Question

In Drosophila (and other organisms) many mutations with large phenotypic effects have been

linked to insertions of transposable elements (TEs). It is unclear, however, whether TE-induced

mutations have played an important role in adaptive evolution. Briefly describe one research

strategy that you think might shed light on the adaptive importance of TE-induced mutations.

You may choose to perform an experiment (for example, introducing TEs into controlled lab

populations) or test a hypothesis by collecting data from natural populations of the same species

(or from different species). Also discuss some of the pitfalls that might be encountered.

Answer 1

Transposable elements are DNA sequences that are a major force in genome evolution that may cause mutations moving from one location to another in a genome. The fruit fly 'Drosophila melanogaster' has been used in genetic research for long due to its characteristics. For understanding the adaptive importance of TE-induced mutations, let us consider a hypothetical data of 177 transposable elements in 10 samples from 7 worldwide natural populations of Drosophila melanogaster.

Firstly, high and low population frequencies were estimated using T-lex2 for reference 177 TE insertions in 10 samples. The TEs were classified based on their population frequencies in high or low recombination regions. High recombination regions had low fixed TEs (72 out of 90) than low recombination regions (25 out of 89).

Further, it was also seen that age and length of TEs could provide information regarding their adaptive role. It was found that TEs in low recombination regions were old due to old TE insertions through different processes, while high frequency and low frequency regions had young TEs. Most of the young and long TEs at high frequencies have high efficiency of selection suggest adaptive role since long insertions lead to ectopic recombination that results in chromosome rearrangement impacting genome structure.  

The genes were checked for behavioural phenotype like olfaction, aggressive nature and stress related to alcohol as shown in Table 1.

Table 1- TE insertions showing evidence of selection with gene association.

TE category	Evidence of Selection	Gene association
OOA	Allele age	immunity
Fixed	Young & Long	alcohol, olfactory, xenobiotics

Thus, by exploring more natural populations adaptive importance of TE-induced mutations in Drosophila and other organisms can be identified using population frequencies, age, length, stress response, behaviour and similar other factors.

Some pitfalls that may be encountered :- 1. The study is limited only to the insertions that are present in the reference genome, so extra details cannot be known.

2. Further, the age and size of de novo insertions cannot be estimated which can hinder the characteristics of adaptive insertions.

3. Seasonal and geographical adaptations are not known for the TEs which can prove for relevant for D. melanogaster.

Different sequencing techniques may come in near future to provide more easy understanding for TE insertions to adaptive evolution.