance over mutation pressure in modulating the codon usage pattern of genes linked with esophageal cancer.     

Characterization of a 320-kb region containing the HEXA gene on bovine chromosome 10 and analysis of its association with BSE susceptibility

Bovine spongiform encephalopathy (BSE) belongs to a group of neurodegenerative diseases known as transmissible prion diseases. Recently, variants in the promoter region of the prion protein ( PRNP ) gene have been shown to have a considerable effect on the susceptibility to BSE. However, a previous genome scan revealed other putative BSE-susceptibility loci. Here, we analysed such a region on BTA10, which contains the functional candidate gene HEXA . Three hundred and twenty kilobases that, besides HEXA , also contain ARIH1 , BRUNOL6 and PARP6 were characterized and screened for polymorphisms. Genotyping of 38 SNPs in Holstein–Friesian animals from the UK (350 diseased and 270 controls) revealed two intronic SNPs that were associated with BSE incidence, with experiment-wise P -values of 3.5 × 10⁻³ and 7.7 × 10⁻³ respectively. Both SNPs were in strong linkage disequilibrium and the rare alleles had a protective effect. These alleles were contained in a haplotype dubbed 'UK-protective' that was significantly overrepresented in the controls with a permuted P -value of 2 × 10⁻³. An association study in German Holstein animals (73 diseased and 627 controls) revealed an opposite effect of the 'UK-protective' haplotype in this population, i.e. it was overrepresented in the diseased animals, although not significant after correction for multiple testing. These findings indicate a causal variant for BSE susceptibility on BTA10 in linkage disequilibrium with the markers studied. Candidate gene analyses of the surrounding region and additional association studies will help to clarify the origin of the protective effects and to identify causal variants for BSE susceptibility on BTA10.