title: A draft de novo genome assembly for the northern bobwhite (Colinus virginianus) reveals evidence for a rapid decline in effective population size beginning in the Late Pleistocene.
abstract: Wild populations of northern bobwhites (Colinus virginianus; hereafter bobwhite) have declined across nearly all of their U.S. range, and despite their importance as an experimental wildlife model for ecotoxicology studies, no bobwhite draft genome assembly currently exists. Herein, we present a bobwhite draft de novo genome assembly with annotation, comparative analyses including genome-wide analyses of divergence with the chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) genomes, and coalescent modeling to reconstruct the demographic history of the bobwhite for comparison to other birds currently in decline (i.e., scarlet macaw; Ara macao). More than 90% of the assembled bobwhite genome was captured within <40,000 final scaffolds (N50 = 45.4 Kb) despite evidence for approximately 3.22 heterozygous polymorphisms per Kb, and three annotation analyses produced evidence for >14,000 unique genes and proteins. Bobwhite analyses of divergence with the chicken and zebra finch genomes revealed many extremely conserved gene sequences, and evidence for lineage-specific divergence of noncoding regions. Coalescent models for reconstructing the demographic history of the bobwhite and the scarlet macaw provided evidence for population bottlenecks which were temporally coincident with human colonization of the New World, the late Pleistocene collapse of the megafauna, and the last glacial maximum. Demographic trends predicted for the bobwhite and the scarlet macaw also were concordant with how opposing natural selection strategies (i.e., skewness in the r-/K-selection continuum) would be expected to shape genome diversity and the effective population sizes in these species, which is directly relevant to future conservation efforts.
authors.affiliation: Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America.
authors.forename: Yvette A
authors.initials: YA
authors.lastname: Halley
authors.affiliation: Molecular Research LP, Shallowater, Texas, United States of America.
authors.forename: Scot E
authors.initials: SE
authors.lastname: Dowd
authors.affiliation: Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: Jared E
authors.initials: JE
authors.lastname: Decker
authors.affiliation: ElanTech Inc., Greenbelt, Maryland, United States of America.
authors.forename: Paul M
authors.initials: PM
authors.lastname: Seabury
authors.affiliation: Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America.
authors.forename: Eric
authors.initials: E
authors.lastname: Bhattarai
authors.affiliation: Genomics and Bioinformatics Core, Texas A&M AgriLife Research, College Station, Texas, United States of America.
authors.forename: Charles D
authors.initials: CD
authors.lastname: Johnson
authors.affiliation: Rolling Plains Quail Research Ranch, Rotan, Texas, United States of America.
authors.forename: Dale
authors.initials: D
authors.lastname: Rollins
authors.affiliation: Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America.
authors.forename: Ian R
authors.initials: IR
authors.lastname: Tizard
authors.affiliation: Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America.
authors.forename: Donald J
authors.initials: DJ
authors.lastname: Brightsmith
authors.affiliation: Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, Texas, United States of America.
authors.forename: Markus J
authors.initials: MJ
authors.lastname: Peterson
authors.affiliation: Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: Jeremy F
authors.initials: JF
authors.lastname: Taylor
authors.affiliation: Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America.
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Seabury
mesh_terms: D000818:Animals; D003088:Colinus / Q000235:genetics*; D003198:Computer Simulation; D019143:Evolution, Molecular; D005260:Female; D023281:Genomics; D055593:Geological Phenomena; D006801:Humans; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D009154:Mutation; D011156:Population Density; D012091:Repetitive Sequences, Nucleic Acid