BIOGEOGRAPHY/PALEOECOLOGY, Fall 2018
SECOND PROBLEM SET

PHYLOGENIES:

1. Here are 14 species of a type of organism known as caminalcules..  Your job is to propose a phylogeny linking them.  Assume the group, as a whole, is 'good' monophyletic group, and all of the types shown represent distinct, living populations.  Proceed by choosing potentially useful 'characters' and identifying two or more 'character-states' (for example, number of eyes might be a character, and character-states could be 0, 1, or 2.  OR you might say character is just 'eyes' and states are 'present' or 'absent'; then number of eyes could be used as another character only for those with eyes present.  
    - Choose at least six characters to work with; list them with the observed states.  
    - Decide how you will interpret states as plesiomorphic or apomorphic (explain your reasoning) (ASSUME that these are vertebrates remotely related to amphibians -- that is, you could use a salamander or a frog as an 'out-group' to help identify plesiomorphic states).
    - Use shared apomorphies ('synapomorphies') to construct an 'optimal' cladogram/phylogeny, trying to minimize the number of state conversions (evolutionary events) required. (i.e., a mazimum parsimony tree).  Identify end-points ('present time') on your cladogram by the numbers below.
    - Identify, on your cladogram, branches where state changes are inferred.
    - Suggest  a division of these 14 species into taxonomic sub-groups (you can give them names if you want).
    - If your phylogeny involves convergences or reversions, point these out.
    - Thinking of your cladogram as a phylogenetic hypothesis, discuss what kinds of additional information (beyond the observed morphology of the creatures) could allow you to test it more rigorously. (Keep in mind that there might be other topologies that are as parsimonious -- or nearly so -- as yours, and parsimony is a somewhat arbitrary criterion.  Also, that  different assumptions about what's ancestral/derived might change everything...)

(you can hand in your cladogram on paper if you prefer.)



2. The diagram below is a proposed 'family tree' or cladogram for squirrels. (J.M. Mercer and V. L. Roth,. 2003. The Effects of Cenozoic Global Change on Squirrel Phylogeny. Science 299:1568-1572) Each terminal branch is one living taxon of squirrels (except for Aplodontia, which is weird rodent called a mountain beaver, and is used here as an 'out-group').  Remember that no extinct taxa are shown. Don't worry about the technological details in the caption; just assume that the relationships shown are correct.  Answer two of the following:
    A. The tree shows two 'basal' lineages (or branches) – Sciurellus and Ratula – that originate very near the 'root' of the squirrel tree – their common ancestry with other squirrels is quite ancient ; each of these two genera has only one species. the three more recently diverging branches each have many genera.  The researchers suggest that these two ancient 'monotypic' lineages required an explanation because it seemed odd that a single species would persist so long 1) without going extinct and 2) without diversifying like the other branches.  Offer an explanatory hypothesis or two.
    B. The researchers say the big diversification of squirrels was rather sudden and more or less simultaneous in all the major branches, and happened at the end of the Eocene at a time of "significant climate change and extinction.”  Why would it make sense that such a dramatic (apparent) diversification within a lineage should coincide with such events?
    C. The little pictures indicate branches that are tree-squirrels, ground squirrels (like chipmunks; that's the little prairie-dog-like symbol in group IV), and flying squirrels; ground and flying squirrels each occur in only one main branch; tree squirrels occur in all three.  What do you think that tells you about the history of these three styles of being a squirrel?


OTHER STUFF (you can do THREE of these -- or do all four and I'll 'score' the best 3):

3.  Isolated, small populations with ranges restricted to relatively small, strictly bounded habitat patches (like an island, or a desert oasis) appear to undergo more rapid selective/evolutionary change than do large species/populations distributed over large geographical areas. Offer at least one hypothesis for why this should be so. (hint: you might consider relationships between selective evolutionary change and non-selective change like ‘gene flow’ or genetic drift -- genetic change that's not directly related to adaptedness.)

4. Dawkins makes a clear distinction between 1) the tendency for Darwinian natural selection to produce specialized  'survival machines' that serve as vehicles for the replicators (genes) that build them, and 2) the potential role in the grand picture of a property he calls 'evolvability' -- the potential, within a lineage or clade, for generating new traits on which selection might act.
A) If individual lineages within a larger taxon or clade tend to become more adaptively specialized over time, what are the likely consequences for particular species lineages over time?  What effect, if any, might this process or tendency have on the replacement of one major group by another?
B) What properties might make an organism "good at evolving"? (these might be at genetic or phenotypic level...).
C) Could the property of 'evolvability' (the potential for rapid evolutionary change) confer fitness benefits on individual organisms?  If not, is there any reason to think that there might be a tendency, over time, for life forms to become more 'evolvable'? 

5. Offer two general hypotheses for why there are no wheeled  mammals (except human extended phenotype); if flight had not already evolved in mammals, would similar reasoning have applied for why there were no flighted mammals?

6. Nearly two million years ago, Homo erectus (or, according to more recent taxonomies, Homo of some pre-sapiens species that should have a different name....) spread out of Africa across all of southern Eurasia. By 100,000 years ago or so,   Homo erectus was gone, and Homo sapiens occupied more or less the same region.  Two general scenarios for this replacement have been proposed:
    The 'Out-of-Africa hypothesis' proposes that H. sapiens originated in east Africa, where our species differentiated from ancestral H. erectus (or similar), and spread outward, replacing H. erectus populations (presumably through competition, but predation not excluded...) as they went. Thus, all H. sapiens share a common ancestor in the earliest H. sapiens populations in Africa.
    The 'Multiregional hypothesis' suggests that H.erectus populations throughout this range were gradually modified, by common selective pressures and as a consequence of frequent immigration/gene flow among populations, so that H. sapiens developed in continuity with H. erectus throughout its range.  In this scenario, the ancestors of, for example, east Asian H. sapiens would be largely or entirely east Asian  H. erectus, and the most recent common ancestor of all H. sapiens would be much earlier, in the H. erectus lineage.
    Address the following questions:
A) Do either of these hypotheses seem more plausible in principle, given what you understand of the processes of natural selection and speciation (explain)?
B) What sorts of archeological/paleontological evidence might be useful in discriminating between the two hypotheses (i.e., do the hypotheses yield different predictions in terms of expected patterns)?
C) What sorts of genetic relationships among existing humans are suggested, and how might these be used to assess the hypotheses?