Talk:Molecular phylogenetics

Untitled
The link http://www.bact.wisc.edu/MicrotextBook/ClassAndPhylo/molPhylogeny.html is outdated. The new link is http://www.bact.wisc.edu/Microtextbook/ I couldn't figure out which section targeted by the old link fits to the new link, therefor I didn't edit the article.

Merge?
Not entirely sure why this article was merged with Molecular systematics, or more importantly, why the two were not merged under the more inclusive heading of "molecular systematics", rather than the narrower concept of "molecular phylogeny". Was a this merge recommended or discussed anywhere? MrDarwin 14:07, 3 July 2007 (UTC)

First sentence
A molecular phylogeny is the result of molecular phylogenetics, isn't it? 203.160.122.99 23:51, 27 October 2007 (UTC)

History
I've just read a bit in Matt Ridley's Nature via Nurture about the history of molecular phylogenetics. Ridley says a Californian called George Nuttall discovered while working in Cambridge University (UK ) that the more closely 2 species were related, the more similar were the immune system responses their blood provoked in rabbits. Then in 1967 Vincent Sarich and Allan Wilson used a more sophisticated version of this immunological analysis to estimate the divergence time of humans and apes as 4 to 5 million years ago, at a time when standard interpretations of the fossil record gave this divergence as from at least 10 to as much as 30 million years ago. Then in the mid-1970s Wilson asked Mary-Claire King (then a Ph.D. student) to do a similar molecular clock analysis using DNA. That's when they found that human and chimp DNA were 99% identical (using their definitions - other definitions lead to a 95% match). I have too many wiki-irons in the fire to do any research on this at present, so I hope someone else will be able to use it. Philcha (talk) 00:22, 10 June 2008 (UTC)


 * We also have some material at DNA-DNA hybridization, Charles Sibley and Jon Ahlquist concerning research of the 1960s and 1970s. Kingdon (talk) 18:45, 10 June 2008 (UTC)

Outline for possible rewrite
Structure of family trees; relative dating; absolute dating; deducing characters of undiscovered common ancestors (last item actually common to all cladistics). Examples: Starting with Nuttall in 1920s (before cladistics!). Sarich, Wilson et al made headlines in 1960s-1980s w analysis of hominids.
 * Lead
 * Concepts
 * Cladisitic approach
 * Applied to various biochemicals - mainly proteins and neucleotides.
 * Prefer traits that are thought neutral under natural selection, to avoid risk of convergence.
 * Applications
 * Paleontology:
 * Sarich, Wilson et al on hominids.
 * Mammals: Afrotheria vs traditional phylogenies; divergence times.
 * DNA barcoding
 * Also used for individuals, e.g. paternity tests, forensics
 * Techniques
 * (need to read up a bit)
 * Issues / controversies
 * Saturation & long-branch attraction can make family tree structures doubtful.
 * Dating:
 * Need for calibration against fossils.
 * Molecular clock assumption (need to research list of possible causes of variation).
 * Uselessly wide error margins of some estimates.
 * History

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Philcha's notes: ---
 * IMO DNA analysis of individuals in paternity tests and forensics does not strictly belong here, as systematics is about species and higher taxa.
 * My biggest concern is that my own knowledge of mol phylo relates entirely to paleontology. -- Philcha (talk) 10:48, 27 August 2008 (UTC)

Regarding techniques: DNA–DNA_hybridization, fingerprinting, or sequencing with varying degrees of completeness (i.e. just a handful of particular genes, or just mitochondria, or just a particular chromosome, or the full genome). An additional issue (which particularly confounds some methods) is that different loci (especially mitochondrial vs nuclear), and different alleles, can have significantly different phylogenies (and this is not restricted to horizontal gene transfer, it is a simple fact of population genetics and is especially emphasised in reticulate evolution). Cesiumfrog (talk) 04:46, 28 March 2015 (UTC)


 * Also, here is one nice example of molecular systematics without using DNA (in this case choosing collagen instead, because this protein is much better preserved in almost million-year-old fossils, and finding that extinct South-american so-called ungulates are most closely related to horses and rhinoceroses not elephants or armadillos). Cesiumfrog (talk) 23:22, 25 April 2015 (UTC)

Paleontology

 * See Cambrian explosion (especially as at late Mar 2008, before attempts to slim down), Evolution of mammals, Evolutionary history of life -- Philcha (talk) 11:56, 27 August 2008 (UTC)

Requested move

 * The following discussion is an archived discussion of the proposal. Please do not modify it. Subsequent comments should be made in a new section on the talk page. No further edits should be made to this section. 

The result of the proposal was move. JPG-GR (talk) 04:01, 3 September 2008 (UTC)

Molecular phylogeny → Molecular phylogenetics — ambiguous title — Philcha (talk) 16:54, 28 August 2008 (UTC)

Survey

 * Feel free to state your position on the renaming proposal by beginning a new line in this section with  or  , then sign your comment with  . Since polling is not a substitute for discussion, please explain your reasons, taking into account Wikipedia's naming conventions.


 * Support. In paleontology, "phylogeny" often refers to a hypothesis about the family tree of a specific set of organisms, sometimes illustrated by a cladogram. One can even speak of a "fossil-based phylogeny" vs a "molecular phylogeny" or, in articles about very early life on Earth (all single-celled), "morphological phylogeny" vs a "molecular phylogeny". "Molecular phylogenetics" would remove ambiguity as it can only refer to the discipline and techniques. -- Philcha (talk) 11:46, 27 August 2008 (UTC) -- Philcha (talk) 16:55, 28 August 2008 (UTC)

Discussion

 * Any additional comments:
 * The above discussion is preserved as an archive of the proposal. Please do not modify it. Subsequent comments should be made in a new section on this talk page. No further edits should be made to this section.

Another proposed rename
I propose putting this back to the name molecular systematics, for the reasons given by user:MrDarwin a couple of years ago - see above. That would also make it clear that the stuff on intra-species uses such as paternity testing should be reduced to the status of an aside. I will return here in a few days/weeks and see if anyone has objected, then do it. seglea (talk) 00:50, 11 October 2009 (UTC)


 * There is indeed some passages conflicting a little bit due to the article dealing with systematics and phylogenetics without clear distinction. There's a part that is somewhat about "criticism", which, in light of everything that is now known, and for basic evolutionary logic since Darwin, can only make sense if it's a "criticism" about systematics, but that wouldn't be even specific to molecular systematics, but would apply to phylogenetic systematics as well, but completely fails if it's intended as a criticism of the techniques described as a means to reconstruc phylogenies. Actually, more than a criticism to phylogenetic systematics, it's an appeal to the worth of other forms of classification. At least that's the only reasonable context for some arguments. That is, is one thing to say that it may be "better" or "equally valid" to simply classify organisms according to, say, their niche, irrespective of phylogenetic relationship -- but that can't possibly be used to argue against the validity of the techniques to construct phylogenetic trees. It's somewhat like saying that, in social science is more important to classify people according to their jobs or social strata, and imply that there is no such thing as "genealogy" or that somehow social strata and professions are better proxies to genealogies than what is actually used in genealogy. --Extremophile (talk) 22:48, 22 June 2010 (UTC)


 * What does molecular systematics include, that the "narrower" term molecular phylogeny/phylogenetics excludes? Cesiumfrog (talk) 05:55, 27 March 2015 (UTC)

Assessment comment
Substituted at 00:19, 30 April 2016 (UTC)