Download Is the Tiger a Copycat? A Phylogenetic Analysis Laboratory

Introduction:
Is the Tiger a Copycat?
A Phylogenetic Analysis Laboratory Investigation
[Name]
[Date]
“Big cats” (the members of the genus Panthera) have been a source of fascination to many people and
cultures, whether prowling in the savannas of Africa or the jungles of India. They are fierce predators that
are not to be taken lightly. With that said, many of the world’s big cat species are endangered in the wild,
with some on the brink of extinction. This leads to questions for conservationists interested in preserving
the species. For instance, if the tiger were to go extinct in nature, might it be possible to keep the species’
genes alive in captivity by inter-breeding with closely related species? The only way to determine whether
this would be possible is to investigate the degree to which tigers are evolutionarily related to the other
cats.
In this investigation, the researcher is going to try to answer the following question: How closely related are
Tigers to other members of the cat family (Felidae)?
Methods:
To find out how closely related the Tiger is to other cats, the research looked at two different genes,
Cytochrome Oxidase Subunit I (COI) and Cytochrome B (CytB). These two mitochondrial genes are commonly
found in most eukaryotic organisms, including the ones that were analyzed in this investigation. Both genes
are involved in producing proteins that aid in the process of cellular respiration in mitochondria.
The animals that were analyzed in comparison to the Tiger (Panthera tigris) were the Lion (Panthera leo),
Leopard (Panthera pardus), Snow Leopard (Panthera uncia), Lynx (Lynx rufus), Domestic Cat (Felis catus),
and as an outgroup, a species of lizard found in Madagascar (Chalarodon madagascariensis).
To obtain the necessary sequences for the two genes, the researcher went to the National Center for
Biotechnology Information’s (NCBI’s) nucleotide resource page at http://www.ncbi.nlm.nih.gov/nuccorend
and searched for the COI and CytB sequences for Tigers. After copying and pasting the Tiger’s COI and CytB
FASTA sequences into two different text files, a sequence BLAST was performed to look for the homologous
gene sequences of the other animals that were being analyzed. Once the appropriate FASTA sequences were
located in the NCBI database, they were copied and pasted into the corresponding text files below the
Tiger’s sequence.
These two text files were then opened and aligned using ClustalX software (available for download at
http://www.clustal.org/clustal2/). Upon closer inspection, some of the FASTA sequences appeared to be
only partial segments of the gene being analyzed. In order to maximize the likelihood of a successful
alignment, excess sequence data was trimmed from the beginning and end of some of the FASTA sequences.
This ensured that the alignment software was only matching up homologous segments of the genes being
compared. By doing this, the researcher hoped to avoid the possibility that some species might appear to be
more closely related to each other simply because they had more data to compare.
After aligning the sequences with ClustalX, two phylogenetic trees were created using the NJplot software
(available for download at http://doua.prabi.fr/software/njplot). A screen shot of the tree was taken of
each tree and then the image was pasted into the document below. To determine which animals were most
closely related to the Tiger, the researcher examined the two phylogenetic trees and looked for which
species shared the most recent common ancestor with Tigers.
One final note: the reason for analyzing the Lizard’s COI and CytB sequences was to indicate the soundness
of the data and to ensure the reliability of the results. For example, if the resulting phylogenetic tree
indicated that the Lion is more closely related to the Lizard than it is to the Tiger, this result would indicate
a problem with the data that was selected for this investigation. On the other hand, if the resulting tree
indicated that the Lizard is the outgroup in comparison to the other cat species, this result would indicate
that the selected data was probably reliable.
Results:
COI Phylogenetic Tree
CytB Phylogenetic Tree
As shown in the two trees above, the Lizard was the outgroup in comparison to the six cat species, as
expected. The species most closely related to the Tiger were the same for each tree (Leopard, Lion, and
Snow Leopard), although the branching patterns above the common ancestor shared by all four species were
different. Lions and Leopards were more closely related on the COI tree, while Lions and Snow Leopards
were more closely related on the CytB tree. Another difference seen in the trees had to do with the
relationship between the two cat species that earlier diverged from the common ancestor of the Tiger,
Leopard, Lion, and Snow Leopard. In the COI tree, the Domestic Cat shared a more recent common ancestor
with the Tiger, Leopard, Lion, and Snow Leopard. In the CytB tree, the Domestic Cat shared a more recent
common ancestor with the Lynx.
Discussion:
The results of this investigation suggest that the Leopard, Lion, and Snow Leopard are the three cats in the
test group that are most closely related to the Tiger, with the Domestic Cat and the Lynx following them,
and lastly the Lizard. The fact that the Lizard was the clear outgroup in both trees serves to confirm the
reliability of the data used in this investigation.
Both phylogenetic trees suggest that the Leopard, Lion, and Snow Leopard share a common ancestor more
recently than the common ancestor the three species share with the Tiger. This observation supports the
conclusion that the Leopard, Lion, and Snow Leopard share the same degree of evolutionary relatedness to
the Tiger. In addition, both trees indicate that the House Cat and Lynx diverged from the Tiger at some
earlier point. This observation supports the conclusion that the Lynx and House Cat are not as closely
related to the Tiger in comparison to the other “big cat” species.
The results of this investigation are consistent with previous research conducted by researchers Brian Davis,
Gang Li, and William Murphy, in which they concluded that Lions and Leopards are most closely related to
each other than either species is related to the Tiger (Walker, 2010). The results also agree with the
traditional taxonomic classification of all of the “big cats” as members of the same genus, Panthera.
One way in which the results of this investigation differ from previous research has to do with the specific
relationships inferred among the members of the genus Panthera. According to a 2011 article by Chinese
researchers, the Panthera phylogeny has Lions and Snow Leopards as most closely related, then Leopards,
(then Jaguars – a species not included in this investigation), then Tigers (Wei, 2011). Excluding Jaguars,
these results can be represented in a nested hierarchy as follows:
(P. tigris (P. pardus (P. leo, P. uncia)))
The nested hierarchies for the COI and the CytB phylogenetic trees generated in this investigation can be
represented as follows:
COI - (P. tigris (P. uncia (P. leo, P. pardus)))
CytB - (P. tigris (P. pardus (P. leo, P. uncia)))
The apparent discrepancy between the COI phylogenetic tree and the research by Wei et al. is probably
explained by the fact that the Chinese researchers used a much larger pool of genetic sequence data,
including the complete mitochondrial genome sequences for each Panthera species.
In conclusion, although the results of this investigation are not enough to definitively determine which cat is
most related to the Tiger, they do show evidence of a relationship between Tigers, Leopards, Lions, and
Snow Leopards. This relationship has already been established by previous phylogenetic analyses conducted
by professional researchers. To further investigate the research question, the researcher would need to look
at a larger variety of gene sequences and a larger group of organisms.
References:
Walker, M. (2010, Feburary 12). Tigers evolved with snow leopards, gene study reveals. Retrieved
from http://news.bbc.co.uk/earth/hi/earth_news/newsid_8512000/8512455.stm
Wei, L., Wu, X., Zhu, L., & Jiang, Z. (2011). Mitogenomic analysis of the genus Panthera. SCIENCE
CHINA Life Sciences, 54(10), 917-930.
FASTA sequences downloaded from http://www.ncbi.nlm.nih.gov/nuccorend
ClustalX software downloaded from http://www.clustal.org/clustal2/
NJplot software downloaded from http://doua.prabi.fr/software/njplot