生命地图：用“分子距离地图”测量和可视化物种的相关性
Map of Life: Measuring and Visualizing Species' Relatedness with "Molecular Distance Maps"
摘要：
我们提出了一种新的方法组合，（i）描绘的DNA序列作为图像的定量特征，（ii）计算这些图像之间的距离，和（iii）使用这些距离输出的地图，其中每个序列是一个共同的欧几里得空间中的一个点。在由此产生的“分子距离图”中，每个点都代表一个DNA序列，任何两个点之间的几何距离反映了相应序列和物种之间的相关程度。分子距离图展示了物种之间关系的令人信服的视觉表示，并可用于分类学澄清，物种识别和进化历史的研究。该方法的优点之一是其普遍适用性，因为不需要序列比对，选择用于比较的DNA序列可以是不同基因组中完全不同的区域。事实上，这种方法可以用来比较任何两个DNA序列。例如，在我们的3，176个线粒体DNA序列的数据集中，它正确地找到了与解剖学上的现代人类（尼安德特人，丹尼索瓦人和黑猩猩）最密切相关的线粒体DNA序列，它发现与它最不同的序列属于黄瓜。此外，我们的方法可以用来比较真实的序列，人工，计算机生成的DNA序列。例如，它被用来确定智人mtDNA和相同长度和相同三核苷酸频率的人工序列之间的距离可以大于相同人类mtDNA和果蝇mtDNA之间的距离。我们证明了这种方法的分类澄清的潜力，通过将其应用到各种各样的情况下，历史上一直有争议的，如属Polypterus，家庭Tarsiidae，和巨大的（超）王国原生生物。
英文摘要：
We propose a novel combination of methods that (i) portrays quantitative characteristics of a DNA sequence as an image, (ii) computes distances between these images, and (iii) uses these distances to output a map wherein each sequence is a point in a common Euclidean space. In the resulting "Molecular Distance Map" each point signifies a DNA sequence, and the geometric distance between any two points reflects the degree of relatedness between the corresponding sequences and species. Molecular Distance Maps present compelling visual representations of relationships between species and could be used for taxonomic clarifications, for species identification, and for studies of evolutionary history. One of the advantages of this method is its general applicability since, as sequence alignment is not required, the DNA sequences chosen for comparison can be completely different regions in different genomes. In fact, this method can be used to compare any two DNA sequences. For example, in our dataset of 3,176 mitochondrial DNA sequences, it correctly finds the mtDNA sequences most closely related to that of the anatomically modern human (the Neanderthal, the Denisovan, and the chimp), and it finds that the sequence most different from it belongs to a cucumber. Furthermore, our method can be used to compare real sequences to artificial, computer-generated, DNA sequences. For example, it is used to determine that the distances between a Homo sapiens sapiens mtDNA and artificial sequences of the same length and same trinucleotide frequencies can be larger than the distance between the same human mtDNA and the mtDNA of a fruit-fly. We demonstrate this method's promising potential for taxonomical clarifications by applying it to a diverse variety of cases that have been historically controversial, such as the genus Polypterus, the family Tarsiidae, and the vast (super)kingdom Protista.
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