[Taxacom] Paraphyletic species: Crocodylus niloticus

[John Grehan]

-----Original Message-----
From: Dan Lahr [mailto:daniel.lahr at gmail.com] 
Sent: Saturday, May 14, 2011 1:29 PM
To: John Grehan
Cc: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Paraphyletic species: Crocodylus niloticus

Dear John and Michael,

> Certainly possibility of older fossils must be acknowledged, but
> can't prevent conclusions based on available evidence. 

Yes they can if the conclusions are really not based on the available evidence. If the fossil record for a certain taxon is only as old as a certain date, that is not evidence for origin at that date. It is only evidence for origin by that date at the minimum.

> I have absolutely no familiarity with crocodile paleontology,
> but my impression from reading the article was that there are 
> older croc fossils which are not C. niloticus, so I am assuming
> there is some degree of confidence to say C. niloticus showed up
> only in Pliocene. Perhaps a vertebrate paleontologist may help 
> here.

Exactly, you are making an assumption

> In any case, I still think they have the correct interpretation > based on *available* fossil record. Of course if older fosils 
> are found the interpretation may change.  It seems to me this is
> indeed an interesting case of transoceanic dispersal.

There is nothing to say that you cannot have that opinion, but that's different from claiming that the paper constitutes a convincing case of transatlantic dispersal. The interpretation is based on a false premise which you acknowledge. The fossils can only provide a minimal estimate no matter how much one may want to believe otherwise.

> As for Michael's further concern:

> Why does everyone always assume that a basal paraphyletic grade
>  in one area represents a center of origin?

> I can't speak for others but that wasn't my assumption and also 
> doesn't seem to me to be the reason the authors interpret that 
> particular region in Africa as the center of origin, but more 
> the case that the American crocs are more derived than old 
> world, as well as Asian-Pacific crocs, i.e., interpretation over
> the phylogenetic branching  pattern.  I believe if the species 
> was not paraphyletic the interpretation would still hold.

Why are you assuming that more 'derived' condition is an indicator of dispersal?

John Grehan


Kind regards,


Dan

On Fri, May 13, 2011 at 10:31 PM, John Grehan <jgrehan at sciencebuff.org> wrote:
> Dan,
>
> Thanks for the paraphyly explanation as I had not seen the original article and it was not covered in the link given by Ken. I have no particular view on that proposed relationship other than having doubts about whether mtDNA can show anything more than variation related to metabolic adaptation.
>
> On dispersal, I presume you have seen Head's comments and that you can now understand how this example of phylogenetic evidence combined with the interpretation of available fossil records does not constitute a convincing case of transatlantic dispersal.
>
> John Grehan
>
> -----Original Message-----
> From: Dan Lahr [mailto:daniel.lahr at gmail.com]
> Sent: Friday, May 13, 2011 4:58 PM
> To: John Grehan
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] Paraphyletic species: Crocodylus niloticus
>
> Hi John,
>
> Paraphyly: The article suggests that C. niloticus is paraphyletic because eastern and western populations constitute independent lineages in their reconstructions: eastern populations are more closely related to New World species than to western populations. It is only an indication of paraphyly as the reconstruction is based on mitochondrial genes.  These are maternally inherited, thus an alternative hypothesis may be coined that females stay more at home than males (one can look at nuclear genes to test this hypothesis).
> It is also worth noting that 6 specimens hardly constitutes comprehensive sampling to definitively conclude paraphyly of the species, in my view this is more of a particularly striking piece of evidence.
>
> DIspersal: The oldest C. niloticus fossils are Pliocene, and the oldest New World Croc fossils are also Pliocene. Because the branching pattern revealed by this study puts C. niloticus + NW crocs in a well-supported clade, one can only conclude that a C. niloticus traveled from Africa to NW in the Pliocene, i.e. around 3.6 Mya. No molecular clock needed, and in fact the authors did not use any implementation of molecular clocks in their analyses.
>
> I do not understand how this example of phylogenetic evidence combined with the interpretation of available fossil records does not constitute a convincing case of transatlantic dispersal.
>
> Kind regards,
>
> Dan
>
> On Fri, May 13, 2011 at 4:16 PM, John Grehan <jgrehan at sciencebuff.org> wrote:
>> It's not an example of transoceanic dispersal at all. That's just the 
>> usual misrepresentation of molecular clock dates as actual or maximal.
>>
>> The article did not give any indication of paraphyly. Please describe.
>>
>> John Grehan
>>
>> -----Original Message-----
>> From: taxacom-bounces at mailman.nhm.ku.edu
>> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Kenneth 
>> Kinman
>> Sent: Friday, May 13, 2011 4:03 PM
>> To: taxacom at mailman.nhm.ku.edu
>> Subject: [Taxacom] Paraphyletic species: Crocodylus niloticus
>>
>> Dear All,
>>       A recent paper indicates that Crocodylus niloticus is 
>> paraphyletic with respect to the clade of Crocodylus species in the 
>> Americas.  Not only a great example of a paraphyletic species, but 
>> also transoceanic dispersal as well.  Link to news story is given below.
>>               ----------Ken
>>
>> http://www.newscientist.com/article/dn20464-crocodiles-swam-the-atlan
>> t
>> ic
>> -to-reach-america.html
>>
>>
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>
>
> --
> Daniel Lahr
> -------------------------------------------------
> PhD candidate
> Organismic and Evolutionary Biology
> U Massachusetts- Amherst
> 319 Morrill Science Center, Amherst
> Amherst, MA 01003
> 413-585-3881
>
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> The Taxacom archive going back to 1992 may be searched with either of these methods:
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--
Daniel Lahr
-------------------------------------------------
PhD candidate
Organismic and Evolutionary Biology
U Massachusetts- Amherst
319 Morrill Science Center, Amherst
Amherst, MA 01003
413-585-3881