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We Exam can trace all of life to a single origin. Natural selection provides the primary mechanism for this
phenomenon
Homology: shared similarity due to common descent in some ancestral species with modification
Structural homology: similarity of morphological traits such as same general limb structure in vertebrates.
Product of descent with modification
Developmental homology: similarity in embryo morphology and/or pattern of tissue traits that get modified in
development so that they dont show up later. (Mammalian order of primates, ancestrally they have a tail and
we and apes dont, but our early development does have a tail, it just disappears later on)
Genetic homology: compare proteins and underlying genetic DNA. Similarity in DNA sequences of genes
from different species. Results in developmental homology and structural homology
Evolutionary perspective: one common origin for all of life on the planet. All life uses same codon to specify
for same amino acids, use ribosomes to make proteins
Darwins theory of evolution by natural selection was complemented by Mendels theory of genetics. Modern
evolutionary synthesis: genetic variation (necessary before any selective force can be applied to a population)
arises through random, spontaneous mutation. Sexual production continually provides more and more
combinations of variations. Changes in allelic frequencies between generations results from genetic drift, gene
flow, natural selection. Speciation, start with one species and end up with to two. Populations are
reproductive and physically and sexually isolated
Selection can maintain genetic variation in a population. Heterozygote advantage: heterozygote genotype has
higher fitness than homozygous genotypes (Sickle-Cell anemia)
Balancing Selection: heterozygote with the higher fitness is balanced by lower fitness of both of the
homozygotes
Directional Selection: natural selection increases the frequency of one allele. Reduces population genetic
diversity over time. If this goes on for a long time, the favored alleles reach a frequency of 1 (fixed), and the
ones no longer found are lost. Selective forces working against individuals of a certain phenotype.
Polygenic: multiple loci, multiple genes each with multiple alleles that are going to control the phenotype. (for
skin color, darker color helps burn prevention and hence mutations)
Directional selection in dog breeding, plants, and cliff swallows. After one selective event in cliff swallows,
only the bigger birds survived. (selective event=6 day cold snap)
Mice have learned how to predate on Albatross chicks because of the way that seabirds raise young. Young
are raised alone on end because they were raised in absence of terrestrial predators. Mice have grown in size
since their arrival and have become carnivorous (from vegetarians). Killing many birds because their original
food is absent, traits become more accentuated.
Stabilizing selection: Individuals with the intermediate traits reproduce more than others, thereby maintaining
intermediate phenotypes in a population and decreasing genetic variation, but does not change the average
value (the parabola after selection becomes narrower because the extremes are becoming less)
Babies with intermediate weight have lowest mortality while the extremes of weight (very low and very high)
have highest mortality rates
Disruptive selection: opposite of stabilizing selection, intermediate phenotypes are not favored and extreme
phenotypes are favored. Maintains genetic variation but does not change the mean value of a trait. Can lead to
speciation (formation of new species) if individual mates preferentially with individual with same trait
(Coloration in Female Mocker Swallowtail Butterflies, Batesian Mimicry. Diversity controlled by the female
W locus. Males are homogametic ZZ, females are heterogametic ZW)
Seedcrackers with very long or short beaks survived long enough to breed, intermediates could not feed
efficiently and died.
Reductive Evolution: evolution does not always have to make organisms more complex. Simpler is often
better. Favors less complex organism, will tend to lose features. Features can be lost. Cave fishes lose their
eyes because they live in complete darkness. Happened independently in different cave systems. Parasitic
barnacle on the crab
Sexual Selection: Mate choice, a type of natural selection. Results in higher fecundity and increased fitness
(greater mating success). Female choice and male-male competition
Anisogamy: reason why males compete more intensely for mates than do females and females are more
choosier. Males make many gametes (sperm) and females make fewer large gametes (eggs) which are more
expensive to make.
Bateman & Trivers principle: several predictions based on differential energy investment in gametes:
1st prediction: male fitness will be limited by the number of mates, whereas female fitness will not.
Females have limited eggs
2nd prediction: because females invest more into each gamete, they should invest more in parental care
of an offspring
3rd prediction: given more investment and care of offspring, females should be choosier about who to
mate with (want the best genes), males compete more for mates
Batemans rule: male fitness improves with more mates; female fitness is limited by resources
Sexual dimorphisms: females prefer to mate with males with particular traits. Traits are being driven by sexual
selection.
Extreme Dimorphism in Anglerfish: body of male will bite female and fuse with female. Steal nutrition from
female, but female is set for life in terms of laying eggs
Intersexual: one sex chooses mates from opposite sex with particular traits (female mate choice selects for
male reproductive traits). Males will get to pass on traits to the next generation.
Intrasexual: competition within a sex, between males selecting for those traits that will make better competing
sons. Genes are going to be inherited by both female/males, but expressed only in males because they are x
linked or sex limited traits (depend on male hormone levels)
Inter and Intra will lead to sexual dimorphism in species
William Hamilton Hypothesis: Bright colors in Male zebra finch advertises their health and hence females
choose mates with brighter colors because they are healthier. Color is due to how much carotenoid chemicals
are in bird
Fisherian Runaway model: model of selection that explains why we see bizarre traits of morphology and
behaviors on part of males. Sexual preference of a particular trait leads to selection which, over time, develops
a greater preference and more pronounced traits until the costs of producing the trait balance the reproductive
benefit if possessing it. (pea fowl)
European giant elk: possible example of runaway sexual selection. Change in climate reduced the amount of
food available to the elk to grow their gigantic antlers. Became extinct
Intrasexual selection (male-male competition)
Male combat: males fight over access to mates
Ritualized displays: use displays to gauge strength of opponent and decide whether or not to fight
(only happens if males appear equally matched)
Sperm competition: males do not physically compete but sperm do, competition for ability to fertilize
egg.
Fighting elephant seals (intrasexual selection): a few male elephant species father majority of offspring each
year. Male-male competition rather than female choice. Variation in reproductive success is high in males.
Variation in reproductive success is relatively low in females
Intrasexual selection often produces more than one successful strategy. May produce distinct male
polymorphisms within populations
Bluegill Sunfish: 3 mating tactics each associated with a distinct morphology and behavior. Parental, sneaker
cuckolder (sneak sperm in) and satellite cuckolder (satellites parental male).
Genotype is what makes up the DNA, hereditary information. Transcribed and translated into proteins which
affect phenotype.
Mutation: restores genetic diversity. Results in mistakes made by enzymes, therefore new alleles are always
added into populations at all gene loci. Only occurs if resulting protein functions differently (then phenotype
will be affected). Only mutations that affect phenotype can be acted upon by natural selection
Point mutation: mutation changes one base into another (A to T, G to C, so on). Results from errors in DNA
replication or from environmental effects (mutagens) like UV radiation, toxins, etc.
When a base-pair mismatch occurs, DNA replication kicks out the mismatch and matches it with a new
matching pair. (see diagram, lecture 25, slide 6)
Mutation rate gap between eukaryotes and prokaryotes
Variation in mutation rates:
Genetic differences in DNA polymerase: protein responsible for DNA replication (all life has DNA,
but not all DNA is the same).
Susceptibility to mutagenic environmental factors
Generation effects, how many times a cell giving rise to a germ cell replicates prior to gamete
formation
Process of transcription and translation:
DNA with nuclear membrane around it. Information on DNA has to be transcribed to mRNA
(unstable within cell)
mRNA will leave the nucleus and go to ribosome (in cytoplasm) where protein is synthesized.
Genes code for proteins
DNA is the hereditary material
Genes consists of specific stretches of DNA
The sequence of bases in DNA specifies the sequence of bases in an RNA molecule
Groups of 3 bases within a sequence of mRNA specify the particular sequence of amino acids
(codons) in a protein
Proteins: put together one amino acid at a time, arranged in a linear chain. Large organic compounds used in
many structures, such as enzymes, structural or mechanical functions, cell signaling, immune responses, cell
adhesion, and cell cycle.
Transcription: copying of DNA information into mRNA (does not have Thymine, only Uracil which is slightly
different
Lead to translation which produces phenotype
Silent mutations/synonymous substitutions: mutations that do not change amino acid sequence of protein
AAAAAG (lyslys). Genotype changes, but phenotype does not, usually fitness neutral
Missense mutations/non-synonymous substitutions: amino acid will change GAA AAA (lysGlu). Change
may be beneficial, neutral, or deleterious
Nonsense mutation : change in nucleotide that results in early stop codon. Premature termination, usually
deleterious
Frameshift mutation: addition or deletion of a nucleotide, maybe in the middle of the genotype. Everything
shifts and changes proteins. Massive missense and deleterious
Neutral Theory of Molecular Evolution: genetic drift can have a major evolutionary role on neutral alleles over
time. Evolution=changes in frequencies of alleles among generations.
New mutations will be either deleterious or neutral, or rarely advantageous
Advantageous mutations result in fixation (positive selection) while deleterious mutations will be
purged from population
Neutral mutations fix with a probability proportional to inverse of population size (genetic drift)
Sickle Cell Anemia: mutation in hemoglobin gene. Change from one amino acid (glutamic acid GAG) to
Valine (GTG). Severely changes shape of hemoglobin. Removed in most areas by purifying selection, except
in areas where malaria is present because it is maintained by balancing selection (balanced polymorphism)
Mutation has to happen in germ line in order for it to be heritable in eukaryotes, because of gamete production.
Non-germ cell (somatic) mutations cannot be inherited. In females, 22 cell divisions before meiosis and 2
during meiosis, giving 23 chromosome replications in total because only 1 replication occurs during 2 meiotic
divisions. In males, a lot more replications. All of these replications make it easier for mutations to occur.
Achondroplasia: abnormal function of protein, not sex linked, homozygous dominant, typically die before or
shortly after birth. Glycine to arginine substitution at codon 1138 of gene
Anagenesis: accumulation of heritable changes that alters the characteristics of species. Microevolution
Cladogenesis: (speciation) evolutionary process that increases diversity by forming new species.
Macroevolution
Typological Species Concept: people viewed species as unchanged, and invariable distinguishing features.
Problems: There are species that mimic other species like butterflies (viceroys). Sexual dimorphism.
Biological Species Concept: A species is a reproductive community of populations (reproductively isolated
from others)that occupies a specific niche in nature. evolutionary component of species with a notion of
reproductive and genetic continuity between individuals in a species. Problems include cases where
populations are partially inter-fertile (interbreeding), populations are potentially inter-fertile but geographically
isolated, populations are asexual, extinct species
Phylogenetic Species Concept: uses pattern of ancestors and descendants to define what a species is.
Allopatric Speciation: When there is geographic isolation of population, will prevent gene flow
Sympatric Speciation: sensation of gene flow can be possible without geographic isolation. Changes in
chromosomes. Non random mating that restricts gene flow
Example of Allopatric: Alpheus snapping pistol shrimp: Partitioned populations (Pacific and Caribbean) cannot
mate successfully because they have speciated.
Mechanisms of Reproductive Isolation:
Temporal: isolation due to different time of breeding
Habitat: isolation due to breeding in different habitats
Behavioral: no interbreeding because courtship displays differ
Gametic barrier: eggs and sperm incompatible
Mechanical: male and female genitalia are incompatible
Jumping Spider Courtship
Assortative mating: affects mate choice. Leads to sexual isolation of color morphs, prelude to speciation
Cicadas temporally offset life cycles.
Example of habitat isolation: Apple maggot flies mate on fruit of native hawthorne, larvae burrow into fruit.
When apples were introduced into North America, some maggot flies used apples for larvae and these larvae,
when grown up, would use apple trees to burrow their larvae.
Example of gametic barrier: Sea Urchin Gamete Recognition Proteins on end of sperm that comes in contact
with egg. Egg only allows Sea Urchin Gamete Recognition Proteins to come through.
Example of mechanical isolation: fleas have complex genitalia. All parts must fit perfectly with female
Postzygotic Reproductive Barriers Hybrid Infertility: Example Male. Cross mare with gametic number of
32 with jackass with gametic number of 31 and get mule with 2n=63, n=? Sterile
Polyploidy: increase in the number of sets of chromosomes in a cell. Instantaneous speciation. Common in
plants, less so in animals. Mutations can only be heritable if they happen in germ line: plants have
indeterminate growth, no fixed pattern and reproductive organs will appear wherever they do. Mutations can
occur on somatic cells that have potential to give rise to reproductive organs in plants.
Tetraploid: failure of cell division in a cell of a growing diploid (2n) plant after chromosome duplication (4n)
Autopolyploidy: happening within a single plant. Mutation that causes nondisjunction among all
chromosomes. speciation in plants. Offspring of tetraploids cannot backcross to parents. Number of
chromosomes doubles, triples, etc.
Allopolyploidy: allo=different. Hybrid produced. Formed from adding genomes from different organisms.
Have more than 2 chromosome sets due to 2 different organisms interbreeding and combining their
chromosomes, are fertile and can breed with each other, but cannot breed with either parent. New biological
species. Example: goatsbeard, allopolyploids formed. Polyploids important in agriculture, wheat is an
allohexaploid (6n) produced by 2 hybridization events. Diploid wheat (2n=14) hybridized with wild ancestor
(2n=14) producing a tetraploid (2n=28) wheat which is hybridized with another wild diploid ancestor (2n=14)
producing hexaploid wheat (2n=42)
Testing Speciation: when can we consider a hybrid a new species? 2 formerly isolated populations return to
sympatry
Individual from formerly isolated populations will get back together and interbreed no reduction in
fitness, gene flow returned to normal. Cohesiveness of original species returned.
2 populations come back together and there is no gene flow, barriers have become fixed. Speciation
has occurred
Stable hybrid zones, 2 species whose ranges overlap slightly and they do hybridize. The hybrids of
that increased fitness are in hybrid zone
Introgression: movement of alleles from one species to another through hybridization, much more frequent
with neutral alleles
Genealogical relationships=ancestor/descendant relationships. Forms the model for Darwins model of
evolution proposing a single origin for all life on Earth.
Phylogeny: study of connections between all groups of organisms genealogically
Systematics: analytical study of the diversity and relationships of organisms, both still living and extinct.
Displayed through cladograms: inferred genealogies of lineages and species
Pleisomorphic: ancestral, inherited from a common ancestor. Not unique to members of a specific group
Apomorphic: derived characteristics, account for differences among organisms. Characterizes an ancestral
species and its descendants
Homologous: structures or genes that are similar because of descent from a common ancestor that had the first
version of that structure or gene
The more similar the variants of structure or gene are to each other, the closer the inferred genealogical
relationship. Variations in homologous genes or proteins maybe also be used to infer genealogical
relationships
Synapomorphies: shared derived changes among different groupings
Outgroup: close relative of vertebrates that acts as a reference lineage
Sister taxa: adjacent branches on a phylogenetic tree (taxon=named group of organisms)
Polytomy: node where more than 2 descendants branch off
Tips: branch endpoints, represent living groups or a groups extinction
Convergent Evolution: give rise to homoplasious structures: structures that superficially appear homologous
but that evolved independently often in response to similar selective environments
Monohyletic: single origin, developed from single common ancestral form
Polyphyletic: multiple origins
Building phylogenetic trees from homologous gene sequences by identifying molecular synapomorphies
Ribosomes can dissociate into small and large subunit. Each subunit has a structural RNA backbone that is
homologous among all life forms that can be sequenced, aligned and analyzed for plesiomorphic and
synapomorphic states.
Samples of earths oldest rock are rare because rocks constantly recycle or sinks to the hot mantle of the Earth
Fossils form when an organism is buried in sediment because oxygen helps decomposition happen. This
prevents decomposition.
Taphonomy: study of the different processes of fossilization
Cretaceous amber, permineralized fossil in Devonian chert, compression fossil in Devonian mudstone.
Hadean Eon: Earth very hot,Earth beginning to cool and liquid water on Earth. Earlier time on Earth
Archaean Eon: First oceans, origin of life, first evidence of oxygenic photosynthesis
Proterozoic Eon: First photosynthetic eukaryotes, formation of landmasses on Earth (continents)
Carbonaceous filamentous: bacteria
Life forms-diverse anaerobic prokaryotes 3 billion years ago. N, CO2, CH4, NH3, H, little O2
Cyanobacterial stromatolites: photosynthetic bacteria that produce oxygen as waste. Changed atmospheric and
oceanic chemistry profoundly. A lot of iron dissolved in ocean oxidized by increased oxygen concentration
from photosynthesis and stromatolites. Forms rust (Iron oxide)
Doushantuo Microfossils: cyanobacteria and multicellular algae, animal embryos in early developmental
stages 570-5880 MA
Ediacaran fossils: 565 MA, animals with simple radial forms and with many body segments and legs
Background extinction: loss of species due to normal levels of ecological and biotic turnover
Mass Extinction: events reflect cataclysmic planet-wide environmental perturbations. At least 5 have
happened in post-cambrian
End0Ordovician mass extinction , global cooling evidenced by glacial deposits in Australia
End-Permian mass extinction killed 90% of species, 250 mya
End-Cretaceous mass extinction killed 75% of species, 65 mya