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 plants by co-option of exapted ancestral enzymes. PNAS 113: 10613–10618

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 with bonobos. Science 354: 477-481

Roux et al 2016 Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence. PLoS Biol 14: e2000234

Series 1: human genome evolution

1. Sulem et al 2015 Identification of a large set of rare complete human knockouts.     Nature Genetics 47: 448–452
2. Hehn et al 2016 Distance from sub-Saharan Africa predicts mutational load in diverse human genomes. PNAS 113: E440-E449
3. Lek et al 2016 Analysis of protein-coding genetic variation in 60,706 humans. Nature 536: 285–291

Series 2: moth coloration

4. van’t Hof 2016 The industrial melanism mutation in British peppered moths is a transposable element. Nature 534: 102–105
5. 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

6. Braasch et al 2016 The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature Genetics 48: 427–437
7. Lien et al 2016 The Atlantic salmon genome provides insights into rediploidization. Nature 533: 200–205
8. Lan and Pritchard 2016 Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals. Science 352: 1009-1013

Series 1 (see also discussion on Razib Khan’s blog):

1. Moorjani et al 2013 Genetic Evidence for Recent Population Mixture in India AJHG 93,: 422–438
2. 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
3. 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):

4. Ku?pper et al 2016 A supergene determines highly divergent male reproductive morphs in the ruff Nature Genetics 48: 79–83
5. 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):

6. Pipoly et al 2015 The genetic sex-determination system predicts adult sex ratios in tetrapods Nature 527: 91–94
7. Barson et al 2015 Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon Nature 528: 405–408
8. Sulem et al 2015 Identification of a large set of rare complete human knockouts Nature Genetics 47: 448–452

1. Zhan et al 2014 The genetics of monarch butterfly migration and warning colouration Nature 514: 317–321
2. Foote et al 2015 Convergent evolution of the genomes of marine mammals Nature Genetics doi:10.1038/ng.3198
3. Artieri and Fraser 2014 Evolution at two levels of gene expression in yeast Genome Res 24: 411-421
4. Gurdasani et al 2015 The African Genome Variation Project shapes medical genetics in Africa Nature 517: 327–332
5. Brawnd et al 2014 The genomic substrate for adaptive radiation in African cichlid fish Nature 513: 375–381
6. Arbeithuber et al 2015 Crossovers are associated with mutation and biased gene conversion at recombination hotspots PNAS 112: 2109–2114
7. Poelstra et al 2014 The genomic landscape underlying phenotypic integrity in the face of gene flow in crows Science 344: 1410-1414
8. 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.

1. Lamichhaney et al 2015 Evolution of Darwin’s finches and their beaks revealed by genome sequencing Nature 518: 371–375
2. Poelstra et al 2014 The genomic landscape underlying phenotypic integrity in the face of gene flow in crows Science 344: 1410-1414
3. Zhan et al 2013 Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle Nature Genetics 45: 563–566
4. Foote et al 2015 Convergent evolution of the genomes of marine mammals Nature Genetics doi:10.1038/ng.3198
5. Arbeithuber et al 2015 Crossovers are associated with mutation and biased gene conversion at recombination hotspots PNAS 112: 2109–2114
6. Zhan et al 2014 The genetics of monarch butterfly migration and warning colouration Nature 514: 317–321
7. Villar et al 2015 Enhancer Evolution across 20 Mammalian Species Cell 160: 554–566
8. Artieri and Fraser 2014 Evolution at two levels of gene expression in yeast Genome Res 24: 411-421
9. Brawnd et al 2014 The genomic substrate for adaptive radiation in African cichlid fish Nature 513: 375–381
10. Gurdasani et al 2015 The African Genome Variation Project shapes medical genetics in Africa Nature 517: 327–332

There are 10, only 8 must remain…

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.

Feb 21: Parker et al. 2013 Genome-wide signatures of convergent evolution in echolocating mammals

Feb 28: Freedman et al 2014 Genome Sequencing Highlights the Dynamic Early History of Dogs

Mar 14: Amborella Genome Project 2013 The Amborella Genome and the Evolution of Flowering Plants

Mar 21: Prado-Martinez et al. 2013 Great ape genetic diversity and population history

Mar 28: Long et al. 2013 Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden

May 2: Linnen et al. 2013 Adaptive Evolution of Multiple Traits Through Multiple Mutations at a Single Gene

May 9: Schmizt et al. 2013 Patterns of population epigenomic diversity

May 16: Corbett-Detig et al. 2013 Genetic incompatibilities are widespread within species

(correction: exchange of dates Prado-Martinez / Corbett-Detig)

Here is the list of suggested papers, in no special order:

1. Freedman et al 2014 Genome Sequencing Highlights the Dynamic Early History of Dogs
2. Amborella Genome Project 2013 The Amborella Genome and the Evolution of Flowering Plants
3. Corbett-Detig et al. 2013 Genetic incompatibilities are widespread within species
4. Moreno-Estrada et al. 2013 Reconstructing the Population Genetic History of the Caribbean
5. Parker et al. 2013 Genome-wide signatures of convergent evolution in echolocating mammals
6. Prado-Martinez et al. 2013 Great ape genetic diversity and population history
7. Orlando et al. 2013 Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse
8. Long et al. 2013 Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden
9. McTavish et al. 2013 New World cattle show ancestry from multiple independent domestication events
10. Linnen et al. 2013 Adaptive Evolution of Multiple Traits Through Multiple Mutations at a Single Gene
11. Schmizt et al. 2013 Patterns of population epigenomic diversity
12. Lappalainen et al. 2013 Transcriptome and genome sequencing uncovers functional variation in humans

• March 8: Alkorta-Aranburu G, Beall CM, Witonsky DB, Gebremedhin A, Pritchard JK, et al. (2012) The Genetic Architecture of Adaptations to High Altitude in Ethiopia. PLoS Genet 8(12): e1003110. doi:10.1371/journal.pgen.1003110
• March 15: Schlebusch et al. (2012) Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History Science 338: 374-379
• March 22: Ellegren et al. (2012) The genomic landscape of species divergence in
  Ficedula flycatchers Nature 491: 756–760
• April 19: Staubach F, Lorenc A, Messer PW, Tang K, Petrov DA, et al. (2012) Genome Patterns of  Selection and Introgression of Haplotypes in Natural Populations of the House Mouse (Mus musculus). PLoS Genet 8(8): e1002891
• April 26: Schloissnig et al. (2013) Genomic variation landscape of the human gut microbiome Nature 493: 45–50
• Mai 3: Blount et al. (2012) Genomic analysis of a key innovation in an experimental Escherichia coli population Nature 489: 513–518
• Mai 17: Groenen et al. (2012) Analyses of pig genomes provide insight into porcine demography and evolution Nature 491: 393–398
• Mai 24: Lachance et al. (2012) Evolutionary History and Adaptation from High-Coverage Whole-Genome Sequences of Diverse African Hunter-Gatherers Cell 150: 457–469