- Information
- AI Chat
Phylogenetics Assignment
Genes, Chromosomes and Populations (GENE222)
University of Otago
Recommended for you
Preview text
1)Using the NCBI (GenBank) database, it was found that sequence 1 is most likely to belong to the genus and species: Phyllium philippinicum, and Phyllium siccifolium, both of which resulted in a 100% identity match. Sequence 2 is most likely to belong to Heteropteryx dilatata. For sequence 3, its most likely match would be Timema knulli. Sequence 4 matched with the genus and species of Eurycnema goliath. And sequence 5 had a 100% identity match to Sceptrophasma hispidulum.
- A pairwise distance matrix for sequence 1 – 5:
- Phylogenetics Assignment – Gene
- region of the gene is 1 – 2)It was found that the particular gene is the cytochrome oxidase subunit I (COI) gene, and the - 5) Construction of a UPGMA tree for sequence 1 – 5: - =
- 6/2 =
- (10+11)/2 = 10 (9+9)/2 = 9 (14+18)/2= - - = 3 3 4. - 1.
- 9/2 = 4.
- (11+10+11)/3=10 (18+14+16)/3=16.
-
-
-
-
-
-
- 1 2 3 4, - - - 4,5 10- 1 2 3 4,
- 4,5 10
- 1 2, 4,
- 2, 4, 5 10.
- 3 18 16.
####### 1 2 3 4,
####### = 3 3 4.
####### 1.
(18+18+14+18)/4=
4 5 2 1 3 = 3 3 4 5 8. (17)/2 =8 1. 0. 3.
- Comparing the UPGMA tree above to the molecular phylogenetic tree below, from the Nature journal), it can be seen that the published tree is more complex. The UPGMA tree used 5 sequences from 5 different species, whereas the published tree used DNA from 57 different species. This allows the phylogenetic tree to be more in depth regarding the amount of DNA sampling that was done. The published tree used nuclear DNA in the forms of ribosomal DNA and histone sampling. This is different to the UPGMA tree as mitochondrial DNA was sampled from all 5 sequences. This poses a difference in the results, as mitochondrial DNA is passed exclusively from the maternal lineage to the offspring, which results in only the maternal lineage being used. This is different to nuclear DNA which is passed down from both parents to the offspring. While the phylogenetic tree has sampled 57 different species, there were 22 ‘outgroups’ or species that do not fall under the stick insect group that the study is focused on.
(Whiting et al 2003 Nature 421:264)
####### 1 2, 4,
####### 2, 4, 5 10.
####### 3 18 16.
1 2 3 4 5 2 11 3 18 18 4 10 9 14 5 11 9 18 6
1, 2, 4, 5 3 3 17
1, 2, 4, 5 3 3 17
(John Waters However, both hypotheses are favoured by different types of parsimony. Equally weighted parsimony favours the least amount of changes in evolution. As the first hypothesis has seven changes in total, and the second has thirteen, the equally weighted parsimony favours the first hypothesis. The weighted parsimony favours the second hypothesis, as losses more likely to occur, let’s say three times as more as gains. Therefore, the first hypothesis has fifteen changes and the second would have thirteen. Which means that the second hypothesis is favoured. I personally think the second hypothesis is more likely to be correct, as the gain of a characteristic that was once lost would not allow the characteristic to be gained identical to when it was lost. It also seems more likely that there would be more wing losses throughout evolution due to changing environments and the changes in predation of the insects that would select for wing loss, instead of changes selecting for wing gain.
Phylogenetics Assignment
Course: Genes, Chromosomes and Populations (GENE222)
University: University of Otago
