phylogenetics

i accidentally wiped most of my notes here sorry

• eukarya: nucleus, cytoskeleton, and organelles
• ophisthokonts: fungal and animal kingdoms incorporated; ophisthen, behind, and kontos, short/pole/pike; single flagellum insertion in the ef1a gene
• animals: collagen, extracellular matrix, and tight junctions; see tissue notes

these notes are from the revisiting of phylogenetics on feb 7. that being said, many of them are reviews of what was touched on on the initial phylogenetics lectures

• reminder that phylogenetics intends to create monophyletic groups which possess the most parsimonious line of assumed evolution
• useful tools for constructing phylogenies:
  • fossils (didn’t… i take notes on this for the textbook…) (yeah.)
    • but unicellular organisms and things that lack bones, shells, or hard structures are difficult to preserve via fossilization
    • transitional fossils: fossilized forms which show intermediate body forms between ancestral and descendant taxa that lived at points in time that are separated by a large period of time
      • useful in macroevolutionary study
      • these link taxa; gradualist, transitional forms
      • predicted by Darwin: if evolution by natural selection is valid, there must be intermediate forms → first found: archaeopteryx (links reptilia and aves)
      • they possess traits from the ancestral taxa and traits that predate the future descendant taxa
      • examples: archaeopteryx (reptilia and aves), cetacea (vestigial pelvic/ankle bones. theyre related to hippo and ungulates… how…)
  • homologies, a subset of shared traits that are shared as a result of a common ancestry
    • “fine-scale taxa” → narrowing to species under genera: shared ancestral vs shared derived characteristics; this is not homologies
    • homologies are broader: ie tetrapods (a superclass) — these are structural, developmental, or genetic
      • tetrapod bones and an ancient lobe-finned fish with homologous tetrapodic bone fins → structural homology
      • embryonic shapes and characteristics in vertebrata → developmental homology
      • dna sequence similarities in eye control genes → genetic homology
• mistakes and sources of error popular in phylogenetic work:
  • can’t (shouldn’t more like) be based on one gene; use multiple genes to show evidence of parsimonious evolution
  • most likely two are reversals of state and convergent evolution (homoplasy and analogous characters)
  • reversal of state: the first descendant of an ancestral taxa has a modification of an original trait, but the second descendant has the original trait
    • A → B → A structure
    • examples: frogs and Gastrotheca guentheri frog teeth
    • take into account other genes and traits which may show that a phylogeny possesses a reversal of state; G. guentheri’s ancestry can be shown by comparisons to an intermediate form of modern frogs vs. the ancestral
  • analogous characters (homoplasy): similar characters that evolved independently of one another as a result of natural selection in similar pressure environments, not common ancestry
    • example: wings in insects, bats, and birds; the bird and bat’s forelimb bones that construct part of the structure of the wing are a homologous character (they are both tetrapods), while the wing structure itself and how it is shaped around the bone is an analogous character
    • example 2: comb-like filter feeding structures in baleen whales and flamingos; this is analogous because other reptilians and mammals do not have similar filter feeding structures. these were not derived from common ancestry, but because of similar selective pressures and competition for food
    • formal definition of convergent evolution: independent evolution of similar traits (analogous characters) in distantly related taxa due to adaptation to a similar way of life

emergence of modern evolutionary theory and natural selection

• charles darwin: “father” of modern evolutionary theory; lived in england, dominated by western christianity conventionalism (church of england)
  • hms beagle 1832-1836 naturalist, galapagos (oceanic)
• manuscript received from alfred russel wallace; scientific paper by arw about indonesian/SEA observations
• joint presentation of identical conclusions + publication of darwin’s manuscript
• separate systems evidence
  • speciation from ancestors, nodes, taxa; no fixed species
  • changes occur when a mutation/variation in a population is reproduced
  • merit of “success” by genetic reproduction; beneficial versions are typical
  • heritable traits and incremental frequency (gradualism/uni)

homology

• different species with similarities in the same geographic area; distinct but similar species → shared ancestry
  • Nesomimus parvulus, Nesomimus trifasciatus, Nesomimus melanotis, Nesomimus macdonaldi
  • why would you have similar but slightly different distinct on the galapagos and not many vastly different species
• homology shared by different species: a type of similarity shared among taxa due to common ancestry
  • structural, genetic, developmental: three levels
    • 1. structural: bones, physical properties, bodily plans
      • vertebrate forelimbs (tetrapods vs. )
        • humerus, carpals, metacarpals, phalanges, distinct human limbs and distinct use; these distinct bones and body plan/patterns (one bone, one bone, many smaller bones) also seen in other tetrapods (frog, bat, porpoise, horse, dolphin, whale, crocodile) but with different functions and different appearances
        • vestigal structures: modern functionless remnant structures (tailbone in humans, pelvic bone and femur in whales and snakes) that had an ancestral use
          • why does an organism have a useless structure that would not have been acquired? debates concept of perfect form
    • genetic (molecular level)
    • developmental embryonic, signs of evolution
      • similar embryos for cat, frog, fish, human, chicken embryos; they are different after maturity, but not in early development
      • why do embryos look like that esp similar vs. perfect form; dissimilarity in maturity
      • parsimonic explanation: common ancestor → branching out caused dissimilarity, but embryonic form was retained based on luca
      • retained gill pouch and tail in chordata embryos (chordata pharyngeal gills); 5 parts of chordata?
  • taxa: any named group regardless of organizational level
  • shared by common ancestry or shared ancestry; each group shares the ancestor who possessed the trait
    • ancestral trait; new descendant branches inherit the characteristic with some modifications
    • not everything has to be different or new; something is in common with the ancestor
  • ancestor, phylogenetics, contrasting old thought
• homologies can compare evolutionary history and similarity of taxa/sister groups
  • human/chimpanzee similarities ~99%, same order; vs human/rabbit, same class; vs human/tunafish, same phylum; vs human/riceplant, same eukaryota
    • 0 vs 8 vs 20 vs 37 differences in cytochrome c amino acid structure
  • degree of similarity/difference between taxa → estimate how long ago taxa shared a common ancestor; see phylogenies and evolutionary track lengths

natural selection

• collection of separate ideas and significance of other influences on darwinism
  • geologists
    • gradualism – james hutton
    • uniformitarianism – charles lyell
    • the earth is older than 6k years and has had millions of years to accumulate incremental geological change
      • applied to evolutionary change
      • underlying hereditary principles emphasized this
  • population dynamics
    • “an essay on the principle of population” treatise – thomas malthus
      • human populations exponentially (geometrically) grow vs agricultural resources grow linear (arithmetically) → class division viewpoint, struggle for survival (when was this written?)
      • leads to population dynamics, carrying capacity, birth/death rate; concluded that maximized reproduction level was limited and not achieved due to natural factors (lack of resources, disease, production)
        • idea of fitness; some organisms do not reproduce and pass heritable traits onto offspring
• descent with modification → evolution
  • natural selection, fitness and success, reproduction, offspring and hereditary traits, gradual change in lineage and diversification, common ancestor

artificial selection

• a control(?) process to compare against natural selection
• selective breeding (dogs, pigeons, plants) for desirable/subjective traits → diversifies extant breeds in a single species; variation increases for heritable traits
• darwin barnacle/plant/pigeon breeding; vs natural selection
  • in artificial selection, people’s subjectivity decides variation and fitness; in natural selection, nature’s subjectivity decides variation and fitness
• a whole ass chapter in origin of species
• provided experimental results validating natural selection and proof of occurrence of natural selection

criteria of natural selection

• what criteria are necessary for natural selection to act on a trait? → what criteria are necessary for evolution by natural selection?
• detailed, necessary terminology, proper understanding of natural selection; thorough, not basic
  • lord help me
• four main criteria; 1-2 pair with one another, 3-4 pair

1. natural selection must act on a single phenotypical trait which possesses variation within a population
   • nature can only act on what it sees?
   • ex. variation in mammalian fur color
   • may be categorical (distinguishable), continuous (gradated), but must exist
2. must be a heritable trait; must have genetic basis
   • must have a genotype that can offspring inherited from parents; valid mechanism for heredity (compare to acquired characteristics)
   • preceded mendelian genetics
3. not all individuals in a population have equal “fitness”
   • malthusian population dynamics; limited by arithmetic growth of available resources
   • struggle for success and fitness: predation, disease
   • fitness is reproductive success: what is the frequency of alleles in the next generation of offspring
   • fitness: how long do you live, how many offspring can you have, and how many can survive; cumulative
   • overproduction of offspring in generations — basic biological fact (birth vs. death rate of any population)
   • not a static, categorical hierarchy of success; continuity in how many offspring each individual who reproduces has and how many survives; not just a y/n metric
   • relative fitness
   • this is meant to be broad but i’m not gonna lie dude this is pretty specific
   • formal definition of fitness: number of surviving fertile offspring
     • “an individual’s genetic contribution to the next generation”
     • fitness is specific to the concept of natural selection and reproduction… nature vs. artificial selection… please be normal and don’t use this to justify eugenics… lol…
4. a particular phenotype and individuals with the given phenotype must have a higher relative fitness than those with different phenotypes
   • natural selection must result from variations in fitness which result from variation in phenotypes

• when all four criteria are met, natural selection culminates in evolution
  • the more relative fit phenotype results in the reproduction of more fertile offspring who inherit the genotype that results in the phenotypical trait. this phenotype is “beneficial” and occurs at incremental increasing frequencies with each given generation.
  • all of these criteria can coalesce/synthesize into a single summarizing paragraph which proves natural selection culminates in evolution rather than a checklist
• natural selection is the driving mechanism behind evolution
• occurrence of natural selection which results in evolution is at a population level
• gradualistic and uniformitarianistic

key concepts

• natural selection acts on an individual level, not on a population or species level
  • example: hanuman langur, india;
    • troops (resident males) vs. satellite males
    • infanticidal behavior among individuals; change in hormones, change in availability of ovulation and relative fitness in a short amount of time
    • in this case, aggressive infanticide amongst male individuals is a phenotypical behavior which promotes relative fitness
      • this is the most insane fucking sentence to read out of context
      • genetic basis which promotes likelihood of infanticidal behavior
• the results of natural selection show at a population level
  • there is no evolution within individuals; genotypical evolution is not individual, but shown through the frequency of populations
  • natural selection acts on the individual
• natural selection only acts on phenotypical variation which is already present/extant in a population
  • if a more relatively fit phenotype is not present in a population, it cannot invent a new rate for it; it cannot invent the trait; it only brings out traits present in the population already
• natural selection leads to the evolution of adaptations: adaptive evolution
  • hardy-weinberg evolution mention
  • natural selection is one of many mechanisms that affects evolution, but it is one of the only ones which results in adaptive evolution
    • genetic drift is random and chance; natural selection is based on the “~fixed” metric of fitness
    • adaptation: a trait that enhances fitness in a specific environment
      • white fur of polar bears vs. black, brown, etc. of grizzly and non-arctic bears due to increased fitness with camouflage
      • black skin and color reflection/absorption
      • hollow hair shafts; air space heats inside shafts with body heat (warm-blooded) and traps heat; wrapping of hot air in a cold vs hot environment
      • adaptive evolution improves survival within an environment in which a population evolves

selected examples of natural selection

peppered moths

• you Already know…
• polymorphic british moths; one gene, two-allele system: black or grey (peppered)
  • AA/Aa black vs aa pepper
• nocturnal; diurnal motionless surface dwellers; vulnerable to predation via birds
• morph color distribution skewed after 1800 (predominant grey) to ~1900 (98% black) due to production of environmental coal-induced smog/soot//pollution via the industrial revolution (1750-1850, esp. 1840s)
  • soot landed on grey lichen on black bark tree surfaces and suffocated lichen
  • change in survivability on a population level → change in relative fitness on an individual level
    
    agent of selection: who/what causes a difference in relative fitness within phenotypical variation
  • possible variations:
    • humans
    • soot
    • birds
  • has to be most direct cause of relative fitness (birds determining survivability by predation and consumption; killing moths directly)
  • try identifying process/effect of natural selection and agent of selection in a provided example

antibiotic resistance

• you also kinda already know ……………
• bacterial infections: pneumonia, pinkeye, impetigo, etc.
• take entire course of antibiotics as directed
  • course will kill first most vulnerable, then eventually all but some resistant individuals
• phenotypic variation in an antibiotic population of heritable natural resistance to the human drug by random chance
• overuse → evolution of dangerous strains that are antibiotic-resistant: tuberculosis, mrsa skin infection; resistance to 3+ drugs, impossible to treat
• no use in flu, viral infections
• agent of selection in this case is antibiotic; effect → increase in antibiotic resistant bacteria in population, directional select

forms of natural selection

1. directional selection → one extreme end is more frequent in the population due to better relative fitness
   • all previous examples of natural selection
2. stabilizing selection → the median gradation is more frequent in the population (the average) than either extreme; must still have less variation in the population, will look narrower
   • distribution of birth weights in human babies; selective pressure enforced by extreme birth weights leading to increased vulnerability to complications, especially before technological developments; heritable trait of birth weight
3. disruptive selection → both extreme ends are more frequent in the population than the median
   • uncommonly called diversifying selection (textbook says disruptive)
   • african seedcracker finches and their ability to crack different types of seeds (lower mandible width and length; disruptive selection in width and even length for those who survived)
4. sexual selection → dimorphism; covered in textbook
   • might fall under directional selection, but is determined by sex and attraction
     

hardy-weinberg equilibrium model

• evolutionary model which discusses when evolution is occurring vs. equilibrium
• solid definition for evolution: any change in the genetic structure of the population (allele and genotype and phenotypic frequencies); phenotypic frequencies result from allelic and genotypic freequencies; generational change
  • allelic frequency: f(A) vs f(a)
  • genotype: f(AA) vs f(Aa) vs f(aa)
  • phenotype: f(gray) vs f(black)
  • remember that individuals don’t evolve, populations evolve
• frequency: (number of actual times of event occurrence) ➗ (number of times event could have occurred)
  • sum of all frequences must equal 1.0!!!!!!!!!!!
• hw derived this model separately of one another similar to darwin/wallace

basic model: conditions of equilibrium

• hwem is a population model consisting of null hypotheses: evolution is not occurring if all 5 conditions are met (equilibrium) vs. occurring if any conditions are violated (evolution)
  • brief overview of five conditions for background context; only context needed in detail after determining calculations and how to use model
  1. must have a large population size
     • must have a reduced likelihood of genetic drift occurring
     • genetic drift: allelic frequencies shift due to chance, not a specific mechanism of evolution
     • at length
  2. mating in relation to the trait studied must be random; no sexual selection/artificial selection?
  3. no gene flow between populations; must be within one population across generations
  4. no mutations shifted the allelic frequency
  5. natural selection must not inform the trait
• in a study of microevolution under hwe, this is regarding a specific, singular trait or a locus on a gene and whether or not it is undergoing evolution

large population size

• as population size increases, the chance/effect of genetic drift decreases
• see below

random mating

• no artificial selection based on trait or sexual selection based on trait; it can be artificial/sexual based on another trait, but not the trait being studied
• two scenarios that occur where mating is directional with regard to the trait:
  1. positive assortative mating: mating where one mate chooses a mate with an identical phenotype of the studied trait
     • always results in evolution in genotypic frequencies and increased homozygosity (disruptive sexual selection?) without changing allelic frequencies
       • allelic frequencies do not change because there is no agent of selection eliminating the alleles in the population; the alleles are simply being paired in non-random ways
     • compare to negative assortative mating
  2. negative assortative mating: mating where one mate chooses a mate with a different phenotype of the studied trait
     • the “foils” of evolution (i am escorted out of the classroom)
     • in an “ideal” situation, results in evolution in genotypic frequencies and increased heterozygosity (disruptive sexual selection?) without changing allelic frequencies
     • in many cases, results in evolution of both genotypic and allelic frequencies
       • consider a situation with more than 2 phenotypes when all individuals sort under negative assortative mating. this is the we know the devil of evolution where one is left behind while the other alleles can continue on (i am escorted off canvas)

gene flow

• gene flow: when an individual leaves a home population and reproduces in another population; the introduction of new alleles into the gene pool of another population (ecosystem? or would this work if multiple populations of a species exist in one environment? is that even possible 🤔)
• in a population which exists in equilibrium, one is studying a closed population
• gene flow has a small effect on the migrated population and a large effect on the immigrated population: it always changes allelic frequencies and has a high chance of introducing new alleles, which will change genotype frequencies in turn (so it always changes allelic and genotype frequencies)

mutations

• no mutations may occur at the locus where the trait occurs in equilibrium
• mutation is always going to change allelic frequencies most likely through introducing new alleles
  • it’s more likely that an allele will mutate into a novel allele rather than into a pre-existing allele in the population (ie A not → a, but A → another allele)
  • this is just a constant. you always have to have this as a given for equilibrium or the lack of (evolution). any presence of mutation will always cause evolution
• note that mutation is a very rare event in reality and almost never occurs in microevolution; it may be a 1/1mil chance in zygotes at a single gene
  • note that microevolution is for single generation studies or even up to a thousand studies; you would need to study macroevolutionary time scales in order for mutation to become a significant factor
  • however, on a macroevolutionary timescale, mutation events are the only way to introduce a new allele (leading into a new trait) into a population; mutation events are more likely to happen and have an incremental, but important (accumulative, gradualist) effect over millions of generations

natural selection

• the tl;dr of this is just it violates the definition of equilbrium/satisfies the definition of evolution
• allele, genotype, and phenotype frequencies can change under natural selection
• natural selection (shrugging) idk what to tell you

modular calculations

• requires knowing something about genetic structure of population via obtaining field research genetic data: know allele frequencies (→ expected genotype frequencies → phenotype) or actual observed genotype frequencies (→ allele frequencies → compare
• alleles have specific variables
  • p (lowercase): dominant allele
  • q (lowercase): recessive allele
• two methods of calculating phenotypic frequencies
  • you must know the frequency of either the genotypes or the alleles in the population (gathered through observational data); otherwise you cannot calculate for equilibrium
  1. calculating genotypic frequencies from allelic frequencies
     • prout square
       • simulation of random reproduction at a population level vs. punnett square
       • resembles punnett square, 2x2
         • horizontal is all possible eggs in gene pool (1.0 sum frequency)
         • vertical is all possible sperm in gene pool
         • intersections are all offspring genotype expected frequencies
     • simplified formulas:
       • p^2 + 2pq + q^2 = 1.0
         • p^2 = exp f(YY)
         • 2pq = exp f(Yy)
         • q^2 = exp f(yy)
     • these result in expected phenotypic frequencies under equilibrium
       • compare these to observed frequencies; if not, there is conclusion of evolution
  2. calculating allelic frequencies from genotypic frequencies:
     • allele frequencies calculated are observed; compare to expected frequency (would be expected from parental generation if evolution is not happening)
     • counting method
       • n = # individuals in the population; placed as a variable
       • based on observed numbers of frequency, not calculated
         • ie obs f(YY) = 0.49, obs f(Yy) = 0.42, obs f(yy) = 0.09
         • 0.49*N times the number of alleles present in the genotype which are being observed (ex. if studying Y, then times 2)
         • sum of all occurrences divided by 2N = frequency of allele (f(?)) in population
         • p = dominant, q = recessive; p+q=1.0
         • 0.09*2N + 0.42N = 0.18N+0.42N= 0.60N / 2N = 0.30 f(y)
• the observed frequencies are calculated, which are compared to the expected frequencies respective to the data
  • the expected frequency is derived from the previous generation, ie the parental generation to the f1 generation, in order to determine if the generation remains in equilibrium
    • comparing allelic frequencies: observed were 0.7 and 0.3 (from the previous example), expected → parental generation allelic frequencies (0.8 and 0.2)
      • in this scenario, the allelic frequencies were gathered and used to calculate the expected phenotypic frequencies first
      • compare meaningfulness via the chi square test: sum of (o-e)sq/e
        • in the allelic case, the frequencies should be converted to whole numbers: you might multiply times n, where n= the number of individuals in the population (eg n=100)
    • comparing genotypic frequencies: genotype were 0.49, 0.42, 0.09, expected are the genotype frequencies
      • compare meaningfulness via chi square as well; multiplying times n
• common mistake made: observed genotype frequency = p^2, so sqrt o = p
  • this cannot be done if the population is not in hardy-weinberg equilibrium
  • squaring the observed frequencies will give another observed frequency for the alleles
  • observed may not be equal to expected (which would occur if population is undergoing evolution)
  • basically just never square the values given of the observed genotype frequencies unless you already know it’s in equilibrium (maybe submitting a proof?)
  • need to use the counting method to determine true allelic frequencies from observed genotype frequencies
  • what is expected under ideal equilibrium conditions is unequal to what is observed when natural selection or other evolutionary trends are acting on a population

genetic drift

• another mechanism of evolution
• under genetic drift, allelic frequencies in a population change due to chance
  • compare to natural selection, where there is an agent of selection acting on the population
• a brief overview of probability: the likelihood of an event to occur
  • the observed frequency of an event is likely to approach or represent the given probability when this event is tested for many times in a large sample size
  • however, in a small sample size, probability and observed frequency often do not match up
    • this is just the result of and explained by chance; even if they do match the expected frequency, the chances of that occurring in a small sample size are infinetismal
  • probability is synonymous with expected frequency, while observed frequency will differ
    • probability is in this case sort of comparable to the expected frequencies under equilibrium that were calculated under hwem
• taking only a small sampling of the alleles in a population gene’s pool for reproduction (aka having a small gene pool or a small population size) will distort the allele frequencies across generations; the random sampling will not represent the expected allelic frequencies (the “probability”); this represents genetic drift
  • what if you only took 10 alleles from a population of thousands, and those represented the f1 generation? the allelic frequency in the f1 generation could be drastically different from the parental all due to chance, or what 10 alleles were sampled from the parental generation.
  • this is specifically known as sampling error
• a formal definition of genetic drift: allelic frequencies chance across generations solely due to chance
  • compare this to natural selection: frequencies change due to relative fitness, while in genetic drift, they only change by chance!!!!!!!!!!
• genetic drift will always exist in a real population; however, the smaller it is, the more likely it is to happen and the more likely it is to be important in determining the evolutionary trend of a population.
  • genetic drift only cannot occur in a population that is infinitely large; you can sim this, but it does not exist in reality (carrying capacity etc etc etc)
• genetic drift is caused by:
  1. chance resulting from sampling error
     • again, this is most likely to occur when the population size is small.
     • consider endangered and vulnerable species which are chronically small
  2. population bottlenecks
     • a population bottleneck is a phenomenon that occurs when a a large population is drastically reduced in size: specifically, a population bottleneck is the sharp reduction and alteration of the population’s gene pool resultant from the presence of very few survivors of a cataclysmic, reductive event
     • below image sums up the difference between bottlenecks and natural selection below
     • 
     • below depicts a population bottleneck graphed on the size of a population
     • 
     • examples in real life: northern elephant seals, antarctic blue whales, american bison
  3. founder event
     • a small sample of a population leaves that population and migrates to create a new population; it’s really similar to gene flow in concept, but also totally different :3
     • also known as a founder effect, but easier to comprehend as a founder event
     • examples: migrated offshore island populations, Amish communities (polydactyly)
  • note that in all cases, due to being occurrences of genetic drift, there is a large element of chance; however, population bottlenecks and founder events are phenomena that, while caused by a specific event, culminate in a small population size and genetic drift that results from chance
• genetic drift often, but not always, results in the loss of genetic variation (see bottlenecks)
• genetic drift can also lead to genetic fixation; but notably, it may lead to fixation of harmful alleles
  • natural selection promotes alleles that benefit the population, but it does not wholly eliminate harmful alleles
  • this just feels like “what if your rng in ffxiv was really bad” actually…

biological classification

• three overarching domains: bacteria, archaea, eukarya
  • these replace kingdoms in modern classifications (plantae, animalia → developed into animalia, plantae, fungi, bacteria, monera)
    • five-kingdom system is now obsolete
  • two domains are prokaryotic; one (eukarya) is eukaryotic
• linnaean classification — carolus linnaeus
  • “nested hierarchy”: levels and smaller groupings
  • traditional five-kingdom system broke down into:
    • phyla
      • class (porifera: hexactinellida, calcarea, demospongiae) (chondricthyes, osteichthyes, mammalia)
        • order (carnivora, cetacea, chiroptera)
          • family (canidae,)
            • genera
              • species
• the species is a distinct group in phenotype from another species within the same genus
• in modern day, the classification system implies taxonomic evolutionary relationships
• taxon: literally just any named group