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1 Οκτ 2013 (πριν από 3 χρόνια και 10 μήνες)

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BIOLOGY 332: BIOINFORMATICS

EXERCISE 4: PHYLOGENY OF ELEPHANT


This exercise is based on Case 1.5 of Lesk

(2008) wherein amino acid sequences are
again used to test the relationships of living and extinct species of elephants.
Elephants are some of the largest land mammal the ever lived on Earth. There are
several questions with regards to the relationships o
f two extant species of
elephants, the African elephant (
Loxodonta Africana
) and the Indian elephant
(
Elephas maximus
) with that of the extinct Siberian woolly mammoth (
Mammuthus
primigenius
).


The wolly

mammoth is believed to have gone extinct about 10,000 years ago, about
the same time man started migration into the Americas. Remains of the woolly
mammoth have been discovered intact in permafrost and considerable
part of the
genome
, as well protein sequ
ences have been deposited in Genbank.


One question is whether we could tell from these sequences alone what species is
more clo
sely related to another species
.

Given the differences are few, do they
represent true evolutionary di
vergence or merely random

drift?


At this point, it is important to distinguish between
similarity

and
homology
.

This is
discus
sed in more detail on page 29 in

Lesk

(2008)
. In some instance
,

similarity in
sequence may not necessarily reflect common closer relationship. It is pos
sible that
a functional
cytochrome b
requires conservation of residues from all other animals
that there is not enough differences to discriminate the branching pattern among
species of the same clade
,

or group. Thus, you will include two other species of
mammals that are more distantly related to the elephants; the hyrax and the
dugongs (or manatee).


The
cytochro
me b

gene is one of 13

protein
-
coding gene
s

of the
eukaryotic
mitochondrial genome. The mitochondria is unique since

it is passed

on only from
m
other

to
offspring
. Thus, mutations in the past generations are reflected in
the
de
scendants and are presumed to

represent unique shared characteristics. This,
however, is based on the assumption, that the ra
te
,

or speed of mutation of all
lineages
in ones

dataset
are relatively the same
,

or constant.
A lineage (or ‘species’)
molecular character may have changed at a certain locus several times and revert
back to a similar character over a short period of time. But those characters are not
the same and repr
esent
evolutionary convergence

or

reversal
. This is most true of
DNA where there are only four character states; G, A, T, and C. an

original A may
change to T, then to C, and C to A, but those As (the original and the derived A) are
not the same. Amino acids, as character, are not as prone to this phenomenon since
there are more than 20 types of amino acids. However, amino acid sequen
ce
alignment of closely
-
related species may not exhibit enough variability to infer
patterns of relationships.



METHOD


Formulate

a hypothesis as to the relationships of the three elephant species, and
their relationship with other mammals, specifically

the hyrax and dugongs. Using
the websites previously used, retrieve and download the cytochrome b protein
sequences of 1) Indian Elephant, 2) African elephant, 3) Siberian woolly mammoth,
4) hyrax, 5) dugong or manatee. Perform multiple sequence alignmen
t using
CLUSTAL W2 and generate a simple phylogeny. An alternative website for alignment
using CLUSTAL and inference of a distance
-
based phylogeny is the Japanese website
Genomenet:
http://www.genome.jp

.
Present your a
lignment as Figure 1 and your
distance
-
based

phylogeny as Figure 2.
Make a sta
t
ement whether your amino acid
alignment and phylogenetic inference support your hypothesis.