Speciation and Transposons

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G_nome
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Speciation and Transposons

The processes of speciation and reproductive isolation are complex, and are not well understood. Transposons are an important force in evolution - I would like to investigate their role in the mysterious route to speciation. One of the initial steps in speciation, postzygotic reproductive isolation, is a phenomena where, after the egg and sperm meet, the zygote is unable to complete development, or dies soon after birth. Postzygotic isolation is critical to prevent the breakdown of speciation, because closely related species may still be geographically close to one another, and are still physically able to copulate. Epigenetic modifications are thought to be relatively less stable than the nucleotide sequence, and may be important in postzygotic isolation. Transposons, which make up 35% of the human genome, have been hypothesized to be critical for proper epigenetic gene regulation, and in proper silencing of the X chromosome in mammals. Many transposons are close to genes, and even when they lack transposable activity they may still have intact promoter/enhancer elements, may form gene/transposon fusions, and may affect genes indirectly by being targeted for methylation.

To investigate their importance in speciation events I would like to use a bioinformatics approach to look at the similarity of sequence and location of LINEs, SINEs, and DNA transposons at a genomic level. Pairs of closely related species would be compared, to see if there are significant differences in sequence and location of transposons within pairs that can have viable offspring vs. those that cannot. I suggest comparing humans and chimps to Mus musculus and Mus spretus, the latter of which can still have viable offspring.

Reference:
Mills RE, Bennett EA, Iskow RC, Luttig CT, Tsui C, Pittard WS, Devine SE. 2006. Recently mobilized transposons in the human and chimpanzee genomes. Am J Hum Genet. 78(4):671-9.

bgood
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I noticed that your Bench

I noticed that your Bench Space profile indicates that you are located in Vancouver. Assuming that you are not actually in her lab already, you may want to try to talk with Dixie Mager or one of her students at the BC Cancer Agency. She studies transposons and their effects on evolution (and is very smart..)

I don't know, but my intuition is that you will want to find organisms that are even more closely related than humans and chimps. Do you know of any datasets containing large numbers of sequences from closely related species - even if not whole genomes? The reason I think this is that you seem to want to prove something quite specific.. to establish that some genetic element has an effect on the particular phenotype of reproductive isolation, it would be best to have a continuous spectrum with lots of examples near the borderline.

G_nome
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Ben makes a good point. My

Ben makes a good point. My suggestion is to check out the NISC comparative genome sequencing project. They are sequencing defined regions (many of which are ENCODE regions) from many mammalian genomes. This might give you the fine-scale data required to accomplish such a study.

NISC comparative strategy paper

Ryan

Jon Moulton
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Or if you want to be really

Or if you want to be really flashy, how about inserting a transposon, screening for insertions that cause reproductive isolation, and isolating the resulting new species? That would be quite a paper ... Experimental Speciation by Transposon Insertion.

- Jon

G_nome
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jonmoulton wrote:Or if you

jonmoulton wrote:

Or if you want to be really flashy, how about inserting a transposon, screening for insertions that cause reproductive isolation, and isolating the resulting new species? That would be quite a paper ... Experimental Speciation by Transposon Insertion.

- Jon

That would be very cool. I wonder what kind of numbers we would be looking at to be able to actually produce a reproductive isolation in captivity?

Sean