Botany picture #140: Pistacia lentiscus

Pistacia lentiscus (Anacardiaceae), France, 2008. This is not the pistacio plant but one of its congeners. When I photographed it on a holiday trip to southern France I was unaware that the species is apparently harvested for a strongly aromatic resin, especially in Greece and Turkey. Read details at Wikipedia if interested.

More 'Framework': Can we trust molecular phylogenetics?

Continuing with extended comments on the book I am reading, Richard Zander's Framework for a Post-Phylogenetic Systematics.

In my previous post, I examined the claim that parsimony analyses are mislead by 'budding' speciation. As indicated then, this does not appear to be plausible unless we deliberately withhold information from the analysis, in which case the analysis itself would not be at fault.

However, it is not only parsimony analyses of morphological data that Zander mistrusts and considers to be too 'mechanistic'. He also claims that molecular phylogenetics cannot be trusted to infer the correct relationships between species. Although he uses different terms, partly of his own invention, his main argument appears to be that the stochastic nature of lineage sorting will often mislead phylogenetic analyses.

Creationists

Yes, perhaps reactions like these are mean, and perhaps those who have been raised in a culture of proud ignorance should be pitied rather than ridiculed, but I cannot help finding the following two links funny, especially the second one:

22 answers for creationists from someone who understands evolution

Creationist questions translated

Botany picture #139: cape weed

Arctotheca calendula (Asteraceae), Australian Capital Territory, 2013. This plant is commonly known here in Australia as cape weed after its introduction from South Africa. As one can see, it is actually quite pretty but it really is an obnoxious weed in disturbed areas and can cover large areas in good years. In contrast to many other daisies it does not have a bristly pappus. Instead, the fruits have a crown of scales and are covered with a large mass of fuzz.

Can parsimony analyses be mislead by 'budding' speciation?

In several places the Framework for a Post-Phylogenetic Systematics argues in favour of inferring relationships between groups of organisms with the informed intuition of the 'classical taxonomist' instead of 'mechanistic' phylogenetic analyses. It presents several arguments, among them the observation that classical taxonomy is generally based on more specimens per species than phylogenetics and the claim that neither parsimony analyses of morphological data nor molecular phylogenies can be trusted to infer relationships correctly.

I kind of get the first of these arguments, at least in principle. Yes, we could mention the large number of newly described species in classical taxonomy that are, at first at least, based on just the type collection. Yes, there seems to be some kind of conflation going on here between species delimitation, which to be done well indeed needs large numbers of specimens, and phylogenetics, which should preferably use only characters that are not variable within the species anyway and thus should theoretically work fine with only one specimen. But still one can at least grant that deep sampling is an advantage of the classical taxonomist's approach. (I would never argue against it anyway - alpha taxonomy and phylogenetics are complementary, not alternatives.)

But I do not at all understand the distrust of phylogenetic analyses. Consequently I would like to take a closer look at these methods, starting with the supposed vulnerability of parsimony analyses of morphological data. Specifically, the claim is that they can be mislead into inferring the wrong relationships if speciation is by budding, in other words if one of the two daughter lineages in a speciation event is morphologically indistinguishable from the ancestor (Framework p. 25, p. 39).

Botany picture #138: Malva neglecta

Malva neglecta (Malvaceae), Australian Capital Territory, 2013. This is an introduced weed, and the flower is tiny for a Malva, but I happen to like the genus.

Two possible meanings of "pseudoextinction"

Continuing to read Richard Zander's recently published Framework for Post-Phylogenetic Systematics.

I had originally intended to discuss general concepts instead of criticizing the book directly, but it probably cannot be avoided entirely; in the present case because I need to lead up to what I would like to discuss afterwards.

Repeatedly the book makes the argument that Hennig's internodal species concept is obviously wrong. To recapitulate, it is the idea that a species can be considered as existing through time between two lineage splits. On the tree of life, a species originates in a speciation event and ends at the next speciation event. Even if one of the products of that next split is morphologically and ecologically indistinguishable from it, it is still considered a new species. Because the ancestral species ends by definition at the split but is not really extinct (it survived, after all, in the form of both descendent species), it is sometimes called pseudoextinct.