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Speidel L, Forest M, Shi S & Myers SR 2019 A method for genome-wide genealogy estimation for thousands of samples. Nat Genet 51:1321-1329. [based on the preprint version downloaded at bioRχiv] all populations show a remarkable increase in …

Paulose J, Hermisson J & Hallatschek O 2019 Spatial soft sweeps: patterns of adaptation in populations with long-range dispersal. PLoS Genet 15:e1007936. soft sweeps become likely when the time taken for an established mutation to fix in t…

Harris RB, Sackman A & Jensen JD 2018 On the unfounded enthusiasm for soft selective sweeps II: examining recent evidence from humans, flies, and viruses. PLoS Genet 14:e1007859. all three examples are prone to extremely high false-positiv…

Jensen JD, Payseur BA, Stephan W, Aquadro CF, Lynch M, Charlesworth D & Charlesworth B 2019 The importance of the Neutral Theory in 1968 and 50 years on: a response to Kern and Hahn 2018. Evolution 73:111-114. inaccuracies can sometimes mo…

Stone GN, Nee S & Felsenstein J 2011 Controlling for non-independence in comparative analysis of patterns across populations within species. Phil Trans R Soc B 366:1410-1424. the phylogeny-based approaches widely used in cross-species anal…

Avice JC & Robinson TJ 2008 Hemiplasy: a new term in the lexicon of phylogenetics. Syst Biol 57:503-507. hemiplasy is a bona fide form of homology (allelic orthology in this case) that nonetheless can give the illusion of homoplasy in an o…

Hahn MW & Nakhleh L 2016 Irrational exuberance for resolved species trees. Evolution 70:7-17. the mapping of traits onto trees generally uses only a single representation of the species tree, ignoring variation in the gene trees used to co…

Copetti D, Búrquez A, Bustamante E, Charboneau JLM, Childs KL, Eguiarte LE, Lee S, LIiu TL, McMahon MM, Whiteman NK, Wing RA, Wojciechowski MF & Sanderson MJ 2018 Extensive gene tree discordance and hemiplasy shaped the genomes of North Am…

Mendes FK, Fuentes-González JA, Schraiber JG & Hahn MW 2018 A multispecies coalescent model for quantitative traits. eLife 7:e36482. the development of models incorporating discordance in order to deal with trait evolution have lagged behi…

Jouganous J, Long W, Ragsdale AP & Gravel S 2017 Inferring the joint demographic history of multiple populations: beyond the diffusion approximation. Genetics 206:1549-1567. we propose a tractable model of ordinary differential equations f…

Jay F, Boitard S & Austerlitz F 2019 An ABC method for whole-genome sequence data: inferring paleolithic and neolithic human expansions. Mol Biol Evol 36:1565-1579. [based on the preprint version downloaded at bioRχiv] the inferred effecti…

Browning SR, Browning BL, Daviglus ML, Durazo-Arvizu RA, Schneiderman N, Kaplan RC & Laurie CC 2018 Ancestry-specific recent effective population size in the Americas. PLoS Genet 14:e1007385. we use identity by descent and local ancestry i…

Ragsdale AP & Gutenkunst RN 2017 Inferring demographic history using two-locus statistics. Genetics 206:1037-1048. methods based on aggregating the statistics of many single loci into an allele frequency spectrum (AFS) have proven powerful…

Bunnefeld L, Frantz LAF & Lohse K 2015 Inferring bottlenecks from genome-wide samples of short sequence blocks. Genetics 201:1157-1169. we extend the site frequency spectrum by counting mutations in frequency classes in short sequence bloc…

Anciaux Y, Chevin L-M, Ronce O & Martin G 2018 Evolutionary rescue over a fitness landscape. Genetics 209:265-279. we will focus on the case where environmental stress causes a reduction of population mean fitness that is harsh enough to t…

Waxman D 2009 Fixation at a locus with multiple alleles: structure and solution of the Wright Fisher model. J Theor Biol 257:245-251. the distribution of allele frequencies in adults is directly determined from the distribution of adult ge…

Shafiey H & Waxman D 2017 Exact results for the probability and stochastic dynamics of fixation in the Wright-Fisher model. J Theor Biol 430:64-77. 6.2. fixing trajectories for a neutral fixation probability Yt + 1 = Bin(N − 1, Yt) / N + 1 …

Kern AD & Hahn MW 2018 The neutral theory in light of natural selection. Mol Biol Evol 35:1366-1371. the neutral theory was supported by unreliable theoretical and empirical evidence from the beginning in light of modern, genome-scale data…

Novembre J & Barton NH 2018 Tread lightly interpreting polygenic tests of selection. Genetics 208:1351-1355. by aggregating small signals of change across many such loci, directional natural selection is now in principle detectable using g…

Racimo F, Berg JJ & Pickrell JK 2018 Detecting polygenic adaptation in admixture graphs. Genetics 208:1565-1584. if a trait is polygenic, positive selection may instead occur by concerted shifts at many loci that all contribute to the vari…

Gao F & Keinan A Explosive genetic evidence for explosive human population growth. Curr Opin Genet Dev 41:130-139. the main limitation of SFS-based methods is that they do not use important information from linkage disequilibrium there is …

Aimé C & Austerlitz F 2017 Different kinds of genetic markers permit inference of Paleolithic and Neolithic expansions in humans. Eur J Hum Genet 25:360-365. previous Paleolithic demographic expansions may have promoted the emergence of fa…

Papp B, Notebaart RA & Pál C 2011 Systems-biology approaches for predicting genomic evolution. Nat Rev Genet 12:591-602. is evolution predictable at the molecular level? this Review investigates recent progresses in mapping evolutionary tr…

Green RM, Fish JL, Young NM, Smith FJ, Roberts B, Dolan K, Choi I, Leach CL, Gordon P, Cheverud JM, Roseman CC, Williams TJ, Marcucio RS & Hallgrímsson B 2017 Developmental nonlinearity drives phenotypic robustness. Nat Commun 8:1970. exce…

Jain K & Stephan W 2017 Rapid adaptation of a polygenic trait after a sudden environmental shift. Genetics 206:389-406. we can observe evolution in action evolution can be so rapid that evolutionary and ecological timescales are confluent …

Jain K & Stephan W 2017 Modes of rapid polygenic adaptation. Mol Biol Evol 34:3169-3175. in contrast to the classical model of directional selection (Charlesworth and Charlesworth 2010), here the strength of selection also depends on the d…

Booker TR, Jackson BC & Keightley PD 2017 Detecting positive selection in the genome. BMC Biol 15:98. Fig. 1 d incomplete/partial sweeps if an advantageous allele increases in frequency, but does not reach fixation, there will still be som…

Galtier N 2016 Adaptive protein evolution in animals and the effective population size hypothesis. PLoS Genet 12:e1005774. the proportion of adaptive amino-acid substitution is found to be positively correlated to species effective populat…

Harris K & Prichard JK 2017 Rapid evolution of the human mutation spectrum. eLife 6:e24284. shifts in generation time or other life-history traits may affect mutational spectra, particularly for CpG transitions most CpG transitions result …