Chapter 26 Homework

Animals that possess homologous structures probably _____.

evolved from the same ancestor

A human is classified in domain _____ and kingdom _____.

Eukarya ... Animalia

A rose bush is classified in domain _____ and kingdom _____.

Eukarya ... Plantae

Based on the results of the 2000 study, how should the portion of the tree extending from branch point 7 be altered?

- Mainland brown bear <ABC brown bear / polar bear

Why do researchers use rRNA in investigations of relationships between taxa that diverged hundreds of millions of years ago?

DNA coding for rRNA changes relatively slowly.

In the five-kingdom system, prokaryotes are placed in the kingdom _____.

Monera

In the five-kingdom system, which kingdom consists primarily of unicellular eukaryotes?

Protista

The tree includes the most recent common ancestor of all living species of bears (branch point 1). What does this tell you about this phylogenetic tree?

This phylogenetic tree is rooted.

By definition a clade is _____.

monophyletic

Molecular clocks are based on the idea that _____.

on average neutral mutations arise at a constant rate

There is(are) _____ eukaryotic domain(s).

one

Now that you have a distance matrix, the next step is to show these relationships graphically with a phylogenetic tree. There are a number of ways to make a phylogenetic tree, but the simplest method uses the information from a distance matrix to cluster more similar samples together into a related group, also known as a clade.In the trees below, the horizontal distance along each line reflects the percent difference between each of the samples. The scale beneath each tree tells you how far along a branch you have to go to have a 0.01 (1%) difference in sequence. Which of the following trees is the best match for the relationships shown in the distance matrix?

- O. nerka < O.keta / O.gorbuscha <Test sample / O. tshawytscha < O. kisutch / S. salar

Now that you know the sequence of the COI gene for your salmon sample, the next step is to align your sequence with standard sequences from each species of salmon. The sequences are lined up next to each other, with gaps introduced to adjust for any insertions or deletions in the DNA sequence from one individual or species to another.A sequence alignment is shown below for the beginning of the COI gene, with standard sequences from the Barcode of Life project. In this exercise, you will align part of your test sample sequence with the alignment below. Each label below contains the same portion of your test sample sequence, but each label starts the alignment in a different position. Drag each one to the target to see which one yields the best alignment.

------CGGCACCGCCCTAAGTCTCTTGATTCGAGC

Once you have obtained your salmon sample from a local store, you need to isolate the DNA from it and make many copies of the COI gene using the polymerase chain reaction (PCR). For a review of how PCR works, see Hint 2. Place the following steps of the DNA extraction and PCR process in the correct order. Not all labels will be used.

1: Cut out a clean section of muscle tissue. 2: Disrupt cell, nuclear, and organelle membranes to release their contents into solution. 3: Eliminate non-Dna molecules using wash buffers. 4: Add Taq, primers, and dNTPs to the DNA sample. 5: Use a thermal cycler to denature, anneal, and extended the target sequence (the COI gene) in 35 cycles.

Examine the trace for the 10-base sequence of the COI gene shown above. Enter the sequence of nucleotides for this section of the COI gene. Use A for adenine, C for cytosine, G for guanine, and T for thymine (e.g., ACGT...). For help reading the trace, see Hint 1.

5'- TACTGATTCG -3'

According to this tree, is the sun bear more closely related to the sloth bear or the polar bear?

According to

Prokaryotic cells are found in the domain(s) _____.

Bacteria and Archaea

Let's take a closer look at how the primers work in PCR. During the denaturing step of PCR, the normally double-stranded DNA is separated by heat into two single strands. These single-stranded DNA molecules are now ready for primers to bind to the appropriate locations within the COI gene. The forward primer is the one that binds to the template strand of the COI gene, while the reverse primer binds to the non-template strand. Both primers are required for Taq DNA polymerase to copy the region in between.Most primers are 18-21 bases long, but for simplicity, we're only showing 10 bases of the COI gene primers here. In the diagram below, place the correct forward and reverse primers into position. The possible forward primers are shown in pink; the possible reverse primers are shown in blue. (See the Hints if you need help getting started.)

Red: 5' - ACATTGGCAC - 3' Blue: 3' - ACTAAGAAAC - 5'

Now that you have aligned your sample's sequence to the standards, you can determine the number of differences between your sequence and each of the standards. To calculate the percent difference between the test sample sequence and each of the standard sequences, count the number of bases that are different between the test sequence and the standard sequence; then divide that number by the total number of nucleotides, and multiply by 100. For simplicity in this question, you will only consider 20 bases, but keep in mind that the full alignment is 640 bases long. For the 20-base sequences shown here, calculate the percent difference between your test sample and each of the species standards.

Salmo: 0 O. gorbuscha: 20 O. keta: 25 O. kisutch: 15 O. nerka: 15 o. tshawytscha: 20

Now let's evaluate the results for the other seven samples your class collected, designated as samples A through G in the phylogenetic tree below. Keep in mind that these samples were processed the same way your test sample was: the DNA was extracted, the COI gene was amplified using PCR, the COI gene was sequenced and aligned to standards, and the percent differences were calculated and used to construct this tree. Using the phylogenetic tree, identify whether each of the sample sequences was labeled correctly or was mislabeled.

Sample A: sold under correct name Sample B: Pacific-for-Pacific Substitution Sample C: sold under correct name Sample D: sold under correct name Sample E: Pacific-for-Pacific Sunstitution Sample F: sold under correct name Sample G: Atlantic-for-Pacific Substitution

In this exercise, you will use the cytochrome c oxidase I (COI) gene to investigate relationships among salmon species. (This gene encodes a protein that functions in the mitochondrial electron transport chain.) You will compare the COI gene sequences from your salmon test samples to the standard sequences for each salmon species. In order for the COI gene to be useful for distinguishing among the different salmon species, which three statements must be true?

The COI gene must be conserved enough that the sequences can be aligned for comparison. The COI gene must be variable enough that there are at least a few differences between each salmon species. The COI gene must be conserved enough that the same PCR primers work for all the species being tested.

Which observation supports the position of eukaryotes at the convergence of the "ring of life"?

The nuclear genome of eukaryotes contains genes from archaeans and from bacteria.

In the two-kingdom system, why were fungi classified in the kingdom Plantae?

They are sedentary.

Based on the revised branch of the tree, what kind of group do brown bears plus ancestral species 7 represent?

a paraphyletic group

Which branch point represents the most recent common ancestor of all bears?

branch point 1

Which branch point represents the most recent common ancestor of the sloth bear and the spectacled bear?

branch point 2

Which branch point represents the most recent common ancestor of the Asian black bear and the brown bear?

branch point 4

Fossil evidence indicates that some dinosaurs had feathers. If birds are indeed descended from dinosaurs, feathers are what kind of character?

shared ancestral character

Which of the following groups of species is a monophyletic group, or clade?

sun bear, Asian black bear, American black bear, ancestral species 5, ancestral species 6

Identify the sister taxon to the polar bear.

the brown bear

Which species is the basal taxon in this tree?

the giant panda