Re: For Sean Pitman: Some real nested hierarchies

In message <0490ee23-0413-4874-a1e3-3f1286b71157@xxxxxxxxxxxxxxxxxxxxxxxxxxxx>, Seanpit <seanpitnospam@xxxxxxxxxxxxxxxxxxxxxxxxxxx> writes
On Mar 11, 3:25 am, Ernest Major <{$t...@xxxxxxxxxxxxxxxxx> wrote:

>http://www.detectingdesign.com/images/EarlyMan/Neandertal3.gif

The GIF you cite above does not support your above claim.

Yes, it does. Did you read the rest of the summary of the paper (a
portion of which is listed below)? If you had you would know that the
gif does exactly what I said it does.

You've snipped your claim - it was "For example, depending upon which sequence or sequence method you use you can get results that suggest that certain groups of living Africans are more closely related to chimps than are other humans and Neandertals?".

Neither the GIF, nor the material you quote from the paper, support your claim. I thought perhaps you had misspoke, but you may be committing the ladder fallacy.

Have you read the paper? The figure 2 that you've copied onto your web doesn't support your claim, but figure 3 blows it out of the water.


>Guitierrez et al., went on to note that:

>    "The main conclusion can be extracted from our analyses: the
>phylogenetic position of the ancient DNA sequences recovered from
>Neandertal bones is sensitive to the phylogenetic methods employed. It
>depends on the model of nucleotide substitution, the branch support
>method, and the set of data used. Ad*** et al. (2001) recovered HVI
>sequences of archaic human bones from Australia, and their phylogenic
>analysis showed that two of the specimens were outgroups even for the
>most ancient African lineages. They concluded that this is evidence
>supporting the multiregional hypothesis. However, a second analysis
>carried out by Cooper et al. (2001) that took into account the
>heterogeneity of rates between sites and a large sample of modern
>humans, showed that both HVI sequences are located among extant
>humans. This case illustrates the influence of the nucleotide
>substitution model on the phylogenetic reconstruction of the human D-
>loop region.
>     The NSG studies used poor parameter models of nucleotide
>substitution for their analysis, whereas we opted for complex
>(parameter rich) models following the likelihood ratio test...  We
>believe that the likelihood mapping values supporting Neandertals as a
>different species might be artifactually increased."

This is not claiming that some "African groups" are more closely related to chimps than Neandertals and other humans; it is arguing that Neandertals may be nested in the modern human crown group, rather than a sister group to it.

Referring to groups seems to be another error on your part. Human populations are not distinguished by the possession of different mtDNA haplotypes, but by the possession of different proportions of mtDNA haplotypes; I expect that the putative outgroups are individuals, not populations.
--
alias Ernest Major

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