title: Phylogenomics using Target-Restricted Assembly Resolves Intrageneric Relationships of Parasitic Lice (Phthiraptera: Columbicola).
abstract: Parasitic "wing lice" (Phthiraptera: Columbicola) and their dove and pigeon hosts are a well-recognized model system for coevolutionary studies at the intersection of micro- and macroevolution. Selection on lice in microevolutionary time occurs as pigeons and doves defend themselves against lice by preening. In turn, behavioral and morphological adaptations of the lice improve their ability to evade host defense. Over macroevolutionary time wing lice tend to cospeciate with their hosts; yet, some species of Columbicola have switched to new host species. Understanding the ecological and evolutionary factors that influence coadaptation and codiversification in this system will substantially improve our understanding of coevolution in general. However, further work is hampered by the lack of a robust phylogenetic framework for Columbicola spp. and their hosts. Previous attempts to resolve the phylogeny of Columbicola based on sequences from a few genes provided limited support. Here, we apply a new approach, target restricted assembly, to assemble 977 orthologous gene sequences from whole-genome sequence data generated from very small, ethanol-preserved specimens, representing up to 61 species of wing lice. Both concatenation and coalescent methods were used to estimate the species tree. These two approaches yielded consistent and well-supported trees with 90% of all relationships receiving 100% support, which is a substantial improvement over previous studies. We used this new phylogeny to show that biogeographic ranges are generally conserved within clades of Columbicola wing lice. Limited inconsistencies are probably attributable to intercontinental dispersal of hosts, and host switching by some of the lice. [aTRAM; coalescent; coevolution; concatenation; species tree.].
authors.affiliation: Department of Entomology, University of Georgia Athens, 413 Biological Sciences Building, Athens, GA 30602, USA.|Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL 61820, USA.
authors.forename: Bret M
authors.initials: BM
authors.lastname: Boyd
authors.affiliation: Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL 61820, USA.|Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.
authors.forename: Julie M
authors.initials: JM
authors.lastname: Allen
authors.affiliation: Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA.
authors.forename: Nam-Phuong
authors.initials: NP
authors.lastname: Nguyen
authors.affiliation: Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL 61820, USA.
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Sweet
authors.affiliation: Departments of Computer Science and Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Tandy
authors.initials: T
authors.lastname: Warnow
authors.affiliation: Department of Biology, University of Utah, Salt Lake City, UT 84112, USA.
authors.forename: Michael D
authors.initials: MD
authors.lastname: Shapiro
authors.affiliation: Department of Biology, University of Utah, Salt Lake City, UT 84112, USA.
authors.forename: Scott M
authors.initials: SM
authors.lastname: Villa
authors.affiliation: Department of Biology, University of Utah, Salt Lake City, UT 84112, USA.
authors.forename: Sarah E
authors.initials: SE
authors.lastname: Bush
authors.affiliation: Department of Biology, University of Utah, Salt Lake City, UT 84112, USA.
authors.forename: Dale H
authors.initials: DH
authors.lastname: Clayton
authors.affiliation: Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL 61820, USA.
authors.forename: Kevin P
authors.initials: KP
authors.lastname: Johnson
mesh_terms: D000818:Animals; D010856:Columbidae / Q000469:parasitology; D016678:Genome / Q000235:genetics*; D058507:Host Specificity; D006790:Host-Parasite Interactions; D008003:Phthiraptera / Q000145:classification* / Q000235:genetics* / Q000502:physiology; D010802:Phylogeny