Tutorial Genomics, Ecology, Evolution, etc

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 …

Motivation: Documenting the genomic variation of 17 inbred strains of mice. Describing the distribution of variants between strains and its relation to phenotypes and gene regulation. Exploring the evolutionary origins of the subspecies that gave rise to the laboratory mouse. –       Structure: The article is divided up in three main parts: i) description of genomic variants, ii) examination of functional consequences of allele-specific variation on transcript abundance, and iii) investigation of the molecular nature of functional variants and their position relative to genes. –       Experimental design: The 17 most widely used mouse strains (liver tissue) were selected for whole genome sequencing on the illumina GAIIx sequencing platform. To estimate error rates and evaluate the method a NOD/ShiLtJ BAC clone library was constructed. 107 BACs from seven loci on chromosomes 1, 6, 11 and 17 from this library were shotgun cloned and capillary sequenced. SNPs, structural variants (inversions, balanced translocations, CNVs), and transposable elements were identified based on a reference genome (the one that had already been sequenced before: C57BL/6J). Bayesian concordance analysis was used to construct gene trees across the genomes of M. m. musculus, M. m. domesticus and M. m. castaneus. M. spretus was used as the outgroup. Allele …

Background                                         Cryptic genetic variation (CGV) is defined as “standing genetic variation that does not contribute to the normal range of phenotypes observed in a population, but that is available to modify a phenotype that arises after environmental change or the introduction of novel alleles” [Gibson & Dworkin, 2004]. As such, CGV fills the gap between : 1.    expressed genetic variation, defined as genetic variation that contributes to the normal range of phenotypes actually present in a population ; 2.     neutral genetic variation, that does not contribute to phenotypes under any likely genetic or environmental conditions ; a typical example of neutral genetic variation would be synonymous substitutions in protein coding sequences. The necessity of the concept of CGV stems from the observation that environmental or genetic perturbations can reveal standing genetic variation that was silent or “cryptic” under standard conditions. CGV relative to a trait can thus be considered as genetic variation that conditionally affects that trait, the conditions or the trait itself being absent in the actual population and environment. A classic example of CGV concept is the scutellar bristle number in Drosophila. The number of bristles on the scutellum is 4 with low variation in wild type Drosophilae; when the …

Background                                         Cryptic genetic variation (CGV) is defined as “standing genetic variation that does not contribute to the normal range of phenotypes observed in a population, but that is available to modify a phenotype that arises after environmental change or the introduction of novel alleles” [Gibson & Dworkin, 2004]. As such, CGV fills the gap between : 1.    expressed genetic variation, defined as genetic variation that contributes to the normal range of phenotypes actually present in a population ; 2.     neutral genetic variation, that does not contribute to phenotypes under any likely genetic or environmental conditions ; a typical example of neutral genetic variation would be synonymous substitutions in protein coding sequences. The necessity of the concept of CGV stems from the observation that environmental or genetic perturbations can reveal standing genetic variation that was silent or “cryptic” under standard conditions. CGV relative to a trait can thus be considered as genetic variation that conditionally affects that trait, the conditions or the trait itself being absent in the actual population and environment. A classic example of CGV concept is the scutellar bristle number in Drosophila. The number of bristles on the scutellum is 4 with low variation in wild type Drosophilae; when the …

Reptiles had major evolutionary novelty: development of amniotic egg, which enabled breeding outside of the water. Until recently, only available genomes from the reptilian lineage were coming from the birds, therefore this paper and accompanying data provides a very valuable resource for further analysis of amniote evolution. The different aspects of lizard genome that were considered: transposable elements microchromosomes and synteny GC content sex determination system egg protein evolution adaptive radiation/ecology Around 30 percent of the lizard genome consists of transposable elements. It is fascinating that unlike in mammals and birds, there is much higher variety of active elements in the lizard genome, but also low rate of their accumulation. When the authors compared the mammalian conserved elements with the lizard genome, they found that several of these elements originate from transposable elements found in the lizard genome. The authors used the term exaptation to describe the process how certain mobile elements that were active in the amniote ancestor have putative function in mammals (most probably as regulatory elements). During the discussion we agreed that this term is not so appropriate since it would imply that the mobile elements had a function in the genome from the beginning (the time …