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The analysis of complex systems frequently poses the challenge to distinguish correlation from causation. Statistical physics hasinspired very promising approaches to search for correlations in time series; the transfer entropy in particular (Hlavackova-Schindler et al., 2007). Now, methods from computational statistics can quantitatively assign significance to such correlation measures. In this study, we propose and apply a procedure to statistically assess transfer entropies by one-sided tests. We introduce to null models of vanishing correlations for time series with memory.We implemented them in an OpenMP-based, parallelized C++ package for multi-core CPUs. Using template meta-programming, we enable a compromise between memory and run time efficiency.

Background: Surface populations of Astyanax mexicanus, living in rivers like their common ancestors, school, while several, independently derived cave populations of the same species have lost schooling behavior., Results: We quantify schooling behavior in individual A. mexicanus and identify quantitative trait loci (QTL) for this trait. We find that the evolutionary modulation of schooling has both vision-dependent and -independent components. We also quantify differences in the lateral line and vision between cavefish and surface fish and relate these differences to the evolutionary loss of schooling behavior. We provide evidence that a monoamine neurotransmitter may have played a role in the evolution of schooling behavior., Conclusions: We find that vision is essential for schooling tendency in A. mexicanus, while the lateral line has a small effect on this behavior. Schooling behavior in A. mexicanus has evolved both through changes in sensory systems and through changes in genetic loci that likely act downstream of sensory inputs., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

The ability to efficiently and accurately determine genotypes is a keystone technology in modern genetics, crucial to studies ranging from clinical diagnostics, to genotype-phenotype association, to reconstruction of ancestry and the detection of selection. To date, high capacity, low cost genotyping has been largely achieved via "SNP chip" microarray-based platforms which require substantial prior knowledge of both genome sequence and variability, and once designed are suitable only for those targeted variable nucleotide sites. This method introduces substantial ascertainment bias and inherently precludes detection of rare or population-specific variants, a major source of information for both population history and genotype-phenotype association. Recent developments in reduced-representation genome sequencing experiments on massively parallel sequencers (commonly referred to as RAD-tag or RADseq) have brought direct sequencing to the problem of population genotyping, but increased cost and procedural and analytical complexity have limited their widespread adoption. Here, we describe a complete laboratory protocol, including a custom combinatorial indexing method, and accompanying software tools to facilitate genotyping across large numbers (hundreds or more) of individuals for a range of markers (hundreds to hundreds of thousands). Our method requires no prior genomic knowledge and achieves per-site and per-individual costs below that of current SNP chip technology, while requiring similar hands-on time investment, comparable amounts of input DNA, and downstream analysis times on the order of hours. Finally, we provide empirical results from the application of this method to both genotyping in a laboratory cross and in wild populations. Because of its flexibility, this modified RADseq approach promises to be applicable to a diversity of biological questions in a wide range of organisms.

Background: Phenotypic and molecular genetic data often provide conflicting patterns of intraspecific relationships confounding phylogenetic inference, particularly among birds where a variety of environmental factors may influence plumage characters. Among diurnal raptors, the taxonomic relationship of Buteo jamaicensis harlani to other B. jamaicensis subspecies has been long debated because of the polytypic nature of the plumage characteristics used in subspecies or species designations., Results: To address the evolutionary relationships within this group, we used data from 17 nuclear microsatellite loci, 430 base pairs of the mitochondrial control region, and 829 base pairs of the melanocortin 1 receptor (Mc1r) to investigate molecular genetic differentiation among three B. jamaicensis subspecies (B. j. borealis, B. j. calurus, B. j. harlani). Bayesian clustering analyses of nuclear microsatellite loci showed no significant differences between B. j. harlani and B. j. borealis. Differences observed between B. j. harlani and B. j. borealis in mitochondrial and microsatellite data were equivalent to those found between morphologically similar subspecies, B. j. borealis and B. j. calurus, and estimates of migration rates among all three subspecies were high. No consistent differences were observed in Mc1r data between B. j. harlani and other B. jamaicensis subspecies or between light and dark color morphs within B. j. calurus, suggesting that Mc1r does not play a significant role in B. jamaicensis melanism., Conclusions: These data suggest recent interbreeding and gene flow between B. j. harlani and the other B. jamaicensis subspecies examined, providing no support for the historical designation of B. j. harlani as a distinct species.

The genetic basis of sexual dimorphisms is an intriguing problem of evolutionary genetics because dimorphic traits are limited to one sex. Such traits can arise genetically in two ways. First, the alleles that cause dimorphisms could be limited in expression to only one sex at their first appearance. Alternatively, dimorphism alleles could initially be expressed in both sexes, but subsequently be repressed or promoted in only one sex by the evolution of modifier genes or regulatory elements. We investigated these alternatives by looking for the expression of sexually dimorphic traits in female hybrids between bird species whose males show different types of ornaments. If modifier alleles or regulatory elements involved in sex-limited traits are not completely dominant, the modification should break down in female hybrids, which might then show dimorphic traits resembling those seen in males. Of 13 interspecific hybridizations examined, we found not a single instance of the expression of male-limited ornaments in female hybrids. This suggests that male ornaments were sex limited from the outset or that those traits became sex limited through the evolution of dominant modifiers -- possibly cis-dominant regulatory elements. Observing hybrid phenotypes is a useful approach to studying the genetics and evolution of dimorphic traits.