Organic Evolution Exam 1

Plato Ideologies of Evolution Vs Aristotle

Plato: Interested in the ethereal, theoretical world (Essentialism), all things have an essence, an idea

Aristotle: Interested in the real world (eternalism and empiricism), what can actually be observed and manipulated

Both believed that life and nature was balanced, life arises from non-life (spontaneous generation)

empiricism and eternalism (aristotle’s ideas)

empiricism: all concepts are based on what can be felt and observed

eternalism: things have no beginning or end

Aristotle was all about believing in only what you can see and observe, looking for patterns and explanations

Aristotle Soul rankings

1. Vegetative Soul (plants)

2. Sensitive soul (animals)

3. Rational Soul (humans)

Lucretius

Began many nature experiments stating that organisms that adapt best to their environment have the best chance of surviving, BIG contrast to modern thought on the subject

Believed that new species were not formed, nature randomly generated many different kinds of species and those who were better survived and those are that which exist now

Stenos Theory of Superposition

• All minerals were originally in solution and gradually settled out of the ocean and created horizontal layers with new ones creating at the top of older ones

• as rocks formed, they could trap animal remains and convert them into fossils

Linnaeus

• interested in classification and identification rather than explanation, was was a firm believer in the fixed world (things never changed because then they would be different than what god created)

• Created the Linnaean system, grouped things based on shared characteristics

Lamarck

• coined the term biology

• believed that classifications were false but useful

• THEORY OF TRANSMUTATION : simple organisms arise by spontaneous generation from nonliving material and have innate power that can adapt them to their environment in response to changes in the environment

  • these characteristics are then passed to offspring

immutable

things are unchanging through time or unable to change

Dawrins Observations from the Galapagos

1. some animals were similar to animals on the mainland but different in species and each island had its own separate species

2. some species were only on the island and no where else

3. animals seemed adapted to a particular way of life

Darwin slowly began to be convinced of inorganic evolution, life changed overtime organically

Wallace Observations

• he begins to notice that many species are well adapted to fit their environment

• concludes that environments are placing some pressure on species and forcing them to adapt in order to compete for resources

Darwin Vs Wallace

Darwin places more emphasis on sexual selection. Those more likely to mate will pass on their traits and genes to more offspring

Wallace places more emphasis on adaptability to environmental pressures, a species better fit will survive (survival of the fittest)

Darwin and Wallace Observations

1. members of a species show variation in morphology and physiology

2. offspring have the same variation as their parents

3. organisms have the physical capability to produce more than they do and the environment changes throughout time

Overall: The environment cannot support everyone, some better fit the environment and those survive and reproduce in numerous amounts, the environment can change at any time, and what is favorable changes

There is NO scale of nature, organisms look the way they do because they adapted for that place, nature is not in balance

Gene Vs Allele

Gene: specific nucleic acids on a chromosome that code for a specific outcome

allele: the different versions of that gene

Mendel’s Laws of Inheritance

1. law of segregation: gametes carry only one of the alleles for each gene

2. Law of independent assortment: genes for different traits must be passed independently

3. Law of dominance: one allele has a stronger signal than the other

Mutationism and Hopeful monsters theory

• mutationism: a sudden single mutation rather than natural selection produces a brand new species

• Hopeful monster theory: a massive mutation occurs and leads to a new species, and just maybe its helpful for survival (super unlikely because two random mutants would need to be beneficial and survive together to reproduce)

Gene Pool, Allele Frequency, Genotype, Phenotype

Gene pool: all the genetic material in a population

Frequency: how often they show up in that pool

genotype frequency: frequency of homozygous dom, hetero, and homo rec.

phenotype: dominant versus recessive phenotype

allele frequency: amount of A or a in the total population

Hardy Weinberg Equilibrium

Under certain ideal conditions, allele frequencies will remain constant from generations in sexually reproducing species if the following conditions are met

1. random mating

2. no mutations

3. population so large that changes in frequency aren’t impactful

4. all individuals survive and reproduce equally

5. no migrations in or out of the population (no gene flow)

p+q=1

p²+2pq+q²=1

If a population does not meet hardy weinberg’s equilibrium, then it is not under ideal conditions and is evolving

Gene flow or migration

• the movement of alleles into or out of the population, thus altering the frequencies

• Impacted by

  • mobility→ can the species move

  • territoriality→ do they want to remain within that area

  • transversability → how walkable is the environment

Avenues of Gene flow (three basic types)

corridors: avenues of a favorable environment, allows movement back and forth for organisms between areas

filters: favorable avenues for dispersal for some, but not all

Sweepstakes: those are rare or accidental routes of dispersal over a major barrier , but those that land in this environment generally find unexploited habitats

while gene flow can provide variability into a species, it can also introduce mutations and rare alleles , a trade off!

Genetic Drift

• also known as sewall wright effect is the change in allelic frequency by random chance (super unpredictable events)

  • example of gene drift: random sampling of gametes through meiosis

• Drift is unbiased (it is random), and its impacts are felt more in smaller populations

• Bottleneck effect: when only a small number of individuals from the original population survive changing the allele frequency at random

• most genetic drift explained by neutral mutations that have no impact so are just passed to offspring and cause drift

random walk process

• alleles can become fixed just by chance in any proportion , there is no discernible pattern or trend

founder effect

• occurs when a few individuals become isolated from the original population and settle in an area without previous species, and the founder allele frequency can be different than the larger parent population

Disassortative vs assortative mating

• mating with a different phenotype

• mating with individuals of the same phenotype

Both have consequences, but disassortative increases genetic variability while assortative will decrease genetic variation. it may be better in either case

Impacts of inbreeding

1. strong female-based sex ratio

2. loss of heterozygote meaning more recessive phenotypes are likely to reappear

Basic structure of genes

1. enhancer/silencer

2. promoter

3. open reading frame

Open reading frame

• span of genetic material that is used to produce a protein through transcription and translation

promoter

• a region of DNA that initiates transcription of a particular gene, transcription factors can bind to promoter to enhance transcription

enhancer/ silencer

• can enhance or suppress gene transcription

synonymous codons and stop codons

codon triplets that code for the same amino acid

stop codons: codons that cause the sequence to stop being read and terminate

Luria-Delbruck fluctuation test and mutations

showed that mutations in bacteria occur randomly before exposure to a challenge. Different bacterial cultures developed very different numbers of resistant bacteria, showing that some mutations happened earlier and were passed on to many descendants. This proved that the environment selects existing mutations rather than causing bacteria to mutate because they need to survive.

Mutation Effect on each part of gene

ORF: alters the product, changes reading frame

Promoter: if or how the gene is read

Enhancer: how much is made

Mutation classifications

1. object: where it happens

2. causes: why it happened

3. consequences: how does it impact gene expression

strand mutations

strand: finest levels, affects individual bases on the DNA strand

• point (single base change)

• Transitions (switch between purines only or pyrimidines only

• transversions: switch between purines and pyrimidines

point mutations that cause no change are called silent mutations

Missense : can be conservative or nonconservative, changes amino acid

nonsense: stops the protein early

chromosomal mutations

• major mutations in chromosome morphology and counting and have significant impact

polyploidy: having three, four, or more complete sets of chromosomes instead of two present in diploids (somewhere the entire genetic code got copied)

aneuploidy: presence of an abnormal number of chromosomes in a cell

1. inversions→ a gene is rotated and inverted within a chromosome

2. translocations→ the location of a piece of chromatin is changed in or between chromosomes

3. unequal crossing over: leading to deleted or duplicated segments of genes and can cause new functions

DDT and biomagnefication

increases in concentration as you go up a trophic level, leading birds to produce fragile eggs and all start to die off, they were not naturally selected for against DDT and reproduced more slowly than insects

selective pressure is on the INDIVIDUAL but success is measured by the POPULATION

Biological fitness

• the reproductive success if a biological entity , the ability to leave offspring in a population

• measured by ability to survive to reproductive age, number of offspring produce by female function, number produced by male function

intrasexual selection versus interselection

intra: fighting physically for mates, its direct competition

inter: indirect competition by showing off

fisherian selection

• female selection traits and male attribute traits will be inherited together and this could lead to more extreme female preferences and male attributes as new mutations occur because genes are inherited together

• “chicks dig it” so it happens

4 types of selection in genetic systems

• selection against the dominate phenotype

  • the dominant allele is lethal or not as beneficial and will eventually be removed from the population, can be one or multiple generations

• selection against the recessive

  • even if the recessive is lethal or not selected for, the heterozygote still has the recessive allele and it will most likely never leave

• selection against the homozygotes (overdominance)

  • alleles must be codominant or incomplete dominance, the heterozygote is better so both alleles are preserved → balanced polymorphism

• selection against the heterozygote (underdominance)

  • the fitness of the heterozygote is worse, all three genotypes still continue to be produced, but the allele in lowest numbers is eventually removed

Variability

• gene variability limits the rate of evolution

• variation comes from:

  • gene migration

  • mutation

  • random mating

  • gene drift

• only natural selection leads to adaptive evolution. new variations arise by chance, and then beneficial ones are sorted out

• Natural selection acts on PHENOTYPE NOT GENOTYPE

what factors impact phenotype

• polygenic traits

  • a trait is controlled by multiple genes that can combine in different ways to produce a result . all the alleles must have incomplete dominance

  • because of independent assortment and additive effect, some are more common than others

directional selection

directional: phenotypes at one extreme die, and the other extreme is preferred and shifted towards (black and white butterfly)

stabilizing selection: both extremes are unfaired and intermediate is favored , common in stable unchanging environments

diversifying selection: favors both extremes and intermediate fails, results in polymorphisms (beetle example )

epistasis vs pleiotropy

epistasis: one gene masks the output of another separate gene

pleiotropy: one gene controls several other traits

• antagonistic pleiotropy: it can positively affect one trait, but negatively effect another (p53 kills cancer cells but can harm stem cells)

clines

cline: the pattern of genotypes and phenotypes over a geographical range

steep: each geographical area has its own unique adapation and phenotypes

smooth cline: phenotypes from environments are not super unique so vary subtly

Biological Species Concept

• Organisms that are able to reproduce(interbreeding) with each other, and not with any other organism are considered to be the same species

  • Problems: some organisms reproduce asexually, some organisms are dead and not possible to observe, and some organisms are able to interbreed (hybridization) even though they are not the same species

Hybridization

• two distinct species are able to reproduce offspring called hybrids in a hybrid zone, which is a zone in which the two species locations mix introducing contact for potential mating

Morphological Species Concept

• organisms are in the same species if they share similar morphological traits in common (an observable feature between them)

  • severely ambiguous because organisms can share similar traits for many reasons and still be different species (monarch butterfly vs non posinuous form, dogs, ants in different casts)

  • sexual dimorphism→ males and females of a species have distinct looks

Ecological species concept

• organisms that develop in the same niche are members of the same species (adapted to a specific set of resources)

  • problems: niche is so objective, and some can be in the same environment but not be remotely similar

Genetic species concept

• a species is a set of individuals with extremely similar or identical genetic sequences

  • used mainly for prokaryote workers

Natural Kind Versus Artificial Kind

• Natural kinds are a natural grouping, instead of an artificial one. A specific property that distinguishes it from all other groups (like protons for elements)

Two categories of reproductive isolation

1. pre-zygote (before a zygote can form, prevents mating)

2. post-zygote (after a zygote is formed→ it is either not viable or infertile )

Mechanisms for pre-zygote reproductive isolation

1. ecological→ the environments don’t interact so the organisms are isolated from each other

2. temporal isolation→ time isnt on their side, they may mate at different times

3. behavioral isolation→ organisms behave in different ways that limit interactions (songs of grasshoppers)

4. structural isolation → the anatomy of the species makes it impossible to mate

5. gametic isolation → the gametes of one species is not compatible with another , they cannot come together to form a diploid cell

6. gametic mortality→ the environment kills the gamete of the partner

Mechanisms for post-zygotic isolation

1. hybrid inviability & sterility→ the hybrid does not reach reproductive age or is sterile

2. hyrbid breakdown→ the hybrid isn’t viable after the first generation

3. zygotic mortality→ the zygote isn’t viable due to chromosomes and dies off

processes of speciation

• anagenesis or phyletic speciation

  • linear, changes are gradual in species over a given time period until the species is distinct from its ancestor

  • cladogenesis → the original lineage splits into new forms creating a branching pattern

3 different categories of cladogenesis ****

• allopatric or geographic isolation

  • populations become separated by a physical barrier. This results in them developing a genetic difference that distinguishes them

  • can be vicariant (a species with a large distribution is divided by a newly arising barrier, they are directionally selected for) or peripatric (part of the original populations on the periphery of the range get isolated, and gene flow is blocked creating differences over time) Genetic Drift

• parapatric→ no physical barrier but the individuals decide not to mate randomly preferring geographic neighbors to individuals in a different part of the populations range

  • needs an environmental cline, hybrids selected against in the hybrid zone, two different forms mate only with others of their own type

• sympatric: same land, something happens that sets them into two different reproductive groups (could be polyploidy, random changes in chromosome number or sexual selection) fly example ,

  • autoploidy→ extra chromosomes from the same species

  • polyploidy→ extra chromosomes from different species

Patterns of Speciation

1. convergent : organisms from different ancestors develop similar traits due to shared environments

2. divergent: descendents become more and more different from each other over time

3. parallel: organisms from the same ancestor develop similar traits like their shared ancestor