Map of life: Measuring and visualizing species’ relatedness with genome distance maps

摘要: We propose a novel combination of methods that (i) portrays quantitative characteristics of a DNA sequence as a black-and-white image,(ii) computes pair-wise distances between these images, and (iii) visually displays each sequence as a point in a common Euclidean space, based on the obtained distance matrix. In a resulting Genome Distance Map each point signifies a genomic sequence, and the geometric distance between any two points is proportional to the relatedness between the species they represent.Genome Distance Maps present compelling visual representations of relationships between species and could be used for taxonomic clarifications, for species identification, placement of species in existing taxonomic categories, as well as for studies of evolutionary history. One of the main advantages of this method is its general applicability. The yardstick that determines that the species closest to human are the Neanderthal, the Denisovan, and the chimp, is also used to determine that the farthest species from human is the cucumber. That same yardstick can also measure the distances between the human mitochondrial genome and artificial computer-generated genomes with the same length and the same single-, di-nucleotide, and tri-nucleotide frequency, and determines that these distances are larger than that between human and the fruit-fly. Furthermore, in general, DNA sample subsequences picked from each genome for distancemeasurement purposes can be chosen from anywhere along each genome, and can be completely independent of each other.