Re: Ancestors [was: Re: And while on the theory of phylogenetic reconstruction...]

[David Marjanovic <david.marjanovic@gmx.at>]

>     Ok, since no-one seems to want to go near this, I'll give it a try...

I wanted to, but I didn't have time until now, and (...unsurprisingly),
you've done it better than I could! :o)

> When ancestors could not be traced, they often left the
> infamous "dotted line" extending towards, but not
> contacting, another lineage.

Shall I scan and upload a few dozen? :^) People were really obsessed with
ancestors, some even used this to "prove" that paraphyletic high taxa are
_necessary_.

> ([...] see the popularity of the term "basal,"
> a politically correct form of "primitive").

That's indeed how it's used a lot. _Properly_, though, "basal" means "as far
away as possible from the clade I'm interested in at the moment". For
example, there is a paper on the phylogenetic position of turtles, which
presents this (widely agreed upon) tree of amniotes

+--mammals
`--+--turtles (traditionally)
   `--+--lizards & snakes
      `--+--crocs
         `--birds

and then says that mammals are the basalmost amniotes (or basalmost living
ones, I forgot). _Is correct_, because the turtles are of interest to the
authors. I bet that many mammalologists would reach for their long knives
upon reading that mammals were basalmost anything, because they'd assume
that "basal" meant "primitive" -- they'd be wrong.

> The approach taken by many
> phylogenetic systematists (including people who would call themselves
> "cladists")

Is there a difference? AFAIK not.

>  Would you consider Pleistocene _Homotherium_ (the "sabertoothed tiger")
> to be a reasonable descendant of Holocene _Felis concolor_
> (the mountain lion), simply because both are found in California?

(Did you mean "ancestor"?)

>     Now, there is a technical aspect of this as well, and it is somewhat
> similar to the situation of hybrid speciation and phylogenetics: nearly
all
> current methods only allow for reconstruction of bifurcating trees, i.e.,
> trees that have 2n-1 branches for n taxa. Although this has been
represented
> as a hypothesis about the pattern of evolution (i.e., that all speciation
is
> bifurcating), and some phylogeneticists dogmatically hold to this
position,
> many others see it as a computational technicality, not necessarily an
> assumption about evolution.

There is a probable example of a real polytomy. Every Mediterranean island
of sufficient size has its own lizard species (*Podarcis*), and
mitochondrial gene studies indicate that they all originated in a polytomy
some 6 million years ago. This fits the time when the Mediterranean dried up
and refilled (several times); when it was dry, one species invaded the
entire area (today there's one that inhabits more or less all Mediterranean
coasts), and when the sea came back, the populations on the islands all
became isolated at the same time, representing a speciation that isn't a
dichotomy but a polytomy with some 8 branches.

> Similarly, at least in theory, the treatment of
> all taxa as terminals is a technical necessity.

If only because the currently available programs can't do otherwise.

> The pattern cladists, and many traditionalists, have spent a great deal of
> time emphasizing the difference between a *cladogram* and a *phylogeny*.

Just today I've had a discussion with just such a traditionalist. :-)

> Probably, in most cases, the two are interchangeable. However, not all
> trees, even if they are "correct" for the data, can be taken as the best
> representation of the phylogeny. As many have noted, simultaneous
> speciation, ancestry and descent, hybridization, and other phenomena that
> are considered very likely to actually occur in nature cannot be
represented
> directly through an analysis (yet).

Don't hold your breath, but there is an approach similar to cladistics that
has been used in linguistics and seems to do just this. I'll send the
citation tomorrow...

> In the case of ancestry and descent, I am
> pretty sure it is not possible for a tree with a taxon
> at a node (i.e., ancestral) to be any more parsimonious
> than one with a taxon on a zero-length branch.

This is obvious.

>     It would help to remember the history of the Clade Wars.

Bit difficult if one was born in 1982! :^)