Background: The red panda (Ailurus fulgens) is a riddle of morphology, making it hard to tell whether it is an ursid, a procyonid, a mustelid, or a member of its own family. Previous genetic studies have given quite contradictory results as to its phylogenetic placement. Results: A recently developed whole genome-based algorithm, the Whole Genome K-mer Signature algorithm was used to analyze the genomes of 28 species of Carnivora, including A. fulgens and several felid, ursid, mustelid, one

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... itid species. This algorithm has the advantage of holistically using all the information in the genomes of these species. Being a genomics-based algorithm, it also reduces stochastic error to a minimum. Besides the whole genome, the mitochondrial DNA from 52 mustelids, mephitids, ursids, procyonids as well as A. fulgens were also aligned to draw further phylogenetic inferences. The results from the whole genome study show that A. fulgens is a member of the mustelid clade (p = 9·10-97). A. fulgens also separates from the mephitid Spilogala gracilis. The giant panda, Ailuropoda melanoleuca also clusters away from A. fulgens, together with other ursids (p = 1.2·10-62). This could be due to the geographic isolation of A. fulgens from other mustelid species. However, results from the mitochondrial study based on the sequence identity matrix seem to place A. fulgens into its own group.Conclusions: The main conclusion that we can draw from this study is that on a whole genome level A. fulgens belongs to the mustelid clade, and not an ursid or a mephitid. This despite the fact that previously some researchers classified A. fulgens and A. melanoleuca as relatives. Since the genotype determines the phenotype, molecular-based classification takes precedence over morphological classifications. This affirms the results of some previous studies, which studied smaller portions of the genome. The mitochondrial results could be due to differing mutational pressures compared to the nucleus. It cannot be said for sure, but it is likely that A. fulgens belongs to the mustelid clade.