Evolution

Evolution

descent with modification. Change in allele frequency and the genetic composition of a population over time.

pattern: revealed by data from many scientific disciplines and are facts/observations about the natural world

process: consists of the mechanisms that produce the observed pattern of change. Represents natural causes of the natural phenomena we observe.

Lamarck proposed a mechanism of how life changes over time. He was _________ about the mechanism he came up with.

incorrect

Use and disuse

the idea that parts of the body that are used extensively become larger and stronger, while those that are not used deteriorate

Ex): gallbladders, appendixes

Inheritance of acquired characteristics

stated that an organism could pass these modifications to its offspring
False; acquired traits are not genetic/passed on

Ex): the development of giraffe's long neck over generations as they stretched their neck more and more

Darwin noticed that Galapagos mockingbirds were

similar, but seemed to be different species

Some were unique to individual islands, while others lived on two or more adjacent islands

They also resembled species living on the South American mainland, but weren't known anywhere else in the world.

Adaptation

inherited characteristics of organisms that enhance their survival and reproduction in specific environments

Darwin realized that adaptation to the environment and the origin of new species were closely related processes

Natural selection

a process in which individuals that have certain inherited traits tend to survive and reproduce at higher rates than do other individuals because of those traits. Heritable differences in phenotype which leads to differential reproductive success.

Darwin centered his explanation of how adaptations arise around this

Darwin's three observations about nature

were explained by descent with modification by natural selection

1. The unity of life - organisms share many characteristics.

2. The diversity of life - All organisms descended from an ancestor that lived in the remote past and gradually accumulated adaptations.

3. How organisms are suited for life in their environments - accumulated adaptations allowed organisms to live in specific ways

None of Darwin's observations were based on

genetics, genes, or alleles
They were not discovered yet!!

Darwin's proposal of natural selection

First, discussed familiar examples of selective breeding of domesticated plants and animals

Then, argued a similar process occurs in nature, based on two observations/inferences

Darwin's first observation

Members of a population often vary in their inherited traits

Darwin's second observation

All species can produce more offspring than their environment can support, and many of these offspring fail to survive and reproduce

Darwin's first inference

Individuals whose inherited traits give them a higher probability of surviving and reproducing in a given environment tend to leave more offspring than do other individuals (fitness)

Darwin's second inference

This unequal ability of individuals to survive and reproduce will lead to the accumulation of favorable traits in the population over generations.

Artificial selection

humans have modified other species over many generations by selecting and breeding individuals that possess desired traits

Artificially selected crops, livestock animals, and pets often bear little resemblance to their wild ancestors

Darwin saw a connection between natural selection and the capacity of organisms to

"over-reproduce"

Only a tiny fraction of offspring complete their development and leave offspring of their own. The rest die in some way

Inheritable traits not only influence an individual's performance, but also their offspring's ability to cope with challenges.

Individuals do NOT evolve, it is the

population that evolves over time.

Natural selection can _____________ only those inheritable traits that _____ among the individuals in a population.

amplify or diminish

differ


if all the individuals in a population are genetically identical for that trait, evolution by natural selection cannot occur

Environmental factors vary from place to place and over time, so a trait that is favorable in one place/time

may be useless or even detrimental in others.

Introduced species and other environmental changes can result in

evolution by natural selection of native species

An example of ongoing natural selection is

the evolution of drug-resistant pathogens.

Ex): S. aureus - resistant to penicillin (had penicillinase), then alternative antibiotics, then methicillin

MRSA and other multi-drug-resistant strains became resistant to antibiotics used to treat it, probably because

bacteria can exchange genes with members of their own and other species (conjugation)

MRSA and soapberry bugs highlight two key points about natural selection

1. Natural selection is a process of editing, not a creative mechanism. Ex): Drugs do not create resistant pathogens; resistant individuals that are already present in the population are favored by natural selection

2. Natural selection depends on time and place. It favors those characteristics in a genetically variable population that provide an advantage in the current, local environment.

Homology

similarity among organisms resulting from common ancestry

Ex): the forelimbs of all mammals show the same arrangement of bones form the shoulder to the tips of the digits, even though the appendages have very different functions (lifting, walking, swimming, flying, etc)
Such anatomical resemblances would be highly unlikely if these structures had arisen anew in each species.

Homologous structures

structures in different species that are similar because of common ancestry. Represents variations on a structural theme that was present in their common ancestor. Shares common ancestry, not necessarily similar function

Ex): the underlying skeletons of the arms/forelegs/flippers/wings of different mammals

homologous structures can also be seen at the

molecular level

Ex): all forms of life use the same genetic code. Some very dissimilar organisms have homologous genes that acquired new functions, while other genes conserved their original function.

Vestigial structures

- remnants of features that served a function in the organism's ancestors. "Leftover" structures of marginal, if any importance to the organism.

Ex): skeletons of some snakes retain vestiges of the pelvis and leg bones of walking ancestors

Convergent evolution

the independent evolution of similar features in different lineages due to similar forces acting on distantly related organisms

Ex): sugar gliders (Australian marsupial) and flying squirrels (North American eutherian) - although they evolved independently from different ancestors. These two mammals have adapted to similar environments in similar ways

Analogy

similarity between two species that is due to convergent evolution rather than to descent from a common ancestor with the same trait

Analogous structures

features from convergent evolution that share similar function, but not common ancestry

Fossils are another piece of evidence for evolution because

it documents the pattern of evolution, showing that past organisms differed from present-day organisms and that many have become extinct.

Fossils can also shed light on

the origins of new groups of organisms

Ex): the fossil record of cetaceans (mammalian order, includes whales, dolphins, and porpoises) and DNA sequence data show that they are closely related to even-toed ungulates (deer, pigs, camels, cows, etc)

Biogeography

the scientific study of the geographic distributions of species. Another type of evidence for evolution

Continental drift

the slow movement of Earth's continents over time

A factor that influences the geographic distribution of organisms. Can be used to predict where fossils of different groups of organisms might be found.

Ex): Horse evolutionary trees - data suggests that the genus of present-day horses originated in N. America.
N. and S. America weren't connected yet, so it's predicted that the oldest Equus fossils should be found on the original continent (N. America)

Endemic

found nowhere else in the world

Darwin explained in "The Origin of Species" that most island species are closely related to species from the nearest mainland or neighboring island, suggesting that

the new species came from the original as it adapted to the new island

Phylogeny

the evolutionary history of a species or group of species

Phylogenetic tree

a branching diagram that represents the evolutionary history of a group of organisms

Branch point

a dichotomy, or two-way divergence of two evolutionary lineages from a common ancestor

Sister taxa

groups of organisms that share an immediate common ancestor and hence are each other's closest relatives

Basal taxon

a lineage that diverges from all other lineages early in the history of its group

Polytomy

a branch point from which more than two descendant groups emerge. Signifies that evolutionary relationships among the taxa are not yet clear

If DNA sequences are closely related

the sequences probably differ at only one or a few sites.

If DNA sequences are distantly related

there will be different bases at many sites and may have different lengths

Aligning Segments of DNA

1. Homologous DNA sequences are identical as species begin to diverge from their common ancestor

2. Deletion and insertion mutations shift what had been matching sequences in the two species.

3. The affected regions in one species will no longer align with the other species because of these mutations.

4. The matching regions realign after a computer program adds gaps in one of the sequences.

Molecular homoplasy

organisms that do not appear to be closely related, but may share coincidental matches in bases of their otherwise very different sequences

Statistical tools have been developed to determine whether DNA sequences that share more than 25% of their bases do so because they are homologous.

Cladistics

an approach to systematics in which organisms are placed into groups called clades based primarily on common descent.

Clade

a group of species that includes an ancestral species and all of its descendants
Clades are nested within larger clades (Ex: Felidae, Canidae -> Carnivora)

Taxa are equivalent to clades (legal) ONLY if

it is monophyletic, signifying that it consists of an ancestral species and all of its descendants.

monophyletic

Pertaining to a group of taxa that consists of a common ancestor and all of its descendants. A monophyletic taxon is equivalent to a clade.

paraphyletic

Pertaining to a group of taxa that consists of a common ancestor and some, but not all, of its descendants.

polyphyletic

pertaining to a group of taxa that includes distantly related organisms but does not include their most recent common ancestor

Synapomorphy

shared, derived character, common between an ancestor and its descendants.

Shared ancestral character

a character that originated in an ancestor of the taxon. Unique to particular clades

Ex): backbones for mammals

Shared derived character

an evolutionary novelty unique to a clade, not found in their ancestors

Ex): hair is shared by all mammals but not found in their ancestors

Maximum parsimony (Occam's razor)

a principle that states that when considering multiple explanations for an observation, one should first investigate the simplest explanation that is consistent with the facts

A minimalist problem-solving approach of "shaving away" unnecessary complications

In the case of trees based on morphology, the most parsimonious tree requires the

fewest evolutionary events, as measured by the origin of shared derived morphological characteristics

If based on DNA, the most parsimonious tree requires

the fewest base changes

Molecular clock

an approach for measuring the absolute time of evolutionary change based on the observation that some genes and other regions of genomes appear to evolve at constant rates.

An assumption underlying the molecular clock is that the number of nucleotide substitutions in related genes is proportional to the time that has elapsed since the genes branched from their common ancestor (divergence time)

The molecular clock of a gene that has a reliable average rate of evolution can be calibrated by

graphing the number of genetic differences (nucleotide, codon, amino acid differences, etc) against the dates of evolutionary branch points that are known from the fossil record

The three domains of life

Eukarya, Archaea, Bacteria

All three branches come from the common ancestor of all life

Horizontal gene transfer

a process in which genes are transferred from one genome to another through mechanisms such as exchange of transposable elements and plasmids, viral infection, and perhaps fusion of organisms

the occurrence of such horizontal transfer events helps explain why tree built using different genes can give inconsistent results

Microevolution

evolution on its smallest scale; a change in allele frequencies in a population over generations

3 main mechanisms that can cause allele frequency change:

1. Natural selection

2. Genetic drift (chance events that alter allele frequencies)

3. Gene flow (the transfer of alleles between populations)

Genetic variation

differences among individuals in the composition of their genes or other DNA sequences

Sources of genetic variation

Formation of new alleles (mutations)

Altering gene number or position

Rapid reproduction (more chances for a mutation)

Sexual reproduction (crossing over, independent assortment of chromosomes, fertilization)

Neutral variation

differences in DNA sequence that do not confer a selective advantage or disadvantage.

Usually from point mutations in noncoding regions or due to the redundancy of the genetic code

Population

a group of individuals of the same species that live in the same area and interbreed, producing fertile offspring.

Gene pool

consists of all copies of every type of allele at every locus in all members of the population

Fixed gene

when only one allele exists for a particular locus in a population and all individuals are homozygous for that allele

assessing whether natural selection or other factors are causing evolution at a particular locus

determine what the genetic makeup of a population would be if it were not evolving at that locus and comparing it to what is actually observed in a population

-No differences = population is not evolving (allele and genotype frequencies remain constant from each generation)

-Differences present = the population may be evolving

Hardy-Weinberg equilibrium

the state of a population in which frequencies of alleles and genotypes remain constant from generation to generation, provided that only Mendelian segregation and recombination of alleles are at work

Hardy-Weinberg equation

p² + 2pq + q² = 1
p + q = 1

Variables

p = frequency of dominant allele
q = frequency of recessive allele
p² = frequency of homozygous dominant genotype
2pq = frequency of heterozygous genotype
q² = frequency of homozygous recessive genotype

Conditions for Hardy-Weinberg equilibrium

1. No mutations - The gene pool is modified if mutations alter alleles or if entire genes are deleted or duplicated

2. Random mating - If individuals tend to mate within a subset of the population, such as their near neighbors or close relatives (inbreeding), random mixing of gametes does not occur, and genotype frequencies change.

3. No natural selection - Allele frequencies can change when individuals with different genotypes differ in their survival or reproductive success

4. Extremely large population size - The smaller the population, the more likely it is that allele frequencies will fluctuate by chance from one generation to the next (genetic drift) No gene flow - By moving alleles into or out of populations, gene flow can alter allele frequencies

Departure from these conditions usually results in

evolutionary change.

The equation describes a hypothetical population that is not evolving.

Individuals in a population exhibit variations in their heritable traits, and those with traits that are better suited to their environment tend to

produce more offspring than those with traits that are not well suited

Genetic drift

a process where chance events can cause allele frequencies to fluctuate unpredictably from one generation to the next, especially in small populations

Founder effect

when a few individuals become isolated from a larger population, the smaller group may establish a new population whose gene pool differs from the source population

Ex): A few members of a population are blown by a storm to a new island. Genetic drift can occur in such a case because the storm indiscriminately transports some individuals (and their alleles), but not others from the source

Bottleneck effect

genetic drift that occurs when the size of a population is reduced, as by a natural disaster or human actions.

the surviving population is no longer genetically representative of the original population and certain alleles may be overrepresented, underrepresented, or absent among the survivors

Effects of genetic drift:

1. significant in small populations - Chance events can cause an allele to be disproportionately over/underrepresented in the next gen. Tends to alter allele frequencies substantially only in small populations

2. Genetic drift can cause allele frequencies to change at random - An allele may increase in frequency one year then decrease the next; the change is unpredictable. Thus, unlike natural selection (consistent), genetic drift causes allele frequencies to change at random over time

3. Genetic drift can lead to a loss of genetic variation within populations - By causing random frequency fluctuation, genetic drift can eliminate alleles from a population. Such losses can influence how effectively a population can adapt to a change in the environment

4. Genetic drift can cause harmful alleles to become fixed - Alleles that are neither harmful nor beneficial can be lost or become fixed by chance. In small populations, genetic drift can also cause alleles that are slightly harmful to become fixed, threatening the survival of a population.

Gene flow

the transfer of alleles into or out of a population due to the movement of fertile individuals or their gametes

Tends to reduce the genetic differences between populations. If extensive enough, it can result in two populations combining into a single population with a common gene pool.

Also affects how well populations are adapted to local environment conditions (Ex: Great tit birds - mainland gene flow prevents central pop from adapting fully to its local conditions)

Adaptive evolution

a process in which traits that enhance survival or reproduction tend to increase in frequency in a population over time

The outcome of natural selection is not random because it favors some alleles over others
Selection acts more directly on the phenotype than on the genotype; it acts on the genotype indirectly, via how the genotype affects the phenotype

Relative fitness

the contribution an individual makes to the gene pool of the next generation relative to the contributions of other individuals

3 modes of natural selection

1. Directional selection - sifts the overall makeup of the population by favoring variants that are at one extreme of the distribution Ex): the lightest/darkest fur color in a light/dark environment

2. Disruptive selection - favors variants of both ends of the distributions. Ex): Light and dark fur colors in a mixed/patchy habitat where intermediates are selected against

3. Stabilizing selection - removes extreme variants from the population and preserves intermediate types. Ex): light and dark fur colors are selected against in an environment that is an intermediate color

Balancing selection

natural selection that maintains two or more phenotypic forms in a population

Includes heterozygote advantage and frequency-dependent selection

Heterozygote advantage

individuals who are heterozygous at a particular locus and display greater fitness than do both kinds of homozygotes

Whether heterozygote advantage represents stabilizing or directional selection depends on

the relationship between the genotype and phenotype.

Ex): Heterozygotes for sickle cell - selection favors heterozygotes in regions with malaria over homozygous dominant individuals (vulnerable to malaria) and homozygous recessive individuals (sickle-cell diseased)

Frequency-dependent selection

the fitness of a phenotype depends on how common it is in the population

Ex): Right/left-mouthed scale-eating fish - selection favors whichever mouth phenotype is least common (the minority). the frequency of either fish oscillates, and balancing selection keeps the phenotype frequencies around 50%

Sexual selection

a process in which individuals with certain inherited characteristics are more like than other individuals of the same sex to obtain mates

Intrasexual selection

selection within the same sex; individuals of one sex compete directly for mates of the opposite sex, usually among males

Intersexual selection/mate choice

individuals of one sex (usually females) are choosy in selecting their mates from the other sex. Choice depends on the showiness of the other's appearance/behavior. Looking for enhancing overall reproductive success

"Good genes" hypothesis

females prefer male traits that are correlated with "good genes." If the trait preferred by females is indicative of a male's over genetic quality, both the male trait and female preference for it should increase in frequency.

Sexual dimorphism

a result of sexual selection; a difference in secondary sexual characteristics between males and females of the same species

Why natural selection cannot fashion perfect organisms

1. Selection can act only on existing variations - Natural selection favors only the fittest phenotypes among those currently in the population, which may not be the ideal traits. New advantageous alleles do not arise on demand

2. Evolution is limited by historical constraints - Evolution does not scrap the ancestral anatomy and build each new complex structure from scratch; rather evolution co-opts existing structures and adapts them to new situations

3. Adaptations are often compromises - Each organism must do many different things. Our versatility and athleticism is owed to our hands and flexible limbs, but it makes us prone to sprains, tears, dislocations, etc. (structural reinforcement sacrificed for agility)

4. Chance, natural selection, and the environment interact - Chance events can affect the subsequent evolutionary history of populations. Not all alleles present in a founding population's gene pool are better suited to a new environment than the alleles that are "left behind." Environments can also change unpredictably.

Speciation

the process by which one species splits into two or more species

Macroevolution

the broad pattern of evolution above the species level

Species (biological species concept)

a group of populations whose members have the potential to interbreed in nature and produce viable, fertile offspring - but do not produce viable, fertile offspring with members of other such groups

Reproductive isolation

the existence of biological factors (barriers) that impede members of two species from interbreeding and producing viable, fertile offspring.

The formation of new species hinges on reproductive isolation. These barriers block gene flow between species and limit the formation of hybrids, offspring that result from an interspecific mating

Barriers are classified according to whether they contribute to reproductive isolation before or after fertilization

Prezygotic barriers - blocks fertilization from occurring, acting in one of three ways:

1. Impeding members of different species from attempting to mate

2. Preventing an attempted mating from being completed successfully

3. Hindering fertilization if mating is completed successfully

Postzygotic barriers - contributes to reproductive isolation after the hybrid zygote is formed, in ways like:

1. Developmental errors may reduce survival among hybrid embryos

2. Problems after birth may cause hybrids to be infertile or decrease their chance of surviving long enough to reproduce

Habitat isolation (prezygotic barrier)

Two species that occupy different habitats within the same area may encounter each other rarely, if at all, even though they are not isolated by obvious physical barriers