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BMC Genomics. 2021 Apr 1;22(1):228. doi: 10.1186/s12864-021-07531-3.
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.
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 mephitid 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 and A. fulgens were aligned to draw further phylogenetic inferences. The results from the whole genome study suggested that A. fulgens is a member of the mustelid clade (p = 9·10). 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). This could be due to the geographic isolation of A. fulgens from other mustelid species. However, results from the mitochondrial study as well as neighbor-joining methods based on the sequence identity matrix suggests that A. fulgens forms a monophyletic group. A Maximum Likelihood tree suggests that A. fulgens and Ursidae form a monophyletic group, although the bootstrap value is weak.
The main conclusion that we can draw from this study is that on a whole genome level A. fulgens possibly 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. However, mitochondrial analyses based on neighbor-joining and maximum likelihood methods suggest otherwise.
小熊猫（Ailurus fulgens）的形态学结构较为复杂，难以确定其所属的分类地位，它既可能是熊科、浣熊科、鼬科的成员，也可能自成一科。先前的遗传研究对其系统发育位置的结论存在较大差异。
本研究使用最近开发的基于全基因组的算法——全基因组 K -mer 特征算法，对包括小熊猫和几种猫科、熊科、鼬科、獾科在内的 28 种食肉动物的基因组进行分析。该算法具有综合利用这些物种基因组中所有信息的优势，并且由于是基于基因组的算法，还将随机误差降至最低。除了全基因组外，还对来自 52 种鼬科、獾科、熊科、浣熊科和小熊猫的线粒体 DNA 进行了比对，以进一步推断系统发育关系。全基因组研究结果表明，小熊猫是鼬科动物的一个分支（p=9.10）。小熊猫与獾科的 Spilogala gracilis 也分开。大熊猫 Ailuropoda melanoleuca 也与小熊猫分离，与其他熊科动物一起（p=1.2.10）。这可能是由于小熊猫与其他鼬科动物的地理隔离。然而，线粒体研究以及基于序列同一性矩阵的邻接法的结果表明，小熊猫形成了一个单系群。最大似然树表明小熊猫和熊科形成一个单系群，尽管其支持值较弱。
本研究的主要结论是，从全基因组水平来看，小熊猫可能属于鼬科，而不是熊科或獾科。尽管先前有研究人员将小熊猫和大熊猫归类为近亲。由于基因型决定表型，因此分子分类优先于形态分类。这证实了先前一些研究较小基因组部分的结果。然而，基于邻接法和最大似然法的线粒体分析结果则不然。
