Fig 1.
Bayesian phylogenetic tree encompassing 164 donkey coding-region sequences (162 domestic and 2 Equus africanus somaliensis).
The tree was rooted using two modern and one ancient horse sequences (not shown). Posterior probabilities are indicated for major nodes, including the two major haplogroups. The geographical provenance of the sequences is color-coded as shown in the legend.
Fig 2.
Median-joining network of worldwide donkey control-region variation reconstructed from 1392 mtDNA sequences.
The size of the nodes is proportional to haplotype frequencies. Nodes are represented as pie charts indicating the haplotype frequencies in different geographical areas: Eastern Africa (AFE), Northern Africa (AFN), Southern Africa (AFS), Western Africa (AFW), America (AME), Arabian Peninsula (ASA), Central-Western Asia (ASC), Eastern Asia (ASE), Sothern Asia (ASS); Balkans (EUB); Eastern Europe (EUE); Italy (EUI) and Western Europe (EUW). DRS indicates the Donkey Reference Sequence for mtDNA (DRS, NC_001788.1).
Table 1.
Summary statistics calculated over the worldwide dataset of donkey mtDNA control-region sequences by geographical region and by country.
Fig 3.
Map of regional Median-joining networks, haplotype and nucleotide diversity values for Europe.
Continental map of Europe showing regional Median-joining networks and histograms of haplotype (h, darker shade) and nucleotide (n, lighter shade) diversity values for haplogroups A (orange shades) and B (green shades). The map was plotted with the getMap and mapCountryData functions of the R package rworldmap [55]. The labelling of geographical areas is the same as in Fig 2. A detailed representation of regional Median-joining networks is given in S8 Fig.
Fig 4.
Map of regional Median-joining networks, haplotype and nucleotide diversity values for Africa and Central America.
Continental maps of Africa (panel a) and Central America (panel b) showing regional Median-joining networks and histograms of corresponding haplotype (h, darker shade) and nucleotide (n, lighter shade) diversity values for haplogroups A (orange shades) and B (green shades). The map was plotted with the getMap and mapCountryData functions of the R package rworldmap [55]. The labelling of geographical areas is the same as in Fig 2. A detailed representation of regional Median-joining networks is given in S8 Fig.
Fig 5.
Map of regional Median-joining networks, haplotype and nucleotide diversity values for Asia.
Continental map of Asia showing regional Median-joining networks and histograms of corresponding haplotype (h, darker shade) and nucleotide (n, lighter shade) diversity values for haplogroups A (orange shades) and B (green shades). The map was plotted with the getMap and mapCountryData functions of the R package rworldmap [55]. The labelling of geographical areas is the same as in Fig 2. A detailed representation of the regional Median-joining networks is given in S8 Fig.