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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  • February 15, 2015
  • 12:44 PM
  • 80 views

Stick Insect Genomes Reveal Natural Selection’s Role in Parallel Speciation

by Esra Durmaz in genome ecology evolution etc

Parallel evolution provides evidence for evolution by natural selection and can cause repeated divergence at specific genes. The parallel evolution of phenotypic traits under similar environmental pressures was estimated to cover almost half of same genomic regions. However, the genomic … Continue reading →... Read more »

Soria-Carrasco, V., Gompert, Z., Comeault, A., Farkas, T., Parchman, T., Johnston, J., Buerkle, C., Feder, J., Bast, J., Schwander, T.... (2014) Stick Insect Genomes Reveal Natural Selection's Role in Parallel Speciation. Science, 344(6185), 738-742. DOI: 10.1126/science.1252136  

  • January 18, 2015
  • 12:30 PM
  • 150 views

The genetics of Mexico recapitulates Native American substructure and affects biomedical traits.

by Marianna Spatola in genome ecology evolution etc

All figures are reproduced from the original paper (Moreno Estrada et al. Science 2014) Summary and personal comments This paper is about genetic diversity among Native Mexico populations Mexico is an interesting region/subject to study human genetic diversity since it … Continue reading →... Read more »

Moreno-Estrada, A., Gignoux, C., Fernandez-Lopez, J., Zakharia, F., Sikora, M., Contreras, A., Acuna-Alonzo, V., Sandoval, K., Eng, C., Romero-Hidalgo, S.... (2014) The genetics of Mexico recapitulates Native American substructure and affects biomedical traits. Science, 344(6189), 1280-1285. DOI: 10.1126/science.1251688  

  • January 3, 2015
  • 07:16 PM
  • 199 views

The genetics of Mexico recapitulates Native American substructure and affects biomedical traits

by Esra Durmaz in genome ecology evolution etc

Mexico, hosted many cultures such as the Olmec, the Toltec, the Maya and the Aztec, conquered and colonized by the Spanish Empire in 1521. The country harbors a large source of pre-Columbian diversity and their genetic contributions to today’s population. … Continue reading →... Read more »

Moreno-Estrada, A., Gignoux, C., Fernandez-Lopez, J., Zakharia, F., Sikora, M., Contreras, A., Acuna-Alonzo, V., Sandoval, K., Eng, C., Romero-Hidalgo, S.... (2014) The genetics of Mexico recapitulates Native American substructure and affects biomedical traits. Science, 344(6189), 1280-1285. DOI: 10.1126/science.1251688  

  • December 15, 2014
  • 04:11 AM
  • 186 views

Electrogenic fish – what’s in charge of the charge?

by Kathrin Garschall in genome ecology evolution etc

Electric organs – organs that are capable of creating and discharging electricity – have evolved independently in at least six different lineages of fish (Torpediniformes, Rajiformes, Mormyroidea, Euteleostei, Siluriformes, Gymnotiformes) and play an important role in communication, navigation, defense and … Continue reading →... Read more »

Gallant, J., Traeger, L., Volkening, J., Moffett, H., Chen, P., Novina, C., Phillips, G., Anand, R., Wells, G., Pinch, M.... (2014) Genomic basis for the convergent evolution of electric organs. Science, 344(6191), 1522-1525. DOI: 10.1126/science.1254432  

  • December 13, 2014
  • 09:56 AM
  • 223 views

Gibbon genome and the fast karyotype evolution of small apes

by Sandra Bosshard in genome ecology evolution etc

Gibbons (Hylobatidae) are small arboreal apes that form a key node in primate evolution. One of the most distinctive phenotype is their high genome plasticity involving large-scale chromosomal rearrangements and karyotype changes. The four gibbon genera (Nomascus, Hylobates, Hoolock, Symphalangus) … Continue reading →... Read more »

Carbone, L., Alan Harris, R., Gnerre, S., Veeramah, K., Lorente-Galdos, B., Huddleston, J., Meyer, T., Herrero, J., Roos, C., Aken, B.... (2014) Gibbon genome and the fast karyotype evolution of small apes. Nature, 513(7517), 195-201. DOI: 10.1038/nature13679  

  • December 10, 2014
  • 07:39 AM
  • 192 views

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  

  • November 30, 2014
  • 03:16 PM
  • 208 views

Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears

by Olesya Pavlova in genome ecology evolution etc

The polar bear (Ursus maritimus) is a carnivorous species which is closely related to the brown bear (Ursus arctos) and is adapted to the severe living conditions of the High Arctic due to the great physiological changes happened during evolutionary … Continue reading →... Read more »

Liu, S., Lorenzen, E., Fumagalli, M., Li, B., Harris, K., Xiong, Z., Zhou, L., Korneliussen, T., Somel, M., Babbitt, C.... (2014) Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears. Cell, 157(4), 785-794. DOI: 10.1016/j.cell.2014.03.054  

  • November 28, 2014
  • 10:54 AM
  • 255 views

Ancient human genomes suggest three ancestral populations for present-day Europeans

by Mila Pajkovic in genome ecology evolution etc

Introduction & Methods The demographic history of the human species has always fascinated us. It is known that the ancestral human lineage appeared in East Africa, and that it subsequently migrated out of Africa towards Eurasia, separating into distinct lineages … Continue reading →... Read more »

Lazaridis, I., Patterson, N., Mittnik, A., Renaud, G., Mallick, S., Kirsanow, K., Sudma..lsate, D., Francken, M., Guinet, J., Wahl, J.... (2014) Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature, 513(7518), 409-413. DOI: 10.1038/nature13673  

  • November 9, 2014
  • 07:39 AM
  • 193 views

Comparative analysis of regulatory information and circuits across distant species

by Franziska Gruhl in genome ecology evolution etc

Development and homeostasis of all organisms is tightly controlled by transcription regulatory factors that are often highly conserved across deep phylogenies. However, it is unclear to what extend the basic components of these networks (e.g. network motifs and structure, binding … Continue reading →... Read more »

Boyle, A., Araya, C., Brdlik, C., Cayting, P., Cheng, C., Cheng, Y., Gardner, K., Hillier, L., Janette, J., Jiang, L.... (2014) Comparative analysis of regulatory information and circuits across distant species. Nature, 512(7515), 453-456. DOI: 10.1038/nature13668  

  • June 25, 2014
  • 08:56 AM
  • 316 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
  • 225 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
  • 388 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
  • 347 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
  • 317 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
  • 292 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
  • 345 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
  • 490 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
  • 549 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
  • 318 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
  • 384 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 »

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