Binhua Liang

Assignment 4 --- PHYLOGENY

March 10, 2007

The problem

Six gamma-globin genes (four human and two chimp) are used for pylogenetic analysis. The question is: is it valid to construct a pylogenetic tree as a single unit, or do different parts of gene have distinct evolutionary histories?

The approach to anwser....

(1) At first, print out the alignments using "Alignment--->Reform? The alignment for working with...
(2) Construct a tree of the entire alignment (Maximum Parsomony with bootstrapping): Outfile; Treefile

      Figure 1. Pylogenetic Tree Produced From The
                 Entire Alignment

        The resulted tree on the left looks very good, which is
        supported by high value of bootstrapping (>92%).

        The gamma globin genes are reported to be subject
        to gene convertion--"noreciprocal transfer of genetic
information", which often occurs in a part of gene. Thus,
some parts of gamma genes may have seperate evolu-
        tionary histories from other region. The next step is to
investigate if different parts of the sequence give differ-
        ent trees (different evolutionary histories).

(3) Decide a strategy to define the parts of sequences which have different evolutionary histories and build sub-tree based on the selected block of sequences.

     In the paper, "Chimpanzee fetal Gr and Ar Globin Gene Nucleotide Sequences Provide Further Evidence of Gene Converstions in Hominine Evolution; Jerry L. Slightom, et.., Mol.Biol.Evol.2(5):370-398. 1985", author postulates a possible conversions in a region of a sequence on two conditions (1) Three or more substtutions and/or insertion/deletion events are required in its descent from its immediate ancestor (2) at least three fewer events would be necessary if the region had instead descended from the homologous region of a paralogous gene in the same taxon.

     We use this criteria to predict the boudaries of conversions of gamma globin gene sequences based on The Alignment. We predicted the following boundaries of converstions of chmip, human A, and human B (gamma globin genes):

     ---chimp: 324-1012, 1013-1183, 1732-1839
     ---humanA: 324-1698
     ---humanB: 324-1176, 1441-1681

     According to the above predicted boundaries of conversions, we divide the whole alignments (2320 bps) into 7 regions, see Figure 1 below:

(4) Building trees based on the above defined regions of sequences, evaluating and comparing the resulted trees through bootstrapping

We built the individual trees based on the above block of defined sequences using "Maximun Parsomony" (DNAPARS). We set "Jumble the sequence order: Yes" and "Resampling: Bootscrap = 100". Output files include: outfile and outtree. We also captured tree images! The all results are as following:

Tree Name	Tree	Out file	Tree file	Tree Name	Tree	Out file	Tree file
I		Click	Click	II		Click	Click
III		Click	Click	IV		Click	Click
V		Click	Click	VI		Click	Click
VI		Click	Click

From the above tree topologies, we can see most of them are different from one built from the whole alignment, except "Tree I". (See figure 2). And the most of resulted trees are supported by bootstrapping...

Except some branches, especially in Tree II & III with the values of bootstrapping <50% (ellipse area, thus Tree II & III not reliable), the most of resulted trees in Figure 2 are very reliable, which are strongly supported by bootstrapping (>70%). Although some branches in Tree I and VI, see figure 2, are not very consistently replicated, their values of bootstrapping are 58% and 60%--- indicating that branches are clustered as above which are more likely true in about 60% of trees and shoud not effect the whole topologies of trees. Thus, the topologies of Tree I, IV, V, VI, and VII should be reliable. Comparing the topologies of Tree I, IV, V, VI, and VII with each other, we found that they are all different. Because each mentioned tree is built from one region of gamma globin gene, which gives a consistant tree across all bootstrapped replicates, it probably has evolved as a coherent unit over time. The above result suggests these regiones defined from above to build different trees (I, IV,V,VI, and VII) may represent different evolutionary histories. Therefore, the gamma globin genes don't evolve as a single unit!

Conlusion

(1) All of parts of alignment of gamma globin gene don't share the same tree since up to 5 regions show different trees.
(2) The whole alignment of gamma globin sequences can be broken up to at least 5 distinct regions, which have separate evolutionary histories from other regions. These 5 regions are defined as following (positions below are based on The Alignment):

      a. 1--324
      b. 1277--1441
      c. 1442--1681
      d. 1732--1839
      e. 1840--2320

In the region 325--1183, we should be more cautious and take more analysis... ...

(3) The tree built from the entire alignment of gamma globin gene is definitely not valid since up to 5 regions have evolved as a coherent unit over time.

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