processes that are happening on earth today also happened in the past and will continue in the future. present is the key to the past.

opposed to catastrophism/ neptunism that says earth was shaped by punctuated great catastrophes, more biblical

• superposition- older rocks are underneath younger
• original horizontality- rock layers originally laid down horizontally/ flat cuz being laid down by a water process
• cross-cutting relations (usually in intrusive igneous rocks)- intrusive rock younger than what its squeezing thru, faults also younger
• included fragments- included are older

easily distinguishable, widespread, over short geological time span, abundant

used for:

"fossil correlation" or biostratigraphy= can tell certain rocks are same age if they have same index fossils in them, can be used over wide areas esp when extinctions

whole body fossils 

preservation of hard parts

petrification

molds and casts

trace fossils (also called ichnofossils- things left behind other than organism itself like footprints or coprilites)

chemical traces (oxygenation of earths atm)

whole body fossils can be mummified, frozen, bog specimens, amber

hard part preservation could be permineralized or petrified

casts and molds are impressions on sediment

trackways

research

exploration

funding and permitting

collection and transport

preparation and replication

measurement and data collection

research and publication

greatest complete fossil of a TRex

illustrates property rights and permitting issues in regard to collecting fossils, especially very rare and special ones

• continents fit together like puzzle pieces/ pangea
• distribution of plants and animals
• hot spots (movement of coeanic islands) and location of earthqakes and volcanic activity
• sea floor spreading= movement (rock record can record magnetic pulls from poles and flips)

convergent

divergent

strike-slip

hot spots that dont move but the islands do as they move with plates

hawaiian are at subduction zones and are explosive cuz hot water turning to extremely hot steam

yellowstone is explosive cuz big thick heavy crust on top so it cant do anything until it gets a small opportunity and by that time the pressure is hugely built up. granite spreads out magma

recycled crust= young, hot, bouyant

subduction= compression= pressure

water gets trapped and becomes really hot steam that builds up pressure

juan de fuca (northern)

and

cocos plate (lower)

stretching of inland basin and range putting eastward pressure and causing uplift

or

portion of subducted plate "peeled" off- shallow subduction = young, hot, bouyant plate

San Andreas

plate went from convergent to strike slp

the thickening and then stretching of crust and then uplifting- bands of mountains (17 mya to present)

this led to

colorado basin, death valley, rocky mountains, and sierra nevade range

1. individuals vary within a pop (no two individuals are exact same)
2. more individuals are produced than can survive
3. variation influences the survival and reproduction of individuals (some will do better than others- competition)
4. and if variation in features is heritable there will be evolution

the variation of individuals from mutations is random

the selective part (which traits are best for surviving and reproducing) is determined by environment and nonrandom)

descent with modification (small changes in gene frequencies in micro can add up to big changes in deep time of earth; evolution works on pops, not individuals)

macro is micro writ large

all evolution is genetic at basic level

ecology is interactions between organisms with each other and their environment, links organisms thru flow of energy

evolution in natural world is a reaction to ecology

evolution gives depth of time to ecology and links organisms via genetic information and shared ancestry

fitness is the relative ability of an individual to survive, reproduce, and propogate genes

selection acts on fitness of individuals to cause changes in average fitness of pop

sexual selection is a subset and has to do with individuals competing for mates- affects ability to pass on genes to next generation so characters not necessarly good in environment can be selected if they help get mates like peacock tails

example of direct observation of evolution and how it illustrates steps of natural selection:

industrial melanism

peppered moth- spread of melanic (darker) form during industrial revolution

in 1950, kettlewell tested pollution hypothesis and found strong support for impact of moth color on susceptibility to bird predation

1958 UK passed a clean air act; 1963 US

moths vary in color pattern, subject to predation, variation affected survival, variation is heritable

example of direct observation of evolution and hot it illustrates steps of natural selection:

malaria control and DDT resistance

malaria infects approx 250 mil per year and kills 1 mill per year

DDT is a chemical that kills mosquito pops but also bad for environment esp for birds

overtime, mosquito's susceptibility to DDT declined

they got more resistant as surviviors reproduced

those few mosquitos that were resistant at beginning (variation in pop) were ones that survived and passed those good traits down (heritability)

like appendixes and tailbones- not useful anymore but not bad so just get smaller generation to generation, not necessarily go away cuz they dont affect survival

are homologous

biogenetic law

"ontogeny recapitulates phylogeny"

ontogenies are development and growth of an individual from zygote to adult and usually involve unequal growth of same parts relative to others

development of organism repeats in concise from the evolutionary history of species

right- organisms during development often show characteristics that are reminiscent of their early evolutionary history (in beginning, our embryo will look similar to embryo of an ancestor)

but

wrong- development doesnt show every single stage and isnt exact (in pictures of embryos, you wont see every single ancestor)

similarity in form between distantly related species as a result of adaption to similar environments

has to do with plate tectonics as diff niches are filled with diff species on diff continents

same ancestry but diff niches= diff adaptations

most fossils of extinct organisms can be classififed into groups of existing organisms (they share similarities due to descent with modification)

observed difference between living and extinct forms become greater as you go back in time

flora/fauna currently are always intermediate between past and future

transitional forms (missing links) are found in fossil record

Cope's rule

lineages tend to evolve larger average body sizes over time (not always true)

Red Queen Hypothesis

predator and prey evolve in tandem just to keep up with each other

there are often evolutionary adaptive races and Cope's rule is a consequence of that so since they are competing to evolve/ survive, everything is getting bigger (possible, not certain)

DNA is the ultimate shared primitive/ ancestral character and in all living things, uses the same code

HOX genes- same in all organisms- instructions for basic body plans are evidence of common ancestry (where to put head and feet, etc)

we all have it and we all have the same code- good evidence for common ancestry

we can also use DNA to look at genes of orgnaisms and species with similar genes are probably related to each other

gives mechanism for inheritance

highest form of reality is not what we see

allegory of the cave

reality is a form that we cannot observe but rather shadows and reflections of reality

there is an essence for all forms we see (in a species, not two individuals are exact same)

everything we see is modeled after one perfect/ ideal form for each thing and we never see this

this is a way to explain variation within species- we are seeing imperfections

he knew extinction was a fact but disagreed with transmutation and evolution

thought fossils appeared abruptly in rock record and then disappear

he didnt believe in deep time cuz of mummified cats and humans- used as examples of fixed species

Hutton- uniformitarianism (evolution not catastrophism)

Malthus- pop growth is not infinite and is checked by earth's resources which are finite (important for natural selection cuz not everyone can survive)

Lyell- geologist that thought about deep time- so many processes happened so long ago and everything we see came from one single cell a long time ago (shared ancestry/ heritability)

Linnaeus

established binomial nomenclature with genus and species name and 3 kingdoms

based on anatomical differences, more concise and accurate than any methods before

cut tails of 900 mice and bred them but their offspring still had tails so it appeared that manipulation was not passed down

developed germ-plasm theory: inheritance only takes place in germ cells

hereditary information moves only from genes to body cells, and never in reverse

has implicationsin our understanding of evolution as it would imply that species arent nearly as separable genetically as we once thought

mutationist theory from Futuyama: new species originate via large-scale rearrangements of the genome- big cuz shuffling of genome- didnt have mechanism for this yet

new species arise out of large scale random occurences.

idea of hopeful monsters- whatever the mechanism of inheritance was, it was from random shuffling and most of the time not good/ failed but every now and then you'd get lucky and a good new species came out

mutation of a really big scale

pangenesis: tiny hereditary particles called gemmules transmitted parent to offspring, formed by cells and aggregated in reproductive organs

allows for lamarckian evolution

countered ideas of blending inheritance

Mendelian inheritance was compatible with gradual natural selection

continuous variation (observed and measured by biologists) could be the result of discreet genetic entities (as postulated by mendel)

law of dominance:

dominant allele is expressed, recessive allele is not, when both are present

law of segregation:

every diploid individual possesses a pair of alleles for a given trait. each parent passes only one copy to offspring (selected at random)

law of independent assortment:

alleles for different traits are inherited independently. in other words, genes sort randomly and independently during gamete formation

one gene affects several different traits

compliment of this is polygenic inheritance:

many genes affect one trait

DNA replication

(double sided DNA unzips and replicates)

transcription of DNA to mRNA

(creation of RNA from one unzipped side- tells it to start and stop)

translation of mRNA to protein

(coding from RNA into things like amino acids using codons- each amino acid has a 3 base codon and the code is redundant)

polymerase

p is frequency of dominant allele

q is frequency of recessive allele at particular locus

p and q are percentages and always add up to 1, or 100%

a statement of how allele frequencies relate to genotype frequencies (they are constant/ in equilibrium) under certain conditions

conditions include:

random mating, large pops, no migration, no mutation, no natural selection

consanguinity tends to increase change that alleles are common by descent ie more homozygous

leads to inbreeding depression: loss in fitness due to mating with close relatives and results in reduced genetic diversity

change in allele frequencies just due to change, which is an effect of limited sampling with each generation- by chance, pops can lose certain alleles over generations

affects small pops more than large cuz they already tend to have less diversity, makes them more susceptible to random events

founder effects and population bottlenecks

how do they relate to conservation of endangered species

applied to founding pops, it is an unrepresentative sampling of the original pop due to change because of small pop

loss of variation= loss of fitness= lower reproductive rates and higher juvenile mortality

2 ways new alleles can enter a population

migration

when pops move and mix it tends to increase diversity, when they move they bring their genes with them and spread them thru new areas resulting in clines. gets out of extinction vortex. gene flow happens during this and increases diversity

mutation

since most of genome doesnt code for proteins, the probability of deleterious mutations is even lower. nevertheless, humans do carry some genetic load- the number of deleterious alleles that would be harmful if homozygous. redundancy/ degeneracy in genetic code. mutation is ultimate source of variation for evolution to work with

stabilizing- intermediate phenotype is most fit

directional- one extreme phenotype is most fit- pushing toward one end or the other 

diversifying- two or more phenotypes are more fit than the intermediate between them. select for extremes- might lead to separation

these all tend to be at micro level but can lead to big things

partly driven by genotype of individual (genes)

but also environmental plays into it

ex: tall but malnourished

also interactions between environment and genotype or other random effects due to noise in system

taxonomy is the classification of species based on anatomical similarities and differences

phylogeny is the study of evolutionary relationships among groups of organisms

phylogenetic trees let us visualize patterns of common descent, putting taxonomy into an evolutionary context

1. fossils- rarely used as sole source of data because so much is many organisms have no hard parts, conditions needed for fossilization are relatively rare, erosion, tectonics, etc destroy fossils, many are buried where we have yet to find them
2. comparative anatomy- most commonly used to build phylogenies prior to relatively cheap and easy molecular methods. organisms grouped by shared morphological, behavioral, or physiological characteristics
3. life-history traits- particularly useful for invertebrates, where the adult stage of life is often dramatically different from larval stages
4. molecular genetics (DNA sequences)- overwhelming majority of trees are now built using DNA sequences cuz they are ideally more objective, there is lots of available data, and they are capable of resolving both old and new relationships
5. DNA is the one most used today

similarity between characters due to common ancestry (human, cat, whale, bat)

organs in two species are homologous only if the same structure was present in their last common ancestor

similarity between characters due to convergent evolution, not common ancestor

(insect, pterosaur, bird, bat)

monophyletic clade- an ancestor plus ALL of its descendants

paraphyletic group- missing some descendents so an ancestor plus some or most of ancestors

sympatric speciation is when a population diverges into two species while occupying the same space

this happened in the East african rift- the earth is pulling apart, creating deep valleys and lakes. cichlids have diversified there

different colors are visible at different depths. fish eyes evolve to see colors at the depth they live. females eventually only recognize beauty of their own kind. the fish in each lake form a clade, so they must have speciated together to want to mate together

this older speciation event was allopatric

genetic drift 

vs

natural selection

genetic drift and natural selection both tend to reduce genetic variation (ie fix alleles)

but genetic drift is more common

selection consitently acts upon functional variation to quickly fix alleles

genetic drift is a random process- randomly acts upon neutral variation to slowly fix alleles

codons are redundant

most DNA is non coding

we want a random process

dispersal 

vs

vicariance

big question is whether a particular distribution of taxa is the result of vicariance or dispersal

vicariance

geographic or climactic barrier to dispersal

dispersal

migration of one or more taxa to a new habitat including plants and animals and can happen by themselves or via other species or environmental changes

knowing the dates of splits

branch lengths mean amount of change from the split of a node-following the 2 branches and measuring the length of them tells you how much change there is- we can get a rate from this and put a scale bar at the bottom

near Indonesia, saw drastic differeces amongst species on either side of this imaginery line- observed abrupt transition from Asian (primates, carnivores, insectivores, pheasants) to Australian (cockatoos, parrots marsupials, terrestrial birds) fauna despite proximity and similar climate and habitat

thought this had to do with history not a creator (aka plate tectonics but he didnt know this yet)

the last time the ice retreated meant another migration of animals back to where they were before the ice took over. pleistocene glaciation

a lot of patterns we see are a result of the ice movement- it made a lot of species go extinct but if it didnt make them extinct, still affected them, made them move

southern= more diverse

northern= genetically younger- founders effect

several species on each side of the pacific, none in the middle= happened from vicariance (separated by the ocean)

the global cooling event likely split the clade in half by rendering the northernmost coastlines uninhabitable

convergent evolution- certain traits converging cuz environment- led to 2 types:

1. astrabe: reduced eyes, long thin bodies cuz live in sand/ rocks. filled similar infaunal niches on each side of pacific

2. chasmichthys: fully developed eyes and larger bodies cuz utilize burrows. also evolved independently on each side of pacific

fossil localities with exceptional preservation

from things like mummification, being frozen, bog specimens, amber