Ch20 Hartwell4e

PowerPo|nt to accompany
Cenet|cs: From Cenes to

Cenomes
Fourth Ed|t|on
Le|and h. hartwe||, Leroy hood, H|chae| L.
Co|dberg, Ann E. Reyno|ds, and Lee H. 8||ver
Prepared by Hary A. ede||
Un|vers|ty of Ceorg|a
1 6opyr|ght @ The HcCraw-h||| 6ompan|es, |nc. Perm|ss|on requ|red to reproduce or d|sp|ay hartwe|| et a|., 4th ed|t|on
8eyord lre lrd|v|dua| 0ere ard 0erore 8eyord lre lrd|v|dua| 0ere ard 0erore
PART V| PART V|
6opyr|ght @ The HcCraw-h||| 6ompan|es, |nc. Perm|ss|on requ|red to reproduce or d|sp|ay hartwe|| et a|., 4th ed|t|on,
6hapter
Evo|ut|on at the
Ho|ecu|ar Leve|
20.1 Tre 0r|g|r ol L|le or Earlr
20.2 Tre Evo|ul|or ol 0erores
20.3 Tre 0rgar|zal|or ol 0erores
20.1 A Corprerers|ve Exarp|e: Rap|d Evo|ul|or |r lre lrrure Resporse ard |r llv
CPA1L8 Cu1LlnL CPA1L8 Cu1LlnL
ClAPTER ClAPTER ClAPTER ClAPTER
6har|es 0arw|n's theory of evo|ut|on 6har|es 0arw|n's theory of evo|ut|on
"0n the 0rigin of 3pecies by Means of hatural 3election"
W Pub||shed |n 1859, based on 5 years of co||ect|ng spec|mens from
around the g|obe
Three pr|nc|p|es:
W Var|at|on ex|sts among |nd|v|dua|s of a popu|at|on
W Var|ant forms of tra|ts can be |nher|ted
W 8ome var|ant tra|ts confer an |ncreased chance of surv|v|ng and
reproduc|ng
6hapter

The or|g|n of ||fe on earth The or|g|n of ||fe on earth
8e|f-rep||cat|ng mo|ecu|es may have |ed to the comp|ex|ty of ce||s
The f|rst step |n ||fe had to fu|f||| three requ|rements:
W Encode |nformat|on by var|at|on of |etters |n str|ngs of a s|mp|e
d|g|ta| a|phabet
W Fo|d |n three d|mens|ons to create mo|ecu|es capab|e of se|f-
rep||cat|on and other funct|ons
W Expand the popu|at|on of successfu| mo|ecu|es through se|ect|ve
se|f-rep||cat|on
6hapter
4
The RNA wor|d The RNA wor|d
198s, Thomas 6ech d|scovered r|bozymes - RNA that can cata|yze
chem|ca| react|ons
6hapter
5
|g 20.1
RNA sat|sf|es a|| three requ|rements of the f|rst
rep||cator: ||near str|ngs encode |nformat|on,
fo|ds |nto a -d|mens|ona| mo|ecu|ar mach|ne,
reproduces |tse|f
|ntr|ns|c d|sadvantages of RNA
W Re|at|ve|y unstab|e
W L|m|ted capab|||ty for -d|mens|ona| fo|d|ng
compared to prote|ns
W No record of |ntermed|ates between an RNA
wor|d and ce|| comp|ex|t|es
Evo|ut|on of ||v|ng organ|sms Evo|ut|on of ||v|ng organ|sms
4.5 b||||on yrs ago - coa|escence of p|anet earth
4. b||||on yrs ago - emergence of |nformat|ona| RNA
.7 b||||on yrs ago - ||fe began
.5 b||||on yrs ago - o|dest foss|||zed ce||s (see F|g .
1.4 b||||on yrs ago - emergence of eukaryotes
W 8ymb|ot|c |ncorporat|on of s|ng|e-ce||ed organ|sms |nto other s|ng|e-ce||ed
organ|sms
W 6omp|ex compartmenta||zat|on of ce|| |nter|or (nuc|eus
1 b||||on yrs ago - ancestors of p|ants and an|ma|s d|verged
.57 b||||on yrs ago - exp|os|ve appearance of mu|t|ce||u|ar an|ma|s
(metazoans and p|ants
6hapter

L|v|ng organ|sms evo|ved |nto three k|ngdoms L|v|ng organ|sms evo|ved |nto three k|ngdoms
6hapter
7
|g 20.3
The |ength of the branches |s proport|ona| to the t|mes of spec|es
d|vergence
The urgess sha|e of southeastern The urgess sha|e of southeastern
r|t|sh 6o|umb|a r|t|sh 6o|umb|a
0ne of the most amaz|ng f|nds |n pa|eonto|ogy!
Enormous d|vers|ty |n body p|ans - many are ext|nct but some st||| ex|st
Punctuated evo|ut|on - short per|ods of exp|os|ve change
A|| bas|c body p|ans of metazoans are represented
6hapter
8
|g 20.1
The evo|ut|on of humans The evo|ut|on of humans
5 m||||on yrs ago - humans arose from a common ancestor to most
contemporary pr|mates
m||||on yrs ago - d|vergence of humans and ch|mpanzees from a
common ancestor
6hapter
9
|g 20.5
8|m||ar|t|es between ch|mps and humans 8|m||ar|t|es between ch|mps and humans
Cenomes are 997 s|m||ar
Karyotypes are near|y the same (see F|g 1.11
No s|gn|f|cant d|fferences |n gene funct|on
0|fferences between spec|es may have been caused by on|y a few
thousand |so|ated genet|c changes
8pec|es-spec|f|c d|fferences probab|y occurred because of a|terat|ons |n
regu|atory sequences
6hapter
1
0NA a|terat|ons form the bas|s of 0NA a|terat|ons form the bas|s of
genom|c evo|ut|on genom|c evo|ut|on
New mutat|ons prov|de a cont|nuous source of var|at|on
Rep|acement of |nd|v|dua| nuc|eot|des |n cod|ng reg|ons:
W 8ynonymous - subst|tut|ons have no effect on encoded am|no ac|d
W Nonsynonymous - subst|tut|ons cause change |n am|no ac|d or
premature term|nat|on codon
0rder and types of transcr|pt|on factor b|nd|ng s|tes |n gene promoters
can be a|tered
Hutat|ons can be de|eter|ous, neutra|, or favorab|e
6hapter
11
6|ass|f|cat|on of mutat|ons accord|ng to effect 6|ass|f|cat|on of mutat|ons accord|ng to effect
Neutra| mutat|ons are not affected by the agents of se|ect|on
W 8urv|ve or d|sappear from a popu|at|on by genet|c dr|ft
W 8ynonymous mutat|ons can produce m|nute advantage or
d|sadvantage
Ava||ab|||ty of d|fferent tRNAs and tRNA-synthetases?
0e|et|ons and |nsert|ons a|most certa|n|y have an effect
Hutat|ons w|th on|y de|eter|ous effects d|sappear because of negat|ve
se|ect|on
Hutat|ons w|th advantageous effects w||| |ncrease |n the popu|at|on
because of pos|t|ve se|ect|on
W Hay become f|xed |n the popu|at|on
6hapter
1
Cene regu|atory networks may dom|nate deve|opmenta| Cene regu|atory networks may dom|nate deve|opmenta|
evo|ut|on evo|ut|on
8ea urch|ns and sea stars d|verged - 5 m||||on yrs ago
ut, they share some bas|c gene networks (F|g .b
6hapter
1
|g 20.a
Cene regu|atory Cene regu|atory
networks |n networks |n
sea urch|ns sea urch|ns
and |n sea stars and |n sea stars
6hapter
14
Rew|r|ng of a gene
regu|atory network can
encode enormous
phenotype change
|g 20.o
An |ncrease |n genome s|ze genera||y corre|ates w|th An |ncrease |n genome s|ze genera||y corre|ates w|th
evo|ut|on of comp|ex|ty evo|ut|on of comp|ex|ty
0up||cat|on and d|vers|f|cat|on of genom|c reg|ons
W 6an occur at random throughout genome
W 8|zes range from a few nuc|eot|des to the ent|re genome
W 6an occur through transpos|t|on or unequa| cross|ng-over
W E|ther the or|g|na| or copy of the gene can accumu|ate mutat|ons
Acqu|s|t|on of repet|t|ve sequences - can make up more than 57 of a
genome
6hapter
15
Transpos|t|on may occur through exc|s|ng and Transpos|t|on may occur through exc|s|ng and
re|nsert|ng the 0NA segment re|nsert|ng the 0NA segment
6hapter
1
|g 20.Za
Transpos|t|on events that produce dup||cat|ons Transpos|t|on events that produce dup||cat|ons
Transpos|t|on through an RNA
|ntermed|ate
6hapter
17
Transpos|t|on through a 0NA
|ntermed|ate
|g 20.Zo |g 20.Zc
Transpos|t|on through Transpos|t|on through
d|rect movement of a 0NA d|rect movement of a 0NA
sequence sequence
After transpos|t|on occurs |n a
germ ce||, the new copy of the
transposon may become f|xed |n
the next generat|on
6hapter
18
|g 20.8
0up||cat|ons resu|t|ng from 0up||cat|ons resu|t|ng from
unequa| cross|ng unequa| cross|ng-- over over
A|so referred to as "|||eg|t|mate
recomb|nat|on"
Hed|ated by sequence s|m||ar|ty
between re|ated sequences |ocated
c|ose to each other
After the |n|t|a| dup||cat|on,
subsequent rounds of unequa|
cross|ng over can occur read||y
6hapter
19
|g 20.9
0up||cated genes can evo|ve |nto 0up||cated genes can evo|ve |nto
pseudogenes or evo|ve new funct|ons pseudogenes or evo|ve new funct|ons
Pseudogenes - nonfunct|ona| genes that resu|ts from random mutat|ons
|n a dup||cated gene
W Loss of regu|atory funct|on, subst|tut|ons at cr|t|ca| am|no ac|ds,
premature term|nat|on, frame-sh|ft mutat|on, a|tered sp||c|ng
patterns
W Accumu|ate mutat|ons at a fast pace
New funct|ons can ar|se |n a dup||cated gene
W Random mutat|ons prov|de se|ect|ve advantage to the organ|sm
W The new gene usua||y has a nove| pattern of express|on
6hapter

Evo|ut|onary h|stor|es are d|agrammed Evo|ut|onary h|stor|es are d|agrammed
|n phy|ogenet|c trees |n phy|ogenet|c trees
6hapter
1
|g 20.10
Ho|ecu|ar c|ock - prov|des a good est|mate
of t|me of d|vergence because rate of
evo|ut|on |s constant across a|| ||neages
Phy|ogenet|c tree |||ustrates
re|atedness of homo|ogous gene or
prote|ns
W Nodes are taxonom|c un|ts
W ranch |engths represent t|me that
has e|apsed
Four |eve|s of gene dup||cat|on have fue|ed evo|ut|on of Four |eve|s of gene dup||cat|on have fue|ed evo|ut|on of
comp|ex genomes comp|ex genomes
At each |eve|, d|vers|f|cat|on and se|ect|on can occur
W Exons dup||cate or shuff|e
W Ent|re genes dup||cate to create mu|t|gene fam|||es
W Hu|t|gene fam|||es dup||cate to produce gene superfam|||es
W Ent|re genome dup||cates to doub|e the number of cop|es of every
gene and gene fam|||es
6hapter

0up||cat|ons create 0up||cat|ons create
mu|t|gene fam|||es mu|t|gene fam|||es
and gene superfam|||es and gene superfam|||es
h|erarch|ca| generat|on of greater
amounts of new |nformat|on at
each |eve|
6hapter

|g 20.11
The bas|c structure of a gene The bas|c structure of a gene
6hapter
4
|g 20.12
0oma|ns |n ant|body prote|ns 0oma|ns |n ant|body prote|ns
0|screte exons can
encode the structura| and
funct|ona| doma|ns of a
prote|n
0up||cat|on of exons, can
create tandem funct|ona|
doma|ns
6hapter
5
|g 20.13
The t|ssue p|asm|nogen act|vator gene evo|ved from The t|ssue p|asm|nogen act|vator gene evo|ved from
shuff||ng of three genes shuff||ng of three genes
New prote|ns w|th d|fferent comb|nat|ons of funct|ons can be created by
exon shuff||ng
6hapter

|g 20.11
0up||cat|ons of ent|re gene can create mu|t|gene fam|||es 0up||cat|ons of ent|re gene can create mu|t|gene fam|||es
Hu|t|gene fam||y - set of genes descended by dup||cat|on and
d|vers|f|cat|on from one ancestra| gene
6hapter
7
|g 20.15
Unequa| cross|ng over can expand and contract gene Unequa| cross|ng over can expand and contract gene
numbers |n mu|t|gene fam|||es numbers |n mu|t|gene fam|||es
6hapter
8
|g 20.1
|ntergen|c gene convers|on can |ncrease var|at|on |n |ntergen|c gene convers|on can |ncrease var|at|on |n
members of a mu|t|gene fam||y members of a mu|t|gene fam||y
A|ternat|ve outcome to
unequa| cross|ng-over
A||ows transfer of
|nformat|on from one gene
to another
6hapter
9
|g 20.1Z
|ncreas|ng the number of a||e|es through |ncreas|ng the number of a||e|es through
gene convers|on gene convers|on
Hajor h|stocompat|b|||ty comp|ex (Hh6 of m|ce - a pseudogene fam||y
was the reservo|r of genet|c |nformat|on to produce a dramat|c |ncrease
|n var|at|on
6hapter

|g 20.18
6oncerted evo|ut|on can |ead to 6oncerted evo|ut|on can |ead to
gene homogene|ty gene homogene|ty
6hapter
1
|g 20.19
Evo|ut|on of gene superfam|||es Evo|ut|on of gene superfam|||es
Cene superfam||y - |arge set of re|ated genes that |s d|v|s|b|e |nto sma||er
fam|||es
Cenes |n each fam||y are more c|ose|y re|ated to each other than to other
members of the superfam||y
Repeated gene dup||cat|on events fo||owed by d|vergence
C|ob|n gene superfam||y - three branches |n a|| vertebrates
W Two mu|t|gene fam|||es (p-||ke genes and d-||ke genes and a s|ng|e
myog|ob|n gene
ox gene superfam||y - four branches |n m|ce, on|y one |n 0rosophila
6hapter

Evo|ut|on of the mouse g|ob|n superfam||y Evo|ut|on of the mouse g|ob|n superfam||y
6hapter

|g 20.20
Evo|ut|on of the Evo|ut|on of the ox ox gene superfam||y of mouse and gene superfam||y of mouse and
0rosophila 0rosophila
6hapter
4
|g 20.21
Repet|t|ve "nonfunct|ona|" 0NA fam|||es const|tute near|y Repet|t|ve "nonfunct|ona|" 0NA fam|||es const|tute near|y
one one--ha|f of the genome ha|f of the genome
Hany repet|t|ve nonfunct|ona| 0NA fam|||es cons|st of retrov|ra| e|ements
that have |ntegrated |nto the host
W Prov|rus can be act|ve or |nact|ve
Long |Nterspersed E|ements - L|NE fam||y
W "8e|f|sh 0NA", encodes reverse transcr|ptase
W Very o|d fam||y, ex|sts |n many organ|sms
W Hay have been source mater|a| for retrov|ruses
8hort |Nterspersed E|ements - 8|NE fam||y (e.g. A|u e|ement |n humans
W 0oes not encode reverse transcr|ptase
W Evo|ved from sma|| ce||u|ar RNAs
6hapter
5
6reat|on of a L|NE gene fam||y 6reat|on of a L|NE gene fam||y
6hapter

|g 20.22
6reat|on of a 8|NE gene fam||y 6reat|on of a 8|NE gene fam||y
8|NEs depend on ava||ab|||ty of reverse transcr|ptase encoded by other
e|ements (L|NEs or retrov|ruses
6hapter
7
|g 20.23
The potent|a| se|ect|ve advantage of The potent|a| se|ect|ve advantage of
se|f|sh e|ements se|f|sh e|ements
8|NEs and L|NEs have had profound |mpacts on who|e-genome evo|ut|on
6ata|yze unequa| homo|ogous crossover events
W These dup||cat|on events can |n|t|ate format|on of mu|t|gene
fam|||es
8ome evo|ved regu|atory funct|ons - can act as enhancers or promoters
6hapter
8
8|mp|e sequence repeats (88Rs 8|mp|e sequence repeats (88Rs
Tandem, nonfunct|ona| repeats scattered throughout mamma||an
genomes
Vary |n s|ze of repeat|ng un|ts ( - 1s of nuc|eot|des
H|crosate|||tes, m|n|sate|||tes, and macrosate|||tes
Very usefu| mo|ecu|ar markers for genome ana|ys|s and genotyp|ng
(6hapter 11
h|gh|y suscept|b|e to unequa| cross|ng-over and are h|gh|y po|ymorph|c
|n s|ze
6hapter
9
6entromeres and te|omeres conta|n 6entromeres and te|omeres conta|n
many repeat sequences many repeat sequences
6entromeres - tandem arrays of noncod|ng sequences that |nteract w|th
m|tot|c and me|ot|c sp|nd|e f|bers
We.g. human a|pho|d 0NA - 171 bp repeat that extends > 1 Hb on e|ther s|de of
centromere |n each chromosome
WEach repeat |s < bp |n |ength
W|ncrease eff|c|ency and|or accuracy of chromosome segregat|on
Te|omeres - tandem arrays of noncod|ng sequences that are at ends of
a|| mamma||an chromosomes
WArrays are 5 - 1 kb |n |ength
WEach repeat |s bp |n |ength
WEssent|a| ro|e |n ma|nta|n|ng chromosome |ength
6hapter
4
A comprehens|ve examp|e: Rap|d evo|ut|on |n the A comprehens|ve examp|e: Rap|d evo|ut|on |n the
|mmune response and |n h|V |mmune response and |n h|V
Evo|ut|onary batt|e at the mo|ecu|ar |eve| between the A|08 v|rus and
ce||s of the |mmune system
After v|ra| |nfect|on, v|rus-spec|f|c |mmune response ensues that can
destroy the pathogen
h|V has a h|gh mutat|on rate and |s ab|e to d|vers|ty and amp||fy |tse|f v|a
se|ect|on
8peed of v|ra| evo|ut|on |s faster than the |mmune response
Effect|ve tr|p|e-drug therap|es act to reduce the rate of v|ra| rep||cat|on
6hapter
41
The |mmune response The |mmune response
0|fferent|ated ce||s secrete
ant|bod|es that destroy or neutra||ze
ant|gens
Expanded numbers of memory T
ce||s and ce||s a||ow a rap|d
response to the
nd
encounter w|th
an ant|gen
6hapter
4
|g 20.21

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