BIO182 Study Guide, I 1

Biology 182: Study Guide, Part I

Purpose: This study guide provides a checklist of terms, concepts and topics covered in Bio182. It is meant to be used in conjunction with your reading of the textbook, lecture notes from class, and your lab notebook. An idealized sequence of study is outlined below:

1) Read the assigned chapter of the textbook before lecture, 2) Complete the MasteringBiology assignment (online), 3) Take detailed notes in lecture (an outline of topics and related facts/examples), 4) Ask questions during/after lecture to clarify any points not understood, 5) Use this study guide to review the main ideas and examples covered in each section, 6) Practice your mastery of this material by rewriting notes from memory, 7) Answer all of the questions at the end of each chapter in your textbook, 8) Review topics with members of your study group (try to ‘mini-teach’ topics), 9) Earn an ‘A’, get a scholarship, earn a degree, and have a fabulous career!

The study guide comes in four parts, one for each written exam. Material is arranged by chapter from your text, although topics may be presented at various times in lecture and lab. This guide is not exhaustive, but it may help you identify concepts that need further clarification. For additional review answer the questions at the end of each chapter. NOTE: Your knowledge of BIO181 is expected for this course. Review the themes of Chapter 1; pay particular attention to the section on evolution, including Linnaeus and his classification scheme, and the scientific method.

PART I. MECHANISMS OF EVOLUTION: Chapters 22-26

Chapter 22. Descent with Modification: A Darwinian View of Life

This chapter introduces the history of evolutionary thought and the Theory of Evolution by Natural Selection, as presented by Darwin in The Origin of Species. The end of the chapter includes recent evidence that further supports evolutionary theory, as well as several recent examples (studies) that demonstrate evolution is a fact, as well as a theory. You should be able to identify some of the most important researchers in this field, and their contributions to our understanding of evolution. Below is a list of names and terms:

Plato: idealism / essentialism natural theology Aristotle: scala naturae (scale of nature) Linnaeus: classification & taxonomy Cuvier: catastrophism Hutton: gradualism Malthus: struggle for existence (humans) Lyell: uniformitarianism Lamarck: evolution by acquired characteristics Mendel: genetics (review 181)

Darwin : evolution by natural selection Wallace: independently hypothesized evolution by natural selection Evolutionary theory ‘evolved’ in Western Europe, a culture based on Greco-Roman philosophy and Judeo-Christian theology. Both traditions considered species ‘fixed’ in nature. Attempts to organize the vast diversity of living things included Aristotle’s scala naturae (scale of nature), and later the classification scheme developed by Linnaeus.

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Linnaeus grouped organisms into a series of ‘nested sets’ based on their shared characters (see Fig. 26.3, more on this topic at the end of this section). Be familiar with his hierarchy of nested sets: Kingdom, Phylum, Class, Order, Family, Genus, species. How did Linnaeus explain the shared characters of the organisms within each of these groupings? How did Darwin explain these shared characters? Which explanation is more parsimonious?

Be able to explain how fossil evidence (e.g. from Cuvier & Lamarck) and new theories in geology (e.g. Gradualism, Hutton & Uniformitarianism, Lyell) set the stage for Darwin’s theory.

Lamarck proposed his own theory of evolution in 1809, and others had suggested evolution had occurred (including Darwin’s own grandfather). Be able to name and describe the evolutionary mechanisms proposed by Lamarck. What is the evidence for or against his hypothesis?

Darwin lived most of his life in the England. He was very familiar with English geology and biodiversity before for his single voyage around the world. The Voyage of the Beagle included surveys of South America and the Galapagos Islands. Be able to describe observations made at both locations and how they influenced Darwin. For example, why were organisms from temperate areas of South America more like organisms from tropical South America than like organisms from England (a temperate climate)? What did these biogeographic patterns suggest?

Be able to describe the observations and inferences that make up the theory of natural selection as summarized by Ernst Mayr (see page 10 of this study guide) and simplified in your text (p. 473). Compare each of these observations and inferences to the changes observed in your ‘lizard’ population from lab (first week).

According to Darwin’s theory, what is the smallest unit of life that can evolve? Explain.

What is artificial selection? How did it influence Darwin?

Much of Darwin’s initial theory developed from the biogeographic distribution of similar organisms (e.g. Galapagos Islands). Be able to describe other examples of biogeography that support the theory that evolution has occurred. Similarly, be able to describe these other lines of evidence that support evolutionary theory.

fossils/paleontology anatomical, embryological & molecular homologies design ‘flaws’

Also know (these terms will be used in Ch. 26 as well):

homology(-ous) analogy(-ous) convergent evolution vestigial organ homoplasy phylogeny

Be able to discuss the difference between evolution as a fact (e.g. soapberry bugs, MRSA, guppies) and the Theory of Evolution by Natural Selection.

How do scientists define ‘theory’?

Be able to define an adaptation as: 1) a new feature, 2) shaped by natural selection, 3) that provides a performance benefit.

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Chapter 23. The Evolution of Populations (Microevolution)

Microevolution is the generation-to-generation change within populations, the smallest possible level of evolution. The study of population genetics describes how a population can change genetically over time. Population genetic studies were central to the Modern Synthesis: the fusion of Darwinian selection and Mendelian genetics. In the early 20th Century, biologists were at conflict between these two pillars of modern biology.

• How could Mendelian genetics explain the range of variability described by Darwin? Or the origin of complex traits (hopeful monster)?

• How could Darwin’s view of genetics (blending hypothesis) explain Mendel’s particulate nature of inheritance (e.g. recessive phenotypes popping up in F2 generations)?

The study of population genetics in real populations, combined with mathematical constructs (e.g. HWE, below) provided the framework for modern biology. Organisms pass down their traits in a particulate nature; natural selection shapes populations such that those traits better able to survive and reproduce become concentrated in subsequent generations.

Chapter 23 focuses on microevolution in four parts: the source and maintenance of genetic variation, the Hardy-Weinberg Equilibrium (HWE), the five mechanisms of evolution, and a focus on natural selection adapts populations to their environment. We will study microevolution in the lab (week 2) with use of the HWE. Therefore, we will introduce the HWE early in this lecture and it will be treated here first of these topics.

The Hardy-Weinberg Equilibrium (HWE) is a mathematical formulation that provides a model for understanding microevolution. It is used to generate predictions of the null hypothesis, the hypothesis that a population is not changing (not evolving). These predictions can then be compared to a real population to see if the real population has changed. Specifically, the HWE compares the allelic and genotypic frequencies of a population from one generation to the next.

The HWE has five assumptions which must be met for the null hypothesis to be true. Be able to name the five assumptions of this model and their counterparts, the five mechanisms of evolution, with examples of each mechanism. Which of these mechanisms is/are expected to adapt a population to its environment?

Assumptions of HWE Type of Microevolution 1. Very large (infinite) population. 1. Genetic drift (bottleneck, founder effect) 2. Isolation from other populations (no gene flow) 2. Gene flow (migration)

3. No net mutations 3. Mutation

4. Random mating (panmictic population) 4. Assortative mating

5. No natural selection 5. Natural selection

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Be able to understand and use the formulas of the HWE to determine the current allelic and genotypic frequencies of a population, and from these data the expected allelic and genotypic frequencies of subsequent generations (you will have several opportunities to practice in lab).

Sample HWE question: (find more HWE problems at the end of this study guide)

Show mathematically and describe in evolutionary terms, why the HWE predicts that a parental population of infinite size with these allelic frequencies: p = 0.6 and q = 0.4, should give rise to offspring with these genotypic frequencies: AA = 0.36, Aa = 0.48, aa = 0.16

Use of the HWE and related statistics demonstrate that populations are, in fact, changing before of our eyes.

The chapter opens with a look at genetic variation within populations: how variation is created and preserved. Be able to answer these questions. What is the source of genetic variation? How much genetic variation exists in natural populations? How is this variation maintained? How important is genetic variation to evolution by natural selection? to other mechanisms of evolution?

What is the neutral theory (p 486)? Why is it hard to test this theory? Darwin described the mechanism of adaptive evolution, natural selection. However, as seen in the HWE, four other mechanisms can change a population’s genetic make-up: genetic drift, gene flow, mutations and non-random mating. Be able to describe these different mechanisms, and to define, describe and use the following terms: population gene pool genetic drift bottleneck effect

founder effect gene flow inbreeding assortative mating polymorphism cline hybrid vigor balanced polymorphism frequency-dependent selection fitness What does natural selection act on or ‘see’: phenotype or genotype? Explain. Be able to describe three modes of natural selection: stabilizing selection, directional selection and diversifying (disruptive) selection, and draw a graph typical of each mode (p 496). What are the costs and benefits of sexual reproduction? What is sexual selection? How does it differ from natural selection? Be able to define anisogamy theory and relate it to the differences between male and female approaches to mate choice. How does sexual selection relate to nonrandom mating? What is group selection? How important is it relative to selection on individuals? Can evolution perfect organisms? Do imperfections in organisms support or refute the theory of evolution by natural selection? Explain and refer to four mechanisms that limit selection.

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Chapter 24. The Origin of Species This chapter addresses the ‘species question’: What is a species? and How do new species arise? Scientists have provided a variety of answers to both of these questions. Moreover, most of these explanations are not exclusive. This chapter provides some of the best examples of how difficult it is to pigeon-hole life. Our focus will be on the different species concepts and how they address the questions above (what is a species? how do they arise?) the problems with each concept, and how they overlap. Pay particular attention to the Morphological Species Concept and Biological Species Concept. Importantly, the Biological Species Concept (BSC), developed by Ernst Mayr (1942) was central to the Modern Synthesis. It emphasized the mechanisms that keep species separated (reproductive isolating mechanisms) and by inference, mechanisms of speciation. Prior to the modern synthesis, most people grouped organisms into species based on their similar appearance: shape (morphology), color, number of bones, fins, etc. the Morphological Species Concept (MSC). Diverse cultures have applied this general method when naming organisms. For example, Ernst Mayr identified and named 137 species of birds in the Arafak Mountains of New Guinea. The native people of these mountains had named 138 types of bird. This method of naming species (MSC) is similar to that of Linnaeus. How common was this method used in the naming of species in the past? What other species concepts are similar to this concept? Ernst Mayr later proposed the Biological Species Concept (BSC). Whereas the MSC focused on similar characters between members within a species, the BSC emphasized characters that keep related species separated, reproductive isolating mechanisms. Be able to describe the differences in these two ways in which species can be identified/named. What kinds of scientists can use the BSC? Who cannot? The key features to the BSC is the notion that individuals of a species can only breed with conspecifics (other members of the same species) to produce viable, fertile offspring. Conversely, they do not mate with members of other species to produce viable, fertile offspring. Note the importance of the BSC to the Modern Synthesis – the union of evolution by natural selection to Mendelian genetics. Members of populations exchange their genetic material and pass them on to new generations. If one population diverges into two separate populations that no longer exchange alleles, each may gradually change in its own way such that they can no longer interbreed, at which point they have evolved into separate (new) species! For example, if two populations become separated by a river or mountain chain, Allopatric Speciation may occur. Mayr and his followers compiled a list of reproductive isolating mechanisms, generalized into the categories below. Be able to describe each category and identify examples from your text/lecture.

Reproductive Isolating Mechanisms

Prezygotic Barriers (before fertilization): Postzygotic Barriers: Habitat Isolation Reduced Hybrid Viability Temporal Isolation Reduced Hybrid Fertility Behavioral Isolation Hybrid Breakdown Mechanical Isolation Gametic Isolation

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Many other species ‘concepts’ (definitions) exist: The Recognition Species Concept differs from the BSC in the mechanism(s) that select for mating between conspecifics (this concept will be discussed in lecture). While the BSC emphasizes the evolution of reproductive isolating mechanisms (selection against mating with other species), the Recognition Species Concept proposes a Specific Mate Recognition System. Selection acts on mate choice so that individuals choose the best possible mate, which will necessarily be a conspecific. Which of these concepts is most consistent with the process of natural selection? How does this relate to Sexual Selection?

Your text mentions one other Species Concept. The Ecological Species Concept separates related forms based on their different ecological roles or niches. Several other types of species concepts have been proposed. One additional species concept worth noting is the Nominal Species Concept. It suggests ‘species’ are simply convenient ‘names’ humans use to group organisms. Be able to compare and contrast these species concepts. Which of these species concepts focus on the process of speciation and which focus on the diagnosis of a species?

Although Species Concepts have generated much controversy, these definitions are important to our explanations of the origin of new species. Speciation may occur under two general geographic scenarios: Allopatric (other country) Speciation and Sympatric (same country) Speciation. Note that these scenarios were an integral part of the BSC when proposed by Mayr. You should be able to discuss each in terms of the reproductive isolating mechanisms that might lead to separate species. Which scenario did Mayr think more commonly led to speciation events?

The classic Allopatric Speciation model describes a large population that becomes separated by a geographical barrier, such that two (still relatively) large populations are created. Over time, the two populations will diverge as they follow their own evolutionary trajectories. Consider the five mechanisms of evolution (Ch. 23) that might be involved in Allopatric Speciation.

Your text also refers to ‘small, isolated populations’ as more likely to diverge. These are also known as peripheral isolates and this model is also known as Peripatric Speciation - a distinct variation of the classic Allopatric model. Evolutionary biologists have argued which model of Allopatric Speciation is more likely to generate new species? Small, isolated populations are likely to occur more frequently compared to the sudden creation of a large geographical barrier separating two large populations. Also, small isolates are more likely to evolve, but mostly due to genetic drift. Whereas two large populations may each have enough genetic diversity for natural selection to shape these populations in new, adaptive ways.

Sympatric Speciation was not thought to be a common scenario, compared to Allopatric Speciation. What might cause a large, interbreeding population to suddenly separate into two separate groups that no longer interbreed? Be familiar with plant examples of allopolyploidy and autopolyploidy.

Be able to define and describe Allopatric, Peripatric, and Sympatric Speciation. Which of these is considered to be the most common for animals? How does reproductive isolation occur in each mode? Which form of speciation occurs on islands? What is the role of islands on speciation and what is an adaptive radiation? How is it different from other scenarios? (Note: We will see in the next chapter that adaptive radiations also follow major extinction events).

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Hybrid Zones provide important examples of incipient speciation. Be familiar with the examples in your text and the three potential outcomes: reinforcement, fusion and stability. Similar examples come from ring species. Ring species consist of several distinct populations or subspecies, with various amounts of contact and interbreeding between the subspecies. Ring species represent living examples of speciation in process. Several examples were provided in earlier editions of your text, such as Peromyscus maniculatus (see attached page). Look at the attachment and then answer these questions. If the other two subspecies went extinct, would you consider P. m. artemisiae a separate species from P. m. nebrascensis? Why or why not? Apply each of the species concepts in answering these questions and explain. Are ring species consistent with the theory of evolution? Explain.

The final section of the chapter evaluates evidence of the mode of speciation. How fast can species arise? How much genetic difference is necessary between two closely related species? Compare and contrast punctuated equilibrium vs. gradualism and the associated evidence.

The explosion of genetic studies provides much new information on both speciation rates and the amount of genetic differentiation required for speciation (e.g. the Japanese snails, genus Euhadra, sunflowers, monkey flowers: Mimulus spp, and Hawaiian Drosophila pp, pages 518-521). Note that a single gene mutation (snail example) can cause reproductive isolation! Be able to use these examples. Importantly, speciation can be fast or slow, with large amounts of variation or only a single gene.

What is Macroevolution? Can the processes of Microevolution explain the larger patterns of evolutionary change? [Answer: Yes!] Explain.

Chapter 25. History of Life on Earth / Read Chapter 26 Before 25! (more details below)

We will study some parts of chapter 25 for our first exam, primarily those sections that focus on the process of evolution, patterns and its study:

- 25.2 (a quick note on fossils and what they tell us of evolution), - 25.4 the History of Extinctions and Adaptive Radiations, - 25.5 the new field of Evo-Devo as the source of Evolutionary Novelties & - 25.6. Evolution is not goal oriented

Major events in biological history will be studied within our second section of the course (25.1-3).

Macroevolution is concerned with large-scale patterns in evolution: e.g. the origin of key adaptations or novelties, mass extinctions, adaptive radiations, and increasing size in some taxa. Chapter 24 introduced this term. Chapter 25 describes large-scale patterns of evolution and some of the developmental changes that lead to novelties (e.g. heterochrony).

Be sure to read section 25.2 and be able to define fossil (Latin: ‘dug up’): the preserved remnants or impressions of an organism that lived in the past, and the example of new groups (e.g.mammals).

What are the limitations of the fossil record? Be able to define or describe these terms:

sedimentary rock relative dating superposition absolute dating radiometric dating half-life carbon-14

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Be able to describe the evidence for plate tectonics (continental drift, 25.4), its explanatory value to current biogeography, and its impact on the history of living things (e.g. the Permian extinction). Be able to define and describe the following:

mass extinction adaptive radiations Pangaea Precambrian Paleozoic Mesozoic Cenozoic impact hypothesis

Be able to compare and contrast global adaptive radiations and regional adaptive radiations. How do these patterns compare to the causes of speciation discussed in Chapter 24?

Scientists have identified five mass extinction events. A possible sixth extinction event may be occurring, the Anthropocene. What is its cause?

Most evolutionary novelties (25.5) are modifications of existing structures. However, the process of modification is often unknown. What is the importance of ‘intermediate forms’ in the fossil record? How would you explain the evolution of a complex character like a wing? For example, ‘What is the adaptive value of half a wing?’ [We will address this question in class.]

Recent studies of regulatory genes have demonstrated that great changes in anatomy and morphology can be created by rather simple changes in the rate and timing of development (heterochrony), and the spatial pattern of expression produced by homeotic genes. The importance of development to the origin of evolutionary novelties has led to the new term, evo-devo, that emphasizes this relationship. Be able to define and present examples of the following:

allometric growth heterochrony paedomorphosis homeotic genes adaptation adaptive divergence

Are species internally driven to change their shape or size? (refer to the evolution of horses)

Chapter 26. Phylogeny (Systematics) & The Tree of Life (will be covered in lab)

This chapter describes Systematics – the branch of modern biology that includes the Classification of living things, from the initial two-Kingdom system of Linnaeus, to modern groupings based on evolutionary hypotheses. All of these methods place groups of organisms into nested sets. Modern systematics generates evolutionary hypotheses of these relationships. In this section, we will focus on the theory and methods used in generating evolutionary hypotheses. We will apply our understanding of this methodology in our two sections on biodiversity (parts II & III of this course).

Systematics consists of Taxonomy (naming) and Classification of taxa (singular taxon – a named group of organisms). Be familiar with the binomial system of naming and the rest of the hierarchical classification system: Domain (new term, includes Kingdoms) Kingdom, Phylum, Class, Order, Family, Genus and specific epithet. The last two, Genus and specific epithet, make up the scientific binomial – the ‘two-name’ descriptor unique for each species.

As noted in the first pages of this study guide, Linnaeus grouped organisms based on their shared characters, but explained the origin of those characters as individually created by god. Darwin suggested these common traits were evidence of a shared, common ancestry. His famous ‘tree’ of life described all living things as descendants of an early ancestor (figure 22.7, p 472).

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Modern schools of systematics include Phylogenetics and Cladistics. These schools share the goal of identifying the true evolutionary relationships between organisms. Because we cannot observe the history of speciation events, we are limited to the generation of evolutionary hypotheses indicating relatedness via common ancestry. These hypotheses are easily illustrated in the form of a phylogenetic tree (phylogenetics) or cladogram (cladistics), much like Darwin’s original.

Various characters may be used to determine evolutionary relationships: morphology, anatomy, embryology, behavior and molecules such as proteins, RNA & DNA. Although Linnaeus created his system for ‘fixed species’ these same classifications are now considered phylogenetic hypotheses – suggestions of the relationships between groups of organisms. You should be able to describe the relationship between taxonomic hierarchies (Phylum, Class, Order, etc.) and phylogenetic hypotheses.

Cladistic analysis uses only specific types of information to create their cladograms (a clade = a branch; aka a monophyletic group, a specific type of taxon). Evolutionarily related groups can be identified by their shared, derived (new) characters known as synapomorphies. You should be able to use the methods of cladistics to create a cladogram or tree, and understand the concepts associated with these trees (e.g. limitations).

To create a phylogenetic tree, it is important to distinguish between homologous vs. analogous characters (aka homoplasies). Be able to define these terms and convergent evolution (previously discussed in Ch. 22). We will practice making trees in lab, but focus on visible characters. Read the sections on molecular characters; they will be referenced, but briefly. Youshouldalsobeabletodefine,describeandusethefollowingterms: Monophyletic Paraphyletic Polyphyletic Clade Apomorphy Derived(new)characterstate Parsimony Synapomorphy Sharedderivedcharacterstate Outgroup Pleisiomorphy Ancestralcharacterstate Ingroup Orthologousgenes Paralogousgenes A phylogenetic hypothesis in the form of a tree carries much information including key adaptations that define groups, relationships between groups, and some time scale (either absolute or relative). You should be able to interpret this information from a tree.

Much of the remainder of our course focuses on the diversity of living organisms. The most important aspects of each group will be presented in the form of trees. You must be able to interpret trees to identify relationships and critical adaptations of these groups.

What is the molecular clock? What affects the reliability of this measure of relatedness? (recall neutral evolution).

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Darwin’sTheoryofEvolutionbyNaturalSelection*

Observation1.Populationshavetremendousreproductivepotential.

Observation2.Populationstendtobestable.

Observation3.Resourcesarelimited.(Malthus1798)

Inference1.Productionofexcessoffspringleadstoastruggleforexistence;

onlyafractionoftheoffspringbornwillsurviveto reproduce.

Observation4.Individualsvarywithinapopulation.

Observation5.Muchofthisvariationisheritable.

Inference2.Somevariantswillbebetterabletosurviveandreproduceintheir

environment.

Inference3.Thereproductivedifferentialbetweenvariantsinthe

populationwillleadtoagradualchangeinthepopulation,with

favorabletraits(adaptations)accumulatingoverthegenerations.

*AfterErnstMayr.1982

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OntheOriginofSpeciesByMeansofNaturalSelection,

orthePreservationofFavouredRacesintheStruggleforLife

CharlesDarwin,1859*

“Fromtheseconsiderations,IshalldevotethefirstchapterofthisAbstracttoVariation

underDomestication.Weshallthusseethatalargeamountofhereditarymodificationisat

leastpossible;and,whatisequallyormoreimportant,weshallseehowgreatisthepowerof

maninaccumulatingbyhisSelectionsuccessiveslightvariations.Iwillthenpassontothe

variabilityofspeciesinastateofnature;butIshall,unfortunately,becompelledtotreatthis

subjectfartoobriefly,asitcanbetreatedproperlyonlybygivinglongcataloguesoffacts.We

shall,however,beenabledtodiscusswhatcircumstancesaremostfavourabletovariation.In

thenextchaptertheStruggleforExistenceamongstallorganicbeingsthroughouttheworld,

whichinevitablyfollowsfromtheirhighgeometricalpowersofincrease,willbetreatedof.

ThisisthedoctrineofMalthus,appliedtothewholeanimalandvegetablekingdoms.Asmany

moreindividualsofeachspeciesarebornthancanpossiblysurvive;andas,consequently,

thereisafrequentlyrecurringstruggleforexistence,itfollowsthatanybeing,ifitvary

howeverslightlyinanymannerprofitabletoitself,underthecomplexandsometimesvarying

conditionsoflife,willhaveabetterchanceofsurviving,andthusbenaturallyselected.From

thestrongprincipleofinheritance,anyselectedvarietywilltendtopropagateitsnewand

modifiedform.”

Frompages4-5oftheIntroduction,firsteditionfacsimile.

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Hardy-WeinbergEquilibrium(HWE):WorksheetTheHWEcomputesexpectedfuturegenotypicandallelicfrequenciesbasedoncurrentallelicfrequencies.[Note:HWEassumesnoevolutionisoccurring.Seepage2forthelistofHWEassumptions.]Thus,tousetheHWEitiscriticaltofirstdeterminethecurrentallelicfrequencies.Onceyouknowtheallelicfrequencies,theywillnotchangeaslongastheHWEassumptionsholdtrue.MostHWEproblemscomeinoneoftwoforms. 1)Youaregiventhefrequencyofhomozygousrecessives 2)YouaregiventhefrequencyofallgenotypesBeforeweworkthrougheachofthesetypesofproblems,let’sreviewthebasicformulas.Formulaforallelicfrequencies: p=frequencyofthedominantallele q=frequencyoftherecessiveallele p+q=1 (giventhereareonlytwoallelesforthisgene)Giventhefrequencyofeitherporq,youcandeterminethefrequencyoftheotherallele: 1-p=q or 1-q=pFormulaforgenotypicfrequencies(showingstepstoreachthefinalformula): (p+q)2 = 12 (p+q)(p+q) = 1 p2+pq+qp+q2 = 1 p2+2pq+q2 = 1 theformwenormallyuseTheseequationstellustheexpectedfrequenciesforhomozygousdominants(p2),heterozygotes(2pq)andhomozygousrecessives(q2)-ifHWEholdstrue. Theseformulasforallelic&genotypicfrequenciesareallyouneedtoworkHWEproblems.

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Example:Youaretoldthatthefrequencyofhomozygousrecessivesinapopulation=.09(9%)andtoassumethatthepopulationisinHardy-Weinbergequilibrium.IfHWEholds,thenthefrequencyofthehomozygousrecessivesshouldequalq2. 0.09=q2Todetermineq,takethesquarerootof0.09=0.3=qOnceyoudetermineqyoucandeterminep: 1-q=p=>1-0.3=0.7=> 0.7=p Nowyouhavetheallelicfrequenciesofpandq,andthesewillnotchangeunderHWE.Tocomputethegenotypicfrequencies,usethesevaluesforp&qintheequationsabove. Theexpectedfrequencyofhomozygousdominants=p2=(0.7)2=0.49 Theexpectedfrequencyofheterozygotes=2pq=2(.7)(.3)=.42 Theexpectedfrequencyofhomozygousrecessives=q2=(.3)2=.09Youcancheckyourworkbyaddingthethreefrequencies(sumshouldequalone).Theproblemsbelowarevariationsonthesametheme.Allgivethefrequencyofhomozygousrecessives,andassumethatHWEholds.Theymayaskfordifferenttypesofanswers(allelicorgenotypicfrequencies)butallrequirethesamegeneralcalculations.Othervariationsarethewayinwhichtheinformationiswrittene.g.thefrequencyofrecessivephenotypesmaybegiveninsteadofthefrequencyofhomozygousrecessives.1.ApopulationinHWEcontainsafrequencyof.16homozygousrecessives.Whatisthefrequencyoftherecessiveallele?Whatisthefrequencyofthedominantallele?2.ApopulationinHWEcontainsafrequencyof.36homozygousrecessives.Whatisthefrequencyoftherecessiveallele?Whatisthefrequencyofthedominantallele?3.Oneinevery10,000peoplearestrickenbyarecessivegeneticdisorder.AssumingHWE,whatisthefrequencyofthisalleleinthepopulation?Whatarethegenotypicfrequencies?4.ApopulationinHWEcontainsafrequencyof.49homozygousrecessives.Whataretheallelicfrequencies?Whataretheexpectedgenotypicfrequenciesinthenextgeneration?5.ApopulationinHWEcontainsafrequencyof.64homozygousrecessives.Whatisthefrequencyoftherecessiveallele?Whatisthefrequencyofthedominantallele?Whatisthefrequencyofthedominantphenotype?

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6.ApopulationinHWEcontainsafrequencyof.01homozygousrecessives.Whataretheexpectedgenotypicfrequenciesinthenextgeneration?7.ApopulationinHWEcontainsafrequencyof.09homozygousrecessives.Whataretheexpectedgenotypicfrequenciesinthenextgeneration?Formorepractice,pickanyvalueforq2andworkoutallthefrequencies.Thesecondtypeofproblemtypicallygivesyouthefrequenciesofallthegenotypes,andthepopulationmaydeviatefromHWE.Theformulasarethesame;themaindifferenceisgettingstartedi.e.determiningtheallelicfrequencies.TocomputeallelicfrequenciesfromgenotypicfrequenciesIprefertoconverttoactualnumbers(notfrequencies)andcountthetotalnumberofeachallele.Eachhomozygotecontainstwoallelesofthesametype;heterozygotescontainoneofeachtypeofallele.Thetotalnumberofallelesshouldequal2xthenumberofindividuals(assumesindividualsarediploid).Problem:Apopulationconsistsof16homozygousdominants(AA),48heterozygotes(Aa)and36homozygousrecessives(aa).Whataretheallelicfrequencies?Solution:Wearegivennumbersofindividualsfromthestart.Now,makeatableandcountoutalleles. ‘A’alleles ‘a’alleles16Homozyg.dominants(AA) => 16x2A=3248Heterozygotes(Aa) => 48x1A=48& 48x1a=4836Homozyg.recessives(aa) => 36x2a=72----- Totals ---------------- ---------------- Total‘A’=80 Total‘a’=120100=Totalindividuals Totalcopiesofalleles(A&a)=200(Note:thetotalnumbersofallelesisdoublethenumberofindividuals)Nowconvertthesenumbersintoallelicfrequencies: frequencyof‘A’=80/200=.4=p frequencyof‘a’=120/200=.6=q (Note:p+q=1; .4+.6=1)

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Onceyouhavedeterminedallelicfrequencies,youcanansweranyadditionalquestionsthattheproblemmightaske.g.expectedgenotypicfrequenciesinthenextgeneration.Tocomparethecurrentgenotypicfrequenciestotheexpectedfrequencies,firstyouneedtoperformtheusualcalculationsforexpectedgenotypes.Second,youcomparethosecalculatedfrequenciestothestartingfrequenciesgiven.Preferablyyouwouldusestatisticsforthiscomparison.Alternatively,youcancompareabsolutevaluesofyourobservedvs.expected.Dotheobservedvaluesdifferfromthoseexpected?Finalnote:AlthoughyourstartinggenotypicfrequenciesmaydeviatefromHWE,yourstartingallelicfrequenciescannotdeviatefromHWE.Theallelicfrequenciesaresimply‘givens’.Theonlywaythatyoucouldseeadeviationinallelicfrequenciesisinthenextgenerationiftheallelicfrequencieschanged(i.e.evolution).However,youwouldnotbeabletocomputethischange.Youcouldonlymeasureallelicfrequenciesfromgenerationtogeneration.Anysignificantchangeinallelicfrequency=evolution.MoreProblems:8.Apopulationconsistsof60AAindividualsand40aaindividuals.WhataretheexpectedallelicandgenotypicfrequenciesinthenextgenerationassumingHWE?IsthecurrentpopulationinHWE?9.Apopulationconsistsof16AAindividuals,48Aa,and36aa.WhataretheexpectedallelicandgenotypicfrequenciesinthenextgenerationassumingHWE?IsthecurrentpopulationinHWE?10.Apopulationconsistsof26AAindividuals,48Aa,and26aa.WhataretheexpectedallelicandgenotypicfrequenciesinthenextgenerationassumingHWE?IsthecurrentpopulationinHWE?RECALL-Hardy-WeinbergEquilibrium:MeasuresmicroevolutionAssumptions of HWE Type of Microevolution (iftheseassumptionsaremet,noevolutionoccurs)1.Verylarge(infinite)population. 1.Geneticdrift(bottleneck,foundereffect)2. Isolation from other populations (no gene flow) 2. Gene flow (migration)

3. No net mutations 3. Mutation

4.Randommating(panmicticpopulation) 4.Assortativemating

5.Nonaturalselection 5.Naturalselection

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Otherstudyideas:-Workwithyourlabpartnertomakeothercombinations.-Tryusingphenotypicfrequenciesinsteadofgenotypicfrequencies.-Whattypeofchangewouldyouexpectifthepopulationmatedassortatively?-OtherquestionscanbefoundatthebackofChapter23inyourtextandMasteringBioAnswerstoproblems.1.GivenHWE,thefrequencyofhomozygousrecessives=q2=.16.Thus,q=.4=thefrequencyoftherecessiveallele.Frequencyofdominantallele=p=.6(1-.4=.6)2.q2=.36thereforeq=.6;p=.43.q2=1/10,000.Thesquarerootof1/10,000=1/100or.01=q.Althoughthisproblemdoesnotaskforthefrequencyofp,youneedtoknowittoworkoutgenotypicfrequencies.p=.99(1-.01).Genotypicfrequencies:p2=(.99)2=.98;2pq=2(.99)(.01)=.0198(or.02),q2=(.01)2=.0001(alreadygiven=1/10,000)4.p=.3,q=.7,p2=.09,2pq=.42,q2=.495.q2=.64;squarerootof.64=.8=q;p=.2 Thethirdpartofthisquestionasksforthefrequencyofthedominantphenotype,whichincludesbothhomozygousdominantandheterozygousgenotypes,orp2+2pq=(.2)2+2(.2)(.8)=.04+.32=.366.p2=.81,2pq=.18,q2=.01 (p=.9,q=.1)7.p2=.49,2pq=.42,q2=.09 (p=.7,q=.3)8.Thereare60x2A’s=120and40x2a’s=80foratotalof200alleles.Startingallelicfrequenciesare:p=.6(120/200);q=.4(80/200).IfatHWE,allelicfrequencieswillnotchange:p=.6;q=.4.Expectedgenotypes:p2=.36,2pq=.48,q2=.16ThestartingpopulationhadNOheterozygotes,butHWEpredicted48%,whichsuggeststhestartingpopulationwasfarfromHWE.9.Startingallelicfrequencies:p=.4,q=.6;UnderHWEtheallelicfrequencieswillnotchange;expectedgenotypicfrequencies:p2=.16,2pq=.48,q2=.36Startingpop.wasinHWE 10.Startingallelicfrequencies:p=.5,q=.5;UnderHWEtheallelicfrequencieswillnotchange;expectedgenotypicfrequencies:p2=.25,2pq=.5,q2=.25Startingpop.wasinHWE(ordarnclose!)

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Ring Species The diagram below shows a partial distribution of the white-footed deermouse, Peromyscus maniculatus. This species can be further divided into four subspecies: P. m. borealis, P. m. nebracensis, P. m. sonoriensis and P. m. artemisiae. Note that P. m. borealis and P. m. sonoriensis do not come into contact, but each of these subspecies mates with members of the other two subspecies: P. m. nebracensis and P. m. artemisiae. However, while P. m. nebracensis and P. m. artemisiae have limited contact, they do not interbreed!

Ring species like the one shown here provide material for debate, especially about the nature of a species and species concepts. Consider the morphological species concept (MSC) and biological species concept (BSC). How would you define each of these subspecies? Are they one species? Two species? Four species? Imagine that P. m. nebracensis and P. m. artemisiae become extinct. Are the two remaining ‘subspecies’ still members of the same species? Note the criteria you use depends on the species concept applied. Be prepared for questions about species concepts and examples of ring species like P. maniculatus.