Tutorial Genomics, Ecology, Evolution, etc

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 …

Bacteria are one of the most ubiquitous living group and exhibit finely tuned adaptations to a wide range of habitats, even the most inhospitable ones. Their ability to evolve rapidly is at the roots of many public health issues, such as the development of resistances to antibiotics or the rapid evolution of seasonal diseases, but can also be of great help to humans by creating new metabolic pathways to transform human-made pollutants and harmful substances. In the early 20th century, new bacterial genomes were still thought to be the result of mutations only, and to be then transmitted vertically within a clonal strain. In the 40’s, the discovery of bacterial DNA recombination through transformation (Avery, MacLeod and McCarty experiment in 1944) or conjugation (Lederberg and Tatum experiment in 1946) shed light on the processes responsible for the rapid ecological differentiation of bacterial strains: an individual can acquire new genes or alleles through recombination that allow it to stand new ecological conditions. In Eucaryotes, genetic exchange and recombination through sexual reproduction is considered the basis of gene-specific transmission and selection among a population. However, the importance of genetic exchange between bacteria in uncoupling selection processes between different genes remains a controversial …

Papers that will be discussed between September and December 2012 : September 7thThe yak genome and adaptation to life at high altitudeQiu et al. 2012 Nature Genetics 44: 946–949 September 14thNuclear Genomic Sequences Reveal that Polar Bears Are an Old and Distinct Bear LineageHailer et al. 2012 Science 336: 344-347Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate changeMiller et al. 2012 PNAS online before print doi: 10.1073/pnas.1210506109 September 21stPopulation Genomics of Early Events in the Ecological Differentiation of BacteriaShapiro et al. 2012 Science 6077: 48-51 September 28thEvolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human ExomesTennessen et al. 2012 Science 6090: 64-69An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 PeopleNelson et al. 2012 Science 6090: 100-104 October 12thHuman gut microbiome viewed across age and geographyYatsunenko et al. 2012 Nature 486: 222–227November 2ndInsights into hominid evolution from the gorilla genome sequenceScally et al. 2012 Nature 483: 169–175The bonobo genome compared with the chimpanzee and human genomesPrüfer et al. 2012 Nature online before print doi:10.1038/nature11128 November 9thIn Situ Evolutionary Rate Measurements Show Ecological Success of Recently Emerged Bacterial HybridsDenef and Banfield 2012 Science 336: 462-466 November …