Bio 345 Exam 1

Scientists belonging to which of the following religious communities use concepts from evolutionary biology in their research?

All religious communities listed

Directional selection increasing bill size towards a new optimum

Bright coloration on a fish that is indicative of genetic quality

Does genetic drift cause beneficial or deleterious alleles to become fixed?

Either one, beneficial or deleterious alleles, can either become fixed or lost; neither one has more of a chance of being fixed

How is it that organisms in the same environment might have different selection pressures?

Environmental pressures that impose natural selection on a species are greatly influenced by the characteristics of the species itself

What is meant by "the theory of evolution"?

Evolution is well-supported by evidence and has survived repeated testing.

Fisher's runaway selection

Ex. Females with preference for long tails tend to mate with males that have a long tail, and so their offspring tend to have the genes both for a long tail and preference for a long tail

What is a proximate cause?

Eyes process light into neural signals

You estimate the size and migration rate of two populations of scorpions on either side of a river. Through your calculations, you deduce that fewer than 1 migrants reach the other shore per generation. What would you predict the genetic divergence (FST) between populations to be?

FST would be near 1, the allele frequencies on either side would likely be different

A trait that is common is an adaptation

False

Natural selection acts on populations, not on individuals.

False

Natural selection results from organism trying to adapt to their environment

False

The goal of evolution is to progress towards becoming the perfect being or species.

False

True or False: Fixation of a particular allele is common in large populations

False

Because evolution is goal oriented, we would expect chimpanzees to evolve more human-like characteristics in the future.

False, evolution is not goal oriented

How does radiometric dating help scientists date fossils?

Fossils are found in sedimentary rock, dating igneous rock above or below it helps scientists determine the relative age of fossils.

Major outcomes of the evolutionary synthesis?

Microevolution and macroevolution. Argued persuasively that mutation, gene flow or migration, natural selection, and genetic drift are the major causes of evolution within species (which Dobzhansky called microevolution)—and that continued over long periods of time, these same causes account for the origin of new species and for macroevolution: the evolution of the major alterations that distinguish higher taxa (genera, families, orders, and classes).

What mutation types would be most and least likely to affect phenotype?

Most: Missense (depends), Nonsense, Frameshift , Regulatory (?) Least: Silent, Point, Missense (depends)

What mutation types would be most and least likely to become fixed in a population?

Most: Regulatory Least: Silent

To convert percentage to frequency

Move decimal place over to the left by 2 places

HWE Equations

p^2+2pq+q^2=1 p=C q=c

Artificial selection

the selective breeding by humans of plants and animals

Uniformitarianism allows evolutionary biology to be an experimental science. Which of the following is an example of uniformitarianism?

Present observations of erosion on a streambank demonstrate how a canyon was formed.

The presence of water-preserving stems and spine-like leaves in plants that are endemic to the deserts of Africa and North America is

an example of different lineages of plants that independently evolved similar adaptations

Polyadenylation mutations

caused by a base-pair substitution of the 5' AAUAAA 3' polyadenylation signal sequence can block 3' proper processing of mRNA

Frameshift mutation

caused by insertion or deletion of a number of nucleotides that are not a multiple of 3 --> causes shift in reading frame results

fixation

change in a gene pool from a situation where there exists at least two variants of a particular gene (allele) in a given population to a situation where only one of the alleles remains

Adaptation

evolutionary process by which, over the course of generations, organisms are altered to become improved with respect to features that affect survival or reproduction (not goal-driven)

Positive selection

fixation of beneficial mutations

Which of the following is universal among organisms, thus implying that all living things derive from a common ancestor?

All of the above

Individual selection

"entities" that differ in survival and reproduction in most discourse evolution are individual organisms with different phenotypes

Orthogenesis

"straight-line evolution" held that the variation that arises is directed toward fixed goals, so that a species evolves in a predetermined direction by some kind of internal drive without the aid of natural selection

5 Basic Features of Genetic Drift

-Drift is unbiased: an allele frequency is as likely to go up as to go down -Random fluctuations in allele frequency are larger in smaller populations -Drift causes genetic variation to be lost -An allele frequency that fluctuates randomly up and down will eventually reach either p=0 or p=1 -Drift causes populations that are initially identical to become different -An allele can become fixed without the benefit of natural selection

What would happen if life evolved proofreading measures that perfectly prevented mutations?

-Natural selection favors lower mutation rates (at least in organisms with sexual reproduction) because most mutations are deleterious -Natural selection is not efficient enough to drive mutation rates to 0 if that were to happen, life on Earth would be deprived of fuel needed for adaptation, leading to extinction -Beneficial mutations spread by natural selection and allow organism to adapt

How does genetic drift/population size affect the likelihood that a new mutation will become fixed in a population?

-When a beneficial mutation first appears, it is present as only a single copy -A mutation that increases fitness has a greater chance of becoming fixed that does a deleterious mutation -A single copy of a new beneficial mutation is almost certain to be lost by drift even if it has a large positive effect on fitness -Mutation's loss by drift can put an evolutionary speed limit on how fast a species can adapt to changing conditions

How can gene flow undermine selection?

-Without gene flow, selection would cause whatever alleles have highest fitness at any place to become fixed there -Without selection (or genetic drift) gene flow would make allele frequencies equal everywhere

What prevents populations from migrating?

-barriers -populations may simply lack genetic variation in a trait necessary for adapting to new environments -gene swamping caused by migration from other parts of a species' range can prevent local adaptation to the extreme conditions at the range edge and prevent the species from expanding outward -biotic interaction can set range boundaries where a species encounters a new competitor, predator, or pathogen

How does population size/drift affect the likelihood an allele with a strong positive or negative effect on fitness will become fixed in a population?

-the genomes of species with large populations tend to be biased towards the codons that are most efficient -adaptation is less precise in species with smaller population sizes -drift can cause deleterious mutations to spread to fixation

Major transitions during evolutionary history, from replicating RNA to humans

1st transition: Origin of cells --> simple organic molecules, which are the building blocks of complex organic molecules, can be produced by abiotic chemical reactions --> some such simple molecules must have formed polymers that could replicate --> Once replication originated, evolution by natural selection could occur

What are the viewpoints on the relationship between religion and evolution?

1) Special Creationism (more literal)= Young earth creationism, progressive creationism, and humans only created 2)Evolution with God= Theistic evolution and deistic evolution 3)Evolution w/out God (less literal)= Agnostic Evolution and Atheistic Evolution

Biogeographic facts make sense if:

1. A species has a definite site or region of origin 2. A species achieves a broader distribution by dispersal 3. a species becomes modified and gives rise to descendent species in the various regions to which it disperses (main take-away: important for Darwin to show that a species had not been created in different places, but had a single region of origin, and had spread from there)

3 main consequences of genetic drift

1. Allele frequencies fluctuate over time, even in the absence of natural selection 2. some alleles are fixed, others are lost 3. separate populations diverge in their allele frequencies

Fundamental Principles of Biological Evolution

1. An individual's phenotype (its observed traits) is distinct from its genotype (its DNA) 2. Acquired characteristics are not inherited 3. Hereditary variations are based on the genes 4. Genetic variations arises by random mutation. Mutations do not arise in response to need 5. Evolution is a change of population, not of an individual 6. Changes in allele frequencies may be random or nonrandom 7. Natural selection can account for both slight and great differences among species 8. Natural selection can alter populations beyond the original range of variation 9. Populations usually have considerable genetic variation 10. The differences between species evolve by rather small steps 11. Species are groups of interbreeding or potentially interbreeding individuals that do not exchange genes with other such groups 12. Speciation (the origin of 2 species from a single ancestor species) usually occurs by the genetic differentiation of geographically isolated populations 13. Higher taxa arise by the sequential accumulation of small differences 14. All organisms form a great Tree of Life (phylogeny)

5 Distinct Components of Darwin's Theory of Evolution

1. Evolution (characteristics of organisms change over time) 2. Common Descent (Darwin argued that species diverged from common ancestors and could be portrayed as one great family tree representing actual ancestry) 3. Gradualism (Darwin's proposition that differences between even radically different organisms have evolved by small steps through intermediate forms, not by leaps) 4. Populational Change (Darwin's hypothesis that evolution occurs by changes in the proportions/frequencies of different variant kinds of individuals within a population) 5. Natural Selection (Darwin's hypothesis, independently conceived by Wallace, that accounts for adaptations)

What are common misconceptions about the Theory of Evolution?

1. Evolution is a theory about the origin of life 2. Natural selection involves organisms trying to adapt 3. Individual organisms can evolve during their lifetime 4. The goal of evolution is to progress towards becoming the perfect being or species 5. If humans came from chimpanzees, chimps should be extinct.

Evolution by natural selection occurs if:

1. There is a correlation between an individual's phenotype and its fitness 2. Variation in the phenotype is correlated between parents and their offspring

What traits are NOT adaptations?

1. Traits that are simply the consequence of physics or chemistry (i.e. hemoglobin is red) 2. Traits that have evolved by other mechanisms such as random genetic drift rather than by natural selection 3. Traits that may have evolved not because it conferred an adaptive advantage, but because it was correlated with another feature that did 4. A character state may be a consequence of phylogenetic history

What are the key conditions of HWE?

1. infinite population size 2. no natural selection 3. no mutation 4. no movement between populations 5. random mating

What are the two important roles that gene flow plays in evolution?

1. it equalizes allele frequencies and so works to erode genetic differences between populations (natural selection can cause 2 populations to become more or less similar, but gene flow only makes them more similar) 2. It introduces new alleles into a population from other populations where they already exist

A population of birds has two alleles for feather color, B (blue) or b (yellow). Bb individuals are green. The alleles are in HWE. If there are 450 blue birds in a population of 5,000, what is the number of green birds in the population?

2,100 green birds

The snow goose (Chen caerulescens) has both a blue and a white morph. Inheritance is Mendelian: BB and Bb individuals are blue, while bb individuals are white.If 280 geese in a population of 7,000 are white, and 6720 are blue, how many of the blue geese would you expect to be carriers of the b allele (i.e., Bb heterozygotes)? Assume the population is at Hardy-Weinberg equilibrium.

2240

According to modern estimates, life originated about _______, and Homo sapiens originated about _______.

3.8 GYA; 200 KYA

Which of the following boxes contains a monophyletic group?

A and B

Cambrian Explosion

A burst of evolutionary origins when most of the major body plans of animals appeared in a relatively brief time in geologic history; recorded in the fossil record about 545 to 525 million years ago; diversification; most dramatic adaptive radiation in the history of life because it transpired over such a short time

Which of the following mutations will be lost most quickly from a population? (Assume the population does not experience strong effects of genetic drift.)

A mutation that adds a premature stop codon.

Which statement best characterizes the distinction between proximate and ultimate causes?

A plankton uses an enzyme to produce light when disturbed. The light scares predators.

Metapopulation

A set of local populations, among which there may be gene flow and patterns of extinction and recolonization.

Which scenario depicts adaptations incorrectly?

A trait evolves in anticipation of a future environmental change.

Which trait cannot describe an adaptation?

A trait that does not change the probability of survival or reproduction, like the color of cave-dwelling fish

Which statement might explain the evolution of a particular trait? It may have evolved because it was correlated with another trait that conferred an adaptive advantage. All statements listed explain the evolution of a particular trait It may have evolved by genetic drift, rather than by natural selection. It may be a necessary consequence of physics or chemistry. It may be a consequence of phylogenetic history.

All statements listed explain the evolution of a particular trait

Darwin suggested that:

Animals unfit to their environment undergo natural selection

Which of the following boxes contains a monophyletic group?

B & D

Benefits and costs of dispersal?

Benefits: · Allows individuals to find habitat that is better now or that will be in the future; when the environment changes in time and space, natural selection favors dispersal if individuals that move have higher fitness on average than those that do not move · If environmental changes wipe out local populations from time to time, any genotype that does not disperse will leave no progeny · Dispersing individuals experience less competition than their siblings that stay at home; genes for dispersal can therefore benefit from kin selection Costs: · Passive dispersal can land an individual in a hostile habitat where there is little or no chance of survival · Active dispersal is also dangerous when patches of good habitat are separated by regions of bad habitat · Energetic trade-offs can also select against dispersal · Deleterious mutations can become fixed by drift in isolated populations

Which of the following accurately describe an adaptation?

Carnivores have strong jaw muscles that help them bite through flesh.

Which of the following is not one of Darwin's theories?

Change via saltations (extreme, sudden changes in an organism's traits)

Why is polymorphism typically higher in the regions between genes, and within introns than within coding regions?

Coding regions (exons) are less variable, particularly the first and second bases of each codon; much of the polymorphism in DNA within species results from random genetic drift acting on selectively neutral mutations

Which observation about a population would not violate the assumptions of the Hardy-Weinberg principle? (Please read the options carefully.)

Cold tolerance differs by genotype, and the population experiences a frost.(NOT ANSWER) Females prefer to mate with red-colored males. Individuals migrate from nearby populations but die prior to breeding. The population size is smaller than 100 individuals. UV radiation induces new mutations at a high frequency.

How do researchers test whether something is an adaptation or not?

Complexity, Design, Experiments, The Comparative Method

Which of the following was not listed as a common misconception about the Theory of Evolution in Dr. Tucker's lecture video?

Darwin's main contributions were Natural Selection and the Theory of Common Descent

Mating fiddler crabs use several types of sexual selection. Males battle each other for territory using their greatly enlarged claws. The best territories are those in the most physiologically stressful area, and only healthy males can maintain them for long. The males also raise their claws to signal females; those that reach the greatest heights are most noticeable because females are attuned to look upwards for predators. Which model of sexual selection is least likely to impact this mating system?

Direct benefits to the female

Imagine a population of Galápagos finches that vary for bill size. If the population mean is near the optimum size for eating the seeds found on the island, what would we expect to occur if their main seed resource goes extinct, and another plant with much larger seeds replaces it?

Directional selection increasing bill size towards a new optimum

How would genetic drift affect two genetically identical populations if they were split?

Drift causes populations that are initially identical to become different

Humans have 23 chromosome pairs. Other members of the Hominidae, including chimpanzees, gorillas, and orangutans, have 24. What structural mutation could have caused this difference?

Fusion

In which situation will gene swamping prevent local adaptation?

Gene flow is high and the patch favoring the alternative allele is small.

Natural selection and genetic drift are the two most important causes of evolutionary change. How do they differ?

Genetic drift is nonadaptive; it changes allele frequency without regard to fitness.

How does random allele loss through time shape what alleles are present today?

Genetic drift is random so random/different copies of genes will become ancestors of future copies

Consider a genetic locus with several alleles. The population size is small, mutation is absent, and none of the alleles has a selective advantage. Which of the following is likely to occur after a long period of time (many generations)?

Genetic variation will decline as alleles randomly go extinct.

What does it mean for two populations if Fst = 0? If Fst = 1?

If Fst = 0, the two populations are expected to be genetically very similar If Fst = 1, the two populations are expected to have very different allele frequencies

What does natural selection require?

If: -· There is a correlation between a phenotypic trait and the number of offspring that individuals leave to the next generation (Means that selection on the trait is occurring, favoring individuals with more extreme phenotypes than average) -there is a correlation between the phenotype of a trait in parents and in their offspring (means that at least some of the phenotypic variation is inherited, causing the individuals with those more extreme phenotypes to pass on their traits to their offspring) Then: the trait will evolve.

How do mutations in germ cells vs. somatic cells differ in how natural selection acts on them?

In mammals, the rate of mutation per nucleotide per replication is greater in somatic cells than in germ cells.

What were Darwin's major contributions to the theory of evolution?

Introduced concept of natural selection, all living things share a common ancestor

What causes genetic drift?

It results from chance events of survival , reproduction, and inheritance

Difference between Darwin's theory of evolution from Lamarck's

Lamarck's does not include the concept of common ancestry; Darwin's theory --> variational theory of change in which the frequency of a variant form increases within a population from generation to generation; Lamarck's --> individual organisms change

Darwin's theory of descent with modification replaced which of the following explanations for the existence of different species:

Lamarck's theory that all organisms originated from nonliving matter separately through spontaneous generation, and progressed along a path to higher complexity due to the action of a "nervous fluid".

Why are mutation rates important?

Mutation is fundamental to genetics and evolution.

Refer to the graph showing fitness effects of mutations in the yeast, Saccharomyces cerevisiae.

Mutations yielding new stop codons have little effect on fitness.

You are studying the prevalence of tail loss in geckos and preliminary results suggest that this trait is tied to the D allele. In the population you observe the following genotype frequencies: D1D1 = 0.25; D2D2 = 0.45. You wonder if the trait is under natural selection. What would you calculate the expected genotype frequencies in this population to be, if they were in HW equilibrium?

N/A

What theories came after Darwin's?

Neo-Lamarckian, orthogenetic, and mutationist theories. These anti-Darwinian ideas were refuted in the 1930s and 1940s by the geneticists, systematists, and paleontologists who reconciled Darwin's theory with the facts of genetics

Darwin's work eventually lead to which of the following well-regarded theories?

Neutral theory of molecular evolution

Is natural selection the same as evolution?

No, selection happens within a generation and may or may not lead to evolution

Which of the following is an example of the evolution of an adaptation? (Consider only the information given.)

Non-random survival and reproduction favors finches with broader beaks, increasing the bill size in the next generation.

About 200 KYA, which major event occurred?

Origin of Homo sapiens

How does population size affect genetic drift and fixation, and why?

Outcomes become more predictable when averaging over a larger number of random events. This is why random genetic drift is stronger in small populations and weaker in large ones. One of the alleles is then fixed. While the allele that is lost can be reintroduced by mutation, drift by itself causes genetic variation to be lost. The loss is faster in smaller populations because they have larger allele frequency fluctuations. The variation among populations generated by drift grows more slowly in large populations than in small ones.

How is it that mating preference can have pleiotropic effects?

Pleiotropic effects: virtually all genes have these, meaning they affect multiple traits --> Causes of evolution of female preferences for elaborate male displays

How does amount of polymorphism correspond with mutation rate?

Polymorphism increases with the effective population size (N_e) and the neutral mutation rate (µ_n)

mutation rate

Probability that an offspring carries a new mutation; humans have the smallest rate of mutation per nucleotide per replication but also the largest mutation rate per genome per generation

How does polymorphism vary along chromosomes and how does recombination affect polymorphism?

Regions with high recombination rates tend to be more polymorphic

Which pair of sequences represents a synonymous mutation? a. UUU → CUU b. GCU → GCA c. GGA → CGA d. UGA → UGG

b. GCU → GCA

Why does natural selection sometimes get stuck far from the optimal?

Selection can only fix those genetic variants with a higher fitness that other genetic variants in a particular population at a particular time; it cannot fix the best of all conceivable variants if they do not arise, or have not yet arisen, and the best possible variants often fall short of perfection because of various constraints

Which term is defined as any consistent difference in fitness among phenotypically different classes of biological entities as a consequence of competition for mates?

Sexual Selection

Imagine a population of lizards became isolated on separate islands after sea levels rose. What relationship would you expect between lizard allelic diversity and island size?

Smaller islands have less allelic diversity than larger ones

How does population size affect whether the effect of selection or drift will be stronger?

Smaller population --> stronger drift, weaker selection Larger population --> stronger selection, weaker drift

Imagine an island archipelago where all of the islands are founded by individuals heterozygous at a particular locus. If there is no migration or mutation, and the alleles at that locus are neutral, what do you expect the island populations to look like after many generations?

Some island populations will have fixed one allele, and other populations will have fixed the other allele.

Which of the following statements about mutations is true?

Some regions of the genome are more likely to accumulate mutations than others.

habitat fragmentation

Splitting of ecosystems into small fragments

Timing of major events in Earth's history (deep history assignment)

Start of Life: 3.8 GYA Origin of Eukaryotes: 2-3.5 GYA Origin of Multicellularity: about 2 GYA Origin of Homo sapiens: about 200 KYA

Application task: Make sure you can pick out which ideas about Evolution can be attributed to Darwin and which cannot.

The Origin of Species contains two major theories. The first is Darwin's idea of descent with modification. It holds that all species, living and extinct, have descended, without interruption, from one or a few original forms of life. The second theory in The Origin of Species is natural selection, which Darwin proposed is the chief cause of evolutionary change.

You make up an imaginary animal based on no animal alive today (just your amazing creativity). Which of the following constraints on a real animal's adaptations fall under necessary constraints of your imaginary animal:

The adaptations must confer a fitness benefit

Which of the following is not an evolutionary transition in the history of living things?

The ancestor of plants from the symbiosis between eukaryotes and bacteria.(NOT ANSWER) Eukaryotes from a symbiosis between bacteria and archaea. Cells from macromolecules packaged in lipid membranes. RNA-based replication from DNA-based replication Multicellular organisms from communities of unicellular organisms.

Commonalities among all living organisms that support the Theory of Evolution

The genetic code, the machinery of replication and protein synthesis, and basic metabolic reactions are among the other features that are universal among organisms and thus imply that they all stem from the LUCA

In the 1930s and 1940s the modern evolutionary synthesis occurred. Which of these was not a major outcome of the evolutionary synthesis?

The integration of genetics, systematics, and paleontology (connecting microevolution with macroevolution). -NOT ANSWER The development of a mathematical theory of population genetics. Support for mutationist theories that suggested new species originated by changes that reorganized the whole genome. Recognition of natural selection as the primary driver of evolution, along with important roles for genetic drift, gene flow, and sexual selection.

HWE is more a tool than a reality. Why?

The key conditions for the Hardy-Weinberg equilibrium are: An infinite population size, No natural selection, No mutation, No movement between populations, and Random mating. No real population meets all of these conditions. Thus, no real population is expected to be exactly in Hardy-Weinberg equilibrium (although the discrepancy may be very small).

How does migration affect HWE?

The mixing of individuals from populations with different allele frequencies generates a systematic deviation from HWE àresults in an excess of homozygotes and a deficit of heterozygotes

Which of these had the least influence on Darwin's theories?

The observation that more individuals are born than the environment can sustain. Ideas from other naturalists of his time. Darwin's work aboard the H.M.S. Beagle where he observed the large amount of variation within species. An understanding of breeding/artificial selection._(NOT THE ANSWER) Knowledge of inheritance, as discovered by Gregor Mendel.

What is considered an important evolutionary transition in the history of living things?

The origin of cells from macromolecules packaged in lipid membranes

MRCA/ Root of the tree

The original branch

If a population of kangaroos (animals that are endemic to Australia) was discovered living on an island northwest of Wallace's line, which of these would be the most likely explanation?

The population was recently founded by kangaroos that dispersed there from Australia.

How does endemicity apply to the distributions of populations?

The populations are found in one area. Populations of high endemicity where there are geographic barriers and evolved in that area. Can cross to new area but non-native to the new area.

What is the name of the idea proposed by Darwin that all species come from pre-existing species?

Theory of Common Descent

Which observations led to Darwin's theory of natural selection?

There is a lot of variation among organisms, and more individuals are born than an environment can sustain

True or False: Large fluctuations in allele frequencies are more common in small populations

True

Where did Darwin think hereditary variation came from?

This was the great gap in Darwin's theory, and he never filled it. The problem was serious because, according to the prevailing belief in blending inheritance, variation should decrease, not increase.

Evolution by natural selection can occur without a new mutation arising in a population.

True

Most systematists today hold the opinion that classifications should consist of monophyletic taxa only.

True

AN adaptation

a characteristic of an organism that evolved by natural selection

cladogenesis

branching of a lineage into 2 or more descendent lineages

How does sexual selection affect fitness (survival and reproduction)?

a male that prevents other males from mating will leave more copies of his genes to the next generation than they will; a trait can evolve by sexual selection IF it increases a male's overall fitness, even if it decreases survival

Taxon/higher taxon

a particular group of organisms assigned to any of these levels (i.e., kingdom, phylum, class, order, family, genus, and species)

Sickle cell disease results from a nonsynonymous point mutation of the HBB gene, producing an altered beta chain of hemoglobin. Beta thalassemia is caused by a mutation to the same gene, but instead of an altered beta chain, the final protein is absent or incomplete. Which of these mutations is the most probable cause of beta thalassemia in a patient without a family history of the disease? a. A nonsynonymous point mutation resulting in a premature stop codon b. A synonymous mutation in an exon c. An inversion in which several codons have their sequence reversed d. A duplication of the HBB gene, creating too much protein product

a. A nonsynonymous point mutation resulting in a premature stop codon

Mutationist Theories

advanced by some geneticists who observed that discretely different new phenotypes can arise by a process of mutation; supposed that such mutant forms constituted new species and thus believed that natural selection was not necessary to account for the origin of species

Structural mutations

affect more than 1 DNA base (insertions, deletions, duplication, inversion, reciprocal translocation, fusion, fission, whole genome duplication)

Regulatory mutations

affect regions such as promoters, introns, and the regions coding for 5'-UTR and 3'-UTR segments of mRNA; 3 types are recognized: promoter mutations, splicing mutations, and cryptic splice sites

Although living or semi-living things might have originated more than once, we can be quite sure that all organisms we know of stem from a single common ancestor because

all share arbitrary features

Linkage disequilibrium

another source of genetic correlation; the nonrandom association between alleles at different loci

Good genes mechanism

another way that female mating preferences evolve; some male displays are correlated with traits that increase fitness --> indicator traits that indicate to females a male's genetic quality

Lineage

any branch on the tree

Node

any branch point on the tree

natural selection

any consistent difference in fitness among different classes of biological entities; may act in conjunction with genetic drift, and it can select for a number of different outcomes in a population

Clade (monophyletic group)

any group that contains an ancestor and all of its descendants

Sister groups

any group that encompasses individuals from 2 different common ancestors

polyphyletic group

any group that encompasses individuals from two different common ancestors

Higher taxon

anything above the species level

In correlated selection, selection favors some combination of character states over others, usually because the characters

are functionally related.

Leks

arenas in which males do nothing but make sexual displays (females visit the lek, mate with the male of their choice, and then leave to rear the offspring with no help from their mate; females receive NO direct benefits from the males here)

Neutral theory of molecular evolution

argues that most of the evolution of DNA sequences occurs by chance rather than by natural selection

Gene flow between populations due to migration causes the populations to

become more similar.

In the late eighteenth century, a typhoon swept through the Pacific atoll of Pingelap, leaving approximately 20 survivors. A large percentage of the present-day inhabitants of Pingelap are color blind. One can conclude, therefore, that the population experienced a

bottleneck

Refer to the graph showing fitness effects of mutations in the yeast, Saccharomyces cerevisiae. Which inference is not supported by the data shown in the graph? a. Most mutations have a relatively small effect on fitness. b. Most mutations are nonsynonymous. c. Mutations yielding new stop codons have little effect on fitness. d. Mutations that improve fitness are relatively rare.

c. Mutations yielding new stop codons have little effect on fitness.

Cline

can develop when the transition between two types of habitats is gradual

Nonsense mutation

codes for premature stop codon; converts a codon encoding an amino acid into a stop codon

sperm competition

common tactic used by males to interfere with each other's reproduction (ex. Penis of Calopteryxhas a structure that basically scoops out the sperm of any males that mated previously with the female --> increases the # of eggs that he will fertilize and decreases the fitness of the other males

Insertions

common; occurs when a segment of a chromosome is left out during replication

Evolutionary Synthesis/modern synthesis/neo-Darwinism

consensus forged by geneticists, systematists, and paleontologists who reconciled Darwin's theory with the facts of genetics; chief principle: adaptive evolution is caused by natural selection acting on particulate (Mendelian) genetic variation; theory developed that showed that mutation and natural selection together cause adaptive evolution

Comparative Method

consists of comparing sets of species to pose or test hypothesis on adaptation and other evolutionary phenomena

Trade-offs

constraint that occurs when increasing fitness in one way decreasing it in another (Ex. With a fixed amount of available energy or nutrients, a plant species might evolve higher seed numbers, but only by reducing the size of its seeds or some other part of its structure)

phenotype screening

count number of new mutations found by the total number of individuals being screened

Are deleterious (harmful to survival or reproduction) or beneficial (increase fitness) mutations more common?

deleterious

A new mutation arises in a population. It is most likely to become fixed in the population at some point in time if it's a:

deleterious (confers lower fitness) mutation present in a large population. neutral mutation present in a small population. neutral mutation present in a large population. highly beneficial (confers higher fitness) mutation present in a small population. (NOT ANSWER) highly beneficial (confers higher fitness) mutation present in a large population. deleterious (confers lower fitness) mutation present in a small population.

Silent mutation

different/wrong base but codes for same amino acid, no effect on protein's structure

direct selection

direct benefits and pleiotropic effects; alleles that affect female mating preferences also influence survival and reproduction, so they themselves are targets of natural selection

Disjunct distributions

distribution gaps in distributions of taxa (distinctly distributed higher taxa typically have different representatives in each area they occupy)

Alternative mating strategies

divergent ways that males of the same species use to acquire matings

Wallace's line is a deep-water boundary that separates islands that differ greatly in their fauna, despite their close proximity and similar climate. Accordingly, these islands are assigned to two different biogeographic realms, each of which has a large number of species that are restricted to that location and found nowhere else in the world. These species are considered ____________.

endemic

What did Carolus Linnaeus do/contribute?

established framework of modern taxonomy; classified "related" species into genera, "related" genera in orders, and so on

Macroevolution

evolution of the major alterations that distinguish higher taxa (genera, families, orders, and classes)

anagenesis

evolutionary change of features within a single lineage (species)

How does female phenotype influence which mate she chooses?

ex. can be influenced by which color her eye is most sensitive to

Reciprocal translocation

exchange of chromosome segments between two non homologous chromosomes

Evolutionary change occurs at the level of the individual.

false

To be a learner and researcher of evolutionary biology, you must dismiss all religious affiliations and beliefs.

false

Wallace's Line

faunal break; sharp break discovered by Wallace in the taxonomic composition of animal species among the islands that lie between southeastern Asia and Australia

Directional selection

favors either an increase or decrease in a trait's mean; reduces phenotypic variance (Ex. Horned lizards: plot of survival against horn lengths shows that lizards with longer horns survive best)

Stabilizing selection

favors individuals whose traits are near the population's mean (ex. baby weights)

Preadaptation

feature that fortuitously serves a new function (Ex. Parrots have strong, sharp beaks used for feeding on fruits and seeds. When domesticated sheep were introduced into New Zealand, some were attacked by an indigenous parrot which pierced the sheep's' skin and fed on their fat)

How does Fisher's runaway selection depend both on male and female phenotypes?

female phenotype expresses preference for trait such as longer tails and the phenotype of the male that the female mates with expresses longer tail

divergence

following cladogenesis, anagenesis, in each of the descendent lineages results in their becoming more different from each other

What happens if s << m?

frequency of the locally adapted allele evolves to 0 and the allele is lost entirely (erosion of adaptation)

What happens if m << s?

gene flow will be largely overwhelmed

How does genetic drift contribute to evolution?

genetic chance between generations --> evolution genetic drift happens even when selection is not at work

infanticide

gruesome kind of male-male competition (ex. Occasionally, dominant male lion in a group will be ousted by one or more rivals; the new males often kill all the young in the group --> decreases number of offspring left to the next generation by previous males, which increases the relative fitness of new males

What ideas did Aristotle develop?

he assigned all creatures a place in his "scala naturae" or "Great Chain of Being", placing plants at the bottom and systematically moving up through more and more 'complex' organisms with humans at the top; implied that each life-form progressively became more and more perfect as they moved to the top

What did Empedocles theorize? (in terms of evolution theories)

he theorized that animal parts arose independently, and then wandered around until they met their respective parts; helped to explain how organisms could be suited to their own unique environment, but did not take into account that the characteristics of organisms change over time

ultimate causes

historical causes, especially the action of natural selection; analysis of this is used for proximate causes (ex. what causes a male bird to sing? --> causes lie in history of events that led to the evolution of singing in the bird's remote ancestors)

phylogeny

history of the events by which species or other taxa have successively arisen from common ancestors

Descent with modification

holds that all species, living and extinct, have descended, without interruption, from one of a few original forms of life

Indirect selection

how preferences evolve with the good genes and Fisher's runaway mechanisms; here, preferred alleles evolve because they are correlated with (in linkage disequilibrium with) alleles at other loci that are not targets of selection

What idea(s) did Chevalier de Lamarck contribute?

hypothesized that different organisms originated separately by spontaneous generation from nonliving matter, starting at the bottom chain of being; a "nervous fluid" acts within each species, causing it to progress up the chain; species originated at different times so we now see a hierarchy of species because they differ in age; argued that species differ from one another because they have different needs, and so use certain of their organs and appendages more than others

"special creation"

idea that each species had been created individually by God in the same form it has today

proximate causes

immediate, mechanical causes of biological phenomena (ex. what causes a male bird to sing? --> action of testosterone or other hormones, the structure and action of the singing apparatus, and the operation of certain centers in the brain)

The wings of auks (alcidae), used for swimming, are called an exaptation because

in the ancestor, wings were used for flight, but they also function well in water.

Neo-Lamarckism

includes several theories based on the old idea of inheritance by modifications acquired during an organism's lifetime (no evidence)

Why is UV light dangerous?

it does not initiate chemical changes but it can cause formation of photoproducts which are abnormal structures with additional bonds involving nucleotides (i.e. thymine dimers and 6-4 photoproduct). Photoproducts that are not repaired cause disruption of replication.

What does LUCA stand for?

last universal common ancestor

Strata

layer of sediments deposited at different times; apply principle that younger sediments are deposited on top of older ones

Selective constraint

loci that experience purifying selection are said to be under this

Biogeographical realms

major regions that have characteristic animal and plant taxa; designated by Wallace based on his Wallace Line observations (realms such as North America, Eurasia and Northern Africa, Central and South America, etc.)

Which model of sexual selection describes males gaining a fitness advantage by preventing other males from mating with the best females?

male-male combat

How is it that female preferences can be a side effect?

mating preferences can arise as side effects of how the courtship signals interact with the environment (as signals propagate, they are filtered by the environment they pass through); different mating displays can be favored by sexual selection depending on the habitat where they are performed

Perceptual bias

mating preferences that evolved by natural selection on pleiotropic effects (In some cases, it appears that the female mating preferences are side effects of features of the sensory system that evolved for reasons unrelated to mating, before the male signals were even present

Exaptation

may be further modified by selection so that the modifications are adaptations for the features new function; very common early stage in the evolution of new adaptations (Ex. The wings of penguins have been modified into flippers that enhance swimming but cannot support flight in air)

Indirect response to selection

means that the trait is evolving because of selection on another trait with which it is correlated

Direct response to selection

means that trait is evolving as the result of selection acting on it

Radiometric Dating

measures the decay of certain radioactive elements in minerals that form igneous rock; can often determine absolute ages of geological events -Ratio of parent to daughter atoms in a rock sample thus provides an estimate of the rock's age (using half-lives) -Only igneous rocks can be dated radiometrically, so the age of a fossil-bearing sedimentary rock must be estimated by dating igneous formations above or below it

Gene flow

mixing of alleles from different populations; results from dispersal

Male-male competition

mode of sexual selection in which males interfere directly with each other

female choice

mode of sexual selection where male's secondary trait's function is to attract females and persuade them to mate ("choice" in this context of sexual selection means any phenotype of the female that biases the type of male she will mate)

whole genome duplication

most extreme type of mutation; occasionally meiosis produces a gamete that carries the entire diploid genome rather than a haploid with just one of each pair of chromosomes, if 2 of these unreduced gametes meet and fertilize each other, an offspring is produced that has 4 copies of each chromosome --> tetraploidy

MRCA

most recent common ancestor

Microevolution

mutation, gene flow or migration, natural selection, and genetic drift are the major causes of evolution within species

Promoter mutations

mutations that alter consensus sequence nucleotides and interfere with efficient transcription initiation

How does genetic drift differ from natural selection?

natural selection can favor one allele over another, but genetic drift does not

founder effect

new population is begun from a small number of individuals; leads to loss of genetic variation

Pigeons are cosmopolitan. That means they are...

not endemic to a specific place

Fitness

number of offspring an individual leaves in the next generation; can be called reproductive success which includes survival because you can't reproduce if you're dead

Inversion

occur when a chromosome breaks in two places and the middle segment is reinserted in the reverse orientation

Pleiotropy

occurs when a single mutation affects multiple traits

Gene swamping

occurs when when gene flow overwhelms adaptation (s << m);

fission

one chromosome breaks into 2

Refer to the graph showing the proportion of warfarin-resistant rats in a population of rats in Wales.

positive selection for warfarin resistance occurred during the warfarin poisoning program, but rats that were not resistant to warfarin increased in frequency after the poisoning program ended.

Hypothetico-deductive method

predictions of what we will find deducted from hypotheses

Uniformitarianism

principle developed by geologists James Hutton and Charles Lyell; holds that the same processes operated in the past as in the present and that the data of geology should therefore be explained by causes we can now observe; adopted by Darwin in his thinking about evolution

Lamarckism/inheritance of acquired characteristics

principle that proposes that just as muscles become strengthened by work, more strongly exercised organs attract and become enlarged by the "nervous fluid" --> believed that such alterations, acquired during an individual's lifetime, are inherited

Purifying selection

process that weeds out non synonymous mutations (which are most likely deleterious) that occur in coding regions of the genome from the population, so they do not contribute to the heterozygosity we observe

Cryptic splice sites

produced by certain base-pair substitution mutations that replace or compete with the original splice sites during pre-mRNA processing

Frequency

proportion of genotype or phenotype

What did Alfred Russell Wallace propose?

proposed (in addition to Darwin) that fitter individuals differ only slightly from the norm of the population, but that a feature such as body size gradually evolves to become more and more different because new, slightly more extreme, advantageous variants continue to arise

genetic drift

random fluctuation in allele frequencies due to sampling effects in finite populations

Splicing mutations

reduce or eliminate normal pre-mRNA splices

Direct benefits

resources that increase the female's survival and reproductive success such as food or care for the offspring; whenever males provide their mates with direct benefits, natural selection favors female preferences for male traits that increase female's fitness

Missense mutation

results in a different amino acid being incorporated into the resulting protein; effect depends on how chemically different the new amino acid is from the wild-type amino acid

Duplication

second copy of a gene is inserted into the genome

Deletions

segment of DNA is added to a chromosome

Sexual selection

selection caused by competition for mates among individuals of the same sex

Point mutation

substitution of a single base

Correlated selection

selection that favors particular combinations of traits (ex. Northwestern garter snake; snakes that are both striped and that escape in a straight line have a higher survival; unstriped snakes who reverse course also have higher survival; other combinations have lower fitness)

phylogenetic method

sequence neutrally evolving piece of chromosome in two species and count number of mutations by which they differ

direct method

sequence the DNA of parents and offspring and look for differences caused by mutation

mutation accumulation

several laboratory populations are established from a single founding population --> each population is maintained under conditions that largely eliminate natural selection so mutation is the only evolutionary process at work --> individuals are sequenced after many generations

Experiments show what? (in terms of whether or not something is an adaptation)

show that a feature enhances survival or reproduction, or enhances performance in a way that is likely to increase fitness, relative to individuals with other features

Population bottleneck

situation in which a large population is reduced to a small size for a small number of generations

Disruptive selection

smallest and largest (more extreme) individuals have higher fitness than individuals near the mean; increases phenotypic variance; makes intermediate individuals less common

Pleiotropy

source of genetic correlation; situation in which a single locus affects more than one trait

Components of fitness

survival and reproduction

Monophyletic

taxon that includes all the named descendants of a particular common ancestor (ex. Class of Aves includes all birds)

Paraphyletic

taxon that includes species that do not exclusively share a common ancestor. A group where there is a missing common ancestor (example when birds and reptiles are separated)

Hardy-Weinberg Equilibrium (HWE)

tells us the relative proportions of genotypes in a population when segregation is the only factor that changes genotype frequencies (p + q = 1 and p^2 + 2pq + q^2 =1)

Endemic

the geographic distribution of almost every species is limited to some extent, and many higher taxa are likewise restricted to a particular geographic region (ex. · Ex. The salamander genus Plethodonis limited to North America and Plethodon caddoensisoccupies only the Caddo Mountains of Western Arkansas)

Male birds with more complicated songs tend to have better developed brains, due to low parasite load and a knack for finding good food. Female birds prefer males with complicated songs. The females choose based on their perception of

the male's song.

Dispersal

the movement of individuals and gametes

The fitness of a biological entity is

the number of offspring it leaves in the next generation.

Fitness

the number of offspring it leaves to the next generation

How does genetic drift affect variation?

there will be fewer heterozygotes than predicted by the Hardy-Weinberg ratios

If you are working in a lab, why must you be very careful around ethidium bromide and acridine orange?

they are potential mutagens (can interact directly with DNA, induce mutations because they often have different base-pairing rules than what they replace, or they slide between the stacked nitrogenous bases of the DNA double helix)

Genetic Correlations

traits are correlated; i.e. if you have long arms, you probably also have long legs; part heritable and genetic; can evolve as gene frequencies change; can cause evolutionary side effects (when selection acts to increase a trait, it will not only cause the mean of the trait to increase, it will also change the means of other traits that are genetically correlated with it)

Evolutionary constraint

traits that lack variation cannot respond to directional selection, so they have an evolutionary constraint that can prevent them from adapting

fusion

two non homologous chromosomes are joined

Sexual selection

variation in mating success causes varying survival and reproduction for males (and females depending on species)

Natural selection

variational theory of change in which the frequency of a variant increases within a population from generation to generation; chief cause of evolutionary change; survival of the fittest

Migration (in context of evolutionary biology, not behavioral biology)

very little migration in the example of salmon born in streams who swim to the ocean, then back to their original stream àalmost all salmon return to breed in the very population where they were born, and there is hardly any mixing of genes between populations in different streams

A population has white and brown mice. The white allele is recessive. If the frequency of brown mice that are homozygous for the brown allele is 0.24, and the frequency white mice is 0.3. What are the expected frequencies of heterozygotes if the population is under HWE?

~0.5

In a population of Galapagos lava lizards, we measure that 1 out of 4,000 lizards (0.025% or 0.00025 of the population) is born with only 4 toes on the front limbs (tt). Assume the population is at Hardy-Weinberg equilibrium. Approximately what percentage of the population will be carriers (Tt) of the trait?

≈ 3%