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UCE are highly conserved short DNA sequences that are shared by different organisms and are particularly useful for phylogeny estimation from genome sequence data (Faircloth et al. UCE have been useful in resolving difficult evolutionary relationships (e.g., birds, Mc Cormack et al. 2008), easily identifiable, the flanking regions show increasing amounts of sequence variability with increasing distance from the UCE, are generally independent loci (Faircloth et al. Genetic variation was also assessed within and between polar, brown, and black bears from North America with single nucleotide polymorphisms (SNP) derived from genome sequences. 2011) as reference to determine sequence variation including single nucleotide variants (SNV), SNP, indels, and UCE among bear species on a whole genome scale.

An analysis of genome sequences estimated the polar bear–brown bear divergence at 4–5 Ma with subsequent periods of gene flow between lineages (Miller et al. In this paper, we reassess the phylogeny of polar bears, brown bears, and black bears using genetic markers not previously used on bears: ultraconserved elements (UCE) derived from genome sequences. UCE can provide a useful measure of phylogeny in bears because they are numerous in the nuclear genome (Stephen et al.

Polar bears and brown bears are thought to have evolved from a common ancestor during the Pleistocene (Kurtén 1964, 1968), and a polar bear fossil from the last interglacial (Eemian) period 110000–130000 years ago established this as their minimum time of divergence (Ingólfsson and Wiig 2008; Alexanderson et al. Molecular clock estimates of the divergence time of polar bears and brown bears vary widely depending on the genetic markers used. DNA libraries for each pool were made from 6 µg genomic DNA using the Illumina Genomic DNA sample kit (Illumina Inc., San Diego, CA).

DNA from 2 to 4 individuals of each species and geographic location were combined to make 7 DNA pools, including 2 pools of polar bears, 2 pools of black bears, 1 pool of ABC brown bears, and 2 pools of other brown bears (non-ABC brown bears, Figure 1 and Table 1).

2011), giant panda (Ensembl 66), domestic dog (; Ensembl 66) genomes using Geneious R6 (2013).

All single hit UCE blast hits were retained from each genome and extended 250bp on both the 5′ and 3′ flanking ends using Geneious R6.

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These include divergences of 2–3 Ma with proteins (Goldman et al. Each bear species’ (polar, brown, and black) genome was sequenced at an average of 25× coverage using the Illumina Hi Seq platform.

RAx ML7.4.2 implements only one of the models tested by MEGA-CC (GTR [general time reversible] model), so we implemented the most complex model suggested by MEGA-CC (GTR Γ I) for each partition of the RAx ML analysis.

The RAx ML analysis included 500 replicates, started from randomized MP starting trees, and used the fast hill-climbing algorithm with all other free parameters estimated.

The 1681 UCE region alignments were concatenated into a 13-partition alignment (996381bp).

Each partition consisted of all UCE region alignments with the same estimated model of molecular evolution as determined by MEGA-CC ().

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