[Taxacom] New lizard species

Sun Jun 6 15:35:05 CDT 2010

Im sorry, but i'm failing to see why so many people on this forum are up in arms. I just joined the forum, and got my inbox filled with responses.

Yes, the paper has some definite weaknesses, which makes me fear about the peer-review here, but im failing to see the reason for the outcry from the taxonomy perspective. From the molecular view alone (which is my background), i agree that the discrete molecular characters supporting of their putative new species should have clearly defined, and i agree it must be re-considered if their diagnoses are valid for the ICZN rules etc. That could of course be a weakness of the need for a character-based definition for formal species delimiation, but surely that's another more general debate?.

Now the problem i have is the such revisonary insigths from molecules alone are not new (though in lizards it perhaps is), and i worry that the outcry is because this work is on vertebrates, not other creatures where there is still a huge wealth of undescribed biodiversity, and where any new perspectives on the species boundaries are entirely welcome. 

What it seems these authors do is determine 4 lineages withn a sampling of 10 'populations' (ie collection sites), using a newly developed approach Yang and Rannala [in press, PNAS]. There are some obvious limitations, like estimating on a fixed guide tree, hence loosing the uncertainty of the original bayesian analyse, (ie 'weak' nodes of 0.89/0.96 Pp seperating the congo north / congo south populations), their sampling scheme is limited (isnt samping always limited by reality?), and the distinct lack of comparable data from other 'species' outside the group (and those pesky outgroup problems). But i am alarmed by the lack of other species, or preferably multiple representatives of other species, which would surely help inform how much genetic divergence is typical for closely related geckos with similar ecologies (ie to clarify geneflow relative to population). They also seem to loose any detail about how the different genetic markers may be providing alternative perspectives on gene flow. It is this lack of detail and insights from 'multiple representatives of other species' that is most worrying to me, as their introduction outlines the need for parameters such as effective population size and mutation rate in the species delimitation model. So, are poor 'estimates' of these parameters heavily influencing their results and biasing their preferred view?

What i suggest are at best perhaps cryptic species, but could well be incipient species, or even just substructure in a widespread population, (and for the record i see only 2 robust lineages..)., but the crux is that my suggestions are subjective, though results here surely indicate more than one 'lineage', suggesting nomenclatural revision maybe needed. But isnt this how 'traditional' taxonomy is always done... some authors suggest a single lineage, others suggest multiple lineages, then typically congruence across multiple robust studies eventually determines the which hypothesis becomes the most widely accepted/generally preferred?. Im of course avoiding the loaded word 'species' here. If multiple future studies converge on a view that indicates fewer 'species' as discrete robust entities, then synonymies will be made. Isnt that how the conventional taxonomic system works already?

Really, i think there is no need for such an outcry from morphologists or others, and im really not sure what a 'classical systematist' is, except maybe one who doesnt use all the modern methods available for giving the most considered insight (bringing all the tools to bear on a question, etc). I would suggest though, that perhaps a published reply and some reanalyses are indeed needed in response to the suggested flaws in this article, though I also suggest any debate to resolve a taxonomic problem, or to encourage more funding / more rigorous analyses of such problems is most welcome. In part, the underlying method of Yang and Rannala (which i dont yet know about) should of course be investigated further, and so i welcome other such 'case studies' on the utility of this and other molecular 'species delimitation methods', which in my opinion are tying to unite perspectives on taxonomy from new molecular datasets with the 'conventional system', not to develop "molecular nonsense species". This is not a study aiming to be devisive of the "linnean system' from 'molecular taxonomy', but to me this is more simply taxonomy using molecular methods, and perhaps one in need of rigorous re-evaluation.

To just question Richard Zander, about his statements [quote] "I think phylogenetic scrambling of taxa will do the same for biodiversity analysis nowadays, with similar sad results. (1) Critical taxa are lumped because they make other taxa paraphyletic (e.g. polar bears don' exist biodiversitywise, cacti are only portulacas, birds are just airborne reptiles), and (2) Critical taxa are buried among a plethora of molecular nonsense species."  Sorry, but isnt such modern revision helping establish the underlying relationships of phyla based on the best available current evidence, and so working towards darwins dream of "true geneological trees for each great kingdom of nature"? or do you want to stick with the old textbooks containing outdated information like that reptiles are a discrete and hence valid group ? That sounds rather like subjective opinion rather than empirical driving research.

stuart.

> > ------------------------------------------------------------------- 

> > 

> > Stuart Longhorn, MSc PhD 

> > PostDoctoral Fellow. 

> > Molecular Evolution and Bioinformatics Lab. 

> > National University of Ireland, Maynooth, IE 

> > 

> > Email: sjl197 at hotmail.com or stul at pdx.edu 

> > 

> > ------------------------------------------------------------------ 

> > 

> > http://www3.imperial.ac.uk/people/a.vogler 

> > http://web.pdx.edu/~stul/

> Date: Sun, 6 Jun 2010 13:45:23 -0500
> From: Richard.Zander at mobot.org
> To: mesibov at southcom.com.au; taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] New lizard species
> 
> I agree with Bob Mesibov's take on the lizard species paper. Although
> there are obvious horrors in the paper, particularly few samples, no
> correlation with morphology or ecology, no statement of what the point
> is in these "species," I think it is time classical systematics takes a
> stand against phylogenetics, particularly its incarnation of the old
> automatic classification promoted by (some) pheneticists. 
> 
> I don't necessarily suggest that "the old ways are best" but they sure
> are better than present-day axiomized systematics. Remember how genetics
> was axiomized in the mid-1900's in the Soviet Union? It killed Vavilov
> in the Gulag and contributed to the famines of the 60's. I think
> phylogenetic scrambling of taxa will do the same for biodiversity
> analysis nowadays, with similar sad results. (1) Critical taxa are
> lumped because they make other taxa paraphyletic (e.g. polar bears don't
> exist biodiversitywise, cacti are only portulacas, birds are just
> airborne reptiles), and (2) Critical taxa are buried among a plethora of
> molecular nonsense species. 
> 
> I think classical systematists should take a stand against structuralist
> empty precision and false "hard science," and make funders realize that
> good systematics means investigation of all data that inform an
> evolution-based classification, including alpha taxonomy (collection and
> delimitation of species), classical systematics (higher categories),
> parsimony of morphology (helps make natural keys), molecular systematics
> (helps show genetic continuity and isolation events in the pedigree of
> specimens used as OTUs), and biosystematics (helps determine extent and
> direction of evolution).
> 
> *****************************
> Richard H. Zander 
> Voice: 314-577-0276
> Missouri Botanical Garden
> PO Box 299
> St. Louis, MO 63166-0299 USA
> richard.zander at mobot.org
> Web sites: http://www.mobot.org/plantscience/resbot/
> and http://www.mobot.org/plantscience/bfna/bfnamenu.htm
> Modern Evolutionary Systematics Web site:
> http://www.mobot.org/plantscience/resbot/21EvSy.htm
> *****************************
> 
> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu
> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Bob Mesibov
> Sent: Friday, June 04, 2010 7:19 PM
> To: TAXACOM
> Subject: [Taxacom] New lizard species
> 
> If you haven't seen it, do read
> 
> Leache, A.D. and Fujita, M.K. 2010. Bayesian species delimitation in
> West African forest geckos (Hemidactylus fasciatus). Proceedings of the
> Royal Society B. Published online as doi:10.1098/rspb.2010.0662
> 
> In a well-argued and very clear paper, the authors plump for
> probabilistic determination of species, and name four *Linnean* species
> on probabilistic grounds. They say '...we are not aware of any
> morphological or ecological characteristics that differentiate these
> lineages,' and therefore diagnose their species as follows (one
> example):
> 
> 'Diagnosis. This species includes all populations that cluster with
> those from the southern portion of the Congolian rainforest included in
> this study (southern Cameroon, Gabon and Congo), with strong support in
> the Bayesian species delimitation model.'
> 
> I don't actually have a problem with the methods used or the argument.
> My concern is that the authors confuse Linnean species with lineages.
> Lineages can be diagnosed within a probabilistic framework. They give us
> an insight into how evolution might possibly have happened. Linnean
> species are those nice, easily recognised things that enable us to
> retrieve biodiversity information, write field guides and feel that we
> have a handle on natural history.
> 
> It's been obvious for a long time that Linnean taxonomy and molecular
> taxonomy were headed in different directions, but this paper (IMO) is a
> clumsy attempt to yoke them back together.
> -- 
> Dr Robert Mesibov
> Honorary Research Associate
> Queen Victoria Museum and Art Gallery, and
> School of Zoology, University of Tasmania
> Home contact: PO Box 101, Penguin, Tasmania, Australia 7316
> 03 64371195; 61 3 64371195
> Webpage: http://www.qvmag.tas.gov.au/mesibov.html
> 
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