Phylogenetic Analysis Homework
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Phylogenetic Analysis Homework
Reconstructing the Evolutionary History of Darwin’s Finches
Due 5:00 pm Wednesday, December 8 (10 points)
Please be sure to complete the Phylogenetic Analysis Tutorial before beginning this assignment.
1. First locate Camarhynchus pauper, the medium tree finch, in both your neighbor-joining tree and in you
matrix of pairwise distances and consider the following question. According to your neighbor-joining tree, is
Camarhynchus pauper (A) more closely related to Camarhynchus parvulus than it is to Camarhynchus
psittacula, (B) more closely related to Camarhynchus psittacula than it is to Camarhynchus parvulus, or (C)
equally related to both Camarhynchus parvulus and Camarhynchus psittacula? Be sure to support you
answer by citing specific values of genetic distance from your pairwise distance matrix! C. pauper,
psittacula, and parvulus are species 7, 8, and 9, respectively, in the distance matrix. [Hint: remember that “more
closely related to” means “shares a more recent common ancestor with” and “equally related to” means “shares
the same most recent common ancestor.”](3 points).
2. Now locate Certhidea olivacea, the wa
ler finch, in both your neighbor-joining tree and in your matrix of
pairwise distances and consider the following question. According to your neighbor-joining tree, is Certhidea (A)
more closely related to Platyspiza crassirostris than it is to Geospiza magnirostris, (B) more closely related
to Geospiza magnirostris than it is to Platyspiza crassirostris, or (C) equally related to both Platyspiza
crassirostris and Geospiza magnirostris? Be sure to support your answer by citing specific values of genetic
distance from your pairwise distance matrix! Certhidea olivacea, Platyspiza crassirostris, and Geospiza
magnirostris are species 13, 12, and 2, respectively, in the distance matrix (3 points).
3. Based on their behavior and ecology, the two species of Cactospiza (Woodpecker Finch and Mangrove Finch)
traditionally have been thought to be closely related to the Camarhynchus tree finches, and some biologists have
even recommended abolishing the genus Cactospiza and placing the Woodpecker Finch and Mangrove Finch in
the genus Camarhynchus. Based on your neighbor-joining tree, do the mtDNA data support a close relationship
etween Cactospiza and Camarhynchus? [Hint: determine what species are Cactospiza’s closest relatives by
ecency of a common ancestor.] Briefly explain why or why not (2 points).
4. The origins of Pinaroloxias (Cocos Finch) has puzzled biologists for years. Many have suggested that
Pinaroloxias may be most closely related to Certhidea (Wa
ler Finch), which it resembles in body size and bill
shape. Based on your neighbor-joining tree, do the mtDNA sequence data support a close relationship between
Pinaroloxias and Certhidea? Briefly explain why or why not. [Hint: determine what species are Pinaroloxias’s
closest relatives by recency of a common ancestor.](2 points).
https:
allegheny.instructure.com/courses/5387/pages/phylogenetic-analysis-tutorial?module_item_id=176436