Chapter 23 - Evolution

Question 0

Phylogeny

Answer 0

The history of descent with branching, much like a geneology of species.

Question 1

On a phylogenetic tree, what does the tip of a branch mean?

Answer 1

A present-day species.

Question 2

What is the aim of taxonomy?

Answer 2

To recognize and name groups of individuals as species, and, subsequently, to group closely related species into the more inclusive taxonomic group of the genus and up through the ranks.

Question 3

What does the taxonomy of a species do?

Answer 3

It communicates information about the features each group possesses.

Question 4

On a phylogenetic tree, what does a node represent?

Answer 4

The last common ancestor of sister species.

Question 5

When did life emerge in its simplest form?

Answer 5

3.5 Billion years ago.

Question 6

What is the aim of phylogenetics?

Answer 6

To discover the pattern of evolutionary relatedness among groups of species or other groups by comparing their morphological or molecular features, and to depict these relationships as a phylogenetic tree.

Question 7

What is a sister group?

Answer 7

groups that are more closely related to each other than either of them is to any other group.

Question 8

Can nodes be rotated on a phylogenetic tree?

Answer 8

Yes. This doesn’t change the relationships or the sister groups.

Question 9

What is the purpose of a phylogenetic tree?

Answer 9

A hypothesis about the evolutionary history of the species.

Question 10

What is a taxon?

Answer 10

A “group” that is named by taxonomy.

Question 11

How can you tell if two species share a common ancestor?

Answer 11

By sharing a node on the tree.

Question 12

What is the tree of life?

Answer 12

A phylogenetic tree for all species.

Question 13

Refer to figure 23.2. Are birds a monophyletic, paraphyletic, or polyphyletic group?

Answer 13

polyphyletic

Question 14

What is a monophyletic classification?

Answer 14

Where all members share a single common ancestor not shared by another species or group of species. Monophyletic classification is the gold standard of naming to maintain the simplest possible classification of a species.

Question 15

What is a paraphyletic classification?

Answer 15

A taxon that includes some, but not all of the descendants of a common ancestor. It’s where you can make 2 cuts at nodes on a tree.

Question 16

What is a polyphyletic classification?

Answer 16

Groupings that do not include the last common ancestor of all members. It’s essentially a mistake made by taxonomists by classifying taxa according to morphological characteristics rather than evolutionary characteristics. It’s when they do not have a common ancestor.

Question 17

List the taxonomic classification from most comprehensive to least.

Answer 17

Domain
Kingdom
Phylum 
Class
Order
Family
Genus
Species

Question 18

What are the three domains of the tree of life?

Answer 18

Eukarya, Bacteria, Archaea

Question 19

What is the definition of a “character”?

Answer 19

The anatomical, physiological, or molecular features that make up organisms. In order to be useful for phylogenetic reconstruction, they must vary among but within a species and have a genetic basis.

Question 20

What is a synapomorphy?

Answer 20

A shared derived character - a homology shared by some, but not all, members of a group.

Question 21

What are character states?

Answer 21

Several observed conditions that can be present or observed.

Question 22

Why would character states be similar?

Answer 22

1. The character state was present in the common ancestor of the two groups and retained over time because of common ancestry
2. The character state independently evolved in the two groups as an adaptation to similar environments (convergent evolution)

Question 23

What is the difference between homology and synapomorphy?

Answer 23

A Homology is a character that is similar in different species because of descent from a common ancestor;
A Synapomorphy is used in cladistics to build a phylogenetic tree - it is a homologous trait that is shared by some but not all members of a group.

Question 24

What are homologous characters?

Answer 24

Characters that are similar because of common ancestry.

Question 25

What are analogous characters?

Answer 25

Similarities in characters due to convergent evolution.

Question 27

If dolphins and bats both utilize echolocation, is this a homologous or analogous character?

Answer 27

It is analogous. Dolphins and bats do not share a common ancestor, but they acquired these traits due to convergent evolution (filling a niche).

Question 27

What are cladistics?

Answer 27

Phylogenetic reconstruction on the basis of synapomorphies.

Question 28

What is parsimony? Provide an example.

Answer 28

Choosing the simpler of two or more hypotheses to account for a given set of observations.
Example: Choosing a phylogenetic tree that requires four changes as the support over the phylogeny that requires five changes.

Question 29

True or False:

All phylogenetic hypotheses are correct.

Answer 29

False. Phylogenetic hypotheses can be strongly or weakly supported. When weakly supported, biologists commonly depict the relationships as unresolved and show multiple groups diverging from one node, rather than just two.
This shows not that this is how speciation occurred, but there is a large gap of evidence to support definitive placing of species on a tree.

Question 30

What do fossils add to a phylogenetic tree?

Answer 30

1. Fossils calibrate a phylogenetic tree, helping to specify when branching occurred.
2. Fossils also provide our only record of extinct species.
3. Fossils place evolutionary events in the context of Earth’s dynamic environmental history, showing major events such as natural disasters and mass extinctions.

Question 31

What exactly is a fossil?

Answer 31

A fossil is the remains of once-living organisms that have been preserved through time in sedimentary rocks.

Question 32

Besides cladistics, what is another way to construct a phylogenetic tree?

Answer 32

Another method is based on distance. This assumes that if the rate of evolution is constant, descendants of a recent common ancestor will have had relatively little time to evolve differences, whereas the descendants of an ancient common ancestor have had a lot of time to evolve distances. In other words, low distance=similarity, which is a result of a common ancestor.

Question 32

How would a phylogenetic tree be able to tell if Patient Zero infected Patients A, B, C, D… with HIV?

Answer 32

HIV samples would be taken from all subjects, and their nucleotides sequenced at a specific loci of the virus to compare the similarities. Those that cluster with that of Patient Zero would be proven to have contracted the virus from Patient Zero, while those patients that do not cluster with Patient Zero would have contracted the virus from a different source.

Question 34

What is required for fossilization? How does it occur?

Answer 34

Fossilization requires the burial of the organism (covering in sand, mud, silt, etc.) If burial doesn’t happen, the organism just degrades and is recycled in biological processes.
Over time, accumulating sediments harden into sedimentary rocks and preserved.
Note that fossilization occurs more readily for marine life because organisms are more likely to be buried than those at a high and dry elevation. Additionally, the composition of the original organism determines how well it will be preserved.

Question 35

True or False:

Molecular data, both in DNA and RNA, forms the basis for phylogeny.

Answer 35

False. Molecular data is an important development that better and more accurately indicates history, but it does not replace comparative morphology in determining phylogeny.

Question 36

How is molecular data used to help establish a phylogenetic tree? Provide an example.

Answer 36

Similar to morphological data, through comparison to an outgroup, we can identify derive and ancestral molecular characters, and generate phylogeny on the basis of molecular synapomorphies.
Example: The sequencing of molecular structure for viruses to identify the phylogeny, which in turn can aid in the development of a treatment for similar viruses and help better understand how these viruses operate.

Question 37

What are three types of fossils and what are they composed of?

Answer 37

Trace fossils - tracks and trails of organisms as they move about.
Molecular fossils - fossils of biomolecules - like lipids and cholesterol, sterols, bacterial, lipids, etc are preserved. DNA usually breaks down rather quickly.

Question 38

What are some examples of well-known fossils that are extremely well preserved?

Answer 38

Burgess Shale - Cambrian period fossil preserved on the bottom of the sea floor in British Columbia.
Messel Shale - 50 myo fossil that was preserved in Germany in O2-poor muds which preserved many mammals.

Question 39

When did animals first appear on earth?

Answer 39

About 600 million years ago.

Question 40

What is the significance of the discovery of Archaeopteryx lithographica?

Answer 40

The fossils are extremely well-preserved, and it clearly suggests a close relationship between birds and dinosaurs. Feathers are also immaculately preserved in this fossil as well.

Question 41

What is the geologic timescale?

Answer 41

The series of time divisions that mark Earth’s long history

Question 41

How do we determine the age of fossils?

Answer 41

Fossils are embedded in different layers which mirror the age that the fossils are relative to each other.
For more specific time periods, scientists calibrate the age of fossils using radioactive decay.

Question 43

What is the significance of the fossil Tiktaalik roseae?

Answer 43

It lived 360 years ago, marking the colonization of land by vertebrates. Tiktaalik had fins, gills, scales like fish, but with a functional neck that could support its body, which is a feature in tetrapods. This supports the phylogeny that all land vertebrates are descended from fish. Further evidence was discovered that show that the limbs of fish and amphibians are shaped by similar patterns of gene expression.

Question 44

What is half-life? How is it used to measure the age of fossils?

Answer 44

Half of C-14 will decay to nitrogen in 5730 years, which is useful for dating materials younger than 50,000 to 60,000 years. Other materials are used for dating older materials, such as Uranium and Lead. Lead has the longest half-life.

Question 45

True or False: Sedimentary rocks that contain fossils also preserve information about the environment in which they formed, such as atmospheric gases or currents.

Answer 45

True.

Question 46

When did recorded diversity drop, how and why?

Answer 46

At several moments in the past 542 million years, brought about by mass extinctions that ended many groups of species but opened opportunities for new species to fill an empty niche.

Question 47

How have mass extinctions shaped the ecological landscape?

Answer 47

Certain species were eliminated, allowing other species to appear or develop. At the end of the Permian Period, a massive volcano eruption resulted in the lack of oxygen, acidification of oceans, and global warming contributed to this. Additionally, changes in the landscape (breaking up of Pangea), separated populations and allowed for speciation.

Question 48

What two methods do we use to reconstruct the history of life on Earth?

Answer 48

The nested similarity observed in the forms and sequences of living organisms; and the direct historical archive of the fossil record.

Question 49

True or False:

Comparative biology and fossils use the same approach to reconstruct the evolutionary past.

Answer 49

False. Comparative biology (morphology, cladistics, molecular analysis), and fossils are two different sources of information for construction the phylogenetic tree. They are complementary and provide evidence of evolution.