Paper List

This Autumn, we will discuss two series of papers: Series 1: Human demography News & Views: Tucci & Akey 2016 Population genetics: A map of human wanderlust.  Nature 538: 179–180 6 Oct 2017: Pagani et al 2016 Genomic analyses inform on migration events during the peopling of Eurasia. Nature 538: 238–242 2 7 Oct 2017: Mallick et al. 2016 The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature 538: 201–206 3 Nov 2017: Malaspinas et al 2016 A genomic history of Aboriginal Australia. Nature 538: 207–214 10 Nov 2017: Skoglund et al 2017 Reconstructing Prehistoric African Population Structure. Cell 171: 59–71.e21 Series 2: Convergent evolution 17 Nov 2017: Levin & Mishmar 2017 The genomic landscape of evolutionary convergence in mammals, birds and reptiles. Nature Ecology & Evolution 1: 0041 24 Nov 2017: Burga et al 2017 A genetic signature of the evolution of loss of flight in the Galapagos cormorant. Science 356: eaal3345 (also see preprint comment by Berger and Bejerano) 8 Dec 2017: Reid et al 2017 The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish. Science 354: 1305-1308 15 Dec 2017: Huang et al 2016 Convergent evolution of caffeine in …

Edit: this Spring’s series has been canceled, but I’m leaving the article list up for the record. For this Spring, the students will need to chose 3 of these 4 series of articles to discuss: Evo-Devo genomics: Lin et al 2016 The seahorse genome and the evolution of its specialized morphology. Nature 540: 395–399 Van Belleghem et al 2017 Complex modular architecture around a simple toolkit of wing pattern genes. Nature Ecology & Evolution 1: 0052 Human populations: Pagani et al 2016 Genomic analyses inform on migration events during the peopling of Eurasia. Nature 538: 238–242 Mallick et al. 2016 The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature 538: 201–206 Malaspinas et al 2016 A genomic history of Aboriginal Australia. Nature 538: 207–214 Convergent evolution: Yeaman et al 2016 Convergent local adaptation to climate in distantly related conifers. Science 353: 1431-1433 Fukushima et al 2016 Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory. Nature Ecology & Evolution 1: 0059 Reid et al 2017 The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish. Science 354: 1305-1308 Speciation: de Manuel et al 2016 Chimpanzee genomic diversity reveals ancient admixture …

This Autumn, we will continue to discuss papers in related series: Series 1: human genome evolution Sulem et al 2015 Identification of a large set of rare complete human knockouts.     Nature Genetics 47: 448–452 Hehn et al 2016 Distance from sub-Saharan Africa predicts mutational load in diverse human genomes. PNAS 113: E440-E449 Lek et al 2016 Analysis of protein-coding genetic variation in 60,706 humans. Nature 536: 285–291 Series 2: moth coloration van’t Hof 2016 The industrial melanism mutation in British peppered moths is a transposable element. Nature 534: 102–105 Nadeau et al 2016 The gene cortex controls mimicry and crypsis in butterflies and moths. Nature 534: 106–110 Series 3: gene and genome duplication Braasch et al 2016 The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature Genetics 48: 427–437 Lien et al 2016 The Atlantic salmon genome provides insights into rediploidization. Nature 533: 200–205 Lan and Pritchard 2016 Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals. Science 352: 1009-1013  

This Spring, we have decided to have a few series of papers on related topics, to discuss one per week: Series 1 (see also discussion on Razib Khan’s blog): Moorjani et al 2013 Genetic Evidence for Recent Population Mixture in India AJHG 93,: 422–438 Basu et al 2016 Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure PNAS online before print van Dorp et al 2016 Evidence for a Common Origin of Blacksmiths and Cultivators in the Ethiopian Ari within the Last 4500 Years: Lessons for Clustering-Based Inference PLOS Genetics 11(8): e1005397 Series 2 (see also perspective in Science Magazine): Ku?pper et al 2016 A supergene determines highly divergent male reproductive morphs in the ruff Nature Genetics 48: 79–83 Lamichhaney et al 2016 Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax) Nature Genetics 48: 84–88 The following form less of a series (although two are sex-related): Pipoly et al 2015 The genetic sex-determination system predicts adult sex ratios in tetrapods Nature 527: 91–94 Barson et al 2015 Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon Nature 528: 405–408 Sulem et …

So here are the papers chosen for our tutorial this Spring (from the list here), in the ordre in wich they will be discussed: Zhan et al 2014 The genetics of monarch butterfly migration and warning colouration Nature 514: 317–321 Foote et al 2015 Convergent evolution of the genomes of marine mammals Nature Genetics doi:10.1038/ng.3198 Artieri and Fraser 2014 Evolution at two levels of gene expression in yeast Genome Res 24: 411-421 Gurdasani et al 2015 The African Genome Variation Project shapes medical genetics in Africa Nature 517: 327–332 Brawnd et al 2014 The genomic substrate for adaptive radiation in African cichlid fish Nature 513: 375–381 Arbeithuber et al 2015 Crossovers are associated with mutation and biased gene conversion at recombination hotspots PNAS 112: 2109–2114 Poelstra et al 2014 The genomic landscape underlying phenotypic integrity in the face of gene flow in crows Science 344: 1410-1414 Lamichhaney et al 2015 Evolution of Darwin’s finches and their beaks revealed by genome sequencing Nature 518: 371–375 An exiting semester in perspective, full of genomes, ecology and evolution.

Like last Spring, we are offering the students following our tutorial Genomes, Ecology, Evolution, etc. the opportunity to chose the 8 papers which we will discuss. Here is the list of papers which we propose: Lamichhaney et al 2015 Evolution of Darwin’s finches and their beaks revealed by genome sequencing Nature 518: 371–375 Poelstra et al 2014 The genomic landscape underlying phenotypic integrity in the face of gene flow in crows Science 344: 1410-1414 Zhan et al 2013 Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle Nature Genetics 45: 563–566 Foote et al 2015 Convergent evolution of the genomes of marine mammals Nature Genetics doi:10.1038/ng.3198 Arbeithuber et al 2015 Crossovers are associated with mutation and biased gene conversion at recombination hotspots PNAS 112: 2109–2114 Zhan et al 2014 The genetics of monarch butterfly migration and warning colouration Nature 514: 317–321 Villar et al 2015 Enhancer Evolution across 20 Mammalian Species Cell 160: 554–566 Artieri and Fraser 2014 Evolution at two levels of gene expression in yeast Genome Res 24: 411-421 Brawnd et al 2014 The genomic substrate for adaptive radiation in African cichlid fish Nature 513: 375–381 Gurdasani et al 2015 The African Genome …

For this new session of our tutorial, these are the papers that we will discuss: Boyle et al 2014 Comparative analysis of regulatory information and circuits across distant species. Nature 512, 453–456 Liu et al 2014 Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears. Cell 157, 785–794 Lazaridis 2014 Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513, 409–413 Wang et al 2014 The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nature Genetics 46, 982–988 Gallant et al 2014 Genomic basis for the convergent evolution of electric organs. Science 344, 1522-1525 Carbone et al. 2014 Gibbon genome and the fast karyotype evolution of small apes.     Nature 513, 195–201 Moreno-Estrada et al. 2014 The genetics of Mexico recapitulates Native American substructure and affects biomedical traits. Science 344, 1280-1285 Soria-Carrasco et al. 2014 Stick Insect Genomes Reveal Natural Selection’s Role in Parallel Speciation. Science 344, 738-742 Dates: 31.10, 7.11, 14.11, 21.11, 28.11, 5.12, 12.12, 19.12.