molecular phylogenetics

Fri Oct 10 10:51:26 CDT 2003

Hi all

on 10/9/03 9:50 AM, John Grehan at jgrehan at SCIENCEBUFF.ORG wrote:

> I did not express myself well here. I am suggesting a situation where one
> can make a species tree because there are differences between he species,
> but that these relationships are all primitive retentions inherited from
> the ancestor rather than being new conditions representing the subsequent
> speciation events. Is this possible?

We have been looking at chloroplast sequence polymorphism in some New Zealand Gnaphalieae (Compositae). There are some reasonably variable cpDNA regions for this group and a number of chloroplast lineages can be resolved. However, some of these lineages have been sampled from very different species (based on morphology or on nuclear sequences) and some species contain several different chloroplast lineages. 

The situation John describes is one possible explanation. Another is introgression. I favour at least some contribution from introgression on the basis of geographical distributions. However, for phylogenetics the key point is that wether a  "gene-tree" will match a "species-tree" depends on parameters such as ancestral poulation size, level of polymorphism, breeding system, period of shared ancestry between divergences etc. Also, it depends on an absence of gene-flow between diverging as well as diverged lineages. In many cases, especially when outcrossing is the norm and populations are continually large, speciation is rapid or punctuated, and one ancestral species gives rise to numerous descendant taxa, "gene-trees" are unlikely to resemble "species-trees". After all, good branches in cpDNA trees are the product of (chloroplast) lineage extinction or sampling.

Ultimately, we all have to accept that the dichotomising tree can be a crude model of genealogical relationships in sexual taxa since every individual is part of multiple lineages. Sequence data make this very clear. In some cases the tree is very usefull, in others it is of dubious value or cannot be extimated reliably. There is no "fix" for these sorts of problems, the only course is to take a holistic view of all the information available for whatever taxa we work with. When sequences do not give credible species trees they still tell us a lot about the process of evolution (which, after all, is not just a series of lineage divergences).

John, these issues are well explored in numerous publications but I found them well communicated  in JC Avise's books "Molecular markers. Natural history and evolution." Chapman and Hall, New York (1994)  and "Phylogeography: The History and Formation of Species." Harvard University Press, Cambridge, MA (2000).


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