those consisting of modifications to more than one part of the genome that have to work in concert to produce the final phenotypic product.
many genes control most traits and most traits are complex
1) genes that encode proteins
2) regulatory elements (DNA sequence)
they control how and where a gene is activated, control the amount, location and timing of gene expression
that gene is actively functioning in that time and space
signal from environment ( can be genetic or actual environment signals)
intial response an trigger multiple downstream effects
the formation of a hard coated spore by bacillus bacteria is triggered by molecules indicting environmental degradation that bind to recpetors on the surface of the bacterial cell.
enviro triggers: dna damage, dessication, irradiation, nutritional deficiences (survival stress)
signals are integrated at master switches/regulators which regulate that downstream response, the downstream effectors realize the "decision"
master regulator is the main character that affects everything onwards
a DNA sequence that carries info that regulates nearby genes
dna sequence that regulate the expression of distant genes
best studied gene cascade in evolution is the hox (homeobox) gene cluster, where we see a gene hierarchies. this gene cluster influences anterior- posterior development (head-tail) and patterns the embryonic segments
can result in major deformations such as legs growing where antenna should be. wt fly X (ant) antennaepedia mutant
d.melanogaster
hox gene cluster evolved after a series of gene duplication and all show sequence homology, they are expressed during development
the hox genes in the genome mirrors position of expression along anterior-posterior axis, hox genes repress other devlopmental genes and body parts are specifiec by developmental genes
antp gene which patterns legs on posterior thorax
The similarity between biological sequences (DNA, RNA, or protein) due to shared ancestry, often indicating similar function or structure.
These are genes or proteins in different species that evolved from a common ancestral gene through speciation. They typically retain the same function across species. For example, the hemoglobin gene in humans and chimpanzees would be orthologous genes.
These are genes or proteins within the same species that have evolved from a common ancestral gene through duplication. They may acquire new functions or sub-functions over time. For example, the two globin genes in humans (alpha and beta) are paralogs, as they arose from a gene duplication event.
segments to be eventually built in adult form
The Eve gene is regulated by multiple enhancer elements, each controlling expression in specific stripes in the embryo.
🧬 Example: Eve has separate enhancers for stripe 2, stripe 3, etc.—each responds to a unique combo of transcription factors. works in embryogenesis before hox genes. The eve gene serves as a model for understanding how cis-regulatory elements like enhancers and promoters control the spatial and temporal expression of a gene, determining its role in development. Changes in regulatory regions (not the coding gene itself) can alter gene expression patterns without disrupting gene function.
🧠 This allows evolutionary changes in body plans through tweaks in gene regulation—Eve stripe enhancers are a model for how this works.
✅ Same gene, different expression = new traits without breaking old ones.
are regions of non-coding DNA that regulate the transcription of nearby genes. These elements include promoters, enhancers, silencers, and insulators.
it normally turns on the eve gene in alternating embryonic segments
a single gene can be affected by different regulatory elements depending on what part of the embryo it is in. cause these regulatory elements to drive gene expression of other genes.
The process by which different factors (such as transcription factors or regulatory elements) control the activity of a gene in various cells, tissues, or conditions, leading to varying levels of gene expression.
through gene duplication whil allows one copy to supply gene function while the other copy can perform a new function
paralogs (selection can act on one of the duplicte genes in novel way)
for both coding sequence variation (different proteins) and regulatory element variation
no mutations/ changes to regulation of genes can change phenotypes as well (where/when the gen is expressed)
horizontal gene transfer
one cell transfers DNA to another species/strain/individual. the fastest way to get genetic variation without sexually reproducing
transduction, transformation, conjugation. most mechanisms of horizontal gene transfer involve bacteria.
1. antifreeze production in some vertebrates
2. carotenoid production in arachnids
gut bacteria in humans getting algae digesting genes from marine bacteria associated with seaweeds used in sushi.
In evolution, genetic variation within a population occurs first, and natural selection acts on this variation, favoring traits that enhance survival or reproduction.
e.coli in 12 flasks, way more cloudies, bacteria multipled greatly --> bacteria acquired additonal method of getting nutrients: abiloty to grow on citrate which they usually dont metabolize. went back and looked at frozen culturals, found mutation rose around 33 K years ago, sequences genomes before, at, and after citrate eating. saw a very fast rise in citrate metabolism.
no, although it doesnt happen, they could reproduce the acquistion of evolutionary novelty randomly
found that mutation invovled a duplication of several genes associated with the usual anarobic digestion of citrate (the citT complex). citrate promoter was duplicated and the mk promoter is active when O2 is avaible, citT genes are now under control of a different promoter when O2 is available
harder to observe adaptions in multicellular organisms because of longer generation times.
chemical or behavioural rather than morphological. snake venom.
researches looked at a phylogeny of genee associated with production of venom in snakes. there are many genes that follow the one that makes a crotamin, a muscle destroying venom
a immune fxn gene (defensin) in vertebrates used in bacterial immune defense. defensin is expressed on the skin of vertebrates. the defensin genes in snakes are expressed in the mouth of venomous snakes
caused a change in regulatory network and the location of expression
garter snakes the produce mild venom, and some lizards, some lizards that do are more related to snakes than other lizards.
that the venom may have orignally evolved in a cmmon ancestor of modern snakes, and these lizards whihc include gila monsters and komodragons. though these venoms do vary.
evolution of development. new field dating from mid -1990s goals of evo devo reasearch range from mechanistic (how does that structure develop) to phylogenetic (where did that structure originate) to theoretical (does development constration evolution)
development
chnages in developmental processes over evolutionary time
developmental steps reflect evolutionary hisotry
development of embryos of both taxa is controlled by homolgous hox genes. though in basal vertebrates the entire hox cluster was duplicated twice, resulting in 4 sets.
yes, since there was gene duplication that happened in vertebrates
hox 13a= expressed in limbs of extant fishes and tetrapods when expressed produces proteins along the outer rim of fin early in development and patterns fin margin. in fish active for quite a whole and then turns off
difference (temporal difference-time); in tetrapod Hox13a becomes active early in development then turned off then turned on again to allow more complex appendages creating digits
ABC complex in dicot plants, infleunce floral structure through various combinations of A-B-C gene expression that determines the face of plant regions. independently evolving equivalents.
in arabidopsis thaliana mutation affecting B results in petals connverting to sepals and stamens to pistils
that precusor to ABC present in ancestor of seed plants before flowers evolved
radial symmetry but bilateral symmetry evolved at least 70 times in the angiosperms.
bilateral symmetry has more effcient pollen transfer
DICH and CYC
if both are mutated in snapdragon flowers then radial symmetry is developed. these pathways control floral bilateral asymmetry in other angiosperm lineages (flowering plants)= same pathway has been recruited repeadeatly independently multiple times
parallel evolution- The process where two or more species independently evolve similar traits or characteristics, often in response to similar environmental pressures, even though they are not directly related.
a design that is so complicated that it implies a designer BUT evolutionary history shows the simple steps that make up the whole
comparative morphology, almost all phyla have some form of light sensing structure (exceptions- sponges and placozoans
can detect presence of light without forming images
crystallins to direct light and opsins to capture light. different specific proteins do these jobs in different categories of organisms
suggests that image forming eyes may have evolved independent multiple times
molecules that react to being struck by a photon, triggers a chemical rxn that produces an electrical signal that can be detected by neurons
vertebrates: ciliary or c opsins (stored in extenstions of retina)
other animals: rhabdomeric or r opsins (stored in infoldings of photosenstive membranes)
all taxa have evidence of both types, just used differently by each group (not creating new genes)
phylogeny of genes that encode opsins have found that they are ancestrally codes receptor for melatonin
key regulator in our circadian rhythym ( sleep/walk cycle) which is regulated by sunlight . several duplications, modification, sorting events which is the reason for distribution and variations of opsins found today.
650 mya- ( evolution of light capturing opsins) from a common ancestor. one copy evolved into melatonin receptors others duplicated again into opsins.
two genes, called "eyeless" in insects and "pax6" in mammals exist as homologs in almost all animals. both resulting in lack of eyes/ eye development issues.
some alleles of eyeless in drosophila, can cause eyes that develop on parts of the body where they arent supposed to be. basic function of pax6/eyeless --> "put pigment here"
in humans and mice pax6 mutations can cause underdeveloped eyes and in fruit flies no eyes.
the evolution of the lens to focus light on receptor cells so it can be ordered into an image.
a protein called a-crystallin, some of the most stable proteins in animals
that a-crystallin shows ancestry with heat shock proteins (molecular chaperones that help other proteins fold after heat denaturation)
cataracts are formed by denaturation of crystallins which clump and form opaque films
features that are inherited from ancestral species that appear to limit current species to life history options
if we look at the simplest light sensing structure --> we can see the "steps" in extant animals. light sensing spot, evolved with a bump like structure, proto lens, involution of light sensing surface, then much more spherical accurate lenses and retina (inside out cellular organization of retina)
more obvious, example. adult mayflies lack functional mouthparts, so egg production depends on energy gathered at larval stages
if they had mouthparts? too heavy to fly and find mates
antagonistic pleiotropy occurs when a mutation with beneficial effects for one trait also causes detrimental effect on other traits
mammals have 7 vertebrae because different values may cause some deletrious effects. giraffe neck has vertebrae therefore same # as humans just much bigger. adding more is deletrious.
the derived giraffe neck for example has to work around the structure of nerves and arteries originally selected for in gilled ancestors, and shows imperfections in 'design'
blood vessel and neural architecture
sometimes, innovation indepedently appear or are lost independently
occurs when similar traits are evolved independently in distantly related taxa ( no shared ancestry)
many marsupials converged on similar body plans to eutherian/placental mammals, they diverged from placental mammals 130 mya = more similar to parallel evolution than true convergent evolution
evolution of flight in both butterflies and birds, they are very distatnly related but they both use wings to fly
similar phenotypes that independently arose with closely related taxa often via independent occurence of similar mutations
A species in which each individual has both male and female reproductive organs at the same time.
🔁 Can often self-fertilize or exchange gametes with others.
🧠 Think: both sex roles in one body, at the same time.
🔗 Examples: earthworms, some snails, flatworms
sperm- in spermatheca
oocytes- produced continously
A form of asexual reproduction where females produce offspring from unfertilized eggs—no male gamete (sperm) is involved.
👶 Offspring are usually genetic clones or near-clones of the mother.
✅ Fast reproduction, no need for mates
❌ Low genetic diversity → reduced ability to adapt to changing environments
🧠 Great for stable environments, risky for changing ones.
no there has been virgin briths with males present recorded. even though it was previously though to be a hail mary pass
combining benefical mutations and generation of novel genotypes
provides opportunity to get good genes which could mean offspring are fitter than parents
Shuffling the decks in meiosis: fertilization can create unique combinanations of alleles for offspring
Because it creates genetic variation, giving more raw material for natural selection to act on.
🧠 Variation = flexibility in adapting to new challenges.
Host–parasite coevolution
🦠 Parasites evolve quickly, so hosts must also evolve rapidly to defend themselves—sexual recombination helps by increasing genetic diversity.
An evolutionary idea that species must constantly evolve just to keep up with their enemies (like parasites). evolutionary pressure that is never escaped because of the rapid evolution of the parasite
🧠 Sex evolved to help hosts "run faster" by producing varied offspring better able to resist parasites.
through genetic variation and outbreeding, sex allows recombination and selection against harmful mutations, helping populations purge them over time.
🧠 Healthy genotypes can be restored by mixing genes.
A process where asexual populations accumulate deleterious mutations over time—because they can’t recombine or remove them.
🔁 Each generation "ratchets up" the mutation load.
🧠 No sex = no reset button on bad mutations.
Sex recombines genotypes, allowing natural selection to weed out harmful mutations and maintain healthy lineages.
✅ Prevents the irreversible buildup of genetic damage.
Two-fold cost of males
❌ Males don’t produce offspring directly, so sexual populations grow half as fast as asexual ones.
🧠 Asexual females double the reproductive rate.
Search cost
🕵️♀️ Males and females must find each other—this takes time, energy, and increases risk of predation or injury.
🧠 More effort = more danger.
Breakup of good gene combinations
🔀 Recombination can disrupt advantageous gene combinations.
Because sexual reproduction creates genetic variation, which:
✅ Helps purge deleterious mutations (Muller’s Ratchet)
✅ Speeds up adaptation (Red Queen Hypothesis)
✅ Increases resilience to changing environments
Sexually reproducing parents pass on only 50% of their alleles to each offspring.
Asexual parents pass on 100% of their genes, making offspring fully related.
It can break up adaptive gene combinations, lowering the offspring's fitness.
Sex increases exposure to infectious agents during mating—this is a cost.
No—STDs affect animals and even plants. It's a widespread evolutionary issue.
The podapolipid mite spreads between beetles during mating—uses sex as a transfer route.
Sex is favored only if its benefits outweigh the costs.
It must:
✅ Produce more offspring, or
✅ Produce more successful offspring
Individuals produce gametes of different sizes—e.g., small sperm and large eggs.
🧠 Leads to male and female sexes.
Both partners produce same-sized gametes—no distinction between sperm and egg.
❌ No true sexes—just mating types or strains.
sexes are based on different intraspecific strategies for relative investment in gametes.
It creates different reproductive strategies and priorities:
Females: few, costly gametes → quality matters
Males: many, cheap gametes → quantity matters
Because sperm are small and numerous (“sperm are cheap”), while eggs are large and few (“eggs are expensive”).
🧠 Males can mate often with little cost; females must be selective.
Their reproductive success is limited by egg number, not mate number.
❗ Mating with a low-quality male can reduce offspring viability.
Access to eggs.
✅ Mating with more females generally increases male success, even if some are low quality.
Females: Reproductive success tied to fecundity (number of eggs); eggs are costly, so mate quality matters.
Males: Reproductive success often tied to access to females, not egg production; sperm are cheap, so quantity of mates matters.
hrough intrasexual competition (e.g., fighting, displays)
Mate attraction (intersexual competition)
In some species, by producing huge amounts of gametes (e.g., sperm in broadcast spawners, pollen in plants)
Competition within one sex (usually males) for access to mates
Aggression, large body size, horns, or other weapons
Often used more as deterrents than actual weapons
🧠 These traits help males outcompete rivals for female access.
Increased sperm output
Traits that improve sperm competition (e.g., fast-swimming sperm, larger testes)
🧠 This strategy is favored when females are rare, dispersed, or dominant.
The greater the variance, the stronger the selection on that sex.
🧠 More variation = more opportunity for traits to give an advantage.
Males, especially in species where a few dominate mating (e.g., harems).
Elephant seals—a few large males control harems and father most offspring, while many males mate rarely or not at all.
In one breeding season, most males sired no offspring, while a few sired many pups.
Female success is more even—most reproduce, and variance is much lower than in males.
Males show greater lifetime reproductive variance, meaning stronger sexual selection acts on them.
🧠 More variance = more “fuel” for natural selection.
Males can’t control which females they fertilize—fertilization is like a lottery.
Produce as many gametes as possible to increase the odds of success.
🧠 Quantity over control—just flood the field and hope for hits.
Males can use post-mating adaptations to increase their chances of paternity.
In species like rats, males produce a chemical plug that blocks the female’s genital tract after mating.
🔒 Prevents other males from mating with her.
In species like Drosophila, males transfer chemicals that reduce the female’s sexual attractiveness after mating.
🧠 Discourages other males from trying to mate with her.
In seed beetles, males have spined genitalia that sweep out sperm from earlier males.
Longer spines increase the chance of removing rival sperm, boosting fertilization success.
🧠 Better tools = better odds.
Yes—males can be polymorphic in both morphology and behavior, using different strategies to reproduce.
Large-bodied males: compete physically (e.g., guarding, fighting)
Small-bodied males: use sneaky tactics or rely on sperm competition
The bluegill sunfish (non-native in Alberta) has three types of males:
Parental males: build nests, guard eggs
Sneaker males: dart in to fertilize eggs covertly
Satellite males: mimic females to sneak past dominant males
🧠 Different paths to reproduction depending on size, timing, and behavior.
Large males (parentals):
🛡️ Build nests, defend territory, protect eggs
🧠 Invest in size and physical defense
Intermediate males (satellites):
🎭 Mimic females to sneak into nests undetected
🧠 Avoids aggression by deception
Small males (sneakers):
🏃♂️ Hide nearby, then dart in to quickly release sperm
🧬 Have large testes to boost sperm output
🧠 Strategy depends on sperm competition
It determines how intense sperm competition will be:
Monogamous females → little or no sperm competition
Polygamous females → high sperm competition
By investing in sperm competition strategies, such as:
Larger testes
More sperm production
By comparing testis size relative to body size—larger testes-to-body ratios are found in species where females mate with multiple males.
🧠 More risk of competition = more investment in sperm.
No—true monogamy is rare. Even in socially monogamous species, extra-pair copulations (EPCs) and extra-pair fertilizations (EPFs) are common.
To increase genetic diversity or offspring quality, even while maintaining a social bond with a partner.
Superb fairy-wrens:
Form pair bonds
But females often mate with neighboring males
EPF rates decrease with distance between territories
🧠 Stay paired, but still hedge genetic bets.
When one sex (usually females) selects mates based on certain traits in the other sex.
🧠 “Mate choice” selection.
Before mating: based on displays, ornaments, calls, etc.
After mating: via cryptic female choice
When a female influences which male’s sperm fertilizes her eggs after mating, often by manipulating sperm in her reproductive tract. It allows females to favor high-quality or genetically compatible mates, even if mating with multiple males.
The evolution of elaborate courtship traits in males, used to attract females.
The species' sensory abilities:
Good vision → visual displays (e.g., color, movement)
Good hearing → acoustic signals (e.g., songs)
Because female preferences can change quickly and are often species-specific, driving rapid trait evolution and even speciation.
Males invest energy not in gametes, but in being chosen—through ornaments, displays, etc.
The peacock’s tail—Darwin’s famous puzzle—explained by runaway selection: female preference for the trait drives its exaggeration over generations.
According to the good genes hypothesis, these traits are costly to maintain and signal high genetic quality or health.
🧠 A long, heavy tail = male is strong enough to survive despite the handicap.
Because choosing the right male can provide direct benefits that improve her own survival or offspring success.
Protection from harassment
🛡️ Ex: In some species, a strong male can guard a female from other aggressive males.
Chemical protection for offspring
💀 Ex: Rattlebox moths—males give females toxic compounds that are passed to eggs to deter predators.
Resources like nests or territories
🏠 Ex: Weaverbirds—males build intricate woven nests, and females choose the best builders.
Yes—some females gain nutritional benefits from males during or after mating.
When the female eats the male during or after mating, gaining nutrients that may help her produce more or healthier offspring.
Sometimes it’s accidental—the male just doesn’t escape fast enough (e.g., mantises, many spiders).
Other times, it's deliberate—the male offers himself as food (e.g., redback spider).
🧠 Ultimate “nutritive gift” = himself.
Choosing a male who provides care for offspring increases their chances of survival—a direct payoff for the female.
🐦 Male cassowaries: incubate eggs and raise chicks.
🪲 Giant water bugs: females lay eggs on male’s back; he carries and protects them until they hatch.
It may reduce disease risk for her and her offspring—strong, healthy males are less likely to carry infections.
Benefits that don’t help the female directly, but improve the fitness of her offspring.
Good genes → offspring have higher viability, e.g., parasite resistance
Sexy sons → sons inherit traits that make them more attractive to future mates
Female sticklebacks prefer redder males.
Redder males = healthier (better parasite resistance)
Offspring of red males were more resistant to tapeworms
🧠 Red is an indirect cue—a “genetic hitchhiker” signaling good genes
Female frogs prefer males with longer and more complex calls
They are costly—longer calls increase predation risk, so only high-quality males can afford to produce them.
Possibly good genes—call length is correlated with offspring performance (e.g., growth, survival).
🧠 Female preference may be based on traits that signal genetic quality—even if they’re risky for males.
When there is greater variation in reproductive success—usually in males.
🧠 More variance = more room for selection to act.
Males often have higher variance in mating success—some mate a lot, others not at all.
✅ Selection favors traits that increase male success.
The sex with greater variance in reproductive success experiences stronger sexual selection
Usually males → leads to more male-specific traits (when females are choosy)
In rare cases (e.g., sex-role reversed species), if females have more variance, then males are choosy, and females evolve sex-specific traits
🧠 Whoever has more to gain (or lose) evolves more traits for competition or attraction.
The ratio of sexually active males to sexually active females.
Often male-biased, since females may be pregnant or caring for young and temporarily unavailable to mate.
Because of Fisher’s Principle: if one sex becomes rare, it has higher reproductive value, so selection balances the ratio back to 1:1.
Because a population with more females would grow faster, since males can fertilize multiple females
In a sexually reproducing, biparental population, males and females must have equal total reproductive success—because each offspring has one mother and one father.
Daughters become rarer → greater reproductive value → selection favors producing more daughters.
Any deviation gives a reproductive advantage to the rarer sex. So natural selection drives the ratio back to equal investment in sons and daughters.
🧠 The average wins—balance is the evolutionary stable strategy.
If the population is male-biased, individuals producing more daughters have higher fitness (red line).
If the population is female-biased, individuals producing more sons have higher fitness (blue line).
✅ Selection favors whatever restores balance → stabilizing at a 1:1 sex ratio.
When males invest heavily in parental care, they become the limiting sex—leading to a female-biased operational sex ratio (OSR).
In Rhamphomyia spp. (dance flies):
Males prefer “fat” females, assuming they have more eggs
Females evolve traits (feathered legs, inflated air sacs) to fake fatness and attract males—sexual deception
🧠 Even females can evolve flashy traits when selection flips!
When an individual starts life as one sex and later switches to the other, producing both types of gametes at different times.
It depends on how body size affects reproductive success:
If larger males gain more mates → change from female to male (protogyny)
If larger females produce more eggs → change from male to female (protandry)
Clownfish: start as males, but if a dominant female dies, a male switches to female to take her role.
🧠 Sex change maximizes fitness based on social and size dynamics.