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 of 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 sequences have been deposited in Genbank.

One question is whether we could tell from these sequences alone what species is more closely related to another species? Given the differences are few, do they represent true evolutionary divergence or merely random drift?

At this point, it is important to distinguish between similarity and homology. This is discussed in more detail on page 29 of Lesk. In some instance similarity in sequence may not necessarily reflect common closer relationship. It is possible 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 cytochrome b gene is one of the protein-coding gene of the mitochondrial genome. The mitochondria is unique since it is past on only from mothers to offsprings. Thus, mutations in the past generations are reflected in the descendants and are presumed to be represent unique shared characteristics. This, however, is based on the assumption, that the rate or speed of mutation of all lineages are relatively the same or constant.

METHODS

You will be using two types of datasets, protein and DNA and determine if the two types of datasets are congruent or if they agree. Congruence among different types of data, or independent sources of evidences is the strongest evidence to support, or reject a hypothesis. Formulate a hypothesis as to the relationships of the three elephant species, and their relationship with other mammals, specifically the hyrax and dugongs. In doing your searches for sequences, it is often better to use scientific names, instead of common names. So use google or Wikipedia to get scientific names.

Submit a scientific paper due the following week.

Protein sequence data

For protein sequence data and and using the websites previously used, retrieve and download the cytochrome b protein sequences of 1) Indian Elephant, 2) African elephant, 3) Siberian woolly mammoth (Mammuthus), 4) hyrax , 5) dugong, 6) manatee, and 7) red kangaroo. You can include any other type mammal to increase your sample size, for a more robust analysis. Perform multiple sequence alignment 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 alignment as Figure 1 and your distance-based phylogeny as Figure 2. Make a statement whether your amino acid alignment and phylogenetic inference support your hypothesis.

Using DNA sequence data.

For DNA sequence data, go to Genbank (https://www.ncbi.nlm.nih.gov/genbank/) and under Nucleotide enter Mammuthus cytb (abbreviation for cytochrome b gene). Copy and paste, or collect files under Select to . Collect other taxa listed above, add more taxa if you wish. Use the Genomenet website for sequence alignment and generate a distance-based phylogeny. An alternative site is http:www.phylogeny.fr . This site will generate alignment and phylogenetic trees under different criteria.