Why does the proportion of transposable elements vary so much across species?

Question

Intuitively, transposable elements (TEs) are harmful as they may cause genome instability. However, some people argue that TEs are also sources of variations, especially regulatory sequences[1].

If TEs are harmful, then their proportions may be low in most species. And if they are beneficial, then their proportions should be high. Either case leads to the conclusion that their proportions should stay close to each other. However, the fact is that the proportion varies greatly across different species:

1. Maize: 85% [2]
2. Human: 45% [3]
3. Arabidopsis: 10% [4]
4. Plasmodium: absent [5]

Why is that? Is there other factors that influences the proportion of TE, such as evolutionary pressure?

---

Reference

[1] Rita R, et al. 2012. Transposable elements: an abundunt and natural source of regulatory sequences for host genes. Annu. Rev. Genet 46:21-42
[2] Schnable PS, et al. 2009. The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112-15
[3] International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921
[4] Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815
[5] Biemont C, Vieira C. 2006. Genetics: junk DNA as an evolutionary force. Nature 443:521-24

Answer 1

I can think of two factors that would influence this, but there are probably more.

1) How do transposable elements (TE) get into the genome in the first place? The answer is both vertically and horizontally. Vertical transmission needs no explanation. Horizontal transmission of TE has been documented in several cases. In some cases, infectious agents can transfer them between species individuals, for instance, viruses can package transposable elements in addition to their own DNA.

http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(10)00123-0

2) How efficient can the TE replicate? For example, in the human genome there are a variety of different types of retrotransposons, but only the L1 element can replicate. Others like Alu and SINEs parasitize their replication machinery and therefore replicate also but at much lower frequencies.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2884099/

So, the difference between species has to do with both of these and probably other factors. I would imagine in the 2nd case, the selective pressures put upon a given species at any point in time, due to infections or inter-species competition, would surely impact the efficiency of TE replication because they are so important to genomic evolution and adaptation.