Bio 191 Exam 3

Postzygotic

after fertilization • Mechanisms that act to reduce the viability or fertility of hybrids • Reduced hybrid viability - incompatibility between genomically-imprinted, nuclear genes (e.g., deer mouse hybrids) - nuclear/mitochondrial incompatibility • Reduced hybrid fertility - meiotic disruption (e.g., mule) • Hybrid breakdown - F1 hybrid viable and fertile but subsequent generations inviable and/or infertile (e.g., Drosophila)

Sympatric speciation in plants occurs most commonly through

allopolyploidy

archaeopteryx

ancient feather

Prezygotic

before fertilization • Mechanisms that impede mating between species or hinder fertilization of ova if members of different species do mate • Pre-mating - habitat isolation - behavioral isolation - temporal isolation • Post-mating - mechanical isolation - gametic isolation

All of the following act to maintain genetic variation EXCEPT

genetic drift

In a small, isolated population of 10 lesser wombat individuals, a meteor impact kills three individuals, all of whom happen to be genotype AA. As a result, the frequency of the A allele decreases from 0.55 to 0.36. This change is gene frequency provides an example of

genetic drift

Which of the following must exist in a population before natural selection can act upon that population?

genetic variation among individuals

The first step in the process of allopatric speciation is

geographic isolation

Christian natural theologians, John Ray and William Paley, ultimately contributed to a scientific understanding of evolution by

guiding researches to the fundamental question of how life works based on the comparative study of anatomy and physiology

The rise of methicillin-resistant Staphylococcus aureus (MRSA) can be considered to be an example of artificial selection because

humans synthesize methicillin and create environments in which bacteria frequently come into contact with methicillin.

To be considered scientific, a theory must be constructed in such a way that

it can be disproved, that is falsified.

The original source of all genetic variation is

mutation

What is the only evolutionary mechanism that consistently leads to adaptive evolution?

natural selection

An experiment carried out on the widow bird indicates that male mating success increased significantly when tails were artificially lengthened, and decreased significantly when tails were artificially shortened. These results provide evidence that

sexual selection is favoring long tails

The most informative characters for phylogenetic reconstruction are

shared, derived characteristics

Define Genotype Frequency

the relative proportion of a particular genotype - represented by a number from 0 to 1

Define Allele Frequency

the relative proportion of an allele at a particular gene locus - again, a number from 0 to 1 • Calculating allele frequencies allows us to quantify and better understand precisely what genetic variation is and how evolution works

Define Gene Pool

the sum total of genetic information present in a population at any given point in time - consists of all alleles (versions of a gene) at all gene loci in all

If two modern organisms are distantly related in an evolutionary sense, then one should expect that

they should share fewer homologous structures than two more closely related organisms

The uptake of naked DNA from the environment by bacteria is known as

transformation

Evolution: fact, fiction or theory?

• "Evolution is just a theory." - implies lack of knowledge or a guess - suggests that there is no evidence that evolution occurs • Theory of evolution by natural selection is a scientific theory - body of interconnected concepts supported by scientific reasoning and experimental evidence that explains the facts - widely accepted because its predictions stand up to thorough and continual testing • Evolution is an accepted scientific fact - genetic changes through time documented in variety of organisms including Homo sapiens

Taxonomy and systematics

• "Taxonomists are trained like performing monkeys - almost solely by imitation" (A.J. Cain, 1960) - lack of conceptual basis for biological classification • Systematics - scientific study of biological diversity and evolutionary relationships among organisms both extinct and modern • Willi Hennig (1950): taxonomic groupings should reflect evolutionary relationships - cladistics and molecular genetic techniques have transformed systematics into rigorous scientific discipline over past 3 decades

Preferred waist-to-hip ratio as an indicator of health and fertility

• 0.1 unit increase in WHR above 0.7 decreases probability of conception by 30% • WHR 3X better than BMI at predicting risk of heart disease • Women with preferred WHR of 0.7 - less susceptible to diabetes, cardiovascular disease and ovarian cancers - enter puberty at younger age • Children of low-WHR teens protected from the cognitive defects often associated with teen birth

Evolution of drug-resistant HIV

• 3TC drug interferes with reverse transcription of HIV RNA into human host cell's DNA - 3TC molecule similar in shape to cytosine-bearing nucleotide - picked up by HIV reverse transcriptase in lieu of C-bearing nucleotide and incorporated into DNA chain - terminates DNA elongation and blocks reproduction of HIV • 3TC-resistant HIV variants can discriminate between 3TC molecule and C-bearing nucleotide • In absence of 3TC, resistant viruses at disadvantage - replicate more slowly • Treatment with 3TC selects for reproduction of resistant viruses

A phylogenetic tree

• A phylogenetic tree is a branching pattern showing ancestor-descendent relationships • Nodes represent common ancestors

Allopolyploidy & speciation

• Allopolyploidy - duplication of combination of chromosomes from different species • Polyploid individuals cannot interbreed successfully with members of either parental species because polyploid individuals have more chromosomes than their parents • Allopolyploidy can result in nearly instantaneous speciation

The origin of new species

• Appearance of new species is the source of biological diversity • Evolutionary theory must therefore explain not only how populations evolve but also how new species originate • Many aspects of Darwin's "mystery of mysteries" now well understood

Sympatric speciation: Rhagoletis pomonella

• Apple maggot fly is pest species on apples and hawthorn • Original host plant was hawthorn (native to North America) • Apple introduced in 1800s and a few females shifted to laying eggs on apples • Males and females show affinity for host plant on which they developed • Molecular evidence that hawthorn and apple flies have diverged genetically in < 200 years

Doctrine of the Continuity of the Germ Plasm August Weismann (1834-1914)

• Argued for 'molecular distinction' between soma and germ cells • Generations linked exclusively by germ cells • Changes to somatic cells have no effect on germ cells • Rules out inheritance of acquired characteristics • Cut tails off 21 generations of rats - 22nd generation still had tails!

Peppered moths and industrial melanism melanism PT2

• B. Kettlewell's experiment (1950s) - released peppered and melanic moths in polluted and unpolluted woods - recaptured more melanic moths in polluted woods; more peppered moths in unpolluted woods - consistent with lower probability of peppered moths escaping bird predation on dark tree trunks • Environmental change and natural selection rapidly altered allele frequency - nearly complete replacement of one allele by another in 50 generations • Clean Air Acts have led to reversal of melanism - frequency of melanic morph outside Liverpool dropped from 93% in 1959 to 15% in 1995 - similar decrease outside Detroit from 89% in 1961 to 15% in 1994

Limits to male & female reproductive success (RS)

• Because sperm are physiologically inexpensive, a male's RS is typically limited by the number of females he can acquire as mates. • Because eggs are costly, a female's RS is typically limited by the resources available for egg production. Females should therefore be much more discriminating in their choice of mate.

Transposon-driven horizontal transfer in bacteria PT1

• CONJUGATIVE TRANSPOSONS combine transposition with horizontal transfer • The multiple-antibiotic-resistant bacterium, CLOSTRIDIUM DIFFICILE (Cdiff), is leading cause of hospital acquired infections in developed world • In the highly virulent and antibiotic resistant Cdiff strain 630, 11% of genome consists of transposable elements most of which are conjugative transposons

Genetic Drift

• Change in allele frequencies due to chance (stochastic) effects • Most important in small populations • An agent that tends to reduce genetic variation as result of extinction of alleles • Generally does not produce a fit between organism and its environment - may result in non-adaptive or maladaptive evolution

What is evolution?

• Charles Darwin - "On the Origin of Species by Natural Selection" (1859) • Descent with modification - All organisms related through descent from common ancestor living in distant past - Spread of descendents into different habitats and slow accumulation of modifications (adaptations) - Descent with modification through mechanism of natural selection • Tree of life

Female choice

• Choice behavior can be difficult to observe - evidence for active choice should include mate rejection • Lek mating system - gathering of males to display to females • e.g., turkeys, cichlid fishes, sage grouse, manakins

Evolutionary systematics

• Classification based on combination of common ancestry and overall phenotypic similarity • New higher taxa erected for groups exhibiting marked phenotypic divergence

Phenetics

• Classification based on overall phenotypic similarity • Uses multivariate statistical methods • All traits given equal weight

Cladistics (phylogenetic systematics)

• Classification based strictly on recency of common ancestry • Aim is to reconstruct phylogeny - i.e., the evolutionary history of a lineage of organisms

Transposon-driven horizontal transfer in bacteria PT2

• Conjugative transposons in Cdiff carry resistance genes for tetracycline and erythromycin • Genome sequence comparisons have shown that many transposable elements present in Cdiff 630 are absent in less virulent and less resistant Cdiff strains

Disadvantages of molecular characters

• Costly in terms of time and money but ... - new Ion Proton sequencer can sequence human genome in few hours for $1,000 • Sequences can be subject to convergence (similarity not due to common ancestry) - because nucleotides can attain only 4 states (GATC), DNA sequences not expected to become 100% different, even after infinite amount of time

Hybrid speciation - the eastern coyote

• Coyote currently inhabiting northeastern US actually hybrid between wolf and western coyote ("coywolf") • More coyote than wolf but significantly larger and fiercer than western coyote (32 - 44 pounds) • Wolf genes enable eastern coyote to kill deer • Young woman recently killed in Nova Scotia by a pair of eastern coyotes

Cladistics is the proper approach

• Critical unit in cladistics is the monophyletic group, that is, common ancestor and ALL its descendent species • Paraphyletic group - common ancestor and some but not all of its descendants

Inheritance: Darwin's Achilles Heel Blending Inheritance

• Darwin accepted prevailing view of blending inheritance - characteristics of an individual result from blending of hereditary determinants from its parents • Critics pointed out that blending of hereditary determinants rapidly depletes genetic variation necessary for natural selection

The reluctant revolutionary

• Darwin began formulating theory of evolution in 1837 • Wrote unpublished paper on evolution by natural selection in 1844 • Received essay on natural selection from Alfred Russel Wallace in 1858 • Why did Darwin prevaricate?

Natural Selection

• Darwin reasoned that different environments could modify species in same way through natural selection - beaks and behaviors of Galápagos finches adapted to foods available on different islands

Artificial Selection

• Darwin very familiar with artificial selection - selective breeding of domesticated plants and animals by humans to produce certain characteristics - results in great variation in traits

Human Evolution: Sickle-Cell Anemia in black Americans of African descent

• Defective hemoglobin molecules stick together and alter shape of red blood cells • Results in impaired oxygen delivery to tissues, intermittent illness and reduced life span

Hardy-Weinberg theorem (rule)

• Developed independently by Hardy in England and Weinberg in Germany in 1908 • Specifies conditions that must be met for population to remain at equilibrium, i.e., for no evolutionary change to occur

The Biological Species Concept (Ernst Mayr 1942)

• Defines species as " ... groups of actually or potentially interbreeding natural populations which are reproductively isolated from other such groups" - a species is composed of populations whose members mate with each other and produce fertile offspring - or would do so, if they came into contact - Phenotypically distinct sub-species of milk snake interbreed and are connected by intermediate populations

Sexual selection

• Differential reproductive success resulting from competition between members of one sex, usually males, to achieve matings and/or fertilizations • Unlike most other forms of natural selection, sexual selection can result in the evolution of traits which may be detrimental to survival

Documented cases of evolution

• Drug resistance in HIV • Industrial melanism in moths • Sickle cell anemia allele in black Americans of African descent • Antibiotic resistance in bacteria

XDR-TB no longer confined to South Africa

• Estimated 40,000 cases per year

Why is systematics important?

• Evolution is a historical process • Testing hypotheses about evolutionary mechanisms requires rigorous data on phylogenetic relationships • Haldane's quip: - "an inordinate fondness for beetles"

M. tuberculosis: grim prospects ahead

• Extensively drug-resistant strain (XDR-TB) has now evolved - resistant to main TB drugs and to two or more of second-line drugs - discovered in 2006 in South Africa when 52 of 53 patients died ~ 2 weeks after TB testing • More than 500 cases of XDR-TB identified in South Africa in 2007 • Enforced isolation of individuals with XDR-TB (see posted Science article)

Early ideas on development and evolution I. von Baer''s law (1828)

• Features common to a higher-level taxon (e.g., class) often appear in development before characters unique to lower-level taxon (e.g., order) • Human and chick are both in class Vertebrata (fishes, amphibians, reptiles, birds and mammals) • At early embryonic stage, all vertebrates possess gill slits and tails • Specific features of vertebrate orders, e.g., feathers in birds, appear later in development

Peahens choose males with good genes

• Females prefer males with many eyespots • Removal of eyespots reduced number of matings • Offspring survival positively correlated with father's eyespot number

How do we calculate allele frequencies?

• First calculate genotype frequencies • Assume a gene with 2 alleles, A, a • Yields 3 genotypes, AA, Aa, aa • Note that: - N denotes numbers of individuals, genotypes and alleles - n denotes frequencies • NAA = number of individuals of genotype AA • NAa = number of individuals of genotype Aa • Naa = number of individuals of genotype aa • NAA + NAa + Naa = N = total number of individuals in population

Negative Frequency Dependent Selection

• Fitness of a genotype increases when it becomes rare • Fitness of a genotype decreases when it becomes common

Allopatric speciation through vicariance: examples

• Formation of Grand Canyon - Harris's antelope squirrel (Ammospermophilus harrisi) inhabits south rim - closely-related white-tailed antelope squirrel (A. leucurus) inhabits north rim • Emergence of Isthmus of Panama

How do we reconstruct phylogeny?

• Fossils • Development • Distribution of character states in living species

Genetic Drift: Founder Effect

• Founder effect occurs when new population is started by few members of original population • Small population size can result in - reduced genetic variation compared to original population - disproportionate representation of rare alleles in founder population • Founder effects important in evolution of organisms on remote oceanic islands - > 500 species of Hawaiian Drosophila descended from single founder ~ 5 mya

Evolution and religion: not necessarily mutually exclusive Francis Collins

• Francis Collins - Director of NIH since 2009 - Director of National Genome Research Institute for 15 years - headed Human Genome Project • Similarities between human genes and those of other mammals, worms and bacteria " ... are absolutely compelling. If Darwin had tried to imagine a way to prove his theory, he could not have come up with something better, except maybe a time machine." - "Asking somebody to reject all of that in order to prove that they really do love God - what a horrible choice."

Gene flow can reduce local adaptation

• Gene flow can oppose natural selection and reduce local adaptation - especially in species with broad geographic ranges, e.g., mountain lions - or when gametes or immature stages are transported from place to place, e.g., heavy-metal tolerance in plants • Benefits of gene flow - restoration of alleles lost through genetic drift - introduction of new beneficial alleles

More HIV

• HIV population in each patient 100% resistant to 3TC within few weeks • Change in genetic composition of population through time

Haeckel: an overzealous evolutionist

• Haeckel's drawings, perhaps deliberately, minimized differences between early-stage embryos of vertebrates Haeckel was correct in showing • increasing differences between species as they develop • strong similarities between earliest embryos of human and other vertebrates However, he was wrong to imply virtually no evolutionary change in early embryos

Now assume A and a alleles are dominant/recessive

• Here, frequencies of AA and Aa genotypes cannot be observed directly because their phenotypes are identical • aa genotype has distinct phenotype and its frequency can be directly observed: naa = Naa/N • Using naa, frequencies of AA and Aa genotypes can be calculated from p^2 + 2pq + q^2 = 1 - naa = q^2 - q = √naa - p = 1 - q - p^2 = frequency of AA genotype - 2pq = frequency of Aa genotype

Evidence for descent with modification: homology

• Homology - underlying similarity between structures with different functions in related species that results from common ancestry • Homologies can be - anatomical - developmental - genetic • Drosophila eyeless gene encodes transcription factor expressed during eye morphogenesis • Eyeless is homologous to Aniridia gene in humans

Reconstructing phylogenies I. Fossils

• In principle, fossils could provide direct evidence of evolutionary transitions • In practice, for most taxa, data are too fragmentary • "Dead fossils may not have left descendants whereas living organisms definitely had ancestors" (Alan Wilson) • Fossils are useful for designating outgroups and estimating divergence time of taxa

Allele frequencies calculated from genotype numbers

• Individuals are diploid - total number of copies of the gene in the population is 2N (twice the number of individuals in the population) • Let the frequency of A = p • and the frequency of a = q .... then • p = (2NAA + NAa)/2N = (NAA + 0.5NAa)/N • q = (2Naa + NAa)/2N = (Naa + 0.5NAa)/N

Peppered moths and industrial melanism PT1

• Industrial melanism - dark individuals predominate in polluted areas • Biston betularia moths exhibit color polymorphism (peppered and melanic morphs) • Color controlled by single gene with two alleles - AA, Aa genotypes produce melanic morph - aa genotype produces peppered morph • Melanic individuals - rare in populations before 1850 - frequency then increased in industrialized areas to almost 100%

Intrasexual competition

• Intrasexual competition for access to mating opportunities - usually male-male competition - evolution of weapons or intimidating signals of strength

Allopatric speciation through vicariance

• Involves emergence of geographic barrier (e.g., new river or mountain range) that divides previously continuous population • Evolution of reproductive isolating mechanisms between populations that are geographically separate

Examples of sexually-selected traits: Weapons

• Larger size of males in many species • Antlers in deer stags • Tusks of bull elephants • Horns in male dynastine beetles

Phenetic versus cladistic classification

• Left column indicates true phylogeny - vertical axis shows time to common ancestry - horizontal axis indicates level of divergence in external morphology • Phenetic and cladistic classifications - concordant in rhino, beetle and butterfly example - not in other two cases • Problem with phenetics - does not distinguish between primitive and derived traits

Sensory exploitation

• Males exploit pre-existing biases in the female's sensory system to increase their attractiveness - Euglossine bees: males produce pheromone that smells like an orchid • Female preference exists before male trait has evolved - in the southern platyfish (Xiphophorus maculatus), females prefer swords but males lack the trait - phylogenetic evidence that preference for swords existed in females before swords evolved

Female facial attractiveness

• Males tend to prefer full lips, narrow chins, high cheek bones and large eyes • Evidence that these traits indicate higher levels of pubertal estrogens and lower levels of androgen exposure

Male facial attractiveness

• Masculine features of male face correlated with testosterone levels during puberty • Testosterone thought to be immunosuppressant • Masculine face an honest signal of health and resistance to pathogens and parasites

The evolution of mate choice Potential benefits

• Material benefits - paternal care; territory quality; nuptial gifts • Genetic benefits - 'good genes'

Particulate genes and blended characters

• Mendel established basic rules governing how traits passed from parents to offspring - Individual has two copies of each hereditary factor (gene) - Each gamete receives one of the two copies present in individual (Law of Segregation) - Copies from different genes transmitted to gametes independently of each other (Law of Independent Assortment) • Mendelism - a controversial model of heredity in 1900 - Many phenotypic characters show continuous (not discrete) variation and apparent blending (not particulate) inheritance - Mendel did not determine physical basis for these patterns of inheritance

Outgroup Comparison

• Monophyletic groups can be identified by shared, derived characters • How do we distinguish between primitive and derived characters? • Outgroup comparison - outgroup is a taxon (species or group of species) that diverged earlier than the taxa under investigation, the ingroup - compare each ingroup species with outgroup to differentiate between shared derived and shared primitive characteristics - assumes that homologies shared by outgroup and ingroup must be primitive characters that predate divergence of both groups from common ancestor

Female attractiveness and reproductive potential (probability of conception)

• Most attractive female phenotype exhibits hormonal profiles indicative of high conception probability • Men's rating of female attractiveness more influenced by female waist size than by hip size

Gene flow (migration)

• Movement of alleles from one population to another by - migration of fertile individuals - transport of gametes or immature stages • in plants: transport by wind or animals • in marine species: transport by water currents - mating of individuals belonging to adjacent populations • Tends to reduce differences in allele frequencies between populations over time

What is polyploidy?

• Multiplication of number of chromosome sets • Autopolyploidy - duplication of chromosome set of single species

Agents of evolutionary change

• Mutation • Genetic drift (in small populations) • Non-random mating • Gene flow (migration) • Selection - natural selection - sexual selection

Mutations caused by transposable elements

• Mutation caused by transposable elements and horizontal gene transfer can be a potent agent of evolutionary change in bacterial populations with important consequences for human health and disease

Natural selection & evolution

• Natural selection occurs when different phenotypes vary in average reproductive success • However, natural selection (a process) is different from evolution by natural selection (selection-driven genetic changes in population across generations) • Natural selection will not produce evolutionary change in population unless phenotypes differ in their genotypes (variation must have genetic basis) • Not all phenotypic variation is heritable - weight and shell morphology in turtles - coloration in map butterflies

What''s different about natural selection? • Natural selection produces adaptations

• Natural selection produces adaptations - traits that increase ability of individuals to survive and/or reproduce in particular environment compared to individuals lacking the traits - other evolutionary forces such as genetic drift, gene flow and mutation can cause maladaptation

Christian natural theology More

• Natural theology scientifically important - guided researchers to fundamental question of how life works • Darwin was admirer of Paley

Molecular Characters Advantages

• No environmental effects • Can evolve in clock-like fashion (rate of substitution constant) • DNA is ubiquitous to life and homologous sequences exist among all taxa • Protein-coding genes provide model of evolutionary change - genetic code degenerate in 3rd position, e.g., CUU, CUC, CUA, CUG all code for the amino acid leucine - changes in third position are synonymous or silent mutations - because most mutations are deleterious, expect higher rate of base substitution at synonymous sites than non-synonymous sites • Different genomic regions evolve at different rates and can therefore be used for phylogenetic questions at different hierarchical levels

Voyage of HMS Beagle (1831-1836)

• On return to England, Darwin - began to see adaptation to environment and origin of new species as closely related processes - Could new species arise from ancestral forms by gradual accumulation of adaptations to different environments? •During voyage, Darwin - collected thousands of specimens - observed adaptations of plants and animals inhabiting diverse environments - visited Galápagos Islands • collected species of finches unique to individual islands

Early ideas on development and evolution: II. Haeckel''s "biogenetic law"

• Ontogeny recapitulates phylogeny • Ontogeny = development of the individual organism • Recapitulate = to repeat the principal stages of • Phylogeny = evolutionary history of species or lineage • In the course of its development, an individual successively passes through the adult forms of its ancestors

The problem with paraphyly

• Paraphyletic groups obscure evolutionary history • Cladistic analysis of fossils indicates that birds and dinosaurs share a common ancestor and therefore constitute a monophyletic group • Dinosaurs have not gone extinct! • Birds are highly modified dinosaurs

Computer programs needed to reconstruct phylogeny

• Parsimony is one of several methods for finding the tree (phylogeny) best supported by character-state data • All methods require evaluating all possible trees • Number of trees increases exponentially with number of taxa - 3 trees with 3 taxa - 15 trees with 4 taxa - 34,459,425 trees with 11 taxa

Evidence for descent with modification: the fossil record

• Pattern of successive evolutionary change in fossils consistent with comparative data from biochemistry, molecular biology and cell biology • Intermediate forms illustrate how major evolutionary transitions occurred - Archaeopteryx intermediate between birds and dinosaurs

Examples of sexually-selected traits: ornaments

• Peacock's tail • Dewlap in male lizards • Elaborate plumage and courtship displays in the cock-of-the-rock • Stalked eyes of some flies, e.g., Plagiocephalus

For simplicity, assume that A and a alleles display incomplete dominance

• Phenotype of heterozygote (Aa) is intermediate between homozygotes (AA, aa) - e.g., crossing red-flowered and white-flowered homozygous snapdragon plants yields pink- flowered heterozygotes • With incomplete dominance, genotype frequencies can be observed directly from phenotypes - frequency of AA = NAA/N = nAA - frequency of Aa = NAa/N = nAa - frequency of aa = Naa/N = naa

Thomas Malthus (1766-1834)

• Political economist • "An Essay on the Principle of Population as it Affects the Future Improvement of Society" (1798) - human suffering (disease, famine, war) results from human population's potential to increase faster than food and other resources - food production increases linearly - population grows geometrically • Malthus's essay profoundly important in Darwin's development of principle of natural selection

Speciation: Reproductive isolating mechanisms

• Prezygotic • Postzygotic

How do we determine the best evolutionary tree?

• Principle of parsimony - commonly used method and simplest to explain - most parsimonious tree requires fewest evolutionary events to have occurred - equals evolutionary tree that minimizes total number of character state changes (steps) across all characters

Charles Lyell (1797-1875)

• Principles of Geology (three volumes, 1830-1833) - incorporated gradualism into theory of uniformitarianism

Transposable elements in humans

• Protein-coding genes, RNA genes and regulatory regions make up less than 2% of human genome • Nearly half (45%) of the 3 billion base pairs is derived from transposable elements (DNA transposons, LTR retrotransposons, SINEs and LINEs) • Many are inactive but LINE-1 family and Alu elements (SINEs) active and implicated in diseases such as cancer

Refining Mendelism

• R.A. Fisher showed mathematically that continuous variation can be produced by multiple Mendelian factors contributing to trait • Mendel worked on discrete traits with simple genetic basis (one gene, 2 alleles, one completely dominant to other) but patterns of inheritance usually more complex - incomplete dominance • two alleles both expressed in heterozygote which exhibits intermediate phenotype (e.g., snapdragons) - codominance • two alleles both expressed in heterozygote which has composite rather than blended phenotype (e.g., MN blood types in humans)

Rapidly-evolving DNA regions

• Rapidly-evolving genomic regions useful for fine-scale phylogenetic resolution at level of populations, species and genera • Mitochondrial genes - have nucleotide substitution rates 10X higher than nuclear genes - useful for reconstructing evolutionary history of the domestic dog - all dog breeds derived from wolves but through four independent domestication events

Allopatric speciation through dispersal and colonization

• Rare dispersal event results in colonization of isolated habitat (e.g., offshore islands) - Galápagos finches - Hawaiian Drosophila

Male-male competition

• Relatively easy to understand and observe • In polygynous species, males compete to monopolize either females or a resource important to females - Harem polygyny (guard females directly) • e.g., elephant seals, horses, deer - Resource defense polygyny • e.g., the Cortez damselfish

Phenotype, Variation, Darwinian Fitness

• Selection acts on the phenotype of the individual - its physical traits, metabolism, physiology and behavior • Phenotypic variation exists among individuals in a population • Certain phenotypic trait variants enhance survival and/or reproduction in a given environment • Individuals possessing those trait variants are 'selected' - they produce more surviving offspring than other individuals • They have higher fitness - Darwinian fitness = survival x reproductive success - the contribution an individual makes to the gene pool of the next generation relative to the contributions of other individuals • Acting on phenotypes, selection indirectly adapts a population to its environment by increasing or maintaining favorable genotypes in the gene pool

Human mate choice

• Several distinctive human traits likely to have evolved through sexual selection • Females - permanently enlarged breasts and buttocks - minimal body hair • Males - V-shaped torso - masculine facial features

Sexual selection and allopatric speciation

• Sexual selection can cause rapid divergence in male sexually selected traits and female mate preferences • Accelerates rate at which mating-stage reproductive isolation evolves • Evidence? - In many closely related species of birds, greatest differences apparent in male sexually selected traits - Of relatively sexually monomorphic and dimorphic sister lineages, the latter is usually more species rich

Sexual dimorphism

• Sexual selection can result in sexual dimorphism - marked difference between sexes in secondary sexual characteristics • Greater sexual dimorphism in polygynous species - single male mates with many females - generates more intense sexual selection - e.g., elephant seals

The ''good genes" model

• Sexually-selected traits signal heritable genetic quality • The Handicap Principle (Zahavi 1975) - some males bear a heritable handicap that reduces viability (e.g., a big bright tail) - only males with "good genes" can survive despite the handicap - females that mate with handicapped males will get better genes (higher viability) for their offspring

Malaria Resistance

• Sickle-cell allele (AS) maintained at relatively high frequency (up to 20%) in many native African populations, although often lethal in homozygous state (ASAS) • AS allele increases malaria resistance - heterozygous individuals with one AS and one normal allele (AN) have highest fitness of the 3 genotypes (ANAN, ANAS and ASAS) • AN and AS co-dominant; heterozygotes produce both normal and defective hemoglobin - known as HETEROZYGOTE SUPERIORITY or HETEROSIS - heterosis acts to maintain AS allele in population

Human evolution: sickle-cell anemia in black Americans of African descent (continued)

• Sickle-cell allele (AS) maintained at relatively high frequency (up to 20%) in many native African populations, although often lethal in homozygous state (ASAS) • AS allele increases malaria resistance - heterozygous individuals with one AS and one normal allele (AN) have highest fitness of the 3 genotypes (ANAN, ANAS and ASAS) • AN and AS co-dominant; heterozygotes produce both normal and defective hemoglobin - known as heterozygote superiority or heterosis - heterosis acts to maintain AS allele in population • In North America, malaria not significant threat - heterozygotes not the most fit - sickle cell allele among black Americans of African descent should therefore decline in frequency through time - it has dropped to 4% - evolutionary change has occurred

Slowly-evolving DNA regions

• Slowly evolving regions useful for broad-scale phylogenetic questions, i.e., higher relationships such as domains, kingdoms and phyla - ribosomal RNA genes evolve slowly, facilitating sequence alignment and enabling comparisons between distantly-related organisms • rRNA sequencing reveals that prokaryotes are composed of two very different groups, Bacteria and Archaea • Phylogenetic analysis indicates that Archaea shares more recent common ancestor with Eukarya than it does with Bacteria

Parapatric speciation

• Speciation alongside - evolution of reproductive isolation between spatially adjacent populations that have limited gene exchange • Occurs in absence of obvious geographic barrier • May occur when a sharp environmental discontinuity develops within the range of a species • Plants growing on mine tailings flower at different times than plants growing in surrounding pastures in Wales - Although continuously distributed, different flowering times have begun to reduce gene flow between metal-tolerant plants and metal-intolerant plants

Sympatric speciation

• Speciation in the same homeland • Development of reproductive isolation without geographic barriers • Fairly common in plants via polyploidy • 47% of flowering plant species are polyploid

Reconstructing phylogenies II. Development

• Structures in early developmental stages may show evolutionary relationships not evident in adults • Sea squirt larvae and frog embryos both have a notochord for body support • Notochord - lost in adult sea squirts - replaced by vertebral column in adult frog

Vestigial traits

• Structures that have marginal or no function in organism but resemble traits possessed by ancestors • Tailbone (coccyx) in humans - ancestral primates were arboreal and tail adaptive for use as prehensile limb and organ of balance - with transition to terrestrial habitat, tail became useless and slowly disappeared - fused vertebrae of human tailbone are vestiges of this tail - documented cases of infants born with 'tails' (coccyx with extra vertebrae) • Other examples include - appendix and wisdom teeth in humans - hip bones and rudimentary hind legs in boa constrictors - fingernails on fins of manatees (sea cows) • Evolutionary relics of structures that served important functions in organism's ancestors

Genetic Drift: Bottleneck Effect

• Sudden change in environment may drastically reduce population size resulting in - change in allele frequencies - potential loss of alleles • Bottlenecks have eliminated genetic variation in - northern elephant seals - cheetahs

Evolution of antibiotic-resistant bacteria I: Mycobacterium tuberculosis PT2

• Surge in infection rates in late 1980s caused WHO to declare TB a global health emergency in 1993 - 9 million new cases of TB and 1.5 million deaths in 2013 - one third of world's population infected with M. tuberculosis - 5-10% of infected individuals develop disease - rate much higher in individuals also infected with HIV • Over last decade, multidrug-resistant strains (MDR-TB) have evolved in many regions of world - resistant to main drugs used to treat TB (rifampicin and isoniazid)

Sympatric speciation: animals

• Sympatric speciation is a more controversial mechanism of speciation in animals • How can reproductive isolation be achieved in absence of barriers to gene flow? • Host plant shifts resulting in sub-populations with assortative mating may be common cause of sympatric speciation in phytophagous insects

Exceptions I: Non-coding DNA

• TRANSPOSABLE ELEMENTST: one category of non-coding DNA - also known as mobile DNAs, transposons, insertion sequences or "jumping genes" - discovered by Barbara McClintock in maize in 1940s • Parasitic, selfish genetic elements that accumulate by TRANSPOSITION (copying themselves to new locations in the genome) • Mutations caused by transposable elements include - inserting into protein-coding genes (and disrupting their function) - inserting into regulatory sequences (and increasing or decreasing protein production) - carrying segments of host DNA sequence to new locations in genome - hindering precise chromosomal pairing during cell division, resulting in chromosomal rearrangements

Haeckel's law: an overzealous law

• Terminal additions to development lead to recapitulation (phylogenetically new features are added to the ancestral ontogeny) • Law is violated most strongly by paedomorphic species - species in which the juvenile morphology of the ancestor is retained throughout life • While Haeckel's law is sufficiently common that recapitulation was noticed, it cannot be used as generally applicable method for phylogeny reconstruction Human skull differs from chimp by retaining fetal skull characteristics present in both species

Hardy-Weinberg and human health

• The Hardy-Weinberg equation (p^2 + 2pq + q^2 = 1) can be used to estimate percentage of population that are carriers for autosomal recessive diseases • Phenylketonuria (PKU) - 1 in 10,000 births - q^2 = 0.0001 - q = √0.0001 = 0.01 - p = 1 - 0.01 = 0.99 - 2pq = 2 x 0.99 x 0.01 = 0.0198 • Therefore, the frequency of PKU carriers (Aa individuals) is ~ 2% of US population

Reconstructing phylogenies III. Character states

• The distribution of character states in a set of organisms provides information on evolutionary relationships • Jaws, lungs, hair, etc. are characters • Absence (0) or presence (1) are character states • Characters can have more than two states

Evolutionary theory is science

• The litmus test for scientific validity is Karl Popper's principle of falsifiability - to be considered scientific, a theory must be constructed in such a way that it is capable of being disproved • Theory of evolution by natural selection is example of the scientific process - Darwin observed differences in related organisms - He proposed hypothesis of natural selection to explain these differences - Predictions of hypothesis tested by analysis of fossil record, genetics, comparative anatomy and comparative genomics • Alternatives to evolution that posit supernatural causes, e.g., Intelligent Design, do not satisfy the falsifiability criterion and are not science

Anisogamy

• The most fundamental difference between males and females lies in the size of the reproductive cells (gametes) they produce • Males produce numerous, small and physiologically inexpensive sperm • Females produce few, large and physiologically expensive eggs

Population genetics

• The study of how populations change genetically over time - concerned with whether particular allele or genotype will become more or less common over time and why - requires mathematical approach

A Population will remain at Hardy-Weinberg equilibrium if:

• There is no mutation • Population is very large (no genetic drift) • Mating combines gametes at random to form genotypes (random mating) • There is no migration into or out of the population (no gene flow) • All genotypes survive and reproduce equally well (no selection)

Why the p's and q's?

• This mathematical formalism can be used to model the conditions under which evolution will and will not occur • When genotype and allele frequencies do not change from generation to generation, the population is said to be at equilibrium, i.e., there is no evolutionary change

The evolution of mate choice Potential costs

• Time and energy devoted to mate searching • Male harassment

Practical implications of horizontal transfer

• Traits acquired through horizontal gene transfer include new metabolic capacities, virulence and antibiotic resistance • Horizontal transfer between soil-dwelling bacteria, as well as between plants and their bacterial symbionts, raises concerns about dangers of releasing bioengineered bacteria into environment • Growing antibiotic resistance linked to horizontal transfer of resistance genes between bacteria via conjugation and transduction

Evolution of antibiotic-resistant bacteria I: Mycobacterium tuberculosis PT1

• Tuberculosis (TB) responsible for - 33% of all deaths in 19th century Paris - 25% of deaths in New York City in 1804 • Virtually 'stamped out' in industrialized countries between 1950 and 1990 due to - improved living conditions - introduction of antibiotics in early 1950s

Mutation

• Ultimate source of genetic variation • Mutation rate generally low in animals and plants - typical gene mutates once per 100,000 cell divisions - only germline mutations transmitted to next generation • Mutation therefore has only minor effects on allele frequencies over short evolutionary time spans • Two exceptions - non-coding regions of DNA can evolve very rapidly due to a combination of relaxed selection and high mutation rates - mutation can rapidly generate genetic variation in bacteria and viruses • short generation times • horizontal gene transfer

Evolution: both fact and theory

• Undeniable that organisms have evolved during history of life on Earth • Mechanisms responsible for this evolution are the domain of evolutionary theory • Understanding in science requires both facts and theories that explain those facts in logical and verifiable manner

Male mate choice: waist-to-hip ratio and female attractiveness

• Waist-to-hip ratio (WHR): the most extreme human sexual dimorphism - Women: 0.60 to 0.80 - Men: 0.85 to 0.95 • Computer manipulation of female images demonstrates that males prefer WHR between 0.6 and 0.7

Georges Cuvier (1769-1832)

• developed paleontology (the branch of science concerned with fossil animals and plants.) • extinctions common in history of life • advocated catastrophism - each boundary between strata represented local catastrophe that destroyed many species - region then repopulated by species from other areas

Calculations reveal two significant points

• p + q = 1 - more generally, regardless of the number of different alleles at a locus, the sum of allele frequencies always equals one • Two populations with markedly different genotype frequencies can have the same allele frequencies

Assume N = 200 individuals in each of two populations • Population 2: 45 AA, 130 Aa, 25 aa In Population 2

• p = (45 + 0.5(130))/200 = 110/200 = 0.55 • q = (25 + 0.5(130))/200 = 90/200 = 0.45

Assume N = 200 individuals in each of two populations • Population 1: 90 AA, 40 Aa, 70 aa In Population 1

• p = (90 + 0.5(40))/200 = 110/200 = 0.55 • q = (70 + 0.5(40))/200 = 90/200 = 0.45

James Hutton (1726-1797)

• promoted gradualism - Earth's geologic features explained by gradual mechanisms still operating today

Reptiles are a paraphyletic group

• taxon created by evolutionary systematics school • includes turtles, lizards, snakes and crocodilians • common ancestor of all reptiles also gave rise to the birds • birds excluded because they have diverged markedly in phenotype

Evolution defined

•Darwin's definition - Descent with modification •Modern definition - Change in the genetic composition of a population through time (across generations)

Darwin's response Pangenesis

•Pangenesis: a more complex theory of inheritance - incorporated both blending inheritance and inheritance of acquired characteristics •Gemmules containing hereditary information from every part of body coalesce in gonads and are incorporated into reproductive cells •Inheritance of acquired characteristics as source of variation - "In variations caused by the direct actions of changed conditions ... certain parts of the body are directly affected by the new conditions, and consequently throw off modified gemmules which are transmitted to the offspring"

A fruit fly population has a gene with two alleles, A1 and A2. Molecular genetic tests show that 70% of the gametes produced in the population contain the A1 allele. If the population is in Hardy-Weinberg equilibrium, what proportion of the flies carry both the A1 and A2 alleles?

(.7)(.3)(2)= 0.42

Parapatric speciation

(speciation alongside) - evolution of reproductive isolation between spatially adjacent populations - results from environmental discontinuity

Allopatric speciation

(speciation in different homeland) - thought to be most common (least controversial) form of speciation - results from geographic separation of populations through • vicariance • dispersal and colonization

Sympatric speciation

(speciation within single locality) - polyploidy in plants - host plant shifts in insects

Blending versus particulate inheritance: fate of a favorable mutation

- Blending Inheritance: The discredited theory that inheritance of traits from two parents produces offspring with characteristics that are intermediate between those of the parents. - Particulate Inheritance: Instead of blending, the offspring inherits a version of a gene, called an allele, from each of the parents. Only one allele is expressed depending on a number of factors.

Genetic Drift: Founder Effect (continued) - Tristan da Cunha

- British settlement founded by 15 colonists in 1814 - high incidence of retinitis pigmentosa • progressive blindness • autosomal recessive disease • mutated allele has 10X higher frequency in Tristan da Cunha than in Britain

Types of natural selection

- Directional selection - Disruptive selection - Stabilizing selection

Uniformitarianism

- Earth shaped by ongoing, observable processes - steady accumulation of minute changes over long time spans - Earth much older than the 6,000 years estimated by theologians • Darwin later applied principle of gradualism to biological evolution

The Evolution of Populations

- Evolution defined as change in the genetic composition of a population through time (across generations) • Individuals do not evolve • Natural selection acts on individuals in a population and the population evolves • Genetic variation is the raw material of evolutionary change - How do we measure it? • What are the forces that cause genetic changes within populations, that is, what are the forces of evolution?

Particulate Theory of Inheritance Gregor Mendel

- Father of genetics • Based on crosses between different varieties of garden pea (e.g., purple-and white-flowered plants) • Parents pass on discrete heritable factors that retain their separate identities in offspring • Heritable factors passed along generation after generation in undiluted form • Published in 1866 but largely ignored until rediscovered in 1900

Christian natural theology • St. Thomas Aquinas (13th century)

- God could be understood by studying his creation - the natural world - adaptations of organisms - evidence of benevolent Creator who designed each species for particular purpose

Two general forms of sexual selection

- Intrasexual competition - Intersexual mate choice

Christian natural theology • Dominated thinking in England for nearly two centuries

- John Ray's "The Wisdom of God Manifested in the Works of the Creation" (1701) - William Paley's "Natural Theology; or Evidences of the Existence and Attributes of the Deity" (1802)

What determines tempo of allopatric speciation?

- Mutation + genetic drift -> Slow allopatric speciation - Natural selection and sexual selection -> Rapid allopatric speciation increases probability that speciation is complete before secondary contact occurs

Mutations

- Mutations in eyeless gene cause major anomalies in Drosophila eye development - Mutations in human Aniridia gene result in absence or partial absence of the iris

Sickle cell allele: mechanisms of malaria resistance Cellular level

- P. falciparum parasite causes low oxygen tension in cell - cells with defective hemoglobin become sickle shaped - removed from blood stream by spleen

Aristotle (384-322)

- Plato's student - organisms arranged in "scale of nature" or Great Chain of Being - linear hierarchy from inanimate matter through plants, lower animals and humans to angels and other spiritual beings

Maintenance of variation

- Removal of variation by directional and stabilizing selection is countered by forms of selection that maintain variation • Temporally oscillating selection in the medium ground finch (Geospiza fortis) favors - short beaks in wet years - long beaks in dry years

Shared, primitive character

- character state that is shared beyond the taxon we are trying to define - character state that is shared by distant common ancestors - lungs are a shared, primitive character of mammals - provides no information on evolutionary relationships

Genetic Drift: Founder Effect (continued) - Amish of Pennsylvania

- descended from ~ 200 18th century German immigrants - suffer high rate of Ellis-van Creveld syndrome • dwarfism, polydactyly and heart malformation • autosomal recessive disease • 12.3% of population are carriers of mutated allele • mutated allele traced to single founding couple

Disassortative Mating

- dissimilar phenotypes mate preferentially (e.g., short with tall) - increases heterozygosity - might be important at MHC loci

Microevolution

- evolution within populations - results from mutation, genetic drift, gene flow, non-random mating, natural and sexual selection

Macroevolution

- evolutionary change above species level - differential speciation and extinction rates among lineages, mass extinctions

Shared, derived character

- evolutionary novelty (trait or character state) that is unique to a particular lineage - character state not shared by distant common ancestors - fur or hair is a shared, derived character state of mammals - provides the basis for cladistic classification

Gene or genomic characters

- frequently called molecular characters - nucleic acid sequence: DNA, RNA - gene order - whole genome

Populations evolve by changes in frequencies of alleles between generations resulting from

- genetic drift - gene flow - especially natural selection

Heterozygote advantage

- greater fitness of heterozygotes maintains two (or more) alleles at locus - sickle cell allele maintained by malaria resistance

First comprehensive theory of evolution Jean-Baptiste Lamarck, 1809

- how things evolve • Organisms continually arise by spontaneous generation • Inheritance of acquired characteristics - organisms develop adaptations to changed environment through use and disuse of organs - acquired characteristics transmitted to offspring • Evolution occurs because organisms have innate drive to become more complex

Inbreeding

- mating between close relatives - extent of inbreeding influenced by population size - exposes lethal recessive alleles and usually depresses fitness - mortality rate for children of first cousins higher than for offspring of unrelated parents - produces a deficit of heterozygotes and an excess of homozygotes

Phenotypic characters

- morphological characters - physiological characters - behavioral characters

What''s different about natural selection? • Natural selection causes allele frequency changes that proceed independently at different loci

- mosaic evolution(!) (different characteristics of a population evolve at different rates) - genetic drift and gene flow tend to act at same rate on all loci

Genetic variation arises by chance through

- mutation (imperfections in DNA replication) - recombination (crossing over of homologous chromosomes during meiosis)

Assortative Mating

- similar phenotypes mate preferentially with one another (e.g., blue-eyed individuals prefer one another as mates) - increases homozygosity at some but not all loci

• Geminate species

- species more closely related to sister species on opposite side of isthmus than to species on same side

Transformation

- take up of naked DNA from surrounding environment and incorporation of foreign DNA into host chromosome

Carolus Linnaeus (1707-1778)

- taxonomy • Classified life's diversity "for the greater glory of God" • Founder of taxonomy • First edition of Systema Naturae published in 1735 - identified species using binomial system of nomenclature (genus name followed by species name) - adopted nested classification system with similar organisms grouped into increasingly general categories (similar species in same genus; similar genera in same family, etc.) - named humans Homo sapiens; placed humans in genus Homo with orangutans and chimpanzees; Homo placed in Primate family • For Linnaeus, similarity between species reflected pattern of their creation • For Darwin, Linnaean hierarchy reflected branching history of tree of life

Varying selection

- temporally oscillating selection favors one phenotype at one time, another phenotype at another time - spatially varying selection favors one phenotype in one environment and different phenotype in second environment

Conjugation

- temporary joining of two bacterial cells and one-way transfer of DNA from donor to recipient

Speciation

- the process by which one genetically-cohesive population splits into two or more reproductively-isolated populations - establishment of reproductive isolation between previously interbreeding populations

Transduction

- transfer of genes from one bacterium to another, with bacterial virus (bacteriophage) acting as carrier of the genes (vector)

Sickle cell allele: mechanisms of malaria resistance Molecular level

- two microRNAs abundant in sickle cells - translocate into P. falciparum cells - fuse with parasite's mRNAs and inhibit translation of essential proteins - impede growth of malarial parasite

Plato (427-347)

- two worlds • real world (invisible, unchanging, perfect and eternal) • illusionary world (perceived through senses, imperfect and transitory) - typological view of nature • single perfect Type for each species in real world • individual variations in illusionary world seen as imperfect copies of real Type

Intersexual mate choice

- usually female choice - evolution of sexually attractive traits and courtship behavior

Speciation (new species formation) occurs gradually as populations become reproductively isolated

- usually involves geographic barriers

Frequency-dependent selection

- fitness of phenotype depends on its frequency within population - may favor common phenotype (positive frequency dependent selection) or rare phenotype (negative frequency dependent selection) - only negative frequency-dependent selection maintains variation

Steps in speciation process

1. Single reproductively-cohesive population 2. Barrier to gene flow splits population into two or more isolated populations 3. Populations gradually diverge 4. Reproductive isolating mechanisms evolve 5. Members of populations incapable of interbreeding 6. Populations now separate species

Define Population

A group of individuals in a particular place that are capable of interbreeding (mating with each other and producing fertile offspring) - e.g., population of coyotes in Washoe Valley

All of the following act to maintain genetic variation EXCEPT A. genetic drift. B. heterozygote advantage. C. negative frequency dependent selection. D. spatially varying selection. E. temporally oscillating selection.

A. genetic drift.

To be considered scientific, a theory must be constructed in such a way that A. it can be disproved, that is falsified. B. it does not challenge accepted scientific dogma. C. it does not conflict with religious teaching. D. only highly trained intellectuals can understand it. E. only technologically advanced instruments can be used to measure its predictions.

A. it can be disproved, that is falsified.

Assuming a gene locus with two alleles (A,a) in a population of 100 individuals, what is the gene frequency, p, of allele A if there are 30 AA genotypes, 60 Aa genotypes and 10 aa genotypes?

A= 60/100 = 0.60

If these conditions hold, it can be shown that:

Allele frequencies remain constant and the genotype frequencies are: nAA = p^2 -->Genotype frequency of AA is p-squared naa = q^2 = (1-p)^2 --> Genotype frequency of aa is q-squared nAa = 2pq = 2p(1-p) --> Genotype frequency of Aa is two times p times q • Total frequency = 1 = p^2 + 2pq + q^2

All of the following were components of Darwin's theory of evolution EXCEPT: A. Competition for resources B. Continual spontaneous generation C. Heritability of traits D. Natural selection E. Variability of traits

B. Continual spontaneous generation

Vestigial traits A. are homologies that can only be observed in embryos. B. are the remnants of structures that were useful to an organism's ancestors. C. constitute evidence that does not support the theory of evolution. D. include highly adaptive traits such as the human brain. E. provide evidence for Lamarck's theory of the inheritance of acquired characters.

B. are the remnants of structures that were useful to an organism's ancestors.

In a small, isolated population of 10 lesser wombat individuals, a meteor impact kills three individuals, all of whom happen to be genotype AA. As a result, the frequency of the A allele decreases from 0.55 to 0.36. This change is gene frequency provides an example of A. gene flow. B. genetic drift. C. mutation. D. natural selection. E. non-random mating.

B. genetic drift.

The original source of all genetic variation is A. independent assortment B. mutation C. natural selection D. recombination E. sexual reproduction

B. mutation

The frequency of an autosomal recessive disease that causes UNR students to descend into a temporary coma during stimulating BIOL 191 lectures ("lectura torpora") is one in every 100 students. Using the Hardy-Weinberg equation, the proportion of students estimated to be heterozygous (carriers) for this dreadful disease is A. 0.01 B. 0.10 C. 0.18 D. 0.81 E. 0.90

C. 0.18

A fruit fly population has a gene with two alleles, A1 and A2. Molecular genetic tests show that 70% of the gametes produced in the population contain the A1 allele. If the population is in Hardy-Weinberg equilibrium, what proportion of the flies carry both the A1 and A2 alleles? A. 0.09 B. 0.21 C. 0.42 D. 0.49 E. 0.70

C. 0.42

What is the only evolutionary mechanism that consistently leads to adaptive evolution? A. gene flow B. genetic drift C. natural selection D. neutral variation E. the bottleneck effect

C. natural selection

Forensic phylogenetic systematics

Case of HIV transmission in Florida dental practice • RNA sequence of HIV proviral envelope gene determined for dentist, 7 infected patients and several local controls (LCs) • Phylogenetic tree indicates that viruses from 5 patients derived from HIV-positive dentist • None of these 5 patients (A, B, C, E and G) at behavioral risk for HIV infection • Patients not infected by dentist (D and F) did have behavioral risk factors for HIV infection

Non-random mating

Changes genotype frequencies but not allele frequencies - Inbreeding, Assortative mating, Disassortative mating

Darwin 5 Components

Competition Variability Natural Selection Heritability Adaptation

Assuming a gene locus with two alleles (A,a) in a population of 100 individuals, what is the gene frequency, p, of allele A if there are 30 AA genotypes, 60 Aa genotypes and 10 aa genotypes? A. 0.09 B. 0.50 C. 0.40 D. 0.60 E. (not enough information is provided)

D. 0.60

DNA sequences in many human genes are very similar to the sequences of corresponding genes in chimpanzees. The scientifically best supported explanation for this similarity is that

D. humans and chimpanzees share a relatively recent common ancestor

Sexual Selection

Differential reproductive success resulting from competition between members of one sex, usually males, to achieve matings and/or fertilizations - can result in evolution of exaggerated male traits detrimental to survival

Directional selection

Directional selection: one extreme phenotype is fittest (e.g., light colored or dark colored individuals) Many examples of strong directional selection associated with • colonization of new environment - colonization of sandy islands by dark deer mice • environmental change - survival after low temperatures and food depletion in cliff swallows

Disruptive selection

Disruptive selection: phenotypes at both ends of the range are fitter than the intermediates Beak length in black-bellied seedcrackers • Juveniles have normal distribution of beak sizes • Birds can specialize either on soft seeds (short beaks) or on hard seeds (long beaks) • Juveniles with intermediate beak lengths die before breeding • Results in bimodal distribution of beak length in adult black-bellied seedcrackers

The uptake of naked DNA from the environment by bacteria is known as A. conjugation. B. genetic drift. C. retrotransposition. D. transduction. E. transformation.

E. transformation.

What was the prevailing belief prior to the time of Lyell and Darwin?

Earth is a few thousand years old, and populations are unchanging

Three schools of systematics

Evolutionary systematics Phenetics Cladistics (phylogenetic systematics)

Which of the following most accurately describes Cuvier's interpretation of fossils found near Paris, France?

Extinction of species can occur but new species cannot evolve.

Do individuals evolve?

Fuuuuuuuuck no, populations evolve not individuals!

Exceptions II: Horizontal transfer in bacteria

Genes may be transferred horizontally between bacteria by - Conjugation - Transformation - Transduction

The frequency of an autosomal recessive disease that causes UNR students to descend into a temporary coma during stimulating BIOL 191 lectures ("lectura torpora") is one in every 100 students. Using the Hardy-Weinberg equation, the proportion of students estimated to be heterozygous (carriers) for this dreadful disease is

Hardy-Weinberg AA=p^2 / Aa=2pq / aa=q^2 / p+q=1 q^2= 1/100 = 0.01 q=0.1 p=0.9 Aa=2pq 2 X 0.9 X 0.1 = 0.18

Variability

Individuals vary in their characteristics (VARIABILITY)

Competition

Many more individuals are born than survive because resources are limited (COMPETITION)

Practical applications of phylogenetics

Phylogenetic reconstruction • important applications in public health Where did HIV come from? • phylogenetic analysis of HIV reverse transcriptase gene indicates that - HIV derived from simian immunodeficiency virus (SIV) - different strains of HIV represent independent transfers from different primate species - 3 independent acquisitions of pandemic HIV-1 from chimps - HIV-2 derived from West African monkeys, primarily sooty mangabey

Which of the following represents an idea that Darwin learned from the writings of Thomas Malthus?

Populations tend to increase at a faster rate than their food supply normally allows.

The evolution of mate choice Manipulation

Sensory exploitation

Natural Selection

Some individuals are more successful in struggle to survive in a given environment than others (NATURAL SELECTION)

Stabilizing selection

Stabilizing selection: The intermediate (average) phenotype is fittest - Stabilizing selection: birth weight • The most common form of selection • Maintains status quo once population adapted to environment • May result from compromise between components of fitness - large babies stronger and healthier - babies too large risk complications of childbirth

Linnaean hierarchy

Systema Naturae (Linnaeus, 1735) - system of taxonomy based on resemblances • Binomial system of nomenclature - two-part name (binomial) for species - genus name plus species name (specific epithet) - both parts together give the species a unique name (e.g., Canis lupus) • Hierarchical classification - similar species grouped into increasingly general categories Do Kings Play Chess On Fiber Glass Stools?

Natural selection

The superior survival and/or reproduction of some phenotypic variants compared to others under the environmental conditions that prevail at the time

Heritability

These survivors pass on their characteristics to next generation (HERITABILITY)

Adaptation

Unequal ability of individuals to survive and reproduce leads to gradual change in population, with favorable characteristics accumulating over generations (ADAPTATION)

Charles Darwin was the first person to propose

a mechanism for evolution that was supported by evidence