Analysis of complete mitochondrial genome sequences increases phylogenetic resolution of bears (Ursidae), a mammalian family that experienced rapid speciation

Abstract

Background: Despite the small number of ursid species, bear phylogeny has long been a focus of study due to their conservation value, as all bear genera have been classified as endangered at either the species or subspecies level. The Ursidae family represents a typical example of rapid evolutionary radiation. Previous analyses with a single mitochondrial (mt) gene or a small number of mt genes either provide weak support or a large unresolved polytomy for ursids. We revisit the contentious relationships within Ursidae by analyzing complete mt genome sequences and evaluating the performance of both entire mt genomes and constituent mtDNA genes in recovering a phylogeny of extremely recent speciation events.

Results: This mitochondrial genome-based phylogeny provides strong evidence that the spectacled bear diverged first, while within the genus Ursus, the sloth bear is the sister taxon of all the other five ursines. The latter group is divided into the brown bear/polar bear and the two black bears/sun bear assemblages. These findings resolve the previous conflicts between trees using partial mt genes. The ability of different categories of mt protein coding genes to recover the correct phylogeny is concordant with previous analyses for taxa with deep divergence times. This study provides a robust Ursidae phylogenetic framework for future validation by additional independent evidence, and also has significant implications for assisting in the resolution of other similarly difficult phylogenetic investigations.

Conclusion: Identification of base composition bias and utilization of the combined data of whole mitochondrial genome sequences has allowed recovery of a strongly supported phylogeny that is upheld when using multiple alternative outgroups for the Ursidae, a mammalian family that underwent a rapid radiation since the mid- to late Pliocene. It remains to be seen if the reliability of mt genome analysis will hold up in studies of other difficult phylogenetic issues. Although the whole mitochondrial DNA sequence based phylogeny is robust, it remains in conflict with phylogenetic relationships suggested by analysis of limited nuclear-encoded data, a situation that will require gathering more nuclear DNA sequence information.

Figure 1

Long-standing unresolved Ursidae phylogeny (tree in the left) and competing hypotheses proposed based on previous sequence data (mtA-E and nuA-B). Trees were constructed from (mtA) combined analysis of partial control region, 12SrRNA, CYTB, tRNA^Pro, and tRNA^Thr mt genes [11], (mtB) MP analysis of complete CYTB, tRNA^Pro, and tRNA^Thr mt genes [12], (mtC) NJ analysis of complete CYTB, tRNA^Pro, and tRNA^Thr mt genes [12], (mtD) combined analysis of partial control region, CYTB, ND4, ND5, COII, and 16SrRNA mt genes [8], (mtE) combined analysis of partial control region, 12SrRNA, complete CYTB, tRNA^Pro, and tRNA^Thr mt genes [13], (nuA) combined analysis of interphotoreceptor retinoid binding protein (IRBP) exon1 and transthyretin (TTR) intron 1 nuclear genes [13], and (nuB) combined analysis of four type I sequence-tagged sites (STS) and IRBP exon 1 nuclear genes [60].

Figure 2

Phylogenetic trees and nodal supports (groups that received more than 50% BS or 0.6 PP were retained) based on analyses of different subsets of mt genome.

Figure 3

Mt genome tree and nodal supports.

Figure 4

Phylogenetic trees based on individual mt genes. Only >50% MP BS are indicated on the branches.

Figure 5

Results of partitioned Bremer support (PBS) analyses to each node on the mt genome tree and comparisons of phylogenetic performance of mt genes among the studies.

Figure 6

Universal primers [35] and newly designed species-specific primers (underlined) used for amplifying Ursidae mt genomes. Locations of new primers are indicated in brackets and correspond to nucleotide numbers from the harbor seal sequence (Accession No. X63726). Eleven mtDNA fragments (mtDNA1-11) covering the entire mt genome are labeled as described in Delisle and Strobeck (2002) [38].