[Taxacom] New molecular propaganda on primate systematics

[Kim van der Linde]

So, what do you think of this response to your own article:

http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2699.2010.02354.x/abstract

Not good enough?

Kim

On 4/24/2011 4:35 PM, John Grehan wrote:
> A nice illustration of the way propaganda is merged with evidence and
> theory is the recent paper "A molecular phylogeny of living primates" by
> Perelman et al 2011 (PLos Genetics 7 (3)).
>
> It begins with the propaganda claim that "The human genome project has
> revolutionized such fields as genomics, proteomics and medicine" and
> then asserts that it lacks a "formal evolutionary context to interpret
> these findings, as the phylogenetic hierarchy of primate species has
> only modest local (family and genus level) molecular resolution with
> little consensus on overall primate relations. In these opening
> sentences the authors only recognize molecular sequence data as the
> evolutionary context of the "human genome project".
>
> This is followed by the assertion that current views concur on the 67-69
> primate genera originating from a common ancestor during the
> Cretaceous/Paleocene boundary roughly 80-90 MYA. These "current views"
> are those of Goodman et al (1988), Groves (2001) and Wilson et al
> (2005). Somehow the authors failed to review the literature properly to
> have been aware of the more recent view by Heads (2009) that suggests an
> earlier Mesozoic differentiation.
>
> Primate taxonomy "initially 'imputed ("imputed?) from morphological,
> adaptive, bio-geographical, reproductive and behavioral traits, with
> inferences from the fossil record is complex". "Complex"??
>
> Earlier molecular studies are seen to be flawed because they have a
> prohibitively large proportion of missing data for each taxon". So here
> we have the interesting observation that the previous molecular
> analyses, which everyone views as so convincing and superior to
> morphology, are now acknowledged to be inadequate - "flawed" even.
>
> But never mind, the solution is quite simple - just add in more of the
> same through "large-scale sequencing and extensive taxon sampling to
> provide a resolved phylogeny that affirms, reforms, and extends previous
> depictions of primate speciation". Against this grandiose claim, the
> "clarity of primate phylogeny forms a solid framework for a novel
> depiction of diverse patterns of genome evolution among primate
> lineages". Just what these novel depictions are I am not quite sure.
>
> Then the introduction ends with another nice piece of propaganda - if
> you want to believe it - "Such insights are essential in ongoing and
> future comparative genomic investigation of adaptation and selection in
> humans and across primates.
>
> So basically, based on the traditional molecular approach of using
> insignificantly small outgroup representation (five species) these
> authors say they base their "comprehensive" molecular phylogeny on
> 34,927 bp - although someone might be able to clarify my impression that
> it is really only 14,683 sites that were informative after the usual
> manipulations one sees in molecular analyses ("in this case correction
> for ambiguous sides"). Of these sites, half are non-coding so I am not
> sure how any direct phylogenetic meaning can be asserted (but some can
> probably correct me for my ignorance here).
>
> In their "resolution" of early primate divergence they note that the
> Tarsiiformes has a broad Holarctic distribution during the Eocene,
> quoting Kay etal (1997). So here we have the first irony, that the
> molecular result is being interpreted in the context of morphological
> analysis of fossils - analysis that I would find suspect anyway as I
> have not seen any credible evidence of fossils more closely related to
> tarsiers than other primates having a "Holarctic" distribution in the
> Eocene.
>
> They decide that they have strong evidence for the placement of tarsiers
> with anthropoids (which is morphologically nonsensical) and they label
> tarsierforms as "ancient" although they fail to note that this would
> mean the anthropoids, as the sistergroup, are "ancient" as well.
>
> As for the rest of the analysis I will confine myself to two points. The
> first is their claim, out of nowhere, that the common ancestors of
> Chiromyiformes and Lemuriformes "likely (which means they really do not
> know) colonized the island of Madagascar prior to 58.6 MYA (maybe 58.7
> MYA?).
>
> On the origin of hominids the authors have the integrity to note that
> "Once contentiously debated, the closes human relative of chimpanzee
> (Pan) within the subfamily Homininae (Gorilla, Pan, Homo) is now
> generally undisputed" even though they could not bring themselves to
> acknowledge the contrary evidence. But at least it's a step up from the
> pretence that there is no contrary evidence. There is hope yet for the
> integrity of primate systematics.
>
> John Grehan
>
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