Classic Selective Sweeps Were Rare in Recent Human Evolution

by UNIL_student in genome ecology evolution etc

With the rise of genomics and theavailability of whole genome sequences, geneticists hope to be ableto understand the recent adaptations humans underwent. Classicselective sweeps, where a beneficial allele arises in a populationand subsequently goes to fixation, leave a specific pattern. Indeed,all variation is erased as the selected allele invades thepopulation, and the neighboring neutral variation is also partiallyswept, with an intensity depending on the linkage with the selectedregion.An ex........ Read more »

Parallel Evolution in Threespine Stickleback

by UNIL_student in genome ecology evolution etc

Hohenlohe, P., Bassham, S., Etter, P., Stiffler, N., Johnson, E., & Cresko, W. (2010). Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags PLoS Genetics, 6 (2) DOI: 10.1371/journal.pgen.1000862 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 ........ Read more »

Paper : genome evolution and adaptation in a long-term experiment with Escherichia coli

by UNIL_student in genome ecology evolution etc

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 confound........ Read more »

RAD tagging adaptation

by UNIL_student in genome ecology evolution etc

The threespine stickleback, Gasterosteus aculeatus, is a small fish that inhabits marine, estuarine and freshwater habitats in the holarctic. It has been previously inferred that in many regions, freshwater populations derived from oceanic ancestors. As soon as the freshwater populations are in different drainage systems, they can be considered as independent of each other. Those natural replicates are one of the reasons why sticklebacks are a model system to study adaptive evolution.Stickleba........ Read more »

Modes of Adaptation in Recent Human Evolution

by UNIL_student in genome ecology evolution etc

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 thei........ Read more »

Bernatchez et al. 2010: On the origin of species: insights from the ecological genomics of lake whitefish

by UNIL_student in genome ecology evolution etc

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 t........ Read more »

Insights into Human Variation

by UNIL_student in genome ecology evolution etc

Higher throughput, better accuracy, and lower costs of DNA sequencing technology revolutionized the field of genetics. Building upon these technological advances, 1000 genomes project marked the new era of human genetics. The ambitious goal of this international project is to build a detailed map of human genetic variation by sequencing 2500 individuals from five major population groups. The first insights into the project results got available upon completion of the pilot phase that covered so........ Read more »

Towards an unbiased study of parallel evolution

by mrr in genome ecology evolution etc

The investigation of parallel evolution is a powerful paradigm to study mechanisms of adaptation.  This review and opinion paper stresses the fact that although remarkable examples have been studied, molecular bases of adaptation are still poorly understood in the vast majority of cases.In rare examples, a genetic variation has been linked to repeated and independent adaptation. In the examples of Mc1r , multiple mutations occurred in the same gene independently leading to different coat co........ Read more »

Positive selection, recombination hot spots and resistance to antimalarial drugs in P. Falciparum: the way to the treatment against malaria ?

by UNIL_student in genome ecology evolution etc

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 th........ Read more »

Cryptic genetic variation promotes rapid evolutionary adaptation in an RNA enzyme (Hayden et al, Nature, 2011)

by Diego in genome ecology evolution etc

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”... Read more »

Elmer & Meyer 2011: Adaptation in the age of ecological genomics: insights from parallelism and convergence

by UNIL_student in genome ecology evolution etc

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 gen........ Read more »

On the origin of species insights from the ecological genomics of lake whitefish: Louis Bernatchez1 et al; Phil. Trans. R. Soc. B (2010)

by UNIL_student in genome ecology evolution etc

@font-face { font-family: "Cambria"; }@font-face { font-family: "AdvPS858B"; }@font-face { font-family: "AdvPS8588"; }@font-face { font-family: "AdvPS8585"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman"; }div.Section1 { page: Section1; } 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 a........ Read more »

An Aboriginal Australian genome reveals separate human dispersals into Asia

by mrr in genome ecology evolution etc

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.BackgroundModern 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 hypothesiz........ Read more »

The evolutionary history of polar bears

by Sacha in genome ecology evolution etc

The study of the Ursus lineage, composed of brown bear (Ursus arctos), black bear (Ursus americanus) and polar bear (Ursus maritimus), provides the ability of addressing the subject of adaptation to extreme (salty and glacial) environments in mammals. Moreover, in last few decades, polar bears won public and media attention, being one of the most charismatic species endangered by global warming and Arctic ice melting. To trace history of innovations and determine response to environmental change........ Read more »

by UNIL_student in genome ecology evolution etc

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 impo........ Read more »

Distinct signatures of diversifying selection revealed by genome analysis of respiratory tract and invasive bacterial populations (Shea et al, PNAS 2011)

by PierreMillon in genome ecology evolution etc

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 mult........ Read more »

Evolutionary consequences of sex: It's not about what you're doing, but who you're doing it with...

by Charlotte Récapet in genome ecology evolution etc

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 bacter........ Read more »

The genome of the green anole lizard and a comparative analysis with birds and mammals

by iris in genome ecology evolution etc

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 a........ Read more »

Rapid Evolution of Enormous, Multichromosomal Genomes in Flowering Plant Mitochondria with Exceptionally High Mutation Rates

by mrr in genome ecology evolution etc

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. Mut........ Read more »