Biology 2C Exam I

Front 1

**What is the Tree of Life?

Back 1

Concept
-all living organisms are related to one another through SHARED ANCESTRY

Phylogeny shown as a tree--a simplified model of the genealogy of life

Shows diversity, relationships, similarities, & differences

Front 2

**What is Phylogeny?

Back 2

Evolutionary History

Front 3

*Classification: Polynomial System

Back 3

Pre-1700's

Organisms grouped into diff. kinds (genus/genera)

EX: Catnip

Nepeta floribus interrupte spicatus pedunculatus

Front 4

*Classification: Binomial System

Back 4

Linneaus (1753)

Genus + Specific Epithet

EX: Catnip

Nepeta cataria

Front 5

*(T/F)

Taxonomy is hierarchical

Back 5

True

Front 6

*What is the hierarchy of taxonomy from broad to specific?

Back 6

Domains

Kingdom

Phylum

Class

Order

Families

Genus+Species

Front 7

*When naming species, especially if its more inclusive (eg genera, families), try to ensure they are ____ groups

Back 7

monophyletic

(MRCA in a single clade contains all descendents)

Front 8

*(T/F)

The Tree of Life is time independent

Back 8

False

Time Dependent

Front 9

*(T/F)

The tree of life is a 4 billion year history of evolution

Back 9

True

Front 10

*(T/F)

Phylogenetic trees are complex models of a much more simple set of biological processes

Back 10

False

Phylogenetic trees are SIMPLE models

Front 11

**What is Speciation?

Back 11

Process
-1 species -> 2 descendent species

On Tree:
-branching (splitting) point

Front 12

*(T/F)

Phylogenies are the result of multiple speciation & extinction events over long periods of time

Back 12

True

Front 13

*(T/F)

Terminal nodes on a tree represent hypothetical ancestral taxa

Back 13

False

Internal nodes

Front 14

What is Biology?

Back 14

scientific study of living organisms, including their characteristics, functions, and interactions

Front 15

What are Cells?

Back 15

basic structural and physiological units of life

Front 16

What is the Cell Theory?

Back 16

all life consists of cells and that all cells come from preexisting cells

Front 17

(T/F)

Evolution by natural selection is responsible for the diversity of adaptations found in living organisms.

Back 17

True

Front 18

The instructions for a cell are contained in its ___

Back 18

genome (made of DNA, which is made of nucleotides)

Front 19

What are Genes?

Back 19

Specific segments of DNA

contain the information the cell uses to make proteins

Front 20

(T/F)

Living organisms regulate their internal environment. They also interact with other organisms of the same and different species. Biologists study life at all these levels of organization

Back 20

True

Front 21

(T/F)

Biological knowledge obtained from a model system may be generalized to other species

Back 21

True

Front 22

(T/F)

Biologists use fossils, anatomical similarities and differences, and molecular comparisons of genomes to reconstruct the history of life.

Back 22

True

Front 23

Life first arose by ____ evolution

Back 23

chemical

Front 24

___ arose early in the evolution of life

Back 24

Cells

Front 25

Why is Photosynthesis is an important evolutionary step?

Back 25

it changed Earth’s atmosphere and provided a means of capturing energy from sunlight

Front 26

(T/F)

The earliest organisms were prokaryotes. Organisms called eukaryotes, with more complex cells, arose later. Eukaryotic cells have discrete intracellular compartments, called organelles, including a nucleus that contains the cell’s genetic material.

Back 26

True

Front 27

**Species are grouped into 3 domains:

Back 27

Archaea, Bacteria, Eukarya

Front 28

**(T/F)

Archaea and Bacteria are domains of unicellular prokaryotes.

Back 28

True

Front 29

Biological species concept distinguishes species on the basis of...

Back 29

reproductive isolation

Front 30

Morphological species concept distinguishes species on the basis of...

Back 30

physical similarities

it often underestimates or overestimates the actual number of reproductively isolated species

Front 31

Lineage species concept distinguishes species on the basis of...

Back 31

branch on the tree of life

Front 32

Speciation usually results from...

Back 32

interruption of gene flow within a population

Front 33

What is Allopatric Speciation?

Back 33

populations are separated by a physical barrier

result from founder events

Front 34

What is Sympatric Speciation?

Back 34

genomes of two groups diverge in the absence of physical isolation

result of disruptive selection (Selection in which phenotypes at both extremes of the population distribution are favored)

occur within two generations via polyploidy, an increase in the number of chromosomes sets

Front 35

(T/F)

Polyploidy may arise from chromosome duplications within a species (autopolyploidy) or from hybridization that results in combining the chromosomes of two species (allopolyploidy)

Back 35

True

Front 36

*A

Back 36

Terminal (Tip) Taxa

Front 37

*B

Back 37

Internal Branches

Front 38

*C

Back 38

Root, Root Node

Front 39

*D

Back 39

Internal Nodes

Front 40

*
(T/F)
"Order" left-to-right has no meaning on a tree

Back 40

True

You can "rotate" tree branches around nodes and not change the meaning of the tree

Front 41

*
What are Bifurcating Trees?

Back 41

Internal node gives 2 descendents

Front 42

***
What are Polytomies?

Back 42

Nodes give 3+ descendents

Reflects UNCERTAINTY about phylogenetic relationships

Front 43

*
What is a Monophyletic Group?

Back 43

group of organisms consisting of MRCA and ALL its descendents

Front 44

*
What is a Clade?

Back 44

a monophyletic group

Front 45

*
What is a Paraphyletic Group?

Back 45

group of organisms consisting of MCRA but EXCLUDES some descendents

Front 46

*
What is a Polyphyletic Group?

Back 46

group of organisms that EXCLUDES MRCA

Front 47

**
What is the relationship between the number of monophyletic groups and the number of internal nodes in a tree?

Back 47

# Internal nodes = # Clades

Excludes Terminal Taxa

Front 48

*
What are Non-Monophyletic Groups

Back 48

Groups that include some but not all descendents of MRCA

Polyphyletic Groups

Paraphyletic Groups

Front 49

**
What are Synapomorphies?

Back 49

Monophyletic groups or clades

UNIQUE characters inherited from common ancestor to that group ONLY

Front 50

*
(T/F)

Synapomorphies are always homologous.

Back 50

True

Front 51

*
(T/F)

Homologous traits are always synapomorphies

Back 51

False

Front 52

**
What are Homologous Traits?

Back 52

Inherited from a common ancestor

Front 53

*
What is Convergence?

Back 53

Evolved INDEPENDENTLY

unrelated species subjected to similar environments

Front 54

*
What are Sister Groups?

Back 54

2 clades or species that are each other's closest relatives

2 descendant taxa of a single node

originate as lineages at the same time

Front 55

*
What is an Ingroup?

Back 55

Set of taxa under study

Front 56

*
What is an Outgroup?

Back 56

1 or more taxa that phylogentically fall outside of group under study

not members of ingroup

usually closely related to ingroup

Front 57

*
What are Derived Traits?

Back 57

Traits that arise or were modified in the ingroup

Front 58

*
What are Ancestral Traits?

Back 58

Features that were present in the common ancestor

Front 59

*
What is a Cladogram?

Back 59

Only RELATIVE BRANCHING ORDER depicted

Branch lengths are meaningless

Front 60

*
What is a Phylogram?

Back 60

Branch length = amt character change

Front 61

*
What is a Chronogram?

Back 61

Branch length = time

Front 62

*
Phylogenetic trees are inferred from the _____ that are observed among species or population (terminal taxa)

(similarities/differences)

Back 62

similarities

Front 63

*
What is a Character?

Back 63

Traits or features of organisms

Front 64

*
What is a Data Matrix?

Back 64

taxon-by-character matrix

Front 65

*
What is the Principle of Parsimony?

Back 65

Least amount of change in character states or evolutionary step

Front 66

*
What is an Unrooted Tree?

Back 66

A tree in which the root has been removed and relationships among taxa are more ambiguous

Shows branch splitting events

Says nothing about time sequence of events

Front 67

*
Basic procedure for finding/searching for the most parsimonious tree.

Back 67

1. Ignore parsimony-uninformative characters.

2. Draw possible trees.

3. For each informative character count the minimum number of steps required on each tree.

4. Sum over all characters to get the “score” (number of steps) for
each tree. The most parsimonious tree(s) is/are the one(s) with lowest score.

5. Root the tree along the branch leading to the outgroup (if known).

Front 68

*
What characters in a data matrix are parsimony-uninformative?

Back 68

Invariant characters (no steps)
-EX: TTTT

One taxon different, others all the same (1 step)
-EX: CCCT

Front 69

*
If there is/are character conflict(s) on a tree, what are some possible solutions?

Back 69

Add more data

Try a different approach

Front 70

*
Model of Evolution

Back 70

model-based approach to phylogeny

Inferring trees under maximum likelihood
-most likely to have evolved

Advantage: more accurate, estimates branch lengths

Disadvantage: complicated, computer intensive

Front 71

*
Transitions v. Transversions

(Nucleotide Substitutions)

Back 71

Transitions
A<->G
C<->T

Transversions
A<->C
A<->T
G<->C
G<->T

Transitions more likely to happen than Transversions

Front 72

*
what is synonymous substitution?

(amino acids)

Back 72

No change in encoded amino acids

Front 73

*
*
what is non-synonymous substitution?

(amino acids)

Back 73

Change in encoded amino acid

Front 74

*
uses of phylogeny

Back 74

Study mode & tempo of evolution

Coevolution

Biogeography

Community phylogenetics

Conservation biology

Front 75

*
Self-Incompatible v. Self-compatible

(flowers)

Back 75

Self-incompatible
-cannot self-fertilize

Self-compatible
-can self-fertilize

Most likely to go from self-incompatible to self-compatible

Front 76

*
Biogeography

Back 76

study of the geographical distribution of organisms.

dispersal and geological events
-determines the distribution of taxa
-origin of taxa
-history of dispersal v. other areas

Front 77

*
Clade Diversification Rates

Back 77

Some taxa have many more species than others

Compare Sister Taxa
-control time
-compare net diversification (# extant species) in sister taxa of diff. traits

Front 78

*
Many plants have canals for holding toxic latex or resin. It provides defense and it evolved independently. What is the conclusion about its Clade Diversification Rate?

Back 78

the clade with canals was more diverse

Front 79

*
Molecular Clock

Back 79

Use the number of mutations along a branch as an indicator of
elapsed time

Rates of molecular evolution are constant
-calibrate rates of molecular divergence
-divergence time estimate

Front 80

*
What if we want to ask WHEN an event occurred on a tree?

Back 80

1) Build tree using DNA

2) Molecular Clock

3) Use other data, like fossils

Front 81

*
Conservation Biology in Phylogenies

Back 81

Phylogenies can inform conservation decisions:

1) Management of introduced “pest” species

2) Identify unsuspected diversity (species, larger clades)

3) Prioritize lineages for conservation based on
-maxing diversity
-emphasize conservation of deeper evolutionary history

Front 82

*
Explain what was needed for life to begin.

Back 82

Hadean-Archaen Earth (~3.8 GYA)

-Energy

-Soup of SPONCH & organic cmpds

-concentration & purity (eg. chirality)

-polymerization

-protection

-sustainable = makes entropy

Front 83

*
Explain how possible sites for life’s origin offer what life needed

Back 83

Shoreline
– Mudflats; clays
– Foam bubbles
– Radioactive beach
(natural fission reaction)

• Micro-caves in undersea
hot vents (~100°C)

• Volcanic hot springs

• Pockets of water in ice
(Snowball Earth)

Front 84

*
Identify current hypotheses for life’s origin

Back 84

-RNA world (genes first;
ribozymes)

• Iron-sulfur world (metabolism
first; acetyl-CoA)

• Thermosynthesis world
(proteins first; ATP synthase)

• Lipid world (membranes first)

• Hybrid world

• Intelligent design

Front 85

*
LUCA

Back 85

Last Universal Common Ancestor

Can be either a Complex cell (surrounded by membrane) or Protocell (no membrane)

Front 86

*
How to test hypotheses for life's origin

Back 86

• Molecular “fossils”
– Ribozymes
– In the genome

• Molecular signatures
– AA sequence of proteins (temp)
– G + C content of DNA (temp)
– Minerals & isotopes (metab)

• Experiments
– Miller-Urey
– PAH world, etc.

Front 87

*
Explain implications of simplified trees

Back 87

• Other branches
• Nodes
• Common ancestors

-Unique and widespread features

Front 88

*
Morphology and Motility of Microbial Eukaryotes

Back 88

Amoeboid

Flagellate
-Ciliate

Non-motile

Variable

Front 89

*
Microbial Eukaryotes: Multicellularity

Back 89

Unicellular

Colonial

Multicellular

Front 90

*
Microbial Eukaryotes: Symbioses

Back 90

Parasitism
-Pathogenicity

Mutualism
-Endosymbiosis
-Ectosymbiosis

Front 91

*
Alveolates

Back 91

Synapomorphy: alveoli or sacs beneath cell membrane

Front 92

*
Apicomplexans

Back 92

Alveolates

-all parasites

-mass of organelles at one tipp (apical complex)
*entry to host's cells
*has plastid DNA

-complex life cycle

Front 93

**
The presence of plastid DNA in the apical complex is evidence that it is the descendant of a(n)

Back 93

Chloroplast

Front 94

*
Dinoflagellates

Back 94

Alveolates

Most marine

Phototrophs & heterotrophs

Accessory pigments

Synapomorphy: 2 flagella (arrangement)
-equatorial groove
-longitudinal groove

Some: cellulose / silica covering

Chloroplast: 2nd or 3rd endosymbiosis

Front 95

*
Ciliates

Back 95

Synapomorphy: network of cilia

Heterotrophs

2 kinds of nucleii
-macro
-micro (sex)

Front 96

*
Stramenopiles

Back 96

aka Heterokonts

Synapomorphy: 2 flagella, unequal size

Front 97

*
Diatoms

Back 97

Stramenopiles

Unicellular or filaments

Carotenoids--yellow or brown

Front 98

*
Brown Algae

Back 98

Stramenopiles

Multicellular & complex

Brown carotenoid (fucoxanthin)

Marine

Front 99

*
Oomycetes

Back 99

Stramenopiles

absorptive heterotrophs

once called fungi, but not closely related

asexual and sexual

Front 100

*
Diplomonads & Parabasalids

Back 100

Excavates

unicellular

no mitochondria
-lost it, once had it

most anaerobic

2 nuclei (giardia lamblia)

STD (trichomonas vaginalis)

Front 101

*
Euglenids

Back 101

Excavates

Single flagella
-some can switch to amoeboid

Photosynthetic or heterotroph
-some can switch

Chloroplasts
-2nd endosymbiosis

Front 102

*
Kinetoplastids

Back 102

Excavates

Unicellular parasites

2 flagella & single mitochondrion

Trypanosomes: pathogens

Front 103

*
Heteroloboseans

Back 103

Excavates

freshwater heterotroph or symbiotroph

change form from amoeboid to flagellate

Front 104

*
Rhizaria

Back 104

unicellular

mostly marine

long thin pseudopodia

Front 105

*
Foraminifernas

Back 105

Rhizaria

Shells of CaCO3 (chalk)

planktonic or in sediments

holes in shell, thread-like, sticky pseudopods catch prey

Front 106

*
Choanoflagellates

Back 106

Opistokont

sister to animals

solitary or colonial

collar of microvilli
-heterotrophs

Front 107

*
Amoebozoans

Back 107

lobe-shaped pseudopods

feed by phagocytosis as predators, parasites, or scavengers

Front 108

*
Plantae

Back 108

includes microbial green & red algae

all chloroplasts from a single primary endosymbiosis
-evidence: peptidoglycan

Front 109

*
Glaucophytes

Back 109

Plantae

unicell or colonial

fresh H2O

chloroplast retains peptidoglycan

Front 110

**
The chloroplast retains a bit of peptidoglycan between the inner and outer membrane. What is peptidoglycan

Back 110

A component of the bacterial cell wall

Front 111

*
Red Algae

Back 111

Plantae

most marine & multicell

red from phycoerythrin; other pigments

alternation of generations wih 3 generations

useful products: agar, carrageenan

Front 112

*
Chlorophytes

Back 112

Plantae

unicell, colonial, multicell

fresh H2O & marine

sister taxa to land plants

Front 113

*
Bacterial Phylogeny is based on...

Back 113

rRNA gene sequences

NOT USEFUL
•form
•function
•ecology

Front 114

**
A synapomorphy of Spirochetes would likely be

a) DNA sequences
b) Spiral shape
c) Metabolism
d) Pathogenicity

Back 114

a) DNA sequences

Front 115

*
(T/F) Bacteria has circular DNA

Back 115

True

Front 116

**
The position of Low GC Gram-positive bacteria on this phylogenetic tree is determined by their

Back 116

rRNA gene sequences

Front 117

*
Biofilms

Back 117

Unicells attach to substrate, makes slime, signalling for more microbes

*Found everywhere!
-moist soil, water, fossil stromatolites, on/in organisms

*Pathogenic
-dental plague, contact lenses, artificial joints

Front 118

*
Microbial Mats

Back 118

Layers of biofilm

Gradients of Light, O2, minerals

Front 119

Back 119

b) Photolithoautotroph