Page 148 - Introduction to Paleobiology and The Fossil Record

MACROEVOLUTION AND THE TREE OF LIFE 135
The vast numbers of DNA and RNA
sequences that are generated daily from the
whole diversity of life are stored as letter
codes in open-access databases. Any investi-
gator may download the sequences of any
particular gene or chromosome for as many
species as are available. There are then two
key processes in extracting a phylogenetic
tree from such data. First, the nucleic acid
sequences must be aligned, that is matched,
so that the code of a particular gene in one
species is lined up with the same sequence in
another species. Alignment can be diffi cult
because species do not differ only in the place-
ment of particular base pairs, but sometimes
gaps in the sequence are introduced, or whole
sections may be repeated. Once the sequences
of a number of species are satisfactorily
aligned, the phylogenetic analysis is carried
out. The base-pair codes are treated like the
presence/absence (1/0) codes in a morphologi-
cal data matrix, and a variety of algorithms
are applied to extract the most likely tree that
explains the data.
The tree of life
Paleontologists and biologists are using mor-
phology and molecules to put together ever-
larger sectors of the tree of life. Desktop
computers are exploding in labs around the
world as analysts ask them to crank out ever-
larger trees. Bear in mind that the number of
n−2
possible trees is N = (2n − 3)!/(2 (n − 2)!).
So for three species, there are three possible
unique trees. For four species, there are 15
possible trees (Fig. 5.12), for eight species
168,210 possible trees, and for 50 species
about the same number as there are atoms in
the universe. You can do these calculations in
table 1.3.1 at http://www.talkorigins.org/faqs/ 1 Consider the four logical steps that sum-
comdesc/section1.html.
And yet 50 species is not a demanding
number. Systematists want to know the com-
plete tree for all 240 species of primates, all
4500 species of mammals (now available:
Bininda-Emonds et al. 2007), and so on.
Mathematicians tinker with the tree-fi nding
software so it finds clever ways to fi nd the
best-fitting tree quickly, even though many
millions or billions of potential trees are con-
sidered and rejected. Another approach is to
link existing trees for parts of the group of
interest to create a supertree that summarizes
A B C B A C A B C
(a)
A B C D A C B D A D B C C D A B
D C A B B D A C D B A C B C A D
A D D A
C B A D B C B C A C B D
C A B D A B C D B A C D
(b)
Figure 5.12 The number of unique trees for
three (a) and four (b) taxa. These cladograms
may be written more simply as (A(BC), (B(AC))
and ((AB)C) for the three-taxon cases, and
((AB)(CD)), ((AC)(BD)), ((AD)(BC)), etc. for the
four-taxon cases. Note that (A(BC)) and (A(CB))
are identical trees, and both versions count as
one.
the information in all existing trees. Research-
ers are currently using all methods and
approaches to draw major sectors of the tree
of life, and such huge trees will allow paleon-
tologists and biologists to carry out many
novel studies of macroevolution.
Review questions
marize natural selection (see p. 119), list
examples for each of numbers 1–3, and
consider how the mechanism could be
disproved.
2 Read books and web sites that present
evidence for intelligent design (ID). List
some specific examples/case studies that
are cited by ID supporters, and present
these in the form of falsifi able scientifi c
hypotheses.
3 Find 10 paleontological case studies on
speciation, by searching the internet with
the key words “phyletic gradualism” and