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    Evolutionary Biology Lecture Guide

    BIO 200

    Jessica Poulin

    Department of Biological Sciences

    University at Buffalo–SUNY 

    7th Edition

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    Copyright © 2017 by Jessica Poulin

    Copyright © 2017 by Hayden-McNeil, LLC on illustrations provided

    Photos provided by Hayden-McNeil, LLC are owned or used under license

    All rights reserved.

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    cal, including photocopying and recording, or by any inormation storage or retrieval

    system.

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    10 9 8 7 6 5 4 3 2 1

    ISBN 978-0-7380-8386-5

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    iii

    Dear Students,

    Welcome to Bio 200—Introduction to Evolutionary Biology! I’m excited to be beginning

    this course with you, as evolutionary biology and its sister fields are the parts o biology I

    love most.

    Tis lecture guide is designed to help you keep on top o all o the material we’ll be discuss-

    ing this semester. Tere’s a lot o it, so the most successul students keep on top o the mate-

    rial as we go and are very organized! For each lecture this guide contains an outline, a list o

    key terms or concepts, a list o people to know, and a list o organisms to know. Tese itemswill help to make sure that you are taking notes on the correct things and understand all the

    parts o lecture I think are most important (i.e., that I will test you on!).

    Te key terms and concepts are listed in the approximate order that they appear in class.

    Many students use the space afer the terms to take notes during class. Others take notes

    in class and then fill in the guide later to cement the concepts we covered. Please use the

    system that works best or you.

    Te paper guide does not contain copies o the slides I will lecture rom. Tese cannot be

    sold due to copyright issues. However, slides will be posted on UBLearns. I SRONGLY

    urge you to print the slides beore coming to class to take notes on.

    As a companion to this guide, you are receiving access to practice questions or the entire

    course. Tese will be posted online (directions or accessing the questions are on UBLearns).

    For each lecture you will be able to work through a set o 10–14 practice exam questions.

    Tese questions are a very good gauge o the exams I will give in class. I strongly recom-

    mend you take your practice test afer going over your notes and that you time yoursel!

    Your midterms will be given during class time, so you have 50 minutes to take a 30 question

    test. Tat’s 1.6 minutes per question. Efficiency is a major key to exam success! As with

    most things academic, practice improves perormance. Tat’s why I provide the practice

    questions.

    Tere are also two old exams or each section o the course (Evolution, Diversity, and Ecol-

    ogy/Final) available. Wait until you have gone to all the lectures rom a given exam, studiedyour notes, taken all the practice tests, AND made your cheat sheet. Ten take the old ex-

    ams as i you were taking a real test (with your cheat sheet and under time). Tis is excellent

    preparation or what it will be like to be in the real exam!

    Good luck—I look orward to working with all o you this term!

    Best!

    Dr. Poulin

     WELCOME

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    iv   Bio 200 Lecture Guide

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     v 

    Table of Contents

    Letter to Students . . . . . . . . . . . . . . . . . . . . . . . . iii

    able o Contents . . . . . . . . . . . . . . . . . . . . . . . . v  

    Evolution Section

    Lecture 2 Material . . . . . . . . . . . . . . . . . . . . . . . . 1

    Lecture 3 Material . . . . . . . . . . . . . . . . . . . . . . . . 5

    Lecture 4 Material . . . . . . . . . . . . . . . . . . . . . . . . 9

    Lecture 5 Material . . . . . . . . . . . . . . . . . . . . . . . . 13

    Lecture 6 Material . . . . . . . . . . . . . . . . . . . . . . . . 19

    Lecture 7 Material . . . . . . . . . . . . . . . . . . . . . . . . 23

    Lecture 8 Material . . . . . . . . . . . . . . . . . . . . . . . . 27

    Lecture 9 Material . . . . . . . . . . . . . . . . . . . . . . . . 31

    Lecture 10 Material . . . . . . . . . . . . . . . . . . . . . . . 35

    Reerence Page or Evolution Material (Exams 1 and 3) . . . . . . . . . . . 39

    Diversity Section

    Lecture 11 Material . . . . . . . . . . . . . . . . . . . . . . . 41

    Lecture 12 Material . . . . . . . . . . . . . . . . . . . . . . . 45

    Lecture 13 Material . . . . . . . . . . . . . . . . . . . . . . . 51

    Lecture 14 Material . . . . . . . . . . . . . . . . . . . . . . . 57

    Lecture 15 Material . . . . . . . . . . . . . . . . . . . . . . . 63

    Lecture 16 Material . . . . . . . . . . . . . . . . . . . . . . . 67

    Lecture 17 Material . . . . . . . . . . . . . . . . . . . . . . . 71

    Lecture 18 Material . . . . . . . . . . . . . . . . . . . . . . . 75

    Lecture 19 Material . . . . . . . . . . . . . . . . . . . . . . . 81

    Lecture 20 Material . . . . . . . . . . . . . . . . . . . . . . . 87

    Lecture 21 Material . . . . . . . . . . . . . . . . . . . . . . . 91

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     vi  Bio 200 Lecture Guide

    Lecture 22 Material . . . . . . . . . . . . . . . . . . . . . . . 95

    Lecture 23 Material . . . . . . . . . . . . . . . . . . . . . . . 99

    Lecture 24 Material . . . . . . . . . . . . . . . . . . . . . . . 103

    Reerence Page or Diversity (Exams 2 and 3) . . . . . . . . . . . . . . 107

    Ecology Section

    Lecture 25 Material . . . . . . . . . . . . . . . . . . . . . . . 109

    Lecture 26 Material . . . . . . . . . . . . . . . . . . . . . . . 113

    Lecture 27 Material . . . . . . . . . . . . . . . . . . . . . . . 117

    Lecture 28 Material . . . . . . . . . . . . . . . . . . . . . . . 121

    Lecture 29 Material . . . . . . . . . . . . . . . . . . . . . . . 127

    Lecture 30 Material . . . . . . . . . . . . . . . . . . . . . . . 131

    Lecture 31 Material . . . . . . . . . . . . . . . . . . . . . . . 135

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    1

    Outline

    ime Scales

    1. Te ormation o the Earth

    2. What happens next: Four eras

    3. A brie tour through the history o time (on Earth)

    Origin of Life

    1. Extra-terrestrial origins?

    2. What is lie?

    3. Te Earth beore lie originated

    4. Four steps

    Key Terms/Concepts

    Note: You do not need to know details about the ormation o the Earth itsel, just the basic

    terms will be fine here.

    1. Protoplanetary disk 

    2. Formation o our sun

    3. Protoplanet

    4. Precambrian supereon

    5. Paleozoic era

    6. Mesozoic era

    7. Cenozoic era

    Lecture 2

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    2

    Lecture 8. Hadean eon (Don’t just tell me it’s the first period o time on Earth; be able to de-

    scribe it.)

    9. Archean eon

    10. Unicellular vs. multicellular

    11. Cyanobacterial mats/stromatolites

    12. Bacterial ossils

    13. Archean ossils

    14. Earliest multicellular lie

    15. rilobites

    16. Archeocyathids

    17. 1st land plants

    18. 1st land animals

    19. Permian extinction

    20. Age o reptiles

    21. 1st mammals

    22. K– extinction event

    23. K– boundary 

    24. Geological clock 

    25. Continental drif and changing geography 

    26. What is lie?

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    3

    27. Four steps to orm lie

    28. Miller and Urey’s experiment

    29. Building blocks o lie

    30. Monomers and polymers

    31. Te importance o clay 

    32. Protobionts

    33. Four reasons we think there was originally an RNA world

    34. Viroids

    People to Know 

    • Stanley Miller

    • Harold Urey 

    Organisms to Know 

    • Cyanobacteria

    • rilobites

    • Archeocyathids

    • Dinosaurs

    •  Morganucodon watsoni

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    4

    Lecture Student Notes and Questions

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    5

    Outline

    History of the Teory of Evolution and Mr. Darwin

    1. Supernatural vs. scientific explanations or creation

    2. History o evolutionary thought

    3. Introducing Mr. Darwin

    4. Darwin’s ollowers

    Key Terms/Concepts

    1. Features o a divinely inspired creation

    2. Common descent

    3. ransmutation o species

    4. Binomial nomenclature

    5. Nested hierarchy o organisms

    6. Sedimentation

    7. Erosion

    8. Gradualism

    9. Great Geological Cycle

    10. “we find no vestige o a beginning [o time], no prospect o an end”

    Lecture 3

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    6

    Lecture 11. “invisible hand”

    12. Competition and sel-interest

    13. Lamarckian evolution

    14. Acquired traits

    15. Populations grow geometrically, while ood supplies only grow linearly 

    16. Te role o disasters in keeping the ood supply in line with the population

    17. Impact o extinction on theories o creation

    18. Catastrophism

    19. “the present is the key to the past”

    20. Uniormitarianism

    21. Atolls

    22. Darwin’s observations on the voyage o the Beagle and their impact on his theory 

    23. Te importance o WHERE the organisms came rom on the Galapagos

    24. Wallace’s line

    25. What’s the big idea?

    People to Know 

    • Anaximander

    • Carolus Linnaeus

    • James Hutton

    • Adam Smith

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    7

    • Jean-Baptiste Lamarck 

    • Tomas Malthus

    • Georges Cuvier

    • Charles Lyell

    • Charles Darwin

    • Alred Russel Wallace

    • Gregor Mendel

    • James Watson

    • Francis Crick 

    Organisms to Know 

    • Glyptodon

    • Mockingbirds

    • Galapagos tortoises

    • Finches

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    8

    Lecture Student Notes and Questions

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    9

    Outline

    Darwin’s Evidence

    1. Darwin’s hypothesis o natural selection

    2. Evidence or Darwin’s hypothesis rom his lietime

    3. Modern evidence

    4. Implications o Darwin’s hypothesis

    5. Evidence to support the implications

    Key Terms/Concepts

    1. Tree actors necessary or natural selection

    2. Five actors necessary or natural selection

    3. Explain evidence that individuals vary 

    4. Explain evidence that organisms overbreed given available resources

    5. Te Grants’ work on the medium ground finch

    6. Daphne Major

    7. Can you analyze the graphs rom the Grants’ work?

    8. El Niño years and La Niña years

    9. Can you explain how the Grants’ data shows evidence o adaptation to environmental

    conditions (better variations have better survival)?

    Lecture 4

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    10

    Lecture 10. I I told you about weather conditions on Daphne Major, could you make predic-

    tions about what would happen PHYSICALLY to the finches there?

    11. Heritability 

    12. What does heritability say about natural selection?

    13. Other issues that made Darwin’s work hard or people to accept

    14. Te age o the earth (how does this support Darwin?)

    15. Fossil evidence o adaptation (how does this support Darwin?)

    16. Percent o living ossils decreases the older the rock strata (how does this supportDarwin?)

    17. Archaeopteryx (how does this support Darwin?)

    18. Modern examples o transitional orms (how does this support Darwin?)

    19. Te horse lineages

    20. Te problem with missing links

    21. What did Darwin know about the proo o his hypothesis beore his death?

    People to Know 

    • Peter Grant

    • Rosemary Grant

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    11

    Organisms to Know 

    • Archaeopteryx

    •  Ambulocetus natans

    • iktaalik

    • Te Equidae

    • Hyracotherium

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    12

    Lecture Student Notes and Questions

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    13

    Outline

    What Darwin Didn’t Know: Mendel and Basic Genetics

    1. Gregor Mendel and the collapse o the blending model

    2. Mendel’s basic process

    3. Monohybrid crosses

    4. Mendel’s five element model and the principle o segregation

    5. Punnett squares

    6. Dihybrid crosses

    7. Principle o independent assortment

    Extending Mendel

    1. Do peas make it too easy?

    2. Gene linkage

    3. Polygenic inheritance

    4. Epistasis

    5. Pleiotropy

    6. Incomplete dominance and codominance

    7. Environmental effects on gene expression

    Key Terms/Concepts

    1. Blending inheritance

    2. Why work with peas?

    3. rue breeding

    4. What does it mean to “cross” something?

    Lecture 5

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    14

    Lecture 5. What is a trait?

    6. Hybrids

    7. Te importance o quantification o results

    8. Monohybrid crosses

    9. P generation

    10. Cross ertilization

    11. F1, F2, etc., generations

    12. Sel-crossing

    13. Monohybrid ratios

    14. Latent traits

    15. Te meaning o the five element model—what conclusions does Mendel draw rom

    each o his elements?

    16. Factors/Genes

    17. Allele

    18. Homozygote/Homozygous

    19. Heterozygote/Heterozygous

    20. Dominant

    21. Recessive

    22. Genotype

    23. Phenotype

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    15

    24. Mendel’s 1st law/Segregation

    25. How do you fill in and analyze a Punnett square?

    26. Where are the gametes on a Punnett square?

    27. Can you determine the parental genotypes rom a Punnett square?

    28. Phenotype vs. genotype ratios

    29. Dihybrid crosses

    30. Dihybrid ratios

    31. Can you find the gametes and parental genotypes rom a dihybrid Punnett square?

    32. Mendel’s 2nd law/Independent assortment

    33. Gene linkage

    34. wo state cases vs. multi-state cases

    35. Polygenic inheritance

    36. Epistasis

    37. How is epistasis different rom polygeneic inheritance?

    38. Given a genotype would you know what color a Labrador was?

    39. Pleiotropy 

    40. Why is sickle cell still around?

    41. Incomplete dominance

    42. Codominance

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    16

    Lecture 43. How does incomplete dominance differ rom codominance? Could you tell them

    apart?

    44. How are blood types determined?

    45. Environmental effects on gene expression

    People to Know 

    • Gregor Mendel

    Organisms to Know 

    • Peas

    • Labradors

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    17

    Student Notes and Questions

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    18

    Lecture Student Notes and Questions

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    19

    Outline

    What Mendel Didn’t Know: Chromosomes and Recombination

    1. Chromosomes are discovered and come in pairs

    2. A brie introduction to mitosis and meiosis

    3. Haploidy, diploidy, polyploidy 

    4. Sex chromosomes: an unusual pair

    5. Recombination via crossing over

    What Does DNA Do?

    1. Understanding how we’ve gone rom actors to DNA

    2. Nucleic acids, the double helix, and a quick tour o DNA replication

    3. Te central dogma (DNA→ RNA→ aa→ Protein)

    4. How central is it?

    5. Codons and translation: A universal code

    6. Closely related species have similar proteins and DNA

    Key Terms/Concepts

    1. Chromosomes

    2. Te implications o paired chromosomes

    3. Human chromosome counts

    4. Karyotype

    5. Chromatid

    6. Sister chromatids

    Lecture 6

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    20

    Lecture 7. Centromere

    8. Homologous pair

    9. Basics o mitosis and meiosis

    10. Cell outcomes o mitosis and meiosis

    11. Basic differences between mitosis and meiosis

    12. Ploidy 

    13. Sex chromosomes

    14. Crossing over/Recombination

    15. How do chromosomes explain gene linkage?

    16. Does recombination eliminate gene linkage?

    17. Te basic structure o DNA

    18. Nucleotides

    19. How does DNA replicate?

    20. What is the central dogma o molecular biology?

    21. ranscription and translation

    22. How are proteins ormed?

    23. Given a DNA or RNA transcript, can you “build” a protein?

    24. Codons and the amino acid table (do not memorize table)

    25. What do comparisons o amino acid sequences (Cytochrome C), gene unctions, or

    DNA sequences tell us about organism relatedness?

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    21

    People to Know 

    • James Watson

    • Francis Crick 

    Organisms to Know 

    • No new organisms or lecture 6

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    22

    Lecture Student Notes and Questions

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    23

    Outline

     Microevolution

    1. What causes evolution?

    2. Allele requencies: A critical measure

    3. Gene flow 

    4. Non-random mating

    5. Genetic drif

     Mutation in Detail 

    1. How do codons get read?

    2. Incorrect readings: a variety o point mutations

    3. Chromosome level mutations

    4. Aneuploidy and polyploidy 

    5. Causes and effects o mutations

    Key Terms/Concepts

    1. Allele requency 

    2. Population

    3. Can an individual evolve?

    4. Microevolution

    5. Microevolutionary orces

    6. Gene flow 

    7. Does gene flow increase or decrease genetic variation?

    Lecture 7

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    24

    Lecture 8. Non-random mating

    9. Assortative mating

    10. Sel-ertilization

    11. Does non-random mating increase or decrease genetic variation?

    12. Genetic drif

    13. Founder effect

    14. Bottleneck effect

    15. How are ounder and bottleneck effects different?

    16. Does genetic drif increase or decrease genetic variation? Founder effects? Bottle-

    neck effects?

    17. Mutation

    18. Where do new genes come rom?

    19. Crick and Brenner’s experiments and their results

    20. Degenerate code

    21. Reading rame and rameshif

    22. Silent, missense, and nonsense mutations

    23. Chromosome level mutations

    24. Nondisjunction

    25. Aneuploidy

    26. Monosomy 

    27. risomy and common trisomys

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    28. Polyploidy 

    29. Causes o mutation (mutagens)

    30. Outcomes o mutation

    People to Know 

    • Francis Crick 

    • Sydney Brenner

    Organisms to Know 

    • No new organisms or lecture 7

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    26

    Lecture Student Notes and Questions

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    27

    Outline

     Natural Selection

    1. Te only adaptive evolutionary orce

    2. Stabilizing selection

    3. Directional selection

    4. Disruptive selection

    5. Balancing selection

    6. Determining fitness

    Sexual Selection

    1. Males and emales have different reproductive strategies

    2. Females choose…

    3. …most o the time (when the exception proves the rule)

    4. Males compete

    5. Females gain by their choosiness

    a. Co-parents

    b. erritory 

    c. When males don’t stick around—theories!

    Key Terms/Concepts

    1. Natural selection

    2. Adaptation

    3. Adaptive

    4. Selective orces (definition and examples)

    5. Fitness

    Lecture 8

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    28

    Lecture 6. Absolute fitness

    7. Relative fitness

    8. Stabilizing selection

    9. Directional selection

    10. Disruptive selection

    11. Balancing selection

    12. Heterozygote advantage

    13. Negative requency dependent selection

    14. Reproductive strategy 

    15. Parental investment

    16. What happens when male and emale parental investment is equal or males invest

    more?

    17. Female choice

    18. Male/Male competition

    19. Sexual dimorphism

    20. Paternal care

    21. erritory deense and resource acquisition

    22. Good genes hypothesis

    23. Handicap principle hypothesis

    24. Runaway selection

    25. Ghost o selection past

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    29

    People to Know 

    • No new people or lecture 8

    Organisms to Know 

    • Fence lizards

    • Pocket mice

    • Salmon

    • Colonial bentgrass, Agrostis tenuis

    • Elephant seals

    • Australian riflebirds

    • Pea owl

    • Long-tailed widowbird

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    30

    Lecture Student Notes and Questions

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    31

    Outline

    Species Concepts and Reproductive Isolation

    1. What is a species?

    2. Morphological species concept

    3. Biological species concept

    4. Prezygotic isolating mechanisms

    5. Postzygotic isolating mechanisms

    Species Formation

    1. How does one species become two?

    2. Allopatric speciation

    3. How is allopatry achieved?

    4. Is sympatric speciation possible?

    5. Neat examples o speciation: Adaptive radiation and ring species

    Key Terms/Concepts

    1. Morphological Species Concept

    2. Biological Species Concept

    3. Reproductive isolation

    4. Prezygotic vs. postzygotic isolating mechanisms

    5. Geographic or ecological isolation

    6. Allopatric/allopatry 

    7. Sympatric/sympatry 

    Lecture 9

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    32

    Lecture 8. emporal isolation

    9. Behavioral isolation

    10. Mechanical isolation

    11. Gametic isolation

    12. Hybrid inviability 

    13. Hybrid inertility 

    14. Hybrid breakdown

    15. How does allopatric speciation occur?

    16. Ways that allopatric isolation can occur (dispersal, vicariance, “the third one”)

    17. How is continental drif related to allopatric speciation and species distributions?

    18. How do the different microevolutionary orces affect the chances o speciation?

    19. Sympatric speciation

    20. Polyploidy 

    21. How might disruptive selection lead to sympatric speciation?

    22. Adaptive radiation

    23. Subspecies

    24. Ring species

    People to Know 

    • No new people or lecture 9

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    33

    Organisms to Know 

    • Liger/igon (no, you don’t have to remember which parents lead to which)

    • Wild lettuce (Lactuca sp.)

    • Blue- and red-ooted boobies

    • Abalone

    • Donkey, Horse, and Mule

    • Cycads

    • Anolis lizards

    • Cichlid fish

    • Pea aphids

    • Silverswords and arweed

    • Rat snakes

    • Salamanders

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    34

    Lecture Student Notes and Questions

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    35

    Outline

    Phylogenetic rees

    1. Introducing trees and tree terminology 

    2. How to make trees rom molecular data

    a. Parsimony 

    3. And i you don’t have molecular data?

    a. Homology and homoplasy 

    4. Putting events on trees

    5. Does taxonomy reflect phylogeny?

    a. Monophyly and paraphyly

    Key Terms/Concepts1. Common descent

    2. Common ancestor

    3. Phylogeny 

    4. How is time represented on a phylogeny?

    5. Branches

    6. Nodes

    7. ips

    8. Great chain o being

    Lecture 10

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    Lecture 9. Why is a phylogeny different than a “great chain”?

    10. Sister taxa

    11. Outgroup

    12. Nodes twist without affecting evolutionary relatedness

    13. Making trees with DNA data

    14. Parsimony 

    15. Do mutations in a single species give more or less inormation or phylogeny build-

    ing than mutations in multiple species?

    16. Non-DNA traits used or making phylogenies

    17. Homoplasious traits/Convergent traits

    18. Homologous traits

    19. Derived traits vs. ancestral traits

    20. Making trees with traits tables

    21. Placing event “tick marks” on trees

    22. Universal common ancestor

    23. Most recent common ancestor

    24. Monophyletic

    25. Prokaryotes

    26. Paraphyletic

    27. Why doesn’t taxonomy always reflect phylogeny?

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    People to Know 

    • No new people or lecture 10

    Organisms to Know

    • No new organisms or lecture 10

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    Lecture Student Notes and Questions

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    Te dates for critical time periods in the Earth’s history:

    Precambrian supereon: 4.6 BYA–543 MYA

    Paleozoic era: 543 MYA–250 MYA

    Mesozoic era: 250 MYA–65 MYA

    Cenozoic era: 65 MYA–now 

    Te Amino Acid Code—Square

    Phe

    Firstposition

    Secondposition Ala = Alanine

    Arg = Arginine

    Asn = Asparagine

    Asp = Aspartate

    Cys = Cystine

    Gln = Glutamine

    Glu = Glutamate

    Gly = Glycine

    His = Histidine

    Ile = Isoleucine

    Leu = Leucine

    Lys = Lysine

    Met = Methionine

    Phe = Phenylalanine

    Pro = Proline

    Ser = Serine

    Thr = Threonine

    Trp = Tryptophan

    Tyr = Tyrosine

    Val = Valine

    Thirdposition

    Leu

    UUU

    U C A G

    U

    C

     A 

    G

    UUC

    UUA 

    UUG

    CUU

    CUC

    CUA 

    CUG

     AUU

     AUC

     AUA 

     AUG

    GUU

    GUC

    GUA 

    GUG

    Leu

    Ile

    Met/start

    Stop Stop

    Stop

    Val

    UCU

    UCC

    UCA 

    UCG

    CCU

    CCC

    CCA 

    CCG

     ACU

     ACC

     ACA 

     ACG

    GCU

    GCC

    GCA 

    GCG

    Pro

    Thr

    Ser

    Ala

    TyrUAU

    UAC

    UAA 

    UAG

    CAU

    CAC

    CAA 

    CAG

     AAU

     AAC

     AAA 

     AAG

    GAU

    GAC

    GAA 

    GAG

    Cys

    Trp

    UGU

    UGC

    UGA 

    UGG

    U

    C

     A 

    G

    U

    C

     A 

    G

    U

    C

     A 

    G

    U

    C

     A 

    G

    CGU

    CGC

    CGA 

    CGG

     AGU

     AGC

     AGA 

     AGG

    GGU

    GGC

    GGA 

    GGG

    His

    Gln

    Asn

    Lys

    Ser

    Arg

    Asp

    Glu

    Arg

    Gly

    ©Hayden-McNeil, LLC

    Reference Page for EvolutionMaterial (Exams 1 and 3)

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    Te Amino Acid Code—Circle

    5'

    3'

    3'

    3'3'

    G

    G

    GG

    G

    G

    G

    G

    G

    G

    GG

    G

    G

    G

    G

    G

    G

    G

    G

    G

    U

    U

    U

    U

    U

    U

    U

    U

    UU

    Phe(F)

    Leu(L)

    Ser (S)

    Tyr (Y)

    Cys (C)

    STOP

    STOP

    Trp (W)

    Leu (L)

    Pro (P)

    His(H)

    Gln(Q)Arg (R)Ile (I)

         S     t    a

        r     t        /        M

         e       t         (           M

            )  Thr (T)

    Remember: AUG codes

    for methionine and  is the

    start codon.

    Asn(N)

    Lys (K)

    Ser (S)

    Arg (R)

    Val (V)

    Ala (A)

    Asp(D)

    Glu(E)

    Gly (G)

    U

    U

    U

    U

    U

    U

    UU

    U

    U

    U

    A

    A

    A

    A

    A   A

    A

    A

    A

    A

    A

    A

    AA

    A

    A

    A

    A

    A

    A

    A

    C

    C

    C

    C

    C

    C   C

    C

    C

    C

    C

    C

    C

    CC

    C

    C

    C

    C

    C

    C

     ©  H a  y

      d  e  n -  M

       c   N  e

        i    l ,  

         L     L

       C

    Reerence Page or Evolution Material (Exams 1 and 3)

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    Outline

    Viruses and the Nature of Life

    1. Lie or not lie?

    2. What are viruses?

    3. Virus structure and reproduction

    4. Slow viruses???

    Te ree of Life

    1. Te real tree o lie vs….

    2. our view o the tree

      a. Our view is biased

    3. Te three domain model is a better system

    4. Diversity is noted in different ways or different organisms

    5. Bacteria and Archaea

    6. Te protists are not monophyletic

    7. Plants, ungi, and animals are (slightly) more understood

    Key Terms/Concepts

    1. What is lie?

    2. Virus structure

    3. Capsid/protein coat

    4. Viral hereditary material

    5. Virions

    6. Helical and Icosahedral shapes

    Lecture 11

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    Lecture 7. Binal

    8. Bacteriophage

    9. Te basics o viral replication

    10. Why do some scientists argue that viruses are not alive? Why do other scientists

    (and your book) disagree?

    11. SE and some examples

    12. How are prions different than viruses?

    13. Why were prions originally called slow viruses?

    14. Prion “replication”

    15. How is the traditional (5 or 6 kingdom) view o the tree o lie biased?

    16. Tree domain model

    17. LUCA

    18. raits shared by all lie-orms

    19. Key traits common to bacteria and archaea

    20. Defining traits o eukaryotes

    21. How is the new eukaryotic tree different rom older views?

    People to Know • No new people or lecture 11

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    “Organisms” to Know 

    • Corona virus

    • obacco mosaic virus

    • Adenovirus

    • Influenza

    • Scrapie

    • Bovine spongiorm encephalopathy (Mad-Cow Disease)

    • Chronic wasting disease

    • Creutzeldt-Jakob disease

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    Lecture Student Notes and Questions

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    Outline

    “Prokaryotes” 

    1. 2/3s o the tree o lie in 1/2 a lecture!

    2. Fundamentally different rom eukaryotes

    3. Early classification

    4. Metabolism

    5. Differentiating archaea and bacteria

    6. Common bacteria

    7. Common archaea

    Key Terms/Concepts

    1. Why is “prokaryotes” in quotes?

    2. Why do we only spend one day on 2/3s o the tree o lie?

    3. Differentiate the “prokaryotes” rom the eukaryotes

    a. Unicellularity 

    b. Internal structure

    c. Chromosomes

    d. Cell division

    Lecture 12

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    Lecture e. Gene transer

    . Cell wall

    g. Flagella

    h. Size?

    4. Colonial or filamentous growth

    5. Nucleoid

    6. Binary fission

    7. Bacterial generation time

    8. Lateral gene transer

    9. Web o lie vs. tree o lie

    10. Peptidoglycan, Pseudomurein

    11. Gram + and Gram – bacteria, Archaea?

    12. Pre-DNA bacterial classification

    a. Shape (bacilli, cocci, spirillum)

    b. Metabolism (anaerobes [acultative, obligate, aerotolerant], aerobes, photoau-

    totrophs, photoheterotrophs, chemoautotrophs, chemoheterotrophs)

    c. Other classification topics

    13. Can you make tick marks on a phylogeny?

    14. Low-GC Gram +

    15. High-GC Gram +

    16. Hyperthermic bacteria

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    17. Hadobacteria

    18. Cyanobacteria

    19. Spirochetes

    20. Chlamydias

    21. Proteobacteria

    22. Crenarcheota

    23. Extremophiles (Termophilic, Cryophilic, Halophilic, etc.)

    24. Euryarcheota

    25. Methanogens

    People to Know 

    • No new people or lecture 12

    Organisms to Know 

    (Some of these are organisms, and some are the diseases caused by the organisms.)

    • Termotoga maritima

    • Bacillus anthracis

    • Botulism

    • uberculosis

    • Actinomyces

    • Deinococcus

    • Syphilis

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    Lecture • Lyme disease

    • Escherichia coli

    • Salmonella

    • Plague

    • Cholera

    •  Methanopyrus

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    Student Notes and Questions

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    Lecture Student Notes and Questions

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    Outline

    Origin of the Eukaryotes

    1. Earliest eukaryotes

    2. Eukaryotic traits

    3. Origin o organelles

    4. Endosymbiosis: mitochondria and chloroplasts

    Protists

    1. Protists are not monophyletic

    2. Protist traits

    3. Building the bridge to multicellularity

    ypes of Protists1. Alveolates

    2. Stramenopiles

    3. Rhizarians

    4. Excavates

    5. Amoebozoans

    6. Choanoflagellates

    Lecture 13

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    Lecture Key Terms/Concepts

    1. Eukaryote traits

    2. How does compartmentalization lead to internal structure?

    3. Why is the loss o the cell wall critical to eukaryotic development?

    4. Formation o organelles

    5. Endosymbiosis leading to mitochondria and chloroplasts—know figures!

    6. How are the protists prooundly paraphyletic?

    7. Variation in protist traits

    a. Locomotion

    b. Cell suraces

    c. Nutrition

    d. Reproduction

    8. Te development o multicellularity 

    9. Protist groups

    a. Alveolates

    i. Dinoflagellates

      ii. Apicomplexa

      iii. Ciliates

    b. Stramenopiles

    i. Brown algaes

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      ii. Diatoms

      iii. Oomycetes (water molds and downy mildews)

    c. Rhizarians (ex.: Foraminierans)

    d. Excavates

      i. Diplomonads and Parabasalids

      ii. Euglenids

    e. Amoebozoans

    i. Loboseans

      ii. Plasmodial and cellular slime molds

    . Choanoflagellates—within Opisthikonts with animals and ungus

    10. Origin o chloroplasts (multiple endosymbiotic events)

    People to Know 

    • No new people or lecture 13

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    Lecture Organisms to Know 

    • Gymnopodium

    • Plasmodium falciparum

    • Paramecium

    • Brown algae (ex.: giant kelp)

    • Sea otters

    • Diatoms

    • White rust

    • Giardia intestinalis

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    Student Notes and Questions

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    Lecture Student Notes and Questions

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    Outline

    Origin of Land Plants

    1. How do plants evolve?

    2. “actics” or land invasion

    3. A general plant lie cycle

    4. Just what is a plant?

    5. Red algae: Te outgroup to the plants

    6. Chlorophytes and stoneworts

     Non-Seeded Land Plants

    1. Moving to land: Embryophytes

    2. Nonvascular plants or Bryophytes: Liverworts, mosses, and hornworts

    3. Te moss lie cycle

    4. Te next big advance: racheid cells

    5. Lycophytes and Monilophytes (Horsetails and Ferns)

    6. Te ern lie cycle

    Key Terms/Concepts

    1. Major ways plants differ rom protists

    2. Challenges o land living

    3. Adaptations to land dwelling

    4. Diplontic lie cycle

    Lecture 14

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    Lecture 5. Haplodiplontic lie cycle

    • Sporangia

    • Spore mother cells

    • Spores

    • Archegonium

    • Antheridium

    • Zygote

    • Embryo

    6. Sporophyte

    7. Gametophyte

    8. How do the events o meiosis and syngamy (ertilization) shape the haplodiplontic

    lie cycle?

    9. Dominant lie stages

    10. Describe different ways to define “plants”

    11. Rhodophyta (Red algaes)

    12. Chloroplast ormation

    13. Primary and secondary endosymbiosis

    14. Chlorophyll types

    15. Chlorophytes

    16. Stoneworts

    17. Nonvascular plants (Bryophytes)

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    18. Seedless vascular plants (racheophytes)

    19. What does it mean to be nonvascular?

    20. raits o bryophytes

    21. Moss lie cycle

    22. racheid cells (xylem and phloem)

    23. Benefits o tracheids

    24. Lycophytes

    25. Microphylls and megaphylls

    26. Monilophytes

    27. Sori

    28. Fern lie cycle

    People to Know 

    • No new people or lecture 14

    Organisms to Know 

    • Giant sequoia, Sequoiadendron giganteum

    • Coast redwood, Sequoia sempervirens

    • Chlamydomonas

    • Volvox 

    • Red algaes (ex.: the species that makes Nori)

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    Lecture • Chara

    • Liverworts

    • Hornworts

    • Mosses

    • Club mosses

    • Horsetails

    • Ferns

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    Student Notes and Questions

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    Lecture Student Notes and Questions

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    Outline

    Seed Plants—Gymnosperms

    1. Te seed is an important advancement

    2. Gymnosperms have naked seeds

    3. Gymnosperm lie cycle

    4. Tere are our groups o gymnosperms

    Seed Plants—Angiosperms

    1. Flowers and ruits

    2. Dissecting a flower

    3. What is a ruit?

    4. Angiosperm lie cycle

    5. Why are angiosperms so successul?

    Key Terms/Concepts

    1. Parts o a seed

    a. Megaspore

    b. Nucellus

    c. Integument

    d. Micropyle

    2. Tree ways seeds are adaptive

    Lecture 15

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    Lecture 3. Homospory vs. heterospory 

    4. Microspore mother cell, microspores, pollen, sperm

    5. Ovules, megaspore mother cell, megaspore, emale gametophyte

    6. Naked seeds

    7. Pollen tube

    8. Why aren’t seed plants dependent on water?

    9. Cycads

    10. Ginkgos

    11. Gnetophytes

    12. Coniers

    13. raits o angiosperms (flowers and ruit)

    14. Flower parts (sepals, petals, anthers, filaments, stamens, ovary, ovules, style, stigma,

    carpel)

    15. ypes o ruits

    16. Egg, Synergids, Antipodals, Polar nuclei

    17. Pollen tube, ube cell, Generative cell

    18. Double ertilization, 2N zygote, 3N endosperm

    19. How is the angiosperm lie cycle different than the gymnosperm lie cycle?

    20. What do we think makes angiosperms so successul?

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    People to Know 

    • No new people or lecture 15

    Organisms to Know 

    • Ginkgo biloba

    • Welwitschia

    • Ephedra (Mormon tea)

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    Lecture Student Notes and Questions

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    Outline

    ouring the Angiosperms

    1. A ossil angiosperm: Archaefructus 

    2. Te most ancestral extant group: Amborella 

    3. Modern groups

    4. Nymphaeales and Austrobaileyales

    5. Chloranthaceae and Ceratophyllum

    6. Magnoliidae, Eudicots, and Monocots

    Coevolution of Plants and Pollinators

    1. Pollination versus ertilization

    2. Abiotic vs. biotic

    3. Abiotic: Water and wind

    4. Biotic: Insects (beetles, bees, butterflies, moths)

    5. Biotic: Birds and bats

    6. Plant goal achievement: rap flowers, a case study

    Key Terms/Concepts

    1. What is the “abominable mystery”?

    2. Te nine clades o angiosperms (ocus on the seven in your book)

    a.  Archaefructus

    b.  Amborella

    c. Nymphaeales

    d. Astrobaileyales

    Lecture 16

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    Lecture e. Chloranthaceae

    . Ceratophyllum

    g. Magnoliids

    h. Eudicots

    i. Monocots

    3. Definition o pollination syndrome

    4. Pollination vs. ertilization

    5. Abiotic vs. biotic (generally and with regard to pollination)

    6. Specific pollination syndromes:

    a. Water

    b. Wind

    c. Beetle

    d. Short- vs. long-tongued bee

    e. Fly 

    . Butterfly 

    g. Moth

    h. Hummingbird

    i. Bat

    7. Coevolution

    8. Nectar guide

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    9. UV spectrum and pollination

    10. What do flowers “get” out o these coevolutionary relationships?

    11. Te example o Aristolochia (trap flowers)

    People to Know 

    • No new people or lecture 16

    Organisms to Know 

    •  Archefructus

    •  Amborella trichopoda

    • Water lily 

    • Star anise

    • Magnolias

    • Nutmeg

    • Rose

    • Pea

    • Daffodil

    • Orchid

    • rap flowers

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    Lecture Student Notes and Questions

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    Outline

    What’s a Fungus? 

    1. Te ungus hike (Not really testable, right?)

    2. Defining traits o ungi

    3. General biology o the ungi

    ypes and Ecology 

    1. Microsporidia

    2. Chytridomycetes

    3. Zygomycetes

    4. Glomeromycetes

    5. Ascomycetes

    6. Basidiomycetes

    7. Fungal ecology: mutualists, saprobes, and parasites

    Key Terms/Concepts

    1. How do ungi fit onto the eukaryotic tree?

    2. “Uniying” ungal traits

    3. Cell types

    4. Fungal body 

    a. Hyphae

    b. Septa

    Lecture 17

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    23. Ascomycetes

    24. Basidiomycetes

    25. Mutualists

    26. Saprophytes

    27. Parasites

    28. Why are ungal diseases hard to treat?

    People to Know • No new people or lecture 17

    Organisms to Know

    (Again, some of these are species and some are diseases caused by fungi.)

    • Batrachochytrium dendrobatidis 

    • Cup ungus

    • Yeast

    • Penicillin

    • ruffles and morels

    • Cheese molds

    • Chestnut Blight

    • Dutch Elm Disease

    • Mushrooms

    • Athlete’s oot

    • Ringworm

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    Outline

     Animal Diversity 

    1. raits o all animals

    2. Te animal body plan evolves through five key transitions

    3. Te new (DNA-based) animal tree

    Te Basal Animals

    1. Non-symmetric and radially symmetric animals

      a. Sponges, Cnidaria (and Ctenophora)

    2. Bilaterians

    a. Arrow worms

      b. Lophotrochozoans: Part 1 (Pretty much, worms)

    i. Bryozoans and Entoprocts

      ii. Flatworms

      iii. Rotiers

      iv. Ribbon worms

     v. Annelids

    Key Terms/Concepts

    1. raits that uniy animals

    2. Symmetry 

    a. Radial

    b. Bilateral

    3. Dorsal, ventral, anterior, posterior

    Lecture 18

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    Lecture 4. Cephalization

    5. Diploblastic development

    6. riploblastic development

    7. Endoderm, ectoderm, mesoderm

    8. Benefits o variable tissues

    9. Protostome vs. deuterostome

    10. Acoelomates, pseudocoelomates, coelomates

    11. Segmentation and locomotion

    12. How has the DNA-based tree changed rom the old morphological tree?

    13. Lophotrochozoans

    14. Ecdysozoans

    15. Sponges

    16. Sponge morphology 

    a. Choanocytes

    b. Water pores

    17. Cnidarians

    18. Polyps

    19. Medusae

    20. Cnidarian digestion

    21. All you need to know about Ctenophorans and Placozoans is that they are other

    phyla o radial, diploblastic animals

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    Lecture • Leeches

    • Polychaetes (ex.: ube worms)

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    Student Notes and Questions

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    Lecture Student Notes and Questions

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    Outline

    Lophotrochozoans: Part 2 (Mollusks)

    1. Mollusks are highly diverse

    2. Mollusk body plan

    3. Mollusk reproduction

    4. Tere are our classes o mollusks

    Ecdysozoans

    1. What is an ecdysozoan?

      a. Nematodes (roundworms) and Horsehair worms

      b. Water bears and Onychophorans (velvet worms)

      c. Arthropods

    Key Terms/Concepts

    1. What did the common ancestor to mollusks look like?

    2. Parts and various roles o the generalized mollusk body plan

    a. Visceral mass

    b. Foot

    c. Mantle

    3. Cephalization in the mollusks

    4. Radula

    5. Mollusk reproduction

    Lecture 19

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    Lecture 6. Polyplacophora (Chitons)

    7. Gastropods

    8. Bivalves

    9. Cephalopods

    10. What makes an ecdysozoan?

    11. Nematodes (Roundworms)

    12. Eutely 

    13. Model organisms

    14. Horsehair worms

    15. Water bears

    16. Onychophorans (Velvet worms)

    17. What did the common ancestor o the arthropods probably look like?

    18. Species richness (number o species) o arthropods

    19. rilobites

    20. Jointed appendages and body segments in arthropods (head, thorax, abdomen)

    21. Exoskeletons in arthropods

    22. Molting in arthropods

    23. Limitations placed on organisms with exoskeletons

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    24. Differentiations between arthropod groups

    a. Arachnids (Chelicerae, eight legs, etc.)

    b. Myriapods (Repeating segments, leg pairs, etc.)

    c. Crustaceans (wo antennae, three-part bodies, etc.)

    d. Insects (Six legs, antennae, three-part bodies, etc.)

    People to Know 

    • No new people or lecture 19

    Organisms to Know 

    • Slugs

    • Snails

    • Nudibranchs

    • Clams

    • Mussels

    • Oysters

    • Scallops

    • Octopus

    • Squid

    • Nautilus

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    Lecture • Horseshoe crab

    • Hookworms

    • Pinworms

    • Caenorhabditis elegans or C. elegans

    • Grasshopper

    • icks

    • Spiders

    • Scorpions

    • Centipedes

    • Millipedes

    • Shrimp

    • Lobster

    • Crab

    • Pill bug

    • Fly 

    • Dragonfly 

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    Student Notes and Questions

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    Lecture Student Notes and Questions

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    Outline

    Echinoderms and Hemichordates

    1. Echinoderms are the first deuterostome

    2. Pentaradial symmetry and endoskeleton

    3. Te water vascular system and tube eet

    4. Echinoderm regeneration and reproduction

    5. Tere are three groups o Echinoderms

    6. Tere’s just not a ton to say about hemichordates: Acorn worms

    Chordates raits and Non-Vertebral Chordates

    1. What makes a chordate?

    2. Lancelets

    3. unicates

    Key Terms/Concepts

    1. What makes a deuterostome?

    2. Ancestral deuterostomes: homalozoans

    3. Echinoderms

    4. Pentaradial symmetry 

    5. Echinoderm larvae

    6. Echinoderm skeletons

    7. Water vasculature system

    Lecture 20

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    Lecture 8. Madreporite and tube eet

    9. Oral surace

    10. Aboral surace

    11. Asexual and sexual reproduction in echinoderms

    12. Extinct echinoderms

    13. Te three groups o echinoderms: Crinoids, Echinozoans, and Asterozoans

    14. Can you name and describe defining organisms in each group?

    15. Hemichordates

    16. Chordate traits

    a. Dorsal hollow nerve cord

    b. Notochord

    c. Pharyngeal gill slits

    d. Post-anal tail

    17. Chordate segmentation

    18. Non-vertebral chordate groups (Lancelets and unicates)

    19. Non-vertebral chordate larvae and chordate traits

    People to Know 

    • No new people or lecture 20

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    Organisms to Know 

    • Sea stars

    • Brittle stars

    • Sea urchins

    • Sand dollars

    • Sea lilies

    • Feather stars

    • Sea cucumbers

    • Acorn worms

    • unicates (Sea squirts)

    • Lancelets

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    Lecture Student Notes and Questions

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    Outline

    What Makes a Vertebrate?

    1. Vertebrate traits

    2. Hagfish: Sister taxa or the first vertebrates?

    3. Lampreys

    Fish

    1. Fish traits and classes

    2. Te evolution o jaws

    3. eeth and the sharks

    4. Bony fish dominate the fish world

    Te Invasion of Land 1. Lobed fish led the invasion o land

    2. Amphibian traits

    3. errestrials challenges led to species like Ichthyostega 

    4. Tree classes o amphibians

    Key Terms/Concepts

    1. Vertebrate traits

    a. Head

    b. Endoskeleton supported by vertebrae

    c. Internal organs

    d. Circulatory system

    Lecture 21

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    Lecture 2. Where to put the hagfish?

    3. Hagfish and lampreys: Cyclostomes

    4. Vertebrate groups

    5. Fish diversity (only ully aquatic group)

    6. Five traits o all fish

    a. Jaws

    b. Paired appendages

    c. Internal gills

    d. Single loop blood circulation

    e. Amino acid deficiencies

    7. Sharks and rays

    8. Te importance o teeth

    9. Cartilage vs. bone

    10. Swim bladders

    11. Ray-finned fish vs. Lobe-finned fish (esp. locomotion)

    12. Challenges o land invasion

    13. Amphibians

    14. raits shared by modern amphibians

    a. Legs

    b. Lungs

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    c. Cutaneous respiration

    d. Pulmonary veins

    e. Partially divided hearts

    15. Major amphibian groups

    16. Age o amphibians

    People to Know 

    • No new people or lecture 21

    Organisms to Know 

    • Sea horses/Leay sea dragons

    • unas

    • Eels

    • Manta rays (rays in general)

    • Coelacanths

    • Lungfish

    • Ichthyostega

    • Frogs and toads

    • Salamanders

    • Mud puppies

    • Caecilians

    • Eryops megacephalus

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    Lecture Student Notes and Questions

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    Outline

    Reptiles

    1. Mastering the art o living on land

    2. raits o modern reptiles

    3. Synapsids and diapsids

    4. Archosaurs and dinosaurs

    5. Modern reptiles

    a. uataras

      b. Lizards and snakes (squamates)

    c. urtles and tortoises

      d. Crocodilians

    Birds1. Where did birds come rom?

    2. Birds share our key traits

    3. Beak and oot morphology determine ecology 

    4. Bird evolution

    Key Terms/Concepts

    1. Reptile perect transition to terrestrial lie

    2. Defining traits o reptiles

    3. Who are the amniotes?

    4. Benefits o the amniotic egg

    5. Internal ertilization

    Lecture 22

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    26. Bird skeletons

    27. Bird lungs

    28. Endothermy in birds

    29. Beak and oot morphology 

    30. General order o bird evolution

    31. Passeriormes (song birds)

    People to Know • No new people or lecture 22

    Organisms to Know 

    • Pelycosaurs

    • Crocodiles

    • Alligators

    • Caimans

    • Gavials

    • Velociraptors

    • Ostriches

    • Ducks and Geese

    • Owls

    • Parrots

    • Woodpeckers

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    Lecture Student Notes and Questions

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    Outline

     Movie: A Winning Design

     Mammals

    1. Te age o mammals

    2. Mammals share five traits

    3. Certain mammals have some pretty cool derived traits

    4. Tere are two groups o mammals

    Key Terms/Concepts

    1. Why do mammals have a winning design?

    2. How do animals in very cold climates stay warm (two reasons)?

    3. Mammals live in highly variable habitats

    4. Mammals gain nutrients rom many different sources

    5. Details about monotreme biology—how are they different rom other mammals?

    6. Size variation among mammals

    7. Mammalian ancestors

    8. Some mammals are extinct

    Lecture 23

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    Lecture 9. Five mammalian traits:

    a. Hair (including various roles o hair)

    b. Mammary glands

    c. Endothermy 

    d. Sweat glands

    e. Placentas

    10. Mammalian teeth

    11. Herbivores’ gut symbionts

    12. Hooves and horns

    13. Prototherians (monotremes) vs. therians

    14. Marsupials

    15. Eutherians

    16. Common ancestor to the eutherians

    17. Rapid radiation o eutherians afer dinosaurs go extinct

    18. Eutherian diversity mirrors the break up o the continents

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    People to Know 

    • David Attenborough

    Organisms to Know 

    • Echidna

    • Platypus

    • Whales and Dolphins

    • Porcupines

    • Hedgehogs

    • Bats

    • Koalas

    • Yapok 

    • Wallaby 

    • Wombat

    • Virginia opossum

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    Lecture Student Notes and Questions

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    Lecture 4. Platyrrhini (New World Monkeys)

    5. Catarrhini

    6. Old World Monkeys

    7. Hominoids (Gibbons, Great Apes, Humans)

    8. Hominins

    9. Differentiating humans and apes

    10. Bipedalism

    11.  Ardipithecus 

    12. Australopithicines ( Australopithecus and Paranthropus sp.)

    13. Homo species

    14. Assimilation hypothesis

    15. “Out o Arica” hypothesis

    People to Know 

    • “Lucy” and “Ardi”

    Organisms to Know 

    • Carpolestes simpsoni

    • Lemurs

    • Lorises

    • Pottos

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    • arsiers

    • amarins

    • Marmosets

    • Squirrel monkeys

    • Howler monkeys

    • Capuchin monkeys

    • Mandrill

    • Baboons

    • Rhesus monkeys

    • Gibbons

    • Orangutans

    • Gorillas

    • Chimpanzees

    •  Ardipithecus ramidus

    •  Australopithicus sp. (afarensis)

    • Paranthropus sp.

    • Homo habilis

    • Homo erectus

    • Homo neanderthalensis

    • Homo sapiens

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    Lecture Student Notes and Questions

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    Important transitions among the three domains:

    F D L

    D

    F A B E

    Amino acid that initiatesprotein synthesis

    Methionine Formyl-methionine Methionine

    IntronsPresent in some

    genesAbsent Present

    Membrane-bounded

    organellesAbsent Absent Present

    Membrane lipid

    structureBranched Unbranched Unbranched

    Nuclear envelope Absent Absent Present

    Number o different

    RNA polymerasesSeveral One Several

    Peptidoglycan in cell

    wallAbsent Present Absent

    Response to the

    antibiotics streptomycin

    and chloramphenicol

    Growth not

    inhibitedGrowth inhibited

    Growth not

    inhibited

    Student Notes and Questions

     

    Reference Page for DiversityMaterial (Exams 2 and 3)

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    Reerence Page or Diversity (Exams 2 and 3)

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    Outline

    Ecology: Evolution in the Present Moment 

    1. What is ecology?

    2. Why talk about ecology in an evolution course?

    3. Adaptations are affected by the biotic and abiotic environment

    Large Scale Climate Patterns

    1. Global patterns in temperature and precipitation

    2. Seasons

    Variation in Climate Patterns

    1. Local variation in climate

    2. Global variation in climate3. Stochasticity

    Key Terms/Concepts

    1. Define ecology 

    2. How is ecology related to evolution?

    3. Abiotic

    4. Biotic

    5. Tree actors influence climate

    6. Intensity o sunlight on Earth varies

    7. Effect o light intensity on temperature

    Lecture 25

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    Lecture 8. Effect o light intensity on rain

    9. Hadley circulation

    10. Hadley cells

    11. Main effects o rising and sinking air streams

    12. Distribution o rain orests

    13. Distribution o deserts

    14. Distribution o temperate orests

    15. Polar deserts

    16. What causes the seasons?

    17. opography or terrain

    a. Slope

    b. Orientation to other eatures

    c. Elevation

    18. Factors that lead to local variation in climate

    a. Rain in the southern hemisphere

    b. Rain shadows

    c. Slope and local drought

    d. North- vs. south-acing slopes

    e. Elevation and temperature

    . Lake effect snow 

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    19. Adiabatic cooling

    20. Less predictable global effects on climate

    a. El Niño

    b. La Niña

    c. Pacific decadal oscillation (PDO)

    21. Stochasticity 

    People to Know • No new people or lecture 25

    Organisms to Know 

    • No new organisms or lecture 25

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    Lecture Student Notes and Questions

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    Lecture 8. Boreal orest

    9. emperate deciduous orest

    10. emperate grassland

    11. Hot desert

    12. Cold desert

    13. ropical evergreen orest

    14. Why don’t biome boundaries exactly match species range boundaries?

    15. Niche

    16. Factors that might be important to a niche

    17. Niche partitioning

    18. Niche packing

    19. Factors affecting density o niche packing

    20. Fundamental niche vs. realized niche

    21. MacArthur’s warblers

    People to Know 

    • Robert Whittaker

    • Joseph Connell

    • Robert MacArthur

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    Organisms to Know 

    • Cactus

    • Euphorbia (member o the Poinsettia amily)

    • Honeyeater

    • Hummingbird

    • Chthamalus barnacles

    • Semibalanus barnacles

    • Warblers

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    Lecture Student Notes and Questions

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    Lecture 2. Symbiont

    3. Why is competition hard to “see”?

    4. Te Ghost o Competition Past

    5. How do you study competition?

    a. Experiments

    b. Comparisons o sympatric and allopatric populations

    6. Exploitation competition

    7. Intererence competition

    8. Interspecific vs. intraspecific

    9. Resources

    10. Resource partitioning

    11. emporal partitioning

    12. Character displacement

    13. Intraspecific competition can lead to less interspecific competition

    14. Predation can limit competition

    15. Disturbance can limit competition

    16. Intermediate disturbance

    17. Competitive exclusion

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    People to Know 

    • Arthur ansley 

    • G.A. Gause

    Organisms to Know 

    • Galium saxatile

    • Galium pumilum

    • Stickleback 

    • Bufo woodhousii 

    • Hyla crucifer 

    • Hydrobia sp. (mud snails)

    • Paramecium caudatum 

    • P. aurelia

    • P. bursari

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    Lecture Student Notes and Questions

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    Outline

    Consumer/Resource Interactions

    1. Predation is universal

    2. Tere are many types o predation/consumption

    3. Consumer species have major effects on prey species

    4. Many predator/prey populations cycle

    5. Coexistence between predators and prey

    Coevolution among Predators and Prey

    1. Prey evolve to avoid predators

    2. What i you’re sessile?

    3. Predators evolve more efficient ways to hunt prey 

    Key Terms/Concepts

    1. Consumer/resource relations

    a. rue predators

    b. Parasitism

    c. Herbivores

      i. Predatory herbivores

      ii. Parasitic herbivores (grazers, browsers)

    d. Detritivores

    2. Extinction via predation

    Lecture 28

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    Lecture 3. Predators lower prey abundance

    4. Predators can restrict prey distribution

    5. Predator/prey cycling

    6. Methods o predator and prey coexistence

    a. Reuges

    b. Cycling

    c. Predators at low abundance

    d. Generalist predators

    7. Prey evolve deenses

    a. Crypsis

    b. Chemical deense

    c. oxicity

    d. Armor

    e. Behavioral deense (alarm calling, distraction displays, fleeing, herds)

    . Predator satiation

    8. Cryptic coloration

    9. Object mimicry 

    10. Aposematic coloration

    11. Batesian mimicry 

    12. Müllerian mimicry 

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    13. How do sessile organisms avoid predation?

    14. How do predators respond to prey deenses?

    a. Search images

    b. Avoid/use toxins

    c. Get past armor

    15. ypes o hunting

    a. Ambush

    b. Stalking

    c. Pursuit

    16. Who would you expect to hunt in each way?

    People to Know 

    • No new people or lecture 28

    Organisms to Know 

    • Paramecium

    • Didinium

    • Klamath weed

    • Chrysolina beetle

    • Megapode

    • Lynx

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    Lecture • Snowshoe hare

    • Bombardier beetle

    • Nudibranch

    • Skunk 

    • Bee

    • Monarch butterflies

    • Viceroy butterflies

    • Armadillos

    • Clams

    • Porcupines

    • Anemones

    • Cactus

    • Sea urchins

    • Vine snake

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    Student Notes and Questions

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    Lecture Student Notes and Questions

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    Outline

    Symbioses

    1. Parasitism

      a. Ectoparasites vs. endoparasites

    b. Multiple hosts

    2. Mutualism

      a. ypes o mutualism

      b. Te importance o stress

    3. Commensalism and ammensalism

    4. Species interactions may change over time or be hard to name

    5. Communities are interactions o species interactions

    6. Keystone species

    Key Terms/Concepts

    1. Coevolution

    2. Symbiosis

    3. ypes o symbiosis

    a. Parasitism

    b. Mutualism

    c. Commensalism

    d. Ammensalism

    Lecture 29

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    Lecture 4. Examples o ectoparasites

    5. Examples o endoparasites

    6. Parasites can have complex lie cycles

    7. Why does parasite spread ofen decline?

    8. Examples o mutualisms

    9. Human mutualisms

    10. ypes o mutualisms

    a. rophic

    b. Deensive

    c. Dispersive

    11. Examples o commensalisms and ammensalisms

    12. Nurse plants

    13. Species relationships can change over time

    14. Species relationships may be unclear

    15. Communities are ormed rom groups o species interactions

    16. Keystones species

    People to Know 

    • No new people or lecture 29

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    Organisms to Know 

    • Lichen

    • Mistletoe

    • Indian Pipe

    • Nematodes

    • Plasmodium

    • Dicrocoelium dendriticum, ants, and deer

    • Cleaner fish and customer fish

    • Honeyguides and honey badgers

    • Acacia and Pseudomyrmex   ferruginea ants

    • ube worms

    • Saguaro and paloverde

    • Oxpecker birds

    • Pisaster (starfish)

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    Outline

    Te Latitudinal Gradient in Species Diversity

    1. A bit on species richness

    2. What is the latitudinal gradient?

    3. Hypotheses or the cause o the gradient

    So, Which Is It?

    1. Energy explains some o the pattern

    2. Problems with energy as a hypothesis

    3. Evolutionary time and niche conservatism: An experiment

    4. Is there ever a simple answer?

    Key Terms/Concepts1. Diversity 

    2. Species richness

    3. Evenness

    4. Species richness and area

    5. Species richness and habitat number (environmental heterogeneity)

    6. Latitudinal gradient in species diversity 

    Lecture 30

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    People to Know 

    • Bradord Hawkins

    Organisms to Know 

    • Spruces

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    Lecture Student Notes and Questions

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    Outline

    Te Teory of Island Biogeography 

    1. Te lesson o Krakatau

    2. Island biogeography explains species distributions in new environments

    3. Immigration and extinction

    4. Reaching equilibrium

    5. Size and isolation

    Why Do We Care? 

    1. errestrial islands: reversing the island model

    2. Real lie data

    3. Protecting the equilibrium

    4. Reserve design

    5. Charismatic megaauna

    Key Terms/Concepts

    1. What is Krakatau an example o?

    2. Basic outlines o the history o Krakatau

    3. Rationales or the new inhabitants o Krakatau (ex.: why are there a lot o birds?)

    4. Te Teory o Island Biogeography 

    5. Immigration decreases over time

    6. Extinction increases over time

    7. Equilibrium species number

    Lecture 31

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    Lecture 8. ime to equilibrium varies by species group

    9. Island size

    10. Island isolation

    11. errestrial islands

    12. How are terrestrial islands different than oceanic ones?

    13. Relaxation

    14. Immigration must be possible to prevent extinction

    15. Reserve design

    16. Corridors

    17. Charismatic megaauna

    18. Specialists

    People to Know 

    • Robert MacArthur

    • E.O. Wilson

    Organisms to know 

    • Coconuts

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    Student Notes and Questions

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    Lecture Student Notes and Questions