Tutorial Genomics, Ecology, Evolution, etc

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 …

Evolution, as explained by Darwin’s theory of origin, is a process of population divergence and speciation by natural selection and adaptation driven by ecological heterogeneity and competitive interactions. Several studies conducted in light of this theory as well as large amount of ecological information, provides a support for the role of divergent natural selection as main cause of evolution. But having a thorough understanding of the genomics underlying these evolutionary process will provide further strong grounds for this theory of evolution. The review “On the origin of species: insight from the ecological genomics of lake whitefish” provides the genetic basis of evolutionary change and diversification driven by natural selection by reviewing the main findings of the long term research program conducting the ecological genomics of sympatric population of whitefish (Coregonus sp) engaged in the process of speciation. The review provides an example as how by applying a combination of multiple research approaches under the conceptual idea of adaptive radiation provides an insight into the evolutionary processes in a non-model species. Adaptive radiation is the evolution of ecological and phenotypic diversity within a rapidly multiplying lineage. Starting with a recent single ancestor, this process results in the speciation and phenotypic adaptation …

From the doctoral school official site Date Location Notice Topics Lecturer(s) 09.09.2011 de 12:15 à 13:15 BiophoreUNIL-SorgeRoom n°4311 On the origin of species: insights from the ecological genomics of lake whitefish Jerome Goudet, Marc Robinson-Rechavi 07.10.2011 de 12:15 à 13:15 BiophoreUNIL-SorgeRoom n° 4311 Adaptation in the age of ecological genomics: insights from parallelism and convergence Jerome Goudet, Marc Robinson-Rechavi 14.10.2011 de 12:15 à 13:15 BiophoreUNIL-SorgeRoom n° 4311 Genome-wide approaches to the study of adaptive gene expression evolution Jerome Goudet, Marc Robinson-Rechavi 21.10.2011 de 12:15 à 13:15 BiophoreUNIL-SorgeRoom n° 4311 Genome evolution and adaptation in a long-term experiment with Escherichia coli Jerome Goudet, Marc Robinson-Rechavi 04.11.2011 de 12:15 à 13:15 BiophoreUNIL-SorgeRoom n° 4311 Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags Jerome Goudet, Marc Robinson-Rechavi 11.11.2011 de 12:15 à 13:15 BiophoreUNIL-SorgeRoom n° 4311 A map of human genome variation from population-scale sequencing Jerome Goudet, Marc Robinson-Rechavi 18.11.2011 de 12:15 à 13:15 BiophoreUNIL-SorgeRoom n° 4311 Plasmodium falciparum genome-wide scans for positive selection, recombination hot spots and resistance to antimalarial drugs Jerome Goudet, Marc Robinson-Rechavi 25.11.2011 de 12:15 à 13:15 BiophoreUNIL-SorgeRoom n° 4311 Classic Selective Sweeps Were Rare in Recent Human Evolution Jerome Goudet, Marc Robinson-Rechavi

Papers that we will discuss between September and November 2011: On the origin of species: insights from the ecological genomics of lake whitefishBernatchez et al. Phil. Trans. R. Soc. B 12 June 2010 vol. 365 no. 1547 1783-1800 Adaptation in the age of ecological genomics: insights from parallelism and convergenceElmer and Meyer. Trends in Ecology and Evolution, June 2011, Vol. 26, No. 6 Genome-wide approaches to the study of adaptive gene expression evolutionFraser. BioEssays Volume 33, Issue 6, pages 469–477, June 2011 Genome evolution and adaptation in a long-term experiment with Escherichia coliBarrick et al. Nature 461, 1243-1247 (29 October 2009) Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD TagsHohenlohe et al. PLoS Genet 6(2): e1000862 A map of human genome variation from population-scale sequencingThe 1000 Genomes Project Consortium. Nature 467, 1061–1073 (28 October 2010) Plasmodium falciparum genome-wide scans for positive selection, recombination hot spots and resistance to antimalarial drugsMu et al. Nature Genetics 42, 268–271 (2010) Classic Selective Sweeps Were Rare in Recent Human EvolutionHernandez et al. Science 331, 920 (2011)