Phylogenetic evidence

Robert Mesibov mesibov at SOUTHCOM.COM.AU
Tue Jul 9 13:54:32 CDT 2002

It isn't clear whether Tom DiBenedetto followed the 'place' thread to its
finish before posting his latest comments, but in any case he has now
opened a different can of worms:

"I actually do not think that there is phylogenetic evidence
in spatial distributions. There is geopgraphic evidence - there is
biogeographic data,
but I don't think it rises to the level of phylogenetic evidence. To be
particular data must have a well-understood set of implications relative to
phylogenetic conclusions (as in character evidence - matching states indicate
common descent). The problem with spatial data is not extracting the
evidence, it is
meeting the basic requirements of evidence."

Haeckel's term 'phylogeny' is now more than 130 years old and it seems to
gain new shades of meaning each time someone sniffs out history in a data
set for the first time. It has a core meaning, though. A phylogeny is a
history of evolutionary events. As history, it's not knowable in the sense
that the melting point of lead (for example) is knowable. Historical
knowledge is historical supposition. We think something happened because we
have evidence that it happened, not because we witnessed it.

OK, so what kind of evidence could be used to erect a phylogenetic
hypothesis, i.e. a guess at a phylogeny? Anything that contains traces of
the history of the evolutionary events in question: fossils, biogeography,
morphological character-states, molecular character-states, host-parasite
relationships, etc etc.

A paleontologist might argue that cladistically working out relationships
between character-states of extant organisms with the blessing of parsimony
is all very nice, and rooting the resulting cladogram in hopes of orienting
it in time is also very nice, but it's not real evidence, is it? It's only
guesswork based on evolutionary endpoints. Now fossils, on the other hand -
there's REAL evidence of evolutionary history!

A molecular evolutionist might argue that morphologists who agonise over
whether two structures are homologous are wasting their time. There are all
sorts of histories possible for complex structures, it's hopelessy messy
evidence, the implications (in developmental genetics) are far from
well-understood. Now gene sequences, on the other hand - there's REAL
evidence of evolutionary history! After all, it's gene change that
underlies all the other changes in organisms, and look how much data we've
got in the genome!

I wish I could apologise and say the last two paragraphs are wildly over
the top but they're not, I could name names... Anyway, we should try to
make sure a phylogenetic hypothesis agrees with all available relevant
evidence. If it doesn't, we don't ignore the annoying facts that don't fit,
we re-examine the hypothesis. We also remind ourselves cheerfully and at
regular intervals that there is no final test, no do-or-die falsification
possible for even our best phylogenetic hypothesis, because we can't
revisit the past, where the truth lives.

Biogeographic evidence may be mutable and "blurry" at higher taxonomic
levels but it does indeed contain traces of history. Every gene, every
organism, every evolutionary event has (or had) an address. It often isn't
easy to use biogeographical evidence but it is REAL evidence nevertheless.

I gave 3 off-the-top-of-my-stack-of-reprints examples of using
biogeographical evidence in an earlier post. The first one concerned
reticulation evolution in a Tasmanian conifer genus. The evidence comes
from total-genome DNA fragment analysis and from geographical mapping: the
putative hybrid occurs only where the putative parents are sympatric.
Imagine for a moment that the putative hybrid had instead been found in New
Zealand. New hypothesis, maybe?

Sticking with Tasmanian plants, I urge Tom to read

McKinnon, G.E., Vaillancourt, R.E., Jackson, H.D. and Potts, B.M. 2001.
Chloroplast sharing in the Tasmanian eucalypts. Evolution 55: 703-711.

Turns out that eucalypt cpDNA haplotype families aren't faithful to
morphospecies lineages. Instead, they're endemic to particular AREAS within
Tasmania, regardless of what eucalypt morphospecies happen to be living
there and housing them. The authors see this as phylogenetic evidence of
massive hybridisation in the past, perhaps when the eucalypt ancestors were
crowded together in Pleistocene glacial refuges. Has Tom got an
interpretation (a phylogenetic hypothesis) for these eucalypts that ignores
the geographical evidence?

Dr Robert Mesibov
Honorary Research Associate
Queen Victoria Museum and Art Gallery
Home contact: PO Box 101, Penguin, Tasmania, Australia 7316
(03) 64371195; 61 3 64371195

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