title: Northern Bobwhite (Colinus virginianus) Mitochondrial Population Genomics Reveals Structure, Divergence, and Evidence for Heteroplasmy.
abstract: Herein, we evaluated the concordance of population inferences and conclusions resulting from the analysis of short mitochondrial fragments (i.e., partial or complete D-Loop nucleotide sequences) versus complete mitogenome sequences for 53 bobwhites representing six ecoregions across TX and OK (USA). Median joining (MJ) haplotype networks demonstrated that analyses performed using small mitochondrial fragments were insufficient for estimating the true (i.e., complete) mitogenome haplotype structure, corresponding levels of divergence, and maternal population history of our samples. Notably, discordant demographic inferences were observed when mismatch distributions of partial (i.e., partial D-Loop) versus complete mitogenome sequences were compared, with the reduction in mitochondrial genomic information content observed to encourage spurious inferences in our samples. A probabilistic approach to variant prediction for the complete bobwhite mitogenomes revealed 344 segregating sites corresponding to 347 total mutations, including 49 putative nonsynonymous single nucleotide variants (SNVs) distributed across 12 protein coding genes. Evidence of gross heteroplasmy was observed for 13 bobwhites, with 10 of the 13 heteroplasmies involving one moderate to high frequency SNV. Haplotype network and phylogenetic analyses for the complete bobwhite mitogenome sequences revealed two divergent maternal lineages (dXY = 0.00731; FST = 0.849; P < 0.05), thereby supporting the potential for two putative subspecies. However, the diverged lineage (n = 103 variants) almost exclusively involved bobwhites geographically classified as Colinus virginianus texanus, which is discordant with the expectations of previous geographic subspecies designations. Tests of adaptive evolution for functional divergence (MKT), frequency distribution tests (D, FS) and phylogenetic analyses (RAxML) provide no evidence for positive selection or hybridization with the sympatric scaled quail (Callipepla squamata) as being explanatory factors for the two bobwhite maternal lineages observed. Instead, our analyses support the supposition that two diverged maternal lineages have survived from pre-expansion to post-expansion population(s), with the segregation of some slightly deleterious nonsynonymous mutations.
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: Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America.
authors.forename: David L
authors.initials: DL
authors.lastname: Oldeschulte
authors.affiliation: Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America.
authors.forename: Eric K
authors.initials: EK
authors.lastname: Bhattarai
authors.affiliation: Genomics and Bioinformatics Core, Texas A&M AgriLife Research, College Station, Texas, United States of America.
authors.forename: Joshua
authors.initials: J
authors.lastname: Hill
authors.affiliation: Genomics and Bioinformatics Core, Texas A&M AgriLife Research, College Station, Texas, United States of America.
authors.forename: Richard P
authors.initials: RP
authors.lastname: Metz
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: Department of Environmental Toxicology, Institute of Environmental and Human Health, Texas Tech University, Lubbock, Texas, United States of America.
authors.forename: Steven M
authors.initials: SM
authors.lastname: Presley
authors.affiliation: Texas A&M AgriLife Extension Service, Dallas, Texas, United States of America.
authors.forename: Rebekah E
authors.initials: RE
authors.lastname: Ruzicka
authors.affiliation: Rolling Plains Quail Research Ranch, 1262 U.S. Highway 180 W., Rotan, Texas, United States of America.
authors.forename: Dale
authors.initials: D
authors.lastname: Rollins
authors.affiliation: Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, United States of America.
authors.forename: Markus J
authors.initials: MJ
authors.lastname: Peterson
authors.affiliation: Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America.
authors.forename: William J
authors.initials: WJ
authors.lastname: Murphy
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; D019143:Evolution, Molecular; D005260:Female; D005787:Gene Frequency; D049810:Genetic Speciation; D054629:Genome, Mitochondrial; D006239:Haplotypes; D008297:Male; D056186:Metagenomics; D008928:Mitochondria / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA