1. Phillips, PC 2005. Testing hypotheses regarding the genetics of adaptation Genetica 123: 15-24.
2. Ehrenreich, IM; Purugganan, MD 2006. The molecular genetic basis of plant adaptation. Amer. J. Bot. 93:953-962.
3. Hughes, AR; Inouye, BD; Johnson, MTJ, et al. 2008. Ecological consequences of genetic diversity. Ecol. Lett. 11: 609-623.
4. Tenaillon, MI; Tiffin, PL 2008. The quest for adaptive evolution: a theoretical challenge in a maze of data. Curr. Op. Plant Biol. 11: 110-115.

Jan 27. Molecular signatures of selection

1. Nielsen, R 2005. Molecular signatures of natural selection. Ann. Rev. Genet. 39: 197-218.
2. Ford, MJ 2002. Applications of selective neutrality tests to molecular ecology. Mol Ecol. 11: 1245-1262.
3. Eyre-Walker, A 2006. The genomic rate of adaptive evolution. TREE 21: 569-575.
4. Namroud, MC; Beaulieu, J; Juge, N, et al. 2008. Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce. Mol. Ecol. 17: 3599-3613.

Feb 3. Roles of regulatory vs. structural genes in adaptation

1. Hoekstra, HE; Coyne, JA 2007. The locus of evolution: Evo devo and the genetics of adaptation. Evolution 61: 995-1016.
2. Stern, DL; Orgogozo, V 2008. The loci of evolution: How predictable is genetic evolution? Evolution 62: 2155-2177.
3. Lynch, VJ; Wagner, GP 2008. Resurrecting the role of transcription factor change in developmental evolution. Ann. Rev. Genet. 39: 197-218.
4. Hanikenne, M; Talke, IN; Haydon, MJ, et al. 2008. Evolution of metal hyperaccumulation required cis-regulatory changes and triplication of HMA4. Nature 453:391-U44.

Feb 10. Spatial environmental heterogeneity I: Clines

1. Storz, JF; Sabatino, SJ; Hoffmann, FG, et al. 2007. The molecular basis of high-altitude adaptation in deer mice. PLOS Genet. 3: 448-459.
2. Schmidt, PS; Zhu, CT; Das, J, et al. 2008. An amino acid polymorphism in the couch potato gene forms the basis for climatic adaptation in Drosophila melanogaster. PNAS 105: 16207-16211.
3. Zhen, Y; Ungerer, MC 2008a. Clinal variation in freezing tolerance among natural accessions of Arabidopsis thaliana. New Phytol. 177: 419-427.
4. Zhen Y; Ungerer MC 2008b. Relaxed selection on the CBF/DREB1 regulatory genes and reduced freezing tolerance in the southern range of Arabidopsis thaliana. Mol. Biol. Evol. 25: 2547-2555.

Feb 17. Spatial environmental heterogeneity II: Localized adaptation

1. Schlotterer, C 2002. Towards a molecular characterization of adaptation in local populations. Curr. Op. Genet. Devel. 12: 683-687.
2. Herrera, CM; Bazaga, P 2008. Population-genomic approach reveals adaptive floral divergence in discrete populations of a hawk moth-pollinated violet. Mol. Ecol. 17: 5378-5390.
3. Savolainen, O; Pyhajarvi, T; Knurr, T 2007. Gene flow and local adaptation in trees. Ann. Rev. Ecol. Evol. Syst. 38: 595-619.
4. Bridle, JR; Vines, TH 2007. Limits to evolution at range margins:Title: Limits to evolution at range margins: when and why does adaptation fail? TREE 22: 140-147.

Feb 24. Adaptation via genome duplication, gene duplication

1. Cliften, PF; Fulton, RS; Wilson, RK, et al. 2006. After the duplication: Gene loss and adaptation in Saccharomyces genomes. Genetics 172: 863-872.
2. Chen, ZZ; Cheng, CHC; Zhang, JF, et al. 2007. Transcriptomic and genomic evolution under constant cold in Antarctic notothenioid fish. PNAS 105: 12944-12949.
3. Beisswanger, S; Stephan, W 2008. Evidence that strong positive selection drives neofunctionalization in the tandemly duplicated polyhomeotic genes in Drosophila. PNAS 105: 5447-5452.
4. Semon, M; Wolfe, KH 2008. Preferential subfunctionalization of slow-evolving genes after allopolyploidization in Xenopus laevis. PNAS 105: 8333-8338.

March 3. Invasive species

1. Dlugosch, KM; Parker, IM 2008. Founding events in species invasions: genetic variation, adaptive evolution, and the role of multiple introductions. Mol. Ecol. 17; 431-449.
2. Rosenthal, DM; Ramakrishnan, AP; Cruzan, MB 2008. Evidence for multiple sources of invasion and intraspecific hybridization in Brachypodium sylvaticum (Hudson) Beauv. in North America. Mol. Ecol. 17: 4657-4669.
3. Brown, JE; Stepien, CA 2009. Invasion genetics of the Eurasian round goby in North America: tracing sources and spread patterns. Mol. Ecol. 18: 64-79.
4. Carroll, SP 2008. Facing change: forms and foundations of contemporary adaptation to biotic invasions. Mol. Ecol. 17: 361-372.

(March 10. No class — Spring Break)

March 17. Experimental evolution

1. Bull, JJ; Molineux, IJ 2008. Predicting evolution from genomics: experimental evolution of bacteriophage T7. Heredity 100: 453-463.
2. Hillesland, KL; Velicer, GJ; Lenski, RE 2009. Experimental evolution of a microbial predator's ability to find prey. Proc Roy. Soc. B. 276: 459-467.
3. Rogers, DW; Greig, D 2009. Experimental evolution of a sexually selected display in yeast. Proc Roy. Soc. B. 276: 543-549.
4. Oxman, E; Mon, U; Dekel, E 2008. Defined order of evolutionary adaptations: Experimental evidence. Evolution 62: 1547-1554.

March 24. Ecological speciation I: Reproductive isolating barriers

1. Mallet, J 2006. What does Drosophila genetics tell us about speciation? TREE 21: 386-393.
2. Turner, TL; Hahn, MW; Nuzhdin, SV 2005. Genomic islands of speciation in Anopheles gambiae. PLoS Biology 3: 1572-1578.
3. Lowry, DB; Modliszewski, JL; Wright, KM, et al. 2008. The strength and genetic basis of reproductive isolating barriers in flowering plants. Phil Trans. Royal Soc. B 363: 3009-3021.
4. Martin, NH; Sapir, Y; Arnold, ML 2008. The genetic architecture of reproductive isolation in Louisiana irises: Pollination syndromes and pollinator preferences. Evolution 62: 740-752.

March 31. Ecological speciation II: Mechanisms of adaptive divergence

1. Seehausen, O; Terai, Y; Magalhaes, IS, et al. 2008. Speciation through sensory drive in cichlid fish. Nature 455: 620-U23.
2. Arias, CF; Munoz, AG; Jiggins, CD, et al. 2008. A hybrid zone provides evidence for incipient ecological speciation in Heliconius butterflies. Mol. Ecol. 21: 4699-4712.
3. Lowry, DB; Rockwood, RC; Willis, JH 2008. Ecological reproductive isolation of coast and inland races of Mimulus guttatus. 62: 2196-2214.
4. Nosil, P; Egan, SP; Funk, DJ 2008. Heterogeneous genomic differentiation between walking-stick ecotypes: "Isolation by adaptation" and multiple roles for divergent selection. 62: 316-336.

April 7. Transposable Elements

1. Lowe, CB; Bejerano, G; Haussler, D 2007. Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. PNAS 104: 8005-8010.
2. Gonzalez, J; Lenkov, K; Lipatov, M, et al. 2008. High rate of recent transposable element-induced adaptation in Drosophila melanogaster. PLoS Biology 6: 2109-2129.
3. Volff, JN 2006. Turning junk into gold: domestication of transposable elements and the creation of new genes in eukaryotes. Bioessays 9: 913-922.
4. Jiang, N; Bao, ZR; Zhang, XY, et al. 2004. Pack-MULE transposable elements mediate gene evolution in plants. Nature 431: 569-573.

April 14. Adaptive Introgression; Horizontal (lateral) gene transfer

1. Arnold, ML; Sapir, Y; Martin, NH 2008. Genetic exchange and the origin of adaptations: prokaryotes to primates. Phil. Trans. Royal Soc. B. 363: 2813-2820.
2. Grant, BR; Grant, PR 2008. Fission and fusion of Darwin's finches populations 363: 2821-2829. Phil. Trans. Royal Soc. B.
3. Keeling, PJ; Palmer, JD 2008. Horizontal gene transfer in eukaryotic evolution. Nature Rev. Genet. 9: 605-618.
4. Bergthorsson, U; Richardson, AO; Young, GJ, et al. 2004. Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. PNAS 101: 17747-17752.

April 21. Evolutionary Convergence/parallelism

1. Arendt J; Reznick D 2008. Convergence and parallelism reconsidered: what have we learned about the genetics of adaptation? TREE 23: 26-32.
2. Steiner, CC; Rompler, H; Boettger, LM, et al. 2009. The genetic basis of phenotypic convergence in beach mice: similar pigment patterns but different genes. Mol. Biol. Evol. 26: 35-45.
3. Gross JB; Borowsky R; Tabin CJ 2009. A Novel Role for Mc1r in the parallel evolution of depigmentation in independent populations of the cavefish Astyanax mexicanus. PLoS Genetics 1: e1000326.
4. Baxter, SW; Papa, R; Chamberlain, N, et al. 2008. Convergent evolution in the genetic basis of Müllerian mimicry in Heliconius butterflies. Genetics 180: 1567-1577.