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Re: primers

Getting back to the original innocent question regarding domestic dogs, the answer seems to be it's not a fair question, but
cladistic analysis of skeletons (after all we dont have dino DNA yet) would result in one species being recognised as many taxon in
a cladogram.

Not automatically. There are many opposite examples -- species that differ hardly or not at all in their skeletons, but quite obviously in soft anatomy and behavior. Lions and tigers, for instance. Or tons of species pairs among small birds. Let alone *Paramecium* -- what was thought to be one species turned out to consist of 27 when it was discovered that members of each of those 27 species mate only with each other, even though all 27 species look identical, according to what I've heard on that.

But first and foremost it's important to keep in mind that cladistics -- morphological as well as molecular! -- doesn't come with a species concept. Cladistics tells you the most probable genealogic tree of your "operational taxonomic units" (the specimens or whatever you've put in your data matrix). It does not give you any criteria to delimit species. However, it is probable that, when analyzed together with wolves, coyotes, jackals, foxes and so on, different dog breeds would pop up in different places all over the tree in a morphological analysis, instead of coming out within the wolves.

Although dogs is an extreme example, how can we then assign different species to dinosaurs that show much smaller variations, that
could be a result of population isolation, for example.

You're right. There's a large amount of guessing involved. This is part of why some people advocate abolishing species in taxonomy...