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…