Author: Marc Robinson-Rechavi

Since their first appearance humans have colonized most parts of the world. They have undergone multiple adaptations to a wide range of disparate habitats, which let to the appraisal of different phenotypes. Thus, dark skin and hair, for example, is an evolutionary adaptation to protect against high amounts of radiation coming from the sun. An adaptive trait can be fixed in a population through the mechanisms of natural selection acting on point mutations or on standing genetic variation.In their article “Classic Selective Sweeps were Rare in Recent Human Evolution” Hernandez et al. 2011 were interested in the modes of natural selection that shaped human adaptations. Up to date, most studies suggest that the principal mode of adaptation is due to positive selection. Therefore, a beneficial mutation appears in a population and is getting rapidly fixed. The decrease in neutral diversity in the linked sites results in the occurrence of a ‘classic selective sweep’. Hernandez et al. 2011 were questioning whether it could be possible that not only selective sweeps but also other types of selection could have been involved in human adaptation. Resequencing data for 179 human genomes from “three” populations (African, Chinese/Japanese and European) was investigated. They assessed average …

Plasmodium Falciparum is a protozoan parasite that cause malaria in human. An estimated 781,000 people died from malaria in 2009 according to the World Health Organization. Different treatments exist against malaria since 1891 such as Atabrine, Chloroquine(CQ) or Artemisinin(ART) but there is not yet any vaccination possible and due to the evolution one can see an increasing in drug resistance of the Falciparum population. Some information at genomic level are at a high importance to determine the resistance to antimalarial drugs. To study possible treatments, a group of researchers worked on Plasmodium Falciparum to detect variation in recombination rate, loci under recent positive selection and genes associated with drug responses. For this work, the researchers used the GWAS method (Genome-Wide Association Studies) which allows to define if a single-nucleotide polymorphism (SNPs) is associated with a trait, here the malaria. The authors collected and adapted 189 independent P. falciparum: including 146 from Asia (specifically, Thailand and Cambodia), 26 from Africa, 14 from America and 3 from Papua New Guinea. Antimalarial drug resistance of Falciparum is different according to their localization, thus the choice of the authors is good but not well-balanced. Using population genetics methods and stratification methods, the authors showed …

The threespine stickleback (Gasterosteus aculeatus) is a coastal and freshwater form species that lives in marine, eustarine and freshwater habits throughout the Northern hemisphere. Previous studies suggested that the freshwater stickleback populations might have diverged independently from oceanic populations less than 10,000 years ago. Indeed, the search for new space might have caused migration to unexplored freshwater habitats. Among threespine stickleback populations, there is a huge phenotypic variation mainly due to adaptation to differences in feeding behaviours and defence mechanisms. For example, the lateral plate armor is present in oceanic populations but has been lost in many derived freshwater populations. This is of particular importance because despite little or no gene flow among freshwater populations, life history traits appear independently in populations of similar habitats. Its evolutionary history and its extraordinary phenotypic diversity made it appropriate for studying the genetic changes that underlie adaptation to new environments. Moreover, recent advances in genome biology and next generation sequencing techniques allowed addressing questions about evolutionary processes acting at a genomic scale in natural populations. In this paper (“Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags”) of Hohenlohe et al. 2010 the main goal was to assess whether the …

Slightly off topic relative to the usual journal-club posts, but I think that this is relevant to understanding where we are going with genomics for studying variability: Next-Gen 101: Video Tutorial on Conducting Whole-Exome Sequencing Research from the National Human Genome Research Institute (from the Nielsen lab blog)

According to Darwin, adaptation is a gradual process. The rate of adaptation is variable and diverse whose reason is unknown. It ’s well known that genomic changes are linked with adaptation, but exact relationship remain elusive. With imperfect knowledge of organism’s genetics and complicated environment, it’s difficult to make clear conclusion. Thus, this paper designed a experiment using tractable model organisms in controlled laboratory environments, in order to minimize the confounding factors and complexity. Moreover, they sequence complete genomes to find the mutations responsible for particular adaptation. In addition, it’s possible to find out whether the dynamics of genomic and adaptive evolution are coupled very tightly or only loosely. In the first step, they sequenced the genomes of E. coli clones sampled at generations 2K, 5K, 10K, 20K and 40K. Through 20K generations , 45 mutations were identified, moreover, the number of mutational differences between accumulated in a ncestral and evolved genomes accumulated in a near-linear fashion over this period. Neutral evolution should accumulate by drift at a uniform rate and are not beneficial. However, in this experiment,they found fitness trajectory shows profound adaptation that is not linear. Particularly, the rate of fitness improvement decelerates over time indicating the rate …

The review by Hunter Fraser discusses the role of gene expression in adaptation, the challenges facing the field, recent genome-wide studies that allow the rejection of the null model of neutrality and how the latter thus help to determine, with some confidence, if positive selection is occurring. He then goes on to discuss questions that can be addressed and the empirical evidence available for answering these. Challenges in studying gene expression adaptation: The author discusses the two important stages at which adaptation can occur – the inherent sequences of proteins and the pattern and level of expression of these proteins. Protein sequence evolution and its role in adaptation have received a lot of attention from the scientific community and have been widely studied. The study of gene expression adaptation (GEA) on the other hand, has been very limited. There are three reasons for this aberration – the little significance attributed to GEA in adaptation as compared to protein sequences until recently (as recent as 2003!), difficulty to characterize gene regulation as compared to deducing DNA sequences, mainly because of its dynamic nature, and thus the unavailability of suitable methods for simple and effective study of GEA. On these lines, the …

Natural selection is one of the two major forces which drive evolution of species, morphs and phenotypes. However, due to the confounding effects of environmental stochasticity, replication at the taxon level is needed for better understanding the influence and importance of natural selection in evolutionary biology. Parallel evolution events, in which related taxons independently evolve similar traits, provide a useful framework to investigate the mechanisms of adaptation using powerful new genomic and transcriptomic tools. In the paper “Adaptation in the age of ecological genomics: insights from parallelism and convergence”, Kathryn Elmer and Axel Meyer reviewed examples of parallel evolution in natural populations of non-model species and compared the genetic bases of their adaptive traits. Inspired by the hypotheses that parallel phenotypes share homologous genetic bases, they investigated the advances allowed by new genomic technique in the field of adaptive evolution. Understanding genetic origins and mechanisms of phenotypic changes will raise insights into the opportunities for species to adapt under ecological pressure. The authors proposed a classification for the nature of genetic variations leading to similar phenotypes among three levels: homologous mutation at the same nucleotides, homologous mutation in the same gene at different nucleotide and non-homologous mutation in different genes. …

In the first paper being discussed in the tutorial (~journal club) of Genomics-Ecology-Evolution etc., the authors (Bernatchez et al.) had a pleasant task of reviewing their own long-term study on white fish species-pair (Coregonus clupeaformis and C.lavaretus). The paper gives a well-structured example how, and also why, a non-model organism can be used to study ecological genomics. One thing is for sure based on this paper; it requires a lot of time and work. The authors have come a long way to actually make their study organism an excellent target for the study of ecological genomics with a large dataset of both ecological and genetic studies. Since the participants of this tutorial have quite different backgrounds, first the discussion was focused on the definitions of the main terms use here, such as “species” and “sympatric”. Can we talk about two sympatric species that are able to hybridize and live in the different water layers? Authors also don’t seem to be quite sure if species is the right term here and sometimes they use terms “species pair” and sometimes “two forms”. I suppose one could discuss the definitions forever but the main point here, however, is that the divergence of these …