Homework 3. Due Wed Feb 6, by noon.
1. Go back to Kevin Padian's
testimony regarding homology, tasmanian wolves, kangaroos,
etc.
Based on the traits presented, draw a phylogeny that shows
the relationship between N. American wolves, dogs, tasmanian
wolves, kangaroos, and oppossums. On the phylogeny,
mark and label the appropriate branches with synapomorphic
characters that unite subgroups.
4pts. Your phylogeny should show
the groupings, and below each group you should show the synapomorphies.
Important ones that clearly group the marsupials separately from the placentals are:
a) placenta; b) # of molars; c) presence/absence
of palatal holes; d) reflected lamina; # of pre-molars; e) presence/absence of
ear bulla; f) presence/absence of para-occipital
process; g) carnassial teeth; position of lacrimal bone;
In addition, you could have added the "overall dog like morphology"
that the creationists seized on.
The following questions refer to the squirrel
article by Mercer et al.
In class we'll cover: What data were used to estimate the
squirrel phylogeny? ; In figure 1, which branch do we have the least confidence
in? Which one(s) do we have the most confidence in?
- 2pts. In figure 2, how did the authors determine the
timing (in years (Ma) before present) of branching events? They used a molecular clock that was calibrated with
the oldest known squirrel fossils, dated 36 Ma (mega-annum). [In
the online supplement, one learns that they used only the IRBP gene because it exhibited more clock-like
behavior than the mt rRNA
genes.]
- 3pts. Aplodontidae
(Mountain Beaver, found only on the PNW coast)
is not a squirrel. Why is it included in the phylogeny? Aplodontia is an outgroup for the squirrel phylogeny. Based on
other evidence (for example, fossil evidence), this group is thought to
have branched off earlier than the squirrel clade, which makes it suitable
as an outgroup. Including an outgroup allows determination of the
order of evolutionary change at each site in the DNA sequence. In turn,
this allows determination of the temporal order of branching events (i.e.
which squirrel clade branched off first, second, etc.).
- 3pts. Do the results suport
the traditional claim that flying squirrels form a group relatively
distant from all other squirrel lineages? No. Flying squirrels form a sister group to North American
Tree squirrels, and are nested well within the squirrel family. This
clearly indicates they are closely related to the N. American tree
squirrels (and that they arose later in the evolution of squirrels rather
than earlier). [If they had arisen earlier, they would be on a branch that
comes off earlier, like that of Ratufa].
- Bishop
thinks that the congruence of major diversification events and major
changes in sea-level or formation of land bridges is remarkable. One
reason is that this congruence required agreement of several independent
types of data: 1) Identifying the nature and timing of
geological/sea-level changes based on the geologic & biological
(non-squirrel) record; 2) The branching pattern of the phylogeny, based on
three different genes; and 3) the calibration of DNA substitution rates
using fossil squirrel ancestors (note, this last item really requires
several independently collected types of data – fossil position in
geologic record, radiometric dating of fossil age, and DNA substitution
rates on each branch).
Questions : 4a) 4pts. What
do these congruences suggest about factors
affecting squirrel diversification? Your answer should refer to figure 3
as an example.
The
fact that these diversification events co-occur with major geographic
changes suggests a causal relationship between geographic changes and
squirrel diversification. [That’s right, squirrels, among the most amazing
of nature’s engineers, caused major changes in sea-level and built
land-bridges….;>)]. Each of these geographic changes allowed
colonization of a new region by squirrels. These regions likely offered
ecological opportunities with low competition for the colonists, and this
likely resulted in the formation of new species (and genera). The fact
that sea-level change later isolated island colonists prevented ongoing
migration and also promoted divergence.
The correspondence
between sea-level change, colonization, and diversification is beautifully
illustrated by figure 3. The timing of the lowest sea level in the entire Pre-pleistocene Cenozoic [65mya-1.5mya]
corresponds precisely to the timing (estimated by molecular clock) of the base
of explosive diversification of squirrel genera on the Sunda
shelf islands. Also at this time, the only lineage to cross Wallace's line
branches off. [Wallaces Line dramatically
separates Asian and New Guinea/Australian faunas].
To sum up: In the words
of the authors (last sentence in abstract), “These precise correspondences
point to an important role for global change in the diversification of a
major group of mammals.”
4b) What does this study suggest about scientist's ability to reconstruct
pre-historical events? You may wish to reference the 7 criteria for
supporting scientific theories or hypotheses.
[Note: The best way to answer was to try to apply
the criteria. It may be the case on questions like this that not all
criteria apply. The study wasn't intended to be a test of the hypothesis
that we can re-construct pre-historical events, because this fact has been
demonstrated ad nauseum
by scientists (and also by the actors on C.S.I.).
However, but I wanted to get you to think about it re-constructing history
and to apply our evaluation criteria.]
4pts.
- If
it better matches the data from a fair test.
The phylogeny
itself, including the scaling of branch lengths to represent time via a
molecular clock, is a hypothesis about history. The test of that
hypothesis is whether the diversification events correspond closely to major
changes in earth history that allowed access to new geographic regions. It
passes this test to an extraordinary degree.
- If
it is confirmed by multiple independent fair tests
Its not clear to me
if there are multiple independent tests, or if we should just regard it
all as one really strong test, but there are a number of facts that could
be regarded as additional tests. For example, if lowered sea level really
promoted colonization and diversification of squirrels on the Sunda Shelf islands, we might expect that other
animals experienced the same thing. The authors point out the fact that flightless
grasshoppers divergence has been pegged to the same time. Another example is that the earliest
known tree squirrel fossils in Africa correspond closely to the base of
the diversification of these squirrels in Africa.
- If
initially conflicting data can be shown to agree I'm not sure we have any
cases of that here.
- If
there are no conflicting lines of evidence
One conflicting
line of evidence is that Rheithosciurus, a giant squirrel from Borneo, nests
very solidly within N. American tree squirrels. The authors choose to
treat this as an anomaly in need of explanation, rather than an indication
that the entire analysis is suspect [one certainly wonders if they mixed
up a sample!]
- If
the fair test that supports it is particularly strong
In my opinion, the test
for correspondence of branching events and land-bridge formation is an
extremely strong one, because it required so many independent sources of
data to correspond exactly. The timing of sea-level change and land-bridge
formation comes from a completely separate scientific discipline with many
independent authors, methods, and data sets. For the diversification times
to correspond to geologic events, branch scaling via molecular clock
required a) the right # of substitutions per branch; b) that the earliest
squirrel fossil be found at a certain layer of the geologic column [also
done by different scientific discipline]; and c) that the radiometric
dating methods obtain accurate dates.
- If
the alternatives are seriously defective conceptually
I.e. no data suggest, or
it is untestable
They are, but this
is not discussed in the paper.
- If
the overall weight of evidence is greatly in its favor
Again, it is, but
its not discussed in the paper.