You are given molecular sequence data for the GULO pseudogene from four species
ID: 212698 • Letter: Y
Question
You are given molecular sequence data for the GULO pseudogene from four species of primates: Pan troglodytes (common chimpanzee, abbreviated Pt below), Pongo pygmaeus (Bornean orangutan, Pp), Homo sapiens (human, Hs) and Macaca fascicularis (crab-eating macaque).
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
Pt
C
A
C
T
A
C
C
T
G
G
T
G
G
G
G
C
T
A
C
G
C
T
T
C
A
C
C
T
G
G
A
G
G
Pp
C
A
C
T
A
C
C
C
G
G
T
G
G
G
G
G
T
A
C
G
C
T
T
C
A
C
C
C
A
G
A
G
G
Hs
C
A
C
T
A
C
C
T
G
G
T
G
G
G
G
G
T
A
C
G
C
T
T
C
A
C
C
T
G
G
A
G
G
Mf
C
A
C
T
A
A
C
C
G
G
T
G
G
G
G
G
T
A
C
G
C
T
T
C
A
C
C
C
A
A
G
G
G
1. Using the molecular data sets above, first identify each variable site on the pseudogene (i.e., locations where not all nucleotides are the same for all 4 species). For example, at location # 6, three species have a C, while one has an A. What are the variable sites on this pseudogene? List them or mark them on the table (2 points)
1b
Use these variable locations as your characters for phylogenetic analysis. Following the same steps as in the previous phylogenetic analyses, construct a phylogenetic tree for the clade that includes chimps, orangutans and humans (with Macaca as an outgroup). (2 points)
1c.
The traditional classification scheme of primates placed orangutans and chimps together in one clade called Pongidae, and humans in a different clade, Hominidae. Is the traditional classification scheme supported by your molecular phylogeny? (4 points)
1d.
A pseudogene is a region of DNA that is derived from a functional gene, but no longer codes for a protein (i.e., it is not expressed at all). In each of these primates, there is also a version of GULO that is functional (i.e., it does code for a protein). Give one reason why you would have more confidence in a phylogenetic tree based on the pseudogene than one based on the functional gene. (2 points)
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26
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28
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32
33
Pt
C
A
C
T
A
C
C
T
G
G
T
G
G
G
G
C
T
A
C
G
C
T
T
C
A
C
C
T
G
G
A
G
G
Pp
C
A
C
T
A
C
C
C
G
G
T
G
G
G
G
G
T
A
C
G
C
T
T
C
A
C
C
C
A
G
A
G
G
Hs
C
A
C
T
A
C
C
T
G
G
T
G
G
G
G
G
T
A
C
G
C
T
T
C
A
C
C
T
G
G
A
G
G
Mf
C
A
C
T
A
A
C
C
G
G
T
G
G
G
G
G
T
A
C
G
C
T
T
C
A
C
C
C
A
A
G
G
G
Explanation / Answer
The traditional classifications scheme of primates placed orangutans and chimps together in one clade called Pongidae, and humans in a different clade, Hominidae.
the variable sites on this pseudogene are at position: 6,8,28,29,30 and 31
Molecular data can provide more robust phylogenies than anatomical data alone, as they are less subject to homoplasies. Many of the molecular changes used to reconstruct evolutionary relationships are random, rare events that are unlikely to occur repeatedly. Molecular data can, roughly, pinpoint the time and relative order in which lineages diverge, while fossil data describe the gain and loss of characters recognized as lineage specific.
The proteins selected are from the mitochondrial origin as mtDNA which codes for mitochondrial proteins, mutate at a better rate compared to nuclear DNA, on the way to deliver a greater beneficial, magnified view of the variety found in a populace, and its records. deliberating that nearby point mutations generate a considerable genetic variant and this transformation being very excessive in mitochondrial DNA the series divergence among those three species using 0, ±1 and ±2 error in same cut sites through one-of-a-kind restriction enzymes. due to the presence of nuclease enzyme in the nucleus only the nuclear region is very less effected with mutation in comparison to the mitochondrial region in cytoplasm so one have more confidence in a phylogenetic tree based on the pseudogene than one based on the functional gene.
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