genome ecology evolution etc

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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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  • June 25, 2014
  • 08:56 AM
  • 152 views

Genetic incompatibilities are widespread within species

by Zheng Yan in genome ecology evolution etc

Epistasis is the phenomenon whereby one polymorphism’s effect on a trait depends on other polymorphisms present in the genome(Hemani et al. 2014). Although it has been proved to shape genetic variation and contribute to differences within and between populations for … Continue reading →... Read more »

Corbett-Detig, R., Zhou, J., Clark, A., Hartl, D., & Ayroles, J. (2013) Genetic incompatibilities are widespread within species. Nature, 504(7478), 135-137. DOI: 10.1038/nature12678  

Hemani, G., Shakhbazov, K., Westra, H., Esko, T., Henders, A., McRae, A., Yang, J., Gibson, G., Martin, N., Metspalu, A.... (2014) Detection and replication of epistasis influencing transcription in humans. Nature, 508(7495), 249-253. DOI: 10.1038/nature13005  

  • May 14, 2014
  • 05:25 AM
  • 79 views

The Amborella Genome and the Evolution of Flowering Plants

by tpillone in genome ecology evolution etc

Amborella trichopoda, an endemic species to New Caledonia, is the most early-diverging taxa of flowering plants (angiosperms, Figure 1). As such, the sequencing of its genome was of considerable interest for the investigation of the emergence and evolution of this … Continue reading →... Read more »

, ., Albert, V., Barbazuk, W., dePamphilis, C., Der, J., Leebens-Mack, J., Ma, H., Palmer, J., Rounsley, S., Sankoff, D.... (2013) The Amborella Genome and the Evolution of Flowering Plants. Science, 342(6165), 1241089-1241089. DOI: 10.1126/science.1241089  

  • May 12, 2014
  • 05:14 AM
  • 209 views

Single and independent mutations lead to an adaptive and complex color phenotype in deer mice living on the light-colored soils of the Nebraska Sand Hills

by Valérie Ducret in genome ecology evolution etc

Pleiotropy of genes is often the main solution to explain genetic basis of complex phenotypes (i.e., those composed of multiple traits). But dissection of those genes or loci are rarely studied, and it remains unclear which of single pleiotropic mutations or … Continue reading →... Read more »

Linnen, C., Poh, Y., Peterson, B., Barrett, R., Larson, J., Jensen, J., & Hoekstra, H. (2013) Adaptive Evolution of Multiple Traits Through Multiple Mutations at a Single Gene. Science, 339(6125), 1312-1316. DOI: 10.1126/science.1233213  

  • May 9, 2014
  • 08:37 AM
  • 221 views

Patterns of population epigenomic diversity

by Delphine Le Roux in genome ecology evolution etc

In my point of vue, this paper is interesting because it’s in my domain of interest but very difficult to understand because they put lot of technical word without definition and they say very often see references, as it’s described … Continue reading →... Read more »

Schmitz, R., Schultz, M., Urich, M., Nery, J., Pelizzola, M., Libiger, O., Alix, A., McCosh, R., Chen, H., Schork, N.... (2013) Patterns of population epigenomic diversity. Nature, 495(7440), 193-198. DOI: 10.1038/nature11968  

  • April 12, 2014
  • 05:17 AM
  • 151 views

Great ape genetic diversity and population history

by Michael Eyer in genome ecology evolution etc

Humans and chimpanzees share about 95% of their DNA. Having this in mind the recently published paper of Prado-Martinez et al. 2013, focusing at identifying great-ape genetic variation and resolving great-ape population history (based on historical-effective population sizes) reflects a … Continue reading →... Read more »

Prado-Martinez, J., Sudmant, P., Kidd, J., Li, H., Kelley, J., Lorente-Galdos, B., Veeramah, K., Woerner, A., O’Connor, T., Santpere, G.... (2013) Great ape genetic diversity and population history. Nature, 499(7459), 471-475. DOI: 10.1038/nature12228  

  • March 13, 2014
  • 01:00 PM
  • 170 views

Towards discovering the evolutionary history of dogs and dog domestication process

by Maria Noemi Llanos Roman in genome ecology evolution etc

In the times in which publishing a paper is not always totally related with the new knowledge´s contribution but leaded by how the researchers sell this new knowledge, it is quite refreshing to find a paper that outstands because deals … Continue reading →... Read more »

Freedman, A., Gronau, I., Schweizer, R., Ortega-Del Vecchyo, D., Han, E., Silva, P., Galaverni, M., Fan, Z., Marx, P., Lorente-Galdos, B.... (2014) Genome Sequencing Highlights the Dynamic Early History of Dogs. PLoS Genetics, 10(1). DOI: 10.1371/journal.pgen.1004016  

  • February 27, 2014
  • 05:16 AM
  • 164 views

Genome-wide signatures of convergent evolution in echolocating mammals (Parker et al., 2013)

by Alberto Merli in genome ecology evolution etc

Phenotype convergence is a fascinating topic in evolution. Usually species evolve by divergence, starting from a common ancestor and then developing different genomic changes that lead to different phenotypes. which are then selected by the environment. Nevertheless, it has been … Continue reading →... Read more »

Parker, J., Tsagkogeorga, G., Cotton, J., Liu, Y., Provero, P., Stupka, E., & Rossiter, S. (2013) Genome-wide signatures of convergent evolution in echolocating mammals. Nature, 502(7470), 228-231. DOI: 10.1038/nature12511  

  • June 19, 2013
  • 01:48 PM
  • 406 views

Evolutionary History and Adaptation from High-Coverage Whole-Genome Sequences of Diverse African Hunter-Gatherers

by Elisa Cavoto in genome ecology evolution etc

“ Hunting and gathering was humanity’s first and most successful adaptation, occupying at least 90 percent of human history. Until 12,000 years ago, all humans lived this way. ” [The Cambridge Encyclopedia of Hunters and Gatherers. Richard B. Lee and … Continue reading →... Read more »

  • May 27, 2013
  • 06:24 AM
  • 415 views

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  

  • May 15, 2013
  • 03:57 AM
  • 249 views

Genomic analysis of a key innovation in an experimental Escherichia coli population

by Romain Savary in genome 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 … Continuer la lecture →... Read more »

  • May 7, 2013
  • 03:38 AM
  • 264 views

Genome Patterns of Selection and Introgression of Haplotypes in Natural Populations of the House Mouse (Mus musculus)

by Martha Serrano in genome ecology evolution etc

  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 … Continuer la lecture →... Read more »

  • April 23, 2013
  • 11:36 AM
  • 287 views

Flycatchers’ genomes bring new insights into the genomic basis of evolution

by Charlotte Récapet in genome ecology evolution etc

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 … Continuer la lecture →... Read more »

Ellegren H, Smeds L, Burri R, Olason PI, Backström N, Kawakami T, Künstner A, Mäkinen H, Nadachowska-Brzyska K, Qvarnström A.... (2012) The genomic landscape of species divergence in Ficedula flycatchers. Nature, 491(7426), 756-60. PMID: 23103876  

  • March 27, 2013
  • 05:30 AM
  • 319 views

Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History.

by Romain Savary in genome ecology evolution etc

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 … Continuer la lecture →... Read more »

Schlebusch, C., Skoglund, P., Sjodin, P., Gattepaille, L., Hernandez, D., Jay, F., Li, S., De Jongh, M., Singleton, A., Blum, M.... (2012) Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History. Science, 338(6105), 374-379. DOI: 10.1126/science.1227721  

  • March 19, 2013
  • 12:30 PM
  • 277 views

The Genetic Architecture of Adaptations to High Altitude in Ethiopia

by Guillaume Cossard in genome ecology evolution etc

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 … Continuer la lecture →... Read more »

Alkorta-Aranburu, G., Beall, C., Witonsky, D., Gebremedhin, A., Pritchard, J., & Di Rienzo, A. (2012) The Genetic Architecture of Adaptations to High Altitude in Ethiopia. PLoS Genetics, 8(12). DOI: 10.1371/journal.pgen.1003110  

  • December 18, 2012
  • 05:11 AM
  • 505 views

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  

  • December 14, 2012
  • 07:51 AM
  • 432 views

Genome-wide analysis of a long-term evolution experiment with Drosophila

by Namrata Sarkar in genome ecology evolution etc

Normal 0 false false false EN-US JA X-NONE ... 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  

  • December 6, 2012
  • 05:31 PM
  • 564 views

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  

  • November 22, 2012
  • 10:21 AM
  • 513 views

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 »

  • October 10, 2012
  • 05:44 AM
  • 534 views

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 »

  • October 3, 2012
  • 11:06 AM
  • 723 views

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  

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