The planetary biology of cytochrome P450 aromatases

Background  

Joining a model for the molecular evolution of a protein family to the paleontological and geological records (geobiology), and then to the chemical structures of substrates, products, and protein folds, is emerging as a broad strategy for generating hypotheses concerning function in a post-genomic world. This strategy expands systems biology to a planetary context, necessary for a notion of fitness to underlie (as it must) any discussion of function within a biomolecular system.     

Male mate choice scales female ornament allometry in a cichlid fish

Background  

Studies addressing the adaptive significance of female ornamentation have gained ground recently. However, the expression of female ornaments in relation to body size, known as trait allometry, still remains unexplored. Here, we investigated the allometry of a conspicuous female ornament in Pelvicachromis taeniatus, a biparental cichlid that shows mutual mate choice and ornamentation. Females feature an eye-catching pelvic fin greatly differing from that of males.     

Myoepithelioma within the carpal tunnel: a case report and review of the literature

Myoepitheliomas of the extremity are rare and usually benign, while a minority display malignant features. This case demonstrates the diagnosis and management of myoepithelioma within the carpal tunnel. Clinical and radiological tumour features were evaluated. Hematoxylin and eosin stained tumour sections were examined, and immunohistochemistry was performed. Histology revealed a nodular mass of epithelioid cells in clusters within a myxoid/chondroid stroma. No mitoses were noted. Cytokeratins, neuron-specific enolase, synaptophysin, glial fibrillary acidic protein, and S100 were positive on immunohistochemistry. A literature review revealed very few prior reports of myoepithelioma in the wrist, and limited data concerning any relationship between recurrence and quality of surgical margins. In this case, wide local excision would have significantly compromised dominant hand function, and therefore a marginal excision was deemed appropriate in the context of bland histological features. Surgical margins noted in future case reports will aid clinical decision making.     

CSS, NIS and dynamic stability for two-species behavioral models with continuous trait spaces

Static continuously stable strategy (CSS) and neighborhood invader strategy (NIS) conditions are developed for two-species models of frequency-dependent behavioral evolution when individuals have traits in continuous strategy spaces. These are intuitive stability conditions that predict the eventual outcome of evolution from a dynamic perspective. It is shown how the CSS is related to convergence stability for the canonical equation of adaptive dynamics and the NIS to convergence to a monomorphism for the replicator equation of evolutionary game theory. The CSS and NIS are also shown to be special cases of neighborhood p^*- superiority for p^* equal to one half and zero, respectively. The theory is illustrated when each species has a one-dimensional trait space.     

Uninvadability in N-species frequency models for resident-mutant systems with discrete or continuous time

The uninvadability concept, that was originally introduced through static comparisons of individual fitness in resident-mutant systems for a single species, is developed for multi-species models with frequency-dependent fitness by extending its equivalent single-species dynamic characterization. This multi-species definition is then reinterpreted in terms of individual fitness functions based on intra and interspecific interactions. The resultant concept is discussed in relation to that of an N-species ESS (evolutionarily stable strategy) and to dynamic stability of monomorphic and polymorphic evolutionary systems.     

The mutation rates of di-, tri- and tetranucleotide repeats in Drosophila melanogaster

In a recent study, we reported that the combined average mutation rate of 10 di-, 6 tri-, and 8 tetranucleotide repeats in Drosophila melanogaster was 6.3 x 10(-6) mutations per locus per generation, a rate substantially below that of microsatellite repeat units in mammals studied to date (range = 10(-2)-10(-5) per locus per generation). To obtain a more precise estimate of mutation rate for dinucleotide repeat motifs alone, we assayed 39 new dinucleotide repeat microsatellite loci in the mutation accumulation lines from our earlier study. Our estimate of mutation rate for a total of 49 dinucleotide repeats is 9.3 x 10(-6) per locus per generation, only slightly higher than the estimate from our earlier study. We also estimated the relative difference in microsatellite mutation rate among di-, tri-, and tetranucleotide repeats in the genome of D. melanogaster using a method based on population variation, and we found that tri- and tetranucleotide repeats mutate at rates 6.4 and 8.4 times slower than that of dinucleotide repeats, respectively. The slower mutation rates of tri- and tetranucleotide repeats appear to be associated with a relatively short repeat unit length of these repeat motifs in the genome of D. melanogaster. A positive correlation between repeat unit length and allelic variation suggests that mutation rate increases as the repeat unit lengths of microsatellites increase.      

The challenge for genetic epidemiologists: how to analyze large numbers of SNPs in relation to complex diseases

Background

Molecular genetic approaches have much to offer population biology. Despite recent advances, convenient techniques to develop and screen highly-resolving markers can be limiting for some applications and taxa. We describe an improved PCR-based, cloning-free, nuclear marker development procedure, in which single-stranded conformation polymorphism (SSCP) plays a central role. Sequence-variable alleles at putative nuclear loci are simultaneously identified and isolated from diploid tissues. Based on a multiple allele alignment, locus-specific primers are designed in conserved regions, minimizing 'null' alleles. Using two undescribed endemic Australian Collembola as exemplars, we outline a comprehensive approach to generating and validating suites of codominant, sequence-yielding nuclear loci for previously unstudied invertebrates.

Results

Six markers per species were developed without any baseline genetic information. After evaluating the characteristics of each new locus via SSCP pre-screening, population samples were genotyped on the basis of either DNA sequence, restriction site, or insertion/deletion variation, depending on which assay was deemed most appropriate. Polymorphism was generally high (mean of nine alleles per locus), and the markers were capable of resolving population structuring over very fine spatial scales (<100 km). SSCP coupled with targeted DNA sequencing was used to obtain genotypic, genic and genealogical information from six loci (three per species). Phylogeographic analysis identified introns as being most informative.

Conclusion

The comprehensive approach presented here feasibly overcomes technical hurdles of (i) developing suitably polymorphic nuclear loci for non-model organisms, (ii) physically isolating nuclear allele haplotypes from diploid tissues without cloning, and (iii) genotyping population samples on the basis of nuclear DNA sequence variation.     

Evolution of Cooperation in a Heterogeneous Graph: Fixation Probabilities under Weak Selection

It has been shown that natural selection favors cooperation in a homogenous graph if the benefit-to-cost ratio exceeds the degree of the graph. However, most graphs related to interactions in real populations are heterogeneous, in which some individuals have many more neighbors than others. In this paper, we introduce a new state variable to measure the time evolution of cooperation in a heterogeneous graph. Based on the diffusion approximation, we find that the fixation probability of a single cooperator depends crucially on the number of its neighbors. Under weak selection, a cooperator with more neighbors has a larger probability of fixation in the population. We then investigate the average fixation probability of a randomly chosen cooperator. If a cooperator pays a cost for each of its neighbors (the so called fixed cost per game case), natural selection favors cooperation if the benefit-to-cost ratio is larger than the average degree. In contrast, if a cooperator pays a fixed cost and all its neighbors share the benefit (the fixed cost per individual case), cooperation is favored if the benefit-to-cost ratio is larger than the harmonic mean of the degree distribution. Moreover, increasing the graph heterogeneity will reduce the effect of natural selection.