bio 221 lec 7+
what are complex adaptions
those consisting of modifications to more than one part of the genome that have to work in concert to produce the final phenotypic product.
what is true about the complexity of traits
many genes control most traits and most traits are complex
parts of the genome involved in complex adaptions can be divided into two broad categories:
1) genes that encode proteins
2) regulatory elements (DNA sequence)
what are regulatory elements
they control how and where a gene is activated, control the amount, location and timing of gene expression
gene expression
that gene is actively functioning in that time and space
what do cascades of gene expression need to respond to
signal from environment ( can be genetic or actual environment signals)
what is a cascade responde
intial response an trigger multiple downstream effects
what is an example of a cascade effect.
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.
how does the cascade effect work bacillus
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
cis acting element
a DNA sequence that carries info that regulates nearby genes
trans acting elements
dna sequence that regulate the expression of distant genes
what is an example of cis regulating gene cascade
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
what happens if there is muation in a hox gene
can result in major deformations such as legs growing where antenna should be. wt fly X (ant) antennaepedia mutant
what organism in the hox cluster best understod
d.melanogaster
when are hox genes expressed and how did they evolve
hox gene cluster evolved after a series of gene duplication and all show sequence homology, they are expressed during development
what is notable about the arrangment of hox genes in the genome
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
what gene is muated when the legs grow out of the head
antp gene which patterns legs on posterior thorax
sequence homology
The similarity between biological sequences (DNA, RNA, or protein) due to shared ancestry, often indicating similar function or structure.
Orthologs
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.
Paralogs:
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.
what does the hox genes pattern
segments to be eventually built in adult form
How does the Eve gene illustrate the role of regulatory elements in gene expression?
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.
cis regulatory elements
are regions of non-coding DNA that regulate the transcription of nearby genes. These elements include promoters, enhancers, silencers, and insulators.
how does the cis regulatory element(switch) effect the eve gene
it normally turns on the eve gene in alternating embryonic segments
what relationship is between a single gene and different regulatory elements
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.
differentially regulate expression
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.
how was the hox gene cluster able to evolve such diverse functions
through gene duplication whil allows one copy to supply gene function while the other copy can perform a new function
duplication provides the oppurunity to create
paralogs (selection can act on one of the duplicte genes in novel way)
what does similar duplicate coding sequences allow for
for both coding sequence variation (different proteins) and regulatory element variation
does the coding sequence have to change for their to be a chnage in phenotype
no mutations/ changes to regulation of genes can change phenotypes as well (where/when the gen is expressed)
gene duplication is a way to allow for gene novelty, what is another method
horizontal gene transfer
horizontal gene transfer
one cell transfers DNA to another species/strain/individual. the fastest way to get genetic variation without sexually reproducing
sometimes the new gene is similar to one the host already has so the process behaves like a gene duplication event, how does this proceed? and involved what?
transduction, transformation, conjugation. most mechanisms of horizontal gene transfer involve bacteria.
there are some rare examples of hgt in multicellular eukaryotes though, what are these (2)
1. antifreeze production in some vertebrates
2. carotenoid production in arachnids
in other cases, the new gene is completly novel (neomorph), what is an example
gut bacteria in humans getting algae digesting genes from marine bacteria associated with seaweeds used in sushi.
what comes first selection or variation
In evolution, genetic variation within a population occurs first, and natural selection acts on this variation, favoring traits that enhance survival or reproduction.
case study example of neomorph
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.
if they repeated this experiment would the novel ability come in the same generation
no, although it doesnt happen, they could reproduce the acquistion of evolutionary novelty randomly
how did this citrate metabolism mutation happen
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
who is it harded to observe emergence of adaptions in unicellular or multicellular and why
harder to observe adaptions in multicellular organisms because of longer generation times.
what are the harder adaptions to target with fossils? what is an example of this?
chemical or behavioural rather than morphological. snake venom.
did the genes for making venom arise within snakes or before them?
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
what is a crotamin simialr to
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
in snakes the defensin gene underwent a duplication, what did this cause?
caused a change in regulatory network and the location of expression
even snakes we consider non venomous produce these same venoms that are found in snakes that have hollow fangs/injection systems, what an example
garter snakes the produce mild venom, and some lizards, some lizards that do are more related to snakes than other lizards.
what does this relationship between snake a lizard show
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.
evo-devo
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)
single celled organism lack
development
morphologcial differences among multicellualr organisms come from
chnages in developmental processes over evolutionary time
ontogeny recapitulates phylogeny- haeckel, means
developmental steps reflect evolutionary hisotry
flies and mice are sepearted by >570 MY yet how is there developent related
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.
can a fly hox gene work in mice
yes, since there was gene duplication that happened in vertebrates
fossil records of transition of fish like fins to tetrapod digit-bearing limb, can we hypothesize what developmental mutation might have been involved?
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
there is hox genes in plants what are these called and what plants
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.
how do mutations effect the ABC complex (hox genes in plants)
in arabidopsis thaliana mutation affecting B results in petals connverting to sepals and stamens to pistils
there are homologues to ABC system present in monocots and maybe gymnosperms what does this imply?
that precusor to ABC present in ancestor of seed plants before flowers evolved
what is the ancestral form of flowers
radial symmetry but bilateral symmetry evolved at least 70 times in the angiosperms.
what is more advatnageous bilateral or radial
bilateral symmetry has more effcient pollen transfer
what two genes are important playwers in networks that control plant asymmetry
DICH and CYC
what happens when DICH and CYC are mutated?
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
bilaterl and radial symmetry is an example of what
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.
irreducibly complex
a design that is so complicated that it implies a designer BUT evolutionary history shows the simple steps that make up the whole
what is the first step of explaning the evolution of the vertebrate eye
comparative morphology, almost all phyla have some form of light sensing structure (exceptions- sponges and placozoans
some single celled eukaryotes have light sensing organisms (ex. nematodinium), what are different about these
can detect presence of light without forming images
all "eyes" use what to direct and capture light
crystallins to direct light and opsins to capture light. different specific proteins do these jobs in different categories of organisms
opsins vary widley (insects vs octupus vs humans) what does this indicates
suggests that image forming eyes may have evolved independent multiple times
what are opsins
molecules that react to being struck by a photon, triggers a chemical rxn that produces an electrical signal that can be detected by neurons
vertebrate opsins are called? what about other animals?
vertebrates: ciliary or c opsins (stored in extenstions of retina)
other animals: rhabdomeric or r opsins (stored in infoldings of photosenstive membranes)
though maybe c opsin and r opsin evolved independently BUT...
all taxa have evidence of both types, just used differently by each group (not creating new genes)
origin of opsin shows what
phylogeny of genes that encode opsins have found that they are ancestrally codes receptor for melatonin
why melatonin? what happened to the melatonin receptor gene.
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.
when and where did opsin originate
650 mya- ( evolution of light capturing opsins) from a common ancestor. one copy evolved into melatonin receptors others duplicated again into opsins.
what is the evidence for deep homology reflected in the developmental genes associated with eye development.
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.
ecotpic eyes come from
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"
mutations can also alter visual pigment development
in humans and mice pax6 mutations can cause underdeveloped eyes and in fruit flies no eyes.
what other structure is detrimental to the eye
the evolution of the lens to focus light on receptor cells so it can be ordered into an image.
what creates lenses in vertebrates
a protein called a-crystallin, some of the most stable proteins in animals
what did phylogenetic analysis show about alpha cystallin
that a-crystallin shows ancestry with heat shock proteins (molecular chaperones that help other proteins fold after heat denaturation)
heat shock proteins are generally very stable, but what can happen later in life
cataracts are formed by denaturation of crystallins which clump and form opaque films
all organisms have to cope with constraints to evolution, phylogenetic constraints are:
features that are inherited from ancestral species that appear to limit current species to life history options
even if we have light sensing pigment and a lens= how do we make an eye
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)
physical constraints example
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
pleiotropic constraints
antagonistic pleiotropy occurs when a mutation with beneficial effects for one trait also causes detrimental effect on other traits
pleiotropic constraint example
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.
derived structures are often built on the scaffold of ancestral forms, how does this relate to the giraffe neck.
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'
land veretebrates lost gills but did not lose..
blood vessel and neural architecture
homoplasy
sometimes, innovation indepedently appear or are lost independently
convergent evolution? example?
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
what is another example of convergent evolution
evolution of flight in both butterflies and birds, they are very distatnly related but they both use wings to fly
parallel evolution
similar phenotypes that independently arose with closely related taxa often via independent occurence of similar mutations
What is a simultaneous hermaphrodite species?
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
where is sperm and oocytes produced in these worms
sperm- in spermatheca
oocytes- produced continously
What is parthenogenesis?
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.
What are the evolutionary consequences of parthenogenesis?
✅ Fast reproduction, no need for mates
❌ Low genetic diversity → reduced ability to adapt to changing environments
🧠 Great for stable environments, risky for changing ones.
do animals only use parthenogenesis when necessary
no there has been virgin briths with males present recorded. even though it was previously though to be a hail mary pass
benefits of sex
combining benefical mutations and generation of novel genotypes
combining benefical mutations
provides opportunity to get good genes which could mean offspring are fitter than parents
generation of novel genotypes
Shuffling the decks in meiosis: fertilization can create unique combinanations of alleles for offspring
Why is sexual reproduction thought to lead to faster evolution?
Because it creates genetic variation, giving more raw material for natural selection to act on.
🧠 Variation = flexibility in adapting to new challenges.
What ecological pressure may select for sexual reproduction?
Host–parasite coevolution
🦠 Parasites evolve quickly, so hosts must also evolve rapidly to defend themselves—sexual recombination helps by increasing genetic diversity.