[Taxacom] Fwd: Bubble science

Sun Apr 28 20:27:59 CDT 2013

Michael and John,

        Wish I had time to respond more fully to this thread, but alas I don't, so must be brief.  However, on the subject of a monkeyless Madagascar, I don't think it is as much a problem as you might think.  

       As I mentioned on Taxacom a couple of years ago, my hypothesis is that woodpeckers are absent from Madagascar primarily due to competitive exclusion (if any woodpeckers ever got there at all). Likewise, I would also hypothesize that if any monkeys rafted to Madagascar that they were also too late, and that the lemurs had already gotten there and diversified into the available niches.    

                     -----------------Ken Kinman

----------------------------------------------------------------------------------------------------------------------

> Date: Sun, 28 Apr 2013 18:54:02 -0400
> From: calabar.john at gmail.com
> To: m.j.heads at gmail.com
> CC: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] Fwd: Bubble science
> 
> 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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> 
> (1) by visiting http://taxacom.markmail.org
> 
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> Celebrating 26 years of Taxacom in 2013.