Phylogenetic Trees (Biointeractive)

Question 1

More distantly related species have had more time elapse since they shared a *; therefore, they have had more time for ** to accumulate in their DNA. Closely related species have had little time to accumulate ** since their last common ancestor, so their DNA sequences are much more **.

Answer 1

• common ancestor
• mutations; mutations
• similar

Question 2

More closely related species tend to share more ** and similar ** than more distantly related species

Answer 2

• anatomical features
• DNA sequences

Question 3

Scientists classify species based on shared features. The more features that are shared, the more likely the species are to be *** in evolution.

Answer 3

closely related

Question 4

Shared anatomical features, such as the presence of a *** , are used to study relationships. But some features, such as the presence of wings, make comparisons difficult or confusing.

Answer 4

backbone

Question 5

Lizards and snakes both have backbones and are classified as vertebrates. Anatomy allows physical trait comparisons but does not allow ***.

Answer 5

genetic comparisons

Question 6

** can also be compared to study relationships.
In sequence comparison, as in anatomical comparison, we look for ** and ** to deduce relationships.
When done properly, sequence comparison can be more ** and less ** than anatomical comparison.

Answer 6

*Molecular sequences (DNA, RNA, protein)
* similarities and differences
* objective and ambiguous

Question 7

** has made many DNA sequences from many different organisms available. It is now possible to directly compare the sequence of genes among many closely or distantly related plants, animals, and microorganisms.

Answer 7

Rapid DNA sequencing technology

Question 8

Evolutionarily related organisms share a common ancestor with an **.
As organisms evolve and diverge, their DNA sequences accumulate differences, also known as **.
Two common types of mutations are called ** and **.

Answer 8

• ancestral DNA sequence
• mutations
• SNPs and Indels

Question 9

One common type of mutation that can be used to track common ancestry is the **
- a change of one DNA base pair into another.

Answer 9

single nucleotide polymorphism (SNP)

Question 10

Another useful class of DNA mutations for tracing relatedness are **. These are **in which one or more nucleotide pairs in a DNA strand are lost or gained.

Answer 10

• insertions and deletions, or “Indels” for short
• mutations

Question 11

Before you can compare sequences, you need to make sure that you are comparing stretches of DNA that are **—i.e., that they are **.
Two sequences need to be *** so that related parts of sequences are lined up against each other and compared.

Answer 11

• evolutionarily related
• homologous sequences
• aligned

Question 12

Comparing non-homologous sequences to determine evolutionary relationships among species is like comparing ***

Answer 12

apples to oranges.

Question 13

There are several different computer programs that can generate an alignment. All of them try to ** the number of matches among all sequences being aligned by ** the positions of the sequences relative to one another and/or by ***.

Answer 13

• maximize
• changing
• adding gaps

Question 14

To compare two DNA sequences, they must be aligned so that the ***.

Answer 14

greatest number of nucleotides match up

Question 15

Each line is one **, and each column is a **.
An *** indicates that all the letters in that column match.

Answer 15

• DNA sequence
• position in the alignment
• asterisk

Question 16

An *** in an alignment is a position where the letters in a column do not match.

Answer 16

Single Nucleotide Polymorphism (SNP)

Question 17

Because an indel is an ** or ** of a pair of DNA bases, an indel in an alignment will be represented by a *** in the alignment.

Answer 17

• addition or removal
• gap (sometimes a dash)

Question 18

You can align **. You might want to compare many sequences if you are trying to determine evolutionary relationships among many organisms.

Answer 18

more than two sequences

Question 19

There are several different ways to create a phylogenetic tree.
One method finds the ** (and therefore likely to be most closely related) sequences in an alignment and then ** to find less closely related sequences.

Answer 19

• two most similar
• works backward

Question 20

Within a tree, the ** represents a species or sequence, or a group of related species/sequences.

Answer 20

end of each branch

Question 21

A place where two branches split apart is called a ** and represents the ** of all the species on those branches.
There may or may not be a shape (like a circle) at a branch point.

Answer 21

• branch point
• most recent common ancestor

Question 22

Some trees have a single branch point from which all branches originate. This is called the ** . The ** closest to the root of the tree represents the most recent common ancestor for all organisms in the tree.

Answer 22

• root of the tree
• node

Question 23

Trees can also be unrooted. These trees only show you ** among compared organisms and do not tell you where the ** is among a group of species.

Answer 23

• relative relationships
• common ancestor

Question 24

** are conveyed by how the branches are arranged and connected to one another. In other words, a tree can be thought of as a *** that can rotate around each node.

Answer 24

• Evolutionary relationships
• mobile

Question 25

Phylogenetic trees can also be drawn with their *** or ***. Again, this does not change the information contained in the tree.

Answer 25

* root above * to the side of the branch points

Question 26

Phylogenetic trees made using DNA sequences are usually very similar to trees made using other evidence, such as ***. In this way, trees can be predictive of traits shared by organisms. Trees can also help clear up **** generated by other methods, such as comparative anatomy.

Answer 26

* comparative anatomy * ambiguities or uncertainties