Author: Marc Robinson-Rechavi

” Where there is life there is wishful thinking “  Gerald F. Lieberman Finding genes which are under positive selection is an important part of any molecular evolution biologists’ work as these genes can be responsible for adaptations in a studied specie. To find such genes, genomic scans are conducted and regions of the genome that show specific patterns, such as selective sweeps, are further studied and sensible biological interpretations are made. In this paper, Pavlidis & al. show that one has to be careful with such biological interpretations as the patterns for positive selection can appear under an a priori known neutrally evolving genome and that it might not be that difficult to come up with a satisfying story about such false-positives. Figure 1 | Flowchart representing the the steps in the simulation. These steps were repeated for all of the 100 simulations. To show the existence of  false-positives in the detection of positive selection patterns, Pavlidis & al simulated 100 data sets of 40 D.melanogaster X chromosomes evolving under a neutral Wright-Fisher model. The D.melanogaster X chromosome, which was sampled in the Netherlands, is believed to have gone through a recent and deep bottleneck. A demographic scenario for …

Sticklebacks are originally marine fish that colonized freshwater habitats after the last glaciation. Adaptation to freshwater environment happened independently in various rivers and lakes around the globe, giving rise to similar phenotypes following natural selection. In a recent study, researchers aimed to identify potential loci repeatedly associated with the divergence between marine and freshwater sticklebacks. An underlying question was to uncover if this adaptation is due to regulatory or protein-coding changes. To ensure that the changes reflected parallel evolution, the authors sequenced a reference freshwater stickleback and 20 other freshwater and marine sticklebacks from both Pacific and Atlantic populations. They selected populations showing characteristic marine and freshwater morphologies (Figure1 a, b). To find loci involved in repeated adaptation to freshwater habitats, the authors used two methods, aiming to identify regions where sequences from freshwater sticklebacks were similar to each other but different from marine sticklebacks. The first method is a self-organizing map-based iterative Hidden Markov Model (SOM/HMM) (Figure1 c). With this method, they identified the 20 most common patterns of genetic relationships (trees) among the 21 individuals. The authors found that for most of the genome, the fish clustered by geography, with fish from Pacific regions being closer to each …

For decades, most researchers have provided some general insights into the nature of adaptation in asexually reproducing populations with small genome, such as bacteria and yeast. They assumed that sexual species evolve the same way these populations do, i.e. their adaptation is driven by the so-called selective sweeps or newly arising beneficial genetic mutation quickly becomes “fixated” on a particular portion of DNA, with the genome-wide haplotype associated with it. When we relate to obligate sexually reproducing systems, this is much more complicated by the fact that selection can act on standing variation, that means that weak selection can act on many pre-existing genetic variants involved in fitness traits. The idea is that short-term evolution have occurred through a so-called “soft sweep” model, which contrasts the hypothesis of the “hard sweep”, where strong selective sweep originates from a single mutation, while all its linked neutral variants are eliminated. Burke et al. compared outbred, sexually reproducing, replicated populations of D. melanogaster selected for accelerated development and their matched control populations on a genome-wide basis, and this is the first time that such a study of a sexually reproducing species has been done.  As shown in figure 1, they used the Illumina …

And they have published an informative article in PLOS One about their first 4 years:http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0050109 More cited papers also have more views of the blog post Biology rules

In this paper, Molly K. Burke and his collogues did an experimental evolution systems, which allows the genomic study of adaptation. They selected outbred, sexually reproducing, replicated populations of Drosophila melanogaster, which experienced over 600 generations of laboratory selection for accelerated development. Short-read sequences from three genomic DNA libraries, were obtained using Illumina platform, they are as follows: a)    A pooled sample of five replicate populations that have undergone sustained selection for accelerated development and early fertility for over 600 generations (ACO); b)   A pooled sample of five replicate ancestral control populations, which experience no direct selection on development time (CO); c)    A single ACO replicate population (ACO1); Figure 1: Phenotypic divergence in the selection treatments     In the above figure, the grey bar indicates values measured in the ACO and CO treatments for each of the five replicate populations. B indicates replicate populations, which represent phenotypes typical of populations kept on two-week generation maintenance schedules. This figure shows a comparative analysis between the ACO population and the population with the CO treatment. Every time, ACO featured significantly differentiated phenotypes, including shorter development time and reductions in pre-adult viability, longevity, adult body size and stress resistance. Furthermore, the CO treatment …

In this paper, Molly K. Burke and his collogues did an experimental evolution systems, which allows the genomic study of adaptation. They selected outbred, sexually reproducing, replicated populations of Drosophila melanogaster, which experienced over 600 generations of laboratory selection for accelerated development. Short-read sequences from three genomic DNA libraries, were obtained using Illumina platform, they are as follows: a)    A pooled sample of five replicate populations that have undergone sustained selection for accelerated development and early fertility for over 600 generations (ACO); b)   A pooled sample of five replicate ancestral control populations, which experience no direct selection on development time (CO); c)    A single ACO replicate population (ACO1); Figure 1: Summary of phenotypic divergence in the selection treatments. In the above figure, the grey bar indicates values measured in the ACO and CO treatments for each of the five replicate populations. B indicates replicate populations, which represent phenotypes typical of populations kept on two-week generation maintenance schedules. This figure shows a comparative analysis between the ACO population and the population with the CO treatment. Every time, ACO featured significantly differentiated phenotypes, including shorter development time and reductions in pre-adult viability, longevity, adult body size and stress resistance. Furthermore, the CO treatment …

How do adaptive phenotypes evolve? This question, despite the increasing availability of genomic and other molecular data, remains still largely unanswered. Among the different aspects investigated, a major point of discussion in this topic is the extent of the contribution of coding versus non-coding variation in the evolution of new traits. Although many research groups suggested that non-coding mutations might play a pivotal role because might avoid pleiotropic effects, still few examples are available to discard a potential major contribution of coding variants in adaptive evolution.The paper from Jones et al. we discussed tried to answer this question by looking at the differences between distinct populations of threespine sticklebacks (Gasterosteus aculeatus). This species, originally found in marine habitats, colonized the freshwater environment evolving specific phenotypic traits, but still maintaining the ability to hybridize with the marine individuals. An important feature of this species, already known from previous studies, is the presence of shared genomic variants in geographically unrelated populations distinguishing the marine from the freshwater populations. This finding suggested the possibility of a parallel adaptive evolution of phenotypic traits due to the reuse of standing genetic variation. To test this hypothesis, Jones et al. generated a reference genomic assembly of …

Microbial species are one of the most ubiquitous living group on Earth’s biosphere, showing incredible ability to thrive even in ambient conditions to the limit of human endurance. By virtue of their rapid growth, bacteria are ideal for unraveling the molecular mechanisms of many evolutionary processes. Their rapidity to respond to changes has been associated to the combined effect of evolutionary processes, species composition or gene expression shifts. Most of the studies have focused so far on isolation and comparison of cultured bacterial population, while very few data are available concerning free-living bacteria. Therefore, it is still controversial how quickly, to which extent and by which mechanism microorganisms evolve in their natural environment.  Two researchers of the University of California, Denef and Banfield, have tried to answer this question, as described in a paper recently published in Science. Their work report evolutionary rate estimates from bacterial populations living in a really challenging site, the hot, humid, low-pH, metal-rich and low-oxygen acid mine drainage in the Richmond Mine (Iron Mountain, CA), over the course of 9 years. This would seem not the ideal model system for conducting such kind of study, for the low accessibility at the sites only in limited …

Despite the recent advances in whole-genome sequencing, two recent studies let us think that we are far from uncovering the genetic basis of common diseases risk. In fact, information relevant to complex diseases might hide within rare or even private genome variations, often too scarce to be studied statistically. We might thus have to change radically our way of thinking of genes-diseases associations to make a step forward and make the DNA talk. Whereas a few, usually rare and severe “genetic disorders” can be traced to variations at one or two locations, or “loci”, in the DNA sequence, most common diseases are the result of complex interactions between protein-coding genes, non-coding DNA and environmental effects. These well-named “complex diseases” include cardiovascular, metabolic, neurologic and psychiatric conditions of great concern to health policies, such as early-onset stroke, myocardial infarction, diabetes, dyslipemia, Alzeihmer’s, bipolar disorder or schizophrenia. Some of these complex diseases have a high heritability, which means that a great part of individual differences in the probability to develop the disease can be explained by differences in genomes. For example, the heritability of early-onset myocardial infarction is about 60% [1]: genomes are more important than environment in explaining the differences in …