ASSIGNMENT 1 OF MOLECULAR ANALYSIS

MUHAMMAD YUNUS
P051140261

SEKOLAH PASCASARJANA
INSTITUT PERTANIAN BOGOR
BOGOR
2015

NTSys Ouput of Data 1 and Data 2

SCa12
SCa6
ICCRI4
ICCRI3
ICS60
DRC16
ICCRI1
ICCRI2
DR38
T SH858
ICS13
RCC72
RCC70
RCC71
DR2
PA300
PA303
UF667
DR1
NIC4
NIC7
GC7
0.60

0.69

0.77

0.85

0.94

Coefficient

Figure 1 Phylogenetic tree of data 1 using SAHN analysis

SCa12
GC7
RCC70
RCC71
ICS13
DR1
NIC4
NIC7
RCC72
DR38
T SH858
ICCRI1
ICCRI2
ICCRI3
ICS60
DR2
DRC16
PA300
PA303
UF667
ICCRI4
SCa6
2.00

4.25

6.50

8.75

Coefficient

Figure 2 Phylogenetic tree of data 1 using NJOIN analysis

11.00

PA300
PA303
DR1
DR2
ICCRI2
DRC15
DRC16
DR38
NIC4
NIC7
ICS13
GC7
UIT 1
RCC70
RCC71
RCC72
ICCRI1
ICCRI3
ICCRI4
RCC78
KEE2
T SH908
Sca6
Sca12
Sca89
ICS60
T SH858
UF667
NW6261
0.73

0.79

0.85

0.91

0.98

Coefficient

Figure 3 Phylogenetic tree of data 2 using SAHN analysis

PA300
RCC72
RCC78
KEE2
T SH908
RCC70
RCC71
DR2
ICCRI2
DRC16
PA303
DR38
ICCRI1
ICCRI3
ICCRI4
Sca6
Sca12
Sca89
UF667
NW6261
ICS60
T SH858
NIC4
NIC7
ICS13
GC7
UIT 1
DR1
DRC15
2.00

4.50

7.00

9.50

Coefficient

Figure 4 Phylogenetic tree of data 2 using NJOIN analysis

12.00

(1) Data1 analysis: Morphological Data

Q1. Based on the output of SAHN Clustering Analysis, what accessions are the closest (the most
related) accessions?
A1. The closest accession are RCC70 with RCC71
Q2. Based on the output of SAHN Clustering Analysis, what accessions are the most distantly
related accessions?
A2. The most distantly related accessions are GC7 with SCa12
Q3. Based on the output of NJOIN Clustering Analysis, set by using OTU no. 2 (SCa6) as
OUTGROUP, what accessions are the closest (the most related) accessions?
A3. The most related accessions are NIC4 with NIC7
Q4. Based on the output of NJOIN Clustering Analysis, set by using OTU no. 2 (SCa6) as
OUTGROUP, what accessions are the most distantly related accessions?
A4. The most distantly reated accessions are SCa6 with SCa12
(2) Data2 analysis: Molecular Marker Data
Q1. Based on the output of SAHN Clustering Analysis, what accessions are the closest (the most
related) accessions?
A1. The closest accession are SCa12 with SCa89
Q2. Based on the output of SAHN Clustering Analysis, what accessions are the most distantly
related accessions?
A2. The most distantly related accessions are NW6261 with PA300
Q3. Based on the output of NJOIN Clustering Analysis, set by using OTU no. 10 (DRC15) as
OUTGROUP, what accessions are the closest (the most related) accessions?
A3. The most related accessions are SCa12 with SCa89
Q4. Based on the output of NJOIN Clustering Analysis, set by using OTU no. 10 (DRC15) as
OUTGROUP, what accessions are the most distantly related accessions?
A4. The most distantly reated accessions are DRC15 with PA300
(3) Based on results of SAHN and NJOIN analysis of Data1:
Q1. Is the answer for Q1 and Q3 the same? (Just answer: YES or NO)
A1. NO
Q2. Is the answer for Q2 and Q4 the same? (Just answer: YES or NO)
A2. NO
Based on results of SAHN and NJOIN analysis of Data2:
Q3. Is the answer for Q1 and Q3 the same? (Just answer: YES or NO)
A3. YES
Q4. Is the answer for Q2 and Q4 the same? (Just answer: YES or NO)
A4. NO
(4) Based on results of Data1 (Morphological Data) vs. Data2 (Molecular Marker Data)
Q1. Is the answer for Step (1) Q1 and Step (2) Q1 the same? (Just answer: YES or NO)
A1. NO
Q2. Is the answer for Step (1) Q2 and Step (2) Q2 the same? (Just answer: YES or NO)
A2. NO
Q3. Is the answer for Step (1) Q3 and Step (2) Q3 the same? (Just answer: YES or NO)
A3. NO
Q4. Is the answer for Step (1) Q4 and Step (2) Q4 the same? (Just answer: YES or NO)
A4. NO