Exam Four Flashcards

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1
Q

What is another term for macroevolution?

A

Speciation

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2
Q

Describe “species”

A

An evolutionary independent unit

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3
Q

Name four biological boundaries to gene flow

A

Physiological (cellular incompatibility), Morphological (anatomical), Behavioral (mate choice), Genetic (chromosomes, genes, alleles)

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4
Q

Describe the Biological Species Concept or BSC

A

If members of separate interbreeding populations mate and produce fertile offspring-> same species

If members of separate interbreeding populations cannot mate (physiology, morphology), will not mate (behavior), or mate and produce infertile (can be viable) offspring (genetics)-> different species

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5
Q

Describe the Morphospecies Concept or MSC

A

Traits/Characteristics

Skeletal and organ system

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6
Q

Describe the Phylogenetic Species Concept or PSC

A

Where well documented (molecular) phylogeny exists

Judgement on how much distance there needs to be for species vs subspecies

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7
Q

What are the three steps of speciation and what concept does it use?

A

1-Elimination or reduction in gene flow (1 population becomes 2)
2-Divergence, until
3-Separate species (by BSC)

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8
Q

Define allopatric speciation and describe the two forms

A

Different range, geographical barrier

Dispersal-From start to “habitat island”
Individuals are able to find compatible places randomly

Vicariance-Geographical barrier forms between a population

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9
Q

Define sympatric speciation

A

Same range

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10
Q

Define parapatric speciation and why it works

A

Nearby/Overlapping range

Reduction in gene flow, not elimination-little in ½ and 2/3 , almost none in ⅓

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11
Q

Which species concept is used for fossils?

A

MSC, morphospecies concept

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12
Q

What kind of speciation is Drosphila clines?

A

parapatric

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13
Q

What kind of speciation is Hawaiian Drosophia?

A

Allopatric-> Dispersal

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14
Q

What kind of speciation is snapping shrimp?

A

Allopatric-> Vicariance

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15
Q

What kind of speciation is hawthorne maggot fly?

A

Sympatric

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16
Q

What are the four levels of divergence?

A

Allele, Gene, Chromosome, and Genome

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17
Q

How does mutation lead to divergence at the allele level?

A

Same mutation do not occur in both populations->

New and different alleles appear in each population independently

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18
Q

How does selection lead to divergence at the allele level with the same selection pressures?

A

under directional selection patterns, different alleles can be fixed or lost

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19
Q

How does selection lead to divergence at the allele level with different selection pressures?

A

homozygote advantage pattern means that different alleles can be fixed or lost

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20
Q

How does selection lead to divergence at the allele level with quantitative traits?

A

Quantitative traits in a adaptive landscape (same selection pressure) can cause different alleles to be fixed or lost

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21
Q

How does nonrandom mating lead to divergence at the allele level?

A

Two populations can become fixed for contributing or non contributing alleles (inbreeding)
Many alleles fixed or lost

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22
Q

What can nonrandom mating lead to that aids in divergence? Give an example.

A

Nonrandom mating can become sexual selection, independent preferences in one population reinforce reduction in gene flow (even in the same or overlapping range)

Hawthorne and apple maggot flies

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23
Q

How can drift lead to divergence?

A

Different alleles fixed or lost in each population (with drift alone)
More likely that they will change then they will follow each other

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24
Q

Describe the founder effect in relation to divergence

A

Founder effect with small population (dispersal) means that initial allele frequencies are different and drift is much stronger

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25
Q

What are the two ways migration can lead to divergence?

A

Alleles introduced into one population and not the other (or change threshold level by changing allele frequencies)

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26
Q

Describe genetic distance

A

Over time two populations will accumulate differences in the actual alleles they have at each locus

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27
Q

How does genetic distance lead to divergence?

A

If two populations have the same genes, but different alleles at every point, mating may become impossible-> BSC
More genetic distance-> more incompatible

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28
Q

What extra thing does the environment at a single locus include?

A

The genotype at other genes -> multilocus selection

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29
Q

What is the simplest way to get macroevolution?

A

Microevolution + time (in thousands of generations)

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30
Q

Relate fitness and speciation by BSC

A

Fitness of hybrids is 0 (do not survive or infertile)

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31
Q

Describe the two ways new genes are created.

A

Unequal crossover-Crossover occurs where there are similar sequences, may make
one with a new region and one with a missing region

Reverse Transcription- A mRNA can be put back into the original DNA

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32
Q

Describe redundany in gene families, name some examples, and explain why it might be helpful.

A

Same function
Ribosomal genes, actin, tubulin, keratin
More is better to produce enough material/protein

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33
Q

How does redundancy, subfunctionalization, neofunctionalization, and nonfunctionalization occur in gene families?

A

One gene retains the original function, while one or more others change (or lose) the function

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34
Q

Describe subfunctionalization in gene families, name some examples, and explain why it might be helpful.

A

Altered function,
hemoglobin proteins and visual pigment proteins, the changed gene can be expressed at different times and have different (but similar) skills

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35
Q

Describe neofunctionalization in gene families, name some examples, and explain why it might be helpful.

A

New function,

Crystallins, can be a preadaptation by providing a new function (or just help)

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36
Q

Describe nonfunctionalization in gene families, name some examples, and explain why it might be helpful.

A

Loss of function, Vitamin C Synthesis Gene and Olfactory receptors, it is the most common and may prevent the wasting of energy (or just be harmful.

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37
Q

Describe chromosome inversions

A

Flipping a section a chromosome where there is no difference in phenotype because all genes are present, just in a different order/location

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38
Q

Describe how chromosome inversions are passed on

A

Inversion heterozygotes have reduced fertility (fitness), but they can still pass on their inversion, Eventually two heterozygoes will mate and produce a homozygote that has no reduced fertility and may have an advantage.

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39
Q

Describe how chromosome inversions lead to speciation

A

When there is normal, heterozygoes, and homozygotes, the hybrid has a much lower fitness and the homozygote may have some advantages (prevent intermating and create new species)

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40
Q

Describe chromosome translocations and describe how they are passed on (with gametes)

A

Parts of non-homologous chromosomes are switched, leading to 2 inviable, 1 translocated, and 1 normal gamete. Eventually two intranslocation heterozygotes will mate and produce a homo with no reduced fertility.

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41
Q

Describe the process of polyploidy and relate it to speciation

A

Diploid plant produces n gametes which go to a 2n zygote. Spindle failure produces a mosaic plant. Two 2n gametes produce a 4n adult. Breeding a 2n gamete with an n produces a sterile 3n adult -BSC

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42
Q

What term describes the speed of polyploidy speciation?

A

Instant (only a few generations)

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43
Q

Describe the hybrid zones and speciation results of a hybrid that has lower fitness

A

Narrow and short lived hybrid zones

Reinforcement of divergence

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44
Q

Describe pre and post-zygotic selection

A

Post-zygotic selection->
Mating and attempting to construct and provision an offspring with low fitness is wasteful

Mate choice preference traits-> Prezygotic selection
Positive assortative mating (inbreeding is selected for)

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45
Q

Describe the relationship between the speed of the formation of pre-zygotic selection and allopatric vs sympatric

A

Hybrid progeny more likely to be produced in sympatric

At the same level (low) of genetic distance, sympatric taxa have much higher prezygotic isolation

Prezygotic mate-selection traits evolve sooner

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46
Q

Describe the hybrid zones and speciation results of a hybrid that has equal fitness

A

Hybrid zone is relatively wide and long lived
Parental populations coalesce (after gene flow is reintroduced)
Not enough divergence

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47
Q

Describe the hybrid zones and speciation results of a hybrid that has higher fitness

A

Hybrid zones depend on whether fitness advantage occurs in new or old habitat
Stable hybrid zone or formation of new species

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48
Q

Describe the formation of higher hybrid fitness in plants

A

Species a has na chromosomes in gametes and species b has nb chromosomes in gametes, so Na + Nb in zygote (sterile)

Failure of the mitotic spindle in one cell ->2na + 2nb (mosaic plant)
Might have a flower, creates egg and pollen with half, zygote with 2na + 2nb (species C)

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49
Q

Describe the formation of higher hybrid fitness in vertebrates

A

Coywolf has a genome composed of 65% coyote, 10% dog, 25% wolf

Skilled at catching prey in forests (wolf), fields (coyote), and city (dog)

Broader diet

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50
Q

Define phylogeny

A

Evolutionary history of a group (taxon)

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51
Q

What two things can a phylogenetic tree tell you?

A

Pattern of branching events and order of speciation events

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52
Q

Define character

A

aspect of the phenotype being compared

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53
Q

Define character state

A

exact value of that trait

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54
Q

In a phylogenetic tree, what is polytomy?

A

When you can’t tell what diverged from what, looks like two v’s with their creases together and a line from the bottom

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55
Q

In a phylogenetic tree, what are branches and what do they show?

A

Lineages; common ancestor or leading to taxon

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56
Q

In a phylogenetic tree, what defines sister taxa?

A

Same branch (recent speciation events)

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57
Q

In a phylogenetic tree, what are clades?

A

A branch with all the taxa included

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58
Q

In a phylogenetic tree, what is the role of roots?

A

They allow you to determine the order of events

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59
Q

What is the most common error in phylogenies?

A

Over-interpretation

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60
Q

In a phylogenetic tree, what is the significance of the order of the taxa on top?

A

Nothing, cannot show relationship

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61
Q

In a phylogenetic tree, what is the significance of the length of lines?

A

Nothing, unless a scale is included

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62
Q

What information are unrooted trees based or not based on?

A

Common ancestors, not order of branching events

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63
Q

In a phylogenetic tree, what is the outgroup?

A

Closest taxa to the root, no common ancestor with others

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64
Q

What are the four steps to estimating a phylogeny?

A

Choose characters, generate all trees, add character states, choose the best one

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65
Q

What is the easiest way to choose the best tree in a phylogeny?

A

Parsimony, the tree with the fewest changes in state (add for each state, may be more than one spot to choose)

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66
Q

What are the four traits of good characters to choose for a phylogeny?

A

Heritable, Variable, Independent, Homologous

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67
Q

Describe synapomorphies

A

Traits evolved in a common ancestor and shared by all descendent taxa

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68
Q

Define homoplasy and name two ways it can form

A

Conflicting information about evolutionary relationships from analogous traits (convergent evolution) or reversal (change back to ancestral)

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69
Q

Describe the method for choosing the best tree based on genetic distance

A

Closer relative-> more shared alleles

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70
Q

Relate maximum likelihood and transitions/transversions

A

Purine to purine (A to G and vice versa) or Pyrimidine to pyrimidine (T to C and vice versa) are transitions and are more likely

71
Q

What was the character used to determine cetacean origins based on morphological characteristics?

A

Shape of astragalus bone (a tarsal, bone in ankle)-> trochleated head present or absent

72
Q

What was the character used to determine cetacean origins based on molecular characteristics?

A

Beta-casein gene (milk protein)

73
Q

Where were whales originally on their tree and where are they now?

A

Closely related to artiodactyls, in the hippo clade

74
Q

Define a transposable element and give the other name

A

Segment of DNA that can copy itself to another location in the same genome (LINE)

75
Q

Describe the use of transposable elements in forming a tree

A

Likelihood that a LINE would copy itself to exactly the same location in two separate transposition events is infinitesimally small (second location is random)

Each different location that a LINE is present or absent in at least one of the taxa is a character

76
Q

Describe the scaling branch length technique relating to fossils and describe its claim

A

Radiometric dating of fossils

Divergence (speciation) must predate their simultaneous existence

77
Q

Describe the scaling branch length technique relating to mutations and describe its claim and cautions

A

Differences due to neutral mutations should be clocklike (a function of mutation rate)

Caution:
Mutation rates vary between distant taxa
Vary between genes

78
Q

How was the origin of HIV discovered?

A

Using parsimony to decide if it was monkeys first or humans (it was monkeys)

79
Q

How did Hawaiian Drosphila make it to the big island? How do we know?

A

Local molecular clock used to estimate original colonization of Hawaiian islands-> Long ago of Koko Seamound (there first, then island hop to big island)

80
Q

What three major groups/clades are birds in?

A

Tetrapods, amniotes, reptilia

81
Q

Name three polyphyletic groups that need to be changed according to monophyletic rules

A

Prokaryotes, dicots, fish

82
Q

How do we know that leafcutter ants and their fungus coevolved?

A

The phylogenies match up

83
Q

Compare IDA with LCUA

A

LCUA -Last universal common ancestor (most recent)

First living thing is also known as IDA (initial Darwinian form)

84
Q

Name and describe the experiment used to test the first step to make a living organism

A

Stanley Miller Experiment took gases and passed them through electrodes, then a cooling jacket, then boiling water. Many repetitions produced amino acids and nucleotide-like molecules. Problem: Gases do not represent atmosphere time

85
Q

Describe the experiment used to test the second step to make a living organism

A

Short nucleic acid bathed with other nucleotides created chance of covalent bonds. The nucleic acid grew (larger average over time). Theory: Clay was substrate, shorelines providedcontinuous washing with dissolved building clock nucleotides or amino acids

86
Q

Why was DNA a poor choice for the first replication?

A

It replicates by encoding proteins that do the catalysis->

Problem: DNA and the proteins needed to replicate it could not have evolved simultaneously

87
Q

Describe the experiment in which the third step to make a living organism was tested

A

RNA attached to bead with a random segment with a PPP end

Another molecule starts with hydroxyl group on a cytosine and includes a tag

The second one is complementary to the first and brings the PPP and HO together

If the phosphodiester linkage is formed, the second section will stay and attach to affinity column

88
Q

Describe how the fourth step to make a living organism may have occurred

A

A membrane forms from the arrangement of the phospholipids in water

The formation of a double-layered sheet allows the hydrophobic fatty acid tails to remain together and away from water

Concentration of building blocks and catalytic components leads to faster replication

89
Q

What are the four steps of the precambrian?

A

Origin of life, LCUA, divergence into eukarya, multicellularity

90
Q

What is the first step of the origin of life?

A

Assemble simple molecules into building blocks for complex polymers

91
Q

What is the second step of the origin of life?

A

Assemble polymers that can store information and catalyze reactions

92
Q

What is the third step of the origin of life?

A

Self-replication

93
Q

What is the fourth step of the origin of life?

A

Add membranes and an energy source to make a living organism

94
Q

What was discovered that became the molecule for step three? Why was it better than DNA?

A

Catalytic RNA was both information carrying and catalytic

95
Q

Name the three examples of the molecule used in step 3

A

Group 1 and 2 introns, ribonuclease P, peptidyl transferase

96
Q

Give the window for LUCA and say why

A

3.85 (sedimentary rocks) to 3.5 (earliest bacteria fossils) BYA

97
Q

Why can’t we use fossils to see what LUCA was like?

A

Chance of fossilization is low, chance of discovery is low, cannot deduce characteristics

98
Q

What characteristics/method is used to find LUCA’s characteristics?

A

Molecular characteristics shared by all cellular organisms are used to firm a phylogeny of the whole life tree

99
Q

What did scientists have to look out for when choosing characteristics to find LUCA’s characteristics?

A

Low mutation rate due to the high genetic distance

100
Q

What clades/branches did the whole life tree form?

A

split between bacteria and a clade of eukarya and archaea

101
Q

Name some monophyletic and non-monophyletic groups on the whole life tree

A

Mono-> animals, plants, fungi (if remove slime molds)

Non-> protists

102
Q

List the three situations in which parsimony of the whole life tree would give a trait to LUCA

A

Alll three, Bacteria and one other, bacteria only

103
Q

List the two situations in which parsimony of the whole life tree would not give a trait to LUCA

A

Archaea/Eukarya only or both

104
Q

What did the tRNA whole life tree reveal?

A

Horizontal gene transfer (transfer of genes across species) is More common than we thought

105
Q

What is the most recent theory of the progression of LUCA to modern life?

A

A community of LUCA’s in which horizontal gene transfer was common

106
Q

Describe the two theories of the formation of the nucleus

A

That early eukaryotic engulfs an archean, which later becomes the nucleus

Eukarya arise as a fusion of a bacterium with an archean

107
Q

Describe the theory of the formation of the mitochondrion

A

Mitochondria was an intracellular parasite, now they are intracellular symbionts of eukaryotic cells

108
Q

Describe the theory of the formation of the chloroplast

A

Came from a bacteria that can photosynthesise

109
Q

Give the three steps to multicellularity

A

Colonial aggregates, division of labor, continued differentiation into specialized tissues and organ systems

110
Q

What factor in the second step to multicellularity allowed increased size?

A

Transport of nutrients, gases, wastes

111
Q

What are the three sections of the third step of multicellularity

A

Need gene regulation, Cell status transmission at division, and reliable spatial patterning

112
Q

Describe homeotic genes

A

Make organs and tissues in the right orientation. In order from head to abdomen.
Some duplications have occured, but it’s still the same gene, a mouse gene can go into a fly. Mammals and fish duplicated a cluster.

113
Q

Give the range of the cambrian radiation

A

543 to 495 MYA

114
Q

What are the three problems with the fossil record?

A

Small # fossilized (not a representative fraction, has taxonomic bias), small # discovered, small # characterized

115
Q

Describe impression/compression fossils

A

2-D

Fine sediment can produce striking detail

116
Q

Describe permimeralized fossils

A

Dissolved minerals enter cells, precipitate, and replace organics

117
Q

Describe cast and mold fossils

A

3-D
Mold-hollow, organism gone
Cast-new material infiltrated mold

118
Q

Describe the required conditions for preserved remains and list a few examples

A

Decay must be prevented

Amber resin, frozen, acid peat bogs, quick-dried, oil-saturated

119
Q

What did the Edicaran fossil field have and what was special about them?

A

First multicellular animals, mostly radial

120
Q

What were the two special things about the Burgess Shale fossil field?

A

Spectacular disparity of body forms
2x as many different forms as today

All major animal phyla represented
Lineages that lead to the major phylums

121
Q

How did symmetry evolve from asymmetric to radial to bilateral?

A

Radial vs bilateral cleavage initiated very early in development

Radial cleavage furrow is angled in the start of a whorl
Bilateral cleavage furrow is at right angles

122
Q

What innovation did triploblasts have?

A

Added mesoderm to the endo and ectoderms

123
Q

What was the first type of gastrulation and what came second?

A

Deuterostome (mouth second) vs protostome (mouth first)

124
Q

What are the three environmental factors that may have aided the rapid diversification?

A

More oxygen, more innovation due to multicellularity, predation and the red queen hypothesis

125
Q

What is the name of the eon that starts with the Cambrian?

A

Phanerozoic

126
Q

Name and describe the starting and ending points of the first era of the Cambian radiation

A

Paleozoic

Cambrian radiation to the end Permian extinction

127
Q

Name and describe the starting and ending points of the second era of the Cambian radiation

A

Mesozoic

Permian extinction to the K-T extinction

128
Q

Name and describe the starting and ending points of the third era of the Cambian radiation

A

Cenozoic

K-T extinction to modern life

129
Q

Name the three causes of adaptive radation

A

New niche, extinction empties a niche, new evolutionary innovation

130
Q

Describe punctuated equilibrium

A

Rapid divergence at speciation followed by long periods of stasis

131
Q

Describe phyletic gradualism

A

Gradual divergence into reproductive isolation

132
Q

What are the three possible causes of punctuated equilibrium?

A

Founder effect
Drift after allopatry
Adaptive landscape

133
Q

Why may punctuated equilibrium not be necessary?

A

More and more transitional forms are found, not all are fossilized in the first place

134
Q

Describe cladogenesis

A

true speciation

Species A goes to Species B and C

135
Q

Describe Anagenesis

A

change from one species to another, they do not coexist in time
Species A goes to Species B

136
Q

Describe the speed, range, and diversity of mass extincions

A

Rapid, global, taxonomicaly diverse

137
Q

Describe the speed, range, and diversity of background extinctions

A

Slow, local, taxonomically narrow

138
Q

What is the largest mass extinction?

A

End Perminan

139
Q

What was the significance of the K-T extinction? When was it?

A

End of dinosaur dominance- allowed mammalian radiation

65 MYA

140
Q

What were the two secondary causes of the severity of the K-T meteor impact?

A

Herbivore diversity was at a cyclic low just before and sex determination may have been affected

141
Q

What are the four consequences of mass extinctions?

A

Random elimination, adaptive radiation, population bottlenecks, and Lazarus taxa

142
Q

What divergence theory did Darwin like?

A

Phyletic gradualism

143
Q

Closest relative

A

chimp

144
Q

Ape synapomorphies

A

absence of tail, joint flexibility, brachiationi

145
Q

African Great Ape synapomorphies

A
Elongated skull
Enlarged brow ridges
Shorter stouter canine teeth
Fusion of certain carpals (wrist)
Enlarged ovaries and mammary glands
Reduced hairiness
146
Q

When did humans diverge from chimps/bonobos and gorillas?

A

5 MYA

147
Q

Group, time, and description-Ardipithecus ramidus

A

Basal hominins, before 4 MYA, Africa, bipedal and arboreal

148
Q

Group and time- Australopithecus genus

A

Early human ancestors or relatives, 4-2 MYA

149
Q

Group, time, and description- Paranthropus genus

A

Early human ancestors or relatives, 4-2 MYA, possible limited tool use

150
Q

Group, time, and description- Homo habilis

A

Early human ancestors or relatives, 4-2 MYA, slightly larger

151
Q

Group, time, and description- Homo rudolfensis

A

Early human ancestors or relatives, 4-2 MYA, cobblestone tool user

152
Q

Group, time, and description- Homo ergaster

A

Middle period, 2-1 MYA, ancestral to others

153
Q

Group, time, and description- Homo erectus

A

Middle period, 2-1 MYA, left Africa to Asia and long lived

154
Q

Group, time, and description- Homo neanderthalensis

A

Recent, <1 MYA, Europe

155
Q

Group, time, and description- Homo sapiens

A

Recent, <1 MYA, global

156
Q

Group, time, and description- Homo floresiensis

A

Recent, <1 MYA, hobbits, java, mix of homo and ape/australopithecine traits

157
Q

Group, time, and description- Homo heidelbergensis

A

Recent, <1 MYA, Europe

158
Q

Describe the hybridization and assimilation theory of our dispersal

A

H. Ergaster diverged into E. Erectus (Asia) and H. heidelbergensis (Europe)
H. heidelbergensis diverged into H. neanderthalensis (Europe) and H. sapiens (global)
H. sapiens maintained gene flow after spreading and still had a little (2-4%) of gene flow with H. erectus and H. neanderthalensis

159
Q

Describe how we find migration history from modern haplogroups

A

Two basic tenets:
New populations will not carry all haplotypes with them, once populations are separated, they will get different mutations

The oldest population will have the most haplogroups
The youngest population will have the fewest overlap with the original
May carry mutations from their former population

160
Q

Name the 5 extinction events

A

K-T, end Permian, late ordovician, end devonian, and end triassic

161
Q

1-1
2-4
3-2
4-4

A

Basal hominins (ardipithecus ramidus)

Early (Australopithecus, Paranthropus, homo habilis, homo rudolfensis)

Middle (homo ergaster, homo erectus)

Recent (H neanderthalensis, sapiens, floresiensis, Heidelbergensis)

162
Q

Are dogs the same species?

MSC, BSC

A

N,Y

163
Q

Is brassica the same species?

MSC, BSC

A

N,Y

164
Q
Are Drosophia (with compound chromosomes) the same species?
(MSC, BSC)
A

Y,N

165
Q

Are marine copepods the same species?

MSC, PSC, BSC

A

Y, N, N

166
Q

Are all African elephants the same species?

PSC, BSC, MSC

A

N,N, Y

167
Q

What are the two clades (not including the one with whales) in artiodactylels?

A

Cow and deer, pig and peccary

168
Q

Describe the Panspermia theory

A

Meteorites brought amino acids to earth

169
Q

Describe the African replacement model of our dispersal

A

H. Ergaster diverged into E. Erectus (Asia) and H. heidelbergensis (Europe)
H. heidelbergensis diverged into H. neanderthalensis (Europe) and H. sapiens (global)

(no gene flow from erectus or neanderthalensis)

170
Q

Where do Old World Monkeys live?

A

Africa and Asia

171
Q

Name the four members of African Great Apes

A

Humans, Common chimps, gorillas, bonobos

172
Q

When did the Pan and Homo genera diverge from each other?

A

5-6 MYA

173
Q

What is the common name for pan paniscus?

A

Bonobos