How to evaluate one specie lost or gain the chloroplast in the evolutionary process via comparative genome?

Question

[fhu2008]

Hello, everyone

Recently, I have sequenced one specie genome and annotated its proteins, the divergence time analysis (Beast 2) based on the 356 single copy genes showed that our nonphotosynthetic specie , other nonphotosynthetic species and the photosynthetic specie have a common non-photosynthetic ancestor, and our sequenced specie was a sister group to a well-supported monophyletic clade that included the nonphotosynthetic species (A and B ) as well as the photosynthetic species (C and D) , the outgroup of the divergence time tree is a nonphotosynthetic species (E).

Can I make a conclusion that 1) all the species (nonphotosynthetic species and photosynthetic species) have a common nonphotosynthetic ancestor? 2) photosynthetic species (C and D) acquired a photosynthetic pathway or in the evolutionary process ?

If not, what analysis should be conducted to evaluate the our specie lost or gain the chloroplast?

Thanks for your kindly answer.

Figure Legends:

Divergence time estimates for 8 species. Estimation analysis was conducted by BEAST2 using normal strict molecular clock analyses of 356 single-copy genes. The MCMC chain length was set to 10,000,000, and other parameters were set to default values.Fossil calibration times were obtained from the TimeTree database.

[Asaf]

How to add a figure: How to add images to a Biostars post

[fhu2008]

Thanks for your good suggestions.

Answer 1

[Vitis]

I think this falls to the area called character evolution, in which you infer the gain, loss and reversion of characters, with the assumption of having a phylogenetic relationship, best obtained from data independent of the characters you're interested. Here, photosynthesis is the character in question and the phylogeny is the phylogenetic framework, hopefully you've obtained the phylogeny from molecular data. The simplest principle in this kind of analysis is parsimony, based on Occam's razor. In evolutionary analysis, it simply states that the pathway requires less steps is more likely. In your case, assuming the phylogeny is accurate (which is very rare itself), one gain of photosynthesis is more likely than three independent photosynthesis loss. It should be noted that this does not mean the simpler pathway is really what happened. Three independent loss is just LESS likely, and there could be other pathways involving character reversions (such as gain of photosynthesis and subsequent loss). For a starter, there is a trimmed down intro here about character evolution:

https://embnet.vital-it.ch/CoursEMBnet/PHYL03/Slides/characters_mwilkinson.pdf

[fhu2008]

Your suggestion is very useful for me, thanks.

Answer 2

[Asaf]

To answer your question, you can't conclude anything, you can only give probabilities. You can use software to evaluate the trait of each ancestor, i.e. the probability that it was photosynthetic or not. However, you have to have an evaluation of the gain and loss probabilities and make some assumptions about them being constant along the tree. Since you don't have a lot of data you can explain it in many ways, each leading to different parameters.

So no, you can't conclude, but you can make claims like if the ancestor was non-photosynthetic then there was one gain event that happened along an edge of length X whereas if the ancestor was photosynthetic then ... and option Y looks more probable than the other since ...

[fhu2008]

Thanks for your good suggestion,

Would you kindly tell me how to evaluate the gain and loss probabilities ?

[Asaf]

BayesTraits is the leading software I think: http://www.evolution.rdg.ac.uk/BayesTraitsV3.0.1/BayesTraitsV3.0.1.html You've got GLOOME which is more towards sequences but can be adjusted to binary traits I think: http://gloome.tau.ac.il/