Author: Marc Robinson-Rechavi

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 …

The Article The authors of this article wanted to find out how the mutational background of adaptation looks like. Specifically, they asked if identical populations adapted to a fixed environment, would adaptation occur via identical mutations or via various alternative pathways. To answer this question they experimentally evolved 115 populations of Escherichia coli to 42.2° Celsius for 2000 generations (6.64 generations of binary fission daily) and sequenced one clone each of every population, what they call “strain” or “line” throughout the paper. All populations originated from the same E. coli B REL1206 ancestral clone. Their system fulfills all of the requirements needed to answer the question: (i) a large number of replicatesfor statistical power, (ii) complete genome sequencing, so that mutations can be identified unambiguously, and (iii) a complex biological system, to ensure that the number of potential adaptive solutions is not trivial. As the experimental environmental change they chose temperature, a rather complex environmental variable since it affects different biological reactions such as respiration, growth and reproduction.  Performance of the different strains was measured as fitness and yield. Fitness was defined as the density after competition of each of the evolved lines against a newly-derived Ara+ mutant of REL1206 …

Theories Genome size and complexity variation has been a long-term debate during the last decades. In multi-cellular eukaryotes, genome expansion is a consequence of noncoding DNA proliferation [1]. Several theories have emerged to explain variation in genome size and complexity. Among them, the most generally accepted are the bulk-DNA hypothesis, followed by the selfish –DNA hypothesis [2]. However, theses hypotheses explain only partially divergent patterns observed in eukaryotes. Mutational burden hypothesis (MBH), which is mostly based on population genetics principles, is a unifying concept that attempts to reconcile different points of view. This hypothesis implies that  “…noncoding element are generally deleterious but proliferate nonadaptively when small effective population reduce the effectiveness of selection relative to genetic drift”. In other words[3], the genome is constantly under two nonadaptative forces: random genetic drift and mutation pressure. What was expected? If the MBH is correct, a genome under high mutation rate would be reduce in term of size and complexity. A glimpse of plant mitochondrial genomes: what make them special Mitochondrial genomes exhibited a broad range of diversity in term of genome structure and diversity among eukaryotes [4]. The plant mitochondrial genome contain usually more than 90% of non coding DNA with usually …

This blog section concerns a trendy debate in science, the human population history, which has extensions into daily life, as it can constitutes a topic of general public curiosity. Therefore, let’s see what is contribution described herein. Background Modern human populations seems to be derived from a single African ancestral population, under the well supported “out of Africa” hypothesis (1). Particularly, for eastern Asian colonization a “single-dispersal” model have been hypothesized (2), which suggest the aboriginal australians are a lineage diversified recently within the Asian cluster. This hypothesis could be summarized in a topological representation, as drawn in figure 1A of the article (Africans,(Europeans,(Asians,Australians))). Recent studies dated the split between Europeans and Asians around 17K-43K years before the present (ybp). In addition, archaeological evidence supports modern humans in Australia back to ~50K ybp. Those inferences are incompatible with the above mentioned hypothesis, at least in a time framework. A second scenario could be hypothesized, with an early branching process and occupation of Australia, and probable later genetic exchange between Asians and Australians, described as (Africans, (Australians,(Asians, Europeans)). This possibility has been non tested so far. Using an ancient, free of current admixtures, aboriginal australian genome, and SNPs data from different …

Diversifying selection is a form of natural selection where intermediate values of a trait become less represented within a population, in favour of extreme values; a process that may subdivide a population between specialized niches and eventually lead to speciation. For instance, it can be theorized that a pathogen colonising several sites of the human body, where it is exposed to wildly different conditions and selective pressures, would have greater chances of survival by expressing a multitude of site-appropriate phenotypes than by reaching an adaptive compromise. While this strategy could be achieved through phenotypic plasticity, it could also result from genetically distinct strains of the pathogen. Streptococcus pyogenes, also known as the group A streptococcus, or GAS, is a Gram-positive human bacterial pathogen. It is responsible for diseases such as impetigo, a localized skin infection, or pharyngitis, the streptococcal “sore throat”, both of which are mild superficial infections. The same bacterium is involved in a wide range of “invasive” infections, i.e. infections of sterile sites such as blood, which can be severe. On an experimental standpoint, S. pyogenes is a useful model for studying bacterial clonal evolution, because its strains exhibit relatively limited amounts of horizontal transfer across portions of …

Diversifying selection is a form of natural selection where intermediate values of a trait become less represented within a population, in favour of extreme values; a process that may subdivide a population between specialized niches and eventually lead to speciation. For instance, it can be theorized that a pathogen colonising several sites of the human body, where it is exposed to wildly different conditions and selective pressures, would have greater chances of survival by expressing a multitude of site-appropriate phenotypes than by reaching an adaptive compromise. While this strategy could be achieved through phenotypic plasticity, it could also result from genetically distinct strains of the pathogen. Streptococcus pyogenes, also known as the group A streptococcus, or GAS, is a Gram-positive human bacterial pathogen. It is responsible for diseases such as impetigo, a localized skin infection, or pharyngitis, the streptococcal “sore throat”, both of which are mild superficial infections. The same bacterium is involved in a wide range of “invasive” infections, i.e. infections of sterile sites such as blood, which can be severe. On an experimental standpoint, S. pyogenes is a useful model for studying bacterial clonal evolution, because its strains exhibit relatively limited amounts of horizontal transfer across portions of …

Diversifying selection is a form of natural selection where intermediate values of a trait become less represented within a population, in favour of extreme values; a process that may subdivide a population between specialized niches and eventually lead to speciation. For instance, it can be theorized that a pathogen colonising several sites of the human body, where it is exposed to wildly different conditions and selective pressures, would have greater chances of survival by expressing a multitude of site-appropriate phenotypes than by reaching an adaptive compromise. While this strategy could be achieved through phenotypic plasticity, it could also result from genetically distinct strains of the pathogen. Streptococcus pyogenes, also known as the group A streptococcus, or GAS, is a Gram-positive human bacterial pathogen. It is responsible for diseases such as impetigo, a localized skin infection, or pharyngitis, the streptococcal “sore throat”, both of which are mild superficial infections. The same bacterium is involved in a wide range of “invasive” infections, i.e. infections of sterile sites such as blood, which can be severe. On an experimental standpoint, S. pyogenes is a useful model for studying bacterial clonal evolution, because its strains exhibit relatively limited amounts of horizontal transfer across portions of …