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Collective blog of the tutorial "Genome Ecology Evolution etc." of the Doctoral school of Biology of the University of Lausanne

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  • November 30, 2011
  • 06:36 AM

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 »

Hernandez, R., Kelley, J., Elyashiv, E., Melton, S., Auton, A., McVean, G., , ., Sella, G., & Przeworski, M. (2011) Classic Selective Sweeps Were Rare in Recent Human Evolution. Science, 331(6019), 920-924. DOI: 10.1126/science.1198878  

  • September 19, 2012
  • 03:17 AM

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 »

Hailer F, Kutschera VE, Hallström BM, Klassert D, Fain SR, Leonard JA, Arnason U, & Janke A. (2012) Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage. Science (New York, N.Y.), 336(6079), 344-347. PMID: 22517859  

Miller W, Schuster SC, Welch AJ, Ratan A, Bedoya-Reina OC, Zhao F, Kim HL, Burhans RC, Drautz DI, Wittekindt NE.... (2012) Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. Proceedings of the National Academy of Sciences of the United States of America, 109(36). PMID: 22826254  

  • November 28, 2011
  • 01:17 PM

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 »

Hohenlohe, P., Bassham, S., Ett er, P., Stiffler, N., Johnson, E., & Cresko, W. (2011) Classic Selective Sweeps Were Rare in Recent Human Evolution. Nature. DOI: 10.1371/journal.pgen.1000862  

  • October 3, 2012
  • 11:06 AM

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 »

Shapiro BJ, Friedman J, Cordero OX, Preheim SP, Timberlake SC, Szabó G, Polz MF, & Alm EJ. (2012) Population genomics of early events in the ecological differentiation of bacteria. Science (New York, N.Y.), 336(6077), 48-51. PMID: 22491847  

  • May 25, 2012
  • 03:04 AM

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 »

Rasmussen, M., Guo, X., Wang, Y., Lohmueller, K., Rasmussen, S., Albrechtsen, A., Skotte, L., Lindgreen, S., Metspalu, M., Jombart, T.... (2011) An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia. Science, 334(6052), 94-98. DOI: 10.1126/science.1211177  

  • March 30, 2012
  • 03:47 AM

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 »

  • November 17, 2011
  • 02:13 PM

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 »

Hohenlohe, P., Bassham, S., Ett er, P., Stiffler, N., Johnson, E., & Cresko, W. (2010) Parallel Evolution in Threespine Stickleback. PLoS Genetics, 6(2). DOI: 10.1371/journal.pgen.1000862  

  • November 7, 2011
  • 07:06 AM

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 »

  • November 4, 2011
  • 09:41 AM

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 »

Barrick, J., Yu, D., Yoon, S., Jeong, H., Oh, T., Schneider, D., Lenski, R., & Kim, J. (2009) Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature, 461(7268), 1243-1247. DOI: 10.1038/nature08480  

  • October 10, 2012
  • 05:44 AM

What could our genomes actually tell about disease risk?

by Charlotte Récapet in genome ecology evolution etc

Despite the recent advances in whole-genome sequencing, two recent studies let us think that we are far from uncovering the genetic basis of common diseases risk. In fact, information relevant to complex diseases might hide within rare or even private genome variations, often too scarce to be studied statistically. We might thus have to change radically our way of thinking of genes-diseases associations to make a step forward and make the DNA talk.Whereas a few, usually rare and severe “gene........ Read more »

  • September 21, 2012
  • 03:19 AM

The yak genome and adaptation to life at high altitude

by Nadja in genome ecology evolution etc

Normal 0 false false false EN-US JA X-NONE ... Read more »

Qiu Q, Zhang G, Ma T, Qian W, Wang J, Ye Z, Cao C, Hu Q, Kim J, Larkin DM.... (2012) The yak genome and adaptation to life at high altitude. Nature genetics, 44(8), 946-9. PMID: 22751099  

  • December 6, 2012
  • 05:31 PM

Parallel evolution in adaptive phenotypes: the case of the threespine stickleback

by Francesco Nicola Carelli in genome ecology evolution etc

How do adaptive phenotypes evolve? This question, despite the increasing availability of genomic and other molecular data, remains still largely unanswered. Among the different aspects investigated, a major point of discussion in this topic is the extent of the contribution of coding versus non-coding variation in the evolution of new traits. Although many research groups suggested that non-coding mutations might play a pivotal role because might avoid pleiotropic effects, still few examples are........ Read more »

Jones FC, Grabherr MG, Chan YF, Russell P, Mauceli E, Johnson J, Swofford R, Pirun M, Zody MC, White S.... (2012) The genomic basis of adaptive evolution in threespine sticklebacks. Nature, 484(7392), 55-61. PMID: 22481358  

  • December 18, 2012
  • 05:11 AM

by Nicla Loviglio in genome ecology evolution etc

Genome-wide analysis of a long-term evolution experiment with Drosophila 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, w........ Read more »

Burke, M., Dunham, J., Shahrestani, P., Thornton, K., Rose, M., & Long, A. (2010) Genome-wide analysis of a long-term evolution experiment with Drosophila. Nature, 467(7315), 587-590. DOI: 10.1038/nature09352  

  • November 30, 2011
  • 10:58 AM

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 »

  • October 3, 2011
  • 03:42 AM

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 »

Bernatchez, L., Renaut, S., Whiteley, A., Derome, N., Jeukens, J., Landry, L., Lu, G., Nolte, A., Ostbye, K., Rogers, S.... (2010) On the origin of species: insights from the ecological genomics of lake whitefish. Philosophical Transactions of the Royal Society B: Biological Sciences, 365(1547), 1783-1800. DOI: 10.1098/rstb.2009.0274  

  • November 26, 2011
  • 08:11 AM

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 »

Mu, J., Myers, R., Jiang, H., Liu, S., Ricklefs, S., Waisberg, M., Chotivanich, K., Wilairatana, P., Krudsood, S., White, N.... (2010) Plasmodium falciparum genome-wide scans for positive selection, recombination hot spots and resistance to antimalarial drugs. Nature Genetics, 42(3), 268-271. DOI: 10.1038/ng.528  

  • November 22, 2012
  • 10:21 AM

Ecological success of recently emerged bacterial hybrids living in the wild

by Nicla Loviglio in genome ecology evolution etc

Microbial species are one of the most ubiquitous living group on Earth's biosphere, showing incredible ability to thrive even in ambient conditions to the limit of human endurance. By virtue of their rapid growth, bacteria are ideal for unraveling the molecular mechanisms of many evolutionary processes. Their rapidity to respond to changes has been associated to the combined effect of evolutionary processes, species composition or gene expression shifts. Most of the studies have focused so far ........ Read more »

  • May 27, 2013
  • 06:24 AM

Analyses of pig genomes provide insight into porcine demography and evolution

by Anna Kostikova in genome ecology evolution etc

Pig domestication has started over 10 000 years ago and has had important consequences on human life, changing our agricultural and medical practices. Much has been argued on whether pig was domesticated independently across multiple locations or it was adopted … Continuer la lecture →... Read more »

Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens HJ.... (2012) Analyses of pig genomes provide insight into porcine demography and evolution. Nature, 491(7424), 393-8. PMID: 23151582  

  • October 19, 2011
  • 02:56 PM

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 »

  • December 10, 2014
  • 07:39 AM

The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication

by Alice Breda in genome ecology evolution etc

Oryza glaberrima is an African species of rice that is not of the same origin as the Asian rice (Oryza sativa) and was independently domesticated from the progenitor Oryza barthii about 3,000 years ago.In this study recently published by Nature … Continue reading →... Read more »

Wang, M., Yu, Y., Haberer, G., Marri, P., Fan, C., Goicoechea, J., Zuccolo, A., Song, X., Kudrna, D., Ammiraju, J.... (2014) The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nature Genetics, 46(9), 982-988. DOI: 10.1038/ng.3044  

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