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In addition to ND2 sequences, we also obtained single nucleotide polymorphism (SNP) data for 48 individuals using the genotyping-by-sequencing (GBS) approach implemented by the Cornell Institute of Genomic Diversity.GBS is a technique for construction of reduced representation libraries for the discovery of SNPs from throughout the genome using Illumina sequencing (Elshire et al.
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.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.Finally, only reciprocal tag pairs are identified as SNPs for further analysis (Lu et al.) with a Markov chain Monte Carlo (MCMC) of 100,000,000 generations sampling every 10,000 generations.Our genetic evidence, together with information from morphology and behavior, suggests that the Bell’s Vireo complex involves two species, each containing two separate subspecies. An inhabitant of some of North America’s most threatened habitat types, including riparian and grassland-shrub habitats, Bell’s Vireo has declined at a rate of approximately 2.7 % per year since the mid-1960s (Sauer et al. Habitat modification associated with agriculture, grazing, urbanization, flood management and wildfire has destroyed, degraded and fragmented vireo breeding habitat, while brood parasitism by the Brown-headed Cowbird ( is state threatened in Minnesota. S., Bell’s Vireo is identified as a high priority conservation target by the Audubon Society’s “Red Watchlist” of species of highest national concern, and by Partners in Flight U. as a “Bird of Conservation Concern” in 14 Bird Conservation Regions.
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.
Species or subspecies delimited solely on the basis of non-genetic data can mislead conservation efforts by misrepresenting the underlying intraspecific variation and evolutionary history (Zink ).
The advent of modern molecular genetic techniques makes it possible to re-assess the intraspecific classification of Bell’s Vireo and evaluate concordance between phylogenetic patterns of genetic variation and the existing morphologically based classification.
The timing of diversification, geographic location, and niche modeling of the east/west divergence suggest vicariance as a mode of diversification for these two lineages.
Analyses of the SNP dataset provided additional resolution and indicated the Least Bell’s Vireo populations are a distinct evolutionary lineage.
5.0 (Gene Codes Corporation), and complementary strands were aligned and read for each individual (Gen Bank Accession numbers KM262667-KM262751).