Key features of DNA-based phylogenetic trees include their topology showing ancestral relationships and branch lengths indicating genetic differences. Trees can be rooted or unrooted, with rooting using an outgroup to indicate the most basal ancestor. The main steps in DNA tree construction are sequence alignment, converting alignment data into a tree, assessing tree accuracy through bootstrap analysis, and using molecular clocks to date branch points. While gene trees are often more accurate than morphology-based species trees, they are not always equivalent as gene trees reflect gene divergence through mutation while species trees indicate reproductive isolation through speciation events. Molecular phylogenetics has many applications including clarifying human/primate relationships, tracing the origins of AIDS, and studying human prehistory through genetic

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Assignment-4 14 -06-15
BTY-05 Intro. To Genomics
Zohaib HUSSAIN sp13-bty-001
Submitted To DR Ismat Nawaz
1. Write in detail the “Key features of DNA-based phylogenetic trees”?
The topology of this tree comprises four external nodes, each representing one of the four
genes that we have compared, and two internal nodes representing ancestral genes. The
lengths of the branches indicate the degree of difference between the genes represented by
the nodes.
Trees may be rooted or unrooted. Rooted trees reflect the most basal ancestor of the tree in
question. There are competing techniques for rooting a tree; one of the most common
methods is through the use of an out group (An organism or DNA sequence that is used to
root a phylogenetic tree)
Figure: The use of an outgroup to root a phylogenetic tree

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The tree of human, chimpanzee, gorilla and orangutan genes is rooted with a baboon gene
because we know from the fossil record that baboons split away from the primate lineage before
the time of the common ancestor of the other four species
 Unrooted trees do not imply a known ancestral root.
2. Main step involved in the “DNA-tree construction”?
DNA tree construction carried out with DNA sequence. Steps in the procedure are as fallows
I. Aligning the DNA sequences and obtaining the comparative data that will be used to
reconstruct the tree. Sequence alignment is the essential preliminary to tree reconstruction.
The data used in reconstruction of a DNA-based phylogenetic tree are obtained by comparing
nucleotide sequences. These comparisons are made by aligning the sequences so that
nucleotide differences can be scored. This is the critical part of the entire enterprise because
if the alignment is incorrect then the resulting tree will definitely not be the true tree.

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Figure: Sequence alignment
II. Converting the comparative data into a reconstructed tree
Once the sequences have been aligned accurately, an attempt can be made to reconstruct the
phylogenetic tree. To date nobody has devised a perfect method for tree reconstruction, and
several different procedures are used routinely
One procedure shown below
Figure 2: simple distance matrix The matrix shows the evolutionary distance between each pair
of sequences in the alignment. In this example the evolutionary distance is expressed as the
number of nucleotide differences per nucleotide site for each sequence pair. For example,
sequences 1 and 2 are 20 nucleotides in length and have four differences, corresponding to an
evolutionary difference of 4/20 = 0.2.

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III. Assessing the accuracy of the reconstructed tree. The limitations to the methods used in
phylogenetic reconstruction lead inevitably to questions about the veracity of the resulting
trees. Statistical tests of the accuracy of a reconstructed tree have been devised but these are
necessarily complex because a tree is geometric rather than numeric and the accuracy of one
part of the topology may be greater or lesser than the accuracy of the other parts. The routine
method for assigning confidence limits to different branch points within a tree is to carry out
a bootstrap analysis(A method for inferring the degree of confidence that can be assigned to a
branch point in a phylogenetic tree)
IV. Using a molecular clock to assign dates to branch points within the tree.
Molecular clocks enable the time of divergence of ancestral sequences to be estimated
Figure : Calculating a human molecular clock

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3. Can a gene tree ever be equivalent to species tree?
The assumption is that the gene tree, based on molecular data with all its advantages, will be a
more accurate and less ambiguous representation of the species tree than that obtainable by
morphological comparisons. This assumption is often correct, but it does not mean that the gene
tree is the same as the species tree. For that to be the case, the internal nodes in the gene and
species trees would have to be precisely equivalent. However, they are not equivalent, because:
 An internal node in a gene tree represents the divergence of an ancestral gene into two genes
with different DNA sequences: this occurs by mutation
 An internal node in a species tree represents a speciation event, this occurs by the population
of the ancestral species splitting into two groups that are unable to interbreed, for example,
because they are geographically isolated.
Figure: The difference between a gene tree and a species tree

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4. Write a note on the applications of the “Molecular phylogenetics”?
Molecular phylogenetics has grown in stature since the start of the 1990s, largely because of the
development of more rigorous methods for tree building, combined with the explosion of DNA
sequence information obtained initially by PCR analysis and more recently by genome projects.
The importance of molecular phylogenetics has also been enhanced by the successful application
of tree reconstruction and other phylogenetic techniques to some of the more perplexing issues in
biology. In this final section we will survey some of these successes.
Examples of the use of phylogenetic trees
 DNA phylogenetics has clarified the evolutionary relationships between humans and other
primates
 The origins of AIDS
Figure: The phylogenetic tree reconstructed from HIV and SIV genome sequences
The AIDS epidemic is due to the HIV-1M type of immunodeficiency virus. ZR59 is positioned
near the root of the star-like pattern formed by genomes of this type.

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 Molecular phylogenetic as a tool in the study of human prehistory
The use of molecular phylogenetic in studies: the study of the evolutionary history of members
of the same species. We could choose any one of several different organisms to illustrate the
approaches and applications of intraspecific studies, but many people look on Homo sapiens as
the most interesting organism so we will investigate how molecular phylogenetics is being used
to deduce the origins of modern humans and the geographic patterns of their recent migrations in
the Old and New Worlds.
Figure: The dark-green area is the ‘Fertile Crescent’, the area of the Middle East where many of
today's crops - wheat, barley, etc. - grow wild and where these plants are thought to have first
been taken into cultivation.