Northern Bobwhite (Colinus virginianus) Mitochondrial Population Genomics Reveals Structure, Divergence, and Evidence for Heteroplasmy

Complete mitogenome of the critically endangered Asian king vulture (Sarcogypscalvus) (Aves, Accipitriformes, Accipitridae): evolutionary insights and comparative analysis

The Asian king vulture (Sarcogypscalvus), also known as the red-headed vulture, is an Old World vulture (Gypini) facing severe population declines. This study aimed to assemble the complete mitogenome of S.calvus, explore its phylogenetic relationships, estimate divergence times, and examine genetic distances and amino acid substitutions. The mitogenome was de novo assembled from genomic DNA extracted from the blood of a female S.calvus. Phylogenetic and pairwise genetic distance analyses were conducted, comparing S.calvus with other members of Gypini, New World vultures (Cathartidae) and various other birds. The assembled mitogenome was 17,750 base pairs in length, comprising 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes and two control regions. Most PCGs used the ATG start codon, except for cytochrome c oxidase subunit 1 (COX1), which employed GTG. Phylogenetic analysis revealed a close genetic relationship between S.calvus and other members of Gypini, with an estimated divergence time of 16.7 million years ago. Genetic distance analysis indicated that S.calvus was more closely related to other Gypini, as well as to Spilornischeela and Circaetuspectoralis (Circaetini)), than to Cathartidae. Conserved amino acid substitutions between Gypini and Cathartidae were primarily observed in the NADH-ubiquinone oxidoreductase chain 1 (ND1) gene. This study provided the first complete mitogenome of S.calvus, offering new insights into its genomic structure, evolutionary history, and genetic relationships.

Accurate Genomic Predictions for Chronic Wasting Disease in U.S. White-Tailed Deer

The geographic expansion of chronic wasting disease (CWD) in U.S. white-tailed deer (Odocoileus virginianus) has been largely unabated by best management practices, diagnostic surveillance, and depopulation of positive herds. Using a custom Affymetrix Axiom single nucleotide polymorphism (SNP) array, we demonstrate that both differential susceptibility to CWD, and natural variation in disease progression, are moderately to highly heritable (h2=0.337±0.079─0.637±0.070) among farmed U.S. white-tailed deer, and that loci other than PRNP are involved. Genome-wide association analyses using 123,987 quality filtered SNPs for a geographically diverse cohort of 807 farmed U.S. white-tailed deer (n = 284 CWD positive; n = 523 CWD non-detect) confirmed the prion gene (PRNP; G96S) as a large-effect risk locus (P-value < 6.3E-11), as evidenced by the estimated proportion of phenotypic variance explained (PVE ≥ 0.05), but also demonstrated that more phenotypic variance was collectively explained by loci other than PRNP. Genomic best linear unbiased prediction (GBLUP; n = 123,987 SNPs) with k-fold cross validation (k = 3; k = 5) and random sampling (n = 50 iterations) for the same cohort of 807 farmed U.S. white-tailed deer produced mean genomic prediction accuracies ≥ 0.81; thereby providing the necessary foundation for exploring a genomically-estimated CWD eradication program.

Annotated Draft Genome Assemblies for the Northern Bobwhite (Colinus virginianus) and the Scaled Quail (Callipepla squamata) Reveal Disparate Estimates of Modern Genome Diversity and Historic Effective Population Size

Northern bobwhite (Colinus virginianus; hereafter bobwhite) and scaled quail (Callipepla squamata) populations have suffered precipitous declines across most of their US ranges. Illumina-based first- (v1.0) and second- (v2.0) generation draft genome assemblies for the scaled quail and the bobwhite produced N50 scaffold sizes of 1.035 and 2.042 Mb, thereby producing a 45-fold improvement in contiguity over the existing bobwhite assembly, and ≥90% of the assembled genomes were captured within 1313 and 8990 scaffolds, respectively. The scaled quail assembly (v1.0 = 1.045 Gb) was ∼20% smaller than the bobwhite (v2.0 = 1.254 Gb), which was supported by kmer-based estimates of genome size. Nevertheless, estimates of GC content (41.72%; 42.66%), genome-wide repetitive content (10.40%; 10.43%), and MAKER-predicted protein coding genes (17,131; 17,165) were similar for the scaled quail (v1.0) and bobwhite (v2.0) assemblies, respectively. BUSCO analyses utilizing 3023 single-copy orthologs revealed a high level of assembly completeness for the scaled quail (v1.0; 84.8%) and the bobwhite (v2.0; 82.5%), as verified by comparison with well-established avian genomes. We also detected 273 putative segmental duplications in the scaled quail genome (v1.0), and 711 in the bobwhite genome (v2.0), including some that were shared among both species. Autosomal variant prediction revealed ∼2.48 and 4.17 heterozygous variants per kilobase within the scaled quail (v1.0) and bobwhite (v2.0) genomes, respectively, and estimates of historic effective population size were uniformly higher for the bobwhite across all time points in a coalescent model. However, large-scale declines were predicted for both species beginning ∼15-20 KYA.