Initial Alignment of Pt verus

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Comparison of mt DNA for the Pt verus subspecies
of Chimpanzee The existence of 2 groups
within The subspecies
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INTRODUCTION In 1900 it has been estimated that
1 2 million Chimpanzees existed, today that
estimate is only 150,000. This species is
divided into smaller discreet groups as their
habitat becomes increasingly fragmented. To
better insure the survival of this species, it is
important that we understand its gene
pool structure.
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Hypothesis Divergent groups exist within the
verus subspecies of Chimpanzee.
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MATERIALS AND METHODS mt DNA sequences for 14
from GenBank were Used in the analysis. The
sequences were analyzed using ClustalW. The
sequences were from Pt verus collected from the
African countries of Mali and the Ivory Coast.
Three of the sequences were from individuals in
protected areas.
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Initial Alignment of Pt verus
6 total sequences (3 Ivory Forest 3
Mali) Genbank IDs Gi556039 (Ivory
Coast) Gi556042 (Ivory Coast) Gi556074 (Ivory
Coast) Gi556049 (Mali) Gi556050
(Maii) Gi556051 (Mali)
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Initial Alignment of Pt verus
6 total sequences (3 Ivory Forest 3
Mali) Genbank IDs Gi556039 (Ivory
Coast) Gi556042 (Ivory Coast) Gi556074 (Ivory
Coast) Gi556049 (Mali) Gi556050
(Maii) Gi556051 (Mali)
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For 4 distinct points on an unrooted tree,
3unrooted trees can be formed
1
2.5
2
original
3
4
2
3
-3.5
Spurious 1
1
4
2
3
0.5
Spurious 2
4
1
Separation Length (2431)-(2314)
therefore separation is not spurious
2
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Additional Genbank Sequences

• 10 Additional Pt verus sequences retrieved
• GenBank sequence similarity
• GB ids
• 6288805
• 4754940
• 6288840
• 6288811
• 6288834
• 6288814
• 4754954
• 4754951
• 4754976
• 4754962

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(No Transcript)
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Additional Filtering

• Sequences Aligned using ClustalW
• Ends Trimmed

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CLUSTAL W (1.81) multiple sequence
alignment Pt_verus_Tai_Forest__Ivory_
TACCACCTAAGTACTGGCTCATTCATTACAACCGCTATGTATTTCGTACA
Pt_verus_Mali_gi_556049_gb
---------------GGCTCATTCATTACAACCGCTATGTATTTCGTACA
Pt_verus_Tai_Forest__Ivory_
-----CCTAAGTACTGGCTCATTCATTACAACCGCTATGTATTTCGTACA
Pt_verus_Mali_gi_556051_gb
---------------GGCTCATTCATTACAACCGCTATGTATTTCGTACA
Pt_verus_Tai_Forest__Ivory_
TACCACCTAAGTACTGGCTCATCCATTACAACCGCTATGTATTTCGTACA
Pt_verus_Mali_gi_556050_gb
---------------GGCTCATTCATTACAACCGCTATGTATTTCGTACA

Pt_verus_Tai_
Forest__Ivory_ TTACTGCCAGCCACCATGAATATTGTACAG
TACCATAATCACCCAACTAC Pt_verus_Mali_gi_556049_gb
TTACTGCCAGCCACCATGAATATTGTACAGTACCATAATCACCCA
ACTAC Pt_verus_Tai_Forest__Ivory_
TTACTGCCAGCCACCATGAATATTGTACAGTACCATAATCACCCAACTAC
Pt_verus_Mali_gi_556051_gb
TTACTGCCAGCCACCATGAATATTGTACGGTACCATAATTACCCAACTAC
Pt_verus_Tai_Forest__Ivory_
TTACTGCCAGCCACCATGAATATTGTACGGTACCATAATTACCCAACTAC
Pt_verus_Mali_gi_556050_gb
TTACTGCCAGCCACCATGAATATTGTACGGTACCATAATCACCCAACTAC


Pt_verus_Tai_Forest__Ivory_
CTATAATACATAAAATCCACTCCCACACCAAAACCTTCACCCCATGCTTA
Pt_verus_Mali_gi_556049_gb
CTATAACACATAAAATCCACTCCCACACCAAAACCTTCACCCCATGCTTA
Pt_verus_Tai_Forest__Ivory_
CTATAACACATAAAATCCACTCCCACACCAAAACCTTCACCCCATGCTTA
Pt_verus_Mali_gi_556051_gb
CTATAACACATAAAACCCAC-CCCACATTAAAACCTTCACCCCATGCTTA
Pt_verus_Tai_Forest__Ivory_
CTATAACACATAAAACCCAC-CCCACATTAAAGCCTTCACCCCATGCTTA
Pt_verus_Mali_gi_556050_gb
CTATAGCACATAAAACCCAC-CCCACATTAAAACCTTCACCCCATGCTTA


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Pt_verus_Tai_Forest__Ivory_
CAAGCACGCACAACAATCAACCTCCAACTGTCGAACATAAGACACAACTC
Pt_verus_Mali_gi_556049_gb
CAAGCACGCACAACAATCAACCTCCAACTGTCGAACATAAAACACAACTC
Pt_verus_Tai_Forest__Ivory_
CAAGCACGCACAACAATCAACCTCCAACTGTCGAACATAAAACACAACTC
Pt_verus_Mali_gi_556051_gb
CAAGCACGCACAACAATCAACCTCTAACTATCAAACATAAAACACAACTC
Pt_verus_Tai_Forest__Ivory_
CAAGCACGCACAACAATCAACCTCTAACTNTCAAACATAAAACACAACTC
Pt_verus_Mali_gi_556050_gb
CAAGCACGCACAACAATCAACCTCTAACTATCAAACATAAAACACAACTC


Pt_verus_Tai_Forest__Ivory_
CAACGACACCCCTCCCCCACCCCGATATCAACAGACCTACCCCTCCCTGA
Pt_verus_Mali_gi_556049_gb
CAACGACNNNNNNNNNNCACCCCGATATCAACAGACCTACCCCCCCCTGA
Pt_verus_Tai_Forest__Ivory_
CAACGACACCCCTCCCCCACCCCGATATCAACAGACCTACCCC-CCTTGA
Pt_verus_Mali_gi_556051_gb
CAACGACACTTCTCCCCCACCCCGATACCAACAAACCTACCCCCCCTTGA
Pt_verus_Tai_Forest__Ivory_
CAACGACACTTCTCCCCCACCCCGATACCAACAAACCTACCCCCCCTTGA
Pt_verus_Mali_gi_556050_gb
CAACGACACCTCTCCCCCACCCCGATACCAACAAACCTACCCCCC-TTGA

Pt_verus_Tai_Fo
rest__Ivory_ CAGAACATAGTACATACAATCATACACCGTAC
ATAGCACATTACAGTCAA Pt_verus_Mali_gi_556049_gb
CAGAACATAGTACATACAATCATACACCGTACATAGCACATTACAGT
CAA Pt_verus_Tai_Forest__Ivory_
CAGAACATAGTACATACAATCATACACCGTACATAGCACATTACAGTCAA
Pt_verus_Mali_gi_556051_gb
TAAAACATAGTACATACAATCACACACCGTACATAGCACATTACAGTCAA
Pt_verus_Tai_Forest__Ivory_
CAAAACATAGTACATACAATCACACACCGTACATAGCACATTACAGTCAA
Pt_verus_Mali_gi_556050_gb
CAAAACATAGTACATACAATCACACACCGTACATAGCACATTACAGTTAA


Pt_verus_Tai_Forest__Ivory_
ACTCTTCCTCGTCCCCACGGATGCCCCCCCTCAGATAGGAAT Pt_veru
s_Mali_gi_556049_gb ATTCTTCCTCGTCCCCACGGATG
CCCCCCCTCAGATAGGAAT Pt_verus_Tai_Forest__Ivory_
ATTCTTCCTCGTCCCCACGGATGCCCCCCCTCAGATAGGAAT Pt_
verus_Mali_gi_556051_gb ATCCATCCTCGCCCCCACG
GATGATCC--------------- Pt_verus_Tai_Forest__Ivor
y_ ATCCATCCTCGCCCCCACGGATGATCCCCCTCA---------
Pt_verus_Mali_gi_556050_gb
ATCCATCCTTGCCCCCACGGATGATCC---------------


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Results and Conclusion

• We found what appears to be two genetically
  distinct groups in the Pt verus subspecies
• Further phylogenetic analysis indicates the
  validity of initial observation
• Data indicates that geographic separation is not
  indicative of genetic separation

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Thats all Folks!(ok, so now wheres my banana?)