This example shows how to construct phylogenetic trees from mtDNA sequences for the Hominidae taxa (also known as pongidae). This family embraces the gorillas, chimpanzees, orangutans and humans.
The mitochondrial D-loop is one of the fastest mutating sequence regions in animal DNA, and therefore, is often used to compare closely related organisms. The origin of modern man is a highly debated issue that has been addressed by using mtDNA sequences. The limited genetic variability of human mtDNA has been explained in terms of a recent common genetic ancestry, thus implying that all modern-population mtDNAs likely originated from a single woman who lived in Africa less than 200,000 years.
This example uses mitochondrial D-loop sequences isolated for different hominidae species with the following GenBank Accession numbers.
% Species Description GenBank Accession data = {'German_Neanderthal' 'AF011222'; 'Russian_Neanderthal' 'AF254446'; 'European_Human' 'X90314' ; 'Mountain_Gorilla_Rwanda' 'AF089820'; 'Chimp_Troglodytes' 'AF176766'; 'Puti_Orangutan' 'AF451972'; 'Jari_Orangutan' 'AF451964'; 'Western_Lowland_Gorilla' 'AY079510'; 'Eastern_Lowland_Gorilla' 'AF050738'; 'Chimp_Schweinfurthii' 'AF176722'; 'Chimp_Vellerosus' 'AF315498'; 'Chimp_Verus' 'AF176731'; };
You can use the getgenbank
function inside a for-loop to retrieve the sequences from the NCBI data repository and load them into MATLAB®.
for ind = 1:length(data) primates(ind).Header = data{ind,1}; primates(ind).Sequence = getgenbank(data{ind,2},'sequenceonly','true'); end
For your convenience, previously downloaded sequences are included in a MAT-file. Note that data in public repositories is frequently curated and updated; therefore, the results of this example might be slightly different when you use up-to-date sequences.
load('primates.mat')
Compute pairwise distances using the 'Jukes-Cantor' formula and the phylogenetic tree with the 'UPGMA' distance method. Since the sequences are not pre-aligned, seqpdist
performs a pairwise alignment before computing the distances.
distances = seqpdist(primates,'Method','Jukes-Cantor','Alpha','DNA'); UPGMAtree = seqlinkage(distances,'UPGMA',primates) h = plot(UPGMAtree,'orient','top'); title('UPGMA Distance Tree of Primates using Jukes-Cantor model'); ylabel('Evolutionary distance')
Phylogenetic tree object with 12 leaves (11 branches)
Alternate tree topologies are important to consider when analyzing homologous sequences between species. A neighbor-joining tree can be built using the seqneighjoin
function. Neighbor-joining trees use the pairwise distance calculated above to construct the tree. This method performs clustering using the minimum evolution method.
NJtree = seqneighjoin(distances,'equivar',primates) h = plot(NJtree,'orient','top'); title('Neighbor-Joining Distance Tree of Primates using Jukes-Cantor model'); ylabel('Evolutionary distance')
Phylogenetic tree object with 12 leaves (11 branches)
Notice that different phylogenetic reconstruction methods result in different tree topologies. The neighbor-joining tree groups Chimp Vellerosus in a clade with the gorillas, whereas the UPGMA tree groups it near chimps and orangutans. The getcanonical
function can be used to compare these isomorphic trees.
sametree = isequal(getcanonical(UPGMAtree), getcanonical(NJtree))
sametree = logical 0
You can explore the phylogenetic tree by considering the nodes (leaves and branches) within a given patristic distance from the 'European Human' entry and reduce the tree to the sub-branches of interest by pruning away non-relevant nodes.
names = get(UPGMAtree,'LeafNames') [h_all,h_leaves] = select(UPGMAtree,'reference',3,'criteria','distance','threshold',0.3); subtree_names = names(h_leaves) leaves_to_prune = ~h_leaves; pruned_tree = prune(UPGMAtree,leaves_to_prune) h = plot(pruned_tree,'orient','top'); title('Pruned UPGMA Distance Tree of Primates using Jukes-Cantor model'); ylabel('Evolutionary distance')
names = 12x1 cell array {'German_Neanderthal' } {'Russian_Neanderthal' } {'European_Human' } {'Chimp_Troglodytes' } {'Chimp_Schweinfurthii' } {'Chimp_Verus' } {'Chimp_Vellerosus' } {'Puti_Orangutan' } {'Jari_Orangutan' } {'Mountain_Gorilla_Rwanda'} {'Eastern_Lowland_Gorilla'} {'Western_Lowland_Gorilla'} subtree_names = 6x1 cell array {'German_Neanderthal' } {'Russian_Neanderthal' } {'European_Human' } {'Chimp_Troglodytes' } {'Chimp_Schweinfurthii'} {'Chimp_Verus' } Phylogenetic tree object with 6 leaves (5 branches)
With view
you can further explore/edit the phylogenetic tree using an interactive tool. See also phytreeviewer
.
view(UPGMAtree,h_leaves)
[1] Ovchinnikov, I.V., et al., "Molecular analysis of Neanderthal DNA from the northern Caucasus", Nature, 404(6777):490-3, 2000.
[2] Sajantila, A., et al., "Genes and languages in Europe: an analysis of mitochondrial lineages", Genome Research, 5(1):42-52, 1995.
[3] Krings, M., et al., "Neandertal DNA sequences and the origin of modern humans", Cell, 90(1):19-30, 1997.
[4] Jensen-Seaman, M.I. and Kidd, K.K., "Mitochondrial DNA variation and biogeography of eastern gorillas", Molecular Ecology, 10(9):2241-7, 2001.