evolution week 1

fact of evolution

forms of life change over time, via descent with modification

theory of evolution

the characteristics of a population are most strongly influenced by the individuals who leave the most-viable offspring.

adaptive evolution

the increase in frequency of beneficial alleles and decrease in deleterious alleles in a population due to selection

adaptive evolution pathway

mutation + inheritance (variation) + population growth (competition and selection) → adaptation → diversification + phylogeny

HIV

RNA retrovirus with the fastest mutation rate of any virus or organism observed to date

implications of HIV mutation rate

AIDS vaccines unlikely to work; HIV evolves more quickly than humans can create new drugs

HIV infection

retrovirus with 2 ssRNA genomes; proteins bind to host T-cells and use reverse transcriptase to replicate RNA → DNA. DNA is inserted into host genome, and the host cell creates virions. HIV attacks macrophages and T-cells

HIV acute phase

early infection with high viral load (0-12 weeks)

HIV chronic phase

later infection, lasting from months to year, with moderate viral load

AIDS

late infection where immune system completely breaks down, leading to organ death

AZT: azidothymidine

thymidine mimic which causes HIV reverse transcriptase to get stuck and impede viral replication. Eventually fails because AZT-resistant mutants eventually occur and flourish

AZT natural selection

in the presence of AZT, natural selection favors reverse transcriptase enzyme mutants that recognize AZT and not use it; slow and careful selected for

evolution by natural selection

random mutations → heritable → selection → adaptation

diversity of life: science

natural explanations, phenomenon; diversity of life on Earth is the result of naturalistic processes

diversity of life: philosophy

purpose of life; existence of a deity; diversity of life on earth is the result of a deity

agnostic

Thomas Henry Huxley: “we shall not say we know or believe that which we have no scientific grounds for professing to know or believe… we know nothing of what may be beyond natural phenomena”

evidence for evolution

patterns change through time; patterns indicate common ancestry; consilience (the interlocking casual explanation across disciplines - geology, physics, chemistry)

Before Darwin theory of special creation

independent origin of all species; all life created on Oct 26, 4004 B.C

microevolution

species change over time; evolution within a species

speciation

lineages split and diverge

macroevolution

new life-forms derive from older forms

common ancestry

all life forms are related

vestigial organs

organs with no apparent function (e.g. tail, appendix, wisdom teeth in humans); (pelvic bone in whales); (kiwi wings); (python hips); (loss of digits during bird development)

vestigial DNA: pseudogenes

remnants of genes that don’t get transcribed

fossils

any trace of an organism that lived in the past; offers evidence of macroevolution

Law of Succession

correspondence between fossils and living organisms from the same location

what do we expect to see in the fossil record?

1. youngest should be similar to living species

2. early life simple, complex species after time

3. cases of evolutionary change within lineages

4. transitional forms: we should see splitting of lineages

transitional forms

evidence of change in progress

evidence of common ancestry

1. nature forms a tree of life: “groups within groups”

2. homology (developmental , molecular

3. convergent evolution

4. developmental homology

5. the central dogma (all have the same components (nucleotides, ribosomes, etc)

6. chirality (left-handed used for AAs, but right-handed would have worked too)

7. shared genetic flaws

8. nested sets of pseudogenes

homology

similarity due to descent

convergent evolution

independent evolution of similar features

analogy

non-homologous, similarity due to structure and function

structural homology

used for different functions

developmental homology

ontogeny recapitulates phylogeny; hypothesized ancestral features revealed during development

molecular homology

all organisms use essentially the same genetic code, similar genes across organisms; different codes would have been good for escaping from pathogens; the central dogma; chirality

consilience

interlocking of casual explanation across discipline

consilience with geology

1. relative dating of fossils: depth gives relative age

2. laws of superposition: younger rocks on top

3. gaps are common: cross-dating can be used

consilience with physics and chemistry

radiometric dating: only works with volcanic rocks; dates layers between fossil beds; isotope decay; begins once magma solidifies

evolution definition

1. descent with modification

   1. change in allele frequencies in a population

natural selection definition

differential reproduction of heritable phenotypes; only one of several processes that cause evolution

how to turn a wolf into a chihuahua

1. start with a population of wolves that have varying sizes and shapes

2. select wolves that are smallest, or look at least a little like a chihuahua

3. breed only these “chihuahua-like” dogs

   1. continue until you have a chihuahua

artificial selection

selecting individuals with certain genes; increase frequency of one allele, remove other

phenotypic variation is caused by…

genetic variation

evolution by natural selection

1. competition due to limited resources

2. individuals within a population are variable

3. some of this variability is heritable

4. individuals vary in ability to survive/ reproduce

5. the survival/ reproduction is nonrandom - individuals with favorable traits do better

population growth

geometric

food supply growth

arithmetic (at best)

what gives rise to adaptation?

the struggle to survive

Darwin observations of population growth

1. the tendency of all species to over-reproduce

2. if more are born than can possibly survive, there must be competition to see which individuals will get enough resources to keep themselves alive

Darwin’s postulates

1. is the population variable?

2. is the variation heritable?

3. is there variability in survival/ reproduction?

4. is survival/ reproduction nonrandom?

oscillating selection

1. there is no “ultimate” goal of evolution

2. selective pressures can vary or change over time

what evolves? populations or individuals?

populations

the 4 postulates in modern genetic terminology

1. because of mutations creating new alleles, and new allele combinations due to segregation and assortment, traits are variable

2. individuals pass alleles to offspring intact (heritability)

3. individuals vary in ability to survive/ reproduce

4. individuals with favorable alleles (and allele combinations) survive or reproduce better (natural selection)