General/Methods:

Andrews KR, Good JM, Miller MR, Luikart G, Hohenlohe PA. 2016. Harnessing the power of RADseq for ecological and evolutionary genomics. Nature Reviews Genetics 17:81-92.

Stevison LS, Woerner AE, Kidd JM, Kelley JL, Veeramah KR, McManus KF, Bustamante CD, Hammer MF, Wall JD. 2015. The time-scale of recombination rate evolution in great apes. Molecular Biology and Evolution:msv331.

Frantzke, A., Koch, M. A., & Mummenhoff, K. Turnip Time Travels: Age Estimates in Brassicaceae (2016). Trends in Plant Science.

Duforet-Frebourg N, Luu K, Laval G, Bazin E, Blum MG. 2015. Detecting genomic signatures of natural selection with principal component analysis: application to the 1000 Genomes data. Molecular Biology and Evolution:msv334.

Fijarczyk, A. and Babik, W. (2015), Detecting balancing selection in genomes: limits and prospects. Mol Ecol, 24: 3529–3545. doi:10.1111/mec.13226

Sharp NP, Agrawal AF. 2016. Low genetic quality alters key dimensions of the mutational spectrum. PLoS Biology 14:e1002419

Dittmar EL, Oakley CG, Conner JK, Gould BA, Schemske DW. 2016. Factors influencing the effect size distribution of adaptive substitutions. Proc Roy Soc B. 283: 20153065

Demographic inference

The following two papers could be read together:

Schrider D, Shanku AG, Kern AD. 2016. Effects of linked selective sweeps on demographic inference and model selection. bioRxiv

Cornille A, Salcedo A, Kryvokhyzha D, Glémin S, Holm K, Wright S, Lascoux M. 2016. Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd’s purse (Capsella bursa‐pastoris). Molecular Ecology 25:616-629.

Mating systems

Hartfield, M. & Glemin, S. (2015) Limits to adaptation in partially selfing species. BioRxiv

Shimizu, K. K. and Tsuchimatsu, T. (2015) Evolution of Selfing: Recurrent Patterns in Molecular Adaptation
– Annual Review of Ecology, Evolution, and Systematics

Brys, R. and Jacquemyn, H. (2016), Severe outbreeding and inbreeding depression maintain mating system differentiation in Epipactis (Orchidaceae). Journal of Evolutionary Biology, 29: 352–359. doi: 10.1111/jeb.12787

S-locus

Charlesworth, D. 2016. The status of supergenes in the 21st century: recombination suppression in Batesian mimicry and sex chromosomes and other complex adaptations. Evolutionary Applications, 9: 74–90. doi: 10.1111/eva.12291

Lin, Z., Eaves, D. J., Sanchez-Moran, E., Franklin, F. C., & Franklin-Tong, V. E. 2015. The Papaver rhoeas S determinants confer self-incompatibility to Arabidopsis thaliana in plants. Science
Lora, J., Hormaza, J. I., & Herrero, M. 2016. The Diversity of the Pollen Tube Pathway in Plants: Toward an Increasing Control by the Sporophyte. Frontiers in Plant Science, 7, 107.

Ancient eDNA/metagenomics

Birks HJB, Birks HH, 2016. How have studies of ancient DNA from sediments contributed to the reconstruction of Quaternary floras? New Phytologist 209: 499-506.

Poinar HN, Schwarz C, Qi J, Shapiro B, et al., 2006. Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science 311: 392-394.

Parducci L, Väliranta M, Salonen JS, et al., 2015. Proxy comparison in ancient peat sediments: Pollen, macrofossil and plant DNA. Philosophical Transactions of the Royal Society of London Series B: Biological Sciences 370: 20130382.

 

Gene expression evolution

Arunkumar, R., Maddison, T. I., Barrett, S. C., & Wright, S. I. 2016 Recent mating-system evolution in Eichhornia is accompanied by cis-regulatory divergence. New Phytologist.

Metzger et al. 2016 Contrasting frequencies and effects on cis– and trans-regulatory mutations affecting gene expression. Molecular Biology and Evolution doi: 10.1093/molbev/msw011 

Gossmann et al. 2016. Transcriptomes of plant gametophytes have a higher proportion of rapidly evolving and young genes than sporophytes. Molecular Biology and Evolution doi:10.1093/molbev/msw044 

Babarinde & Saitou  2016  Genomic locations of conserved noncoding sequences and their proximal protein-coding genes in mammalian expression dynamics. Molecular Biology and Evolution doi:10.1093/molbev/msw058 

Léon-Novelo et al. 2014. A flexible bayesian method for detecting allelic imbalance in RNA-seq data. BMC Genomics 15:920