[Taxacom] Bubble science

[JF Mate]

 No big deal. She´s just following the time-honoured tradition of selective
literature review. She can´t fit the entire primate literature in her
intro! What would be the point anyway?, she works with lemurs and
bushbabies, so great apes are not even the subject. And as for the paper
itself, it is a tribute to the journal and of Morris Goodman (who was at
one point the editor of said journal).


Best

Jason


On 27 April 2013 15:55, 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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