How are gene duplication and loss used in phylogenetic analysis?

We can use gene duplication and loss to determine if our proteins are related or not. If there are two genes in a cluster but one of them is missing, it means that they recently diverged from each other. If both genes are still present, then they have been evolving together for a longer period of time.

What is the purpose of gene duplication?

The primary function of gene duplication is to create more copies for mutation. If one copy mutates and becomes non-functional, there will be another copy that can take over its function.

What is the purpose of gene loss?

The primary function of gene loss is to reduce unnecessary genes, which saves space and energy.

What are some common pitfalls in phylogenetic analyses that involve gene duplication or loss?

One pitfall that can occur when using gene duplication or loss is homoplasy, which means the convergent evolution of a character. This happens when a gene gains a new function, and can cause us to incorrectly cluster our proteins into the wrong group.

Another pitfall is not being able to identify an orthologous relationship between two genes if they’ve both been lost from their original species or have different evolutionary rates. We can use “paralogs” as an alternative, which are two genes that have diverged from one another in the same species.

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