Exam 1 Flashcards

Question

Early Evolutionary Thought | Erasmus Darwin

Answer 1

Erasmus Darwin 1731-1802 Charles Darwin’s grandfather Species evolve into each other Linear progressive evolution--evolve toward increasing complexity No extinction

Answer 2

Jean-Baptiste Lamark (1744-1829) Organisms progress upward in response to environment Spontaneous generation from inanimate ancestors Trend towards increasing complexity Change acquired during lifetime is passed on to offspring No extinction, rather, transformation

Answer 3

George Cuvier (anatomist) compared bones of living animals to extinct ones and reconstructed their appearance William Smith: fossils were distinctive in each different rock layer; could be used to identify rocks in different parts of the country (England) Others demonstrated the phenomenon over Western Europe

Answer 4

Everything is made of matter Can be studied by science A materialistic world view emphasizes matter, physical processes over spiritual causes Simple, observable physical processes used to explain more complex events Gods/spirits not used as explanations for phenomena

Answer 5

Catostrophic events (geologic upheavals, Biblical Flood) could explain geological features (mountains, lakes)

Answer 6

Gradualists Change occurs slowly over long periods of time Cumulative action of everyday processes (sedimentation, erosion) explains geology A materialistic world view (emphasizes matter, physical processes over spiritual causes)

Answer 7

1798-1826—Thomas Malthus—resource limitation Thomas Malthus (1766-1834) Noted the geometric rise in the human population (vs. the arithmetic rise in agricultural production) Developed the idea of limitation of natural resources Too many people and not enough food -->famine, disease, conflict

Answer 8

1859 - Darwin publishes the Origin of Species. - Son of a doctor - “Landed gentry” - Abandoned medical training - Began theological training at Cambridge - An avid collector and naturalist - Engaged as ship’s naturalist aboard the Beagle - Captain Robert FitzRoy - At sea 1831-1836 - Mission: study geology and biology of S. America - Travels mainland and islands - Collects huge numbers of specimens - Back in England, studies mockingbirds, finches - Island forms are similar to mainland forms due to colonization and change - Develops idea of “transmutation”--species change from one to another

Answer 9

Publishes “Vestiges” in 1844 Argues in favor of evolutionary change Initially popular; subsequently widely denounced Darwin intimidated by public reception

Answer 10

South Seas naturalist Independently discovers evolution via natural selection Writes to Darwin to ask for his comments

Answer 11

Darwin and Wallace co-publish an article on their findings in 1858 Journal of the Proceedings of the Linnean Society “On the tendency of species to form varieties; and on the perpetuation of the varieties and species by natural selection”

Answer 12

Charles Darwin, 1859 Elaborated, expanded ideas set forth in the paper Used ideas from artificial selection (captive breeding) to support key arguments An intellectual sensation

Answer 13

“Descent with Modification” New species are produced from existing species Explains underlying similarities Explains diversity of organisms Explains pattern of the fossil record Doesn’t explain the precise mechanism, though

Answer 14

“Natural Selection” More offspring are produced than can survive Offspring vary in quality More robust or better equipped survive better Survivors pass on these traits to their offspring

Answer 15

1. Species are related by evolution, branching from common descent 2. Species change through time, they aren’t static 3. There is variation within species

Answer 16

Charles Darwin did not understand heredity (used “variation”) Gregor Mendel (1822-1884)—genetics of inheritance Importance of Mendel’s work not understood until years after his death

Answer 17

-Did not understand how variability was generated (mutation) -Did not know how variations are passed to offspring -Thought that traits “blend” (But phenotypes may blend; genotypes don’t)

Answer 18

Darwin’s ideas disputed for many years Between 1932-1953, genetics were incorporated with Darwin’s ideas Theory of Evolution is re-stated as the Modern Synthesis (Evolutionary Synthesis) Gradual evolution Origin of new species (macro-evolution) can be explained via natural selection on individuals (micro-evolution) Some individuals are more successful than others Individuals that survive and reproduce are those best adapted to environment Over time, these adaptive alleles will become more frequent in the population

Answer 19

result of small genetic changes acted on by natural selection

Answer 20

Mutation creates new alleles; shuffling leads to variation within a population Alleles are passed to offspring

Answer 21

Evolutionary processes tend to be invisible We see the products of evolution, not the process

Answer 22

Darwin used natural selection to explain adaptation process Lacked examples of natural selection Used examples of artificial selection in plants and animals

Answer 23

- Individuals in a population vary - Variations are heritable - Some variants survive and reproduce better than others - Individuals with the best variations (adaptations) are selected -Those “winners” become more common in the population over time - Darwinian evolution - Natural selection is a testable theory - Each postulate can be tested - Natural selection exploits genetic variance to increase fitness - It is an editor, not a writer - Mutation is a writer, creating new forms

Answer 24

gradual change in populations (gene frequencies) over time

Answer 25

The ability of an individual organism to survive and reproduce in its environment

Answer 26

A trait or characteristic of an individual that increases its fitness relative to individuals without the trait

Answer 27

-75% white with yellow dot, 25% all yellow 1. Population contained variation (white and all yellow individuals) 2. Variation in color was heritable (determined by different experiment) SS; Ss = white, ss = yellow

Answer 28

Counted bee visits (pollination = reproduction) Counted seeds produced (# seeds = # offspring) Answer: Yes!

Answer 29

Found some individuals received more bee visits Some individuals had higher reproductive success Answer: No! Some individuals are preferred!

Answer 30

Yes! Frequency of white flowers increased slightly in the population.

Answer 31

Yes! Ground finches vary in size. (All individuals were banded and measured).

Answer 32

Yes! Birds with larger beaks can crack larger, tougher seeds than birds with smaller beaks, which have to eat smaller seeds

Answer 33

Yes! There are allele differences in beak size.

Answer 34

During drought, only large seeds are available Birds with smaller beaks can’t eat them, so they starve Significant change in beak size due to natural selection can be observed over just one generation

Answer 35

- Natural Selection acts on individual organisms (they are either selected or not) - But change is seen in population characteristics over time - Natural Selection acts on phenotypes - But evolution consists of changes in allele frequencies - Natural selection does not look to the future! - Organisms do not plan for their evolutionary future! - Evolution is always “behind the curve” - Natural selection acts on existing traits - However, new traits can evolve - Selection acts on individuals - NOT for the good of the species

Answer 36

- Mutations can produce new alleles | - Meiosis and fertilization shuffle the possible allele combinations to create new genotypes

Answer 37

Genes may affect multiple traits Selecting for one trait may affect another in a different way

Answer 38

Ecological processes are visible - Birth - Death - Feeding - Competition - Predation Evolutionary processes tend to be invisible We see the products of evolution, not the process

Answer 39

= mechanism of evolution - Genetics - Natural selection - Molecular evolution - Speciation - Extinction

Answer 40

Genetics is at the core of evolution - Variation of genome - Transmission of genetic info

Answer 41

First to describe how heredity works Pea plants

Answer 42

One copy of the whole genome

Answer 43

Two copies of the whole genome

Answer 44

Multiple copies of the whole genome

Answer 45

There is no nucleus in bacteria, and the genome is a large, double-stranded, closed circle of DNA, without packaging.

Answer 46

In eukaryotic cells, the DNA is packaged in linear chromosomes, usually more than one chromosome for each cellular genome. Eukaryotic cells have their DNA wrapped around a backbone of proteins called histones.

Answer 47

= bundle of DNA

Answer 48

= an organism’s complete set of DNA (all chromosomes)

Answer 49

= locations of particular genes

Answer 50

= region of DNA (that codes for a protein)

Answer 51

= alternative forms of a gene at a given locus

Answer 52

Chromosomes recombine during meiosis - “Crossing over” - Ends (“feet”) break off - “Feet” recombine with other “legs” - Foot/leg recombinations are random

Answer 53

Genes on non-homologous chromosomes assort independently of each other Different gametes can be produced from the same sets of chromosomes

Answer 54

Randomly - Many sperm are available, only one gets to pair with each egg - Which sperm wins is random

Answer 55

- Point mutations - Frameshift - Inversions (Translocations) - Duplications (and deletions) - Genome Duplications

Answer 56

One nucleotide is replaced (e.g. adenine replaces a thymine) Description: Base pair substitutions in DNA sequences. Mechanism: Chance errors during DNA synthesis or during repair of damaged DNA. Significance: Creates new alleles

Answer 57

“Flips” a piece of chromosome so gene order along chromosome changes Description: Flipping of a chromosome segment, so order of the genes along the chromosome changes. Mechanism: Breaks in DNA caused radiation or other insults. Significance: Alleles inside the inversion are likely to be transmitted together, every unit.

Answer 58

Duplication of a short piece of DNA Description: Duplication of the short stretch of DNA, creating an extra copy of the sequence. Mechanism: Due to unequal crossing over during meiosis or retrotransposition. Significance: Redundant new genes may acquire new functions by mutation.

Answer 59

Duplication of entire genome Description: Addition of a complete set of chromosomes. Mechanism: Errors in meiosis or (in plants) mitosis. Significance: May create new species; Massive gene duplication.

Answer 60

(look at slide #75) 1. HIV virion 2. Binding 3. Fusion 4. DNA synthesis 5. DNA splicing 6. Transcription 7. Translation 8. New virion assembly 9. Budding 10. Muturation

Answer 61

-Dendritic cells capture a virus and prevent bit of its proteins to naive helper T cells. Once activated, these naive cells divide to produce effector helper T cells. (76)

Answer 62

- Effector helper T cells help stimulate B cells displaying the same bits of viral protein to mature into plasma cells, which make antibodies that bind and in some cases inactivate the virus. - Effector helper T cells also help activate killer T cells, which destroy host cells infected with the virus. (77)

Answer 63

-Most effector T cells are short lived, but a few become long-lived memory helper T cells. (78)

Answer 64

Macrophages, effector helper T cells, and memory helper T cells all have CD4 and CCR5 proteins on their cell membranes. These proteins are HIV’s entry point into the host.

Answer 65

- After initial infection, viral load increases rapidly, plummets, then gradually rises over time (years) - In acute stage, CD4 T-cell numbers crash, rebound, then decline over the long term (years) - Immune system is activated in acute stage, then plateaus at a high level over the long term (years)

Answer 66

HIV activates the immune system directly AND indirectly. Immune response and damage are ongoing. Eventually, the immune system is exhausted and can no longer function properly. This is the beginning of full-blown AIDS. (81)

Answer 67

- HIV’s reverse transcriptase uses nucleotides from the host cell to make a DNA strand complementary to the HIV virus’ strand. - The anti-AIDS drug AZT mimics a normal nucleotide (T), but lacks an attachment site for the next nucleotide in the chain. AZT therefore blocks replication of the HIV virus.

Answer 68

Individual HIV patients evolve resistance to AZT. As therapy continues over time, higher percentages of virions have acquired partial resistance. Higher and higher doses of AZT are required to suppress HIV virions. In most patients, AZT resistance evolves within six months.

Answer 69

Viral strains late in AZT treatment are genetically different from those found early in treatment. Reverse transcriptase is prone to errors, and HIV’s genome has no correction mechanism --> the highest mutation rate of any organism known so far. Some of these mutations cause an amino acid substitution that makes AZT less likely to bind to HIV’s reverse transcriptase, leading to resistance. Resistance is adaptive, so virions that have it reproduce and pass on their resistance. Virions without this mutation fail to reproduce. Over time, the resistant virions dominate the population and the patient no longer responds to AZT.

Answer 70

- Mutation - Errors in reverse transcription generate a variable population. Some variants differ in resistance to AZT. - Resistance (or susceptibility) is passed from parents to offspring. - During treatment with AZT, many virions fail to reproduce. - The variants that persist are the ones that can reproduce in the presence of AZT. - Result: The composition of the population had changed over time.

Answer 71

Using a single anti-retroviral drug such as AZT will cause rapid selection for drug resistance. A solution has been to use a “cocktail” of multiple drugs (HAART). As more AIDS patients use the multiple-drug “cocktail,” deaths from opportunistic infections decrease. However, the virus remains, and side-effects of treatment are significant. HAART uses a “cocktail” of multiple drugs. Treatment prolongs the lives of AIDS patients. However, resistance still arises in patients who miss doses.

Answer 72

Survivors tend to have a mutant CCR5 co-receptor (Δ32 allele; Δ32 is missing 32 base pairs that most people have) This CCR5 mutation prevents HIV from entering cells-->prevents infection Un-infected Europeans tend to have one or two copies of Δ32; infected Europeans don’t Humans have genetic variation for disease (HIV) resistance. HIV-resistant people have a mutant CCR5 co-receptor (Δ32 allele) HIV resistance can also be conferred by mutations in the CD4 receptor.

Answer 73

Allele frequency varies significantly in different countries. CCR5-Δ32 allele affects resistance to HIV infection. (91,92)

Answer 74

Monkeys transmitted SIV virus to chimpanzees Chimpanzees transmitted SIV to humans (HIV-1) Pet monkeys and/or contact through hunting probably transmitted SIV to humans (HIV-2) Two different sources of infection Multiple transmissions of SIV strains to great apes (chimps, gorillas) At least three separate infection events from great apes to humans (HIV-1 group M, N, O, P)

Answer 75

Human HIV is derived from primate SIV In monkeys, SIV generally causes little to no illness

Answer 76

- HIV-1 has a mutation that fails to suppress the host’s immune system, allowing for indefinite reproduction of the virus (most viruses would try to shut down the immune system of the host) - All hosts eventually die - If a parasite (e.g. HIV) is to survive, it has to leave the host and find a new one - Hosts vary in their resistance to HIV; viruses vary in their ability to move from one host to another (transmission) - Strains good at getting transmitted will survive; strains that are bad at being transmitted will die with the host

Answer 77

Continuous evolution of new epitopes (short pieces of viral protein) keeps virus population ahead of immune system response and assures rapid replication Viral population replication within a host becomes progressively more aggressive—later strains cause more damage than strains from earlier in infection Evolution of strains that can infect naïve T-cells (CXCR4 co-receptor). This speeds up collapse of the immune system.

Answer 78

HIV strains that use the CXCR4 co-receptor appear later in the life of the patient, when the patient is sicker HIV strains that use the CXCR4 co-receptor cause the patient’s immune system to collapse, resulting in death of the host HIV strains that use the CXCR4 co-receptor don’t get transmitted to new hosts, so they go extinct when the host (patient) dies

Answer 79

Frequencies of alleles and gene combinations - How often are certain combinations seen in a population? - Rare? Common?

Answer 80

= how genes determine an organism’s characteristics - Are all genes expressed at birth? - How do genes interact with each other? - How is gene expression related to environment?

Answer 81

- Survival and fertility are what natural selection acts upon - Organisms with a survival advantage tend to survive and reproduce - Trait becomes more common over time

Answer 82

= a part of the genome or a gene locus

Answer 83

= what the organism’s physical traits are (e.g. what it looks like)

Answer 84

= members of a (sexually reproducing) species living within a given area

Answer 85

= How much the selected population varies from the overall population The selection differential = S __ __ S = X whole pop — X selected pop

Answer 86

The selected sub-group gets to breed The change in the offspring relative to the original population = the Response to Selection = R __ __ R = X offspring — X whole pop.

Answer 87

The response (R) to selection = heritability (h2) times the selection differential (S) R = h2 S

Answer 88

Heritability equals the response to selection divided by the selection differential h2 = R/S

Answer 89

- Able to select for extreme phenotypes (high oil or high protein) - Selection effects are cumulative over time - Many genes are involved -Selection process can be reversed - Significant genetic variation is maintained over time - All 4 strains evolved from a single ear of corn

Answer 90

Populations are a mix of different phenotypes Natural selection may affect different phenotypes in different ways - Directional selection - Stabilizing selection - Disruptive selection - Frequency-dependent

Answer 91

- A typical population has a variety of phenotypes (look at slide 119) - The traits follow a normal distribution (120)

Answer 92

Favors one extreme phenotype in the population (look at slide 121)

Answer 93

Favors intermediate phenotypes (look at slide 122)

Answer 94

Penalizes intermediates and favors both extreme phenotypes (look at slide 123)

Answer 95

Perissodus microlepis - Scale-eating fish displaying “handedness” for mouth shape - Right-handed fish attack the left flank - Left-handed fish attack the right flank - “Mouth handedness” is genetically determined - Prey fish guard against the prevalent phenotype; suffer more attacks from the un-guarded side - In this way, the rare phenotype is favored for a time, then becomes common and loses out to the other phenotype, now rare

Answer 96

- 3 different morphs: Orange, Blue, and Yellow. - Orange: aggressive and territorial; large territories - Blue: guard mates to prevent sneaking; lose to aggressive orange males - Yellow: non-territorial sneakers (resemble females) -Females appear to prefer to mate with the rare type - Type is genetically controlled - Frequency of male types therefore fluctuates as the rare “preferred” type becomes more common and less desirable

Answer 97

- A Visible Case of Natural Selection - Two morphs, dark and light - As industry and coal dust coated trees, light form was more visible, and eaten more often by birds - Dark morph became more common in cities

Answer 98

Fitness = ave. reproduction of an individual/genotype over its lifetime Fitness reflects differences in net reproduction Fitness = (total reproduction) x (survival probability)

Answer 99

Heterozygote is better than both homozygote I.e sickle cell Look up!

Answer 100

-genetic disease ``` AA = normal Aa = carrier, partially affected aa = afflicted w/ sickle-cell ``` Normal red blood cells curve into a sickle shape These cells form clots in the blood vessels Victim suffers pain, bleeding, organ damage, death

Answer 101

Heterozygote has an advantage over both other genotypes: malaria resistance An example of heterozygote superiority

Answer 102

``` If there is no selection.... If there is no migration.... If the population is large.... If mating is random.... If there is no mutation…. ``` Then meiosis and recombination do not alter allele frequencies

Answer 103

Hardy-Weinberg equilibrium occurs when there is no change in allele frequencies Equilibrium is reached in 1 generation and remains stable unless acted on by some other force Hardy-Weinberg equilibrium explains why dominant alleles don’t replace recessive alleles in a population Hardy-Weinberg equilibrium is RARE in nature!

Answer 104

Hardy-Weinberg says no

Answer 105

Consider a population with two alleles, A and a. p = freq. of “A” allele q = freq. of “a” allele p + q = 1 Calculates allele frequencies in population

Answer 106

p^2 (AA) + 2pq (Aa) + q^2 (aa) = 1 ``` p = freq. of “A” allele q = freq. of “a” allele pq = “Aa” alleles (2pq because “Aa” or “aA”) ``` Calculates genotypes in population

Answer 107

...then evolutionary processes are occurring!

Answer 108

- Selection.... - Migration (gene flow).... - Small populations (inbreeding).... - Non-random reproduction.... - Mutation - Random chance events (genetic drift)

Answer 109

- Increases gene flow - Moves genes between populations - Prevents alleles from disappearing from population - Introduces mutations into larger population

Answer 110

May, 2006 Good weather causes mass birch tree flowering in Scandinavia Pollen deposited throughout Britain

Answer 111

When related individuals mate - Reduces heterozygosity (Aa) - Increases homozygosity (AA, aa) - Reduces genetic variance - Can increase the chance of getting a recessive genetic disorder (CF, TS) But inbreeding can vary by degree

Answer 112

Reduction of fitness Reduction of functional characters

Answer 113

F = inbreeding coefficient - ~measures deviation from random mating Ranges from 0.0 - 1.0 0 = not inbred 1 = highly inbred

Answer 114

When an allele occurs 100% of the time, it has been “fixed” in the population Inbred lines remain “true to their breed”: deviants are rare

Answer 115

A large population gets sub-divided Several distinct, isolated populations result Mutations occur, but not they are not the same in all the populations (diff. mutations, diff. frequencies)

Answer 116

Loss of genetic diversity of the species That’s why we care about small populations

Answer 117

= a random fluctuation in allele frequencies due to sampling error Leads to fixation of some alleles Leads to loss of other alleles Leads to an overall decline in genetic variation over time

Answer 118

Larger populations are less likely to be affected Small populations more likely to lose alleles due to random fluctuations Affects small populations more dramatically and more quickly Can contribute to speciation by causing an isolated population to diverge

Answer 119

Either/Or One type or the other - Brown fur vs. black fur - Spots vs. no spots - Pink flower vs. blue flower

Answer 120

Continuous; on a spectrum - Height - Weight - Fertility - Longevity

Answer 121

Phenotype = Genotype + Environment

Answer 122

Variance in Phenotype = Variance in Genotype + Variance in the Environment VP = VG + VE (See slide 47)

Answer 123

Shows the amount of dispersal around a mean (the amount of variation) (See slide 48)

Answer 124

Different genes can interact with each other How a gene is expressed (gene expression) is a result of additive and/or full dominance

Answer 125

VA = genetic variation with no dominance or gene interaction (epistasis)

Answer 126

h^2 = heritability Heritability = the relative importance of heredity in character development ~The resemblance of offspring to parents h^2 = VA / VP VA = Additive genetic variance VP = Phenotypic variance -Value of h2 ranges from 0 to 1.0 0 = inheritance not important to trait (low h2) 1 = inheritance very important to trait (high h2) - Size tends to be highly heritable - Fertility tends to be less heritable

Answer 127

Consider a colonization event where some individuals leave the population and form a new population Allele frequencies in a new population are likely to be different than those in the original population

Answer 128

Amish - High incidence of Ellis van Creveld syndrome (dwarfism + polydactyly; hole in the heart; nail and teeth deformity) - One couple carried in 1744, passed to children - Intermarriage spread trait

Answer 129

Afrikaners in South Africa - Originated from a few Dutch settlers - High incidence of Huntington’s disease - Founders carried Huntington’s disease allele at higher fq. than general population; over time it spread through S. African population

Answer 130

Achromotopsia on Pingelap Island, Micronesia - Typhoon killed most residents of island - One survivor carried mutation - Achromotopsia now affects ~6% of island residents - Only 1 in 33,000 in general population

Answer 131

-Cheetahs -Florida panthers -Northern elephant seals --Heavily hunted in 1800’s --Population crashed to ~20 individuals --Now population ~30,000 --Reduced genetic variation compared to Southern elephant seals (a less hunted population) (See slide 60)

Answer 132

Size of an ideal randomly mating population (no selection, mutation, or migration) that would lose genetic variation (via drift) at the same rate as is observed in the actual population

Answer 133

Factors affecting effective population size (Ne): Variations in mating success Non-random mating Unequal sex ratios Correlations in repro success (inbreeding) Fluctuations in population size

Answer 134

Biological Species Concept Phylogenetic Species Concept Morphospecies Species Concept -Biologists usually use the Biological Species Concept

Answer 135

Examines phylogenetic trees and finds smallest groups (distinct branch tips) Based on statistically significant differences in traits used to estimate phylogeny (family tree)—can be tested using DNA (See slide 66)

Answer 136

Based on morphological differences between groups But variation may not be indicative of different species; careful grouping necessary Morphology may not reflect genetic diffs.

Answer 137

There is reproductive isolation between 2 populations Members of the 2 populations do not reproduce successfully

Answer 138

Failure to mate Offspring are produced but are not fertile

Answer 139

Pre-zygotic isolating mechanisms (prevent formation of an embryo) Usually have relatively low fitness costs POST-zygotic isolating mechanisms (act after fertilization occurs) Usually have a high fitness cost

Answer 140

- Different habitats - Different mating seasons - No sexual attraction - Fertilization problems - Coital problems (organs may not match up)

Answer 141

Successful mating occurs, but offspring is sterile Mating occurs, but offspring does not survive

Answer 142

- Populations become separated - Each has an independent evolutionary fate (they evolve separately) - Geographical separation of populations fosters speciation - Dispersal barriers lead to independent evolutionary tracks for each population - 2 separated populations may experience different environmental conditions - This leads to adaptation to those different conditions - Can lead to allopatric speciation (see slide 86)

Answer 143

Geographically separated populations = allopatric | See slide 84

Answer 144

See slide 87

Answer 145

Transposable elements are different in different populations When reunited, genomes may no longer be compatible (i) Genomes may evolve duplications (ii) One population has a larger genome that is incompatible with the other population due to size differences (e.g. muntjacs) Chinese muntjac = 46 chromosomes Indian muntjac = only 6 chromosomes

Answer 146

Sympatric populations occur in the same geographic area Therefore, it is hard for complete population isolation to occur (See slides 96,97)

Answer 147

- Disruptive selection may occur - Extreme phenotypes are favored - Intermediate phenotypes are eliminated -Hybrids of the extremes will be intermediate and will be selected against - Extremes will succeed better if they mate with similar phenotypes - polyploidy - Differences in insect/plant host associations may cause sympatric speciation - Fruit flies can eat several types of fruit, but they tend to stay put on a single type - Flies in different regions choose different plant hosts - This leads to geographic isolation on a micro scale

Answer 148

Some organisms gain extra copies of chromosomes = polyploidy Polyploid plants are no longer compatible with normal plants—> reproductive isolation Normal plants = sexual reproduction Polyploid plants = vegetative reproduction via clones/runners (See slide 102)

Answer 149

1. Disruptive selection may occur 2. Polyploidization 3. Differences in insect/plant host associations 4. Assortative mating 5. Sensory drive

Answer 150

mating with someone that's your type. There is variety but you pick the mate that most resembles you

Answer 151

integration of environmental factors along with sexual Selection , mating preferences, acting together

Answer 152

When a species mates with another species and they produce offspring

Answer 153

- Alleles to spread across populations - New hybrids = new types - Inviable/infertile hybrids

Answer 154

Area where local conditions permit hybridization to occur Especially if 2 allopatric populations resume contact

Answer 155

Normally have reduced fitness relative to parents, but sometimes have better fitness Plants especially have hybrids with higher fitness (See slides 110, 112-116)

Answer 156

Can have extra chromosomes: allopolyploidization 1 parent contributes an extra set of chromosomes Offspring is triploid

Answer 157

A. jeffersonianum x A. laterale salamanders hybridize 1 parent contributes an extra set of chromosomes Triploid offspring are produced 2 hybrid combos are possible: extra chromosomes can be contributed by either parent species Parents reproduce sexually Offspring reproduce parthenogenetically (asexually)!

Answer 158

Also called adaptive radiation When many new species arise in a relatively short period of evolutionary time Often happens on islands Many niches are empty Little or no competition Species can evolve to fill an ecological vacuum

Answer 159

Darwin’s finches Anolis lizards

Answer 160

1830 — Charles Lyell: Principles of Geology ``` Charles Lyell (1797-1875) Founder of modern geology ``` Recognized that rock layers represented depositions of different layers of fossils Uniformitarianistic world view--change is gradual 1830: wrote Principles of Geology, an important book in its day; greatly influenced Charles Darwin.

Answer 161

Phylogeny Pattern of events that happen as a group diversifies Sequence of lineages (what appeared when) Generated by inference since most of our data is incomplete

Answer 162

Phylogeny = a diagram depicting the evolutionary history of a group of organisms descending from a common ancestor Pattern of events that happen as a group diversifies Sequence of lineages (what appeared when) Generated by inference since most of our data is incomplete

Answer 163

= a diagram depicting the evolutionary history of a group of organisms descending from a common ancestor

Answer 164

A way to establish relationships between organisms - What characters do they share? - How closely related are they? - When did major evolutionary events happen? - Oldest organisms at the base - Younger species at the tips - Shape and orientation varies Three different styles of trees that all express the equivalent relationships (see slide 11) -Groups that are more closely related should share more traits -Groups that are less related should share fewer traits (See slide 15-17)

Answer 165

Three trees that all express the equivalent relationships, regardless of branch length

Answer 166

These trees depict equivalent relationships, despite the fact that certain internal branches have been rotated so that the order of the tip labels is different.

Answer 167

Traits used must be independent (change in one character cannot change another character) Characters must be homologous (similarity in traits is due to a common ancestor)

Answer 168

Similarity in traits is due to a common ancestor Synapomorphies = shared traits derived from a common ancestor Evolutionary relationships are revealed by shared derived traits (synapomorphies) A structure present in an ancestor species is retained in a descendent, but the structure may be highly modified (see slide 23)

Answer 169

= shared traits derived from a common ancestor -Synapomorphies reveal relationships (See slide 20, 21) - Synapomorphies identify evolutionary branch points - Synapomorphies are nested (each branching event adds more shared derived traits) - Mutations can create synapomorphies, and you can map these changes onto a phylogenetic tree - But…reversals may obscure the correct phylogeny. - If a reversal has occurred, similar traits are NOT homologous (they are not synapomorphies) - Reversals ("back-mutations") can remove synapomorphies - (See slide 26)

Answer 170

= phylogenetic tree created by clustering synapomorphies | See slide 25

Answer 171

A monophyletic group includes all of the descendants of the ancestor under investigation (See slide 27)

Answer 172

Ancestral character

Answer 173

Derived character

Answer 174

- More than one tree may be possible - How do you determine the best tree? 1. Make a matrix of character states 2. Draw all possible trees 3. Mark evolutionary events on trees 4. Count number of events needed for pattern 5. Compare trees: which has the fewest transitions? Fewest transitions = most parsimonious - Problems can arise in making a tree - Homoplasy = similarity of characters NOT due to a shared common ancestor

Answer 175

We may not know anything about the common ancestor (no characters) Similar evolutionary novelties sometimes evolve independently in different lineages (homoplasy) Evolutionary novelties may evolve, then are lost (reversal), returning to ancestral condition

Answer 176

= similarity of characters NOT due to a shared common

Answer 177

Convergent organisms may look very similar or have similar structures. Convergent organisms may play similar roles in the environment, but they have: - Different evolutionary histories - Different ancestors - Different DNA - Organisms evolve solutions to environmental problems - Natural selection favors similar traits in similar environments See slides 58-60

Answer 178

- Different evolutionary histories - Different ancestors - Different DNA

Answer 179

``` Thorny devil (Agamidae; Moloch horridus) from Australia (left) and Horned toad (Phrynosomidae; Phrynosoma coronatum) from Texas ( See slide 59,60) ``` - Different families - Both desert species - Ant specialists

Answer 180

Perform similar functions NOT derived from the same structure Result of similar evolutionary pressures, not shared heritage Shark claspers; squid hectocotylus (see slide 62)

Answer 181

Monophyletic group = clade (related species with a common ancestor) -- taking ancestor and all its descendants Non-monophyletic group -- looks at ancestor and SOME descendants (See slide 64)

Answer 182

A polytomy occurs when there is not enough information to resolve evolutionary relationships into dichotomies The result is “flat” trees or multiple branches emerging from the same point (See slide 66)

Answer 183

Two hypotheses about the origin of whales: A. Whales are artiodactyls and belong inside that group Alternatively, B. Whales are relatives of artiodactyls and belong next to that group (See slide 67-75, 77,78,80)

Answer 184

Branch lengths are proportional to number of nucleotide substitutions per site (per branch) Optimize branch lengths Compare alternative trees to predicted chance of certain sequences

Answer 185

Maximum likelihood/BMCMC: - What is the chance that alternative trees are supported by the data? - Given certain parameters, what is the likelihood that a certain tree will occur? - Highest likelihood = better tree

Answer 186

You’ve used parsimony and/or maximum likelihood to make your tree; now just how sure are you about its accuracy? You could collect more data and re-run your analysis, or you could bootstrap Bootstrapping creates a new data set (bootstrap replicates) from existing data to compare trees with/without certain branches; see which is correct 1. Make new data set: here, randomly select 6 nucleotides from the pool for each animal. 2. Construct a new tree based on this random selection. 3. Rinse. Repeat. 100-1,000+ times. 4. Majority-rule consensus model = new tree that contains all the monophyletic groups that appear in at least 50% of the bootstrap replicates 5. What percentage of replicates have this monophyletic grouping pattern? This number = bootstrap support = confidence in your clade

Answer 187

Select characters carefully Use more characters Use more species Use multiple techniques

Answer 188

A species ceases to exist anywhere in the world | Species with larger geographic ranges survive longer See slide 99,100

Answer 189

- New species arise - Some go extinct - Some evolve - Some remain relatively unchanged over time Existing species represent a balance between extinction and new species (See slide 90)

Answer 190

- Disease - Predation - Competition with other species - Pollinator loss - Habitat loss - Habitat fragmentation

Answer 191

- Climate change - Excessive heat - Drought - Salinity - Ice Age - Volcanic activity

Answer 192

When an unusually high number of extinctions occur

Answer 193

Permian/Triassic mass extinction - 250 MYA - A catastrophic species loss—the “great dying” - Wiped out >50% of all families - Wiped out >90% of all species - Why?

Answer 194

What caused the P-T extinction? - Not entirely clear - Massive tectonic movement of continents - Alteration of ocean currents - Change in climate - CO2 buildup to toxic levels - Asteroid impact?

Answer 195

Also known as the K-T extinction - 65 MYA - Dinosaurs wiped out - 50% of all genera What caused the K-T extinction? -The Alvarez hypothesis:

Answer 196

Asteroid impact Tosses up giant dust cloud Affects climate and sunlight Plant and animal die-off

Answer 197

- Iridium layer at K-T boundary - Iridium is common in asteroids - Shocked quartz, found with asteroid impacts - Micro-tektites - Chicxulub crater: impact site (See slide 113-117)

Answer 198

- The physical environment can affect abundance and distribution of species - Organisms adapt to their environment

Answer 199

- Temp - Heat - Cold - Water - Gas exchange - Light - Body size - Metabolism - Energy acquisition - Energy use - Nutrient acquisition (how do they get the food) - Waste elimination

Answer 200

- Enzymes work best in a narrow temperature range - Freezing destroys cells - Heating de-natures proteins - Temp affects water balance - Water balance affects Temp - Light levels affect Temp - Temp affects metabolism - Organisms regulate their body Temp - Have different strategies

Answer 201

-animals are cool/warm to touch

Answer 202

-body Temp varies

Answer 203

-body Temp stays constant

Answer 204

-generate heat internally via metabolism

Answer 205

-need external heat source