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Bri MT

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Evo eco with Bri
« on: October 28, 2019, 10:23:49 pm »
+11
Heyo,

I was going to only start this next week but it's a good productive distraction method so Here. We. Go.

This thread is intended to serve 2 purposes:
1) Get me to actually remember stuff for my evo eco exam
2) Provide some insight into evo eco for the many, many, many of you who haven't had much exposure to it.

You (hypothetically): "What is evo eco?"
Me: Evolutionary ecology!
You (hypothetically): "What is evolutionary ecology?"
Me: A combo of evolutionary biology and ecology
You (hypothetically): "Uhhh.... more info?"
Me: There are many patterns that can be observed in how organisms (living things) interact with their environments and other organisms - ecology examines these patterns. We'll get into what evolution is later, but suffice to say that evolutionary ecology looks at what patterns exist in the natural world and the processes responsible for them
You (hypothetically): "Ok but why should I care?"
Me: You're on an academic site - do I really need to justify why you should care about learning??
You (hypothetically): "Yes. Yes you do"
Me: Ok. If you care about extinction, how species came to be as they are, or how we can predict and influence how species will change in the future you should care about evolutionary ecology. This can be applied to your favourite charismatic megafauna (the cute/cool animals society tends to like), disease carrying vectors (e.g. mozzies), ourselves & a whole host of other taxa.


I may slip into assuming VCE bio knowledge at points - if I use a term or concept and you don't know what it means please feel free to ask regardless of your level of bio background :)


- topic 1: crash course into evolution and natural selection
- topic 2: life history strategies - investing yourself vs investing in your kids
- topic 3: evolution of sex - why eukaryotes have sexual and asexual reproduction
- topic 4: sex allocation - nature's better at balanced sex ratios than parliament
- topic 5: evolution of aging - why do we decline as we get older?
Up next:
- topic 6: sexual selection & dimorphism - how & why females are usually more picky with mates
« Last Edit: November 10, 2019, 08:45:24 pm by Bri MT »

Geoo

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Re: Evo eco with Bri
« Reply #1 on: October 28, 2019, 10:38:45 pm »
+2
Oooo, looking forward to this!
How come you chose evo eco?
2020: VCE 93.2
2022: BSci/Arts (Chemistry/Pharmacology and French)@Monash

Bri MT

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Re: Evo eco with Bri
« Reply #2 on: October 28, 2019, 11:10:15 pm »
+4
Oooo, looking forward to this!
How come you chose evo eco?


1. I have an evo eco exam in a couple of weeks and even though I'm confident I'll remember the concepts I'm not so confident I'll remember case studies, authors' names, dates etc. I'm hoping this thread will help me with that
2. Going into semester I was looking forward to evo eco the least but it's actually been a great unit & I want to share my understanding and appreciation with people

Thank you! :)

Bri MT

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Re: Evo eco with Bri
« Reply #3 on: October 29, 2019, 12:18:31 am »
+6
Topic 1: Crash course in Evolution and Selection

Natural selection is: differential survival and reproduction of individuals due to differences in phenotype

(Phenotype refers to expressed traits. E.g. having blue eyes. Genotype refers to genetic make-up E.g. having DNA which codes for blue eyes)

Macro-evolution: Morphological change across time or long-term change across species. I.e. descent with modification

There's lots of lines of evidence to support evolution but today I'll be focusing on a few case studies mentioned in the lectures.

1. We would hypothesis that if extant (currently existing) species have come to exist through a process of descent with modification then there should be evidence of transitional forms in the fossil record.

So, if we're saying that birds are descendants of dinosaurs then there should be species in the fossil record that's a bit like a bird and a bit like the other dinosaurs.

Bam! Enter Archaeopteryx which had modern flight feathers but also a reptilian body including teeth, long tail and sets of 3 claws and lived approximately 150 million years ago.

Does Archaeopteryx truly represent a transition between birds and dinosaurs or is it simply a misleading example? There are more transitional forms in the fossil record & anatomical studies in the 1970s do suggest that Archaeopteryx is likely to have descended from therapods, which turn out to commonly have feathers. This all helps us confirm our theory.

2. Vestigial traits

Maybe we don't want to look at fossils for our evidence. Maybe we want to look at extant species living right now. The existence of useless traits that are carry-overs from species' evolutionary past further supports macro evolution. Let's consider some examples.
- Kiwis have vestigial wings
- Rubber Boas have vestigial hindlimbs
- Humans have appendixes
- Whales have hips

Maybe you trust the whales' hips not to lie but you're still a bit confused on how macro evolution occurs. Let's zoom into micro evolution to take a closer look.

Microevolution is: Rapid phenotypic change within populations over successive generations due to changes in allele frequency

Oh no. Now we have more jargon. Let's break it apart.

- We've sections of DNA called genes which encode for proteins or functional RNA (for our purposes, dw about knowing what RNA is)
- Genes are considered the molecular units of heredity
- The DNA sequences which make up genes can experience changes, known as mutations, where the sequence changes
- This means there can be different versions of the same genes, which we call alleles
E.g. There are genes for eye colour, and some alleles code for blue eyes, some code for brown eyes etc.

So when we talk about microevolution, we are talking about changes in phenotype based on changes in the frequency of different versions of genes.

Let's look at an example: Threespine stickleback, Gasterosteus aculeatus
This is a fish which comes in two forms. The marine (i.e. ocean-dwelling) form is fully armoured with lateral plates and pelvic structure & the freshwater form has reduced armour with vestigial pelvic structure.

Some threespine stickleback were taken from a marine system and introduced into Loberg Lake in 1990 (all this happened in Alaska). At the start, the frequency of the fully plated phenotype was almost 1 (i.e. not quite 100% of the sticklebacks had the marine form). Over generations, the frequency of the lightly plated phenotype increase and the frequency of the fully plated phenotype decreased. By 2001 more than 70% of the sticklebacks had the lightly plated phenotype rather than the fully plated phenotype.

The process:
For evolutionary adaptation 4 things must occur:
1. Phenotypic variation. There needs to be difference in individuals for selection pressures to act on
2. Genetic variation: At least part of the phenotypic variation needs to be heritable. I.e. the genes you have need to impact the phenotypic variation
3. Competition: There canít be enough resources for each organism to survive and produce the same number of offspring
4. Differential performance: Some variants survive and produce offspring at a higher rate than others

Applying this to a classic case study: Darwinís finches
1. There was variation in the beak depth of the finch population (this variation was approximately normally distributed, which is v. common for this type of trait)
2. A plot comparing midparent beak depth (average beak depth of parents) to the midoffspring beak depth (average beak depth of offspring) in 1978 and 1976 shows that the line of best fit for each year has the same slope but different intercept. This provides strong evidence that beak depth is heritable
3. In 1977 there was a drought. Heaps of finches died (big bottleneck) Ė thus, there was competition for survival. This is related to seed abundance crashing in the same year. Large and hard seeds were more likely to survive the drought
4. Finches with deeper beaks were more likely to survive, and finches born after the drought had deeper beaks on average than those born before.

Thatís an example of directional selection Ė being closer to an extreme is rewarded, so the population average shifts in that direction over generations. E.g. if faster cheetahs are more likely to survive & reproduce, youíd expect the average speed of cheetahs to increase over generations and this would be directional selection.

Letís now look at stabilising selection using goldenrod galls. Youíve got the golden rod plant which as part of its defences produces galls around foreign invaders. Youíve also got goldenrod gall flies, which are bad at flying and spent their life on the plants. The flies lay their eggs in the plant, juveniles eat the plant & secrete chemicals, and generally spend a lot of time in the gall formed around them.

Parasitic wasps attack the galls and inject their eggs, with wasp larvae eating fly larvae. The wasps are super effective at attacking small galls and not other gall sizes. You might think then that large galls are ideal, but birds also attack galls and theyíre good at attacking large galls. What ends up happening, is that the medium sized galls are best at surviving. Thus, natural selection acts to reduce the range of gall sizes and increase the frequency of the intermediate trait.

Thatís stabilising selection Ė where survivorship is grouped around an intermediate trait. What if rather than looking at selection resulting in increased similarity, we consider selection favouring being different?

Letís use the case study of elderflower orchids to examine this. These flowers come in yellow and purple, with neither the yellow nor the purple flowers offering a food reward (nectar) to visiting bees (European bumblebees are their main pollinator). So if youíre a bee and you land on a purple flower only to find that it didnít give you food, youíre likely to try a yellow flower next rather than another purple flower. Thus, if there are many purple elderflower orchids itís better to be a yellow elderflower orchid and vice versa for if there are many yellow elderflowers. This was experimentally tested by Luc Giford and colleges who set up orchids in arrays of 50 plants. There were 2 arrays for each of the following yellow flower frequencies: 0.1, 0.3, 0.5, 0.7, 0.9.  These experiment confirmed that the rarer phenotype was more successful, making this a case of negative frequency dependent selection.


SoÖ is selection is the only reason for change in allele frequencies across generations? Nope. Thereís stochastic (random) genetic change as well, which we call genetic drift


« Last Edit: November 08, 2019, 05:48:26 pm by Bri MT »

Bri MT

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Re: Evo eco with Bri
« Reply #4 on: November 05, 2019, 10:51:37 pm »
+9
Topic 2: Life History

First things first, life history is the pattern of allocation, throughout an individual's life, of time and energy to growth, somatic maintenance & reproduction.

In other words, life history describes how an organism invests in growing, (ah ah ah ah) staying alive (staying alive), and producing offspring (including finding a mate if necessary etc.). Organisms can't have it all, and there are different life history strategies for trying to maximise contribution to the gene pool.


An important aspect of this is how many times an organism reproduces - the below examples are semelparous.

North Giant Pacific Octopus:
- lives for a few years
- has 10,000s of eggs in a single reproductive episode then dies

Agile antechinus:   (it's basically a marsupial equivalent of a mouse)
- Has one breeding season then all of the males and 85-90% of the females die
- The high death rate may be linked to the breeding season being violent and testosterone being an immune suppressant

Sockeye Salmon (we'll be hearing more about these later)
- Has one reproductive episode in its lifetime lasting a few weeks where 100s of eggs are laid
- They take on spawning colouration (new aesthetic for breeding season) and there's male competition for spawning

You may have noticed that the common thread in this is dying after only one bout of reproduction - and that's what semelparity is all about

Let's now look at an example close to home (though not too close rn I hope...) : the redback spider. Redbacks are a gonochoristic species, meaning that 2 sexes are needed for reproduction.

The females are much much larger than males, and they're the ones that have the distinctive colouration we think of for redbacks: black with that signature red. On the other hand males are pretty small and are largely brown. Another interesting difference between the sexes is that immediately after mating the female will eat the male 65% of the time.

You might be thinking, well this is dumb how could evolution have resulted in this? Surely natural selection wouldn't promote this??  Rest assured, there's an explanation. You see, in nature, less than 20% of redback males will find a mate before dying. Chances are that males will only be able to reproduce once anyway, so they may as well invest all of their resources (including their lives) into it (from an evolutionary stand point anyway - I doubt the spider would be knowingly sacrificing himself for his kids). Females which eat the males produce more eggs which means that a male which gets eaten has increased reproductive success.


Next up: iteroparity case studies

Ok, adding this in now:

Coast Redwood
- Produces millions of seeds each year (once it's reached 10-15 years of age)
- However, less than 15% of seeds will be viable (able to survive & develop properly)
- Each tree lives for hundreds of years

Humpback whale
- Reaches reproductive maturity at 5 years old
- Lives for around 40 - 100 years
- One calf / juvenile whale  at a time (the mother is called a cow)
- Usually they won't have offspring every year - more like every two years

iteroparity: multiple reproductive bouts across lifetime


You might be thinking, why not just have an organism that:
- is constantly reproducing
- matures at birth
- and live forever

Wouldn't natural selection love that? Yeah sure, this might be great, but there's trade offs and constraints that prevent existence of this "Darwinian demon"

First up, we'll look at ecological constraints with Seychelle's warbler (Acrocephalus sechellensis)
- It lives on Cousin's island (off the east coast of Africa) which was bought to turn the island into a reserve and save the birds
- The birds have small patches of land (territories) which they defend from intraspecific competition (i.e. they don't want other Seychelle's warblers there) so they get the yummy insects that live there all to themselves
- As conservation was being successful, the population of the warblers increased, following the characteristic sigmoidal curve of population growth which qce bio students would be familiar with.
->For those of you who aren't qce bio students (or haven't covered this yet) in the sigmoidal curve, population growth starts off exponential when the population as small but once the graph starts becoming very vertical, population growth starts slowing down until it becomes asymptotic as it approaches the carrying capacity (K).
- At the vertical-ish bit of the sigmoidal curve there really weren't many territories left compared to the number of birds so - much like millennials  "not leaving the nest" - kids stayed at home  and helped out parents rather than moving out into their own territories.

In other words, habitat saturation (ecological constraint) resulted in cooperative breeding and delayed dispersal.

This is a nice theory, but how about actually getting evidence for this?

Translocation experiment
-There's an island near Cousin island called Aride island which didn't have Seychelle's warblers on it
- Researchers took 16 males and 13 females to Aride island from Cousin's island 
- Helpers only started to be seen only after ecological constraints set it (did this by tracking the number of high quality and medium quality territories - at the start it was only high quality ones but as the amount available decreased birds had to settle for lower quality)

Next, we'll examine evolutionary constraints

- As survival increases, fecundity (number of offspring) decreases
- I.e. there's a phenotypic trade-off where investment in one trait (in this case survival) comes at the expense of another (in this case fecundity)
We can show this relationship with the following formula
Reproductive Value (RV) = Current reproductive + Residual Reproductive Value (RRV)
or basically: When thinking about reproductive value consider both the current reproduction and future reproduction (which will only be possible if the organism invests in growth and survivorship)

If you reproduce a lot early in life, you won't have invested as much in surviving and you'll have reduced ability to reproduce later.

Case study: collared flycatcher (bird found east of Stockholm)

Observation:
Female birds that started breeding at 1 year old had clutch sizes of around 5.9 whereas female birds that started breeding at 2 years of age had clutch sizes of around 6.6

Brood manipulation experiment:
- Adding eggs to some birds nests: artificially increasing clutch size
- The ones given extra eggs in the first year had decreased clutch sizes in later years
- This is evidence that current reproduction decreases future reproduction

Comparative studies:
- When comparing different species there's a clear trend of decrease in body size as fertility rate per year increases
- We can approximate body size as being equivalent to somatic investment - i.e. investment in growth and survival
- Thus reproductive investment decreases as somatic investment increases and vice versa


So far we've been operating under the assumption that each member of a species is going to follow the same life history pattern as every other member of that species that's the same sex, but this isn't always true. There can be distinct life history strategies within the same sex of a species & these are known as alternative reproductive tactics.

Going back to the sockeye salmon you might remember that they are semelparous and males compete for access to females' eggs.
- In this case, (hooknose) males fight each other and literally form a queue behind the female based on who wins
- But some males (jacks) don't play by the rules and try to sneak in
- Jacks are smaller than hooknoses, but at 1 year old (before they differentiate into these two morphs) the fish that will become jacks are roughly the same size as hooknoses - they're not just making the best of a bad situation
- At maturity males want to be either small (jacks, good at hiding) or large (hooknoses, good at fighting); being an intermediate size reduces reproductive success
- if there are lots of hooknoses, you don't want to be a hooknose since the chances of you being at the front of the queue will be slim -> so being a jack is better
- if there are lots of jacks, it's going to be hard to hide -> so being a hooknose is good
- thus, there's negative frequency dependent (disruptive) selection

Next case study: dung beetles
- Two different morphs: small horns and large horns
- bimodal distribution of horn length and normal distribution of body size
- Males with large horns roll dung to the opening of a burrow as a gift for the female in the borrow, and sit under the dung guarding the borrow entrance from other males who want access to the female beetle & her eggs
- Males with small horns dig a tunnel and sneak in under the guarding male (it wouldn't be effective for males with large horns to do this as the large horns would get in the way of borrowing). The small horn males are also smaller in body size which helps


In thinking about life history strategies, we can also consider parental investment in offspring, which is related to the amount of offspring an individual should produce in a given year.

David Lack thought that selection would favour the clutch size which produces the most surviving offspring.

Lack's hypothesis assumes that as clutch size increases, the probability of an individual in the clutch surviving decreases. This makes sense - more siblings to compete with for resources isn't a great start in life. It also holds up when we look at data on European starlings

We take the probability of an individual surviving given a particular clutch size and multiply it by the clutch size to get the predicted number of surviving individuals from a particular nest. This gives us the optimal clutch size. Interestingly there's conflict here between what the parent and offspring want - the parent wants to produce the clutch size which maximises its reproductive value while the offspring wants a smaller clutch size to maximise its likelihood of survival.

Boyce and Perrins (1978) tested Lack's hypothesis by studying 4,489 Great Tit clutch sizes from 1960-1982. (The Great Tit population in Wytham Woods is well studied by Oxford University so there was lots of info available)

When they crunched the data the predicted optimal clutch size was 12ish eggs but the mean number of eggs was 8.53. Clearly, 12 is not the same as 8.53 so something has gone wrong here, or - as it turns out - multiple things have gone wrong.

Here's some additional assumptions of Lack's hypothesis; these ones don't really hold up:
1. No trade-offs between current reproduction and future reproduction - we know this isn't true, remember the collared flycatcher
2. Clutch size only affects offspring survival - not true, it also effects the daughter's clutch size (shown w/ collared flycatchers)
3. No year on year variation in what optimal clutch size is

Another consideration in life history is how much parents invest into the size of their offspring.
in Lack's hypothesis, one assumption is that all eggs are equal size - this is actually a decent assumption for birds

There's a trend in fruit flies and fish (not sure why these were the two examples given but ok) where as clutch size increases egg volume decreases.

You can then take the relationship between number of offspring and size of offspring & combine it with survival probability of offspring based on size to find the optimum size  of offspring in terms of parental investment. This was explored by Smith and Fretwall in 1974

When this is applied to salmon in hatcheries, the equilibrium egg mass is smaller than what's found in wild populations.
« Last Edit: November 10, 2019, 08:52:42 pm by Bri MT »

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Re: Evo eco with Bri
« Reply #5 on: November 08, 2019, 06:59:13 pm »
+7
Topic 3: Evolution of Sex

Before we go into why sexual reproduction exists and there are different sexes, a bit of context is useful.

We can break the tree of life into 3 main domains:
- Archaea (e.g. some chemosynthetic organisms)
- Bacteria (e.g. Thermos aquaticus famous for taq polymerase & cyanobacteria which is sometimes [misleadingly] called blue-green algae)
- Eucarya (e.g. plants and animals)

We can also break organisms into two different groups:
- Prokaryotes (bacteria and archaea) 
- Eukaryotes (eucarya)
[fun fact: archaea is more closely related to eucarya than to bacteria]

There are some differences between prokaryotes and eukaryotes, with the most important one being the prokaryotes don't have a nucleus or membrane bound organelles as a rule. Basically, us eukaryotes like to make different segmented off areas within our cells and prokaryotes don't do that. As you may have guessed, that's not the difference between prokaryotes and eukaryotes we'll be examining in this post.

Prokaryotes  Eukaryotes
No membrane bound organelles  Yes membrane bound organelles
single celled  can be multicellular
big circle of DNA plus plasmids  linear chromosomes
Reproduction is asexual (only)  Reproduction can be asexual or sexual

Before I get too carried away with myself for coding a table in the forums let's move on.

You might then think that sexual reproduction evolved at some point in the eukaryotes, it was clearly superior and thus all its descendants are sexual while those that descended from a different ancestor didn't have such luck and here we are. That isn't the case, and it can't be the case because organisms which reproduce asexually isn't a monophyletic group (i.e. the most recent common ancestor of all sexually reproducing organisms has some descendants which reproduce asexually). This means that sexual reproduction and/or asexual reproduction has to have evolved multiple times.

So why might asexual reproduction evolve? What are the benefits?

Well, consider 2 populations each with four individuals and the difference being sexual vs asexual reproduction. Each generation the (semelparous) organisms have 2 offspring then the parents die
In the sexual one we'll assume even sex ratios (i.e. 50/50 male/female):
- 1 male + 1 female produces 2 offspring, 1 male + 1 female produces 2 offspring  : total of 4 offspring
- now the offspring are parents, process repeats and 4 offspring are produced
- now the offspring are parents, process repeats and 4 offspring are produced

ok, so after 3 generations we still have 4 organisms. cool

What about with asexual reproduction?
- 4 individuals (often classed as females) produce 2 offspring each: total of 8 offspring
- 8 females produce 2 offspring each: total of 16 offspring
- 16 females produce 2 offspring each: total of 32 offspring

after 3 generations we have 32 organisms. I think asexual reproduction wins.

This demonstrates the twofold cost of sexual reproduction. Since the amount of offspring in a sexually reproducing population is constrained by the number of females, this can be described as asexual females producing twice as many daughters as sexual females.

So given that asexual individuals can spread their genes into a population much faster than sexual individuals, why is it that sexual reproduction exists?

There are 3 major ideas around this:
(note: I'm just using these names so I can remember them - I've made them up)
1. Addressing Muller's Ratchet
2. Wisemann's adaptation benefit of 1904
3. Mortiz et.al 1991 & the Red Queen


Before I can explain what these ideas are, you need to understand recombination (i.e. crossing over) - a process which occurs in meiosis.

It goes like this: you have 2 copies of each chromosome - one from each of the gametes (e.g. sperm, egg) which combined to form the zygote that developed into you. When you make/made your gametes, those two copies can cross over, switching alleles (i.e. versions of a gene) and recombing into two new chromosomes with a unique combination of alleles compared to your parents chromosomes.

The benefits of this fall into two categories:
- Removing deleterious ("bad") alleles without getting rid of everything attached to it (addressing Muller's Rachet)
- Increasing genotypic diversity (Wisemann's adaptation benefit of 1904, Moritx et. al 1991 and the Red Queen)

1. Addressing Muller's Ratchet
- Recall that mutations are random changes in DNA
- Most of these random changes will not be beneficial to the organism - and there will be more changes which reduce fitness than increase it
- Over time, these mutations will accumulate (even though selection opposes them - remember that stochasticity/randomness plays a role)
- In an asexual population you can't get rid of these deleterious mutations without removing/killing all organisms with this trait
This is Muller's Ratchet

In a sexual population, however, recombination means that you can chuck the deleterious mutations on one chromosome (which has a 50% chance of being passed down to each of your offspring) thus allowing you to have offspring without the deleterious mutations (and with the beneficial mutations originally on the same chromosome as a deleterious one)

2. Wisemann's adaptation benefit of 1904Mortiz et.al 1991 & the Red Queen
Since we can get all of these funky new combinations of alleles on chromosomes and you have 2 different copies of each chromosome, that more genotypic diversity.

What's good about genotypic diversity? It gives more things for natural selection to act on.

At this point I'm going to split off and focus just on Wisemann's adaptation benefit of 1904

This means that the chance of a beneficial genotype (combination of alleles) existing in the population is increased. In natural selection, the proportion of that genotype is increased in the population across time - benefitting future generations.

This is supported by research showing that sexual strains of yeast had higher fitness than asexual strains when evolving under stressful environmental conditions. There were no differences under benign conditions. (Goddard et al 2005 Nature)

Going back to  Mortiz et.al 1991 & the Red Queen
This is focused not so much on being better but rather on being ok. The Red Queen Hypothesis describes co-evolution where populations need to keep evolving just to not be disadvantaged by the evolution of other populations. (It's named after a conversation between Alice and the Red Queen in one of Lewis Carrol's books where the Red Queen says you need to run to stay in the same place.)

In regards to the evolution of sex, this is focused on parasites. Parasites tend to have a shorter lifespan than their hosts, which means they can undergo adaptive evolution faster than hosts e.g. bacteria often go through 70 generations in just one day. This means that they'll be able to adapt to whatever resistance the host has fast. Therefore, to compensate for this disadvantage, the host wants to make sure that when they do increase their genotypic variation they do it by a lot (more variation = more likely to have lots of new ways of being resistant). Since sexual reproduction creates many novel/new genotypes, this favours sexual reproduction.

A study into a species of Australian geckos (Heteronotia binoei) found that sexually reproducing geckos had fewer parasites than parthenogenetic geckos (Moritz et al. 1991) - supporting this theory.

Note: a parthenogenetic gecko is a gecko that developed from an unfertilised egg.
« Last Edit: November 08, 2019, 10:50:38 pm by Bri MT »

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Re: Evo eco with Bri
« Reply #6 on: November 09, 2019, 12:10:12 pm »
+8
Topic 4: Sex Allocation

Fisher's Principle states that parental strategies should evolve towards equal investment in offspring of the two sexes* and it assumes that both sexes are equally costly to produce

*Two sexes is a simplification when we look at the real world - not everything falls neatly into male or female

The logic of Fisher's Principal is this:
- If you have uneven sex ratios, then the less common sex is going to have better mating prospects than the more common sex
- So, any alleles which encode for a bias towards the less common sex will have a selective advantage
- That/those allele/s will increase in frequency in subsequent generations, and thus the less common sex will become more common
- As the population approaches a 1:1 ratio (perfectly balanced, as all things should be) the selective advantage of that/those allele/s will decrease
- If the 1:1 ratio is overshot read again from the start

If you remember topic 1, you may recall that this is negative frequency-dependent selection at work


How is sex determined:
Like basically all of bio, both heritable and non-heritable factors can influence this.

Let's start off with genetics:
In haplodiploid  species, sex is determined by how many sets of chromosomes an organism receives. e.g. in  the knopper gallwasp Andricus quercuscalcis females have 2 sets of chromosomes (diploid - like humans) whereas males have 1 set of chromosomes (haploid).

However, you're probably more familiar with sex chromosomes being used to determine sex. For example, humans use the XY system where XX encodes for female development and XY encodes for male development, chooks use the ZW system where ZW encodes for females and ZZ encodes for males, and some species use different chromosomal systems such as XO.

Let's now go to environment:
Temperature
Gammarus duebeni uses as system where sex determination is based on the hours of sunshine in a day. More sunshine = more males.  Or, in more technical words, sex is determined by the photoperiod.

Chelonia mydas (i.e. green sea turtle) uses a system where temperature determines sex. This follows a sigmoidal curve, with higher temperatures resulting in more females. From a conservation stand point, this is concerning in the face of global climate change.
(this wasn't the given example but I've got the scientific names of my favourite sea turtles memorised so might as well use that, right?)

Note that the sigmoidal curve is 1 major pattern of temperature dependent sex determination with the other one being a u shape.

Social
Some species change their sex based on the population they're in. For example, in Finding Nemo, we would expect Nemo's dad to become female after Nemo's mum died. Additionally, Nemo's mum would have been born male.

Anti-biotics
Antibiotics can also influence sex determination - in parasitic wasps from the Trichogramma genus at least.
Wasps from this genus which usually display thelytoky (female to female parthenogenesis) swapped to arrhenotoky( unfertilised eggs develop into (haploid) males and fertilised eggs develop (diploid) females) in the presence of antibiotics.

Parasites
Wolbachia is a parasitic bacteria which is maternally inherited. Thus, it's in Wolbachia's interest to have female offspring produced and it biases sex ratios by increasing the relative fitness of females.

sidenote: some people in my course have done cool work with the world mosquito program in using Wolbachia to tackle the spread of disease by a particular species of mosquito (Aedes aegypti)

So if an endosymbiotic parasite can bias the sex ratio, can parents ever vary the sex ratio of their offspring?

The Trivers and Willard Hypothesis suggests that in polygynous species mothers in good condition should produce sons and those in poor condition should produce daughters.
In a polygynous species access to reproductive females is monopolised by one male - meaning that most females will reproduce but many males won't. Thus, any sons will need to be highly competitive and whereas this isn't so much of a concern for daughters.
Note that the population sex ratio should still be maintained at 1:1

Assumptions:
Parental condition is positively correlated with offspring condition (even once the offspring are at reproductive age), and that it's more important for this to be higher in male offspring as opposed to female offspring. Additionally, the Trivards and Willard hypothesis also assumes differences in cost to the mother of producing high quality sons compared to daughters.

A case study in Red Deer (Clutton Brock et al. 1984) supports this hypothesis.

Since Red Deer use the XY system and the ability of the mother to bias the sex ratio is more limited than for species using the ZW system such as Seychelle's Warbler. (Remember XX codes for females and ZW codes for females)

« Last Edit: November 10, 2019, 06:10:56 pm by Bri MT »

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Re: Evo eco with Bri
« Reply #7 on: November 10, 2019, 07:36:17 pm »
+7
Topic 5: Evolution of Aging

Aging seems a bit counter intuitive - surely we should live forever and be able to reproduce forever in order to pass down our genetics as many times as we can?

You might be thinking that evolution didn't want aging and it's just an inevitable result of telomere shortening during DNA replication but a) the role of telomere shortening in aging is less clear now (even though it was thought of as a driver of aging) and b) there are evolutionary reasons for aging. As promised, we'll be diving into those but first, case studies.

Collared flycatchers (Remember this birbs from earlier?)
- There's a linear increase in offspring produced from 1 to 3 years old, and from 3 y/o up until the  5+ y/o category there's a linear decrease (never going as low as the 1 year old rate was)
- Probability of survival is basically constant across all years (there's a decline w/ age but it's not statistically significant)

Red Deer 
Since males & females operate differently in this system (as demo'd in previous post) we'll look at them separately

Males:
- Offspring per year is about 0 until 5 y/o, then follows a hill shape with the max at 9ish years old
- Survivorship is basically constant until 9-10 y/o where it takes a steep plunge

Females:
- offspring per year follows a sigmoidal shape at the start (0-5 years) after which it's basically constant until a gradual decline past 13 y/o
- Survivorship is basically constant until 9-10 y/o where it gradually declines

Drosophila melanogaster if you've done much uni bio I won't need to tell you that these are fruit flies
Drosophila are a favourite for experiments involving genetics an evolution for a fair few reasons and the short amount of time it takes for them to reproduce is one.
- If you do chem their fecundity looks a bit like a Maxwell Boltzmann curve where the reaction is at a low temp.
- Otherwise here's my description attempt: from 0 - 4 days of age their mean number of offspring increases from about 6 to 80-ish. It stays around that level until 12 days and at 16 days old they only produce 65-ish offspring per day. From there fecundity declines and looks like it's approaching an asymptote of 0 offspring/day which is just about reached at 48 days
- The graph of survivorship (only reason to be dying is aging in this graph) looks like the right half of a hill with the flat-ish bit ending at about 16-20 days old.

Homo sapiens ("wise man" -> us, apparently)
- Human maximum performance, as measured by athletic records in running (100m, 1500m & 10,000m), shotput, high jump, and long jumps appears to be highest at 20-something and then curve downwards. (As a 20 year old this isn't great news)
- Human female mortality per year follows a u-shape with death being about 10% likely at 0 y/o and almost 0% at 15. After 40 years old it starts slowly angling upwards and picks up quite fast around 65 y/o onwards Note: this is based on a hunter-gatherer population in Paraguay. In comparison, chimpanzee females also follow a u-ish shape but that cuts off in the 40s while harbor porpoises have a very steep u-ish shape that cuts off at about 25
-Females: offspring per year is about 0 until 15 and rapidly increases until 0.14-ish at 20 and stays around that until the early 30s where it declines. By 60 years old it's 0
-Males: offspring per year is about 0 until the late teens. It around the max between the early 30s and early 40s. It declines like the bottom left quarter of a circle and hits 0 in the late 80s
- Both above fecundity descriptions are based Gems' research in 2014 on a polygynous human population in Northern Ghana

Explaining the trends:
- Natural selection only cares about survival in so far as it impacts reproduction
- So an allele that increases the chance you die before you reach peak reproduction will be heavily selected against
- An allele that increases the chance you die after you've already passed peak reproduction will be weakly selected against
- Natural selection doesn't really act on anything that happens after you've got about 0% chance of reproducing
- e.g. this helps explain why genetic diseases like Huntington's persist

Now you might ask, but why does reproduction decline later in life?
Even if aging doesn't exist, the chances of someone being alive are reduced the further into their future you look due to external mortality hazards. To survive to a late age, you need to have survived every year before that without drowning, being eaten by a bear, being bashed up too bad in a fight, catching the plague etc.
Therefore, natural selection favours early life reproduction - so you can pass on your genes before you die. If a population has higher extrinsic mortality pressures, reproduction will be pushed earlier and earlier. Thus, we would also expect these populations to age faster & have shorter lifespans.

In a study on Drosophila melanogaster (Stearns et al. 2000) evidence was proved for:
a) high extrinsic mortality pushing reproduction earlier
b) high extrinsic mortality leading to the evolution of high intrinsic mortality (i.e. more dying from aging)
I.e. we were right about lifespan evolving via natural selection on reproductive age

As to how ageing evolves, the two main hypotheses are antagonistic pleiotropy and mutation accumulation.

Mutation accumulation  - Peter Medawar
- genetic variation is increased by having new alleles emerge through mutation
- genetic variation is decreased through purifying selection
- selection is weaker as you get older past the ages of highest fecundity
- so, deleterious ("bad") alleles expressed when you're older are less likely to be selected out and thus remain in the population

In other words, deleterious alleles that act late in life are maintained in mutation-selection balance and result in senescence.

Antagonistic Pleiotropy - George Williams
- A pleiotropic gene affects multiple traits
- In this case, there are mutations which are maintained and/or selected for under natural selection because they have a benefit before or during reproductive but the cost of this is increased senescence.
- I.e. aging results from genetic trade offs

Note that one prediction specific to mutation accumulation is that traits should have higher levels of genetic variation as age increases. Evidence for this was shown in D. melanogaster (Hughes et. al 2002). Evidence for an allele influencing both age and fertility (in opposite directions) was shown in D. melanogaster (Lin et al 1998), thus antagonistic pleiotropy (maybe I'll be able to spell it before the exam :P) and mutation accumulation both have evidence supporting them.



Edit: fixed typo
« Last Edit: December 10, 2019, 05:07:26 pm by Bri MT »

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Re: Evo eco with Bri
« Reply #8 on: November 11, 2019, 10:27:32 pm »
+6
Topic 6: Sexual selection & dimorphism

Sexual selection is a form of selection which occurs within one sex due to competition within members of that sex for reproduction with members of the other sex (according to Darwin)

Historically there wasn't all that much agreement on sexual selection.
Alfred Russel Wallace thought that traits used for male-male competition made sense but was critical of the idea of traits being developed for inherent beauty and female mate choice based on that. Darwin emphasised the need for aesthetic taste in animals and was mocked for this pretty widely - Wallace's views were more popular at this time. It was suggested that ornamental traits had evolved to provide camouflage.

In terms of timeline, this discussion was happening from the 1880s to 1950s, after Darwin's famous origin of species and the descent of man had been published (in 1859 and 1871 respectively). In 1903 Morgan made the study of genetics more prominent with research on Drosophila. Morgan suggested 'an interesting fiction' could be made about ornamental traits but that it would be unlikely to be believed and less likely to have evidence provided for it. 27 years later, Fisher - who had a statistics background - published the genetical theory of natural selection. Fisher provided a verbal model The "Runaway": "an interesting fiction" describing how exaggerated traits could evolve.

How the Runaway model works:
- Some individuals have a trait that's expressed in males. Initially, this trait has a selective advantage. It must also have a genetic basis
- There is also a genetic basis for preference towards that trait, with this being expressed in females
- Females with the preference will tend to mate with males with the trait & their offspring will inherit both the preference and the trait (which one is expressed will depend on the sex of the offspring in question)
- Because the trait expressed in males has a selective advantage, the proportion of offspring carrying both the advantageous trait and the preference increases across successive generations
- This is an example of directional selection

As for Morgan doubting that anyone would believe it, from the 1960 to late 1990s the amount of paper published on sexual selection compared to natural selection climbed to be about equal. This was helped by Lande publishing a mathematical model of it the runaway effect 1981 which helped validate it.

So how far will the Runaway run?
One answer is "until the model reaches equilibrium" but that's not very descriptive so:
-It will reach a balance between natural and sexual selection, depending on their relative strengths (the line of equilibrium is more steep as the importance of natural selection increases)
- The strength of genetic correlation between the preference and trait determines the lines of motion. If the genetic correlation is too strong / these lines are too steep, there won't be a stable equilibrium and the trait will "runaway"

Case study: Stalk-eyed flies (Wilkinson & Reillio 1994)
- male eyestalk length is normally distributed
- 3 groups of males were sampled: short stalks, intermediate stalks, and long stalks
- females were sampled randomly
- after 13 generations the preferences of females and the traits of the males were as expected based on Runaway model predictions (except that females in the intermediate group had a preference for long stalks)

~To be continued~

Bri MT

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Re: Evo eco with Bri
« Reply #9 on: November 12, 2019, 02:52:07 pm »
+7
Alright since today is exam day and I'm less than a 1/3 of the way through the course I'm going to leave this post here with key points/areas. If anyone wants me to expand on them lmk and I can, otherwise I'll just pick out topics that I think are most relevant to highschool after my exams are done/

- Allopatric speciation:
-> vicariance (e.g. Alpheus)  vs dispersal (e.g. Drosophila)
- Sympatric speciation:
--> requirements:
---> sister taxa
---> rule out allopatric phase
---> sympatric
---> reproductive isolation
--> conditions:
---> Philopatry (stay in the same area) + assortative mating (mate w/ similar orgs)
---> Discontinuity of ecosystem (e.g. Howea palms  (Savolainen et al. 2006)
---> New range of niches available
----> disruptive selection
----> host switch
----> habitat switch

- Phylogenies
-> Paraphyletic includes ancestor whereas polyphyletic does not. Unresolved -> polytomy
->Parsimony analysis: fewest evolutionary changes. Use any homologous traits + neutral genetic markers ( esp. silent SNP). Bootstrap -> reliability

- Interactions: cooperation (e.g. groupers and moray eels hunting together), selfish, altruistic, spitelful
- Inclusive fitness: consider both direct & indirect.
- Kin Selection: Hamilton's rule  Benefits * Probability an allele is shared > costs  (e.g. pied kingfisher)
- In haplodiploidy: r = .75 for sisters & .25  or .5 for brother-sister  (direction is important).
- costs & benefits also important
- Eusociality: overlap in generations b/w offspring and parent with cooperative care of young and castes of non-reproductive individuals
- reciprocal altruism (e.g. vampire bats sharing blood, cleaner fish)
- Group selection poorly supported (lemmings don't commit suicide)
- multi-level selection: group composition influences phenotype

- synonymous base changes can create changes (but less likely than other options)
- About 10% of human genes are essential. Each of us have about 100 knock outs & 20 cases where both copies of the gene have been knocked out
- Evidence for gene duplication: drosophila salivary glands (Bridges 1936)
- subfunctionalisation and neofunctionalism as potential results of duplication
--> case study: Antarctic zoarcids antifreeze, DNA sequence analysis
-> For a beneficial mutation time to fixation is inversely proportional to s (measured strength of selection)
- Deviations from Hardy Weinberg Equilibrium
--> chi squared test for significance (sum of (obs - exp)^2/(exp))

- Wright-Fisher Model
-> haploid, constant n, asexual, discrete generations, sampling w/ replacement for ne, no selection or mutation
-> Pr(fixation) for a neutral allele is 1/N
-> All neutral alleles eventually fixed or lost
-> Time to fixation dependent on N
-> If s < 1/N then the selective advantage won't be "seen" by natural selection
-> Founders effect case study: Fanconi's Anemia
- U, the genomic mutation rate, is about 100 in humans

- molecular genetic control vs quantitative genetic control
- quantitative traits usually related to fitness, more likely to be adaptive
--> measured through VP (variation through phenotype) = VG + VE
--> VG = VA (additive) + VD (dominance) + VI (interaction/epistatic)
--> h^2 (narrow-sense heritability) = VA/VP    , VA predicts evolutionary potential
--> 0<h^2<1 is based on family studies and estimates the population's adaptive potential
--> Allelic diversity (unlike richness) is not corrected for sample size
--> Heterozygosity is related to the short term ability for populations to evolve


- Long term human Ne (effective population size)  is about 10,000
--> On average in wildlife population Ne = N/10
--> factors accounted for in Ne: sex ratios, changes in population and family sizes, inbreeding, overlapping generations
--> Ne is the harmonic (not arithmetic) mean of previous generations' Ne values
--> Ne/N ratio useful for planning migrations
--> All types of selection more effective at higher Ne

- balancing selection (heterozygous advantage, environmentally dependent, negative frequency dependent, epistasis)

- Demes: subpopulation units defined in absence of panmixia
- landscapes have temporal and spatial distributions, these + natural history or organisms will significantly influence metapopulation structure
- ephermal vs stable structures (Wright's island model (e.g. aphids), stepping stone (e.g. gallwasp invasion), isolation by distance (basically any spp in continuous habitat) )
- Wright's F statistics assume island model + no directional changing
--> Fst: compares allele frequencies across sub-populations. 0 <Fst<1. Low geneflow -> low Fst
-->Fis: compared heterozygosity with HWE expectations -1<Fis<1. Less homozygotes than expected -> low Fis

- Genetic connectivity is highly dependent on Nm (number of genetically effective disperses)
- Demographic connectivity is highly dependent on the relative contributions of dispersers (Nm doesn't influence it)
- Sometimes Fst approximately = 1/(1+4Nm) is used BUT this ignores time and population size which are both important
-Isolation with migration estimates account for Ne and time using a coalescent approach
- Ecological direct methods (e.g. radio-tracking, GPS-tracking) and genetic direct methods (e.g. parentage and assignment tests)  can also be used for estimating dispersal
- linkage disequilibrium is used for assignment testing in STRUCTURE which also clusters genotypes


- Environmental Association Analysis: correlating alleles w/ enviro (and separating results from population history)
- Transcriptome: genes used in tissue of an organism at time of sampling from that tissue
--> can be used to analyse responses to pattern of seasonal changes shifting (e.g. phenology not keeping up with anthropogenic climate change)
- correlative vs mechanistic modelling of species distributions (e.g. Aedes aegypti)
- Breeder's equation R=h^2 * S limited by generation, conditions of measurement & type of variation
- Regulatory genes are primary drivers of rapid adaptive evolution
- Mitochondria can be highly involved in evolution, including through mitochondrial-nuclear interactions


Erutepa

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Re: Evo eco with Bri
« Reply #10 on: December 04, 2019, 12:42:14 pm »
+6
Unfortunately those last couple posts slipped under my radar and I missed them when they were posted so I am a bit late on the reply.
Thanks for sharing this evo eco content - I have personally found it very interesting to read both becuase of the content itself but also due to the rather engaging way you lead us through the topics. While I did get lost occasioanlly on a bit of content, overall I think you did a great job of breaking the topics down. The case studies were particularly interesting for me - when learning evolution in unit 3/4 bio I think I didn't give as much attention to learning examples and looking for proof of different evolutionary ideas which is something I think is not only important but makes the content a bit more meanigfull.

I think that this thread would have been a great resource to have while studying 3/4 bio. While bits of this evo eco thread are within the course and help reinforce such content, I think the most valuable thing I got out of this was adding depth to my fundamental understanding of how evolution works and how to go about talking about it. Hopefully next year's bio students can discover this thread and use it to compliment and improve their understanding of evolution.

Interms of what else I'd like you to go over from the list, the things that jumped out at me mostly were the things that i have read a bit about, but don't really grasp all that well. These are:
 - sympatric speciation
 - Interactions (particulalry altruism and about how group selection is poorly supported)
 - how synonymous base changes can create change and the evolutionary explanation for why we keep all this 'non essential' DNA around
 - mitochondrial-nuclear interactions in evolution

There were alot of things in that list though that I just completly didn't understand haha. So if there are anythings that you are particulalrly passionate about I would love to hear them.
Don't feel obliged to explain the above things I have listed though.
Thanks again for putting in this effort!
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Bri MT

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Re: Evo eco with Bri
« Reply #11 on: December 10, 2019, 02:38:31 pm »
+4
Unfortunately those last couple posts slipped under my radar and I missed them when they were posted so I am a bit late on the reply.
Thanks for sharing this evo eco content - I have personally found it very interesting to read both becuase of the content itself but also due to the rather engaging way you lead us through the topics. While I did get lost occasioanlly on a bit of content, overall I think you did a great job of breaking the topics down. The case studies were particularly interesting for me - when learning evolution in unit 3/4 bio I think I didn't give as much attention to learning examples and looking for proof of different evolutionary ideas which is something I think is not only important but makes the content a bit more meanigful.
Thank you! I'm glad to hear it :)

If there's anything you're still lost on & would like clarification please let me know.

Yeah, even when I did the old VCE bio study design they focus on knowing multiple lines of evidence (e.g. transitional forms in the fossil record) but don't cover experimental evidence.

I think that this thread would have been a great resource to have while studying 3/4 bio. While bits of this evo eco thread are within the course and help reinforce such content, I think the most valuable thing I got out of this was adding depth to my fundamental understanding of how evolution works and how to go about talking about it. Hopefully next year's bio students can discover this thread and use it to compliment and improve their understanding of evolution.
I hope so! I'll likely be making evolution content for QCE & since that goes more in-depth than VCE it should be useful for VCE students too.

Interms of what else I'd like you to go over from the list, the things that jumped out at me mostly were the things that i have read a bit about, but don't really grasp all that well. These are:
 - sympatric speciation
 - Interactions (particulalry altruism and about how group selection is poorly supported)
 - how synonymous base changes can create change and the evolutionary explanation for why we keep all this 'non essential' DNA around
 - mitochondrial-nuclear interactions in evolution

There were alot of things in that list though that I just completly didn't understand haha. So if there are anythings that you are particulalrly passionate about I would love to hear them.
Don't feel obliged to explain the above things I have listed though.
Thanks again for putting in this effort!

- Sympatric speciation I can definitely explain (I'll go through a variety of mechanisms for it)
- Altruism I'll be able to go into a fair bit (we actually had an exam question on kin selection & inclusive fitness). There's not too much for me to say about group selection, it's mostly just that individual selection pressures are too high.
- Some of this I can already cover but I'll also do some extra research because imo it's really interesting
- Yep, will do :)

No worries!

This post is basically a placeholder to say I will get around to addressing these & haven't forgotten :) 

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Re: Evo eco with Bri
« Reply #12 on: December 10, 2019, 04:38:12 pm »
+6
Wow, I didn't even know that evolutionary ecology was a thing... But this is all super duper interesting, and I can't wait for unit 4 biology so I can learn more about topics like inheritance and evolution.

Thank you for sharing this! I'm feeling very excited about all of these new ideas I can potentially talk about in my research investigation next year :)
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