Background

The Dodo (Raphus cucullatus) was a flightless bird native to the island of Mauritius. It became extinct in the 1600’s and is one of the most famous examples of human-induced extinction. Having evolved in the absence of significant predators, it was fearless of humans and was extirpated by a combination of hunting and nest predation by human-introduced pigs, monkeys, cats, rats, and dogs.

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It has been variously suggested that Dodo’s were a type of parrot, ostrich, rail, albatross, or vulture (Owen 1846). Theodore Reinhardt suggested that it was most closely related to pigeons, which was later supported after the examination of the Oxford museum specimen (Strickland and Melville 1848). While this theory has been generally accepted, the complete evolutionary history of the Dodo remained unknown until recently. In this lab, you will use genetic data from museum specimens to reconstruct the Dodo phylogeny.

Phylogenetic Tree 1:

You have been give a data file (named cytb) with the species names and genetic sequences of the cytochrome b (cytb) gene from the mitochondria of 35 species of birds. The data is in the FASTA forma, which can be seen in the following example:

>seq0
FQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKKIEKF
>seq1
KYRTWEEFTRAAEKLYQADPMKVRVVLKYRHCDGNLCIKVTDDVVCLLYRTDQAQDVKKIEKFHSQLMRLME LKVTDNKECLKFKTDQAQEAKKMEKLNNIFFTLM
>seq2
EEYQTWEEFARAAEKLYLTDPMKVRVVLKYRHCDGNLCMKVTDDAVCLQYKTDQAQDVKKVEKLHGK
>seq3
MYQVWEEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSVCLQYKTDQAQDVK
>seq4
EEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSVVSYEMRLFGVQKDNFALEHSLL
>seq5
SWEEFAKAAEVLYLEDPMKCRMCTKYRHVDHKLVVKLTDNHTVLKYVTDMAQDVKKIEKLTTLLMR
>seq6
FTNWEEFAKAAERLHSANPEKCRFVTKYNHTKGELVLKLTDDVVCLQYSTNQLQDVKKLEKLSSTLLRSI
>seq7
SWEEFVERSVQLFRGDPNATRYVMKYRHCEGKLVLKVTDDRECLKFKTDQAQDAKKMEKLNNIFF
>seq8
SWDEFVDRSVQLFRADPESTRYVMKYRHCDGKLVLKVTDNKECLKFKTDQAQEAKKMEKLNNIFFTLM
>seq9
KNWEDFEIAAENMYMANPQNCRYTMKYVHSKGHILLKMSDNVKCVQYRAENMPDLKK
>seq10

You will begin by adding the cytb sequence data from two extinct taxa to your fasta file: the Dodo (Raphus cucullatus) from Mauritius island and it’s presumed relative the Rodrigues Solitaire (Pezophaps solitaria) from Rodrigues island. Both of these birds have been extinct for hundreds of years but DNA was isolated from specimens originally collected for (and preserved in) natural history museums. You will use GenBank to download the sequence data and add it to your cytb file. Through GenBank, you can find sequence data by searching for the species and gene names, the name of a journal article (if there is a published article for which sequences have been deposited in GenBank), or the Accession number (each sample’s unique ID) if you know it.

  1. In your browser, go to the following website: http://www.ncbi.nlm.nih.gov/genbank
  2. Verify that the pull-down menu at the top of the page is set for “Nucleotide”
  3. Type the following Accession number in the search bar and click “Search”: AF483338.1
    1. What species did this sequence come from?
    2. What gene is this?
    3. What is the title of the journal article that this sequence was used for?
    4. What journal did this article appear in?
    5. List the authors of the article
  4. Click “FASTA” under the GenBank Accession number,
  5. Copy the FASTA sequence and paste it at the end of your cytb file (you may want to change the name to match the format of the rest of the file).
  6. Repeat steps 3-5 with Accession number: AF483337.1
    1. What species did this sequence come from?
    2. What gene is this?
    3. Is this sequence data from the same journal article as the previous sequence?
  7. Save the file as cytb-2.fa

cytb-1.fa

cytb-2.fa

Before creating your tree, your sequence data must first be aligned. To do this, you will use the program Muscle.