Complex Interplay of Evolutionary Forces in the ladybird Homeobox Genes of Drosophila melanogaster

Tandemly arranged paralogous genes lbe and lbl are members of the Drosophila NK homeobox family. We analyzed population samples of Drosophila melanogaster from Africa, Europe, North and South America, and single strains of D. sechellia, D. simulans, and D. yakuba within two linked regions encompassing partial sequences of lbe and lbl. The evolution of lbe and lbl is highly constrained due to their important regulatory functions. Despite this, a variety of forces have shaped the patterns of variation in lb genes: recombination, intragenic gene conversion and natural selection strongly influence background variation created by linkage disequilibrium and dimorphic haplotype structure. The two genes exhibited similar levels of nucleotide diversity and positive selection was detected in the noncoding regions of both genes. However, synonymous variability was significantly higher for lbe: no nonsynonymous changes were observed in this gene. We argue that balancing selection impacts some synonymous sites of the lbe gene. Stability of mRNA secondary structure was significantly different between the lbe (but not lbl) haplotype groups and may represent a driving force of balancing selection in epistatically interacting synonymous sites. Balancing selection on synonymous sites may be the first, or one of a few such observations, in Drosophila. In contrast, recurrent positive selection on lbl at the protein level influenced evolution at three codon sites. Transcription factor binding-site profiles were different for lbe and lbl, suggesting that their developmental functions are not redundant. Combined with our previous results on nucleotide variation in esterase and other homeobox genes, these results suggest that interplay of balancing and directional selection may be a general feature of molecular evolution in Drosophila and other eukaryote genomes

A genetically encoded calcium indicator for chronic in vivo two-photon imaging

Neurons in the nervous system can change their functional properties over time. At present, there are no techniques that allow reliable monitoring of changes within identified neurons over repeated experimental sessions. We increased the signal strength of troponin C-based calcium biosensors in the low-calcium regime by mutagenesis and domain rearrangement within the troponin C calcium binding moiety to generate the indicator TN-XXL. Using in vivo two-photon ratiometric imaging, we show that TN-XXL exhibits enhanced fluorescence changes in neurons of flies and mice. TN-XXL could be used to obtain tuning curves of orientation-selective neurons in mouse visual cortex measured repeatedly over days and weeks. Thus, the genetically encoded calcium indicator TN-XXL allows repeated imaging of response properties from individual, identified neurons in vivo, which will be crucial for gaining new insights into cellular mechanisms of plasticity, regeneration and disease

Morphological and molecular variation within an ocean basin in wedge-tailed shearwaters (Puffinus pacificus)

Micro-evolutionary processes that underpin genetic and morphological variation in highly mobile pelagic vertebrates are virtually unknown. Previous findings preferentially invoke vicariant isolation due to large-scale physical barriers such as continental landmasses, followed by genetic drift. However increasingly, evidence for divergence by non-random processes (e.g. selection, plasticity) is being presented. Wedge-tailed shearwaters are wide-ranging seabirds with breeding colonies located such that they experience a variety of environmental pressures and conditions. Previous work on this species has provided evidence of inter-colony divergence of adult morphology and foraging modes, as well as chick developmental patterns, suggesting that reinforcement among colonies is possible. In order to evaluate the micro-evolutionary processes driving this observed variation, our study compared patterns of gene flow with morphological and environmental variation among four colonies of wedge-tailed shearwater breeding within the Indo-Pacific Ocean basin. Estimates of gene flow differed according to the genetic marker used; most likely, this is a function of different mutation rates. Nuclear introns suggest that gene flow among wedge-tailed shearwater breeding colonies within the Indo-Pacific Ocean basin is substantial, however microsatellite markers imply that gene flow is reduced. In general, levels of genetic divergence were relatively low and did not correlate with geographic distance, morphological distance or environmental differences (sea-surface temperature and chlorophyll a concentration) among colonies. We suggest that genetic drift alone is unlikely to be the major source of morphological variation seen in this species. Instead, we propose that non-random processes (selection, plasticity) underpin morphological diversity seen in this and possibly other seabird species