Chapter 1 Intro Biological Evolution--Study Version

7/21/2019 Chapter 1 Intro Biological Evolution--Study Version

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Assigned readings

Chapter 1 of Zimmer and Emlen text--The virus and the whale: how scientists

study evolution.


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iological evolution

Any change in the inherited traits !geneticstructure" of a population that occurs fromone generation to the next.

#ote that evolution is apopulationprocessthat occurs from generation to generation.

The a$ove de%nition is a de%nition ofMicroevolution.


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iological evolution

The microevolutionary changes ingenetic structure of a population over

time can lead to su$stantial changes inthe morphology of organisms over timeand the origin of new species.

&uch changes are referred to asMacroevolution.


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'hy study evolution(

Evolution explains the diversity of life.All living things are related to each other

and are the products of millions of yearsof evolution.

)nderstanding evolution allows us tounderstand why the living world is the

way it is. 'e can understand e.g.* thesimilarities and di+erences $etweenspecies* as well as their adaptations andtheir distri$utions.


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There are also practical reasons tostudy evolution.

Evolution allows us to understand theevolution of disease organisms such as

viruses and $acteria and com$at them.


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Evolution also gives us insight intosuch ,$ig uestions as:

,/ow did we get here( and ,/ow did thought and language

evolve(


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Evolution case studies

Whales: mammals gone to sea

0iruses: the deadly escape artists


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/ow do we now whales aremammals(

'hales share synapomorphies!shared derived characters" withmammals

2ammary glands

Three middle ear $ones

&ingle 3aw $one !dentary"

/air !in developing em$ryos" &imilarities with %sh 4streamlining* %ns5

arose through convergent evolution


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'hale evolution

'hales are auatic mammals thatevolved from terrestrial ancestors

through the process of naturalselection $y which individuals thatpossessed traits that $est %tted themto life in water left $ehind the most

o+spring.


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6ossil whales

The evolution of whales is welldocumented $y fossil discoveries.

2odern whales have peg-lie teeth or$aleen for feeding. Early fossil whalessuch as Dorudon!78 mya" howeverhad more complex teeth that weresimilar to those of contemporaryterrestrial mammals.


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Dorudon


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Dorudonand modern whales sharenumerous features of the sull in

common* including a distinctively thic-walled ectotympanic $one.

The same distinctive $one is found inPakicetus a terrestrial wolf-lie animalfrom 98 mya.


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Pakicetus

Pakicetusalso possesses a distinctiveanle $one called the astragalus. n

Pakicetusit has a dou$le-pulley liemorphology and this structure is foundonly in artiodactyls !hoofed mammalssuch as cows* pigs and deer".


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6ossils reveal lins to land mammals

Shape of astragalus connects to artiodactyls


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These and other fossil discoveries haveena$led $iologists to construct a

phylogentic tree !a tree of $ranchingrelationships" that depicts theevolutionary history of the group.


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Evolution case studies

'hales: mammals gone to sea

Viruses: the deadly escape artists


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0iruses

;our text has a nice discussion of theevolution of the


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#atural /istory of /0>A?&

Acuired immune de%ciency syndrome!A?&" caused $y /uman

mmunode%ciency 0irus !/0". ?isease %rst descri$ed in 1@1.

Transmitted through transfer of $odily


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&cale of pro$lem

2ore than B8 million people so farinfected.

2ortality so far a$out 8 million. Dro3ected mortality $y 88 --@8 million

lives

esponsi$le for a$out 9F of all deathsworldwide.

Approx. *888 deaths per day.


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The /umanmmunode%ciency 0irus

/0* lie all viruses* is an intracellularparasite

DarasitiGes macrophages and T-cells ofimmune system

)ses cells enGymatic machinery tocopy itself. Hills host cell in process.


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/0 $inds to two protein receptors oncellIs surface : C?7 and a coreceptor*

usually CC9. /ost cell mem$rane and viral coat fuse

and virus contents enter cell.


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'hat the virus inserts

#A genome

everse transcriptase: transcri$es viral

#A into ?#A ntegrase: this enGyme splices ?#A into

host ?#A

Drotease: this enGyme involved inproduction of viral proteins


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0iral ?#A inserted in host ?#Aproduces /0 m#A and all

components of virus 0iral particles self assem$le and $ud

from host cell.


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/0 $udding fromhuman immune cell


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/0 hard to treat

ecause /0 hi3acs the hostIs ownenGymatic machinery: ri$osomes*

transfer #As* polymerases* etc. it ishard to treat.

?rugs that targeted these would targetevery cell in the hosts $ody


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Drogress of an /0 infection

Three stages

Acute

Chronic A?&


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Acute

0iral load increases rapidly

C?7 helper T cell level declines

mmune system mo$iliGes 0iral load declines* C?7 T cell level

increases


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Chronic

/0 not eliminated

0iral load increases slowly

C?7 helper T cell levels slowly decline


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A?&

C?7 helper T cell level drops so lowimmune system fails.

Datient vulnera$le to all infections Jife expectancy of only -K years


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/ow /0 causes A?&

/uman $ody responds to infection with/0 $y mo$iliGing the immune system.

The immune system destroys virusparticles


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/ow /0 causes A?&

/0 invades immune system cellsespecially helper T cells.

These helper T cells have a vital role inthe immune system. 'hen a helper T cell is activated !$y

having an antigen 4a piece of foreign

protein5 presented to it* it $egins todivide into memory T cells and e+ectorT cells.


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2emory T cells

2emory T cells do not engage incurrent %ght against the virus.

nstead they are long-lived and cangenerate an immune response uiclyif the same foreign protein isencountered again.


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E+ector T cells

E+ector T cells engage in attacing thevirus. They produce signaling moleculescalled chemoines that stimulate cells

to produce anti$odies to the virus.

E+ector T cells also stimulatemacrophages to ingest cells infected withthe virus.

n addition e+ector T cells stimulate illerT cells to destroy infected cells displayingviral proteins.


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'hy is /0 hard to treat(0iral disguise

6irst round of infection with /0reduces the pool of C?7 /elper T cells

!those that can recogniGe and attac/0".

Joss of C?7 cells costly* $ut immunesystem now primed to recogniGe viral

protein. 'hatIs the pro$lem(


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0irus mutatesand the proteins on itsouter surface !gp18 and gp71"

change. These surface proteins are not

recogniGed $y the immune systemsmemory cells.

2utants survive immune systemonslaught and $egin new round ofinfection


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Each round of infection reduces thenum$ers of helper T cells $ecause theyare infected $y virus and destroyed.

6urthermore* $ecause each lineage of Tcells has a limited capacity for replicationafter a %nite num$er of rounds of

replication the $odyIs supply of helper Tcells $ecomes exhausted and the immunesystem eventually is overwhelmed andcollapses.


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'hy is /0 hard to treat(?rug resistance.

AZT !aGidothymidine" was the %rst /0wonder drug

t wors $y interfering with /0Isreverse transcriptase* which is theenGyme the virus uses to convert its#A into ?#A so it can $e inserted in

the hostIs geneome.


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AZT is similar to thymidine !one of 7$ases of ?#A nucleotides" $ut it has an

aGide group !#K" in place of hydroxylgroup !L/".

An AZT molecule added to ?#A strandprevents the strand from growing. TheaGide $locs the attachment of nextnucleotide in the ?#A chain.


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AZT successful in tests although withserious side e+ects.

ut patients uicly stoppedresponding to treatment.

Evolution of AZT-resistant /0 inpatients usually too only a$out Bmonths.


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/ow does resistant virusdi+er(

The reverse transcriptase gene inresistant strains di+ers genetically fromnon-resistant strains.

2utations are located in active site ofreverse transcriptase.

These changes selectively $loc the

$inding of AZT to ?#A $ut allow othernucleotides to $e added.


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/ow did resistancedevelop(

/0 reverse transcriptase very errorprone.

A$out half of all ?#A transcriptsproduced contain an error !mutation".

/0 highest mutation rate nown.

There is thus 0AATL# in the /0population in a patient.


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/igh mutation rate maes theoccurrence 3ust $y chance of AZT-resistant mutations almost certain.

#AT)AJ &EJECTL# now starts to actin the presence of AZT


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&election in action

The presence of AZT suppressesreplication of non-resistant strains.

esistant strains are ETTE A?ADTE?to the environment.

esistant strains reproduce morerapidly. There is thus ?66EE#TAJ

EDL?)CT0E &)CCE&& of /0strains. esistant strains produce moreo+spring.


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&election in action

esistant strains replicate and pass ontheir resistant genes to the nextgeneration.

Thus resistance is /ETAJE.


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&election in action

AZT-resistant strains replace non-resistant strains. The /0 gene poolchanges from one generation to thenext.

E0LJ)TL# has occurred: emem$er

E0LJ)TL# is change in the gene poolfrom one generation to the next.


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Evolution of /0 population in an individual patient


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Drocess of natural selection

There is variation in population= somemem$ers of population $etter adaptedthan others

Thatvariation afects reproductivesuccess= there is di+erential reproductivesuccess as a result of natural selection.

ecausethevariation is heritable=$ene%cial alleles passed to o+spring andalleles $ecome more common in nextgeneration.


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)sing selection to devise$etter treatment regimens.

&everal di+erent types of drugs have$een developed to treat /0. everse transcriptase inhi$itors !e.g. AZT".

Drotease inhi$itors !prevent /0 fromproducing %nal viral proteins fromprecursor proteins".

6usion inhi$itors prevent /0 entering cells.

ntegrase inhi$itors prevent /0 frominserting /0 ?#A into hostIs genome.

i l i d i


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ecause /0 mutates so rapidlytreatment with a single drug will not $esuccessful for long.

s there a $etter way(

) i l i d i


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2ost successful approach has $een touse multi-drug coctails !referred to as/AAT 4/ighly Active Anti-etroviral

Treatments5

/AAT coctails usually use threedi+erent drugs in com$ination !e.g. two

reverse transcriptase inhi$itors and aprotease inhi$itor".

) i l i d i


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)sing multi-drug coctails sets theevolutionary $ar higher for /0.

To $e resistant a virus particle mustpossess mutations against all threedrugs. The chances of this occurring isa single virus particle are very low.

) i l ti t d i


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f the same drugs were provided inseuence to an /0 population eachtime it faced a new drug it would needonly a single mutation to gainresistance* which would then spreadthrough the population.

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L+ering drugs one at a time isanalagous to providing a stairway that/0 must clim$. L+ering multipledrugs at once reuires /0 to leap fromthe $ottom to the top in a single$ound* which is much more diMcult

) i l ti t d i


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2ulti-drug treatments have provenvery successful in reducing viral loadand reducing mortality of patients.


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) i l ti t d i


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/owever* /0 infection is not cured.eservoir of /0 hides in resting white$lood cells. Datients who go o+ /AATtherapy experience increased /0loads.

) i l ti t d i


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6or patients on /AAT whether /0replication is stopped completely or not iscrucial. n some /0 appears dormant

and no replication means no evolution.

n other patients replication occurs*

although slowly. /owever* this allows /0to mutate and resistance to develop. &ofar* few /AAT regimens are e+ective formore than K years.

) i l ti t d i


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Lther downside of /AAT therapy isthat many patients experience severeside e+ects.

These patients have diMcultiesmaintaining their treatment regimen.

)sing selection to de ise


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ecause of severe side e+ects of/AAT therapy some doctors haveadvocated ,drug holidays for theirpatients !i.e. to have patients stoptaing drugs for a while". 6rom anevolutionary perspective does this

seem lie a good idea or not(


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Lrigins of /0

'here did /0 come from(

/0 similar to viruses in moneys called&0 !simian immunode%ciency virus".

To identify ancestry of /0 scientists

have seuenced various /0 strainsand compared them to various &0strains.


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Lrigins of /0

/0-1 is most similar to an &0 found inchimps and /0- is most similar to an&0 found in a money called the sootymanga$ey.


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Lrigins of /0

/0-1 occurs in three di+erentsu$groups !called 2*# and L" and eachappears closely related to a di+erentchimpanGee &0 strain.


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Lrigins of /0

Thus appears that /0-1 3umped tohumans from chimps on at least Koccasions.

2ost liely acuired through illing and$utchering chimps and moneys in the

,$ushmeat trade.

'hen did /0 move to


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'hen did /0 move tohumans(

&euence data from several group 2strains has $een used estimate when /0moved from chimps to humans.

Hor$er et al. !888" analyGed nucleotideseuence data for 19@ samples of /0-1

strain 2. Constructed a phylogenetic treeshowing relatedness to a commonancestor of the 19@ samples.


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'hen did /0 move to


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'hen did /0 move tohumans(

Extrapolating $ased on rates of changeof di+erent strains suggests thatsu$group 2 pro$a$ly infected humansin the early 1@K8Is.


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ene%ts of evolutionary


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ene%ts of evolutionaryunderstanding

To summariGe: our understanding ofevolutionary $iology has ena$led us tounderstand why /0 is so hard to treat*devise treatment methods that taeevolution into account and reconstructthe liely history of the disease.

Common misconceptions


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Common misconceptionsa$out Evolution

The process of Evolution is widelymisunderstood and most people haveonly a vague understanding of theprinciple mechanisms !naturalselection* genetic drift" $y which itoccurs.

As a result there are manymisperceptions a$out how evolution

occurs.


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Evolution is ,3ust a theory

All scienti%c theories are $aced $y multiple linesof evidence

A theory is not 3ust a ,hunch. All theories provide

$road* overarching explanations for ma3or aspects ofthe natural world and have $een extensively testedover time.

Lther scienti%c theories

Nravity

Dlate tectonics

Nerm theory

Evolutionary theory is overwhelmingly accepted$y scientists

Evolutionary $iologists understand


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Evolutionary $iologists understandeverything a$out the history of life

iologists continually discover newinformation a$out life and the$iological world.

All that new information %ts or isunderstood within the context of anevolutionary framewor * $ecauseevolutionary theory provides a unifyingframewor for all $iology.

Evolution explains the


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Evolution explains theorigin of life

Evolution deals with how life haschanged after it originated

Lther scienti%c %elds address the origin

of life* $ut an understanding ofevolution especially the process ofnatural selection* is relevant todiscussions of lifeIs origins.

Evolutionary $iologists


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Evolutionary $iologistssearch for missing lins

#ewspaper reports always seem tofocus on ,missing lins. n reality* thefossil record is very incomplete and%nding a direct ancestor of a particularorganism is unliely.

Availa$le evidence strongly supports

relationships $etween current and pastspecies and fossil evidence sheds lighton how traits evolved.

Evolution violates the second


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Evolution violates the secondlaw of thermodynamics

The second law holds that disorderincreases in closedsystems !entropyalways increases".

/owever* the Earth is nota closedsystem $ecause the sun provides a

constant input of energy.

Evolution is natural


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Evolution is naturalselection

#atural selection is a cruciallyimportant mechanismof evolutionarychange $ut it is not the only one

Lther mechanisms include:

Nenetic drift

&exual selection


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Evolution is entirely random

Evolution includes random and non-randomcomponents

2utations occur randomly

/owever* natural selection is completely non-

random and it results in the spread of mutationsthat increase the survival and reproduction of theorganisms that possess them.

Convergent evolutionalso demonstrates

that evolution is non-random Dhenotypes are predicta$le when environments

are similar

Lrganisms evolve


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Lrganisms evolveadaptations they ,need

Evolution cannot identify or anticipatethe needs of an organism

2utations do not occur $ecause they

would $e adaptive in an environment

f $ene%cial mutations happento occur $ychance they may increase in freuencythrough selection

Evolution is a march of


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Evolution is a march ofprogress

Evolution is not ladder-lie #ew species result from $ranching events

Evolutionary patterns are $ush-lie not ladder-lie.

Evolution always moves


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Evolution always movesfrom simple to complex

Evolution can also move from complexto simple

e.g. mitochondria evolved from free-living

$acteria

Darasitic tapeworms do not possess a gut$ecause they live attached to theintestines of their host and have no needto digest their own food. They 3ust a$sor$predigested nutrients from theirsurroundings.

Evolution results from individuals


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Evolution results from individualsadapting to environment

Evolution only wors on inherited traits

Acuired changes are not passed too+spring. #o matter how much you

practice a musical instrument you cannotpass that a$ility on to your child.

PopulationsevolveO individuals do not

Evolution results from changes in allelefreuencies that result from the success orfailure of individuals to reproduce !e.g. as aresult of natural selection or sexual

selection"

Lrganisms are perfectly


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Lrganisms are perfectlyadapted to their environment

#atural selection can only wor withavaila$le variation

Constrained $y physical limitations and

development

2any traits involved in trade-o+s

e.g. human $rain siGe

&tructures may have to perform multipledi+erent tass and cannot $e eually goodat all of them

Evolution happens for the


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Evolution happens for thegood of the species

Evolution selects traits that are$ene%cial for individuals or their genes

Traits that are $ad for individuals !or

genes" will not $e selected even if they aregood for the species

Evolution promotes


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Evolution promotessel%shness and cruelty

#atural selection favors traits thatincrease reproductive success

?i+erent conditions select for di+erent

traits

Cooperative traits are $ene%cial undermany conditions.

Cruelty is a human concept #ature is notcruel. ather #ature is pitilesslyindi+erent.

Evolution sees peaceful


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Evolution sees peacefulharmony in nature

#atural selection favors traits thatincrease reproductive success

Can result in overexploitation of resources*

ha$itat destruction* the extinction of otherspecies and many other non-harmoniousoutcomes.

Jife can $e divided into


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Jife can $e divided intohigher and lower forms

All of life is adapted to the environment innumerous ways

Environments di+er so the adaptations to succeed indi+erent environments di+er also.

Lne organism is not ,superior to another organism3ust $ecause we thin itIs simpler. 6or example* a3elly%sh is $eautifully adapted to the role of a


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Evolution has produced asta$le diversity of life

Extinction means diversity is not sta$le 2ore than @@F of all species that have ever

existed are extinct.

There has and always will $e constantturnover in the diversity of life.

Documents

Chapter 1 Intro Biological Evolution--Study Version