[Taxacom] nucler vs plastid trees

[Michael Heads]

Incongruent trees for different characters (including genes) are very
common and are a fundamental aspect of life. They are usually explained by
introgression or by incomplete lineage sorting (ancestral polymorphism).

In the latter process, the ancestor is polymorphic with, say, a north-south
break or cline, BEFORE the new phylogenetic break starts to form. This old
variation can be inherited. The new round of phylogeny can result in, say,
an east-west break or cline, and the two sets of variation now present in
the descendant are incongruent, in phylogeny and biogeography.

This is discussed in my Australasia book in the sections 'Incongruence in
patterns of variation in different genes and characters' (p. 27) and
'Examples of incongruence and incompete lineage sorting' (p. 29).

On Fri, Feb 26, 2016 at 7:23 AM, John Grehan <calabar.john at gmail.com> wrote:

> My thanks for all the comments and responses (some off list). I get the
> impression that its a bit of an unresolved problem. However, its does not
> seem to be an impediment to the widespread use of molecular analyses (and
> its virtual supplanting of morphology). I do not have the level of
> comprehension to make any judgment bout the incongruence. From what some
> have indicated, the incongruence problem might even render molecular trees
> uninformative. I certainly have no argument with the issue of morphology
> coding genetic traits as I have argued for over a decade for the orangutan
> relationship.
>
> My present focus is in the sue of molecular trees for biogeographic
> reconstruction since that is pretty much all that is available to me.
> However it is good to have some idea of how others view the nuclear and
> plastid (or mitochondrial) incongruence. Theoretical questions aside, the
> molecular trees repeatedly show extensive clade allopatry at all levels or
> organization, as was extensively demonstrated by Heads (2012, 2014). The
> bizarre aspect of this allopatry is that it is almost always attributed to
> grand global migrations as if the taxa all new where to go in order to
> occupy different localities (a sort of global musical chairs, where the odd
> taxon out - the one who does not find a 'chair' - becomes extinct).
>
> John Grehan
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> Channeling Intellectual Exuberance for 29 years in 2016.
>



-- 
Dunedin, New Zealand.

My books:

*Panbiogeography: Tracking the history of life*. Oxford University Press,
New York. 1999. (With R. Craw and J. Grehan).
http://books.google.co.nz/books?id=Bm0_QQ3Z6GUC
<http://books.google.co.nz/books?id=Bm0_QQ3Z6GUC&dq=panbiogeography&source=gbs_navlinks_s>



*Molecular panbiogeography of the tropics. *University of California Press,
Berkeley. 2012. www.ucpress.edu/book.php?isbn=9780520271968



*Biogeography of Australasia:  A molecular analysis*. Cambridge University
Press, Cambridge. 2014. www.cambridge.org/9781107041028



*Biogeography and evolution in New Zealand. *Taylor and Francis, Boca Raton
FL. 2016. www.tandf.net/books/details/9781498751872/