Following sequencing, SNP discovery and genotyping were performed using a network based analysis pipeline, UNEAK (Universal Network Enabling Analysis Kit), a protocol developed for species without a reference genome (Lu et al. The UNEAK pipeline is designed to overcome complexities that impede SNP discovery, such as repeats, paralogs, and sequencing errors.Briefly, sequence reads were trimmed to 64 bp, and then all identical reads were pooled to form distinct tags.An HKY model of evolution was determined to be the most appropriate model for all codon positions according to j Model Test v2.1.6 (Darriba et al. A preliminary analysis determined that the data were sufficiently clocklike and therefore the analysis was run with a strict molecular clock and a standard substitution rate of 0.0115 (2.3 % divergence my) was used to generate a maximum clade credibility tree with a burn-in of 1000 samples that could then be visualized with FIGTREE v1.3.1.RAx ML was used to construct a ML tree with a GTR G model of sequence evolution imposed for the separate codons and nodal support was assessed via bootstrapping, and the best tree was visualized with FIGTREE v1.3.1.Our goal was to infer broad scale phylogeographic patterns in the Bell’s Vireo complex using genetic markers from across the genome.We compared these data to past and present niche models for the species to provide further ecological and historical insight into observed genetic patterns.
This new information has implications for the federal, state and other listing status of Bell’s Vireo throughout its range.) is a species of conservation concern throughout its U. Thus, a variety of federal and state laws, as well as non-governmental programs, guide the conservation of Bell’s Vireo throughout its range.), no previous genetic studies have focused on the Bell’s Vireo, despite its conservation significance.The PCR products were purified using Exo Sap before being submitted to Macrogen, Inc (Rockville, MD) for sequencing.Following sequencing, the data were imported into Sequencher, vers.Therefore, the current taxonomy used to guide management decisions may misrepresent the true evolutionary history for the species.We sequenced 86 individuals for ND2 and genotyped 48 individuals for genome-wide SNPs to identify distinct lineages within Bell’s Vireo.