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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  • December 14, 2016
  • 07:43 AM
  • 196 views

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

by Christian de Guttry in genome ecology evolution etc

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons About 450 mya bony vertebrates radiated into Lobe-finned fish, from which tetrapods appeared later, and Ray-finned fish, which include Teleost (Fig.1). Nowadays they make up to 96 percent of … Continue reading →... Read more »

Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J.... (2016) The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature genetics, 48(4), 427-37. PMID: 26950095  

  • December 8, 2016
  • 03:14 PM
  • 110 views

ExAC presents a catalogue of human protein-coding genetic variation

by Kamil S. Jaron in genome ecology evolution etc

Exploration of variability of human genomes represents a key step in the holy grail of human genetics – to link genotypes with phenotypes, it also provides insights to human evolution and history. For this purpose Exome Aggregation Consortium (ExAC) have … Continue reading →... Read more »

Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB.... (2016) Analysis of protein-coding genetic variation in 60,706 humans. Nature, 536(7616), 285-91. PMID: 27535533  

  • May 16, 2016
  • 03:22 PM
  • 29 views

Identification of a large set of rare complete human knockouts

by Anna Marcionetti in genome ecology evolution etc

High throughput genotyping and sequencing has led to the discovery of numerous sequence variants associated to human traits and diseases. An important type of variants involved are Loss of Function (LoF) mutations (frameshift indels, stop-gain and essential sites variants), which … Continue reading →... Read more »

Sulem, P., Helgason, H., Oddson, A., Stefansson, H., Gudjonsson, S., Zink, F., Hjartarson, E., Sigurdsson, G., Jonasdottir, A., Jonasdottir, A.... (2015) Identification of a large set of rare complete human knockouts. Nature Genetics, 47(5), 448-452. DOI: 10.1038/ng.3243  

  • May 13, 2016
  • 04:35 AM
  • 595 views

Sex-dependent dominance of a large effects locus in Atlantic salmon

by Casper van der Kooi in genome ecology evolution etc

Many male and female-specific traits share a common genetic basis. Selection on these traits may, however, differ between the sexes, leading to sexual conflict. Sex-dependent dominance, where the dominant allele in one sex is recessive in the other, is expected … Continue reading →... Read more »

Barson, N., Aykanat, T., Hindar, K., Baranski, M., Bolstad, G., Fiske, P., Jacq, C., Jensen, A., Johnston, S., Karlsson, S.... (2015) Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon. Nature, 528(7582), 405-408. DOI: 10.1038/nature16062  

  • May 6, 2016
  • 12:52 PM
  • 311 views

Supergenes and social organization in a bird species

by Cindy Dupuis in genome ecology evolution etc

      Cindy Dupuis, Xinji Li, Casper van der Kooi   The development of new molecular mechanisms and next generation sequencing techniques have advanced our knowledge on the genetic basis underlying phenotypic polymorphism. Over the coarse of recent years, … Continue reading →... Read more »

Küpper C, Stocks M, Risse JE, Dos Remedios N, Farrell LL, McRae SB, Morgan TC, Karlionova N, Pinchuk P, Verkuil YI.... (2016) A supergene determines highly divergent male reproductive morphs in the ruff. Nature genetics, 48(1), 79-83. PMID: 26569125  

  • May 27, 2015
  • 08:47 PM
  • 705 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
  • 517 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
  • 619 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
  • 606 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
  • 440 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
  • 706 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
  • 704 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
  • 600 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
  • 517 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
  • 577 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
  • 638 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
  • 583 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
  • 643 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
  • 718 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
  • 592 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  

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