Entering edit mode
7.6 years ago
Farbod
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3.4k
Dear Friends, Hi (I am not native in English, So be ready for some misunderstanding)
Most fishes lay eggs, some are live-bearing but they do not have a real placenta. in the other hand, most mammals have placenta. I like to compare an egg laying fish (e.g zebrafish), a live-bearing fish (e.g Amazon Molly) and a mammal (e.g mouse) to find the genes that are important in this evolutionary pathway.
but I do not know where to begin and to do this?
I will appreciate any suggestion.
One of my friends suggested :"you should use Ensembl to get your sequences for each clade. You should align sequences within each clade and identify the consensus sequence. It would then be easy to compare 3 or 4 consensus sequences (each belonging to a clade) at the genomic level but you could start with the sequence of known genes."
but I could not use his help maybe because I did not get his point.
Which genes would those be and what would be the selection criteria?
Hi, yes. That is the heart of the question.
Yes but that's your job as the scientist.
There's a lot of differences between a mammal and a zebrafish. Most of those differences have nothing to do with egg-laying. How will you separate that out?
Let's just state the obvious - it is probably not that simple - there is not just one, two or three genes that do this or that - if it were like that most of these problems would already be solved.
As always reality is a lot more complicated - and most of the progress builds on small incremental understanding of the world. So try different selection criteria, perhaps you will help incrementally solve this problem.
Dear Istvan Hi, I was thinking about collecting all the genes located in reproduction GO and pathways and compare them between these 3 species. What do you think ?
Istvan is right. You need to break this (huge) question down. By a lot. To a much smaller question that is actually possible to answer. The starting point is more likely to be "bio" rather than "informatics".
Incidentally, I googled Amazon Molly and those fish are weird! Also, they are not truly bearing live young (like a mammal), they carry eggs internally. There is also not a single discrete evolutionary branch between eggs vs live. It seems to have occurred at multiple points across multiple lineages (e.g. "mammals" include monotremes, marsupials and eutherians).
You might want to start by focusing on a single branch point, preferably between two closely related species that only differ in their mode of reproduction.
Dear jotan1982, Hi and thank you.
Yes, you are right about "Amazon Molly are weird and are not truly bearing live young", I just did not mention any details to simplify my question.
By the way, Amazon Mollies do not need males for reproduction !
About your correct suggestion that "start by focusing on a single branch point, preferably between two closely related species that only differ in their mode of reproduction", imagine that we have the zebrafish (egg) and guppy (lives) which are more or less close, Now how and where you suggest that I should begin ?
I'm a molecular biologist so the first thing I would do is, consult with an evolutionary biologist ;) Then I would look through the literature to see how other people might have answered similar questions. Then I might ask myself, is it a loss of function or is it gain of a new function? Which might give some clues about whether I'm looking for evolutionarily novel genes or degeneration of previously functioning genes.
But seriously, I would go and consult with someone who has experience with these topics and ask them to advise me.
There are times when you should be innovative and creative, and times when it's silly to reinvent the wheel.
Hi and thank you, I have seen some papers (maybe in Science mag) about the relationship of curing blindness in human and blind cave fishes genetics. I think I should have a look at their pipeline.