60 posts · 42,462 views
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 13, 2016
- 04:35 AM
- 380 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
- 188 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
- 586 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
- 436 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
- 520 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
- 516 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
- 342 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 »
Artieri, C., & Fraser, H. (2013) Evolution at two levels of gene expression in yeast. Genome Research, 24(3), 411-421. DOI: 10.1101/gr.165522.113
- March 23, 2015
- 11:22 AM
- 600 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
- 606 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
- 505 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
- 457 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
- 526 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
- 572 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
- 511 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
- 582 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
- 619 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
- 530 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
- 631 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
- 498 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
- 655 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
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