Chapters 22-25 (Evolution) (1)

Mechanisms of Evolution 1

Chapter 22: Descent with Modification“Evolution” = change over time

= descent with modification (=Darwin’s definition)= the changes in a population’s genetic composition over time

Important People to Know: Aristotle : proposed that all living things could be arranged in a system of plants (herbs, tree,

shrub) and animals (water, land, air)and each group of organisms was permanent and perfect Carolus Linnaeus : father of taxonomy (=the science of classification) who developed a

binomial system for naming organisms according to their genus and species James Hutton : father of modern geology who proposed that immense changes in Earth’s

geology are the cumulative result of slow but continuous processes Georges Curier : developed paleontology, the study of fossils. Fossils are remnants or traces of

past organisms, usually found in sedimentary rocks formed through the compression of layers of sand and mud into superimposed layers called strata. He advocated catastrophism, the idea that the extinctions and differences in the fossils found in different strata are the result of local sudden catastrophic events and not indicative of evolution.

Charles Lyell : developed a theory of uniformitarianism, stating that the rates of geological processes have remained the same through Earth’s history and continue in the present

Jean Baptist Lamarck : Lamarck’s hypothesis explained the mechanism of evolution with 2 principles: the use and disuse of body parts leading to their development or deterioration, and the inheritance of acquired characteristics. - Although present genetic knowledge rejects his mechanism, Lamarck proposed several key

evolutionary ideas: that evolution is the best explanation for the fossil record and that adaptation to the environment is the main result of evolution.

Thomas Malthus : organisms can overproduce and outgrow the food supply

Alfred Russel Wallace

Darwin took 2 ideas from the observations of Hutton and Lyell: Earth must be very old, and very slow processes can produce substantial change, perhaps even in living species

Darwin’s Research Darwin sailed on the HMS Beagle and went on a voyage collecting thousands of specimens of

South America, observing the various adaptations of organisms living in very diverse habitats, and making special note of the geographic distribution of the distinctly South American species

Adaptations are characteristics that help organisms survive and reproduce in specific environments

Darwin proposed that adaptations arise through natural selection, a process in which individuals with beneficial inherited traits produce more than offspring without those traits.

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The Origin of Species Darwin published his book On the Origin of Species by Means of Natural Selection His book developed 2 main points:

1) Descent with modification as the basis of life’s unity and diversity- All organisms are related through descent from some unknown ancestor and develop

increasing modifications as they adapt to various habitats- The history of life is like a tree, with a common ancestor at the fork of each new branch,

and present day species at the tips of the latest branches -Darwin figured out the idea of this branching idea of life from looking at the taxonomy developed by Linnaeus provided a hierarchical organization

2) Natural selection as the mechanism that matches organisms with their environment- Using the example of artificial selection in the breeding of domesticated plants and

animals, Darwin found evidence that selection in a population can lead to substantial evolutionary change

- Darwin studied Malthus and found support for the capacity of organisms to overproduce

- Natural selection results in the evolution of populations, not individuals.- Natural selection affects only those traits that are heritable – acquired traits cannot

evolve.- Natural selection depends on the specific environment factors present in a region at a

given time. If the environment changes, different adaptations will be favored.

Scientific Support for EvolutionDirect Observations of Evolutionary Change

J. Endler observed variations in the color patterns of male guppies that correlate with the intensity of predation- the more predators, the less brightly colored fish.- He transported guppies from pools with active predators to pools with less active predators

and observed an increase in the number of size and colored spots (in 15 generations) This is an example of evolution in a natural setting over a relatively short period of time

The evolution of drug resistance in HIV demonstrates 2 facets of natural selection: 1. It is an editing, not a creative, mechanism that selects for variations already present in a

population. 2. It is regional and temporal, selecting for traits that are beneficial in the local environment at

that current time.

The Fossil Record The fossil record documents that present and past organisms differ, and that many species have

become extinct. Fossils also trace the evolution of new groups, as in the origin of whales from land mammals.

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The major branches of evolutionary descent established with evidence from anatomy and molecular data have been tested and supported by the sequence of fossil forms found in the fossil record.

Homology Homology is similarity resulting from common ancestry.

- The forelimbs of all mammals are homologous structures, containing the same skeletal elements regardless of function or eternal shape.

Comparative anatomy and embryology illustrate that evolution is a remodeling process in which ancestral structures become modified for new functions- Vestigial organs are rudimentary structures, of little or no value to the organism, that are

historical remnants of ancestral structures. Homologies can be seen on a molecular level.

- DNA, RNA, and an essentially universal genetic code, which have been passed along through all branches of evolution, are important evidence that all forms of life descended from the earliest organisms and are thus related

Homology is evident on different hierarchical levels, reflecting evolutionary history in a nested pattern of descent.- An evolutionary tree diagrams ancestral relationships. - Each branch point represents the common ancestor of all the species beyond that point. - Evolutionary trees are hypotheses based on available data that represent patterns of

evolutionary descent. Distantly related organisms may appear similar as a result of convergent evolution, the

independent evolution of similar characteristics.- These analogous structures arise as a result of evolutionary adaption to similar

environments.

Biogeography The geographic distribution of species, or biogeography, has been influenced by continental

drift, the slow movements of Earth’s continents. The single land mass called Pangaea formed 250 million years ago and began to break apart 200

million years ago. - The gradual separation of continents helps to explain and predict where fossils of different

groups and their descendants are found Islands often have endemic species, found nowhere else and usually closely related to species

on the nearest island or mainland. Widely separated areas having similar environments are not likely to be populated by closely

related species. - Rather, each area is more likely to have species that are taxonomically related to those of

their region, regardless of environment.

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Chapter 23: Evolution of Populations Individuals are selected for or against by natural selection, but populations actually evolve. Microevolution is changes in allele frequencies of a population over generations

Mutation and sexual reproduction produce the genetic variation making evolution possibleGenetic Variation

Variation in an individual genotype leads to variation in an individual phenotype Not all phenotypic variation is heritable. Environment can affect phenotype. For example, you

can dye your hair or build muscles. Natural selection can only act on variation with a genetic component Discreet characteristics can be classified on an either-or basis and are very distinct phenotypes.

They are usually determined by a single gene locus. Quantitative characteristics vary along a continuum within a population. They are usually

affected by 2 or more gene loci.- These characteristics represent most of the heritable variation within a population

Measures of genetic variation look at both gene variability and nucleotide variety. - The average heterozygosity of a population is the average percent of loci that are

heterozygous. - Nucleotide variability measures the average percent of differences in nucleotide sites

between individuals of a population.

Geographical Variation Most species exhibit geographic variation: regional genetic differences between populations A cline is a graded change or variation in a character along a geographic area.

- Clines may parallel an environment gradient. - For example: the number of plants changes as you go up a mountain

Mutation Mutations are any change in the DNA sequence. Only mutations in gametes are passed on to offspring

- Most mutations occur in somatic cells and cannot be passed on to the next generation. Point mutations that occur in noncoding DNA or do not change the amino acid sequence of a

protein are often harmless. - Mutations that do alter the phenotype are usually harmful. - Rarely, however, a mutant allele may enhance an individual’s reproductive success.

Chromosomal mutations are more often deleterious.- Duplication of small DNA segments, introduced by transposons or errors in cell division,

may provide an expanded genome with extra loci that could eventually take on new functions by mutation.

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Mutation rates are low in animals and plants and on average occur in 1 in 100,000 genes per generation.

Mutation rates are higher in viruses and prokaryotes due to their short generation spans.

Sexual Reproduction Sexual reproduction can shuffle existing alleles into new combinations in each individual. This allows organisms to survive in a changing environment In sexual reproduction, the 3 processes of crossing over, independent assortment, and random

fertilization all create unique genetic combinations in offspring and increase variation.

The Hardy Weinberg equation can be used to test whether a population is evolving Populations and Gene Pools

A population is a localized group of individuals capable of interbreeding and producing fertile offspring.

The gene pool is the term for all the alleles at all the loci present in a population. A locus is fixed if all individuals in a population are homozygous for the same allele More often, 2 or more alleles are present in the gene pool in some relative frequency.

- In a case with 2 alleles at a particular gene locus, the letters p and q represent the frequencies of the 2 alleles within a population, and p + q = 1

The Hardy-Weinberg Equation The Hardy-Weinberg equation predicts allele frequencies in an unchanging environment Hardy-Weinberg equilibrium is a non-evolving gene pool there are no population changes Allele frequency determines the proportion of gametes that will contain that allele

H-W equation: p2 + 2pq + q2 = 1 Allele frequencies:

- p is the frequency of the dominant allele- q is the frequency of the recessive allele

Genotype frequencies: - p2 = homozygous dominant frequency- 2pq = heterozygous dominant frequency- q2 = homozygous recessive frequency

Phenotype frequencies: - p2 + 2pq = dominant phenotype frequency- q2 = recessive phenotype frequency

Number of individuals:- Multiply the frequency by the total population

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Maintaining the Hardy-Weinberg Equation Hardy-Weinberg equilibrium is maintained only if all of the following 5 conditions are met:

1) No natural selection (no differential survival and reproductive success) 2) No gene flow (no movement of alleles into or out of populations)3) No mutations4) Random mating (nonrandom mating changes genotype frequencies)5) An extremely large population to offset “chance fluctuations” (no genetic drift)

- Genetic drift is any “chance fluctuations” (=any changes that result from random chance)

Natural selection, genetic drift, and gene flow can alter allele frequencies in a populationNatural Selection

Individuals that have traits that are better suited to their environment tend to be more successful in producing viable, fertile offspring and pass their alleles to the next generation in disproportionate numbers, resulting in adaptive evolution

Genetic Drift Genetic drift describes how allele frequencies fluctuate unpredictably from one generation to

the next- Tends to reduce genetic variation through losses of alleles - These changes are often due to some random factor loss of alleles is not due to selection

Founder effect occurs when a few individuals become isolated from a larger population- Allele frequencies in the small founder population can be different from those in the larger

parent population Bottleneck effect occurs when some disaster or other factor leads to a sudden reduction in

population size - The resulting gene pool is unlikely to represent the genetic makeup of the original

population - Genetic drift will remain a factor until the population grows large enough for chance events

to be less significant Genetic drift:

1. Is significant in small populations2. Causes allele frequencies to change at random3. Can lead to a loss of genetic variation within populations4. Can cause harmful alleles to become fixed

Gene Flow Gene flow is the migration of individuals and movement of alleles among populations

- Alleles can be transferred through the movement of fertile individuals or gametes - Gene flow tends to reduce differences between populations over time

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Natural selection is the only mechanism that consistently causes adaptive evolutionA Closer Look at Natural Selction

Natural selection results in adaptive evolution by acting on an organism’s phenotype Relative fitness is measured by who is most likely to leave most offspring

- It is measured by the contribution an individual makes to the gene pool of the next generation relative to the contributions of other individuals

- It depends on the entire genetic and environment context in which it is expressed Types of Selection

1. Directional selection – occurs when one extreme is selected against and the other extreme survives - Most likely to occur during periods of environmental change

2. Disruptive selection – occurs when the environment favors individuals on both extremes of a phenotypic range

3. Stabilizing selection – acts against extreme phenotypes and favors the more intermediate forms, tending to reduce phenotypic variation

As natural selection increases the frequencies of alleles that enhance survival and reproduction, the match between organisms and their environment increases.

Sexual Selection Sexual selection is the selection for traits that enhance an individual’s chances of obtaining

mates Dimorphism is when the male looks different than the female Intrasexual selection is when individuals of one sex (usually males) compete for mates of the

opposite sex Intersexual selection is when individuals of one sex (usually females) are choosy in selecting

their mate- Is also called mate choice

Male showiness due to mate choice can increase a male’s chances of attracting a female, while decreasing his chances of survival (example: peacocks)

Maintaining Genetic Variation1. Diploidy: maintains genetic variation in the form of hidden recessive alleles in heterozygotes by

allowing these alleles to persist in the population2. Balancing selection: occurs when natural selection maintains stable frequencies of 2 or more

phenotypic forms in a population 3. Heterozygous advantage: heterozygotes have a higher fitness than both homozygotes, and

have survival and reproductive advantages - Example: sickle cell anemia – carriers are malaria resistant

4. Frequency dependent selection: when the fitness of a phenotype declines if it becomes too common in the population

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5. Neutral variation: appears to confer no selective advantage or disadvantage - Variation in noncoding regions of DNA or alleles that do not affect fitness may change

randomly by genetic drift

Why no “perfect” organisms? Natural selection can only act on variations that are available: new alleles don’t arise as they’re

needed. Each species has evolved from a long line of ancestral forms, many of whose structures have

been co-opted for new situations. Adaptations are often compromises between the need to do several different things, such as

swim and walk. And finally, chance events affect a population’s evolutionary history.

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Chapter 24: The Origin of Species Speciation, the origin of new species, is at the focal point of evolutionary theory. Microevolution explains evolutionary changes and adaptations that evolve within a population,

confined to one gene pool. Macroevolution involves evolutionary change above the species level and considers broader

changes

The biological species concept emphasizes reproductive isolationThe Biological Species Concept

A species is defined as a group of populations whose members have the potential to interbreed in nature and produce viable, fertile offspring, but don’t breed successfully with other populations- Gene flow between populations holds the phenotype of a population together

Reproductive isolation is the existence of biological factors (=barriers) that impede 2 species from producing viable, fertile hybrids.- Hybrids are the offspring of crosses between different species.- Reproductive isolation can be classified by whether it occurs before or after fertilization.

Prezygote barriers block fertilization from occurring by preventing mating between species or preventing successful fertilization if gametes meet.

Postzygote barriers prevent a hybrid zygote from developing into a viable, fertile adult.

The biological species concept doesn’t work for species that are asexual, such as prokaryotes.

Other Definitions of Species Most species have been identified on the basis physical characteristics, an approach called the

morphological species concept. The ecological species concept defines species on the basis of the role they play and resources

they use in the specific environments in which they are found. In the phylogenetic species concept, a species is an evolutionary lineage that represents one

branch on the tree of life and has distinct morphology or molecular sequences.

Speciation can take place with or without geographic separation Allopatric Speciation

Allopatric speciation occurs when geographic isolation interrupts gene flow between 2 subpopulations

Geographic separation alone is not a reproductive barrier in the biological sense. Intrinsic reproductive barriers may arise coincidentally as allopatric populations go down

different evolutionary paths due to mutation, genetic drift, and natural selection

Sympatric Speciation

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In sympatric speciation, the reproductive barriers prevent gene flow between populations that share the same area.

Mistakes during cell division may lead to polyploidy, the presence of extra sets of chromosomes.

An autopolyploid has more than 2 sets of chromosomes that have all come from the same species.- Failures in cell division can produce tetraploids (4n) which can fertilize themselves or other

tetraploids, but can’t reproduce with diploids from the parent population, resulting in reproductive isolation in just one generation.

Polyploidy species may also arise through allopolyploidy. - Interspecific hybrids may propagate asexually, but are usually sterile due to difficulties in the

meiotic production of gametes. - Future mitotic or meiotic mistakes can result in the production of a fertile polyploid.

Polyploid speciation has been frequent and important in plant evolution. Sympatric speciation in animals may involve isolation within the geographic range of the parent

population based on different resource usage. Sexual selection may also lead to sympatric speciation.

Hybrid zones provide opportunities to study factors that cause reproductive isolationPatterns within Hybrid Zones

Hybrid zones are areas where diverging allopatric populations come back into contact and members of the different species interbreed

For example:- In the hybrid zone found between the yellow-bellied toad and the fire-bellied toad, the

frequencies of alleles specific to one species range from 100% near that species edge of the hybrid zone to 0% at the edge near the other species.

- What keeps these hybrids from introducing the alleles of each other’s species into the parent populations?

- Their poor survival and reproduction mean that these hybrids produce few viable offspring if they mate with the parent species.

Hybrid Zones over Time There are 3 possible outcomes for populations in a hybrid zone:

Reinforcement: natural selection may strengthen prezygotic barriers to reproduction when hybrids are less fit (=less viable and reproductive) than individuals of the parent species.

Fusion: weak reproductive barriers may allow sufficient gene flow that barriers break down even more and the two hybridizing species fuse into a single species.

Stability: many hybrid zones appear to be stable, with hybrids continuing to be formed, but with the two parent gene pools remaining separate.

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Time of Evolution 1. Gradualism(Darwinian Evolution) : gradual divergence- organisms change over long periods

of time 2. Punctuated equilibrium : long periods of stasis punctuated by episodes of relatively rapid

speciation and change - In the fossil record, new forms appear rather suddenly, persist unchanged for a long time,

and then disappear.

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Chapter 26: Phylogeny and the Tree of LifePhylogeny is the evolutionary history of a species or group.Systematics is the discipline focused on classifying organisms and determining evolutionary relationships.

Phylogenies show evolutionary relationshipsBinomial Nomenclature

Each species is assigned a 2-part Latinized name – a binomial – consisting of the name of the genus and the specific epithet, designating one species in that genus

Hierarchical Classification Taxonomy is concerned with naming and classifying species. In the Linnaean taxonomic system, genera are grouped into families, which are then grouped

into orders, classes, phyla, kingdoms, and then domains. A taxon is a taxonomic unit at any level.

Linking Classification and Phylogeny A phylogenetic tree represents hypotheses about evolutionary relationships among groups,

with branching patters that may reflect their Linnaean classification. The “phylocode” system of classification is based totally on evolutionary relationships, only

naming groups that include a common ancestor and all descendants. Each dichotomous branch point on a phylogenetic tree represents the divergence of two taxa

from a common ancestry. - Sister taxa share the most recent common ancestor. - Trees are rooted with the oldest branch to the left. - A polytomy is a branch point involving more than 2 descendants, indicating that these

evolutionary relationships are not yet clear. Phylogenetic trees show patterns of descent but do not usually indicate when species evolved or

the amount of genetic change in each lineage. - Also, species next to each other on the tree indicate that they shared a common ancestor,

not that one evolved from the other.

Morphological and Molecular HomologyMorphological and Molecular Homologies

Homologies are similarities due to shared ancestry The more similar morphologies or DNA sequences are, the more likely that organisms are closely

related

Sorting Homology from Analogy Analogy is similarity due to convergent evolution, in which unrelated species develop similar

features because natural selection has led to similar adaptations.

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Homoplasies are analogous structures. In general, when 2 complex structures share many similar features, they more likely were

inherited from a common ancestry In molecular comparisons, the more nucleotide sequences shared between comparable genes,

the more likely the genes are to be homologous.

Evaluating Molecular Homologies Molecular comparisons are complicated by insertion or deletion mutations that change the

lengths of homologous regions of DNA. - Computer programs identify similar sequences and then insert gaps in order to align

homologous DNA segments properly for nucleotide comparisons. - The matching bases between organisms that are not closely related may be molecular

homoplasies. - Mathematical tools have been developed to identify “distant” homologous between

extremely divergent sequences Molecular systematics uses DNA and other molecular comparisons to infer evolutionary

relationships

Phylogenetic trees Cladistics

Classification based on common descent forms the basis of cladistics A clade consists of an ancestral species and its entire descendant species. Such a clade is

monophyletic. A paraphyletic group excludes some species that share a common ancestor with other species in the group, and a polyphyletic group includes several groups with different ancestors.

Shared ancestral characters are found in a particular clade but evolved in an ancestor that is not part of that clade.

Shared derived characters are evolutionary novelties that are unique to a particular clade. To determine the branching sequence of a group of related species, the group is compared to an

outgroup, a species or group of species that diverged before the group being studied (the ingroup)

A comparison of the number of characters in each taxon of the ingroup indicates the sequence in which shared derived characters evolved and determines the branch points used to produce a phylogenetic tree.

Phylogenetic Trees with Proportional Branch Lengths The branching pattern of most phylogenetic trees is relative rather than absolute, indicating only

the order in which members of each clade last shared a common ancestor. The branch length of some trees can be scaled to reflect rates of evolutionary change (for

instance, number of changes in DNA sequence) or time (using the dates of branch points as indicated in the fossil record)

Maximum and Maximum Likelihood

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Systematists use morphological characters or molecular comparisons to choose among many possible phylogenetic trees using the principle of maximum parsimony – the smallest number of evolutionary changes is the simplest explanation and thus the best hypothesis to consider first.

According to the principle of maximum likelihood, a tree can be found that represents the most likely sequence of events, given a certain set of assumptions (such as equal rates of DNA changes).- Computer programs search for the most parsimonious and most likely trees

Phylogenetic Trees as Hypotheses The most parsimonious tree based on the fewest number of evolutionary changes represents

the best hypothesis of the relationship among a set of species. A hypothesis of phylogenetic relationships becomes more reliable with ore data that can be

compared. Phylogenetic hypotheses can be used to make and test predictions. In phylogenetic bracketing, features shared by two closely related organisms are predicted to

be found in their common ancestor and all its descendants. - Fossil discoveries support the prediction that the ancestor of birds and crocodiles, and

therefore also dinosaurs, built nests and brooded their eggs.

From Two Kingdoms to Three Domains Historically, taxonomists divided the diversity of life into two kingdoms- plants and animals In the five-kingdom system, the prokaryotes were set apart from the eukaryotes and placed in

the kingdom Monera The kingdom Protista contained mostly unicellular eukaryotes, while kingdoms Plantae, Fungi,

and Animalia consisted of multicellular eukaryotes The current three-domian system creates a taxon above the kingdom levels The domains Bacteria and archaea, although both consisting of single-celled prokaryotes, differ

in many characteristics The domain Eukarya includes all the eukaryotes: plants, fungi, animals, and many groups of

single-celled organisms.

R strategists: reproduce a lot – large populations (fish, insects, fruit flies)K strategists: don’t reproduce a lot – small populations (cheetahs, humans, birds)

Phylogenic treeDivergent evolution/Adaptive radiation: organisms become more different over time

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Chapters 22-25 (Evolution) (1)

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Transcript of Chapters 22-25 (Evolution) (1)