Talk:Ancestral reconstruction

PLoS Computational Biology Topic Page proposal
We are planning to rewrite and extend this page, and submit it as a Topic Page at PLOS Computational Biology. For detailed information about Topics Pages see: http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002446. Please contact us if you have any objections or suggestions about the proposed article. --Artpoon (talk) 16:53, 8 May 2013 (UTC)
 * The draft is available at http://topicpages.ploscompbiol.org/wiki/Ancestral_reconstruction . -- Daniel Mietchen (talk) 03:37, 10 March 2014 (UTC)
 * Reviews are available for this Topic Page. -- Daniel Mietchen (talk) 11:49, 2 October 2014 (UTC)

Merger
I added the merger as the article paleogenetics and Ancestral reconstruction covert the same topic. The ancestral reconstruction is better cited and longer (I just added correct references in the other a second ago). I'd avoid using the term "paleogenetics" as Archaeogenetic, the study of ancient DNA, is etymologically too similar to paleogenetics, despite the latter term being used by Pauling in 1963, so has temporal precendence over Ancestral reconstruction.--Squidonius (talk) 00:05, 2 May 2011 (UTC)


 * If I may weigh in on this proposed merger, my own experience as an active researcher in phylogenetics is that the term "ancestral reconstruction" (including "ancestral state reconstruction" and "ancestral sequence reconstruction"), is more widely recognized than the term "paleogenetics" (which I have never encountered until now). I respectfully suggest that the search term Paleogenetics be redirected to an expanded Wikipedia page on Ancestral Reconstruction (which is currently a stub) that incorporates content from the former--Artpoon (talk) 16:53, 8 May 2013 (UTC)


 * Different fields of science use different names for similar things. Folks coming from a background in genetics say Ancestral reconstruction. Anthropologists say Paleogenetics, for example, Paleogenetics: Ancient DNA in Anthropology and Paleogenetics of cattle domestication. Archeologists say Archaeogenetics, for example, From molecular genetics to archaeogenetics and Archaeogenetics: DNA and the Population Prehistory of Europe. So all the terms seem notable. Paleogenetics and Archaeogenetics have a lot of overlap insofar as prehistoric anthropology and archaeology have a lot of overlap. It is no so clear to me that paleogenetics and Ancestral reconstruction cover the same topic. Ancestral reconstruction is the generic phylogenetics term covering all living things, whether there is any relation to man or not. But from what I have seen, paleogenetics is mostly (except for Pauling) used in an anthropological context; it is a specialization of phylogenetics to anthropology. I'm not strongly opposed to a merger, but I think it needs to be made clear that these are two different concepts often used in different domains of science. --Mark viking (talk) 19:45, 17 May 2013 (UTC)


 * I do not think there is much to merge here, despite partial overlap: paleogenetics is about the analysis of preserved genetic materials (typically ancient DNA), ancestral sequence reconstruction is about inferring ancestral sequences (of nucleic acids or proteins) by way of analyzing sequences that have been obtained by sequencing of multiple fresh or preserved specimens (typically of a different species), and ancestral state reconstruction is about inferring ancestral phenotypes, again on the basis of what is known about sequences in related taxa. -- Daniel Mietchen - WiR/OS (talk) 20:07, 17 May 2013 (UTC)


 * Good points. Would it be adequate to make brief note of the initial linkage with Zuckerkandl and Pauling, and subsequent divergence of the term "paleogenetics" (including a link to that page) without merger? -- Artpoon (talk) 05:45, 24 May 2013 (UTC)


 * I also agree that there isn't too much to merge. It seems to me that paleogenetics is more of an application of Ancestral Reconstruction than a subtopic or something that it should be combined with. I think that this article is missing much more important things such as specifics about the maximum likelihood, maximum parsimony, or Bayesian inference. There are also some more specifics about parsimony and the assumptions that are made in this entire process that raise its reliability. Amandaxrasmussen (talk) 03:27, 9 October 2013 (UTC)

Merging with PLoS Comp Biol topic page
I am one of the authors of the page mentioned above. It's been reviewed and accepted, and is available here: http://compbiolwiki.plos.org/wiki/Ancestral_reconstruction

I'm going to be incorporating most of the existing text on this page into that article, and putting the merged version here. This is in line with what was done on the viral phylodynamics page. Please let me know if you have any concerns.

Rmcclosk (talk) 17:12, 3 December 2015 (UTC)


 * Done! Here's a summary of what I changed and merged from the existing topic page.
 * The bit in the introduction about "filling in gaps" in phylogenetic trees was a bit unclear. I've changed this to indicate that we are examining parts of phylogenetic trees which correspond to the possibly distant past, thereby clarifying the evolutionary history of the species in the tree. I also reworded the part about modern genetic sequences being a variation of ancient ones.


 * The sentence "One of the most prominent examples is tracing the evolution that took place from ape to man", which I've moved into the history section, seems important but has no citation. I've left it in and added a "Citation needed" tag.


 * I moved the methods overview into the front of the new methods section, but shortened/rewrote it significantly, since much of the information (like which method came first) is contained in the body of the relevant section.


 * There were some things in the existing methods that seemed to refer to phylogenetic tree reconstruction, not ancestral state reconstruction. For example, from maximum parsimony: "In other words, you accept a phylogenetic tree which has the transition from one state to another represented with the least possible number of changes." I removed these.


 * This sentence under Parsimony was out of context and removed: "The Cambrian Explosion represented a period of time with a pronounced increase in the variation of organisms in phyla."


 * This sentence from maximum likelihood is wrong and was rephrased: "The method of maximum likelihood involves assuming the phenotypes that developed, the ones that you see, were those that were statistically most likely."


 * The subsections "Trait reconstruction", "DNA and protein reconstruction", and "Genome reconstruction" have all been integrated into the relevant parts of Applications.


 * There was a bit of a methods overview at the beginning of "Trait reconstruction" that I took out, since it's redundant given the existing overview at the beginning of the methods section.


 * The second paragraph under "DNA and Protein reconstruction" was pretty nicely written, so I just copied it verbatim into the "Molecular Evolution" part of Applications. The third paragraph is more of an overview, and was put at the beginning of the Applications section.


 * Rmcclosk (talk) 17:52, 3 December 2015 (UTC)
 * The PLOS version was finally published this week. I've added the respective source template. -- Daniel Mietchen (talk) 18:34, 14 July 2016 (UTC)

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 * Added archive https://web.archive.org/web/20150910050917/http://ancestors.bioinfo.uqam.ca/ancestorWeb/ to http://ancestors.bioinfo.uqam.ca/ancestorWeb/
 * Added archive https://web.archive.org/web/20151208053710/http://www.lillo.org.ar/phylogeny/VIP/index.htm to http://www.lillo.org.ar/phylogeny/VIP/index.htm
 * Added archive https://web.archive.org/web/20151211193105/http://carmelab.huji.ac.il/software.html to http://carmelab.huji.ac.il/software.html
 * Added archive https://web.archive.org/web/20150307220356/http://markov.uoregon.edu/software/lazarus/ to http://markov.uoregon.edu/software/lazarus/
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