Re: Article: On Phylogenetic Trees

In article <ehmjj1$kek$1@xxxxxxxxxxxxxxxxxxx>, <anon1@xxxxxxx> wrote:

[me, last December:]
Lamarck also had a tree of life, earlier.

[anon@xxxxxxx:]
It's my understanding that neither Lamarck nor Darwin had *a* single
tree of life, rather each had multiple trees of life, with Lamarck's
trees comprising very small clades (one genus, or one family many
genera), while Darwin's trees comprised larger clades. Furthermore
Lamarck believed firmly that evolution was strictly segregated within
these family groups, whereas Darwin allowed for the possibility of a
single all-inclusive clade or at least a very small number of master
clades.

Lamarck's tree was not as small as you imply. For example, all multicellular
animals were in one tree. That's a heck of a lot bigger than "very small
clades"

[me:]
If one wants to use trees properly, you want not only a single estimate
of the tree, but some information about the uncertainty of different parts
of the tree.

If branch lengths are shown by numbers as well as visual length of
segments, upper and lower bounds should be shown for any branch whose
length isn't known to the precision of the numbering system.

That would be nice, but usually we can't do that.
.....
(Actually the numbers I usually see in published cladograms are
actually confidence levels, usually above 90, sometimes only in the
80's, not branch lengths, right? I'm not sure really. Enlighten me?

Usually they are the numbers of times (out of 100) that the branch was
supported in bootstrap-sampled data sets. This does not translate directly
into percent chance that the group is wrong, alas. In other cases the
numbers are percents of support in a Bayesian inference, with an assumed
prior distribution of trees.

[me:]
Lamarck did come (after some resistance) to a tree of life, fifty years
before Darwin.

So it's no wonder he didn't go so radical as Darwin later did. What
Lamarck proposed was radical for his time, and apparently the French
later recanted it, even as the British continued to embrace it, and
then what Darwin proposed would have been a mortal sin in Lamarck's
time but was merely radical in his time, while Lamarck's proposal was
tame in Darwin's time, already well accepted everywhere, and *still*
accepted outside France.

No, Lamarck's view had some influence outside science (see Adrian Desmond's
wonderful book "The Politics of Evolution" which about that era) but
Lamarck's views were rejected by most scientists both inside and outside
France. They were not "accepted everywhere".

Lamarck was a really bright guy, and it's just that he didn't have
Malthus's shoulders to stand on as Darwin and Wallace did. I think
Malthus deserves half the credit for the theory of evolution by
competition per fitness and survival of the fittest, since he did the
ground work in the population dynamics whereby the Darwin/Wallace is
merely a corollary.

I disagree. The discovery of natural selection was far more substantive
than "merely a corollary".

But Darwin and Wallace deserve a majority of the
credit for their groundwork in Galapagos and East Indies respectively
that led to the idea of largescale common descent and (see below)
abolition of the idea of fixed ideal forms.

They deserve almost all of the credit for natural selection. It is also
pretty well accepted that Darwin's observations in other places such as
South America played a more important role than his observations in the
Galapagos. The Galapagos, and particularly its finches, gets overpublicized
in accounts of the story (the excellent work on finches by David Lack and Peter
Grant is over a century later). Also Darwin didn't come to natural selection
until long after his return from the voyage.

----
Joe Felsenstein joe@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Department of Genome Sciences and Department of Biology,
University of Washington, Box 357730, Seattle, WA 98195-7730 USA

.

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