Tutorial Genomics, Ecology, Evolution, etc

In this paper Richard E. Lenski and colleague are showing an example of how efficient adaptation by natural selection is. During 20 year they have been growing twelve populations of Escherichia coli in glucose medium containing also abundant citrate, this famous long-term evolution experiment called LTEE allowed the evolution to run for 40’000 generations in controlled laboratory conditions. Surprisingly after 31’000 generations some mutants appeared that were able to use citrate, as a source of carbon instead of glucose, the inability to use citrate is one of the frame that define E.coli as a species. Researcher Zachary D. Blount dissected all the mechanism in using whole genome re-sequencing of 29 clones along the population history (Fig.1). Three steps are analyzed in details, as they were necessary to permit the evolution of Cit+ trait, potentiation, actualization and refinement. The phylogeny (Fig.1) highlight two clades that coevolved and were maintain with the new Cit+ clade around generation 20’000 (Fig 1.). Moreover after the evolution of the citrate clade around 36’000, bacteria that have Cit+ phenotype have a SNP that is causing a defect in methyl directed mismatch DNA repair such that mutants accumulate SNPs much faster than any other clades. (Fig.1 inset). …

  1. How genomes evolve in natural populations? is a question that, despite to be a long-standing search for geneticists, recent molecular genomic approaches may help to understand. Their evolution among natural populations may be shaped by forces derived from different processes, such as as mutation, neutral evolution, negative or positive selection and demographic changes (Nosil & Feder 2011). In addition, the study of population divergences and species formation has an important temporal context. That is, the point in time during the evolutionary trajectory of the set of populations or related species we aim to study, can display different patterns. For instance, during initial stages the level of genome differentiation may be low. Then, as divergence proceeds (by intrinsic or extrinsic forces) this level is expected to increase in the genome, in either a clustered or an interspersed way. Further, hybridization between differentiated populations may produce the secondary infiltration of genomic regions of one population into the other. The study of the genomic complexity in natural populations may shed light into the population dynamics and the relevant processes during species evolution. 2. Staubach et al. (2012) used natural populations of house mice (Mus musculus) subspecies (M. m. domesticus which does …

How exactly do lineages diverge to the point that they can be considered separate species, and especially reach reproductive isolation, is still an ongoing question in evolutionary biology. Classical views of speciation hypothesize the existence of speciation genes, defined as loci contributing to reproductive isolation (Nosil and Schluter 2011). Although such loci have been clearly described in a few cases (Presgraves 2010), the mechanisms remain impossible to generalize. Two central issues remain unresolved: Whether genetic incompatibilities arise mostly through adaptive or neutral mutations; Whether these isolating mutations occur at specific loci in the genome. In a recent paper, Hans Ellegren and his colleagues at Uppsala University describe the new insights brought by the comparison of whole genome data from two sister species of Old World flycatchers. The collared flycatcher Ficedula albicollis and the pied flycatcher F. hypoleuca (fig. 1) have been separate species for about 2 millions years, and their reproductive isolation is still incomplete as they can produce fertile male hybrids (but infertile females). Consistently, gene flow is strongly reduced but not null between the two species. The researchers first established a map of the flycatcher genome by assembling short reads from a collared flycatcher and using the known …

Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History. The origin of modern Human is clear with evidences coming from many different disciplines. Africa is the continent where the highest genetic diversity is found; this clue associated to fossils records strongly supports the theory of a African origin with a migration out of Africa around 100’000 years ago (Templeton, 2002). Moreover other populations in the world confirm this pattern in showing a subset of this diversity. The history of the emergence of modern human is more debated, especially in two points, for the inside story of African divergence between groups and for the number of times the out of Africa occurred. In this study the focus is made on the internal history of Africa. In order to respond to a lack of study about genome-wide in different ethnic groups of African, the authors focused on the deepest mitochondrial lineages known that are represented by the different click-speaking ethnic groups of southern Africa. A number of 220 individuals of 11 groups were genotyped for SNPs, resulting in ~2.3 million of markers. Populations were characterised by their languages subdivision as well as by their mode of subsistence (hunters-gatherers and …

Human populations have colonized high altitude (HA) habitats (above 2500m of altitude) multiple times and independently. HA habitats are essentially characterized by lower biodiversity and low levels of oxygen availability, also called hypoxia. Classically, organisms respond to this decreased oxygen saturation (O2 sat) by increasing their hemoglobin (Hb) concentration. Nonetheless, such an acclimatization process is often associated with health issues and often results in altered reproductive success. Thus, long-term survival at HA may have brought about adaptations to counter these outcomes in human populations, such as the Andean, Tibetan or Ethiopian highlander populations. Several studies have intended to look for signatures of natural selection in these populations, asking several interesting questions about the nature and strength of selection at the phenotypic level, as well as its effect on the genome. Thus, it has been found that human populations don’t respond in the same way to similar selective pressures associated with HA : Andean highlanders show a large increase in Hb levels, while Tibetans and the Amhara (Ethiopian ethnic group that colonized HA habitat more than 5 ky ago) show little. Genomic studies conducted on Tibetan highlanders have found single nucleotide polymorphisms (SNPs) that are significantly associated with variation in Hb …

These are the articles we will be discussing this spring: March 8: Alkorta-Aranburu G, Beall CM, Witonsky DB, Gebremedhin A, Pritchard JK, et al. (2012) The Genetic Architecture of Adaptations to High Altitude in Ethiopia. PLoS Genet 8(12): e1003110. doi:10.1371/journal.pgen.1003110 March 15: Schlebusch et al. (2012) Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History Science 338: 374-379 March 22: Ellegren et al. (2012) The genomic landscape of species divergence in Ficedula flycatchers Nature 491: 756–760 April 19: Staubach F, Lorenc A, Messer PW, Tang K, Petrov DA, et al. (2012) Genome Patterns of  Selection and Introgression of Haplotypes in Natural Populations of the House Mouse (Mus musculus). PLoS Genet 8(8): e1002891 April 26: Schloissnig et al. (2013) Genomic variation landscape of the human gut microbiome Nature 493: 45–50 Mai 3: Blount et al. (2012) Genomic analysis of a key innovation in an experimental Escherichia coli population Nature 489: 513–518 Mai 17: Groenen et al. (2012) Analyses of pig genomes provide insight into porcine demography and evolution Nature 491: 393–398 Mai 24: Lachance et al. (2012) Evolutionary History and Adaptation from High-Coverage Whole-Genome Sequences of Diverse African Hunter-Gatherers Cell 150: 457–469

” Where there is life there is wishful thinking “  Gerald F. Lieberman Finding genes which are under positive selection is an important part of any molecular evolution biologists’ work as these genes can be responsible for adaptations in a studied specie. To find such genes, genomic scans are conducted and regions of the genome that show specific patterns, such as selective sweeps, are further studied and sensible biological interpretations are made. In this paper, Pavlidis & al. show that one has to be careful with such biological interpretations as the patterns for positive selection can appear under an a priori known neutrally evolving genome and that it might not be that difficult to come up with a satisfying story about such false-positives. Figure 1 | Flowchart representing the the steps in the simulation. These steps were repeated for all of the 100 simulations. To show the existence of  false-positives in the detection of positive selection patterns, Pavlidis & al simulated 100 data sets of 40 D.melanogaster X chromosomes evolving under a neutral Wright-Fisher model. The D.melanogaster X chromosome, which was sampled in the Netherlands, is believed to have gone through a recent and deep bottleneck. A demographic scenario for …

Sticklebacks are originally marine fish that colonized freshwater habitats after the last glaciation. Adaptation to freshwater environment happened independently in various rivers and lakes around the globe, giving rise to similar phenotypes following natural selection. In a recent study, researchers aimed to identify potential loci repeatedly associated with the divergence between marine and freshwater sticklebacks. An underlying question was to uncover if this adaptation is due to regulatory or protein-coding changes. To ensure that the changes reflected parallel evolution, the authors sequenced a reference freshwater stickleback and 20 other freshwater and marine sticklebacks from both Pacific and Atlantic populations. They selected populations showing characteristic marine and freshwater morphologies (Figure1 a, b). To find loci involved in repeated adaptation to freshwater habitats, the authors used two methods, aiming to identify regions where sequences from freshwater sticklebacks were similar to each other but different from marine sticklebacks. The first method is a self-organizing map-based iterative Hidden Markov Model (SOM/HMM) (Figure1 c). With this method, they identified the 20 most common patterns of genetic relationships (trees) among the 21 individuals. The authors found that for most of the genome, the fish clustered by geography, with fish from Pacific regions being closer to each …

For decades, most researchers have provided some general insights into the nature of adaptation in asexually reproducing populations with small genome, such as bacteria and yeast. They assumed that sexual species evolve the same way these populations do, i.e. their adaptation is driven by the so-called selective sweeps or newly arising beneficial genetic mutation quickly becomes “fixated” on a particular portion of DNA, with the genome-wide haplotype associated with it. When we relate to obligate sexually reproducing systems, this is much more complicated by the fact that selection can act on standing variation, that means that weak selection can act on many pre-existing genetic variants involved in fitness traits. The idea is that short-term evolution have occurred through a so-called “soft sweep” model, which contrasts the hypothesis of the “hard sweep”, where strong selective sweep originates from a single mutation, while all its linked neutral variants are eliminated. Burke et al. compared outbred, sexually reproducing, replicated populations of D. melanogaster selected for accelerated development and their matched control populations on a genome-wide basis, and this is the first time that such a study of a sexually reproducing species has been done.  As shown in figure 1, they used the Illumina …

And they have published an informative article in PLOS One about their first 4 years:http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0050109 More cited papers also have more views of the blog post Biology rules