BI582: "Next-gen" Molecular Ecology - Readings for Discussion - Spring 2010

25 January - Gene Expression

Cheviron ZA, Whitehead A, Brumfield RT (2008) Transcriptomic variation and plasticity in rufous-collared sparrows (Zonotrichia capensis) along an altitudinal gradient. Molecular Ecology 17, 4556-4569.

Stillman JH, Tagmount A (2009) Seasonal and latitudinal acclimatization of cardiac transcriptome responses to thermal stress in porcelain crabs, Petrolisthes cinctipes. Molecular Ecology 18, 4206-4226.

Hodgins-Davis A, Townsend JP (2009) Evolving gene expression: from G to E to G x E. Trends in Ecology & Evolution 24, 649-658.

1 February - Disease

Blanchong JA, Samuel MD, Scribner KT, et al. (2008) Landscape genetics and the spatial distribution of chronic wasting disease. Biology Letters 4, 130-133.

Margos G, Gatewood AG, Aanensen DM, et al. (2008) MLST of housekeeping genes captures geographic population structure and suggests a European origin of Borrelia burgdorferi. Proceedings of the National Academy of Sciences of the United States of America 105, 8730-8735.

Rosenblum EB, Poorten TJ, Settles M, et al. (2009) Genome-wide transcriptional response of Silurana (Xenopus) tropicalis to infection with the deadly chytrid fungus. PLoS One 4, e6494.

Venkatesan M, Rasgon JL (in press) Population genetic data suggest a role for mosquito mediated dispersal of West Nile virus across the western United States. Molecular Ecology.

8 February - Tanscriptomics

Toth AL, Varala K, Newman TC, et al. (2007) Wasp gene expression supports an evolutionary link between maternal behavior and eusociality. Science 318, 441-444.

Yoder-Himes DR, Chain PSG, Zhu Y, et al. (2009) Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proceedings of the National Academy of Sciences of the United States of America 106, 3976-3981.

Zhu HS, Casselman A, Reppert SM (2008) Chasing Migration Genes: A Brain Expressed Sequence Tag Resource for Summer and Migratory Monarch Butterflies (Danaus plexippus). Plos One 3, e1345.

Background reading:

Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics 10, 57-63.

16 February - Human Evolutionary Genomics

Coop G, Pickrell JK, Novembre J, et al. (2009) The role of geography in human adaptation. Plos Genetics 5.

Monot M, Honore N, Garnier T, et al. (2009) Comparative genomic and phylogeographic analysis of Mycobacterium leprae. Nature Genetics 41, 1282-U1239.

Novembre J, Johnson T, Bryc K, et al. (2008) Genes mirror geography within Europe. Nature 456, 98-U95.

22 February - Prokaryote-Eukaryote Symbiosis

Degnan PH, Yu Y, Sisneros N, Wing RA, Moran NA (2009) Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors. Proceedings of the National Academy of Sciences of the United States of America 106, 9063-9068.

Moya A, Pereto J, Gil R, Latorre A (2008) Learning how to live together: genomic insights into prokaryote-animal symbioses. Nature Reviews Genetics 9, 218-229.

Wier AM, Nyholm SV, Mandel MJ, et al. (2010) Transcriptional patterns in both host and bacterium underlie a daily rhythm of anatomical and metabolic change in a beneficial symbiosis. Proceedings of the National Academy of Sciences of the United States of America 107, 2259-2264.

1 March - Molecular Ecology Special Issue, 1

Tautz et al. (2010) Next generation molecular ecology. Molecular Ecology 19, 1–3.

Whittall et al. (2010) Finding a (pine) needle in a haystack: chloroplast genome sequence divergence in rare and widespread pines. Molecular Ecology 19, 100–114.

Ferguson et al. (2010) Characterization of a hotspot for mimicry: assembly of a butterfly wing transcriptome to genomic sequence at the HmYb⁄Sb locus. Molecular Ecology 19, 240–254.

15 March - Molecular Ecology Special Issue, 2

Harr B, Turner LM (2010) Genome-wide analysis of alternative splicing evolution among Mus subspecies. Molecular Ecology 19, 228-239.

Wolf JBW, Bayer T, Haubold B, Schilhable M, Rosenstiel P, Tautz D (2010) Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow. Molecular Ecology 19, 162-175.

22 March - Genomics of Adaptation

Renaut S, Nolte A, Beratchez L (2010) Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonus spp. Salmonidae). Molecular Ecology 19, 115-131.

Hohenlohe PA, Bassham S, Etter PD, Stiffler N, Johnson EA, Cresko WA (2010) Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genetics 6, e1000862.

5 April - Microbial Symbioses

Ley RE, Hamady M, Lozupone C, et al. (2008) Evolution of mammals and their gut microbes. Science 320, 1647-1651.

Mandel MJ, Wollenberg MS, Stabb EV, Visick KL, Ruby EG (2009) A single regulatory gene is sufficient to alter bacterial host range. Nature 458, 215-U217.

Turnbaugh PJ, Hamady M, Yatsunenko T, et al. (2009) A core gut microbiome in obese and lean twins. Nature 457, 480-U487.

22 April - Zebra Finch Genome & Recombination

Warren WC, Clayton DF, Ellegren H, et al. (2010) The genome of a songbird. Nature 464, 757-762.

Clayton DF, Balakrishnan CN, London SE (2009) Integrating genomes, brain and behavior in the study of songbirds. Current Biology 19, R865-R873.

Backstrom N, Forstmeier W, Schielzeth H, et al. (2010) The recombination landscape of the zebra finch Taeniopygia guttata genome. Genome Res 20, 485-495.

Balakrishnan CN, Edwards SV (2009) Nucleotide variation, linkage disequilibrium and founder-facilitated speciation in wild populations of the zebra finch (Taeniopygia guttata). Genetics 181, 645-660.

26 April - Phylogenomics and Speciation

Hallstrom BM, Janke A (2008) Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations. BMC Evolutionary Biology 8.

Kane NC, King MG, Barker MS, et al. (2009) Comparative genomic and population genetic analyses indicate highly porous genomes and high levels of gene flow between divergent Helianthus species. Evolution 63, 2061-2075.

Kriegs JO, Churakov G, Kiefmann M, et al. (2006) Retroposed elements as archives for the evolutionary history of placental mammals. PLoS Biology 4, 537-544.