ORIGINAL ARTICLE doi:10.1111/evo.13386 Integrating phylogenomic and population genomic patterns in avian lice provides a more complete picture of parasite evolution Andrew D. Sweet,1,2,3 Bret M. Boyd,1,4 Julie M. Allen,1,5 Scott M. Villa,6 Michel P. Valim,7 Jose L. Rivera-Parra,8 Robert E. Wilson,9 and Kevin P. Johnson1 1Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Illinois 61820 2Program in Ecology, Evolution, and Conservation Biology, School of Integrative Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61820 3E-mail:
[email protected] 4Department of Entomology, University of Georgia, Athens, Georgia 30602 5Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 6Department of Biology, University of Utah, Salt Lake City, Utah 84112 7Bioterio´ da Universidade Iguac¸u, Av.Abılio´ Augusto Tavora,´ 2134, RJ 26275, Brazil 8Departamento de Petroleos, Facultad de Geologia y Petroleos, Escuela Politecnica Nacional, Quito, Ecuador 9Institute of Arctic Biology, University of Alaska, Fairbanks, Alaska 99775 Received August 14, 2017 Accepted October 23, 2017 Parasite diversity accounts for most of the biodiversity on earth, and is shaped by many processes (e.g., cospeciation, host switching). To identify the effects of the processes that shape parasite diversity, it is ideal to incorporate both deep (phylogenetic) and shallow (population) perspectives. To this end, we developed a novel workflow to obtain phylogenetic and population genetic data from whole genome sequences of body lice parasitizing New World ground-doves. Phylogenies from these data showed consistent, highly resolved species-level relationships for the lice.