Change in Allele frequency in a population over time

1. finding and describing biological diversity

2. understanding the processes that shape the diversity

1. how many species

2. how are they similar or different

3. variation within species

4. how are they related

1. how do organisms come to fit their environment

2. what limits diversity

3. origin of novel traits- how

-retrovirus (RNA as genetic material)

-viral replication- retrotranscription (RNA to DNA)

-blocks retrotranscription of HIV

-interfere with enzyme active site

-work then not work in the long run

-1000 fold increase of no effect in 2 years

-when stop AZT- decrease in HIV resistance

1. population- heterogenous pool of virions

2. variation- highest mutation rate ever observed b/c error-prone retrotranscription (at least one have retrotranscriptase enzyme that works when AZT is present)

3. heritable- AZT resistance passed on

4. survival and reproduction- host immune response, rate of replication, ability to invade host cells (AZT overwhelmingly determine survival of certain HIV)

1. % resistant to AZT increase over time

2. AZT strong selective pressure (rapid viral evolution)

3. evolution come at a cost- resistant virions less fit overall

1. occurs in a lot of animals and is usually harmless

2. in sootey mangabeys- no disease but in chimps- SAIDS

1. the science of inferring historical relationships and evolutionary histories of species and populations

2. comparing viral gene sequences

- from SIV

- multiple origins: HIV-1 from chimps and HIV-2 from mangabeys

-coherent group of propositions that can be used to explain a class of phenomena

-broad and unifying conceptual framework that coherently explains diverse observations

-tentative explanation to an observation, phenomenon, or scientific problem that can be tested by further investigation

-used to evaluate the accuracy of a theory

-something that has actual existance

-used to test hypothesis

-interpreted in the context of theory

if theory is supported by overwhelming evidence- it's treated factual

ex. earth flat/geocentric orbit of sun around earth both proved wrong after repeated tests of theory

ex. evolution is factual

1858: Darwin and Wallace = evolution and natural selection

1859: Darwin publish origin of species by means of natural selection

1. change is due to operations of natural law

2. progressive change from simple to complex

3. new simple organisms created by spontaneous generation

4. mechanism of evolution- inheritance of acquired characteristics

1. created at the same time, created separately by God, immutable (never change)

2. social unrest- industrialization, urbanization, authoritarian, conformist

1. natural law (organic and inorganic org.)

2. complex from simple; simple from simple

3. descent with modification- all descend from one or few original species

4. natural selection

Change through time:

- Domestic species (wild to domestic)

 -Natural populations  

-Vestigial organs 

- The law of succession

-Transitional forms

Common ancestry:

- homology: structural, embryology, molecular

-change makes a phylogenetic tree

soapberry bugs in Florida

-balloon vine (native) vs. golden rain tree (invasive)

-beak length change after invasion (long to short)

-conclusions: species not immutable, diverse descendants emerge from one

- organs w/o function

ex. snake "legs", whale back "legs", wisdom teeth, appendix

- in fossil record

-new species continuously appear throughout strata

-fossils laid down in layers in order of when they existed (deeper is older)

-fossils remains of living organisms

-The kinds of animals and plants found as fossils change through time. When we find the same kinds of fossils in rocks from different places, we know that the rocks are the same age

fossils that are intermediate between older taxa and living species

ex. archaeopteryx lithographica- theropod dinosaurs to birds evolution

1. structural - tetrapod limbs have similar skeletal structures despite divergent function

2. embryology- embryos of dissimilar adult species look similar

3. molecular- universal genetic code, Hox genes code for body patterning early in development: anterior-posterior expression order conserved across species; humans duplicated hox genes

-malthus theory essay on the principles of population

-food supply increase linearly, population exponentially

-population exceed food eventually

1. variation in population

2. heritable variation (phenotypes)

3. survival and reproduction vary among individuals based on heritable qualities FITNESS(therefore more animals are born than will survive)- fight for survival begin when population meet resources on malthus' graph) FITNESS

4. selection not random- more favorable trait dominate surviving population

(change in composition of population is evolution by natural selection)

- nonrandom differences in survival and reproduction of heritable phenotypes in population

1. show us natural selection

2. show us speciation (species multiply)

&

1. 1977 drought of Isla Daphne Major

2. seed abundance plummet

3. seed characteristics change (large and hard)

4. population crash of finches

proportional contribution of an individual's genes to future generations

1. survival

2. reproduction

3. quality of offspring

4. environment

- individuals not species

-existing traits

-phenotypes (evolution=change in genotype)

-nonrandom

-fitness is not circular

-short-sighted

-not lead to perfection

1. shared derived characters =monophyletic

2. taxa related by descent from a common ancestor

3. relationship drawn in a tree

-shared derived

-determine monophyletic groups

-symplesiomorphy

-autopomorphy

-shared ancestral

-derived character only in one taxon

-plesiomorphic

-apomorphic characters

-outgroup- ancestral

-ingroup- monophyletic synapomorphies

similarities that result from factors other than common ancestry (environmental)

-character similarity resulting from independent responses to similar environment ex. green tree boa (new guinea) and green tea python (south america) both arboreal and green and coiled

-hierarchical method of naming

-species is the most fundamental unit of biological classification

-ecosystem function not understood without characterizing species

-mitigation of biodiversity loss requires species identification

-economical importance ex. phytophthora ramorum (sudden oak death by parasite of previously unknown species)

1. every grouping is a clad (monophyletic)

2. names involve characters that represent that

group

3. evolutionary transition can be represented

4. we can reconstruct the tree

1. classification and naming

2. molecular clocks

3. forensics

4. biogeography (study of where organisms occur and how they came to be there) ex. pangaea

5. ancestral human relationships

6. adaptation

1. a trait modified by selection that (evolutionary history of change)

2. enhances survival and adaptation of an animal (existing variation) compared to another that doesn't have the trait

3. a trait that arises repeatedly and independently in association with a similar selective force is probably caused by that force (homoplasy)

4. convergent evolution, parallel evolution, and homoplasy support adaptation

-phylogenetically independent contrasts

-group size and testes size correlated by looking at sister taxa and comparing their group size and testes size

-if lineages diverged to have different group sizes- do the testes sizes show a positive correlation with the group size?

molecular: same genetic code (codons), nucleic acids, DNA, RNA, similar proteins as enzymes, shared biochemical pathway (ATP as source of energy in all organisms)

cellular: all have cells, all cells have similar cellular components (cytoplasm, membrane bound, chromosomes, ribosomes)

LUCA (life)= (bacteria + (archaea +eukarya))

eukarya= chromalveolates + rhizaria + plantae + excavata + unikonts

-shared characteristics of bacteria and archaea (not monophyletic)

-no nucleus or membrane bound organelles (chloroplasts and mitochondria)

-morphological: limited (cocci, bacilli, spirilla)

-diverse nutritional metabolism: energy=photo(light)/chemo(inorganic chem)

carbon source=hetero(organic)/auto(co2)

ex. most prokaryotes chemohetero

1.binary fission(asexual, mistakes in DNA rep=variation, otherwise no variation ok in stable environment)

2. conjugation (lateral transfer of genes using f factor in plasmid)

3. phage conversion (using virus)

4. transformation

-contain peptidoglycan

-gram +/- staining where +=cell wall outside, -=cell wall between outer and inner membranes

-autopomorphy for bacteria

1. spirochetes - helical & motion, teeth, biofilm, modified flagellum

2. chlamydia- STD

3. cyanobacteria-photosynthetic, nitrogen fixers (heterocysts with no photosystem II), internal membranes

4. proteobacteria- metabolically diverse paraphyletically

1. acidophiles

2. methanogens (obligate anaerobes)

3. halophiles

-all have nucleus

-all have membrane bound organelles (mitochondria and chloroplasts and plastids)

-alveoli

-photoautotrophs

1. alveolates

a.ciliates (2 nuclei, aquatic, cilia),

b. unnamed taxon of

-apicomplexin (apical complex malaria) and -dinoflagellates (cellulose, 2 flagella equatorial and posterior, tertiary endosymbiosis of chloroplast, red tides)

2. stramenopiles= 2 unequal flagella one with tubular hairs

a. brown algae (fucoxanthin, secondary)

b. diatoms (silica cell wall)

-ventral feeding groove

1. unnamed group= reduced/lacking mitochondria

a. diplomonad = no mito., 2 nuclei, intestinal parasite

b. parabasalid= anaerobic, STD

2. unnamed group= mitochondrial cristae disc-shaped

a. euglenid= pellicle under plasma

b. kinetoplastids= kinetoplast (big mitochondrion)

-filose pseudopodia

1. foraminiferans=calcareous test

2. radiolarians

1. phylogenies= group by synapomorphies to derive patterns of common ancestry

2. fossils= geological (relative dating) and biological (evidence of ancient life)

-dissected shark's head

-sufficient similarity

-object in rock looked like it was alive- maybe it was alive; if it was alive then the hard rock was soft sediment

1.superposition= younger on top, older on bottom

2. original horizontality=layers deposited horizontally and then deformed to various latitudes later

3. lateral continuity= layers assumed to have continued laterally far from where they currently end

4. cross cutting= whatever cuts across a layer came after the layer

-geological cycle

-world is old

-even the oldest rocks made up of materials from the ruins of former continents

-assume physical law is constant in time and space

-geology is not scientific unless can explain geological observations using modern physical processes

-use known modern processes to explain ancient patterns (present is key to past= uniformitarian)

-modern rates of change may not be representative because catastrophes can happen

-timescales of multiple fossils

-ex of biostratigraphy= scallops at chesapeake bay

-radiometric clocks

-half lives (parent to daughter isotope ratio)

-use igneous rocks

-assumptions= no other forms of decay, no daughter at t=0

-fossils are the basis

-began to be used in present form since 1830

-hard parts

-modes of preservation: original material (most info), mold and cast (surface features), traces, impression (carbonaceous film), mineralization

-must avoid degredation (buried quickly)

-no oxygen

ex. marine environment more favorable

-lagerstatten: particularly well preserved

ex. archaeopteryx late jurassic limestone solnhofn/ cambrian burgess shale marine preserve soft parts

-transitional forms: only direct evidence of descent with modification

-extinct taxa

-past morphologies and developmental pattern

-past diversity patterns

-past environment

-first appearance of fossil- minimum date for phylogenies

-deep time and evolution : tempo (rate) and mode(pattern)- pretty ambiguous

anagenesis vs cladogenesis

implications of anagenesis applied to cladogenesis

-rate of evolutionary change within a lineage

-rate of divergence (change between lineages); speciation

-if evolutionary change is in the anagenic mode, then rates of evolution = rate of anagenesis

1. morphological = mean value of character through time, can change at different rates within same lineage, no correlation between molecular-genetic- and morphological rates of change

a. transitions and gaps at a finer temporal scale

b. expected gradualism (Darwin) vs. punctuated equilibrium (stasis interrupted by rapid periods of change (cladogenesis))

c. stasis- why? 

2. taxonomic= origination and extinction rate, duration of taxa

-allopatric speciation

-dispersal (population move to another place) (peripatry), and vicariance (population split)

-peripatric speciation= rapid change punctuation

-stasis is data

-between speciation= stasis (lack of change)

-stabilizing selection (explanation)

-environmental tracking (implication)

-constraint (explanation)