#import "template.typ": *
#show: ams-article.with(
  title: "Reading notes: Signalling",
  authors: (
    (
      name: "<NAME>",
      department: [Department of Biology],
      organization: [Wake Forest University],
      location: [Winston Salem, NC 27101],
      email: "<EMAIL>",
      url: "www.michaeldewittjr.com"
    ),
  ),
  abstract: "Caveat Emptor",
  bibliography-file: "integratedbio.bib",
)

#set heading(numbering: "1.")
#let today = datetime.today()


Mechanisms of learning are different amongst all animals.

Generally all animals can learn something (where animal is taken as a broad catgory).

Molecular models of learning are just *models* and not proven laws.

Some definitions of learning

- Conditioned learning  is an approach where learning takes place through negative or positive reinforcement (generally just negative). This is a simple form of learning.
- *Unconditioned stimulus* - the stimulus under no learning or experience
- *Conditioned experience* - the training conditions
- *Conditioned response* - what is the desired behaviour or taught response
- *Habituation* - retraiing to lose a conditioed response if repeated with some experienced result
- *Associative learning* - connection between cause and effect.
- Opelant (instrumental) - the animal makes a decision which has consequences

There is an unresolved debate between the relative importance between conditioning and cognitiion.

- *Transitive Inference* using known relationships to deduce new relationships (e.g., A > B, B > C => A > C)

== Cleaner Fish Paper

Cleaner fish (cleaner #link(https://en.wikipedia.org/wiki/Bluestreak_cleaner_wrasse)[Wrasse]) clean off the growths from fish. Cleaner fish are well marked so that they can be seen by "clients". There is competition between the clients to get return customers. They employee different strategies based on the presence of familiar and unfamiliar clients.
General strategy is to serve the new fish first rather than return clients due to potential loss of new customer pool.

Why don't the sharks eat the cleaner fish?
- Payoff of having parasite removal vs eating the fish
- Neurotransmitter of "I'm cleaning you, don't eat me" or biomolecular signalling
- How do cheaters get punished?
- Are some behaviours learned based on social cues and observation

Local cleaner-fish density determines social complexity of their world in a single  (Experimentally controllable) variable

All cleaner fish are born females.

== Ways of recognizing self

- Private self-awareness - you know what you like
- Kinesthetic visual-matching - your movements are matched by the image in the mirror ("public")

Animals that do this:
- Chimps and gorillas
- elephants
- dolphins
- horses
- magpies
- cleaner-fish?

Doing the experiment with fish in the traditional sense is challenging because it is a severe intervention (e.g., stress when fish removed from water, disruption of scales). Generally, the mirror test fails with non-visual creatures.

Mirror neurons fires the same way if you see someone do something your neurons will fire in the same way. This could be a mechanism for emphathy and is likely conditioning.

Guppies. Females choose the males.

Why? Females can only mate once per season vs males who can mate many times. Thus female function is expensive so males must compete.

Males are brightly coloured males are more desirable which could indicate higher fitness due to the ability to survive despite being brightlycolored


== Moving into Sexual Selection

Physiological mechanism--really involving testosterone. and the role that it plays in causing males to do the things they do to attract mates.

Genetic discrimination
One particular gene is present in aboit 93% in the prison population but only 50% in the the general population
Individuals with that gene also receive longer sentences
It's male.
Across mammals testorone has high longevity penalty.

Maximizing an animals probability of surviving to maturity

Survival is one component of fitness. Without reproduction is 0 unless you reproduce regardless of how long you live.
For man but not all animals that involves sexual selection: variation in mating success
And usable males are under much stronger sexual selection than females, because females invest much more in offspring than males; each egg is more metabollically expensive to product than a sperm, so they are produced in smaller quantities than sperm.
Therefore eggs are in limited supply and males must compete for access to them.

- Sexual selection is strong and is imposed on every generation (unlike regular selection which in many cases vaies in strength and direction)
- There is a cost in this choice
- Females pay some cost
- Sexually selection is strong enough that within a few generations before all males have the same high quality of alleles to offer there will be little or no variation among male fitness

So how is there still any variation in male quality for females to select on?
- Not mutation isn't plausible because mutation is not fast enough
- Recombination would speed up selection of alleles
- Alleles carried by males might not be beneficial for females (e.g., things that females like might not be good for male)
- Abiotic changes
- Biotic changes (e.g., predators will adapt to a new adaptation)

One type of biotic interaction seems particular likely to impose constant selection for new or rare genotypes: parasites and their hosts.

== Red Queen Hypothesis

Parasites target the most abundant host genotype (the biigest resource pool for their offspring)

You have to run as fast as you can to stay in one place

That reduces the fitness of that host genotype and one or more other hos genotypes then becomes more abundant

Now the most sucessful are those adapted to the most abundant host genotype

Frequency-depedent selection perpetually favors rare genotypes preventing the alleles making up that genotypes from being lost; in other words, it maintain genetic variation instead of eliminating it.

Alleles that were previously fit are now targets for parasites, so they become a disadvantage.

== Fancy Plummage

Free of parasites if you have nice fur, brightly colored feathers etc, indicate you likely dont have a lot of parasites


Most males do not produce offspring (exponentially distributed--mostly zero and a few with all)
Females have almost equal express


Lyre bird probably selects for intelligence, survivability, and likelihood of surviving their surroundings

Golden collared manakins make have bright plummage (no parasites), clearing (making a clearing takes lots of energy), loud wing snaps (showing athleticism, strenght, energy budget).

== Lack of sexual selection

Less obvious selection occurs when male component is larger (but still less than females)


Why don't males cheat, especially with morphological sexual selective features?
- might be an inordinate cost that can't be born
- High quality males pay a lower price than low quality males for reproduction.
- Forces son to bear the cost of this selective feature
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== Honest signals

Sexually selected traits that signal high fitness are thought to be impossible to fake (impossible for inferior males to produce).
Females that prefer signals that can be faked are at a disadvantage, selection favors demales that demand an honest signal of genetic quality.

An alternative non-adaptive theory for why females the traint that they do; the sensory bias hypothesis. Rather than an indicator of henetic purpose it is an accident.

**Proximal** explanations tend to be mechanistic on short time scales - e.g. during the breading season testoterone levels in their blood increases in male; by binding to testoterone receptors in key brain regions, alterning behvaiours. E.g., winning a fight boosts your testosterone and makes you more likely to win the next fight.

**Ultimate** explanations focus on the bigger pictures - that mating dance evolved vecause its an accurate indicator of a male's fitness. it indicates good neuromuscular coordination and it demands a lot of energy.

Testosterone has a role is sexual selection. prop

Aromatase is an enzyme that converts thalamus and amygdala turns testoerone in men to estrogen. This makes testosterone less effective (dumber guys) and is used for estrogen-sensitive cancers.

Testerone is a cholestrol, once in the cell it turns on transcription factors altering gene expression

Testosterone has some effects that don't appear tied to the transcription e.g. relatedto protein kinase A to release energy

== Manekins

Testosterone has a large impact on multiple genes which are regulated.

Testosterone binds to androgen receptor



SH: Wing puscle
PEC: Chest muscle
Flutamide: T and AR agonist
NTC: Novel transcript clusters
AR: androgen receptor
ARE: Androgen receptor elements
ER: Estrogen receptor
WGCNA: Weighted gene co-expression network analysis
RPKM:reads per kb of exon per 106 mapped RNA Seq reads qq
PCA: Principal component analysis

3-4 question; half a page to a page. Diagrams and figures allowed.

At lot worse to get too hot than to get hot. Proteins don't work or fold correctly

Reponse is generally
- Work to maintain a constant balance (mammal homeostatis)
- Tie temperature to environment (ectotherms)

Wood frogs can survive freezing.

== Thermostats
- Invertebrates the thermostat is the hypothalamus
- Receives sensory input about body temperature
- If body is cooler than set point, the hypothalamus induces reduces that raise body temperature; if warmer than set point, begins measures to cool it

=== warming
- Blood vessels constrict
- muscles shiver
- thyroid for hormones
- breathing rates

=== cooling
- blood vessels dialate
- skin perspires
- sweat gland

== Endothermy
- most of heat comes from the metabolic rate of internal organs: liver, spleen, gut, kidneys
- regulating the permeability of inner mitochrondial membrane determines how much heat is produced, e.g., endotherms can separate oxidative phosphorlation from electron transport, causing, "proton leak" across the inner mitochrondrial membrane, producing more heat and less ATP. Diverts energy to heat vs ATP
- the rate of heat loss, and the temperature of particular organs or region, can be regulated by a variet of mechanisms, e.g., constricting or dilating blood vessels
- Endotherms have a high cost of energy with a high payoff of having enzymes operating at peak efficiency so more mass

== Ectothermy
- Behavioural thermoregulation: choosing their location, their coloration, their orientation relative to the sun, or some combination of those.
  - This has a cost of devoting time to do this

- Thermoconformation: just let their body temperature vary with their surroundings
- in a few extreme cases allow themselves to freeze

== Behavioural thermoregulation does have costs
- greater exposure/ vulnerability to predators
- time not available/ less available for feeding, courtship

What would you expect to determine whether an extotherm choose thermoregulation or conformation?


Habitats vary in the costs and hazards of behavioural thermoregulation
- for example if sunny locations are scarce, it might be more costly for a lizard with a lower than ideal temperature to warm up
- if hard to find sun then costs a lot.

As air temperature increases, body temperature generally increases.
Any deviation are behavioural regulation

== Plasticity and acclimation (adaptation)

- both endotherms and ectotherms can adjust thermal performance curves and temperature set points in response to a particular challenge (e.g., climate, pathogens)
- e.g., to induce a fever, "pyrogens" (compounds produced either by your own body or by pathogens) raise the set point

How do ectotherms like a desert iguana deal with bacterial infection that cause endotherms to raise their body temperature.

Desert iguana experimentally injected with bacteria raise their set points running a behaviour fever?

Partial endothermy: some ectotherms generate heat but only when/where it matters most.

Prioritizes brains and eyes. e.g., swordfish and tuna heat their brains and in some cases their eyes, to about 5 deg above surrounding seawater

== Heat shock proteins

Proteome stability, heat hardening and heat-shock protein expression profiles in cataglyphis desert ants.

HSC70 -
HSP - heat shock proteins
HSF - transcription factors
HSE - transcription effectors
heat harderning - response to heat

Heat shock proteins are chaperones; this means that they help protein fold correctly. These can refold or prevent denaturing of proteins.

homologs - came from same ancestry
paralogs - homolog within a lineage

Orthologs are genes derived from a single ancestral gene in the last common ancestor of the compared species. This short, simple definition includes two distinct, explicit statements that are important to rationalize; furthermore, it does not include other requirements that might seem natural but are not actually intrinsic to orthology. First, the requirement of a single ancestral gene is central to the concept of orthology. Once the ancestral genome is shown to have contained two paralogous genes that gave rise to the genes in question, it will be incorrect to consider the latter orthologs, even if, on some occasions, there may be the appearance of orthology (see below). Second, the definition specifies the presence of an ancestral gene in the last common ancestor of the compared species rather than in some arbitrary, more ancient ancestor. Of course, this definition assumes the existence of a distinct common ancestor of the compared species, a proposition sometimes challenged for prokaryotes owing to the high incidence of HGT (see discussion below).

Paralogs are genes related via duplication. Note the generality of this definition, which does not include a requirement that paralogs reside in the same genome or any indication as to the age of the duplication leading to the emergence of paralogs (some of these duplications occurred at the earliest stages of life's evolution but the respective genes nevertheless qualify as paralogs).

= Exams

Architecture of regulatory pathways and learning/ behaviour

Look for common themes (e.g., the fish transitive inference, the testorone paper).

Something along the lines of a sprandral vs adaption

People have spectulated on origins of heat shock protein. genes can get mutations that have phenotypic protens can correct (E.g., mutations coudl accumulate after being corrected by heat shock. then when exposed to a new environment it could be a step change). Evolutionary "capacitance".
This doesn't make sense from an evolutionary perspective. you don't know the future.
