[Taxacom] Fwd: Bubble science

[Michael Heads]

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
>



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