**Genetic 564 Undergraduate Capstone course at University of Wisconsin Madison**

## What is a phylogeny?

A

**phylogeny**refers to an illustration of a biological relationship over time. Phylogeny is not to be confused with a**genealogy**which is based on known decedents and statistically probability.[1] Fig. 1Fig.1

## How to construct a phylogenic tree?

The foundation of any phylogenetic tree is the data one is attempting associated biological relationships. Biological material such as DNA, RNA, or protein are sequenced and later are processed using computational statistically methods.[2] The four main statistically techniques used to construct phylogenic trees are bayesian inference, maximum likelihood/parsimony and distance matrixes,

Bayesian Inference : Probability of distribution based on

Maximum Likelihood: Given assumptions and rules about biological changes (DNA) over time, the tree reflects the

Maximum Parsimony: Assumes tree requires

Distance Matrices: depends on measurements of

Bayesian Inference : Probability of distribution based on

**prior knowledge and data.**Maximum Likelihood: Given assumptions and rules about biological changes (DNA) over time, the tree reflects the

**most likely**sequence.Maximum Parsimony: Assumes tree requires

**fewest evolutionary**events is the most likely.Distance Matrices: depends on measurements of

**genetic distance**between the sequences, and therefore they require multiple sequence alignment.## The Phylogeny of PAX8

To construct a consensus phylogenetic tree for PAX8 I used two platforms. The first being

**Neighborhood Joining**uses these statistics to determine which species are most closely related. It calculates the branch lengths which can be different lengths. While**A****verage Distance**links the most closely related species and joins them with equal branch lengths. [3] One assumption is that species being compared have diverged a common ancestor. Under each of the two platforms two statistical approached underline each the phylogenetic tree construct methods.**BLOSUM**scores sequences system and calculates the similarity (*See Distance Matrix*).**Percent identity**calculates the percentage of identical segments of sequences between two species.[3] The species used to construct the PAX8 phylogenic tree can be found on the**homology page**and protein sequences (FASTA) were aligned to create the following phylogenic trees.

## Conclusion

Pax8 as characterized today derived and evolved from ancestral gene beyond the Drosophila melanogaster (Fruit Fly) dPAX2. Both the Zebra fish and Western Clawed Frog as expected were confined to separate and distant branch despite being vertebrates. All mammals scored to be in the same clade as predicted suggesting

**PAX8 is highly conserved both in function and sequences among mammalian species compared to fish, amphibians and invertebrates.**## PAX8 Consensus Phylogenetic Tree

## Additional Material

sequence_alignment_phylogeny_.clustal | |

File Size: | 12 kb |

File Type: | clustal |

References:

[1]Kingman, J.F.C. (1982) ‘On the genealogy of large populations’,

[2]Yang Z, Rannala B. Molecular phylogenetics: principles and practice. Nat Rev Genet. 2012 Mar 28;13(5):303-14. doi: 10.1038/nrg3186.

[3] http://genetics564.weebly.com/homology--phylogeny.html

[1]Kingman, J.F.C. (1982) ‘On the genealogy of large populations’,

*Journal of Applied Probability*, 19(A), pp. 27–43. doi: 10.1017/S0021900200034446.[2]Yang Z, Rannala B. Molecular phylogenetics: principles and practice. Nat Rev Genet. 2012 Mar 28;13(5):303-14. doi: 10.1038/nrg3186.

[3] http://genetics564.weebly.com/homology--phylogeny.html