Bioinformatics Worksheet

QUESTION 1

1. What set of relationships are now shown?

   		cnidarians are sister to protostomes
   		chordates are sister to cnidarians
   		cnidarians and echinoderms evolved from chordates
   		chordates are sister to echinoderms

1.5 points

QUESTION 2

1. What is the Newick format of the correct tree?

   		((((Bbelcheri,Hsapiens),Aplanci)),(((Hvulgaris,Myessoensis),(Dgigantea,Nvectensis))));
   		(((((Bbelcheri,Hsapiens),Aplanci),Myessoensis)),(((Hvulgaris,Nvectensis),Dgigantea)));
   		(((((Bbelcheri,Hsapiens),Aplanci),Myessoensis)),((Hvulgaris,(Dgigantea,Nvectensis))));
   		(((((Bbelcheri,Myessoensis),Hsapiens),Aplanci)),((Hvulgaris,(Dgigantea,Nvectensis))));

1.5 points

QUESTION 3

1. What is the log likelihood of the optimal tree that IQ-TREE found?

1.5 points

QUESTION 4

1. Which amino-acid exchange rate model was did we use?

   		LG
   		Blosum62
   		cpREV
   		VT

1.5 points

QUESTION 5

1. Which amino acid frequencies did we use to estimate the tree?

   		+F, empirical AA frequencies from the data.
   		+FO, ML optimized AA frequencies from the data.
   		+FQ,Equal AA frequencies.
   		AA frequencies are given by the model

1.5 points

QUESTION 6

1. Which rate heterogeneity did we use to estimate the tree?

   		+I+G invariable site plus discrete Gamma model
   		Gamma with 5 categories (G5)
   		+I+R invariable site plus FreeRate model.
   		FreeRates with 4 categories (R4)
   		FreeRates with 10 categories (R10)

1.5 points

QUESTION 7

1. What is the least frequent amino acid in the alignment?

   		W (Tryptophan)
   		S (Serine)
   		R (Arginine)
   		L (Leucine)

1.5 points

QUESTION 8

1. What is the most frequent amino acid in the alignment?

   		R (Arginine)
   		W (Tryptophan)
   		S (Serine)
   		L (Leucine)

1.5 points

QUESTION 9

1. Based on our discussion of unroooted trees, and your visualization of the unrooted tree, what is the oldest divergence event on the unrooted tree?

   		There is no time on this tree, so we can’t tell.
   		The divergence between a large clade of 59 genes and another large clade of 90 genes. The smaller of the two clades includes genes such as GBX, MOX, and MNX (motor neuron and pancreas homeobox).
   		The divergence between Bilaterians and Cnidarians.
   		The divergence between dlll (DISTALLESS) proteins and all other hox proteins.
   		The divergence between Nvectensis.LOC5518689 homeobox protein engrailedli (homeobox protein engrailed-like ceh-16) and all other proteins.

1.5 points

QUESTION 10

1. Compare the cladogram and phylogram. What has changed in the cladogram, compared to the phylogram?

   		The lengths of the branches in the tree are all equal.
   		Branch lengths have all been multiplied by a factor of 2.
   		The branch lengths have been calibrated with a molecular clock so they are proportional to time.
   		Branch lengths are now proportional to the number of substitutions along each branch.

1.5 points

QUESTION 11

1. Carefully examine the midpoint rooted tree. What is the oldest divergence event on the midpoint rooted tree?

   		There is no time on this tree, so we can’t tell.
   		The divergence between Bilaterians and Cnidarians.
   		The divergence between a large clade of 59 genes and another large clade of 90 genes. The smaller of the two clades includes genes such as GBX, MOX, and MNX (motor neuron and pancreas homeobox).
   		The divergence between dlll (DISTALLESS) proteins and all other hox proteins.
   		The divergence between Nvectensis.LOC5518689 homeobox protein engrailedli (homeobox protein engrailed-like ceh-16) and all other proteins.

1.5 points

QUESTION 12

1. How many genes are included in the clade that includes the common ancestor and all the descendents of any gene labelled in the phylogeny as “barHlike” or “BarHlike”? (The hyphen has been removed; other places this is: BarH-Like).

1.5 points

QUESTION 13

1. Compare the **species** phylogeny you made to the gene phylogeny. In particular, examine the area of the phylogeny around the *Nematostella* Hox-C5 gene. Are the species relationships reflected in the gene tree?

   		There is no consistency between the known species relationships and the gene family relationships in the tight junction protein clade.
   		Yes, all species relationships are reflected perfectly in tight junction protein clade, although some species contain multiple gene copies.
   		There is strong evidence of horizontal gene transfer in this tree.
   		The species relationships are sometimes observable, but typically one or more species seems to be missing a gene or one or more species has mulitple copies of a gene.

1 points

QUESTION 14

1. Locate the Hox-C5 gene in humans and the Hox-C5 gene in Nematostella. What does the tree tell you about the relationship between these gene copies?

   		It is not possible to determine the relationships between Hox-C5 in human and Nematostella from this phylogeny.
   		The genes called Hox-C5 in human and Nematostella are clearly in distant gene lineages according to the phylogeny, and likely should be given different names to reflect this.
   		There has been a single duplication and deletion event, but otherwise these are the genes.
   		The are one to one orthologs.