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Kalinka A.T.,Institute For Populationsgenetik
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution | Year: 2015

The roots of modern evo-devo can be traced back to the comparative anatomy of the 19th century. Inheriting from this tradition, the field has maintained a mechanistic approach to understanding the origins of distinct animal morphologies. While this focus has produced a valuable body of work, we argue here that a fuller understanding of why species diverge morphologically must be centered on the selective forces driving divergence, and these forces ultimately reside in the ecological context in which organisms live and reproduce. We discuss reasons why we expect many morphological novelties to evolve largely secondarily to, and often as a by-product of, primary selection on life-history traits. By shifting the focus to proximate evolutionary causes, our perspective necessarily prioritises selection experiments as a means of empirical testing. We outline experimental approaches designed to dissect the role of ecological variables in the evolution of animal development and morphology, and we show how methods and advances in fields as diverse as population genomics and ecological stoichiometry can contribute to progress in this direction. © 2014 Wiley Periodicals, Inc.

Schlotterer C.,Institute For Populationsgenetik
Trends in Genetics | Year: 2015

Although considered an extremely unlikely event, many genes emerge from previously noncoding genomic regions. This review covers the entire life cycle of such de novo genes. Two competing hypotheses about the process of de novo gene birth are discussed as well as the high death rate of de novo genes. Despite the high death rate, some de novo genes are retained and remain functional, even in distantly related species, through their integration into gene networks. Further studies combining gene expression with ribosome profiling in multiple populations across different species will be instrumental for an improved understanding of the evolutionary processes operating on de novo genes. © 2015 The Author.

Kofler R.,Institute For Populationsgenetik | Schlotterer C.,Institute For Populationsgenetik
Bioinformatics | Year: 2012

Summary: An analysis of gene set [e.g. Gene Ontology (GO)] enrichment assumes that all genes are sampled independently from each other with the same probability. These assumptions are violated in genome-wide association (GWA) studies since (i) longer genes typically have more single-nucleotide polymorphisms resulting in a higher probability of being sampled and (ii) overlapping genes are sampled in clusters. Herein, we introduce Gowinda, a software specifically designed to test for enrichment of gene sets in GWA studies. We show that GO tests on GWA data could result in a substantial number of false-positive GO terms. Permutation tests implemented in Gowinda eliminate these biases, but maintain sufficient power to detect enrichment of GO terms. Since sufficient resolution for large datasets requires millions of permutations, we use multi-threading to keep computation times reasonable. © The Author(s) 2012. Published by Oxford University Press.

Kofler R.,Institute For Populationsgenetik | Schlotterer C.,Institute For Populationsgenetik
Molecular Biology and Evolution | Year: 2014

Standing genetic variation provides a rich reservoir of potentially useful mutations facilitating the adaptation to novel environments. Experimental evolution studies have demonstrated that rapid and strong phenotypic responses to selection can also be obtained in the laboratory. When combined with the next-generation sequencing technology, these experiments promise to identify the individual loci contributing to adaption. Nevertheless, until now, very little is known about the design of such evolve & resequencing (E&R) studies. Here, we use forward simulations of entire genomes to evaluate different experimental designs that aim to maximize the power to detect selected variants. We show that low linkage disequilibrium in the starting population, population size, duration of the experiment, and the number of replicates are the key factors in determining the power and accuracy of E&R studies. Furthermore, replication of E&R is more important for detecting the targets of selection than increasing the population size. Using an optimized design, beneficial loci with a selective advantage as low as s = 0.005 can be identified at the nucleotide level. Even when a large number of loci are selected simultaneously, up to 56% can be reliably detected without incurring large numbers of false positives. Our computer simulations suggest that, with an adequate experimental design, E&R studies are a powerful tool to identify adaptive mutations from standing genetic variation and thereby provide an excellent means to analyze the trajectories of selected alleles in evolving populations. © 2013 The Author.

Kofler R.,Institute For Populationsgenetik | Betancourt A.J.,Institute For Populationsgenetik | Schlotterer C.,Institute For Populationsgenetik
PLoS Genetics | Year: 2012

Transposable elements (TEs) are mobile genetic elements that parasitize genomes by semi-autonomously increasing their own copy number within the host genome. While TEs are important for genome evolution, appropriate methods for performing unbiased genome-wide surveys of TE variation in natural populations have been lacking. Here, we describe a novel and cost-effective approach for estimating population frequencies of TE insertions using paired-end Illumina reads from a pooled population sample. Importantly, the method treats insertions present in and absent from the reference genome identically, allowing unbiased TE population frequency estimates. We apply this method to data from a natural Drosophila melanogaster population from Portugal. Consistent with previous reports, we show that low recombining genomic regions harbor more TE insertions and maintain insertions at higher frequencies than do high recombining regions. We conservatively estimate that there are almost twice as many "novel" TE insertion sites as sites known from the reference sequence in our population sample (6,824 novel versus 3,639 reference sites, with on average a 31-fold coverage per insertion site). Different families of transposable elements show large differences in their insertion densities and population frequencies. Our analyses suggest that the history of TE activity significantly contributes to this pattern, with recently active families segregating at lower frequencies than those active in the more distant past. Finally, using our high-resolution TE abundance measurements, we identified 13 candidate positively selected TE insertions based on their high population frequencies and on low Tajima's D values in their neighborhoods. © 2012 Kofler et al.

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