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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, tRNAPro, and tRNAThr mt genes , (mtB) MP analysis of complete CYTB, tRNAPro, and tRNAThr mt genes , (mtC) NJ analysis of complete CYTB, tRNAPro, and tRNAThr mt genes , (mtD) combined analysis of partial control region, CYTB, ND4, ND5, COII, and 16SrRNA mt genes , (mtE) combined analysis of partial control region, 12SrRNA, complete CYTB, tRNAPro, and tRNAThr mt genes , (nuA) combined analysis of interphotoreceptor retinoid binding protein (IRBP) exon1 and transthyretin (TTR) intron 1 nuclear genes , and (nuB) combined analysis of four type I sequence-tagged sites (STS) and IRBP exon 1 nuclear genes .
All other relationships within the genus Ursus remained an
unresolved polytomy (Figure 1). .
Additionally, analyses of different genes within the mt genome have
resulted in inconsistent branching patterns being reported in the
Ursidae (Figure 1A–E).
Previous molecular studies relevant to Ursidae phylogeny provided
either an inconsistent view on the issue or weak statistical
support for discriminating alternative hypotheses (Figure 1).
Based on the largest available mt data set from Ursidae, our
genome phylogeny provides strong evidence that within genus Ursus,
the sloth bear is the sister taxa of all the other five ursines,
and that the latter group is divided into the brown bear/polar bear
and the two black bears/sun bear assemblages, upholding and
strengthening the hypothesis drawn by our previous analysis of the
five fragments of mtDNA  (Figure 1E).
The necessity of including other unlinked genes for phylogenetic
resolution of the Ursidae is also illustrated by the fact that our
recent study on two nuclear genes, transthyretin (TTR) and
interphotoreceptor retinoid binding protein (IRBP), has united the
sloth bear and the sun bear as sister taxa with high statistical
support  (Figure 1 nuA), a relationship not consistent with mt
gene analyses, including the present study.
Yu, Li; Li, Yi-Wei; Ryder, Oliver A; Zhang, Ya-PingJournal: BMC Evolutionary Biology
Issue 1DOI: 10.1186/1471-2148-7-198Published: 2007-12-01Institution(s):
Yunnan University, Kunming Institute of Zoology, Zoological Society of San Diego
This image is from the article titled "Analysis of complete mitochondrial genome sequences increases phylogenetic resolution of bears (Ursidae), a mammalian family that experienced rapid speciation"
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