This is a great question! (for a change, in researchgate, where, I'm afraid, questions tend to be too naive and uninformed and that in other internet fora would be answered with an unpolite RTFM)

I think it will be most useful to put together a comprehensive bibliography clear cases of adaptive evolution.

Adaptive and neutral in-vitro evolution has been done with TEM beta lactamase. The "warning" here is, to my mind, that the experimental selection protocols are not necessarily modeling adequately "natural evolution" (e.g. population genetics effects, etc). However, such work could be very useful for understanding positive vs negative selection, and other classic evolutionary issues.

Sorry if I cannot at this point provide a comprehensive list, but I put some examples:

Adaptive in-vitro evolution of tem-1

http://www.ncbi.nlm.nih.gov/pubmed/21408208

http://www.ncbi.nlm.nih.gov/pubmed/18687656

Neutral:

http://www.ncbi.nlm.nih.gov/pubmed/18495157

Hi, your question made me think of this article:

https://www.researchgate.net/publication/259989782_Effector_Specialization_in_a_Lineage_of_the_Irish_Potato_Famine_Pathogen?ev=prf_pub

Enjoy

Article Effector Specialization in a Lineage of the Irish Potato Fam...

Yes, this is exactly the kind of studies I am looking for! Thank you!

There are two great studies on visual pigments and odorant receptors:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2795536/

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2533215/

This is a great question! (for a change, in researchgate, where, I'm afraid, questions tend to be too naive and uninformed and that in other internet fora would be answered with an unpolite RTFM)

I think it will be most useful to put together a comprehensive bibliography clear cases of adaptive evolution.

Adaptive and neutral in-vitro evolution has been done with TEM beta lactamase. The "warning" here is, to my mind, that the experimental selection protocols are not necessarily modeling adequately "natural evolution" (e.g. population genetics effects, etc). However, such work could be very useful for understanding positive vs negative selection, and other classic evolutionary issues.

Sorry if I cannot at this point provide a comprehensive list, but I put some examples:

Adaptive in-vitro evolution of tem-1

http://www.ncbi.nlm.nih.gov/pubmed/21408208

http://www.ncbi.nlm.nih.gov/pubmed/18687656

Neutral:

http://www.ncbi.nlm.nih.gov/pubmed/18495157

There are several groups that regularly use those codon models to generate hypotheses about the functional implications of amino acid substitutions, which they directly test via site-directed mutagenesis and biophysical analysis. Two groups that immediately come to mind are:

1. Sara Sawyer's group works on host-virus arms races:

http://www.sbs.utexas.edu/sawyer/Sawyer_Lab_Website/Publications.html

A specific example from the Sawer group is:

Demogines A, Abraham J, Choe H, Farzan M, Sawyer SL (2013) Dual Host-Virus Arms Races Shape an Essential Housekeeping Protein. PLoS Biology, 11(5): e1001571.

(This one won the Omenn prize in 2013)

2. Belida Chang's group works on visual pigments:

http://labs.eeb.utoronto.ca/chang/pubs.html

Recent papers by Chang's group separate the biophysical analysis and the molecular evolution, but I believe that joint analyses are "in the works".

Here is an older commentary (2005) by Ziheng Yang about the overall approach with some examples:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC552944/

One last example in fluorescent proteins:

http://link.springer.com/article/10.1007%2Fs00239-005-0129-9

Hi Romain,

The examples that come to mind are articles by Harmit Malik and the people in his lab.

http://www.ncbi.nlm.nih.gov/pubmed/?term=%22malik+hs%22

They usually test the ability of different primate antiviral proteins to restrict specific viruses, and were often able to identify the adaptive amino acid changes responsible for the differences in susceptibility to viruses in different primates.

One really impressive example: PMID: 23084925

So, this is not per se in vitro introduction of the identified amino acid changes, but their approach is very close and very powerfull.

Antonio, Julian, Joseph, David: Thank you for your answers, they were very helpful.

It seems that the majority of these studies, apart from immunity-related genes, are on proteins where we can measure a reaction to different visual wavelengths.

I now remember this paper:

Looking for Darwin in Genomic Sequences—Validity and Success of Statistical Methods

Weiwei Zhai, Rasmus Nielsen, Nick Goldman and Ziheng Yang

http://mbe.oxfordjournals.org/content/29/10/2889.long

They cited some studies, based on opsin (Bielawski et al. 2004), TRIMalpha (Sawyer et al. 2005), viral protein (Moury and Simon 2011), antifreezing (Deng et al. 2010) and MHC, the classical example:

"Numerous examples now exist in which the results of such statistical analysis were validated by functional assays in the laboratory (e.g., Bielawski et al. 2004; Sawyer et al. 2005; Deng et al. 2010; Moury and Simon 2011). Even when structural information is available, it is rarely precise enough to pinpoint codons under positive selection, and the site-based model may still be very useful. This appears to be precisely the case with the MHC, the exemplar of positive selection, as demonstrated by Yang and Swanson (2002)."

I found an old paper, with a mixture of dN/dS and experimental validation:

Identification of Residues in Glutathione Transferase Capable of Driving Functional Diversification in Evolution. A NOVEL APPROACH TO PROTEIN REDESIGN

Ylva Ivarsson, Aaron J. Mackey, Maryam Edalat, William R. Pearson and Bengt Mannervik

http://www.jbc.org/content/278/10/8733.full

Any older paper than this one?

I found another one, quite recent:

Functional Consequence of Positive Selection Revealed through Rational Mutagenesis of Human Myeloperoxidase

http://mbe.oxfordjournals.org/content/29/8/2039.full

"Taken together, our data provide further support for the in silico predictions of positive selection and highlight the correlation between positive selection and functional divergence. Our data demonstrate that directly probing the functional importance of positive selection can provide important insights into understanding protein evolution."