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what is HIV?

what is HIV?

Description

School: Florida State University
Department: Biology
Course: Evolution
Professor: Darin rokyta
Term: Spring 2016
Tags: evolution
Cost: 50
Name: Exam1 Study Guide
Description: These notes cover all five chapters that will be included on exam 1. This outline includes detailed notes from the book and class lectures.
Uploaded: 02/03/2016
35 Pages 9 Views 15 Unlocks
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Same time next week teach? Can't wait for next weeks notes!



Evolution Ch. 1 01/30/2016


what is HIV?



A case for evolutionary thinking: Understanding HIV

∙ 1.1 The Natural History of the HIV/AIDS Epidemic

o Worst epidemics in human history:

 1. Influenza 1918

 2. The Black Death 1347-52

 3.New world smallpox 1520

o AIDs is among the worst epidemics in human history

 First recognized 1891

 HIV infected > 65 million

 Every day 13400 newly infected with HIV and 8500 die  

of AIDS

 Infection rates much lower in industrialized countries

o HIV contracted when a bodily fluid holding the infection  

contacts a mucous membrane or bloodstream of an  

uninfected person

o Intro of effective long-term drug therapies for HIV prompted  increase in risky sexual behaviors as infection rates for other  

STIs rose in yr 2000

o What is HIV

 Intracellular parasite that can’t reproduce on its own


what is the study of same organ in different animals under every variety of form adn function?



 Uses cells in human immune system to make copies of  

itself, kills host cell in the process

 Extracellular form called virion

 Replication initiated by attaching to two surface proteins

of host cell (CD4 and a coreceptor)

 Virion envelope fuses with host cell membrane  

and spills virion contents into cell

∙ Contents include diploid genome, reverse  

transcriptase, integrase, and protease

 Flow of genes RNA-> DNA

 Difficult to treat b/c HIV uses host cell machinery so any  drug that interrupts virus life cycle also interferes with  host cell functioning

o How does HIV cause AIDS

 HIV parasitizes helper T cells, immune system depleted  of helper T cells(which respond to invading  

pathogens)leaving host susceptible to secondary  


what caused te Cambrian explosion?



infections

 In clinical trial: human HIV patients treated with  

antiretrovirals+immunosuppressant had higher helper T count than those treated with antiretrovirals alone If you want to learn more check out Subculture means what?

 T-cell capacity for replication diminishes with each  division

∙ 1.2 Why does AZT work in the short run, but fail in the long run? o Rationale behind AZT: drugs that block reverse transcriptase  should kill retroviruses with minimal side effects

 AZT mimics nucleotide to reverse transcriptase picks it  up but it lacks the binding site for the next nucleotide  o Early tests: AZT worked and stopped loss of marcohphages  and T-cells in AIDS patients

 Also had serious side effect: stopping DNA synthesis in  host cells

o Patients stopped responding to treatment after a few years  use

 Patients cellular physiology changed: long term  

exposure to AZT could cause natural thymaine kinase  production to decrease If you want to learn more check out How do environmental factors limit growth and survival?

 Virions become resistant to AZT disruption (~6 mo.) o Difference in resistant vs susceptible virion

 Viral strains present late in in treatment were  

genetically different from those present before  

treatment

 Mutations with AZT resistance occur on active site of  reverse transcriptase

o no conscious manipulation took place; reverse transcriptase is error prone

o change over time in the composition of the viral population is  evolution by natural selection

o when AZt therapy is stopped, AZT resistant population begins  to decrease (back-mutations)

o evolution by natural selection

 is NOT unidirectional or irreversible

 can occur in any population with heritable variation in  reproductive success

∙ 1.3: Why is HIV fatal

o Evolution by natural selection: an automatic process that  happens whenever a population shows the necessary  heritable variation and reproductive success. Traits conducive  to surviving and reproducing spread throughout the  

population; traits conducive to dying without issue disappear o Short-sighted evolution

 Epitopes: short pieces of viral protein displayed on  surface of virion or infected cell that help antibodies and killer-T cells recognize HIV

 Epitopes mutate; those that better evade the immune  system replicate more increasing their population If you want to learn more check out What is pyramidal neurons?

 Evolution of HIV contributes to collapse of immune  system

 Continuous evolution towards novel epitopes  

enables viral population to stay ahead of immune  

response to replicate in high numbers

 Viral population in host evolves towards ever more

aggressive replication  

 At least half of all hosts strains of HIV can infect  

naïve T cells

o Correlation between lethality and transmission

 Syndey blookbank cohort has a relatively benign strain  of HIV

 Genome lacks part of gene for viral protein Nef.

 Nef helps HIV virions enter host cells Don't forget about the age old question of Marginal opportunity cost on the supply curve.

 Loss of this function limits damage ot host  

immune system (b/c lower viral loads)

 Second level of selection: those that are god at getting  transmitted to new hosts will become more common  over time

 Poor transmission may be due to reduced ability of Nef deficient virions to infect new cells

 w/ fewer virions in body fluid reduced chance of  

transmission  

∙ 1.4 Why are some people resistant to HIV

o resistant indivuduals might have unusual forms of coreceptors that thwart HIV entry to cell

o resistant genome distribution does not reflect HIV distribution  allele CCR5-delta-32 may have recently been favored by natural selection in European populations

 allele could have risen to high frequency by chance as a result of genetic drift

o there are also costs to the delta-32 allele such as increased  susceptibility to west nile virus If you want to learn more check out what are the types of Highly Invasive Methods?

∙ 1.5: Where did HIV come from

o HIV virus derived from primate’s SIVs

o How do researchers reconstruct evolutionary history  Phylogenetic tree shows historical relationships among  a group of organisms/viruses Don't forget about the age old question of A detailed schedule showing the expected sales for the budget period.

 Done by comparing nucleotide sequences

o The origin of HIV

 HIV-2 Probably transmitted from sooty mangabeys (pets and food) to humans in west Africa

 Chimps as food transmitted SIVcpz to humans evolved  into HIV-1

 Virus jumped from chimps to humans on three separate  occasions  

o HIV diversity and the difficulty of developing a vaccine  Vaccine would need to contain epitopes from all strains  of HIV

 Likely for transmission of SIV to humans to occur again  Aim for regional vaccine has a higher probability for  success

The Pattern of Evolution

∙ Scientific theories have two components: a statement about an  existing pattern and a process that explains that pattern o Theory of special creation

 Part one:  

 Species do not change through time

 They were created independently of one another

 They were created recently

 Part two: separate and independent acts of creation by  a designer

∙ Darwin’s evidence against theory of special creation: o Species are not immutable but change through time o Species are not derived independently but from common  ancestors

o The earth and life are considerably more than 6000 yrs old ∙ 2.1: Evidence of change through time

o evidence (for descent with modification) from living species  monitoring natural populations microevolution can be  directly observed  

 monitoring the bodies of living organisms shows  

evidence for macroevolution

 direct observation of change through time

 soapsberry bugs

∙ feed using long beaks to attack inflated fruit

capsules on host plants

∙ before 1925 bugs in FL lived exclusively on  

native host

∙ gardeners introduced an Asian relative of  

this plant with flat fruit

∙ bugs living on flat capsuled host had much  

shorter beaks than the bug living on round  

capsuled host

∙ short beaked are descended from long

beaked, just evolved when they switched to  

a new host

∙ alternative explanation: as they grow the  

bugs develop a beak just long enough to  

reach the seeds of the fruit they find

o refuted by results because the two  

populations are genetically different

 vestigial organs

 vestigial structure: useless or rudimentary version of a body part that has an important function in in  other, closely allied, species

∙ ex: flightless bird w/ stubby wings; boa w/  

remnants of hind limbs; human tailbone and

muscles on hair follicles

 vestigial traits also occur at molecular level

∙ chromosome 6 has one that disables the  

production of CMAH, which most mammals  

make in abundance

 evidence: threespine sickleback: small fish  

∙ marine have heavy body armor while  

freshwater have light body armor

∙ when each were mated with each other in a  

lab offspring were heavily armored; F2  

generation consisted of 1.heavily armored 2.

Fully plated w/ vestigial pelvic structure 3.  

Lightly plated with full pelvic structure 4.  

Lightly armored (suggests control by 2  

mendelian genes)

o evidence from the fossil record

 fossil: trace of organism that lived in the past

 fossil record: total worldwide collection of fossils  the fact that fossils exist that are unlike living species  today is evidence that life changes over time

 three specific observations are evidence of evolution  1. The fact of extinction

 list of extinct species directly refutes that unusual  forms in the fossil record would eventually be  

found as living species

 creationsists argued that species had died in  

seried of biblical floods

 Darwin and other interpreted extinct species as  relatives of living ones

 2. Law of succession

 general pattern of correspondence btwn fossil and living forms from the same locale

 3. Tranitional forms

 fossil record should capture evidence of  

transformations in progress: transitional species  

with a mix of features

 archaeopteryx: crow sized animal with feathers  

and ability to fly; skeleton was reptilian with teeth  

and three clawed hands and a boney tail

∙ documents transition from dinosaurs to  

birds

o evidence of descent with modification

∙ 2.2 Evidence of common ancestry

o intro to tree thinking

 Darwin invented phylogenetic trees

o Ring Species

 Documents one species splitting into two  

 Ex: Siberian greenish warbler; geographic range forms a ring around Siberian plateau

 Individuals recognize each other as the same  

species and interbreeding occurs everywhere they

meet except for where the NE form meets the NW  

form  

o Homology: the study of likeness; the same organ in different  animals under every variety of form and function

 Structural and developmental homology

 Underlying design of vertebrate forelimbs is  

similar even though function and appearance  

differ

 Inherited fundamental design from a common  

ancestor

 Embryo observation

∙ Embryos are similar b/c all vertebrates  

evolved from the same common ancestor  

and some developmental stages have  

remained similar as reptiles, birds, and  

mammals diversified

 Molecular homology

 All organisms use the same nucleotide triplets to  

specify same amino acid w/ few exceptions

∙ Reduces deleterious effects of point  

mutations/translational errors

 A unique genetic code could have been  

advantageous in preventing spread of disease  

btwn species so why do all organisms use the  

same one? It was inherited from a common  

ancestor

 Genetic flaw on chromosome 17 of humans

∙ Causes unequal crossing over by incorrect  

insertion of CMT1A repeat which results in  

multiple copies or no copies of PMP-22 gene

∙ Common chimps and bonobos share this  

repeat; its absent in gorillas orangutans and

other examined species

∙ Humans more closely related to chimps and  

bonobos

 Processed pseudogenes: nonfunctional copies of  

normal genes that originate when processed  

mRNAs are accidentally reverse transcribed to  

DNA and inserted at a new location

∙ Readily distinguished because they lack  

introns and promoters

∙ Estimate age of pseudogene because the  

older it is the more mutations it will have  

accumulated

∙ Older processed pseudogenes should be  

shared by a greater variety of species

 Modern concept of homology

 Homology underlies use of model organisms in  

biomedical research and drug testing

o Relationships among species

o Evidence of common ancestry

∙ 2.3: The age of Earth

o uniformitarianism: claim that geological processes taking  place now operated similarly in the past

o the geologic times scale

 relative dating: object was to determine rock age  

relative to other strata based on the following  

assumptions

 younger rocks are deposited on top of older rocks

 lava and sedimentary rocks were originally laid  

down in horizontal position

 rocks that intrude into seams in other rocks are  

younger than their host rocks

 boulders, cobbles, or other fragments are older  

than their host rock

 earlier fossil life forms are simpler than more  

recent forms and more recent forms are more  

similar to existing forms

o radiometric dating: assigns absolute ages

 uses unstable isotopes of naturally occurring elements  half-life

 planet about 4.6 billion yrs old

 fossils back 2 billion yrs

∙ 2..4: is there necessarily a conflict between evolutionary biology  and religion

o methodological naturalism and ontological naturalism  methodological naturalism: the only hypothesis  

researchers propose to account for natural phenomena  and the only explanations the accept are ones that  

involve strictly natural causes

 ontological naturalism : the position that the natural  world is all there is  

 methodological assumes nothing else exists but  

ontological believes this

Estimating Evolutionary Trees

∙ 4.1: The logic of Phylogeny Inference

o most closely related taxa should have the most in common  o synapomorphies identify monophyletic groups

 only certain types of homologous characters are useful  in estimating phylogenetic trees

 synapomorphy: homologous trait that is shared among  certain species and is similar because it was modified in a common ancestor; shared, derived traits

 monophyletic group: includes an ancestor and all its  descendants

 bacteria and mammals use genetic code to put them in  the same monophyletic clade

 bacteria are identified from eukaryotes by  

synapomorphies such as cell walls containing  

peptidoglycan while eukaryotes have a nuclear  

envelope

 all synapomorphies are homologous traits but not all  homologous traits are synapomorphies

 synapomorphies identify evolutionary branch points

 speciation starts when two populations become  genetically isolated; once genetic separation  

occurs the species evolve independently and  

some homologous traits undergo changes (these  changed traits are synapomorphies

o cladistics approach

 must identify which traits are more ancient and which  are more derived

 outgroup analysis: the character state in the  

group of interest is compared to the state in a  

very close relative that clearly branched off earlier  each brank on tree corresponds to one or more  synapomorphies

 clustered synapomorphies make a cladogram

 synapomorphies identified in cladograms by a bar  across the branch and a description of accompanying  traits/labels

 evolution of tetrapods

 identified by evolution of limbs in vertebrates

 moist, scaleless sil and exchanging gases across skin  link amphibia

 amniotic egg distinguished amniota

o problems in reconstructing phylogenies

 similar traits may have evolved independently in  different groups of species

 not all similar traits are homologues

 convergent evolution: occurs when natural  

selection favors similar structures as solutions to  problems posed by similar environments  

 octopuses and vertebrates did not inherit  

sophisticated camera eye from a common  

ancestor; they individually evolved because both  species depend on sight to find food and avoid  

danger

 hippopotamuses and crocodiles have eyes on the  tops of their head because they spend a lot of  

their time submerged in water, not because of a  

common ancestor

 ex: wings of bats and birds, streamline shape of  sharks and whales, limbless bodies of snakes and  legless lizards

 species can even share nucleotide sequences  without having a common ancestor

∙ reversals: common in DNA; 25% chance of  

reversal to the previous state; similar traits  

are not homologous and aren’t  

synapomorphies

 homoplasy: convergence and reversal; similarities  

not due to homology

 distinguishing homology from homoplasy

 most efficient to analyze many traits instead of  

just one or a few

 comparing the two results: development of  

camera eye in octopuses and vertebrates:  

assuming common ancestor the tree would  

undergo six changes while assuming convergent  

evolution implies only two changes

 parsimony: biologists consider convergence most  

likely hypothesis

 homoplasius morphological traits aren’t as similar  

as they initially appear

∙ octopus eyes: light sensitive cells oriented  

toward opening while in vertebrates they  

are in the opposite direction

∙ octopus change the shape of their eyeball to

focus while vertebrates change the shape of

the lens

 developmental pathways and and alleles observed

in diff species will be similar if they have a  

common ancestor  

 resolving conflicts in data sets: the role of parsimony  minimizes the confusing effects of homoplasy and  

is most accurate  

 parsimony favors the simpler explanation

∙ 4.2: the phylogeny of whales

o choosing characters: morphology and molecules

 1. Skeletal and other morphological characteristics

 2. DNA sequences and other molecular traits

 each path has pros and cons

 morphological traits essential when the species only  exists as a fossil and is very compelling when  

homoplasy and homology can be distinguished  

 slow and painstaking work

 molecular characters have a reduced cost and a large  number of nucleotide can be analyzed very quickly.

 Mathematical models can minimize homoplasy

 Helps identify reversals

 Homoplasy can be difficult to identify in molecular data

o Finding the best tree implied by the data

 Parsimony with a single morphological trait

 Skeletal character closely relate cetaceans and  ungulates

 Ungulates two major groups: perissodactyls  

(horses and rhinos) and the artiodactyls (cows  

deer pigs camels hippos)

 Morphological data identifies artiodactyla as  

monophyletic  

∙ Synapomorphies include skull and dental  

characteristics and ankle bone(astragalus:  

unusual pulley shape at both ends)

 How close are whales and artiodactyla

∙ If whales are closely related to hippos then a

logical evolutionary scenario is assumed

∙ After extinction of dinosaurs mammals  

made living in shallow water habitats and  

some, whales, became fully aquatic over  

time while other remained semi-aquatic

∙ Whale-hippo relationship implies dolphins  

and porpoises are closely related to  

completely terrestrial forms

∙ Astralagus suggests hippos and whales are  

not closely related b/c parsimony. The trait  

would have been gained just to have been  

lost again by whales

 Whales have no ankles but some fossils whales  have had hind limbs

∙ Some features of the pulley shaped  

astragalus are in the earliest whales  

suggesting that they are descended from an

artiodactyl

∙ Controversial though b/c possible that the  

bones may have belonged to a different  

artiodactyl

 Parsimony with multiple molecular characters

 Over 60 traits analyzed

 Computer generates all possible trees then maps  each character

 Most parsimonious pattern of character change is  noted for each character

 Best tree implies fewest character changes across all characters

 Only 15 of the 60 traits were usable; others were  either inherited from the common ancestor and  

variable yet uninformative

 Synapomorphies must group two or more taxa  Determined whales and hippos are closest  

relatives

∙ Homoplasy evident

 Whale hippo hypothesis most parsimonious

 Searching among possible trees

 When lower than 11 taxa a computer program can evaluate all possible trees (exhaustive search

guarantees optimal tree will be found)

 Agreement among search methods strengthens  findings

o Evaluating the best tree

 Using other methods besides parsimony: maximum  likelihood and Bayesian inference

 Likelihood computes probability that alternative  trees are supported by the data

 When competing trees arise choose the one with  the highest likelihood  

 Bayesian method asks what the probability of a  particular tree being correct is

 Provide an objective criterion  

 Evaluating particular branches: bootstrapping

 Bootstrapping: evaluating branches based on  

parsimonious trees; computer creates new data  

set from existing one by repeated sampling. New  data set used to estimate a phylogeny. The more  times a branch occurs in a bootstrapped sample  

the more confident we can be that the branch  

actually exists

 Under 50% certainty is put in a polytomy (point of  uncertainty)

o Resolving conflict

 More confidence in trees that are estimated with   larger data sets,

 characters subject to less homoplasy

 inference methods most appropriate to data in  question

 wait for additional data independent of traits analyzed  to date

 short or long interspersed elements (SINES/LINES)

 whales/hippos: no homoplasy in the dataset

 new fossils

o take home messages

∙ 4.3: using phylogenies to answer questions

o classification and nomenclature: is there such a thing as a  fish?

 Systematics: effort to name and classify species

 Linnaean: genus and species according to morphological traits (phenetic approach)

 Those based on evolutionary relationships are cladistics  approaches; should be tree based; only monophyletic  groups named

 Paraphyletic groups including some but not all  

descendants of a common ancestor should not be  

named

 Tree based scheme “fish” would have to include  

tetrapods

o Using molecular clocks: when did humans start wearing  clothes

 Molecular clock allows us to date events not  

documented in the fossil record

 Mutations in DNA that aren’t expressed in phenotype  and therefore aren’t acted upon by natural selection  

accumulate at a rate equal to the mutation rate

 Estimate when two species diverged: document number of different neutral mutations observed in two species  multiply by calibration rate

 Head lice similar to body lice. Body lice live in clothes so must have diverged around the time humans started  

wearing clothing

 Our species originated 100,000-200,000 yrs ago

o Analyzing phylogeny: how did chameleons get from Africa to  india

 Phylogeography: using phylogenies to help determine  why species are found where they are

 Evidence shows that chameleons diversified via  

dispersal to new habitats instead of occurring as the  

supercontinent broke up

 Explains presence on volcanic islands that were  

never part of supercontinent

o Co-speciation: when new species of aphids form, what  happens to the bacteria that live inside their cells

 Coevolution: when natural selection occurs during  

interactions such as predation, parasitism, and  

mutualism

 Cospeciation: occurs when a population splits into two  groups that become genetically isolated and then begin  to diverge genetically

 Aphids are parasitized by wasps so they may house  bacteria that come from the wasp as opposed to  

ancestral species

The Cambrian Explosion and Beyond

∙ 565 MYA first animals appear in fossil record

o jellyfish + sponges found are multicellular but small ∙ 543 to 506 MYA is the Cambrian period, when most of todays living  animal phyla surfaced

∙ five episodes of extinction

∙ start of Cambrian to present is called Phanerozoic eon ∙ 18.1 The nature of the fossil record

o how organic remains fossilize

 fossil: any trace left by an organism that lived in the  past

 four general categories of fossils

 compression fossils: result when organic material  

is buried in water or wind borne sediment before it

decomposes; the pressure leaves an impression in

the material below

 casts and molds: originate when remains decay  

after being buried in sediment.

∙ Molds: unfilled spaces

∙ Casts: form when new material fills the  

space and hardens into rock

 Permineralized fossils: form when structures are  

buried in sediments and dissolved mineral  

precipitate in the cells; preserves details of  

internal structures

 Unaltered remains: preserved in environments  

that discourage loss from weathering,  

consumption by scavengers, and decomposition  

by bacteria/fungi

 Key features of specimen that fossilization depends on  Durability

 Burial

 Lack of oxygen

 Most fossils found in depositional environments (deltas,  beaches, lakeshores)

o Strengths and weaknesses of the fossil record

 Bias in the fossil record

 Geographic: fossils tend to come from low land  

and marine habitats

 Taxonomic: marine organisms dominate fossil  

record but make up only 10% of extant species

 Temporal: earth’s crust is constantly recycled  

when tectonic plates subduct and mountains  

erode (ability to sample life forms should decline  

with time

o Life through time: an overview

 Time scale: eons, eras, periods, epochs, stages

 Phanerozoic eon: paleozoic era, Mesozoic era, and  Cenozoic era

∙ 18.2: The Cambrian Explosion

o The Ediacaran Fauna

 Earliest dated at 565MYA and youngest at 544MYA at  end of Proterozoic era

 Mostly compression and impression fossils

 No shells or hard parts

 Include sponges, jellyfish, and comb jellies

 Asymmetrical or radial symmetry

 Difficult to determine if complex bilaterally symmetric  animals were present at this time

 Evidence supports that bilaterians evolved prior to Cambrian

 635-551MYA

 apparent embryos found fossilized

 trace fossils: remnants of burrows, fecal pellets, tracks  difficult to interpret

 bilaterally symmetric animals were small but present  pre-cambrian period

o The Burgess Shale Fauna

 Variety of large complex bilaterally symmetric forms  Arthropods, mollusks, vertebrates, and schinoderms  520-515MYA

 mostly impression and compression fossils

 little overlap with ediacaran fauna

 several chordates found, including jawless invertebrates  had segmented trunk muscles and a notochord  had a problematica phylum that are now being  redescribed and more successfully categorized

 major morphological innovations

 large body size, segmentation, limbs, antennae,  shells, external skeletons, notochords

o phylogeny and morphology

 dipoblasts and tripoblasts

 ctendephora cnideria and dipoblastic (have two  embryonic tissue types)

 tripoblasts have three

 present n both tripoblasts and dipoblasts:

∙ ectoderm: cells prodice adult skin and  

nervous system

∙ endoderm: cells produce gut and associated

organs

 mesoderm

∙ unique to tripoblasts

∙ develops into gonads, heart, muscle,  

connective tissue, and blood

 tripoblasts

∙ most have one plane of symmetry

 dipoblasty and radial symmetry evolved before  tripoblasty and bilateral symmetry

 protostomes and deuterostomes

 gastrulation: mass movement of cells that  

rearranges embryonic cells after cleavage and  

defines the ectoderm, endoderm, and mesoderm  protostomes: gastrulation forms mouth first

 deuterostomes: gastrulation forms anal region  first

 lophotrochozoans and ecdysozoans

 lineages of protostomes

 ecdysozoa are molting animals

 lophotrochozoans have a feeding structure called  lophophore

o was the Cambrian explosion really explosive?

 Origin of bilaterians

 Analyze differences in hemoglobin amino acid  sequences

 ~900 MYA

 chrodates and echinoderms diverged~1000MYA

 protostomes and deuterostomes  

diverged~1200MYA

 discrepancy between estimated time clock and fossil  record suggest lineages leading to bilateria diverged  over Proterozoic but mostly existed as small larva-like  organisms that didn’t show up in the fossil record

o what caused the Cambrian explosion

 Cambrian explosion filled many ecological niches

 Environmental changes that made varying was of life  possible

 Rising oxygen concentration in sea water (due to  

photosynthetic algae) key to multicellularity and  

large size and higher metabolic rate

∙ Larger size prerequisite for evolution of  

tissues  

∙ Higher metabolic rate needed for powered  

movement

∙ 18.3 Macroevolutionary patterns

o adaptive radiations: occur when a single or small group of  ancestral species rapidly diversify into a large number of  descendant species that occupy a wide variety of ecological  niches

 ecological opportunity as a trigger

 occurs when small number of individuals or  

species is suddenly presented with a wide and  

abundant array of resources to exploit

 EX: finches colonizing islands with few  

competitors and many resources

 Mass extinction events or dispersal and  

colonization

 Morphological innovation as a trigger

 Diversification of arthropods: associated with  

jointed limbs, which allow them to move and find  

food

 Adaptive radiations in land plants

 Radiation of terrestrial plants form aquatic  

ancestors in early Devonian ~400MYA

∙ Evolved waxy cuticle and stomata

∙ Alteration of generation

 Cretaceous explosion of flowering plants ~110MYA

∙ Made pollination efficient; flower triggered  

this radiation

o Stasis

 Theory of punctuated equilibrium: most morphological  change occurs during speciation

 Demonstrating stasis

 Does change occur in conjunction with speciation  

events or independently

 Is rapid change followed by stasis or continuous  

change

 Necessary that ancestral species survive long  

enough to co-occur w/ new species in the fossil  

record: phyletic transformation or anagenesis

 Stasis and speciation in bryozoans

 Relatively few species meet the requirements for  

stasis studies

 Cheilostome bryozoans show a pattern of stasis  

punctuated by rapid morphological change

 What is the relative frequency of stasis and gradualism  No one process occurs alone

 Why does stasis occur

 Looking at “living fossils” species that show  

little/no morphological change over time

 Horseshoe crabs: show just as much genetic  

divergence as other arthropod clades even though

far less morphological change occurred  

 Stasis is not from a lack of genetic variability

 Habitat tracking/ dynamic stasis: zigzag evolution;

large fluctuations that average to stasis when  

quantified

∙ 18.4: Mass Extinctions

o mass extinctions: over 60% of species that were alive went  extinct over the course of 1 million yrs

o five mass extinction events during the Phanerozoic  (responsible for 4% of all extinctions in this period)

o background extinctions: occur at normal rates

 likelihood of a particular lineage to become extinct is  constant and independent of how long the taxa have  existed  

 survivorship curves show the proportion of an original  sample that survives for a particular amount of time  almost all produce a straight line: probability of  extinction was constant

 in marine organisms extinction rates vary with how far  larvae disperse: those that disperse survive longer than  species whose young develop directly from egg

 species with larger geographical ranges survived longer  than those with limited ranges

o cretaceous-Tertiary: high impact extinction:

 Evidence for the impact event (of the K-T extinction  Asteroid evidence

∙ iridium concentration in sediment

∙ shocked quartz

∙ tiny glass particles called microtektites

∙ hit at an angle to splash material NW

∙ crater discovery

 killing mechanisms

 consequences of ejected material

∙ vaporization of anhydrite and sea water  

would have contributed to influx of sulfur  

dioxide to atmosphere creating an acid rain

∙ sulfur dioxide also scatters solar radiation  

which would have led to global cooling;  

enhanced by dust-sized carbonate, granitic,  

and other particles that were ejected

∙ soot deposits suggest wildfires occurred

∙ impact strong enough for mass earthquakes

and setting off volcanoes  

∙ impact would have made a tsunami in the  

atlantic ocean

 effects on oceans

∙ primary productivity of phytoplankton  

dramatically reduced

∙ temperature and chemical gradients would  

have been disrupted

 decline of organisms occurred over proceeding  500,000 yrs

 extant and selectivity of extinctions

 extinctions were not distributed evenly among  taxa

 wider geographical ranges less susceptible to  

elimination

o recent extinctions: the human meteorite

 Polynesian Avifauna

 ~2000 species of birds extinct over past two  

millennia in pacific region as a result of human  

colonization

 human predation along with introduction of  

mammalian predators brought with the colonizers   habitat destruction: slash and burn agriculture,  permanently irrigated fields

 is a mass extinction event currently underway

 focus on habitat loss due to expanding human  population

 predicting how habitat destruction will impact  extinction rates

∙ multiply number of species found per  

hectare in diff. environments by rate of  

habitat loss measured from satellite photos

∙ quantify rate that well-known species are  

moving from threatened to endangered to  

extinct status in the lists maintained by  

conservation groups

∙ estimate the probability that all species  

currently listed as threatened or endangered

will actually go extinct over the next 100-

200 yrs

 suggested that extinctions now occurring at 100  to 1000 times the normal rate of extinction

 where is the problem most acute

 tropical rain forests b/c they’re so rich in species

 tropics have been relatively unaffected by humans

so they don’t have the resilience to human impact

of other areas

 more than double the amount of cleared forest is  

effected due to “edge effects”

Darwinian Natural Selection

∙ 3.1: Artificial Selection: Domestic Animals and Plants o Darwin bred pigeons

o Tomato  

 All species of wild tomato have small fruit (think grape  tomato)

 Ancestor probably had tiny fruit

 Chromosome 2 gene called fw2.2 encodes a protein  made during early fruit development  

 Represses cell division (more protein, smaller  

fruit)

 Changes in promoter alter timing of production  

and amount made

 All wild tomatoes tested have a high production allele  All cultivated tomatoes have low production alleles o Artificial selection can change more than size

∙ 3.2: Evolution by natural selection

o Darwin’s postulates result in descent with modification  Individuals within populations are variable

 The variations among individuals are passed from  

parents to offspring

 In every generation, some individuals are more  

successful at surviving and reproducing than others

 The survival and reproduction of individuals are not  randomly they are tied to the variation among  

individuals. The individuals with the most favorable  

variations are naturally selected

o If differences among individuals in a population can be passed to offspring and is there is differential success in those  individuals surviving/reproducing then some traits will be  passed on more frequently than others

o Characteristics will change slightly with each succeeding  generation

o Selection happens to individuals but populations are what  change

o Darwinian fitness: the ability of an individual to survive and  reproduce in its environment

 Relative nature important in determining fitness

 Adaptation: a trait or characteristic that increases its  fitness relative to individuals without the trait

o Darwin’s mechanism of evolution: Natural Selection  Each of the four postulates can be verified  

independently  

∙ 3.3: the evolution of flower color in an experimental snapdragon  population

o postulate 1: there is variation among individuals

 snapdragons varied in flower color

 ¾ were white with two spots of yellow on lower lip

 ¼ had all yellow flowers

o Postulate 2: some of the variation is heritable

 12 were SS, 24 Ss, and 12 ss

o testing postulate 3: do individuals vary in their success at  surviving or reproducing

 researchers made sure all plants survived but didn’t  ensure all plants reproduced

 free living bumblebees pollinated the plants

 tracked the number of times a bee visted each flower to see reproduction success by exporting pollen

 reproductive success by making seeds was tracked by  counting the number of seeds produced by each fruit.   The plants showed considerable variation in their  

reproductive success

o Testing postulate $: is reproduction nonrandom?

 Expected that one color would attract more bees than  the other

 Yellow spots on white flowers thought to be nectar  guides: attracted twice as many bees as the yellow  

flowers

 White plants also produced more seeds per fruit

o Testing Darwin’s prediction: did the population evolve?  The next generation in this experiment has a higher  proportion of white flowers (increased from 75% to 77%  of offspring)

∙ 3.4: the evolution of beak shape in Galapagos finches o beak morphologies reflect diversity of foods they eat o focus: medium ground finch studied by Grant and Grant on  Isla Daphne Major

 only one spot on island can pitch a camp

 few finches migrate on and off the island

 population small enough to be studied exhaustively  primarily seed eaters; beak size correlated with seed  size across finch species

o testing postulate 1: Is the finch population variable?  All traits investigated on tagged finches are variable o Testing postulate 2: is some of the variation among individuals heritable?

 Heritability of a trait: the proportion of the variation  observed in a population that is due to variation in  

genes

 Stronger correspondence in beak size between relatives  Issues in estimating heritability

 Misidentified paternity

 Conspecific nest parasitism

 Maternal effects

 Shared environments

 Ground finches with larger beaks make BMP4 mRNA  earlier and in larger quantities than finches with smaller  beaks

o Testing postulate 3: do individuals vary in their success at  surviving or reproducing?

 Severe drought in 1977

 Killed 84% of finches; assumed died of starvation  Fewer seeds were produced for consumption

 Medium ground finches did not attempt to breed  Decline in population simultaneous with decline in seed  production

 More offspring are produced each generation than  survive to breed

 Third postulate is universally true

o Testing postulate 4: are survival and reproduction nonrandom  Types of seeds varied drastically during drought, not just amount

 Seeds typically ranged from small and soft to large and  hard

 Small soft seeds were consumed first during the drought and left only large hard seeds

 Only large birds with deep narrow beaks can crack and  eat the large hard seeds

 Avg survivor had a deeper beak than avg nonsurvivor  Larger birds are favored in drought conditions while  smaller birds are favored in wet years

o Testing Darwin’s prediction: did the population evolve  All four postulates true in this finch population therefore  predicts a change in composition of population

 Chicks that hatched in 1978, year after the drought, had deeper beaks

 Small evolutionary changes over short time spans can  accumulate into larger changes over longer time spans ∙ 3.5: The nature of Natural Selection

o natural selection acts on individuals but its consequences  occur in populations

 selected individuals don’t change, they survived  

through the selection event

o natural selection acts on phenotypes but evolution consists of  changes in allele frequencies

 evolution is dependent of selection of traits with genetic basis, those that are selected for due to environmental  changes wont be passed on to next generation

o natural selection is not forward looking

 evolution is always a generation behind any changes in  the environment

o new traits can evolve, even though natural selection acts on  existing traits

 evolution of new traits possible for two reasons

 during reproduction in all species mutations  

produce new alleles

 during reproduction in sexual species meiosis and  

fertilization recombine existing alleles into new  

genotypes

 mutation, selection, and recombination together  

produce a new phenotype

 preadaptation: a trait that is used in a novel way and is  eventually elaborated by selection into a completely  

new structure; happenstance

o natural selection does not lead to perfection

 phenotypes evolve that “compromise” between  

opposing agents of selection

 ex: large fish tail that attracts females also slows  

down escape form predators

o natural selection is nonrandom but is not progressive  mutation and recombination are random but natural  selection is not  

 evolution by natural selection is non random ; it  

increases adaptation to environment  

 there is no trend toward more advanced, complex forms of life

 contemporary tapeworms have evolved to be  

more simpler than their ancestors (no digestive  

track)

o fitness is not circular

 favorable doesn’t necessarily mean favorable; only  requirement for natural selection is for certain heritable  variants to do better than others

o selection acts on individuals, not for the good of the species  if an altruistic allele existed that reduced bearers fitness to increase the fitness of others that allele would quickly disappear

 infanticide enhances the fitness of some individuals and does not occur for the good of the species

∙ 3.6: The evolution of Darwinism

o problems with Darwin’s theory that had to be resolved  Nothing was known about mutation so there was no  idea as to how variability was generated in populations  Critics argued that natural selection would stop  

when variability ran out

 1900s showed mutations occur in every  

generation and every trait

 Darwin didn’t know anything about genetics and had no  idea how variations are passed on to offspring

 Mendel’s experiments were rediscovered to show  

how variation is heritable

 Blending inheritance was the belief at the time  

that argued favorable mutations would merge into

existing traits and be lost

 Lamarck’s hypothesis was that species evolve  

through inheritance of changes wrought in  

individuals (incorrect)

∙ Ex: if a person were to lift weights to  

become muscular then their offspring would

be more muscular as well

 Age of earth was estimated at 15-20 MYO at the time  Kelvin calculated that there was a transition from  

a hot to cold sun and hot to cold earth that gave a

limited window when life on earth was possible,  

too narrow to allow Darwin’s gradual changes

o The modern synthesis

 Gradual evolution results from small genetic changes  that are acted upon by natural selection

 The origin of species and higher taxa, or  

macroevolution, can be explained in terms of natural  

selection acting on individuals (microevolution)

 Restatement of darwin’s postualtes in terms of the  synthesis

 As a result of mutation creating new alleles, and  

segregation and independent assortment shuffling

alleles into new combinations, individuals within  

populations are variable for many traits

 Individuals pass their alleles on to their offspring  

intact

 In every generation, some individuals are more  

successful at surviving and reproducing than  

others

 The individuals that survives and reproduce, or  

who reproduce the most, are those with the  

alleles and allelic combinations that best adapt  

them to their environment

 Outcome: alleles associated with higher fitness increase in frequency from one generation to the next

o This view of life

∙ 3.7: The debate over “scientific creationism” and intelligent design  creationism

o history of the controversy

 scopes trial of 1925: scopes violated the butler act  prohibiting teaching evolution in schools

 butler act stayed until 1967

 it was overturned when the supreme court ruled it  violated separation of church and state

 intelligent design theory: infers the presence of a  

designer form the perfection of adaptation in  

contemporary organisms

o perfection and complexity in nature

 Darwinism predicts that complex structures have  

evolved through a series of intermediate stages

 Ex: eyespots in unicellular organisms that undergo  structural changes when they absorb light; similar to  

more complex eyes’ photoreceptors

 The argument from biochemical “design”

 If complexity is irreducible then it can’t have  

functional precursors (cilium) and therefore can’t  

have been produced by natural selection

o Other objections

 Evolution by natural selection is unscientific because it  is not falsifiable and because it makes no testable  

predictions

 Darwin’s four postulates are independently  

testable

 Because earth was created as little as 6,000-8,000  years ago, there has not been enough time for  

Darwinian evolution to produce the adaptation and  

diversity observed in living organisms

 Radiometric dating deny this

 Earth is actually 4.6 billion years old

 Because organisms progress from simpler to more  complex forms, evolution violates the second law of  

thermodynamics

 “natural processes tend to move toward a state of

greater disorder” – the entropy of an isolated  

system never decreases

∙ true for only closed systems, which  

organisms are not

 energy is constantly being added to living systems

so the second law doesn’t apply to evolution

 no one has ever seen a new species formed, so  

evolution is unproven. Because evolutionists say that  speciation is too slow to be directly observed evolution  is un-provable and based on faith

 we can’t observe atoms directly but there is still  

evidence to infer they exist

o what motivates the controversy

 concern is what evolution means to human morality and behavior

Mutation and Genetic Variation

∙ Mutation is the only process that creates completely new alleles o Ultimate source of genetic variation

∙ Selection, drift, and migration act on this newly produced variation ∙ 5.1: Where New Alleles Come From

o pyrimidines: cytosine and thyamine

o purines: adenine and guanine

o The nature of mutation

 DNA mRNA protein

 Each of the 64 codons specified a specific amino acid  Genetic code highly redundant, 20 AA to 64 codons  Allele: versions of the same gene that differ in base  sequence

 Mutation: any type of change in base sequence of DNA  First mutation characterized on molecular level: change  in human gene for hemoglobin that results in sickle-cell  disease

 Difference in hemoglobin due to a single AA  

change at position 6 in the protein chain caused  

by a single base substitution in hemoglobin gene

 Mutant allele has adenine instead of thymine at  nucleotide 2 in the codon for AA 6 (point  

mutation)

 Point mutations caused by

 Random errors in DNA synthesis or random errors  in repair of sites damaged by chemical  

mutagens/radiation

 Catalyzed by DNA polymerase

 Transition: when a purine is substituted for a  

purine or pyrimidine for a pyrimidine

 Transversion: when a purine is substituted for a  pyrimidine or vice versa

 Transitions more common b/c they cause less  

disruption to double helix during synthesis and are therefore less likely to be recognized as an error

 Changes in first or second position of codon almost  always change the AA specified while redundancy  allows for the third to be replaced without detriment

 Replacement (nonsynonymous) substitutions are point  mutations that result in an AA change

 Silent site (synonymous) substitutions show no AA  change

o Mutation rates

 Loss of function mutations: changes in DNA tha  inactivate a gene leading to a complete lack of gene  product

 Cause most observable mutant phenotypes

 Achondroplasia(dwarfism) and hemophelia

 Estimating mutation rates based on observable  phenotypes results in an underestimate because silent  site mutation are most replacement substitutions have  more subtle effects and aren’t detected in phenotype

 Mutation rate per cell division is approx. equal in all  organisms

 Recent work: direct estimates of mutation rates

 2.1*10^-8 mutations per site per generation

 more than half of the mutations were indels  

(inserted or deleted)

 investigating natural selection on mutation rate

 DNA polymerases vary in their accuracy

∙ Tradeoff between accuracy and speed

 Higher mutation rates are more adaptive when  

organisms colonize new environments to which  

they’re poorly adapted  

o The fitness effects of mutations

 The vast majority of mutations are deleterious; if they  accumulate then fitness declines

 Most mutations are only mildly deleterious and reduce  fitness by ~2% when heterozygous

 Selection coefficient: the difference in fitness btwn each  experimental population and the control

 Alleles with no effect are neutral

∙ 5.1: Where New Genes Come From

o gene duplications: most important source of new genes  result from either

 retrotransposition

∙ these genes lack introns and regulatory  

sequences

∙ code for a poly A tail and found far from  

original gene

 unequal cross over: a chance mistake caused by  

the proteins involved in managing genetic  

recombination that occurs during meiosis

∙ one chromosome contains a deletion and  

the other a redundancy

∙ found back to back and contain the same  

introns

o rates of gene duplication

 4.4 megabases of DNA added to each genome per  million years

o The fate of duplicated genes

 Original gene carries out its same function while the  duplicated gene may accumulate mutations

 Over time its function may change and become a  

new gene instead of an extra copy

 Globin gene family in humans

∙ Alpha cluster on chromosome 16 an beta  

cluster on chromosome 11

∙ Each are expressed at different times in  

development

∙ Fetal hemoglobin has a higher affinity for  

oxygen

∙ Product of gene duplication

 Pseudogenes: nonfunctional loci that are not transcribed  Paralagous: genes that are duplicated then diverge in  sequence

 Orthologous: homologs of genes found in different  species

∙ 5.3: Chromosome Mutations

o inversions

 result when radiation causes two double strand breaks  in a chromosome that then detaches, flips, and re

anneals in its original location

 inverts gene order

 affect genetic linkage (tendency for alleles of different  genes to assort together in meiosis)

 heterozygous inversions (only one chromosomes  

contains an inversion) the sequences can’t align  

properly when homologs synapse

 successful crossing over very rare

 creates supergene

 polymorphic for at least one inversion: chromosomes  with and without the inversion exist

 cline: regular change in the frequency of an allele or an  inversion over a geographic area

o genome duplication

 occurs when homologous chromosomes fail to separate  in meiosis one or if sister chromatids don’t separate in  meiosis two

 cells have double the number of chromosomes of the  parent cell

 production of a tetraploid(4n) results when a diploid  gamete plant self-fertilizes

 tetraploidy can become established  

 polyploidy: organisms with more than two chromosome  sets

 common in plants and rare in animals b/c self

fertilization is more common in plants

o polyploidy and speciation

 diploid and tetraploid populations can become separate  species (triploid can not)

o gene duplication and genetic innovation

 in flowering plants, polyploidy formation occurs just as  frequently as point mutations in individual genes

 genome replication event occurred early in evolution of  ray-finned fish

 most morphologically and ecologically diverse

∙ 5.4: Measuring genetic variation in natural populations o instead of one wild type allele at a very high frequency (like  the classic view suggested) most populations have an array of alleles

o determining genotypes

 PCR can make copies of a desired region of a gene that  can be put through gel electrophoresis

o Calculating allele frequencies

 Count allele copies and divide by total number of alleles tested

o How much genetic diversity exists in a typical population  To summarize allele data researchers use mean  heterozygosity and the percentage of polymorphic  genes

 Mean heterozygosity

 Avg frequency of heterozygotes across loci

 Fraction of genes that are heterozygous in the  genotype of the avg individual

 Percentage of polymorphic loci

 Fraction of genes in a population that have at  least two alleles

 Allozyme electrophoresis

 Isolate and stains proteins to see products of  

particular genes

 Different alleles would show up in a gel  

electrophoresis differently

 Selectionist theory: genetic diversity is maintained by  natural selection: in favor of rare individuals, in favor of  heterozygotes, or in favor of different alleles at different times and places

 Neutral theory: most of the alleles at most polymorphic  loci are functionally and selectively equivalent and are  maintained by genetic drift

 Maintains genetic diversity b/c its not eliminated  by selection

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