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BIOEE 1780 > Prelim 1 > Flashcards

Prelim 1 Flashcards

1
Q

Fossil

A

remains, traces, or impressions of once living organisms ie. skeleton, impression, cast, trace, or coprolite (poop); most found in sedimentary rocks

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2
Q

Forces that impede fossilization

A

natural processes such as predators/scavengers, bacterial decay (soft tissue), dissolution in water (soft and hard tissue), or physical disturbance (wave action, wind)

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3
Q

Conditions that promote fossilization

A

rapid burial, protection from physical disturbance ie. quiet, deep water, anaerobic conditions (prevent bacterial decay)

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4
Q

Sedimentary rock formation

A

formed from the deposition of sediment falling to the bottom of a body of water

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5
Q

What gets preserved in fossils of animals

A

hard parts ie. teeth, bone, chitinous exoskeleton, or calcium carbonate shells

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6
Q

What gets preserved in fossils of plants

A

seeds, pollen, leaves, wood, rarely flowers (fragile petals)

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7
Q

What gets preserved in fossils of microbes

A

bacteria, microbial mats ie. stromatalites are formed from biofilms of cyanobacteria that trap sediment which eventually harden and form layers

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8
Q

Types of preservation

A

original remains (skeletal body, other body elements), permineralization/petrification, trace fossils, impression fossils, casts and molds

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9
Q

Permineralization/petrification

A

process where minerals are deposited in tiny holes within bones, or wood and over time completely replacing the original organism and all that remains is a stone structure

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10
Q

Impression fossils

A

made up of carbonaceous film imprint of an organism

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11
Q

Lagerstatten

A

German word that means “storage place”, place where fossils are exceptionally preserved (numerous and well preserved)

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12
Q

Burgess Shale

A

a famous Lagerstatten from the Cambrian which has yielded many of the organisms that contribute to our understanding of the Cambrian explosion

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13
Q

How do we know the age of a fossil?

A

relative and absolute dating

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14
Q

Geological chronology

A

the science of dating geological layers and fossils

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15
Q

4 principles relative dating is based on

A

superposition, original horizontality, lateral continuity, and cross-cutting

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16
Q

Principle of superposition

A

geological layers are formed by laying one on top of the other so that the youngest layer is on top

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17
Q

Principle of original horizontality

A

layers are first deposited horizontally and then they may be deformed later such as from the movement of continental plates

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18
Q

Principle of lateral continuity

A

layers continue laterally over distances; each layer is deposited at the same so that even if erosion has removed some of the layer, the layer is still the same layer after the gap

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19
Q

Principle of cross-cutting

A

if there is a cross-cutting layer or intrusion in rock layers, the intrusion is always younger than any of the layers it is cross-cutting

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20
Q

Index fossils

A

fossil organisms that are only found in a particular rock layer and are also geographically widespread so that the layers can be stratiagraphically correlated with each other in different locations according to the principle of lateral continuity

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21
Q

How was geological time scale (GTS) created?

A

by correlating layers based on index fossils; derived from the spatial distribution of rocks and the vertical sequence of rocks and contained fossils

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22
Q

How/when did absolute dating become possible

A

with the discovery of radioactivity in the late 19th century

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23
Q

Absolute dating

A

done by examining the radioactive decay of unstable isotopes

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24
Q

Radioactive decay

A

decay of a parent isotope gives rise to a stable daughter isotope at some characteristic rate of decay

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25
Q

Which rocks can be absolute dated

A

only igneous rocks; clock starts ticking when rock solidifies (daughter isotope is 0 in molten rock); sedimentary rock decays too quickly (carbon decays too quickly)

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26
Q

Radiometric dating: half lives

A

0 half lives = 100% parent isotope; 1 half life = 50%; 2 half lives = 25%; 3 half lives = 12.5% etc.

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27
Q

Uranium-lead effective dating range

A

10 million - 4.6 billion years

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28
Q

Potassium-argon effective dating range

A

100,000 - 4.6 billion years

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29
Q

Carbon-14 effective dating range

A

100 - 100,000 years

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30
Q

Phylogeny

A

a visual representation of the evolutionary history of populations, genes, and species

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31
Q

Tips of phylogenetic tree

A

represent groups of descendant taxa; most often species but can also represent molecules or populations

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32
Q

Branches of phylogenetic tree

A

lineages evolving through time between successive speciation events

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33
Q

Node of a phylogenetic tree

A

a point in a phylogeny where a lineage splits (a speciation event)

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34
Q

Clade/monophyletic group

A

an organism and all of its descendants; consists of the most recent common ancestor and all of its descendants

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35
Q

Paraphyletic clade

A

an ancestor and a group of taxa but it is not monophyletic because some of the descendants are missing

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36
Q

“Tree Thinking”

A

using data to construct trees, and reading trees to determine evolutionary relationships

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37
Q

Pedigree vs Phylogeny

A

pedigree: individuals, 2 ancestors, unlimited descendants; phylogeny: populations, 1 ancestor, 2 descendants (except for a polytomy)

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38
Q

How do we infer relatedness in a phylogeny

A

based on sharing of derived characteristics

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39
Q

Character

A

anything inherited (genetically determined, or DNA sequence itself) that can be used to determine relationships; morphological, physiological, (traits) or molecular (DNA sequence)

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40
Q

Ancestral state

A

the historical state of a character

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41
Q

Derived state

A

the more recently evolved state of a character

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42
Q

Synapomorphies

A

shared derived traits which are phylogenetically informative

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43
Q

Polytomy

A

describes an internal node of a phylogeny with more than 2 branches (the order in which the branching occurred is not resolved)

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44
Q

Choosing optimal phylogeny

A

select tree with the smallest number of character state changes (most common for morphological characters); select tree that is the most probably (based on probability methods, typically used for DNA mutations)

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45
Q

What are phylogenies used for?

A

map characters, trace the origins of epidemics, or to inform taxonomy; is it NOT a depiction of the degree of similarity

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46
Q

Bootstrap/posterior probability as branch support

A

statistical confidence assigned to certain branches

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47
Q

Neutral theory of molecular evolution

A

at the fine scale level, most new mutations are not favored or disfavored by natural selection (synonymous mutations); neutral mutations will arise at random and random processes (ie. genetic drift) will determine their fate in a population; since mutations arise at an average rate, they can be used to date the nodes on a molecular phylogeny

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48
Q

Graphic variations of a phylogeny

A

Cladogram (branching only); Phylogram (degree of change); Chronogram (calibrated to real time)

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49
Q

Parsimony inference

A

the best phylogeny is the one that explains the observed character data by positing the fewest evolutionary changes

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50
Q

Homology

A

shared traits because they are inherited from a common ancestor

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51
Q

Autapomorphy

A

a trait that does not help us distinguish between two trees because it is only in one lineage

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52
Q

Homoplasy

A

when similar characteristics are not due to common ancestry but instead arise by convergent evolution or evolutionary reversals; can create the mistaken impression that two species are closely related when they are not

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53
Q

Vestigial

A

a trait that has become functionless in the course of evolution (but still is present)

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54
Q

Ideal characters for phylogenies

A

have low rates of evolutionary convergence and/or reversal

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55
Q

What do different speeds of evolving characters show ie. fast vs slow)

A

slowly evolving characters ( including DNA sequences) can show the relationship between distant taxa while rapidly evolving characters (including DNA sequences) can reveal relationships between closely related taxa

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56
Q

Index case

A

source of the outbreak ex. someone who is initially affected brings a human pathogen to a new geographic location and transmits the disease to a few other recipients

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57
Q

Outbreak

A

when a disease continues to be transmitted

58
Q

Last Universal Common Ancestor (LUCA)

A

molecular characteristics: used nucleic acids (DNA OR RNA) as hereditary material, used a molecular mechanism to replicate this material, used the same triplet genetic code for amino acids, used similar biochemical pathways for energy ie. ATP;

cellular characteristics: had a plasma membrane, unicellular, lacked organelles

59
Q

Who are the prokaryotes?

A

archaea and bacteria; not monophyletic

60
Q

Characteristics of Prokaryotes

A

always unicellular but are capable of forming large colonial groups called biofilms ie. dental plaque; divide by binary fission, horizontal (lateral) gene transfer

61
Q

Stramatolites

A

rocks that are formed from biofilms of cyanobacteria trapping layers of sediment; 3.7 bya stramatolites are the earliest evidence of life

62
Q

Prokaryotes vs Eukaryotes

A

eukaryotes have a membrane bound nucleus and membrane bound organelles ie. mitochondria and chloroplast

63
Q

Peptidoglycan

A

only present in the cell walls of bacteria; gram positive: more; gram negative: less

64
Q

Membrane linkages between 3 Domains of Life

A

bacteria and eukarya have ester-linked membrane lipids while archaea have ether-linked membrane lipids which enable arachae to live in extreme conditions since ether linkages are more stable

65
Q

Coccus/cocci

A

round, spherical shaped bacteria

66
Q

Bacillus/bacilli

A

rod-like shaped bacteria

67
Q

Spirilium/spirilla

A

spiral shaped bacteria; have filaments that run along the long axis and use these filaments to move and can be highly mobile

68
Q

Staphyloccocus

A

unnamed taxon; genus that contains bacteria which live on your skin; most of the time they are harmless but can cause harmful and even deadly staph infections

69
Q

Bacillus anthracis

A

unnamed taxon; source of deadly anthrax

70
Q

Cyanobacteria

A

photoautotrophs meaning that they harvest carbon from carbon dioxide and use sunlight to break up the carbon dioxide and make glucose (photosynthesis); gave rise to chloroplasts via endosymbiosis

71
Q

Proteobacteria

A

well known human pathogens; exhibit the highest metabolic diversity of any organismal group (including animals); E.coli, Yersinia pestis, Vibrio cholerae, Salmonella

72
Q

E. coli

A

proteobacteria; lives in our GI tract but can also cause deadly food poisoning

73
Q

Yersinia pestis

A

proteobacteria; cause of bubonic plague

74
Q

Vibrio cholera

A

proteobacteria; causes cholera

75
Q

Salmonella

A

proteobacteria; causes food poisoning

76
Q

Spirochetes

A

spiral shaped bacteria with axial filaments: motile; Lyme disease, syphillis

77
Q

Chlymdias

A

small obligate parasites meaning that they cannot live outside of a host; can cause STDs and other strains can cause eye infection and even pneumonia

78
Q

What synapomorphy unites Eukarya and Archae

A

having DNA with histones and certain introns

79
Q

Characteristics of Viruses

A

don’t have a membrane bound nucleus, lack mitochondria, parasites, lack ATP and molecular machinery for replication

80
Q

Why are viruses placed outside the tree of life?

A

they lack ATP and can’t replicate without a host

81
Q

Binary fission vs. mitosis

A

binary fission: DNA is replicated, simple, no nucleus; mitosis: chromosomes replicated, forms 2 membrane bound nuclei; both create 2 daughter cells

82
Q

Characteristics of Archae

A

no membrane bound nucleus, no membrane bound organelles, no peptidoglycan in cell walls, ether linked membrane lipids, extremophiles but can also be found in soil, ocean plankton and microbiomes

83
Q

Methanogen

A

type of archaea; contribute to global warming by producing methane; also present in our gut microbiome

84
Q

Halophiles

A

survive in highly saline environments; typically archaea

85
Q

Characteristics of Eukaryotes

A

membrane enclosed nucleus, mitochondria, some have chloroplast, relatively large and complex

86
Q

Origin of eukaryotes

A

flexible cell membrane (loss of cell wall) -> infolding (increases surface area: volume) -> cytoskeleton forms from microtubules -> internal membranes with ribosomes -> infolded membrane encloses DNA forming the nucleus -> flagellum formed from microtubules -> endosymbios leads to mitochondria and chloroplasts

87
Q

Endosymbiosis

A

results from the incomplete phagocytosis of a bacterium where a mutualistic symbiotic relationship forms

88
Q

Characteristics of Protists

A

not a monophyletic group, eukarya that are not animals, fungi, or plants,

89
Q

Alveolates

A

unicellular protist; has sacs (alveoli) beneath cell membrane, secondary endosymbiosis of red algae; dinoflagellates, ciliates including Paramecium, Plasmodium -malaria

90
Q

Ciliates

A

covered with cilia which allows for controlled movement ie. Paramecium

91
Q

Dinoflagellates

A

have 2 flagella: one in an equatorial groove and the other longitudinal; tertiary endosymbiosis; themselves endosymbionts of coral; red tide, bioluminescence

92
Q

Plasmodium - Malaria

A

intracellular parasites, chloroplast is vestigial, complex of proteins at the apical prominence attach to and penetrate the host cell

93
Q

Stramenopiles

A

have 2 unequal flagellas one of which has tubular hairs ; brown algae and diatoms

94
Q

Brown algae

A

multicellular, some are very large, secondary endosymbiosis of red algae, found in kelp forests

95
Q

Diatoms

A

secondary endosymbiosis of red algae; unicellular, lost double flagella , deposit silica -> shells

96
Q

Excavates

A

reduced or lost mitochondria; euglenids, Giardia, Tyrpanosoma-sleeping sickness, Chagas’ disease, leishmaniasis

97
Q

Giardia

A

most common intestinal parasite, water borne

98
Q

Euglenids

A

have mitochondria, one large anterior flagellum, secondary endosymbiosis of green algae

99
Q

Trypanosoma

A

free living or parasite; some cause debilitating and deadly disease; single large mitochondria; sleeping sickness, Chagas’ disease, leishmaniasis

100
Q

Amoebozoans

A

lobe-shaped pseudopods, move by cytoplasmic streaming; slime molds, amoeba

101
Q

Darwin’s 3 Postulates

A

Natural selection will occur when: 1. individuals are variable in some trait 2. at least some of this variation is heritable 3. there is a struggle to survive or reproduce and some are better at it than others

102
Q

What causes phenotypic variation?

A

genetic differences, environmental differences, interactions between genes and the environment; (measurement error, ontogenic differences)

103
Q

Ontogenic differences

A

variation in phenotypes across development, occurs mostly before sexual maturation

104
Q

Heritability

A

the proportion of within-population variation in a trait that comes from genetic factors

105
Q

Natural selection

A

the non-random process by which biological traits become more or less common in a population as a result of the differential reproductive success of their bearers; one mechanism of evolution

106
Q

Selection differential/coefficient (S)

A

the difference between the population mean of a trait before and after selection

107
Q

Response to selection (R)

A

the difference between the mean of a trait before selection and the mean of that trait in the next generation

108
Q

Directional selection

A

favors phenotypes at one end of a distribution, the population evolves in that direction

109
Q

Stabilizing selection

A

favors values toward the middle of the distribution; fitness of organisms at either end is lower

110
Q

Disruptive selection

A

favors phenotypes toward the ends of the distribution

111
Q

Frequency dependent selection

A

occurs when the fitness of a genotype depends on its frequency in a population

112
Q

Negative frequency dependent selection

A

a phenotype has the greatest selective advantage if it is rare

113
Q

Positive frequency dependent selection

A

a phenotype has the greatest selective advantage if it is common

114
Q

Hamilton’s rule

A

a helping behavior can spread in a population if the cost to the donor is smaller than the benefit to recipient weighted by relatedness; if rB > C

115
Q

Senescence

A

a decline with age in per capita reproductive performance, physiological function, or the probability of survival

116
Q

Antagonistic pleiotropy

A

when a genetic variant with beneficial effects on one trait also has a detrimental effect on some other trait

117
Q

Fitness

A

an individual’s proportional representation in the gene pool of subsequent generations; can only be assessed relative to the fitness of other individuals

118
Q

Direct fitness

A

determined by the number of offspring an organism produces (and that survive to maturity) over its entire lifetime

119
Q

Life history

A

the timing and duration of key events during a liftetime (ie. age and duration of reproduction); often involves tradeoffs between present and future reproduction

120
Q

Current repro success

A

number of offspring

121
Q

Future repro success

A

of offspring times the likelihood of survival

122
Q

Survival vs reproduction

A

inverse relationship; high survival, delayed reproduction; low survival, high reproduction

123
Q

Extrinsic mortality

A

the rate at which external events (predation, starvation, infectious disease) leads to death in a population

124
Q

Intrinsic mortality

A

the rate at which internal events (aging, disease, mutation) lead to death in a population

125
Q

Individual selection

A

differential performance (fitness) of individuals causes some genotypes to replace others

126
Q

Group selection

A

differential performance (fitness) of groups of individuals causes some genotypes to outcompete and replace others (populations unstable)

127
Q

Altruism

A

behaviors that are costly to the individual performing them but benefit one or more others

128
Q

Inclusive fitness

A

direct fitness + indirect fitness

129
Q

True altruism

A

reduces inclusive fitness; rare because it is evolutionary disadvantageous

130
Q

Kin selection

A

selection arising from the indirect fitness benefits of helping relatives

131
Q

Locus

A

the position of a gene on a chromosome

132
Q

Allele

A

one copy of a gene at a locus

133
Q

Genotype

A

pair of alleles at a single locus; determines phenotype

134
Q

Microevolutionary forces the disturb Hardy-Weinberg equilibrum

A

natural selection, non-random mating, genetic drift, gene flow, mutation

135
Q

Hardy-Weinberg equilibrium

A

predicts what the allele frequencies and genotype frequencies would be if the population was not experiencing any evolution

136
Q

Equation for phenotypic variance in a population

A

Vp = Vg + Ve; Vg = Va + Vd + Vi

137
Q

Broad sense heritability

A

H2 = Vg/Vp; proportion of phenotypic variance that is due to genotype

138
Q

Narrow sense heritability

A

h2 = Va/Vp; proportion of phenotypic variance that results from additive (simple) genetic variance; remember that Vp = Vg + Ve

139
Q

Breeder’s equation

A

R = h2 * S

140
Q

Plastids

A

organelles derived from cyanobacterial endosymbionts

BIOEE 1780 (1 decks)

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