[Taxacom] New lizard species

[Robin Leech]

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
>
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