Are rates of species diversification correlated with rates of morphological evolution?

Some major evolutionary theories predict a relationship between rates of proliferation of new species (species diversification) and rates of morphological divergence between them. However, this relationship has not been rigorously tested using phylogeny-based approaches. Here, we test this relationship with morphological and phylogenetic data from 190 species of plethodontid salamanders. Surprisingly, we find that rates of species diversification and morphological evolution are not significantly correlated, such that rapid diversification can occur with little morphological change, and vice versa. We also find that most clades have undergone remarkably similar patterns of morphological evolution (despite extensive sympatry) and that those relatively novel phenotypes are not associated with rapid diversification. Finally, we find a strong relationship between rates of size and shape evolution, which has not been previously tested.     

Are adrenal and testicular androgen levels correlated?

To investigate the reported correlation between adrenal and testicular serum androgen levels, testosterone, DHEAS and androstenedione were measured in the serum of 92 healthy young males. Testosterone and androstenedione were found to have a weak but statistically significant correlation, while no correlation existed between testosterone and DHEAS, or DHEAS and androstenedione. These results indicate that although common steroidogenic pathways lead to androgen synthesis in both adrenals and testes, the regulation of steroid production in these glands is influenced by different factors. The correlation of testosterone with androstenedione can be attributed to their peripheral interconversion as well as to the fact that half of androstenedione is of testicular origin. Various other aspects of the androgen regulation mechanism such as ACTH stimulation and the role of aging, are presented and discussed.     

Regulation of RNA function by aminoacylation and editing?

The chemical modification of nucleic acids is a ubiquitous phenomenon. Aminoacylation of tRNAs by aminoacyl-tRNA synthetases (ARSs) is a reaction essentially devoted to protein synthesis but it is used also as an emergency mechanism to recycle stalled ribosomes, and it is required for genome replication in some RNA viruses. In several aminoacyl-tRNA synthetases a correction mechanism known as editing is present to prevent aminoacylation errors. Genome data reveal a growing number of open reading frames encoding ARS-like proteins. This strongly suggests the existence of a widespread and nonconventional machinery for aminoacylation and editing. Here we review the different biological functions of aminoacylation and editing; also we propose an evolutionary scenario for the origin of these two reactions, and hypothesize an extant role for RNA charging and editing outside the genetic code.     

Is the Trypanosoma brucei REL1 RNA ligase specific for U-deletion RNA editing,and is the REL2 RNA ligase specific for U-insertion editing?

It was shown previously that the REL1 mitochondrial RNA ligase in Trypanosoma brucei was a vital gene and disruption affected RNA editing in vivo, whereas the REL2 RNA ligase gene could be down-regulated with no effect on cell growth or on RNA editing. We performed down-regulation of REL1 in procyclic T. brucei (midgut insect forms) by RNA interference and found a 40-50% inhibition of Cyb editing, which has only U-insertions, as well as a similar inhibition of ND7 editing, which has both U-insertions and U-deletions. In addition, both U-insertion and U-deletion in vitro pre-cleaved editing were inhibited to similar extents. We also found little if any effect of REL1 down-regulation on the sedimentation coefficient or abundance of the RNA ligase-containing L-complex (Aphasizhev, R., Aphasizheva, I., Nelson, R. E., Gao, G., Simpson, A. M., Kang, X., Falick, A. M., Sbicego, S., and Simpson, L. (2003) EMBO J. 22, 913-924), suggesting that the inhibition of both insertion and deletion editing was not due to a disruption of the L-complex. Together with the evidence that down-regulation of REL2 has no effect on cell growth or on RNA editing in vivo or in vitro, these data suggest that the REL1 RNA ligase may be active in vivo in both U-insertion and U-deletion editing. The in vivo biological role of REL2 remains obscure.     

Are summit metabolism and thermogenic endurance correlated in winter-acclimatized passerine birds?

Small birds exhibiting marked winter improvement of cold tolerance also show elevated summit metabolic rates (maximum cold-induced metabolic rate) in winter relative to summer. However, relatively large increases in cold tolerance can occur with only minor increments of maximum cold-induced metabolic rate and geographic variation in cold tolerance is not always positively correlated with variation in maximum cold-induced metabolic rate. Thus, it is uncertain whether maximum cold-induced metabolic rate and cold tolerance are phenotypically correlated in small birds and no previous study has directly examined this relationship. I measured maximum cold-induced metabolic rate and cold tolerance (i.e., thermogenic endurance) over three winters in black-capped chickadees Poecile atricapillus, American tree sparrows Spizella arborea, and dark-eyed juncos Junco hyemalis. For raw thermogenic endurance data, residuals of maximum cold-induced metabolic rate and thermogenic endurance from mass regressions were significantly and positively correlated in juncos and tree sparrows, and their correlation approached significance for chickadees. Log10 transformation of thermogenic endurance and mass data gave similar results. These data provide the first direct evidence for a phenotypic correlation between maximum cold-induced metabolic rate and thermogenic endurance in small birds, although much of the variance in thermogenic endurance is explained by factors other than maximum cold-induced metabolic rate and the degree of correlation differs among species. Nevertheless, these data suggest that physiological adjustments producing elevated thermogenic endurance also produce elevated maximum cold-induced metabolic rate in small birds.     

Are per-incident rape-pregnancy rates higher than per-incident consensual pregnancy rates?

Is a given instance of rape more likely to result in pregnancy than a given instance of consensual sex? This paper undertakes a review and critique of the literature on rape-pregnancy. Next, it presents our own estimation, from U.S. government data, of pregnancy rates for reproductive age victims of penile-vaginal rape. Using data on birth control usage from the Statistical Abstract of the United States, we then form an estimate of rapepregnancy rates adjusted for the substantial number of women in our sample who would likely have been protected by oral contraception or an IUD. Our analysis suggests that per-incident rape-pregnancy rates exceed per-incident consensual pregnancy rates by a sizable margin, even before adjusting for the use of relevant forms of birth control. Possible explanations for this phenomenon are discussed, as are its implications to ongoing debates over the ultimate causes of rape.     

Transglycosylation: a mechanism for RNA modification (and editing?)

The vast majority of the ca. 100 chemically distinct modified nucleosides in RNA appear to arise via the chemical transformation of a genetically encoded nucleoside. Two notable exceptions are queuosine and pseudouridine, which are incorporated into tRNA via transglycosylation. Transglycosylation is an extremely efficient process for incorporating highly modified bases such as queuine into RNA. Transglycosylation is also a requisite process for "isomerizing" an N-nucleoside into a C-nucleoside as is the case for pseudouridine formation. Finally, transglycosylation is an attractive possibility for certain RNA editing events (e.g., pyrimidine to purine conversions) that cannot occur via the known, more straightforward enzymatic reactions (e.g., deaminations). This review discusses what is known about the mechanisms of transglycosylation for the queuine and pseudouridine RNA modifications and will speculate about a potential role for transglycosylation in certain RNA editing events.     

4SALE – A tool for synchronous RNA sequence and secondary structure alignment and editing

Background  

In sequence analysis the multiple alignment builds the fundament of all proceeding analyses. Errors in an alignment could strongly influence all succeeding analyses and therefore could lead to wrong predictions. Hand-crafted and hand-improved alignments are necessary and meanwhile good common practice. For RNA sequences often the primary sequence as well as a secondary structure consensus is well known, e.g., the cloverleaf structure of the t-RNA. Recently, some alignment editors are proposed that are able to include and model both kinds of information. However, with the advent of a large amount of reliable RNA sequences together with their solved secondary structures (available from e.g. the ITS2 Database), we are faced with the problem to handle sequences and their associated secondary structures synchronously.     

Are RNA Viruses Adapting or Merely Changing?

RNA viruses and retroviruses fix substitutions approximately 1 million-fold faster than their hosts. This diversification could represent an inevitable drift under purifying selection, the majority of substitutions being phenotypically neutral. The alternative is to suppose that most fixed mutations are beneficial to the virus, allowing it to keep ahead of the host and/or host population. Here, relative sequence diversification of different proteins encoded by viral genomes is found to be linear. The examples encompass a wide variety of retroviruses and RNA viruses. The smoothness of relative divergence spans quasispeciation following clonal infection, to variation among different isolates of the same virus, to viruses from different species or those associated with different diseases, indicating that the majority of fixed mutations likely reflects drift. This held for both mammalian and plant viruses, indicating that adaptive immunity doesn't necessarily shape the relative accumulation of amino acid substitutions. When compared to their hosts RNA viruses evolution appears conservative. Received: 16 November 1999 / Accepted: 10 March 2000     

Are physiological and behavioral immune responses negatively correlated? Evidence from hormone-linked differences in men's face preferences

Behaviors that minimize exposure to sources of pathogens can carry opportunity costs. Consequently, how individuals resolve the tradeoff between the benefits and costs of behavioral immune responses should be sensitive to the extent to which they are vulnerable to infectious diseases. However, although it is a strong prediction of this functional flexibility principle, there is little compelling evidence that individuals with stronger physiological immune responses show weaker behavioral immune responses. Here we show that men with the combination of high testosterone and low cortisol levels, a hormonal profile recently found to be associated with particularly strong physiological immune responses, show weaker preferences for color cues associated with carotenoid pigmentation. Since carotenoid cues are thought to index vulnerability to infectious illnesses, our results are consistent with the functional flexibility principle's prediction that individuals with stronger physiological immune responses show weaker behavioral immune responses.