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 (d XY = 0.00731; F ST = 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, F S) 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.
Highlights
The northern bobwhite (Colinus virginianus; hereafter bobwhite) is one of 32 species belonging to the family Odontophoridae (New World quail), with wild populations historically ranging throughout the United States of America (i.e., USA, U.S.), Mexico and parts of the Caribbean [1, 2]
A recent bobwhite mitochondrial DNA study for representatives of the four putative subspecies described west of the Mississippi River revealed a general lack of distinct phylogeographic structure, evidence for demographic expansion following the Pleistocene, and an apparent discordance between patterns of mtDNA diversity and subspecies designations; with all inferences based on the analysis of a 353 bp fragment of the bobwhite mitochondrial control region [3]
Using a probabilistic variant detection algorithm previously described [36], we predicted 344 segregating sites corresponding to 347 total mutations (n = 338 single nucleotide variants (SNVs), 8 indels, and 1 multi-nucleotide variant, MNV), which included 49 putative nonsynonymous SNVs distributed across 12 protein coding genes
Summary
The northern bobwhite (Colinus virginianus; hereafter bobwhite) is one of 32 species belonging to the family Odontophoridae (New World quail), with wild populations historically ranging throughout the United States of America (i.e., USA, U.S.), Mexico and parts of the Caribbean [1, 2]. The male masked bobwhite is unequivocally the most phenotypically and geographically distinct (i.e., black head; Sonora, Mexico); with the eastern, plains, and Texas bobwhites exhibiting more subtle variation in male plumage and body size [2, 3]. A recent bobwhite mitochondrial DNA (mtDNA) study for representatives of the four putative subspecies described west of the Mississippi River revealed a general lack of distinct phylogeographic structure, evidence for demographic expansion following the Pleistocene, and an apparent discordance between patterns of mtDNA diversity and subspecies designations; with all inferences based on the analysis of a 353 bp fragment of the bobwhite mitochondrial control region [3]. Given the availability of a draft nuclear and mitochondrial genome assembly for the bobwhite [36], large-scale genetic studies are both possible and warranted, especially considering the apparent decline of wild bobwhite populations across the majority of their historic U.S range [8, 9, 12,13,14,15]
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