Question

1. Analysis based on two individual genes (gene trees) may imply two different phylogenetic relationships among a group of species. List three possible reasons for this (1), and explain how one of them works (2). If only one phylogenetic tree accurately represents the true evolutionary history of these species, what might we do in order to determine which one is correct (2)?  

Answer 1

It is true that phylogenetic analysis using two different genes may imply two different phylogenetic relationship among a group of species. This may be because:

1. Different origin of the two genes. plants and animals acquired mitochondria (Both plants and animals) and plastid (Only plants) during endosymbiosis at different periods of time. Thus, any gene of mitochondria in a species may come from different bacteria at different time. Also, any gene of plastid in plants may differ in different species due to their different origin.

2. Frequency of recombination in a gene: Different genes have differing tendency to change. Thus, differing recombinations in genes may indicate different phylogenetic origin.

3. Gene duplication and extinction: If a large dataset comprises paralogous copies of any gene (descended from the same ancestral gene by gene duplication), phylogeny will reflect the duplication history rather than true divergence.

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In order to determine which of the phylogenetic tree correctly represents the phylogenetic history, we will need to include more similar or different genes. And, the phylogenetic tree which corresponds to most of the genes under study will almost correctly represent the phylogenetic relationship among organisms.

The phylogenetic analysis is mainly done by maximum likelihood and maximum persimony methods. However, if the replicate the analysis with UPGMA (unweighted pair group method with arithmetic mean) with multiple replicating analysis will provide more or less correct phylogenetic relationship.

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