Intro to Biological Anthropology Homework II Fall 2024C/C++

Java Python Intro to Biological Anthropology

Homework II

Fall, 2024

Part 1: Exercise in Sytematics/Phylogenetic Biology

Once long ago, mighty herds of snuphalupaghi roamed the sidewalks and back alleys of Sesame Street. Seven different species of this massive and impressive family of beasts have been identified in the fossil record, and all are believed to be extinct. Reconstructing the evolutionary history of this fascinating group of creatures has nonetheless been a difficult task. Some, but not all, of the species were contemporaries of one another.

Analysis of the stratigraphy in which the fossils were found reveals that one of the species, snuphalupaghous generalis (species A – see below) was the oldest. It surely provided the  root stock of an adaptive radiation of snuphalupaghi that quickly diversified to dominate a  Sesame Street as yet unpopulated by Oscar the Grouches, Cookie Monsters, Big Birds, Elmos, and other sundry Jim Henson creations.

Your job, as curator of the National Museum of Muppetology, is to reconstruct the evolutionary history of the snuphalupaghi using what little data we have about them. Fortunately, the fossil record has allowed us to track three sets of homologous features in all seven of the species. These three sets of homologous traits and the different forms of each found in the seven species of snuphalupaghi are as follows:

Molar Enamel:

Thick; Thin; Medium

Shape of the Orbits (eye sockets of skull)

             Round, Square

Tail Shape

Curly; Straight, None

The seven species of snuphalupaghi along with their associated traits are as follows:

Species:	A	B	C	D	E	F	G
Enamel:	Medium	Medium	Thick	Thin	Thick	Thick	Medium
Orbit:	Round	Square	Round	Square	Round	Round	Square
Tail:	Curly	Curly	Curly	Straight	Curly	Curly	None

The muppetologists who excavated these seven fossil species were careful to contextualize them within Sesame Street’snow well understood stratigraphy. This, of course, gives us a clear picture of the relative ages of the different fossil species. 

Closest to Surface                          D        E        F        G                  

Mid-level                                            B                     C                      

Deepest Stratum                                             A                                  

Your answer will be given in the form. of a branching tree diagram (phylogenetic tree) that represents the evolutionary (including likely ancestor-descendent) relationships. Be sure to label each node of your diagram with the appropriate letter of each species.  You may assume three things in your analysis.

1) Traits of the same type are homologous – not analogous – structures.

2) Once a trait is lost, it is notre-evolved in descendant lineages.

3) Evolutionary lines might bifurcate, trifurcate, or even lead to a single new species through anangenic change.

The stratigraphy given above will allow yo Intro to Biological Anthropology Homework II Fall, 2024C/C++ u to determine which species were older and which were contemporaries of one another. Assume a complete fossil record and create the most parsimonious phylogenetic tree. The key to this exercise lies in differentiating between ancestral and shared-derived traits to hypothesize the evolutionary (phylogenetic) relationships between the fossil species of snuphalupaghi.

Report Your Phylogenetic Tree Here (28 points)

Part 2: Who Am I? (16 points)

For each of the following sets of traits and descriptors, give the name of the most specific primate taxon that possesses ALL of the given features. In other words, don’treport a suborder or superfamily name if a family or even a genus is sufficient to include all primates sharing the three sets of traits. In each case, you will need to be no more specific than the taxa Ihave asked you to know for the final exam.

1)        fused mandibular symphasis

post-orbital septum (full post-orbital closure)                                                           

three premolars per quadrant of mouth

2)        full 360 degree rotation of shoulder

no tail                                                                                                                         

fist walking

3)        fused frontal bone

sectorial premolars                                                                                                    

quadrupedal anatomy

4)        post-orbital bar with no post-orbital closure

dental comb                                                                                                                

all members live in Madagascar

Part 3:  Molecular Evolution Exercise

Below are reported nucleotide sequences for an intron in the same gene for 4 different species of animals.

A

C G T A A T A C T A G G T A T T C A T T A C T G G T G C T G A T A C G C G C G

B

C G T G A C A C G A G G A A T T C A G T T C T G T T G C T G C T A G G C C C G

C

C G T A A T A C G C G G T G T T C A G T A C T G G T G C T G A T A G G C G A G

D

C G T A T C G A G A T G T A T A C G G T A C A G G T A G T C C T A G C C G C G

Difference Matrix and Topology (36 points)

Report the differences you’ve observed between the nucleotide sequences of the different species in the matrix below.

	A	B	C	D
A
B
C
D

Use the differences in your matrix to create a rooted tree topology showing the evolutionary relationships between creatures A,B, C, & D. Write your topology out on the chart below