Denver DR, Howe DK, Wilhelm LJ, Palmer CA, Anderson JL, Stein KC, Phillips PC & Estes S 2010 Selective sweeps and parallel mutation in the adaptive recovery from deleterious mutation in Caenorhabditis elegans. Genome Res 20:1663-1671. DNA …

Paul JS & Song YS 2010 A principled approach to deriving approximate conditional sampling distributions in population genetics models with recombination. Genetics 186:321-338.

Jenkins PA & Song YS 2010 An asymptotic sampling formula for the coalescent with recombination. Ann Appl Prob 20:1005-1028.

Griffiths RC, Jenkins PA & Song YS 2008 Importance sampling and the two-locus model with subdivided population structure. Adv Appl Prob 40:473-500.

Hazle T & Bonen L 2007 Comparative analysis of sequences preceding protein-coding mitochondrial genes in flowering plants. Mol Biol Evol 24:1101-1112. we examined the nucleotide sequences preceding 23 mitochondrial protein-coding genes hel…

Kubo T & Newton KJ 2008 Angiosperm mitochondrial genomes and mutations. Mitochondrion 8:5-14. the sizes of angiosperm mitochondrial genomes have expanded since plants colonized the land although the genomes have lost some genes during this…

Palmer JD, Adams KL, Cho Y, Parkinson CL, Qiu Y-L & Song K 2000 Dynamic evolution of plant mitochondrial genomes: mobile genes and introns and highly variable mutation rates. PNAS 97:6960-6966. we summarize our recent studies showing that …

Bafna V & Pevzner PA 1995 Sorting by reversals: genome rearrangements in plant organelles and evolutonary history of X chrmosome. Mol Biol Evol 12:239-246. table 1 presents the results of our program on a series of experimental data by Pal…

Palmer JD & Herbon LA 1988 Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence. J Mol Evol 28:87-97. the rate of rearrangements is extraordinarily faster in plant mtDNA than in cpDNA and animal mtDNA we shall use "…

Kuo D, Licon K, Bandyopadhyay S, Chuang R, Luo C, Catalana J, Ravasi T, Tan K & Ideker T 2010 Coevolution within a transcriptional network by compensatory trans and cis mutations. Genome Res 20:1672-1678. a trans mutation has occurred very…

Emerson JJ, Hsieh L-H, Sung H-M, Wang T-Y, Huang C-J, Lu HH-S, Lu M-YJ, Wu S-H & Li W-H 2010 Natural selection on cis and trans regulation in yeasts. Genome Res 20:826-836. expression polymorphism in yeast is common for both cis and trans …

Connallon T & Clark AG 2010 Sex linkage, sex-specific selection, and the role of recombination in the evolution of sexually dimorphic gene expression. Evolution 64:3417-42.

Charlesworth B 2010 Molecular population genomics: a short history. Genet Res 92:397-411. it is interesting to note that Alan Robertson and Bill Hill (Robertson & Hill, 1983) used the results of Orkin et al. (1982) to infer that the mean n…

Genetics Research (GRH) 50 years celebration we have made a selection of papers freely available until 31 December 2010 these papers include the most-read paper of each decade*, as well as some well-cited papers+ from more recent issues * …

Streisfeld MA & Rausher MD 2010 Population genetics, pleiotropy, and the preferential fixation of mutations during adaptive evolution. Evolution 65:629-642. fixation bias can be strong ..., likely due to differences in the magnitude of del…

Chevin L-M, Martin G & Lenormand T 2010 Fisher's model and the genomics of adaptation: restricted pleiotropy, heterogenous mutation, and parallel evolution. Evolution 64:3213-3231. if all loci exhibit a similar and large degree of pleiotro…

Hohenlohe PA, Phillips PC & Cresko WA 2010 Using population genomics to detect selection in natural populations: key concepts and methodological considerations. Int J Plant Sci 171:1059-1071. as with genomewide association studies, epistat…

Schatz MC, Delcher AL & Salzberg SL 2010 Assembly of large genomes using second-generation sequencing. Genome Res 20:1165-1173. the scaffolding phase of assembly focuses on resolving repeats by linking the initial contigs into scaffolds, g…

Young AL, Abaan HO, Zerbino D, Mullikin JC, Birney E & Margulies EH 2010 A new strategy for genome assembly using short sequence reads and reduced representation libraries. Genome Res 20:249-256. the WGS assembly was conducted at the upper…

Zerbino DR & Birney E 2008 Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829. Vervet

Klingenberg CP 2010 Evolution and development of shape: integrating quantitative approaches. Nat Rev Genet 11:623-635. modularity is a general property of biological systems from molecular interactions to ecosystem function developmental m…

Barton NH 2010 Genetic linkage and natural selection. Phil Trans R Soc Lond B 365:2559-2569. can we really believe that natural populations are subject to the homogeneous selection envisaged by the current view of molecular evolution? almo…

Hall MC, Lowry DB & Willis JH 2010 Is local adaptation in Mimulus guttatus caused by trade-offs at individual loci? Mol Ecol 19:2739-2753. local adaptation is largely controlled by non-overlapping loci reduced gene flow prevents the evolut…

Kaessmann H 2010 Origins, evolution, and phenotypic impact of new genes. Genome Res 20:1313-1326. the observation of numerous functional retrogenes in various genomes (detailed below) immediately raises the question of how retrocopies can …

Kaessmann H, Vinckenbosch N & Long M 2009 RNA-based gene duplication: mechanistic and evolutionary insights. Nat Rev Genet 10:19-31. intron gains are rare events during evolution intron loss seems to be more frequent in mammals, for exampl…

Okamura K & Nakai K 2008 Retrotransposition as a source of new promoters. Mol Biol Evol 25:1231-1238. we identified 29 gene pairs in the human genome, consisting of a functional retrotransposed gene and its parental gene a large part of th…

Coop G, Witonsky D, Di Rienzo A & Pritchard JK 2010 Using environmental correlations to identify loci underlying local adaptation. Genetics 185:1411-1423. loci involved in local adaptation can potentially be identified by an unusual correl…

Ralph P & Coop G 2010 Parallel adaptation: one or many waves of advance of an advantageous allele? Genetics 186:647-668. we study various models of parallel mutation in a continuous, geographically spread population adapting to a global se…

Hancock AM, Witonsky DB, Ehlera E, Alkorta-Aranburu G, Beallc C, Gebremedhind A, Sukernike R, Utermannf G, Pritchard JK, Coop G & Di Rienzo A 2010 Human adaptations to diet, subsistence, and ecoregion are due to subtle shifts in allele fre…

Hancock AM, Witonsky DB, Gordon AS, Eshel G, Pritchard JK, Coop G & Di Rienzo A 2008 Adaptations to climate in candidate genes for common metabolic disorders. PLoS Genet 4:e32.