Download Mechanisms of Evolution 1 Chapter 22: Descent with Modification

Mechanisms of Evolution
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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
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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
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Adaptations are characteristics that help organisms survive and reproduce in specific
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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
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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
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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
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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 Evolution
Direct Observations of Evolutionary Change
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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
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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
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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
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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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Mechanisms of Evolution
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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 possible
Genetic Variation
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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
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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
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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
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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
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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
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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
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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 mutations
4) 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 population
Natural Selection
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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
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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 populations
2. Causes allele frequencies to change at random
3. Can lead to a loss of genetic variation within populations
4. Can cause harmful alleles to become fixed
Gene Flow
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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 evolution
A Closer Look at Natural Selction
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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
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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 Variation
1. Diploidy: maintains genetic variation in the form of hidden recessive alleles in heterozygotes by
allowing these alleles to persist in the population
2. 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
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Variation in noncoding regions of DNA or alleles that do not affect fitness may change
randomly by genetic drift
Why no “perfect” organisms?
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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 isolation
The Biological Species Concept
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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
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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
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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 isolation
Patterns within Hybrid Zones
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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
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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 Life
Phylogeny is the evolutionary history of a species or group.
Systematics is the discipline focused on classifying organisms and determining evolutionary
relationships.
Phylogenies show evolutionary relationships
Binomial Nomenclature
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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
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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
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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 Homology
Morphological and Molecular Homologies
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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
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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
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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
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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
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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
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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
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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 tree
Divergent evolution/Adaptive radiation: organisms become more different over time
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