http://morrell-lab.cfans.umn.edu/pastmeetings/pastmeetings.htm Past Lab Meetings
Lab Meetings - Journal Club - 2009 - 2016

This is an archive of our lab meeting schedule.

Page Updated: 08 June 2016

06/06/2016
Kono et al. Genomic prediction in barley. Manuscript.
Discussion Leader:
Tom Kono

05/31/2016 - Note Special Date
Cooke TF, Yee M-C, Muzzio M, Sockell A, Bell R et al. (2016) GBStools: A statistical method for estimating allelic dropout in reduced representation sequencing data. PLoS Genet 12: e1005631.
Discussion Leader:
Paul Hoffman

05/23/2016
Brandvain Y, Wright SI (2016) The limits of natural selection in a nonequilibrium world. Trends Genet 32: 201-210.
Discussion Leader:
Skylar Wyant

05/16/2016
Bryan J, Cranston K, Kitzes J, Nederbragt L, Teal T et al. (2016) Good enough practices for scientific computing. Available: http://swcarpentry.github.io/good-enough-practices-in-scientific-computing/ via the Internet.
Discussion Leader: Felipe Reyes

05/09/2016
Rogers RL, Cridland JM, Shao L, Hu TT, Andolfatto P et al. (2014) Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans. Mol Biol Evol 31: 1750-1766.
Discussion Leader: Shawn Goggins

05/02/2016
Campos JL, Charlesworth B, Haddrill PR (2012) Molecular evolution in nonrecombining regions of the Drosophila melanogaster genome. Genome Biol Evol 4: 278-288.
Discussion Leader:
Li Lei

04/25/2016
McMullen MD, Kresovich S, Villeda HS, Bradbury P, Li H et al. (2009) Genetic properties of the maize nested association mapping population. Science 325: 737-740.
Discussion Leader: Alex Ollhoff


04/18/2016
Xu S, Jia Z (2007) Genomewide analysis of epistatic effects for quantitative traits in barley. Genetics 175: 1955-1963.
Discussion Leader: Alex Susko

04/11/2016
Chamala S, Feng G, Chavarro C, Barbazuk WB (2015) Genome-wide identification of evolutionarily conserved alternative splicing events in flowering plants. Front Bioeng Biotechnol 3: 33.
Discussion Leader:
Chaochih Liu


04/04/2016
Tuttle EM, Bergland AO, Korody ML, Brewer MS, Newhouse DJ et al. (2016) Divergence and functional degradation of a sex chromosome-like supergene. Curr Biol 26: 344-350.
Commentary: Campagna L (2016) Supergenes: The genomic architecture of a bird with four sexes. Curr Biol 26: R105-7.
Discussion Leader: Tom Kono

03/28/2016
Rodgers-Melnick E, Bradbury PJ, Elshire RJ, Glaubitz JC, Acharya CB et al. (2015) Recombination in diverse maize is stable, predictable, and associated with genetic load. Proc Natl Acad Sci USA
Discussion Leader: Paul Hoffman

03/21/2016
Takuno S, Ran J-H, Gaut BS (2016) Evolutionary patterns of genic DNA methylation vary across land plants. Nature Plants 2: 15222.
Commentary:
Schneeberger K (2016) Plant genic methylation: Conserved for 400 million years. Nature Plants 2: 16003.
Discussion Leader: Shawn Goggins

03/14/2016
Spring Break

03/07/2016
Slotte T, Hazzouri KM, Ågren JA, Koenig D, Maumus F et al. (2013) The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat Genet 45: 831-835.
Discussion Leader:
Ana Poets

02/29/2016
Morrell PL, Toleno DM, Lundy KE, Clegg MT (2006) Estimating the contribution of mutation, recombination and gene conversion in the generation of haplotypic diversity. Genetics 173: 1705-1723.
Discussion Leader:
Li Lei

02/22/2016
Clegg MT, Allard RW, Kahler AL (1972) Is the gene the unit of selection? Evidence from two experimental plant populations. Proc Natl Acad Sci USA 69: 2474-2478.
Discussion Leader:
Skylar Wyant

02/15/2016
Bolon YT, Stec AO, Michno JM, Roessler J, Bhaskar PB et al. (2014) Genome resilience and prevalence of segmental duplications following fast neutron irradiation of soybean. Genetics 198: 967-981.
Discussion Leader:
Chaochih Liu

02/08/2016
Hudson RR (2001) Two-locus sampling distributions and their application. Genetics 159: 1805-1817.
Discussion Leader:
Tom Kono

02/01/2016
Yang J, Lee SH, Goddard ME, Visscher PM (2011) GCTA: a tool for genome-wide complex trait analysis. Am J Hum Genet 88: 76-82.
Discussion Leader: Jeff Neyhart
Optional:
Yang J, Lee SH, Goddard ME, Visscher PM (2013) Genome-wide complex trait analysis (GCTA): methods, data analyses, and interpretations. Methods Mol Biol 1019: 215-236.

01/25/2016
Weiblen GD, Wenger JP, Craft KJ, ElSohly MA, Mehmedic Z, Treiber EL, Marks MD 2015. Gene duplication and divergence affecting drug content in Cannabis sativa. New Phytol 208: 1241–1250.
Discussion Leader: Colin Pierce


01/22/2016 - 2:oo pm - Note Special Date & Time
Henn BM, Botigué LR, Peischl S, Dupanloup I, Lipatov M et al. (2015) Distance from sub-Saharan Africa predicts mutational load in diverse human genomes. Proc Natl Acad Sci USA
Discussion Leader:
Li Lei

01/12/2016
Plant & Animal Genome Meeting

01/05/2016
Lande R, Schemske DW 1985. The evolution of self-fertilization and inbreeding depression in plants. I. Genetic models. Evolution 39: 24–40.
Discussion Leader: Alex Susko


12/29/2015
Christmas Holiday

12/22/2015
Christmas Holiday

12/15/2015
Pourkheirandish M, Hensel G, Kilian B, Senthil N, Chen G, Sameri M, Azhaguvel P, Sakuma S, Dhanagond S, Sharma R et al. 2015. Evolution of the grain dispersal system in barley. Cell 162: 527–539.
Discussion Leader:
Paul Hoffman

12/10/2015 2:00 pm - Note Special Date & Time
Lamichhaney S, Berglund J, Almén MS, Maqbool K, Grabherr M, Martinez-Barrio A, Promerová M, Rubin CJ, Wang C, Zamani N et al. 2015. Evolution of Darwin’s finches and their beaks revealed by genome sequencing. Nature 518: 371–375.
Discussion Leader:
Felipe Reyes

12/01/2015
Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis - a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 88: 9828-9832.
Discussion Leader: Benjamin Campbell


11/24/2015
Tsuda K, Sato M, Stoddard T, Glazebrook J, Katagiri F (2009) Network properties of robust immunity in plants. PLoS Genet 5: e1000772.
Discussion Leader:
Li Lei

11/17/2015
Kessner D, Novembre J 2015. Power analysis of artificial selection experiments using efficient whole genome simulation of quantitative traits. Genetics 199: 991–1005.
Discussion Leader:
Ana Poets

11/10/2015
Li Lei’s terrific new Arabidopsis manuscript! (We will email a copy to meeting participants.)
Discussion Leader: Tom Kono

11/03/2015
Renaut S, Rieseberg LH 2015. The accumulation of deleterious mutations as a consequence of domestication and improvement in sunflowers and other compositae crops. Mol Biol Evol 32: 2273–2283.
Discussion Leader:
Shawn Goggins

10/27/2015
Branca A, Paape TD, Zhou P, Briskine R, Farmer AD, Mudge J, Bharti AK, Woodward JE, May GD, Gentzbittel L et al. 2011. Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula. Proc Natl Acad Sci U S A 108: E864–70.
Discussion Leader:
Jeff Neyhart

10/20/2015
Reading the Classics
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
Discussion Leader: Alex Susko & Fumi Katagiri

10/13/2015
Poets AM, Mohammadi M, Seth K, Wang H, Kono TJY et al. (2015) The effects of both recent and long-term selection and genetic drift are readily evident in North American barley breeding populations. biorxiv
Discussion Leader:
Chaochih Liu

10/08/2015 - 1:00 pm - Note Special Date & Time
Joint Meeting Brandvain, Goldberg, McGaugh, Moeller, Morrell, & Tiffin Lab Groups
Leffler EM, Gao Z, Pfeifer S, Segurel L, Auton A, Venn O, Bowden R, Bontrop R, Wall JD, Sella G et al. 2013. Multiple instances of ancient balancing selection shared between humans and chimpanzees. Science 339: 1578–1582.
Discussion Leader: Lex Flagel

10/06/2015
Short presentations on current projects.
Discussion Leaders: Lab Members


09/29/2015
Reading the Classics
Kimura M, Crow JF 1964. The number of alleles that can be maintained in a finite population. Genetics 49: 725–738.
Discussion Leader: Peter Morrell

09/22/2015
Huang BE, Verbyla KL, Verbyla AP, Raghavan C, Singh VK et al. (2015) MAGIC populations in crops: current status and future prospects. Theor Appl Genet 128: 999-1017.
Discussion Leader: Benjamin Campbell

09/15/2015
Makarevitch I, Waters AJ, West PT, Stitzer M, Hirsch CN et al. (2015) Transposable elements contribute to activation of maize genes in response to abiotic stress. PLoS Genet 11: e1004915.
Discussion Leader:
Tom Kono

09/08/2015
Bradburd G, Ralph PL, Coop G 2015. A spatial framework for understanding population structure and admixture. BioRxiv
Discussion Leader:
Shawn Goggins

09/02/2015
Leinonen T, McCairns RJ, O’Hara RB, Merilä J (2013) Q(ST)-F(ST) comparisons: evolutionary and ecological insights from genomic heterogeneity. Nat Rev Genet 14: 179-190.
Discussion Leader: Alex Susko


08/26/2015
Rasmussen MD, Hubisz MJ, Gronau I, Siepel A (2014) Genome-wide inference of ancestral recombination graphs. PLoS Genet 10: e1004342.
Discussion Leader:
Chaochih Liu & Yaniv Brandvain

08/19/2015
Gaut BS, Diez CM, Morrell PL (in review) Genomics and the contrasting dynamics of annual and perennial domestication.
Discussion Leader:
Paul Hoffman

08/12/2015
Assaf ZJ, Petrov DA, Blundell JR (2015) Obstruction of adaptation in diploids by recessive, strongly deleterious alleles. Proc Natl Acad Sci U S A 112: E2658-E2666.
Discussion Leader:
Tom Kono

08/05/2015
O’Reilly PF, Birney E, Balding DJ (2008) Confounding between recombination and selection, and the Ped/Pop method for detecting selection. Genome Res 18: 1304-1313.
Discussion Leader: Peter Morrell

07/29/2015
Pfeifer B, Wittelsbürger U, Ramos-Onsins SE, Lercher MJ (2014) PopGenome: an efficient Swiss army knife for population genomic analyses in R. Mol Biol Evol 31: 1929-1936.
Discussion Leader: Fengli Fu

07/24/2015 - 1:30 pm - Note Special Date
Burke MK, Liti G, Long AD (2014) Standing genetic variation drives repeatable experimental evolution in outcrossing populations of Saccharomyces cerevisiae. Mol Biol Evol 31: 3228-3239.
Discussion Leader: Peter Morrell

07/15/2015
Summer Institute in Statistical Genetics

07/10/2015 - 1:30 pm - Note Special Date
Diez CM, Trujillo I, Martinez-Urdiroz N, Barranco D, Rallo L et al. (2015) Olive domestication and diversification in the Mediterranean Basin. New Phytol 206: 436-447.
Discussion Leader:
Paul Hoffman

07/01/2015
Beaumont MA, Balding DJ (2004) Identifying adaptive genetic divergence among populations from genome scans. Mol Ecol 13: 969-980.
Discussion Leader:
Tom Kono

06/24/2015 - 3:00 pm - Note Special Time
Anderson JE, Kantar MB, Kono TY, Fu F, Stec AO et al. (2014) A roadmap for functional structural variants in the soybean genome. G3 4: 1307-1318.
Discussion Leader: Jean-Michel Michno

06/17/2015
Pease JB, Hahn MW (2015) Detection and polarization of introgression in a five-taxon phylogeny. Syst Biol
Discussion Leader:
Chaochih Liu & Tom Kono

06/10/2015
Schubert M, Jonsson H, Chang D, Der Sarkissian C, Ermini L et al. (2014) Prehistoric genomes reveal the genetic foundation and cost of horse domestication. Proc Natl Acad Sci USA 111: E5661-E5669.
Discussion Leader: Justin Anderson


06/03/2015
Meirmans PG (2015) Seven common mistakes in population genetics and how to avoid them. Mol Ecol
Discussion Leader: Alex Susko


05/27/2015
Vann L, Kono T, Pyhajarvi T, Hufford MB, Ross-Ibarra J (2015) Natural variation in teosinte at the domestication locus teosinte branched1 (tb1). PeerJ 3: e900.
Discussion Leader: Austin Dobbels


05/20/2015
Tiffin P, Ross-Ibarra J (2014) Advances and limits of using population genetics to understand local adaptation. Trends Ecol Evol 29: 673-680.
Discussion Leader: Alex Susko

05/13/2015
Hellenthal G, Busby GB, Band G, Wilson JF, Capelli C et al. (2014) A genetic atlas of human admixture history. Science 343: 747-751.
Discussion Leader: Fengli Fu

05/06/2015
Jain M, Fiddes IT, Miga KH, Olsen HE, Paten B, Akeson M (2015) Improved data analysis for the MinION nanopore sequencer. Nat Methods 12: 351-356.
Discussion Leader: Diana Trujillo

04/29/2015
Poets AM, Fang Z, Clegg MT, Morrell PL (in review) Barley landraces are characterized by geographically heterogeneous genomic origins.
Discussion Leader:
Tom Kono

04/22/2015
Levins R (1966) The strategy of model building in population biology. Am Sci 54: 421-431.
Discussion Leader:
Mikey Kantar

04/15/2015
Voytas DF, Gao C (2014) Precision genome engineering and agriculture: opportunities and regulatory challenges. PLoS Biol 12: e1001877.
Discussion Leader: Justin Anderson

04/08/2015 - 4:00 pm - Note Special Time
Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM et al. (2015) Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 4: 7.
Discussion Leader:
Mikey Kantar

04/01/2015
Decaens T, Porco D, Rougerie R, Brown GG, James SW (2013) Potential of DNA barcoding for earthworm research in taxonomy and ecology. Appl Soil Ecol 65: 35-42.
Discussion Leader:
Kyungsoo Yoo

03/25/2015
Cheverud JM, Routman EJ (1995) Epistasis and its contribution to genetic variance components. Genetics 139: 1455-1461.
Discussion Leader: Alex Susko

03/18/2015
Spring Break

03/11/2015
Huynh LY, Maney DL, Thomas JW (2010) Contrasting population genetic patterns within the white-throated sparrow genome (Zonotrichia albicollis). BMC Genet 11: 96.
Discussion Leader:
Chaochih Liu

03/06/2015 - Note Special Date
Bhatia G, Patterson N, Sankararaman S, Price AL (2013) Estimating and interpreting FST: the impact of rare variants. Genome Res 23: 1514-1521.
Discussion Leader: Peter Morrell

02/25/2015
Gravel S (2014) When is selection effective? BioRxiv
Discussion Leader: Tom Kono

02/18/2015
Nordborg M, Tavaré S (2002) Linkage disequilibrium: what history has to tell us. Trends Genet 18: 83-90.
Discussion Leader: Ana Gonzales

02/11/2015
Bachtrog D, Mank JE, Peichel CL, Kirkpatrick M, Otto SP et al. (2014) Sex determination: why so many ways of doing it? PLoS Biol 12: e1001899.
Discussion Leader: Kiran Seth

02/02/2015
Fu W, Gittelman RM, Bamshad MJ, Akey JM (2014) Characteristics of neutral and deleterious protein-coding variation among individuals and populations.Am J Hum Genet 95: 421-436.
Discussion Leader: Justin Anderson

01/26/2015
Korneliussen T, Albrechtsen A, Nielsen R (2014) [ANGSD: Analysis of Next Generation Sequencing Data.] BMC Bioinformatics 15: 356.
Discussion Leaders: Tom Kono & Peter Morrell

01/20/2015 - Note Special Date
Berg JJ, Coop G (2014) A population genetic signal of polygenic adaptation. PLoS Genet 10: e1004412.
Discussion Leader: Kiran Seth

01/12/2015
International Plant and Animal Genome Meeting

01/05/2015
Davis JK, Mittel LB, Lowman JJ, Thomas PJ, Maney DL et al. (2011) Haplotype-based genomic sequencing of a chromosomal polymorphism in the white-throated sparrow (Zonotrichia albicollis). J Hered 102: 380-390.
Discussion Leader:
Weidong Wang

12/29/2013
Christmas Holiday

12/22/2013
Christmas Holiday

12/15/2014
Reading the Classics
Coyne JA, Orr HA (1989) Patterns of speciation in Drosophila. Evolution 43: 362-381.
Coyne JA, Orr HA (1997)
“Patterns of Speciation in Drosophila” Revisited. Evolution 51: 295-303.
Discussion Leader: Mikey Kantar

12/08/2014
Mangin B, Siberchicot A, Nicolas S, Doligez A, This P et al. (2012) Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness. Heredity (Edinb) 108: 285-291.
Lin CY, Xing G, Xing C (2012)
Measuring linkage disequilibrium by the partial correlation coefficient. Heredity (Edinb) 109: 401-402.
Discussion Leader:
Yaniv Brandvain

12/01/2014
Nicholson G, Smith AV, Jónsson F, Gústafsson Ó, Stefánsson K et al. (2002) Assessing population differentiation and isolation from single-nucleotide polymorphism data. J R Stat Soc Ser B Stat Methodol 64: 695-715.
Balding DJ, Carothers AD, Marchini JL, Cardon LR, Vetta A et al. (2002) Discussion on the meeting on’Statistical modelling and analysis of genetic data’. J R Stat Soc Ser B Stat Methodol 64: 737-775.
Discussion Leader:
Peter Morrell

11/24/2014
Toleno DM, Morrell PL, Clegg MT (2007) Error detection in SNP data by considering the likelihood of recombinational history implied by three-site combinations. Bioinformatics 23: 1807-1814.
Discussion Leader:
Chaochih Liu

11/17/2014
McVean G (2007) The structure of linkage disequilibrium around a selective sweep. Genetics 175: 1395-1406.
Discussion Leader: Tom Kono

11/10/2014
Coop G (2013) Notes on Population Genetics. Davis: University of California. 54 p.
Chapter 1: Allele and genotype frequencies
Discussion Leader: Ana Poets
Code and images are
here.

11/03/2014
Springer NM (2013) Epigenetics and crop improvement. Trends Genet 29: 241-247.
Discussion Leader: Diana Trujillo


10/27/2014 - 2:30 pm - Note Special Time
Stinchcombe JR, Hoekstra HE (2008) Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits. Heredity (Edinb) 100: 158-170.
Discussion Leader: Justin Anderson


10/20/2014 - 2:30 pm - Note Special Time
Avise JC, Wollenberg K (1997) Phylogenetics and the origin of species. Proc Natl Acad Sci USA 94: 7748-7755.
Discussion Leader: Chaochih Liu

10/17/2014 - 1:00 pm - Note Special Date & Time
Munoz-Amatriain M, Cuesta-Marcos A, Endelman JB, Comadran J, Bonman JM et al. (2014) The USDA barley core collection: genetic diversity, population structure, and potential for genome-wide association studies. PLoS One 9: e94688.
Discussion Leader: Allison Haaning

10/06/2014
Gusev A, Lowe JK, Stoffel M, Daly MJ, Altshuler D et al. (2009) Whole population, genome-wide mapping of hidden relatedness. Genome Res 19: 318-326.
Discussion Leader: Peter Morrell

09/29/2014
Thornton KR, Foran AJ, Long AD (2013) Properties and modeling of GWAS when complex disease risk is due to non-complementing, deleterious mutations in genes of large effect. PLoS Genet 9: e1003258.
Discussion Leader:
Tom Kono

09/26/2014 - 2:30 pm - Note Special Date & Time
Goff SA (2010) A unifying theory for general multigenic heterosis: energy efficiency, protein metabolism, and implications for molecular breeding. New Phytol
Discussion Leader: Ana Gonzales

09/15/2014
Kovalic D, Garnaat C, Guo L, Yan Y, Groat J et al. (2012) The use of next generation sequencing and junction sequence analysis bioinformatics to achieve molecular characterization of crops improved through modern biotechnology. Plant Gen 5: 149-163.
Discussion Leader: Kiran Seth

09/10/2014
Moreno-Estrada A, Gignoux CR, Fernandez-Lopez JC, Zakharia F, Sikora M et al. (2014) Human genetics. The genetics of Mexico recapitulates Native American substructure and affects biomedical traits. Science 344: 1280-1285.
Discussion Leader: Diana Trujillo


09/03/2014
Guerrero RF, Kirkpatrick M (2014) Local adaptation and the evolution of chromosome fusions. Evolution
Discussion Leader: Justin Anderson

08/27/2014
MPGI 5th Annual Fall Symposium, Beyond Genomes: Epigenetic Inheritance

08/20/2014
Crawford JE, Lazzaro BP (2012) Assessing the accuracy and power of population genetic inference from low-pass next-generation sequencing data. Front Genet 3: 66.
Discussion Leader:
Chaochih Liu

08/13/2014
Reading the Classics
Risch N, Merikangas K (1996) The future of genetic studies of complex human diseases. Science 273: 1516-1517.
Kruglyak L (1999)
Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nature Genet 22: 139-144.
Discussion Leaders: Derek Nedveck & Mikey Kantar


08/06/2014
Soy14 - Molecular and Cellular Biology of Soybean

07/30/2014
Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB et al. (2014) A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet 46: 707-713.
Gaut BS (2014)
The complex domestication history of the common bean. Nat Genet 46: 663-664.
Discussion Leaders:
Ana Gonzales & Chaochih Liu

07/23/2014
Graur D, Zheng Y, Price N, Azevedo RB, Zufall RA et al. (2013) On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol 5: 578-590.
Discussion Leader: Mikey Kantar

07/16/2014
Yoder JB, Stanton-Geddes J, Zhou P, Briskine R, Young ND et al. (2014) Genomic signature of adaptation to climate in Medicago truncatula. Genetics 196: 1263-1275.
Discussion Leader: Kiran Seth

07/09/2014
Jeremy Yoder’s - Evolution 2014 Talk - Population genetic and genomic identification of locally adapted loci
Jeremy will discuss simulations he is using to experiment with approaches for identifying loci contributing to local adaptation. Come and enjoy!

07/02/2014
21st Triennial North American Barley Researchers Workshop

06/25/2014
Cromie GA, Hyma KE, Ludlow CL, Garmendia-Torres C, Gilbert TL et al. (2013) Genomic sequence diversity and population structure of Saccharomyces cerevisiae assessed by RAD-seq. G3 (Bethesda) 3: 2163-2171.
Discussion Leader: Kiran Seth

06/18/2014
Takuno S, Gaut BS (2013) Gene body methylation is conserved between plant orthologs and is of evolutionary consequence. Proc Natl Acad Sci USA 110: 1797-1802.
Discussion Leader: Allison Haaning

06/12/2014
Fumagalli M, Vieira FG, Korneliussen TS, Linderoth T, Huerta-Sanchez E et al. (2013) Quantifying population genetic differentiation from next-generation sequencing data. Genetics 195: 979-992.
Discussion Leader:
Ana Gonzales

06/03/2014
Gonzales AM, Fang Z, Clegg MT, Morrell PL (in prep) Analysis of barley landrace provenance.
Discussion Leader: Justin Anderson


05/27/2014
Reading the Classics
Kimura M (1969) Number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics 61: 893-903.
Discussion Leader: Derek Nedveck

05/20/2014
Andolfatto P (2005) Adaptive evolution of non-coding DNA in Drosophila. Nature 437: 1149-1152.
Discussion Leader: Ana Gonzales

05/13/2014
Rogers RL, Cridland JM, Shao L, Hu TT, Andolfatto P et al. Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans. Mol Biol Evol
Discussion Leader: Justin Anderson

05/06/2014
Reading the Classics
Milkman R (1976) Roger Milkman-selection is the major determinant. Trends Biochem Sci 1: N152-N154.
Kimura M (1976)
The neutral theory as a supplement to Darwinism. Trends Biochem Sci 1: N152-N154.
Nei M (1976)
The cost of natural selection and the extent of enzyme polymorphism.Trends Biochem Sci 1: N247-N248.
Discussion Leaders: Derek Nedveck & Mikey Kantar

04/29/2014
Kono TJY, Fu F, Mohammadi M et al. (in preparation) Bad mutations.
Discussion Leader: Amber Eule-Nashoba

04/24/2014
Joint Meeting Brandvain, Goldberg, Moeller, Morrell, & Tiffin Lab Groups
Mimura M, Ono K, Goka K, Hara T (2013) Standing variation boosted by multiple sources of introduction contributes to the success of the introduced species, Lotus corniculatus. Biol Invasions 15: 2743-2754.
Discussion Leader: Derek Nedveck

04/22/2014
Baldwin-Brown JG, Long AD, Thornton KR (2014) The power to detect quantitative trait loci using resequenced, experimentally evolved populations of diploid, sexual organisms. Mol Biol Evol
Discussion Leader: Diana Trujillo


04/15/2014
Ralph P, Coop G (2013) The geography of recent genetic ancestry across Europe. PLoS Biol 11: e1001555.
Discussion Leader:
Tom Kono

04/08/2014
Crisci JL, Poh YP, Bean A, Simkin A, Jensen JD (2012) Recent progress in polymorphism-based population genetic inference. J Hered 103: 287-296.
Discussion Leader: Allison Haaning

04/01/2014
Xu S, Jia Z (2007) Genomewide analysis of epistatic effects for quantitative traits in barley. Genetics 175: 1955-1963.
Discussion Leader: Justin Anderson


03/28/2014
Joint Meeting Brandvain, Goldberg, Moeller, Morrell, & Tiffin Lab Groups
Chantha SC, Herman AC, Platts AE, Vekemans X, Schoen DJ (2013) Secondary evolution of a self-incompatibility locus in the Brassicaceae genus Leavenworthia. PLoS Biol 11: e1001560.
Discussion Leader:
Emma Goldberg

03/25/2014
Reading the Classics
Lander ES, Botstein D (1989) Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185-199.
Discussion Leader: Derek Nedveck

03/18/2014
Li H, Durbin R (2011) Inference of human population history from individual whole-genome sequences. Nature 475: 493-496.
Discussion Leader:
Ana Gonzales

03/11/2014
Freedman AH, Gronau I, Schweizer RM, Ortega-Del V, Diego, Han E et al. (2014) Genome sequencing highlights the dynamic early history of dogs. PLoS Genet 10: e1004016.
Discussion Leader: Chaochih Liu & Peter Morrell

03/04/2014
Hollister JD, Ross-Ibarra J, Gaut BS (2010) Indel-associated mutation rate varies with mating system in flowering plants. Mol Biol Evol 27: 409-416.
Discussion Leader: Diana Trujillo


02/28/2014
Joint Meeting Brandvain, Goldberg, Moeller, Morrell, & Tiffin Lab Groups
Rasmussen M, Anzick SL, Waters MR, Skoglund P, DeGiorgio M et al. (2014) The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature 506: 225-229.
Discussion Leader: Tom Kono

02/25/2014
Hartfield M, Glemin S (2014) Hitchhiking of deleterious alleles and the cost of adaptation in partially selfing species. Genetics 196: 281-293.
Discussion Leader: Ron Okagaki

02/18/2014
Arbiza L, Gronau I, Aksoy BA, Hubisz MJ, Gulko B et al. (2013) Genome-wide inference of natural selection on human transcription factor binding sites. Nat Genet 45: 723-729.
Discussion Leader: Allison Haaning

02/11/2014
Nielsen R, Korneliussen T, Albrechtsen A, Li Y, Wang J (2012) SNP calling, genotype calling, and sample allele frequency estimation from New-Generation Sequencing data. PLoS One 7: e37558.
Discussion Leader:
Tom Kono

02/04/2014 - 2:30 pm - Note Special Time
Reading the Classics
Lewontin RC, Krakauer J (1973) Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics 74: 175-195.
Discussion Leader: Derek Nedveck

01/28/2014
Han E, Sinsheimer JS, Novembre J (2013) Characterizing bias in population genetic inferences from low coverage sequencing data. Mol Biol Eval
Discussion Leader:
Ana Gonzales

01/24/2014
Joint Meeting Brandvain, Goldberg, Moeller, Morrell, & Tiffin Lab Groups
Skoglund P, Malmstrom H, Raghavan M, Stora J, Hall P et al. (2012)
Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe. Science 336: 466-469.
Discussion Leader:
Yaniv Brandvain

01/21/2014
Slatkin M (2009) Epigenetic inheritance and the missing heritability problem. Genetics 182: 845-850.
Discussion Leader: Justin Anderson

01/14/2014
International Plant and Animal Genome Meeting

01/07/2014
Fay JC, Wyckoff GJ, Wu CI (2001) Positive and negative selection on the human genome. Genetics 158: 1227-1234.
Discussion Leader: Kiran Seth

12/31/2013
Christmas Holiday

12/24/2013
Christmas Holiday

12/17/2013
Gonzales AM, Fang Z, Clegg MT, Morrell PL (in prep) Barley landraces - SNP Analysis.
Discussion Leader:
Tom Kono

12/12/2013 - Note Special Date
Guo M, Rupe MA, Wei J, Winkler C, Goncalves-Butruille M et al. (2013) Maize ARGOS1 (ZAR1) transgenic alleles increase hybrid maize yield. J Exp Bot
Discussion Leader:
Peter Morrell

12/13/2013 - 10:30 am - Note Special Date & Time
Joint Meeting
Moeller, Morrell, & Tiffin Lab Groups
Moreno-Estrada A, Gravel S, Zakharia F, McCauley JL, Byrnes JK et al. (2013) Reconstructing the population genetic history of the Caribbean. PLoS Genet 9: e1003925.
Discussion Leader:
Dave Moeller

12/03/2013
Nicholson G, Smith AV, Jónsson F, Gústafsson Ó, Stefánsson K et al. (2002) Assessing population differentiation and isolation from single-nucleotide polymorphism data. J R Stat Soc Ser B Stat Methodol 64: 695-715.
Discussion Leader: Zhou Fang

11/26/2013
Epperson B.K., 1999. Gustave Malecot, 1911-1998. Population genetics founding father. Genetics 152: 477-484.
Discussion Leader: Ron Okagaki

11/19/2013
Berg J.J., Coop G., 2013. The population genetic signature of polygenic local adaptation. J arXiv preprint arXiv:1307.7759
Discussion Leader: Ana Gonzales

11/15/2013 - 2:30 pm - Note Special Date & Time
Joint Meeting with Blekham, McCue, Moeller, & Tiffin Lab Groups
Brandvain Y., Slotte T., Hazzouri K.M., Wright S.I., Coop G., 2013. Genomic identification of founding haplotypes reveals the history of the selfing species Capsella rubella. PLoS Genet 9: e1003754.
Discussion Leader: Tom Kono

11/12/2013
Reading the Classics
Hill WG, Robertson A (1966)
The effect of linkage on limits to artificial selection. Genet Res 8: 269-294.
Discussion Leader: Ron Okagaki


11/05/2013
van Heerwaarden J, Hufford MB, Ross-Ibarra J (2012) Historical genomics of North American maize. Proc Natl Acad Sci U S A
Discussion Leader: Xin Li

10/29/2013
Rosenberg NA, Li LM, Ward R, Pritchard JK (2003) Informativeness of genetic markers for inference of ancestry. Am J Hum Genet 73: 1402-1422.
Discussion Leader: Zhou Fang

10/22/2013
Loh PR, Lipson M, Patterson N, Moorjani P, Pickrell JK et al. (2013) Inferring admixture histories of human populations using linkage disequilibrium. Genetics 193: 1233-1254.
Discussion Leader: Tom Kono

10/15/2013
Rosenberg NA, Mahajan S, Ramachandran S, Zhao C, Pritchard JK et al. (2005) Clines, clusters, and the effect of study design on the inference of human population structure. PLoS Genetics 1: e70.
Discussion Leader: Zhou Fang

10/08/2013
Fang Z, Gonzales AM, Clegg MT, Muehlbauer GJ, et al. (in preparation) Two genomic regions contribute disproportionately to population structure in wild barley.
Discussion Leader: Allison Haaning

10/04/2013 - 2:30 pm - Note Special Date & Time
Joint Meeting with
Blekham, McCue, Moeller, & Tiffin Lab Groups
Long Q, Rabanal FA, Meng D, Huber CD, Farlow A et al. (2013) Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden. Nat Genet 45: 884-890.
Discussion Leader: Peter Tiffin

09/24/2013
King EG, Macdonald SJ, Long AD (2012) Properties and power of the Drosophila synthetic population resource for the routine dissection of complex traits. Genetics 191: 935-949.
Discussion Leader: Tom Kono

09/17/2013
Richman AD, Uyenoyama MK, Kohn JR (1996) Allelic diversity and gene genealogy at the self-incompatibility locus in the Solanaceae. Science 273: 1212-1216.
Discussion Leader: Kelly Tweito

09/10/2013
Flowers JM, Molina J, Rubinstein S, Huang P, Schaal BA, Purugganan MD (2012) Natural selection in gene-dense regions shapes the genomic pattern of polymorphism in wild and domesticated rice. Mol Biol Evol 29: 675-687.
Discussion Leader: Tom Kono

08/29/2013
King EG, Merkes CM, McNeil CL, Hoofer SR, Sen S et al. (2012) Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource. Genome Res
Discussion Leader: Vikram Vikus

08/22/2013
Beleza S, Johnson NA, Candille SI, Absher DM, Coram MA et al. (2013) Genetic architecture of skin and eye color in an African-European admixed population. PLoS Genet 9: e1003372.
Discussion Leader: Allison Haaning

08/14/2013 - 10:00 am - Note Special Date & Time
Hudson RR, Bailey K, Skarecky D, Kwiatowski J, Ayala FJ (1994) Evidence for positive selection in the superoxide dismutase (Sod) region of Drosophila melanogaster. Genetics 136: 1329-1340.
Discussion Leader: Justin Anderson

08/08/2013
Morrell, P.L., Rieseberg, L.H. 1998. Molecular tests of the proposed diploid hybrid origin of Gilia achilleifolia (Polemoniaceae). Am J Bot 85:1439–1453.
Discussion Leader: Zhou Fang

08/01/2013
Cutter AD, Payseur BA (2013) Genomic signatures of selection at linked sites: unifying the disparity among species. Nat Rev Genet 14: 262-274.
Discussion Leader:
Ana Gonzales

07/26/2013 - Note Special Date
McVean G (2009) A genealogical interpretation of principal components analysis. PLoS Genet 5: e1000686.
Discussion Leader: Vikram Vikus

07/18/2013
Deleterious Mutations Jigsaw
Lopes AM, Aston KI, Thompson E, Carvalho F, Goncalves J et al. (2013) Human spermatogenic failure purges deleterious mutation load from the autosomes and both sex chromosomes, including the gene DMRT1. PLoS Genet 9: e1003349.
Discussion Leaders: Allison Haaning, Tom Kono

Peischl S, Dupanloup I, Kirkpatrick M, Excoffier L (2013) On the accumulation of deleterious mutations during range expansions. J arXiv preprint arXiv:13061652
Discussion Leaders: Kelly Tweito, Ana Gonzales

Simons YB, Turchin MC, Pritchard JK, Sella G (2013) The deleterious mutation load is insensitive to recent population history. J arXiv preprint arXiv:13052061
Discussion Leaders: Margie Stringfield, Justin Anderson

Szpiech ZA, Xu J, Pemberton TJ, Peng W, Zollner S et al. (2013) Long runs of homozygosity are enriched for deleterious variation. Am J Hum Genet
Discussion Leaders: Mikey Kantar, Diana Trujillo

07/11/2013
Society for Molecular Biology & Evolution (SMBE) Meeting 2013 - Chicago

07/04/2013
Independence Day

06/27/2013
Sousa V, Hey J (2013) Understanding the origin of species with genome-scale data: modelling gene flow. Nat Rev Genet 14: 404-414.
Discussion Leader: Diana Trujillo

06/20/2013
Petersen JL, Mickelson JR, Rendahl AK, Valberg SJ, Andersson LS et al. (2013) Genome-wide analysis reveals selection for important traits in domestic horse breeds. PLoS Genet 9: e1003211.
Discussion Leaders:
Justin Anderson

06/13/2013
Reading the Classics
Smith JM, Haigh J (1974)
The hitchhiking effect of a favorable gene. Genet Res 23: 23-35.
Discussion Leader: Mikey Kantar


06/06/2013
Charlesworth B 2012. The effects of deleterious mutations on evolution at linked sites. Genetics 190: 5–22.
Charlesworth B 2013. Background selection 20 years on: The Wilhelmine E. Key 2012 Invitational Lecture. J Hered 104: 161–171.
Discussion Leaders: Fengli Fu & Mohsen Mohammadi

05/30/2013
Lin Z, Li X, Shannon LM, Yeh CT, Wang ML et al. (2012) Parallel domestication of the Shattering1 genes in cereals. Nat Genet 44: 720-724.
Discussion Leader: Amber Eule-Nashoba

05/23/2013
Guerrero RF, Rousset F, Kirkpatrick M (2012) Coalescent patterns for chromosomal inversions in divergent populations. Philos Trans R Soc Lond B Biol Sci 367: 430-438.
Discussion Leader: Tom Kono

05/17/2013
Fuller DQ, Willcox G, Allaby RG (2012) Early agricultural pathways: moving outside the ‘core area’ hypothesis in Southwest Asia. J Exp Bot 63: 617-633.
Discussion Leader: Peter Morrell

05/10/2013
Takebayashi N, Morrell PL (2001) Is self-fertilization an evolutionary dead end? Revisiting an old hypothesis with genetic theories and a macroevolutionary approach. Am J Bot 88: 1143-1150.
Igic B, Busch JW (2013) Is self-fertilization an evolutionary dead end? New Phytol 198: 386-397.
Discussion Leaders:
Ana Gonzales & Tom Kono

05/03/2013
Joint Meeting with McCue, Moeller, & Tiffin Lab Groups
Ober U, Ayroles JF, Stone EA, Richards S, Zhu D, Gibbs RA, Stricker C, Gianola D, Schlather M, Mackay TF, Simianer H (2012) Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster. PLoS Genet 8: e1002685.
Discussion Leader: Vikram Vikus

04/26/2013
Fuller DQ, Willcox G, Allaby RG (2011) Cultivation and domestication had multiple origins: arguments against the core area hypothesis for the origins of agriculture in the Near East. World Archaeology 43: 628-652.
Discussion Leader: Tom Kono

04/19/2013
Reading the Classics
Felsenstein J (1974) The evolutionary advantage of recombination. Genetics 78: 737-756.
Discussion Leader: Mikey Kantar

04/12/2013
Parker GA, Smith JM (1990) Optimality theory in evolutionary biology. Nature 348: 27-33.
Shoval O, Sheftel H, Shinar G, Hart Y, Ramote O et al. (2012) Evolutionary trade-offs, Pareto optimality, and the geometry of phenotype space. Science 336: 1157-1160.
Discussion Leader: Ron Okagaki

04/05/2013
Fu W, O’Connor TD, Jun G, Kang HM, Abecasis G, Leal SM, Gabriel S, Altshuler D, Shendure J, Nickerson DA, Bamshad MJ, Akey JM (2013) Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature 493: 216-220.
Karakoc E, Alkan C, O’Roak BJ, Dennis MY, Vives L et al. (2012)
Detection of structural variants and indels within exome data. Nat Methods 9: 176-178.
Discussion Leader: Ahmad Sallam

03/29/2013
Gan X, Stegle O, Behr J, Steffen JG, Drewe P et al. (2011) Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 477: 419-423.
Discussion Leader:
Tom Kono

03/22/2013
Spring Break

03/15/2013
Yang S, Yuan Y, Wang L, Li J, Wang W et al. (2012) Great majority of recombination events in Arabidopsis are gene conversion events. Proc Natl Acad Sci USA
Discussion Leader: Amber Eule-Nashoba


03/08/2013
Reading the Classics
Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7: 256-276.
Discussion Leader: Mikey Kantar

03/01/2013
Morrell PL, Gonzales AM, Meyer KKT, Clegg MT (in prep) Resequencing data indicate a modest effect of domestication on diversity in barley: a cultigen with multiple origins.
Discussion Leader:
Zhou Fang

02/22/2013
Joint Meeting with McCue, Moeller, & Tiffin Lab Groups
Rockman MV (2012) The QTN program and the alleles that matter for evolution: all that’s gold does not glitter. Evolution 66: 1-17.
Discussion Leader: Peter Tiffin

02/15/2013
Lu J, Tang T, Tang H, Huang J, Shi S, Wu CI (2006) The accumulation of deleterious mutations in rice genomes: a hypothesis on the cost of domestication. Trends Genet 22: 126-131.
Discussion Leader: Amber Eule-Nashoba


02/08/2013
Reading the Classics
Gould SJ, Lewontin RC (1979) The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. Proceedings of the Royal Society B: Biological Sciences 205: 581-598.
Discussion Leader: Mikey Kantar

02/01/2013
Comeron JM, Ratnappan R, Bailin S (2012) The many landscapes of recombination in Drosophila melanogaster. PLoS Genet 8: e1002905.
Discussion Leader: Peter Morrell

01/24/2013
Turchin MC, Chiang CW, Palmer CD, Sankararaman S, Reich D et al. (2012) Evidence of widespread selection on standing variation in Europe at height-associated SNPs. Nat Genet 44: 1015-1019.
Discussion Leader:
Ana Gonzales

01/17/2013
Pickrell JK, Pritchard JK (2012) Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet 8: e1002967.
Discussion Leader: Tom Kono

01/10/2013
International Plant and Animal Genome Meeting

01/03/2013
Christmas Holiday

12/27/2013
Christmas Holiday

12/20/2012
Swanson-Wagner R, Briskine R, Schaefer R, Hufford MB, Ross-Ibarra J, Myers CL, Tiffin P, Springer NM (2012) Reshaping of the maize transcriptome by domestication. Proc Natl Acad Sci U S A 109: 11878-11883.
Discussion Leader:
Zhou Fang

12/13/2012
Leffler EM, Bullaughey K, Matute DR, Meyer WK, Segurel L et al. (2012) Revisiting an old riddle: what determines genetic diversity levels within species? PLoS Biol 10: e1001388.
Sella G, Petrov DA, Przeworski M, Andolfatto P (2009) Pervasive natural selection in the Drosophila genome? Plos Genet 5: ARTN e1000495.
Discussion Leader:
Ana Gonzales & Peter Morrell

12/06/2012
van Heerwaarden J, Hufford MB, Ross-Ibarra J (2012) Historical genomics of North American maize. Proc Natl Acad Sci USA
Discussion Leader: Emily Combs

11/28/2012
Kono TY, Seth K, Stupar RM, Morrell PL (in prep) SNP annotation and SNP metadata collection without a reference genome.
Discussion Leader: Zhou Fang

11/22/2012
Thanksgiving Holiday

11/16/2012
Hahn MW (2008) Toward a selection theory of molecular evolution. Evolution 62: 255-265.
Discussion Leader: Ron Okagaki


11/08/2012
Reading the Classics
Tajima F (1983)
Evolutionary relationship of DNA sequences in finite populations. Genetics 105: 437-460.
Discussion Leader: Mikey Kantar

11/01/2012
Ralph P, Coop G (2012) The geography of recent genetic ancestry across Europe. J Arxiv preprint arXiv:12073815
Discussion Leader: Ron Okagaki


10/25/2012
Mayer KF, Waugh R, Langridge P, Close TJ, Wise RP et al. (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature
Discussion Leader: Peter Morrell

10/19/2012
Joint Meeting with the Smith Lab
Fang Z, Eule-Nashoba A, Powers C, Kono TY, Morrell PL et al. (in prep) Multiple genomic regions indicate a response to selection for Fusarium head blight resistance in a barley experimental breeding population.
Discussion Leader: Vikram Vikus

10/11/2012
Fang Z, Gonzales AM, Durbin ML, Meyer KKT, Miller BH, Volz KM, Clegg MT, Morrell PL (in prep) Tracing the geographic origin of weedy Ipomoea purpurea in the Southeastern United States.
Discussion Leader: Tom Kono

10/04/2012
Lee CR, Mitchell-Olds T (2011) Quantifying effects of environmental and geographical factors on patterns of genetic differentiation. Mol Ecol 20: 4631-4642.
Discussion Leader:
Ana Gonzales

09/27/2012
Gonzales AM, Fang Z, Durbin ML, Meyer KKT, Clegg MT et al. (in press) Nucleotide sequence diversity of floral pigment genes in Mexican populations of Ipomoea purpurea (morning glory) accord with a neutral model of evolution. J of Heredity
Discussion Leader: Amber Eule-Nashoba


09/21/2012
Joint Meeting with McCue, Moeller, & Tiffin Labs
Wang C, Zollner S, Rosenberg NA (2012) A quantitative comparison of the similarity between genes and geography in worldwide human populations. PLoS Genet 8: e1002886.
Discussion Leader: Jeremy Yoder

09/13/2012
Whittington HR, Deede L, Powers JS (2012) Growth responses, biomass partitioning, and nitrogen isotopes of prairie legumes in response to elevated temperature and varying nitrogen source in a growth chamber experiment. Am J Bot 99: 838-846.
Discussion Leader: Peter Morrell

09/06/2012
Morrell PL, Buckler ES, Ross-Ibarra J (2012) Crop genomics: advances and applications. Nat Rev Genet 13: 85-96.
Discussion Leader: Zhou Fang

08/30/2012
Microbial and Plant Genomics Institute
3rd Annual Fall Symposium

08/23/2012
Eichten SR, Swanson-Wagner RA, Schnable JC, Waters AJ, Hermanson PJ, Liu S, Yeh CT, Jia Y, Gendler K, Freeling M, Schnable PS, Vaughn MW, Springer NM (2011) Heritable epigenetic variation among maize inbreds. PLoS Genet 7: e1002372.
Discussion Leader: Peter Morrell

08/16/2012
Warmuth V, Eriksson A, Bower MA, Canon J, Cothran G et al. (2011) European domestic horses originated in two holocene refugia.PLoS One 6: e18194.
Warmuth V, Eriksson A, Bower MA, Barker G, Barrett E et al. (2012)
Reconstructing the origin and spread of horse domestication in the Eurasian steppe. Proc Natl Acad Sci U S A 109: 8202-8206.
Discussion Leader: Tom Kono

08/09/2012
Zhong SQ, Dekkers JCM, Fernando RL, Jannink JL (2009) Factors affecting accuracy from genomic selection in populations derived from multiple inbred lines: A barley case study. Genetics 182: 355-364.
Discussion Leader: Vikram Vikus

08/02/2012
Hoban S, Bertorelle G, Gaggiotti OE (2011) Computer simulations: tools for population and evolutionary genetics. Nat Rev Genet 13: 110-122.
Discussion Leader: Emily Combs

07/26/2012
Reading the Classics
Kreitman M (1983) Nucleotide polymorphism at the alcohol dehydrogenase locus of Drosophila melanogaster. Nature 304: 412-417.
Discussion Leader: Mikey Kantar

07/19/2012
Mackay TF, Richards S, Stone EA, Barbadilla A, Ayroles JF et al. (2012) The Drosophila melanogaster Genetic Reference Panel. Nature 482: 173-178.
Discussion Leader:
Peter Morrell

07/12/2012
Novembre J, Ramachandran S (2011) Perspectives on human population structure at the cusp of the sequencing era. Annu Rev Genomics Hum Genet 12: 245-274.
Discussion Leader: Tom Kono

07/05/2012
Wegmann D, Kessner DE, Veeramah KR, Mathias RA, Nicolae DL et al. (2011) Recombination rates in admixed individuals identified by ancestry-based inference. Nat Genet 43: 847-853.
Discussion Leader: Ron Okagaki

06/28/2012
Horton MW, Hancock AM, Huang YS, Toomajian C, Atwell S et al. (2012) Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel. Nat Genet 44: 212-216.
Gaut BS (2012)
Arabidopsis thaliana as a model for the genetics of local adaptation. Nat Genet 44: 115-116.
Discussion Leader: Amber Eule-Nashoba


06/21/2012
Engelhardt BE, Stephens M (2010) Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis. PLoS Genet 6:
Yang WY, Novembre J, Eskin E, Halperin E (2012)
A model-based approach for analysis of spatial structure in genetic data. Nat Genet 44: 725-731.
Discussion Leader: Vikram Vikus & Ana Gonzales

06/14/2012
Moeller DA, Geber MA, Tiffin P (2011) Population genetics and the evolution of geographic range limits in an annual plant. Am Nat 178 Suppl 1: S44-57.
Discussion Leader: Peter Morrell

06/07/2012
Hufford MB, Xun X, van Heerwaarden J, Pyhäjärvi T, Chia J-M, Cartwright RA, Elshire RJ, Glaubitz JC, Guill KE, Kaeppler SM, Lai J, Morrell PL, Shannon LM, Song C, Springer NM, Swanson-Wagner RA, Tiffin P, Wang J, Zhang G, Doebley J, McMullen MD, Ware D, Buckler ES, Yang S, Ross-Ibarra J (in press) Population genomics of domestication and improvement in maize. Nature Genetics
Discussion Leader: Mikey Kantar


05/31/2012
Otto SP, Whitlock MC (1997) The probability of fixation in populations of changing size. Genetics 146: 723-733.
Discussion Leader: Amber Eule-Nashoba

05/24/2012
Tang H, Choudhry S, Mei R, Morgan M, Rodriguez-Cintron W et al. (2007) Recent genetic selection in the ancestral admixture of Puerto Ricans. Am J Hum Genet 81: 626-633.
Discussion Leader: Ana Gonzales

05/17/2012
Ng PC, Henikoff S (2003) SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res 31: 3812-3814.
Ng PC, Nickerson DA, Bamshad MJ, Shendure J (2010) Massively parallel sequencing and rare disease. Hum Mol Genet 19: R119-24.
Discussion Leader: Tom Kono

05/10/2012
Lawson DJ, Hellenthal G, Myers S, Falush D (2012) Inference of population structure using dense haplotype data. PLoS Genet 8: e1002453.
Gattepaille LM, Jakobsson M (2012)
Combining markers into haplotypes can improve population structure inference. Genetics 190: 159-174.
Discussion Leaders: Ana Gonzales & Peter Morrell

05/03/2012
Haun WJ, Hyten DL, Xu WW, Gerhardt DJ, Albert TJ et al. (2011) The composition and origins of genomic variation among individuals of the soybean reference cultivar Williams 82. Plant Physiol 155: 645-655.
Discussion Leader: Mikey Kantar

04/26/2012
Fournier-Level A, Korte A, Cooper MD, Nordborg M, Schmitt J et al. (2011) A map of local adaptation in Arabidopsis thaliana. Science 334: 86-89.
Discussion Leader: Amber Eule-Nashoba


04/19/2012
Marth GT, Yu F, Indap AR, Garimella K, Gravel S et al. (2011) The functional spectrum of low-frequency coding variation. Genome Biol 12: R84.
Discussion Leader:
Zhou Fang

04/12/2012
Pyhäjärvi T, Kujala ST, Savolainen O (2011) Revisiting protein heterozygosity in plants—nucleotide diversity in allozyme coding genes of conifer Pinus sylvestris. Tree Genetics & Genomes 7: 385-397.
Discussion Leader:
Tom Kono

04/05/2012
Dumont BL, Payseur BA (2011) Genetic analysis of genome-scale recombination rate evolution in house mice. PLoS Genet 7: e1002116.
Discussion Leader: Mikey Kantar

03/29/2012
Tenaillon O, Rodriguez-Verdugo A, Gaut RL, McDonald P, Bennett AF et al. (2012) The molecular diversity of adaptive convergence. Science 335: 457-461.
Discussion Leader: Ron Okagaki

03/22/2012
Blackman BK, Rasmussen DA, Strasburg JL, Raduski AR, Burke JM et al. (2011) Contributions of flowering time genes to sunflower domestication and improvement. Genetics 187: 271-287.
Discussion Leader: Mikey Kantar


03/15/2012
Spring Break

03/08/2012 (location - 138 Cargill)
Joint Meeting with the Smith Lab
Illumina Genotyping -
GenomeStudio and Alchemy
Wright MH, Tung CW, Zhao K, Reynolds A, McCouch SR et al. (2010) ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations. Bioinformatics 26: 2952-2960.
Discussion Leaders: Karen Beaubien, Ana Gonzales, and Maria Munoz
If you need an Minnesota Supercomputing Institute (MSI) account to participate, register here:
https://www.msi.umn.edu/tutorial/802

03/01/2012
Zhao K, Tung CW, Eizenga GC, Wright MH, Ali ML et al. (2011) Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat Commun 2: 467.
Discussion Leader:
Ana Gonzales

02/23/2012
Macdonald SJ, Long AD (2007) Joint estimates of quantitative trait locus effect and frequency using synthetic recombinant populations of Drosophila melanogaster. Genetics 176: 1261-1281.
Discussion Leader: Vikram Vikus

02/16/2012
Albrechtsen A, Nielsen FC, Nielsen R (2010) Ascertainment biases in SNP chips affect measures of population divergence. Mol Biol Evol 27: 2534-2547.
Discussion Leader: Zhou Fang

02/09/2012
Reading the Classics
Lewontin RC, Hubby JL (1966) A molecular approach to the study of genic heterozygosity in natural populations. II. Amount of variation and degree of heterozygosity in natural populations of Drosophila pseudoobscura. Genetics 54: 595-609.
Discussion Leader: Amber Eule-Nashoba

02/02/2012
Saintenac C, Jiang D, Akhunov ED (2011) Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome. Genome Biol 12: R88.
Discussion Leader:
Zhou Fang

01/26/2012
Reading the Classics
Lewontin RC, Krakauer J (1973) Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics 74: 175-195.
Discussion Leader: Mikey Kantar

01/19/2012
International Plant and Animal Genome Meeting

01/13/2012
International Plant and Animal Genome Meeting

01/06/2012
Christmas Holiday

12/29/2011
Christmas Holiday

12/22/2011
Nair, S.K., Wang, N., Turuspekov, Y., Pourkheirandish, M., Sinsuwongwat, S., Chen, G., Sameri, M., Tagiri, A., Honda, I., Watanabe, Y., Kanamori, H., Wicker, T., Stein, N., Nagamura, Y., Matsumoto, T., Komatsuda, T. 2010. Cleistogamous flowering in barley arises from the suppression of microRNA-guided HvAP2 mRNA cleavage. Proc Natl Acad Sci U S A 107:490–495.
Discussion Leader:
Ana Gonzales

12/15/2011
Wakeley J (2005) The limits of theoretical population genetics. Genetics 169: 1-7.
Discussion Leader: Peter Morrell

12/08/2011 (location - 138 Cargill)
Joint Meeting with the Smith Lab
UNIX Shell Scripting and Job Queueing on Linux Clusters
http://manuals.bioinformatics.ucr.edu/home/linux-basics
Discussion Leader: Tom Kono and Erin Treiber
If you need an Minnesota Supercomputing Institute (MSI) account to participate, register here:
https://www.msi.umn.edu/tutorial/786

11/30/2011
Joint Meeting with McCue, Moeller, & Tiffin Labs
Studer A, Zhao Q, Ross-Ibarra J, Doebley J (2011) Identification of a functional transposon insertion in the maize domestication gene tb1. Nat Genet 43: 1160-1163.
Discussion Leader: Tom Kono

11/24/2010
Thanksgiving Holiday

11/17/2011
Fay JC (2011) Weighing the evidence for adaptation at the molecular level. Trends Genet
Discussion Leader: Raffa Teixera

11/10/2011
Macdonald SJ, Long AD (2007) Joint estimates of quantitative trait locus effect and frequency using synthetic recombinant populations of Drosophila melanogaster. Genetics 176: 1261-1281.
Discussion Leader: Peter Morrell

11/03/2011
Ju YS, Kim JI, Kim S, Hong D, Park H et al. (2011) Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals. Nat Genet 43: 745-752.
Discussion Leader: Mikey Kantar

10/26/2011 (note date, time, and location 371 Bioscience - 12:30 pm)
Joint Meeting with McCue, Moeller, & Tiffin Lab Groups
Cao, J., Schneeberger, K., Ossowski, S., Gunther, T., Bender, S., Fitz, J., Koenig, D., Lanz, C., Stegle, O., Lippert, C., Wang, X., Ott, F., Muller, J., Alonso-Blanco, C., Borgwardt, K., Schmid, K.J., Weigel, D. 2011. Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet
Discussion Leader:
John Stanton-Geddes

10/20/2011
Emasculation and pollination of barley
Discussion Leader: Kevin Smith

10/13/2011
McHale LK, Huan WJ, Xu WW, Bhaskar PB, Hyten DL et al. (in review) Structural variation hotspots in the soybean genome localize to clusters of biotic stress response genes. - see email for weblink
Discussion Leader: Tom Kono

10/06/2011
Kover PX, Valdar W, Trakalo J, Scarcelli N, Ehrenreich IM et al. (2009) A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana. Plos Genet 5: ARTN e1000551.
Discussion Leader: Ana Gonzales

09/28/2011 (note date)
Joint Meeting with McCue, Moeller, & Tiffin Lab Groups
Vonholdt BM, Pollinger JP, Earl DA, Knowles JC, Boyko AR et al. (2011) A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids. Genome Res 21: 1294-1305.
Discussion Leader: Tim Paape

09/22/2011
McHale LK, Huan WJ, Xu WW, Bhaskar PB, Hyten DL et al. (in review) Stuctural variation hotspots in the soybean genome localize to clusters of biotic stress response genes. - see email for weblink
Discussion Leader: Tom Kono

09/15/2011
Coop G, Pickrell JK, Novembre J, Kudaravalli S, Li J et al. (2009) The role of geography in human adaptation. PLoS Genet 5: e1000500.
Discussion Leader: Mikey Kantar

09/08/2011
Ossowski S, Schneeberger K, Lucas-Lledo JI, Warthmann N, Clark RM et al. (2010) The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327: 92-94.
Discussion Leader: Emily Combs

09/01/2011
Microbial and Plant Genomics Institute
2nd Annual Fall Symposium

08/25/2011
Coop G, Witonsky D, Di Rienzo A, Pritchard JK (2010) Using environmental correlations to identify loci underlying local adaptation. Genetics 185: 1411-1423.
Discussion Leader: Hongyun Wang

08/18/2011
Sakai AK, Lane MJ (1996) National Science Foundation funding patterns of women and minorities in biology. BioScience 46: 621-625.
Discussion Leader: Kiran Seth

08/11/2011
Moyle LC, Nakazato T (2010) Hybrid incompatibility “snowballs” between Solanum species. Science 329: 1521-1523.
Discussion Leader: Ana Gonzales

08/04/2011
Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W et al. (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475: 348-352.
Discussion Leader: Peter Morrell

07/28/2011
Altshuler DL, Durbin RM, Abecasis GR, Bentley DR, Chakravarti A et al. (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
Discussion Leader:
Ana Gonzales

07/21/2011
Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18: 1851-1858.
Discussion Leader: Robert Schaefer

07/14/2011
Haasl RJ, Payseur BA (2011) Multi-locus inference of population structure: a comparison between single nucleotide polymorphisms and microsatellites. Heredity 106: 158-171.
Discussion Leader: Zhou Fang

07/07/2011
Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S et al. (2009) Genome sequence, comparative analysis, and population genetics of the domestic horse. Science 326: 865-867.
Discussion Leader: Ron Okagaki

06/30/2011
Yang Z, Rannala B (2010) Bayesian species delimitation using multilocus sequence data. Proc Natl Acad Sci U S A 107: 9264-9269.
Discussion Leader: Beau Miller

06/23/2011
Molina J, Sikora M, Garud N, Flowers JM, Rubinstein S et al. (2011) Molecular evidence for a single evolutionary origin of domesticated rice. Proc Natl Acad Sci U S A 108: 8351-8356.
Discussion Leader: Ana Gonzales

06/16/2011
Evolution Meeting 2011

06/09/2011
Mackay TF, Stone EA, Ayroles JF (2009) The genetics of quantitative traits: challenges and prospects. Nat Rev Genet 10: 565-577.
Discussion Leader: Kiran Seth

06/02/2011
Nielsen R, Paul JS, Albrechtsen A, Song YS (2011) Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet 12: 443-451.
Discussion Leader: Jessica Petersen

05/26/2011
Morrell PL, Toleno DM, Lundy KE, Clegg MT (2006) Estimating the contribution of mutation, recombination and gene conversion in the generation of haplotypic diversity. Genetics 173: 1705-1723.
Discussion Leader: Peter Morrell

05/19/2011
Guo F, Dey DK, Holsinger KE (2009) A Bayesian hierarchical model for analysis of SNP diversity in multilocus, multipopulation samples. J Am Stat Assoc 104: 142-154.
Discussion Leader: Amber Eule-Nashoba

05/12/2011
Reading the Classics
Cavalli-Sforza LL (1966) Population structure and human evolution. Proc R Soc Lond B Biol Sci 164: 362-379.
Discussion Leader: Ron Okagaki

05/05/2011
Huynh LY, Maney DL, Thomas JW (2010) Chromosome-wide linkage disequilibrium caused by an inversion polymorphism in the white-throated sparrow (Zonotrichia albicollis). Heredity 106: 537-546.
Discussion Leader: Zhou Fang

04/28/2011
Macdonald SJ, Long AD (2007) Joint estimates of quantitative trait locus effect and frequency using synthetic recombinant populations of Drosophila melanogaster. Genetics 176: 1261-1281.
Discussion Leader: Nichol Schultz

04/21/2011
Ralph P, Coop G (2010) Parallel adaptation: one or many waves of advance of an advantageous allele? Genetics 186: 647-668.
Discussion Leader: Jessica Petersen

04/14/2011
Burke MK, Dunham JP, Shahrestani P, Thornton KR, Rose MR et al. (2010) Genome-wide analysis of a long-term evolution experiment with Drosophila. Nature 467: 587-590.
Discussion Leader: Margaret Taylor

04/07/2011
Joint Meeting with McCue, Moeller, & Tiffin Lab Groups
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J (2011) Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea luxurians. Genome Biol Evol
Discussion Leader:
Ana Gonzales

03/31/2011
Cuesta-Marcos A, Szucs P, Close TJ, Filichkin T, Muehlbauer GJ, Smith KP, Hayes PM (2010) Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure. BMC Genomics 11: ARTN 707
Discussion Leader: Emily Combs

03/24/2011
Barley diversity manuscript - see email for weblink
Discussion Leader: Ana Gonzales

03/17/2011
Spring Break

03/10/2011
Li Y, Vinckenbosch N, Tian G, Huerta-Sanchez E, Jiang T et al. (2010) Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet 42: 969-972.
Discussion Leader: Krista Fritz

03/03/2011
Lohmueller KE, Indap AR, Schmidt S, Boyko AR, Hernandez RD et al. (2008) Proportionally more deleterious genetic variation in European than in African populations. Nature 451: 994-997.
Discussion Leader: Peter Morrell

02/24/2011
Chun S, Fay JC (2009) Identification of deleterious mutations within three human genomes. Genome Res 19: 1553-1561.
Discussion Leader: Beau Miller

02/17/2011
Joint Meeting with McCue, Moeller, & Tiffin Lab Groups
Casto AM, Feldman MW (2011) Genome-wide association study SNPs in the Human Genome Diversity Project populations: does selection affect unlinked SNPs with shared trait associations? PLoS Genet 7: e1001266
Discussion Leader: Tim Paape

02/10/2011
Sabeti PC, Walsh E, Schaffner SF, Varilly P, Fry B et al. (2005) The case for selection at CCR5-Delta 32. Plos Biol 3: 1963-1969-ARTN e378.
Discussion Leader: Annette McCoy

02/03/2011
To Be Determined (Maize LD manuscript)
Discussion Leader: Zhou Fang

01/27/2011
Joint Meeting with McCue, Moeller, & Tiffin Lab Groups
Lam HM, Xu X, Liu X, Chen W, Yang G et al. (2010) Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet 42: 1053-1059.
Discussion Leader: Emily Combs

01/20/2011
Albrechtsen A, Moltke I, Nielsen R (2010) Natural selection and the distribution of identity-by-descent in the human genome. Genetics 186: 295-308.
Discussion Leader: Amber Eule-Nashoba/Ron Okagaki

01/13/2011
Kirkpatrick M, Barton N (2006) Chromosome inversions, local adaptation and speciation. Genetics 173: 419-434.
Discussion Leader: Zhou Fang

01/06/2011
Pluzhnikov A, Donnelly P (1996) Optimal sequencing strategies for surveying molecular genetic diversity. Genetics 144: 1247-1262.
Discussion Leader: Peter Morrell

12/30/2010
Christmas Holiday

12/23/2010
Christmas Holiday

12/16/2010
Coalescent Simulation
http://home.uchicago.edu/~rhudson1/source/mksamples.html
Discussion Leader: Ana Gonzales

12/09/2010
Padhukasahasram B, Marjoram P, Wall JD, Bustamante CD, Nordborg M (2008) Exploring population genetic models with recombination using efficient forward-time simulations. Genetics 178: 2417-2427.
Discussion Leader:
Peter Morrell

12/02/2010
Joint Meeting with McCue, Moeller, & Tiffin Lab Groups
Dickson SP, Wang K, Krantz I, Hakonarson H, Goldstein DB (2010) Rare variants create synthetic genome-wide associations. PLoS Biol 8: e1000294.
Discussion Leader: Peter Tiffin

11/25/2010
Thanksgiving Holiday

11/18/2010
Komatsuda T, Pourkheirandish M, He C, Azhaguvel P, Kanamori H et al. (2007) Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene. Proc Natl Acad Sci USA 104: 1424-1429.
Discussion Leader: Ron Okagaki

11/11/2010
Hancock AM, Witonsky DB, Gordon AS, Eshel G, Pritchard JK et al. (2008) Adaptations to climate in candidate genes for common metabolic disorders. Plos Genet 4: ARTN e32.
Discussion Leader: Jessica Petersen

11/04/2010
Li H, Homer N (2010) A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform 11: 473-483.
Discussion Leader: Peter Morrell

10/29/2010
Clark RM, Linton E, Messing J, Doebley JF (2004) Pattern of diversity in the genomic region near the maize domestication gene tb1. Proc Natl Acad Sci U S A 101: 700-707.
Discussion Leader: Zhou Fang

10/21/2010
Joint Meeting with McCue, Moeller, & Tiffin Lab Groups
Gossmann TI, Song BH, Windsor AJ, Mitchell-Olds T, Dixon CJ et al. (2010) Genome wide analyses reveal little evidence for adaptive evolution in many plant species. Mol Biol Evol 27: 1822-1832.
Discussion Leader: Tim Paape

10/14/2010
Haddrill PR, Thornton KR, Charlesworth B, Andolfatto P (2005) Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. Genome Res 15: 790-799.
Discussion Leader:
Peter Morrell

10/07/2010
Hudson RR (1990) Gene genealogies and the coalescent process. Oxford Surveys in Evolutionary Biology 7: 1-42.
Second half of the chapter.
Discussion Leader:
Peter Morrell

09/30/2010
Durand E, Tenaillon MI, Ridel C, Coubriche D, Jamin P et al. (2010) Standing variation and new mutations both contribute to a fast response to selection for flowering time in maize inbreds. Bmc Evol Biol 10: ARTN 2.
Discussion Leader: Vikram Vikus

09/23/2010
Andolfatto P, Nordborg M (1998) The effect of gene conversion on intralocus associations. Genetics 148: 1397-1399.
Jeffreys AJ, May CA (2004)
Intense and highly localized gene conversion activity in human meiotic crossover hot spots. Nat Genet 36: 151-156.
Discussion Leader:
Peter Morrell

09/16/2010
Atwell S, Huang YS, Vilhjalmsson BJ, Willems G, Horton M et al. (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465: 627-631.
Discussion Leader: Nichol Schultz

09/09/2010
Zhai W, Nielsen R, Slatkin M (2009) An investigation of the statistical power of neutrality tests based on comparative and population genetic data. Mol Biol Evol 26: 273-283.
Discussion Leader: Ana Gonzales

09/03/2010
Lockton S, Ross-Ibarra J, Gaut BS (2008) Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata. P Natl Acad Sci Usa 105: 13965–13970
Discussion Leader: Peter Morrell

08/27/2010
Albrechtsen A, Nielsen FC, Nielsen R (2010) Ascertainment biases in SNP chips affect measures of population divergence. Mol Biol Evol 27: 2534-2547.
Discussion Leaders: Zhou Fang

08/20/2010
Karasov T, Messer PW, Petrov DA (2010) Evidence that adaptation in Drosophila is not limited by mutation at single sites. Plos Genet 6: ARTN e1000924.
Discussion Leader: Krista Fritz

08/13/2010
Baudat F, Buard J, Grey C, Fledel-Alon A, Ober C et al. (2010) PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice. Science 327: 836-840.
Discussion Leader:
Peter Morrell

08/06/2010
No Meeting

07/30/2010
No Meeting

07/23/2010
Yang J, Benyamin B, McEvoy BP, Gordon S, Henders AK et al. (2010) Common SNPs explain a large proportion of the heritability for human height. Nat Genet 42: 565-569.
Discussion Leader:
Molly McCue

07/16/2010
Hudson RR (1990) Gene genealogies and the coalescent process. Oxford Surveys in Evolutionary Biology 7: 1-42.
Discussion Leader: Diego Coelho


07/09/2010
An introduction to libsequence & phred/phrap/consed/polyphred
Thornton K (2003)
Libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics 19: 2325-2327.
Discussion Leaders: Ana Gonzales / Zhou Fang

07/02/2010
Fay JC, Wu CI (2000) Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
Discussion Leader: Jessica Petersen


06/25/2010
Morrell PL, Clegg MT (2007) Genetic evidence for a second domestication of barley (Hordeum vulgare) east of the Fertile Crescent. Proc Natl Acad Sci USA 104: 3289-3294.
Discussion Leader: Godwin Macharia

06/18/2010
Eckert AJ, van Heerwaarden J, Wegrzyn JL, Nelson CD, Ross-Ibarra J et al. (2010) Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda L., Pinaceae). Genetics 185: 969-982.
Discussion Leaders: Diego Coelho / Kevin Volz


06/11/2010
Ross-Ibarra J, Tenaillon M, Gaut BS (2009) Historical divergence and gene flow in the genus Zea. Genetics 181: 1399-1413.
Discussion Leader:
Zhou Fang

06/04/2010
Plagnol V, Padhukasahasram B, Wall JD, Marjoram P, Nordborg M (2006) Relative influences of crossing over and gene conversion on the pattern of linkage disequilibrium in Arabidopsis thaliana. Genetics 172: 2441-2448.
Discussion Leader: Ana Gonzales

05/28/2010
Price AL, Tandon A, Patterson N, Barnes KC, Rafaels N et al. (2009) Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet 5: e1000519.
Discussion Leader: Zhou Fang

05/21/2010
Gaut BS, Long AD (2003) The lowdown on linkage disequilibrium. Plant Cell 15: 1502-1506.
Discussion Leaders: Peter Morrell


05/14/2010
Green RE, Krause J, Briggs AW, Maricic T, Stenzel U et al. (2010) A draft sequence of the Neandertal genome. Science 328: 710-722.
Discussion Leaders: Ana Gonzales / Diego Coelho

05/07/2010
Linux Basics
http://manuals.bioinformatics.ucr.edu/home/linux-basics
Discussion Leaders: Ana Gonzales / Zhou Fang

04/30/2010
Feng L, Sebastian S, Smith S, Cooper M (2006) Temporal trends in SSR allele frequencies associated with long-term selection for yield of maize. Maydica 51: 293-300.
Discussion Leader: Godwin Macharia

04/23/2010
Charlesworth D, Willis JH (2009) FUNDAMENTAL CONCEPTS IN GENETICS The genetics of inbreeding depression. Nat Rev Genet 10: 783-796.
Discussion Leader: Hao Zhou

04/16/2010
Pickrell JK, Coop G, Novembre J, Kudaravalli S, Li JZ et al. (2009) Signals of recent positive selection in a worldwide sample of human populations. Genome Res 19: 826-837.
Discussion Leader: Zhou Fang

04/09/2010
Metzker ML (2010) APPLICATIONS OF NEXT-GENERATION SEQUENCING Sequencing technologies - the next generation. Nat Rev Genet 11: 31-46.
Discussion Leader: Vikram Vikus

04/02/2010
Vonholdt BM, Pollinger JP, Lohmueller KE, Han E, Parker HG et al. (2010) Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature 464: 898-902. - Supplemental Information & analytical methods
Discussion Leader: Peter Morrell

03/26/2010
Vonholdt BM, Pollinger JP, Lohmueller KE, Han E, Parker HG et al. (2010) Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature 464: 898-902.
Discussion Leader: Peter Morrell

03/19/2010
Spring Break

03/12/2010
Chen H, Morrell PL, Ashworth VE, de la Cruz M, Clegg MT (2009) Tracing the geographic origins of major avocado cultivars. J Hered 100: 56-65.
Discussion Leader: Ana Gonzales


03/05/2010
Chen H, Morrell PL, de la Cruz M, Clegg MT (2008) Nucleotide diversity and linkage disequilibrium in wild avocado (Persea americana Mill.). J Hered 99: 382-389.
Discussion Leader: Ana Gonzales

02/26/2010
Long AD, Langley CH (1999) The power of association studies to detect the contribution of candidate genetic loci to variation in complex traits. Genome Res 9: 720-731.
Discussion Leader: Liana Nice


02/19/2010
Rockman MV, Kruglyak L (2008) Breeding designs for recombinant inbred advanced intercross lines. Genetics 179: 1069-1078.
Discussion Leader: Peter Morrell

02/12/2010
Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ et al. (2009) The genetic architecture of maize flowering time. Science 325: 714-718.
Discussion Leader: Peter Morrell

02/05/2010
Zhao KY, Aranzana MJ, Kim S, Lister C, Shindo C et al. (2007) An Arabidopsis example of association mapping in structured samples. Plos Genet 3: ARTN e4.
Discussion Leaders: Vikram Vikus / Stephanie Nevara

01/29/2010
Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C et al. (2005) The pattern of polymorphism in Arabidopsis thaliana. PLos Biol 3: e196.
Discussion Leader:
Zhou Fang

01/22/2010
Wright SI, Bi IV, Schroeder SG, Yamasaki M, Doebley JF et al. (2005) The effects of artificial selection on the maize genome. Science 308: 1310-1314.
Discussion Leader: Chris Taylor

01/12/2010
Plant & Animal Genome Meeting

01/05/2010
Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK et al. (2002) Genetic structure of human populations. Science 298: 2381-2385.
Discussion Leader: Peter Morrell

12/23/2009
Rosenberg NA, Nordborg M (2002) Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat Rev Genet 3: 380-390.
Discussion Leader: Peter Morrell

12/17/2009
Voelkerding KV, Dames SA, Durtschi JD (2009) Next-generation sequencing: from basic research to diagnostics. Clin Chem 55: 641-658.
Discussion Leader:
Zhou Fang

12/10/2009
Gore MA, Chia JM, Elshire RJ, Sun Q, Ersoz ES et al. (2009) A first-generation haplotype map of maize. Science 326: 1115-1117.
Discussion Leader: Peter Morrell

12/03/2009
Wakeley J (2008) Coalescent Theory: An Introduction. Roberts & Company Publishers. Chapter 1 (continued).
Discussion Leader: Chris Taylor

11/26/2009
Thanksgiving Holiday

11/19/2009
Wakeley J (2008) Coalescent Theory: An Introduction. Roberts & Company Publishers. Chapter 1.
Discussion Leader: Ana Gonzales

11/12/2009
Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF et al. (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc Natl Acad Sci USA 98: 9161-9166.
Discussion Leader: Ana Gonzales

11/05/2009
Stumpf MP, McVean GA (2003) Estimating recombination rates from population-genetic data. Nat Rev Genet 4: 959-968.
Discussion Leader: Peter Morrell