[Taxacom] New molecular propaganda on primate systematics

[John Grehan]

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