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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  • May 27, 2015
  • 08:47 PM
  • 164 views

Evolution of Darwin’s finches and their beaks revealed by genome sequencing

by Andrea Vucicevic in genome ecology evolution etc

Introduction Darwin’s finches from Galapagos and Cocos Island are classic example of young adaptive radiation, entirely intact because none of the species having become extinct as a result of human activity. They have diversified in beak sizes and shapes, feeding … Continue reading →... Read more »

Lamichhaney, S., Berglund, J., Almén, M., Maqbool, K., Grabherr, M., Martinez-Barrio, A., Promerová, M., Rubin, C., Wang, C., Zamani, N.... (2015) Evolution of Darwin’s finches and their beaks revealed by genome sequencing. Nature, 518(7539), 371-375. DOI: 10.1038/nature14181  

  • May 9, 2015
  • 06:34 AM
  • 137 views

The genomic substrate for adaptive radiation in African cichlid fish

by Olesya Pavlova in genome ecology evolution etc

Evolutionary diversification among species attracts the attention of scientist during long time. Adaptive radiation underlies evolution and comprises the rapid adaptation of a single lineage to its changed environment which provides new resources and opens new environmental niches. Among all … Continue reading →... Read more »

Brawand, D., Wagner, C., Li, Y., Malinsky, M., Keller, I., Fan, S., Simakov, O., Ng, A., Lim, Z., Bezault, E.... (2014) The genomic substrate for adaptive radiation in African cichlid fish. Nature, 513(7518), 375-381. DOI: 10.1038/nature13726  

  • May 8, 2015
  • 08:12 AM
  • 135 views

The genomic landscape underlying phenotypic integrity in the face of gene flow in crows

by Thomas Martignier in genome ecology evolution etc

The role of interspecific gene flow in species diversification has long been debated and is increasingly appreciated. However, the effect of gene introgression on phenotypic divergences and genome heterogeneity remain unclear in case of early speciation. To investigate these questions … Continue reading →... Read more »

Poelstra, J., Vijay, N., Bossu, C., Lantz, H., Ryll, B., Muller, I., Baglione, V., Unneberg, P., Wikelski, M., Grabherr, M.... (2014) The genomic landscape underlying phenotypic integrity in the face of gene flow in crows. Science, 344(6190), 1410-1414. DOI: 10.1126/science.1253226  

  • May 7, 2015
  • 12:43 PM
  • 172 views

Crossovers are associated with mutation and biased gene conversion at recombination hotspots

by Andrea Vucicevic in genome ecology evolution etc

Meiosis is an important biological process by which combination of various types of the genes called alleles, are segregated and packed in each germ cell waiting to be transferred and expressed in descendants. This combinations of alleles are products of … Continue reading →... Read more »

Arbeithuber, B., Betancourt, A., Ebner, T., & Tiemann-Boege, I. (2015) Crossovers are associated with mutation and biased gene conversion at recombination hotspots. Proceedings of the National Academy of Sciences, 201416622. DOI: 10.1073/pnas.1416622112  

  • April 7, 2015
  • 11:42 AM
  • 46 views

Evolution at two levels of gene expression in yeast

by Jialin Liu in genome ecology evolution etc

Protein abundances mainly determined by the balance of transcriptional and translational regulation. Because of the limited technology for the translational research, however, gene expression evolution was based almost entirely on studies of transcriptional regulation. With the quickly development of ribosome profiling–isolating and … Continue reading →... Read more »

  • March 23, 2015
  • 11:22 AM
  • 203 views

Convergent evolution of the genomes of marine mammals

by Amaury Avril in genome ecology evolution etc

Convergent evolution is defined by the independent evolution of similar traits in different lineages, in order to adapt to similar environmental conditions. Examples of this phenomenon include adaptations to altitude in humans, independent evolution of flight in birds and bats … Continue reading →... Read more »

Foote, A., Liu, Y., Thomas, G., Vinař, T., Alföldi, J., Deng, J., Dugan, S., van Elk, C., Hunter, M., Joshi, V.... (2015) Convergent evolution of the genomes of marine mammals. Nature Genetics, 47(3), 272-275. DOI: 10.1038/ng.3198  

  • March 22, 2015
  • 02:30 PM
  • 176 views

The African Genome Variation Project shapes medical genetics in Africa.

by Andrea Komljenovic in genome ecology evolution etc

  Despite being the world’s most genetically diverse continent, only a handful of studies attempted to understand the genetic risks for diseases of the African populations. This study shines light not only on the genetic diversity to help learn more … Continue reading →... Read more »

Gurdasani, D., Carstensen, T., Tekola-Ayele, F., Pagani, L., Tachmazidou, I., Hatzikotoulas, K., Karthikeyan, S., Iles, L., Pollard, M., Choudhury, A.... (2014) The African Genome Variation Project shapes medical genetics in Africa. Nature, 517(7534), 327-332. DOI: 10.1038/nature13997  

  • March 8, 2015
  • 07:20 AM
  • 164 views

The genetics of monarch butterfly migration and warning colouration

by Lucas Marques Da Cunha in genome ecology evolution etc

The monarch butterfly (Danaus plexippus) has a large distribution worldwide. It occurs in North, Central, and South America, Caribbean, and it has recently dispersed to other locations, such as Oceania and Africa. Two traits of this butterfly are incredibly intriguing: … Continue reading →... Read more »

Zhan, S., Zhang, W., Niitepõld, K., Hsu, J., Haeger, J., Zalucki, M., Altizer, S., de Roode, J., Reppert, S., & Kronforst, M. (2014) The genetics of monarch butterfly migration and warning colouration. Nature, 514(7522), 317-321. DOI: 10.1038/nature13812  

  • February 15, 2015
  • 12:44 PM
  • 202 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
  • 259 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
  • 316 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
  • 279 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
  • 328 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
  • 312 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
  • 299 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
  • 366 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
  • 275 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
  • 388 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
  • 292 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
  • 481 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  

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