[Taxacom] Fwd: Bubble science

[John Grehan]

Mike, that's putting it in a nutshell. Those darned monkeys are supposed to
have hopped, skipped, jumped and otherwise rafted their way all across the
Atlantic, but somehow could not face the terrors of sea passage to
Madagascar, or even the smaller water gaps to Australia. Yoder gives her
Lemur story plausibility only by leaving out everything that might be to
the contrary.

John


On Sun, Apr 28, 2013 at 3:41 PM, Michael Heads <m.j.heads at gmail.com> wrote:

> Hi John,
>
> The authors who support dispersal of lemurs to Madagascar never mention the
> other half of the problem - why are there no monkeys on Madagascar? Monkeys
> are agile, tough and smart and can disperse anywhere warm.
>
>
> On Sun, Apr 28, 2013 at 1:56 AM, John Grehan <calabar.john at gmail.com>
> wrote:
>
> > Science in a bubble
> >
> >  In these days of mass communications and electronic accessibility of
> > information one would think that the present world of research would be
> > much advanced over what prevailed 20 or even 10 years ago. Then it was
> much
> > more difficult to track down all pertinent information and publications
> and
> > it took a lot more time and digging (literally digging through books and
> > journals at times). Now there are electronic resources that would reduce
> > that time and effort and improve efficiency of coverage (although I find
> I
> > still miss items).
> >
> >  All those improvements are nothing if they are not sought, and in some
> > sciences they definitely are not. Primate biogeography and systematics is
> > one such area, where researchers live in science bubbles that float away
> by
> > their denial of anything other. This is amply illustrated in a recent
> paper
> > by Anne Yoder (2013) titled “The lemur revolution starts now: The genomic
> > coming of age for a non-model organism” (Molecular Phylogenetics and
> > Evolution 66: 442–452).
> >
> >  In the abstract she states “New technologies for gathering and analyzing
> >
> > genomic data will allow investigators to build upon what can now be
> > considered a nearly-known phylogeny of the Lemuriformes in order to ask
> > innovative questions about the evolutionary mechanisms that generate and
> > maintain the extraordinary breadth and depth of biological diversity
> within
> > this remarkable clade of primates.”
> >
> >  Her thesis is that the phylogeny of the Lemuriformes is “nearly-known”
> > through genomic data (sequence analysis). The tensions in her thesis
> begin
> > early in the introduction where she states
> >
> >  “Although the first decade or so of this revolution relied upon indirect
> > measures of genetic distance such as DNA–DNA hybridization, numerous
> > breakthroughs in our understanding of evolutionary relationships were
> > achieved, such as the (very controversial, at the time) finding that
> > chimpanzees are more closely related to humans than to gorillas (Sibley
> and
> > Ahlquist, 1984).”
> >
> >  She does mention that there was some opposition to the chimpanzee model:
> >
> >  “Several authors took exception to these results in particular, both in
> > terms of the obvious incongruence with the morphological details shared
> by
> > chimpanzees and gorillas (reviewed in Holmquist et al., 1988), but also
> due
> > to various subtleties of statistical analysis (Farris, 1985; Templeton,
> > 1985).”
> >
> >  This borders on the truly bizarre, that it is worth mentioning
> > morphological ‘details’ shared by chimpanzees and gorillas, but never
> mind
> > the existence of those shared by humans and orangutans. Bubble science at
> > work.
> >
> >  Of course, in the mind of Yoder (and pretty much all of her
> > contemporaries) the truth of phylogeny lies in DNA sequences alone:
> >
> > “The dispute was for many settled decisively by Felsenstein (1987) who
> > employed a maximum likelihood mixed model analysis of variance method to
> > show that there was indeed significant support for the human-chimp clade
> > contained within the DNA–DNA hybridization data published by Sibley and
> > Ahlquist, 1984.”
> >
> >  Her principle focus is on the origins of Madagascan lemurs. She notes
> > that:
> >
> > “…in the early to mid-1980s, nearly all primate classifications (Fleagle,
> > 1988; Schwartz, 1986; Szalay and Delson, 1979) placed one of the
> lemuriform
> > groups, the dwarf and mouse lemurs (family, Cheirogaleidae), into the
> > Lorisiformes due to their shared and otherwise unique condition of the
> > cranial blood supply (Cartmill, 1975; Szalay and Katz, 1973).”
> >
> >  The biogeographic consequences of these relationships are seen as:
> >
> > “In both cases, that of the dwarf lemurs and of the aye–aye, a
> > paraphyletic Lemuriformes would necessitate at least two crossings of
> > the Mozambique Channel (Yoder, 1996; Yoder et al., 1996a).”
> >
> >  But of course only if one assumes dispersal or constructs a divergence
> > model requiring such crossings.
> >
> >  Under the section on lemur biogeography Yoder states:
> >
> >  “In order to ask how lemurs arrived in Madagascar, however, we first
> need
> > to understand when.”
> >
> >  “Given that Madagascar has been surrounded by an oceanic barrier for at
> > least 88 my, we must conclude that dispersal, not vicariance, would have
> > been the mode of their arrival.”
> >
> >  We must? Must? Oh yes, Yoder has said so and so shall it be. And as to
> > how they arrived, one must surely appeal to the only remaining
> implausible
> > alternative:
> >
> >  “With these terrestrial routes rejected, we are left with one remaining
> > alternative: implausible as it may seem (Stankiewicz et al., 2006),
> lemurs
> > must have dispersed via rafting across a formidable oceanic barrier,
> > perhaps aided by an ancestral capacity for heterothermia (Kappeler,
> 2000).”
> >
> >  Must have, must have, and must have. If it is said enough times it will
> > be so.
> >
> >  To Yoder, timing is everything, but divergence estimates (from sequence
> > analysis) are variable:
> >
> >  Estimated ages range from the late-Cretaceous (Arnason et al., 2008), to
> > the early- to middle-Paleocene (Perelman et al., 2011; Roos et al., 2004;
> > Yoder et al., 2003, 1996a; Yoder and Yang, 2004) to the early- to
> > middle-Eocene (Dos Reis et al., 2012; Yoder et al., 1996a).
> >
> >  With all this variation Yoder asks:
> >
> >  But how do we decide which estimate is best supported? She notes that
> > there are a variety of problems with rate estimation and the “problematic
> > nature” of the fossil record. She concludes with the view that these
> > problems will be overcome in the technological advances of phylogenomics
> > and in the end:
> >
> >  “we can begin to explore what might have been the specific adaptive
> > advantage that allowed lemurs to endure what must have been a treacherous
> > journey from Africa to Madagascar, and potentially, the genetic
> advantages
> > that allowed them to cement their survival and diversification upon
> > arrival.”
> >
> >  Yoder’s paper reads to me as a case of a world view that is established
> > by leaving out what might otherwise expose the internal tensions. The
> > possibility that morphogenetic evidence may represent an alternative
> model
> > is dismissed out of hand. And the problematic nature (never really
> > specified) of fossil calibration is never identified, never mind that the
> > traditional use of fossil calibration in divergence estimates
> consistently
> > misrepresent minimal ages as actual or maximal.
> >
> > Most glaring is the total absence of the vicariance model based on
> > molecular evidence presented in Heads (2012) and (2009). Now perhaps
> Yoder
> > may be forgiven for having missed the book as it may not have been
> reviewed
> > in Molecular Phylogenetics and Evolution, but missing the 2009 article
> > borders on the fantastic. If Yoder failed to do any basic literature
> search
> > on the web, then surely one of her many colleagues would have brought it
> to
> > light. But perhaps not? This is the trouble with science living in a
> bubble.
> >
> >
> > John Grehan
> >
>
>
>
> --
> Wellington, New Zealand.
>
> My new book: *Molecular panbiogeography of the tropics. *
> University of California Press, Berkeley.
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