Primate Mitochondrial DNA Distance Matrix

Distance matrix of 12 primate species based on mitochondrial DNA sequences. This classic dataset from Hayasaka et al. (1988) shows nucleotide substitutions per site and is frequently used in phylogenetics education.

Usage

primates

Format

A dist object with 12 taxa:

Human

Homo sapiens (great ape)

Chimpanzee

Pan troglodytes (great ape)

Gorilla

Gorilla gorilla (great ape)

Orangutan

Pongo pygmaeus (great ape)

Gibbon

Hylobates lar (lesser ape)

Japanese_macaque

Macaca fuscata (Old World monkey)

Rhesus_macaque

Macaca mulatta (Old World monkey)

Crab_eating_macaque

Macaca fascicularis (Old World monkey)

Barbary_macaque

Macaca sylvanus (Old World monkey)

Squirrel_monkey

Saimiri sciureus (New World monkey)

Tarsier

Tarsius syrichta (prosimian)

Lemur

Lemur catta (prosimian)

Source

Table 4 from Hayasaka K, Gojobori T, Horai S (1988). "Molecular phylogeny and evolution of primate mitochondrial DNA." Molecular Biology and Evolution, 5(6), 626-644. doi:10.1093/oxfordjournals.molbev.a040524

Details

Values represent the number of nucleotide substitutions per site between species, computed from mitochondrial DNA sequences. The phylogenetic pattern shows great apes clustering together, macaques forming a tight group, and prosimians (Tarsier, Lemur) as outgroups.

References

Hayasaka K, Gojobori T, Horai S (1988). "Molecular phylogeny and evolution of primate mitochondrial DNA." Molecular Biology and Evolution, 5(6), 626-644. doi:10.1093/oxfordjournals.molbev.a040524

Examples

data(primates)
tree <- fast_nj(primates)
plot(tree, type = "unrooted", no.margin = TRUE, lab4ut = "axial")


# The four macaque species cluster tightly together
# Great apes (Human, Chimp, Gorilla, Orangutan) form another cluster