[Taxacom] New lizard species

Sat Jun 5 22:47:56 CDT 2010

I see your point Stephen, but I think in the case of node-based identity,
this leads to a circular argument. Don't get me wrong, I do not have a
problem with molecular data being used to diagnose taxa (nor with
"splitting", particularly as a pragmatic exercise in learning more about
species ... or even  biota), but molecular diagnoses should be explicit.
Node-based taxa are self-fulfilling and, because they are analysis
dependent, nebulous.

On Sat, Jun 5, 2010 at 8:19 PM, Kim van der Linde <kim at kimvdlinde.com>wrote:

> That is very well possible. It could be a population on the verge of
> splitting, they might even have developed mating barriers and be real
> cryptic species to be distinguished by bar-coding like two Zaprionus
> species of the same region: Yassin, A., Capy, P., Madi-Ravazzi, L.,
> Ogereau, D. & David, J. R. (2008). DNA barcode discovers two cryptic
> species and two geographical radiations in the invasive drosophilid
> Zaprionus indianus. Molecular Ecology Resources 8, 491-501.
>
> Or it is a solid case of oversplitting that has nothing to do with
> speciation and everything to do with isolated populations, insufficient
> sample sizes etc.
>
> Who knows?
>
> Kim
>
> On 6/5/2010 7:01 PM, Robin Leech wrote:
> > Or, it could be that they just have not looked carefully enough for
> > morphological characters. My suggestion is to give the specimens,
> > several from each DNA group, to a lizard taxonomist.
> > On several occasions I have looked at collections of spiders and at
> > first glance figured that they were all representatives of the same
> > species.
> > but, when I sorted according to locality, then looked again, I did find
> all
> > the morphological characters I needed. I am sure that most morphological
> > taxonomists have had this experience.
> > And I will acknowledge that these lizards might represent a population
> that
> > is on the verge of splitting - has done so with DNA, but has not done so
> > yet
> > with morphology.
> > Robin
> >
> > ----- Original Message ----- From: "Kim van der Linde" <
> kim at kimvdlinde.com>
> > To: "Robin Leech" <releech at telusplanet.net>
> > Cc: "TAXACOM" <taxacom at mailman.nhm.ku.edu>
> > Sent: Saturday, June 05, 2010 2:55 PM
> > Subject: Re: [Taxacom] New lizard species
> >
> >
> >> Yes, that would be a way out of it, but they state explicitly that there
> >> are no morphological or ecological difference. So, we have four lineages
> >> described as species.
> >>
> >> Kim
> >>
> >> On 6/5/2010 4:40 PM, Robin Leech wrote:
> >>> Why don't we take the individuals that have solid DNA differences,
> >>> then when these are sorted, start looking for external morphological
> >>> characters that confirm the DNA?
> >>> Robin
> >>> ----- Original Message -----
> >>> From: "Kim van der Linde"<kim at kimvdlinde.com>
> >>> To: "TAXACOM"<taxacom at mailman.nhm.ku.edu>
> >>> Sent: Saturday, June 05, 2010 12:26 PM
> >>> Subject: Re: [Taxacom] New lizard species
> >>>
> >>>
> >>>> I just read the article, and I have mixed feeling about the article.
> >>>>
> >>>> 1. The central idea is that we can determine species limits by
> >>>> estimating where solid differences in the DNA can be found, as
> >>>> estimated
> >>>> using specific Bayesian methods.
> >>>>
> >>>> 2. The species concept used here is a strict phylogenetic species
> >>>> concept. Whether or not this corresponds with species using the
> >>>> biological species concept is unclear.
> >>>>
> >>>> 3. The number of individuals used for some populations is as low as
> >>>> one.
> >>>> if you have a single outlier. Humm, so much for an estimate of
> >>>> population variance, which is at the heart of the idea.
> >>>>
> >>>> 4. The use of guid trees is problematic at least. Why 4 species, and
> >>>> not
> >>>> 5, 6 or 3. If you a priori start with 4, you of course can find
> >>>> four. As
> >>>> long as you have well-supported nodes with a posterior probability
> >>>> of 1,
> >>>> you can determine species. The fact that the 10-species guide tree
> >>>> provides FIVE species should have resulted in major alarm bells.
> >>>>
> >>>> 5. They use the SAME data to first estimate the species, and then to
> >>>> estimate the probability of those species. This is a circular process.
> >>>> You need two separate data sets to do this. This sounds way to much to
> >>>> self-conformation.
> >>>>
> >>>> Overall, I am not buying this article. Maybe when it is done properly,
> >>>> with sufficient number of individuals per population, independent data
> >>>> sets and a search algorithm that determines what number of species is
> >>>> actually explaining the data the best, I might be persuaded to accept
> >>>> these phylogenetic species, in the context of phylocode.
> >>>>
> >>>> Kim
> >>>>
> >>>>
> >>>> On 6/4/2010 8:19 PM, Bob Mesibov wrote:
> >>>>> 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.
> >>>>
> >>>> --
> >>>> http://www.kimvdlinde.com
> >>>>
> >>>> _______________________________________________
> >>>>
> >>>> Taxacom Mailing List
> >>>> Taxacom at mailman.nhm.ku.edu
> >>>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> >>>>
> >>>> The Taxacom archive going back to 1992 may be searched with either of
> >>>> these methods:
> >>>>
> >>>> (1) http://taxacom.markmail.org
> >>>>
> >>>> Or (2) a Google search specified as:
> >>>> site:mailman.nhm.ku.edu/pipermail/taxacom your search terms here
> >>>>
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>>
> >>> Taxacom Mailing List
> >>> Taxacom at mailman.nhm.ku.edu
> >>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> >>>
> >>> The Taxacom archive going back to 1992 may be searched with either of
> >>> these methods:
> >>>
> >>> (1) http://taxacom.markmail.org
> >>>
> >>> Or (2) a Google search specified as:
> >>> site:mailman.nhm.ku.edu/pipermail/taxacom your search terms here
> >>>
> >>
> >> --
> >> http://www.kimvdlinde.com
> >>
> >> _______________________________________________
> >>
> >> Taxacom Mailing List
> >> Taxacom at mailman.nhm.ku.edu
> >> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> >>
> >> The Taxacom archive going back to 1992 may be searched with either of
> >> these methods:
> >>
> >> (1) http://taxacom.markmail.org
> >>
> >> Or (2) a Google search specified as:
> >> site:mailman.nhm.ku.edu/pipermail/taxacom your search terms here
> >>
> >
> >
>
> --
> http://www.kimvdlinde.com
>
> _______________________________________________
>
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>
> The Taxacom archive going back to 1992 may be searched with either of these
> methods:
>
> (1) http://taxacom.markmail.org
>
> Or (2) a Google search specified as:  site:
> mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
>

-- 
Dr Anthony C. Gill
Assistant Director for Collections
International Institute for Species Exploration
School of Life Sciences
PO Box 874501
Arizona State University
Tempe
AZ 85287-4501
USA.

Phone: (480) 965-8620
Fax: (480) 965-6899
E-mail: gill.anthony at gmail.com
http://sols.asu.edu/faculty/agill.htm
http://species.asu.edu/