Bioinformatics Toolbox 3.4

Building a Phylogenetic Tree for the Hominidae Species

Phylogenetic trees are constructed from mtDNA sequences for the Hominidae taxa (also known as pongidae). This family embraces the gorillas, chimpanzees, orangutans and the humans.

Contents

Introduction

The mitochondrial D-loop is one of the fastest mutating sequence regions in animal DNA. Therefore, useful for comparing closely related organisms. The origin of modern man is a highly debated issue that has recently been tackled 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 originated from a single woman who lived in Africa less than 200,000 years.

Gather Sequence Data from GenBank®

Get some data from GenBank®, these are the accession codes for mitochondrial D-loop sequences that have been isolated for different hominidae species.

%        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';
       };

for ind = 1:length(data)
    primates(ind).Header   = data{ind,1};
    primates(ind).Sequence = getgenbank(data{ind,2},'sequenceonly','tru
e');
end

If you don't have a live web connection, you can load the data from a MAT-file using the command

%load primatesdemodata       % <== Uncomment this if no Internet connecti
on

Build a UPGMA Phylogenetic Tree using Distance Methods

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 will pairwise align them before computing the distances.

distances = seqpdist(primates,'Method','Jukes-Cantor','Alpha','DNA');
UPGMAtree = seqlinkage(distances,'UPGMA',primates)

    Phylogenetic tree object with 12 leaves (11 branches)

Render the UPGMA phylogenetic tree

h = plot(UPGMAtree,'orient','top');
title('UPGMA Distance Tree of Primates using Jukes-Cantor model');
ylabel('Evolutionary distance')

Build a Neighbor-Joining Phylogenetic Tree using Distance Methods

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 (using the seqpdist function) to construct the tree. This method clusters using the minimum evolution method

NJtree = seqneighjoin(distances,'equivar',primates)

    Phylogenetic tree object with 12 leaves (11 branches)

Render the NJ phylogenetic tree

h = plot(NJtree,'orient','top');
title('Neighbor-Joining Distance Tree of Primates using Jukes-Cantor model')
;
ylabel('Evolutionary distance')

Comparing Tree Topologies

Notice that the trees that are created have different topologies. The neighbor-joining tree groups Chimp Vellerosus in a clade with the gorillas and 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 =

     0

Exploring the UPGMA Phylogenetic Tree

Find the closest species to the 'European Human' entry (3).

names = get(UPGMAtree,'LeafNames')
[h_all,h_leaves] = select(UPGMAtree,'reference',3,'criteria','distance','thr
eshold',0.6);
% h_all has now all the nodes within 0.6 of patristic distance to the 'Europ
ean
% Human' leave.
% h_leaves has only the leaf nodes within 0.6 of patristic distance to (3)
subtree_names = names(h_leaves)

names =

    '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 =

    'German_Neanderthal'
    'Russian_Neanderthal'
    'European_Human'
    'Chimp_Troglodytes'
    'Chimp_Schweinfurthii'
    'Chimp_Verus'

Reduce the tree to the sub-branch of interest

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')

    Phylogenetic tree object with 6 leaves (5 branches)

With view you can further explore/edit the phylogenetic tree using an interactive tool. See also phytreetool.

view(UPGMAtree,h_leaves)

References:

[1] I.V. Ovchinnikov, et al., "Molecular analysis of Neanderthal DNA from the northern Caucasus", Nature 404(6777), 2000, pp. 490-493.

[2] A. Sajantila, et al., "Genes and languages in Europe: an analysis of mitochondrial lineages", Genome Research 5(1), 1995, pp. 42-52.

[3] M. Krings, et al., "Neandertal DNA sequences and the origin of modern humans", Cell 90(1), 1997, pp. 19-30.

[4] M.I. Jensen-Seaman and K.K. Kidd, "Mitochondrial DNA variation and biogeography of eastern gorillas", Molecular Ecology 10(9), 2001, pp. 2241-2247

Suggest an enhancement for this demo.