L27-Molecular Evolution+Evolution in Geological Time

Mutations Frameshift mutations can cause major amino acid changes, resulting in genetic diseases -anemia due to unbalanced globin protein production (thalassemia)

Mutations Chromosomal mutations that affect copy number (‘ploidy’) and rearrangements Arise frequently during meiosis generally lethal trisomy 21-Down’s

Gene duplications

Gene duplications -”supplies raw material for biological evolution” -Jianzhi Zhang, TREE -redundant functions facilitate emergence of new functions through the acquisition of mutations (1 gene /100 My in verts.) --leucine biosynthesis + TCA cycle --red + green sensitive opsins in humans

A

duplication&

divergence

B C

1 2

enzyme

substrate

Gene duplications and new functions Subfunctionalization- paralogous ’division of labor’ Neofunctionalization-paralogs evolve novel attributes RNASE -> RNASE1 + RNASE1B -facilitates persistence on plant material -N acquired from cellulolytic gut bacteria

A

duplication&

divergence

B C

1 2

enzyme

substrate

Gene duplications -retention of ancestral functions balanced by acquisition of mutations Duplicate genes acquire deleterious mutations and are pseudogenized

enzyme

substrate

A

gene lossB C

1 2

moonlighting

Evolutionary forces behind gene duplication Dykhuisen-Hartl theory: random mutations are fixed in one gene under relaxed purifying selection, which is the result of reduced functional constraint provided by the redundancy >no need for positive selection

Evolutionary forces behind gene duplication Dykhuisen-Hartl theory: random mutations are fixed in one gene under relaxed purifying selection, which is the result of reduced functional constraint provided by the redundancy >no need for positive selection Multifunctional specialization: positive selection drives a multifunction-encoding gene to specialize, as enabled by the redundancy.

Mutations in nonprotein coding DNA Transcriptional regulation mutations can interfere with appropriate temporal or conditional expression Mobile genetic elements (transposons) likely not under selection, and can change, as well as introduce indel mutations (Micro)satellites repetitive sequences dispersed throughout the genome -Huntington’s (>35 CAG repeats) -useful for phylogenetic/forensic analyses

Measuring genetic change

transitional states are not always available multiple substitutions can obscure evolutionary history

Measuring genetic change Models of sequence evolution used to correct for differences between observed and expected species divergence

DNA substitution models of evolution Jukes-Cantor (homologous) -equal probability of character change Kimura Two-Parameter -pur->pur changes more likely than pur->pyr

DNA substitution models of evolution Felsenstein 1981 (F81) -similar to JC and K2P -accounts for base composition (25-75%) -assumes even distribution of base composition Thermus and Deinococcus are closely related but trees using base composition may not group them

DNA substitution models of evolution Felsenstein 1981 (F81) -similar to JC and K2P -accounts for base composition (25-75%) -assumes even distribution of base composition Hasegawa-Kishino-Yano 1985 (HKY85) -merges K2P and F81 Likelihood tests are used to evaluate the appropriateness of the model.

Frequencies of substitutions by nucleotide feature Empirical evidence about rates of change in different regions can parameterized to inform models sequence evolution

Nonuniform nucleotide site variation Limitations on sites that can vary can impact the rate of sequence divergence (A) can vary at 80% of sites at a rate of 0.5%/My but (B) varies at 50% of sites at a rate of 2%/My While site changes saturate more rapidly in (B) than (A), one might incorrectly infer that (B) is evolving more quickly.

Models of molecular evolution Haemoglobin alpha-globin present in most verts Comparison of a.a. changes between increasing different species shows a proportional increase in seq. distance Steady rate of change suggests that a-globin behaves in like a molecular clock

Models of molecular evolution Natural selection acts to remove deleterious mutations (purifying) while fixing those that confer fitness benefits (positive) -experimental evidence showed that at many loci up to an average of 30% polymorphism exist with an average heterozygosity of 11% If most mutations are deleterious, how can so much variation be maintained in populations

Models of molecular evolution If most mutations are deleterious, how can so much variation be maintained in populations? Neutral mutations are those that do not confer selective costs

What type of mutation would most likely be neutral?  

A.  synonymous  B.  frameshi1  C.  nonsynonymous  D.  4  nucleo7de  indel  

Models of molecular evolution If most mutations are deleterious, how can so much variation be maintained in populations? Neutral mutations are those that do not confer selective costs Motoo Kimura 1st proposed the neutral theory of evolution in 1969 -deleterious and selectively removed -neutral and slight chance of fixation

Models of molecular evolution Functional constraint strongly impacts the frequency of deleterious and neutral mutations and the rate of substitutions. Alpha-globins (essential for hemoglobin function) are under considerable functional constraint.

L27-Molecular Evolution+Evolution in Geological Time

Walker, J.D., Geissman, J.W., Bowring, S.A., and Babcock, L.E., compilers, 2012, Geologic Time Scale v. 4.0: Geological Society of America, doi: 10.1130/2012.CTS004R3C. ©2012 The Geological Society of America.

237

70

80

90

100

110

120

130

140

150

160

170

180

190

210

200

220

230

240

250

5

10

15

20

25

30

35

40

45

50

55

60

65

750

1000

1250

1500

1750

2000

2250

2500

2750

3000

3250

3500

3750

260

280

300

320

340

380

360

400

420

440

460

480

500

520

540

4000

HIS

T

AN

OM

.

CH

RO

N.

C31

C32

C33

31

32

33

M0rM1

M5

M10

M12M14M16M18M20

M22

M25

M29

M3

RA

PID

PO

LAR

ITY

CH

AN

GE

S

30 C30

C3434

1 C1

C2

C2A

C3

C3A

C4

C4A

C6

C6A

C6B

C6C

C7

C8

C9

C10

C11

C12

C13

C15C16

C17

C18

C19

C20

C21

C22

C23

C24

C25

C26

C27

C28

C29

C7A

C5

C5A

C5B

C5CC5D

C5E

2

2A

3

3A

4

4A

5

5B

5A

5C

6

6A

6B

7

8

9

10

11

12

13

1516

17

18

19

20

21

22

23

24

25

28

29

26

27

7A

6C

5D

5E

30 C30

PALEOZOIC

PER

MIA

ND

EVO

NIA

NO

RD

OVI

CIA

NSI

LUR

IAN

MIS

SIS

-S

IPP

IAN

PE

NN

SY

L-VA

NIA

N

CAM

BRIA

NC

ARBO

NIF

ERO

US

AGE(Ma) EPOCH AGE PICKS

(Ma)PERIOD

252

260

254

265269272279

290296

304307

299

323

331

347

359

372

383388393

408411

419423426

433430

439441

427

444445

453458

470467

478

485

494497501505

490

509 514

521

529

541

GZHELIANKASIMOVIAN

MOSCOVIAN

BASHKIRIAN

SERPUKHOVIAN

VISEAN

TOURNAISIAN

FAMENNIAN

FRASNIAN

GIVETIANEIFELIAN

EMSIAN

PRAGIANLOCHKOVIAN

315

PRECAMBRIAN

PR

OTE

RO

ZOIC

AR

CH

EA

N

AGE(Ma)

EON ERABDY.

AGES(Ma)

1000

1200

1800

2050

2300

1400

1600

2500

2800

3200

3600

4000

Lopin-gian

MIDDLE

Guada-lupian

Cisura-lian

LLANDO-VERY

EARLY

EARLY

FURON-GIAN

Epoch 3

Epoch 2

TERRE-NEUVIAN

LATE

LUDLOW

LATE

MIDDLE

WENLOCK

541

635

850

MESOZOIC

TR

IAS

SIC

JUR

AS

SIC

CR

ETA

CE

OU

S

AGE(Ma) EPOCH AGE PICKS

(Ma)

MAGNETICPOLARITY

PERIOD PERIOD

LATE

EARLY

LATE

EARLY

MIDDLE

LATE

EARLY

MIDDLE

MAASTRICHTIAN66.0

72.1

83.686.389.8

93.9

100

113

126

131134

139

145

152

157

166164

CAMPANIAN

SANTONIANCONIACIAN

TURONIAN

CENOMANIAN

ALBIAN

APTIAN

BARREMIANHAUTERIVIAN

VALANGINIAN

BERRIASIAN

TITHONIAN

KIMMERIDGIAN

OXFORDIANCALLOVIANBATHONIANBAJOCIANAALENIAN

TOARCIAN

PLIENSBACHIAN

SINEMURIAN

HETTANGIAN

NORIAN

RHAETIAN

CARNIAN

LADINIAN

ANISIAN

OLENEKIANINDUAN

168170174

199

191

201

209

241

228

252250247

RA

PID

PO

LAR

ITY

CH

AN

GE

S

CENOZOICAGE(Ma) EPOCH AGE PICKS

(Ma)

MAGNETICPOLARITY

PERIODH

IST.

AN

OM

.

CH

RO

N.

QUATER-NARY PLEISTOCENE*

MIO

CE

NE

OLI

GO

CE

NE

EO

CE

NE

PALE

OC

EN

E

PLIOCENEPIACENZIAN

0.011.8

3.6

5.3

7.2

11.6

13.8

16.0

20.4

23.0

28.1

33.9

37.8

41.2

47.8

56.0

59.2

61.6

66.0

ZANCLEAN

MESSINIAN

TORTONIAN

SERRAVALLIAN

LANGHIAN

BURDIGALIAN

AQUITANIAN

CHATTIAN

RUPELIAN

PRIABONIAN

BARTONIAN

LUTETIAN

YPRESIAN

DANIAN

THANETIAN

SELANDIAN

CALABRIANHOLOCENE

PALE

OG

EN

EN

EO

GE

NE

GELASIAN 2.6

183

CHANGHSINGIAN

WORDIANROADIAN

WUCHIAPINGIANCAPITANIAN

KUNGURIAN

ASSELIANSAKMARIAN

ARTINSKIAN

PRIDOLILUDFORDIAN

GORSTIANHOMERIAN

RHUDDANIAN

TELYCHIANAERONIAN

SHEINWOODIAN

HIRNANTIAN

SANDBIANKATIAN

DARRIWILIANDAPINGIAN

AGE 10JIANGSHANIAN

PAIBIANGUZHANGIAN

DRUMIANAGE 5AGE 4

AGE 3

AGE 2

FORTUNIAN

FLOIAN

TREMADOCIAN

EDIACARAN

CRYOGENIAN

TONIAN

STENIAN

ECTASIAN

CALYMMIAN

STATHERIAN

OROSIRIAN

RHYACIAN

SIDERIAN

NEOPRO-TEROZOIC

MESOPRO-TEROZOIC

PALEOPRO-TEROZOIC

NEOARCHEAN

MESO-ARCHEAN

PALEO-ARCHEAN

EOARCHEAN

HADEAN

EARLY

EARLY

MIDDLE

MIDDLE

LATE

LATE

*The Pleistocene is divided into four ages, but only two are shown here. What is shown as Calabrian is actually three ages—Calabrian from 1.8 to 0.78 Ma, Middle from 0.78 to 0.13 Ma, and Late from 0.13 to 0.01 Ma.

The Cenozoic, Mesozoic, and Paleozoic are the Eras of the Phanerozoic Eon. Names of units and age boundaries follow the Gradstein et al. (2012) and Cohen et al. (2012) compilations. Age estimates and picks of boundaries are rounded to the nearest whole number (1 Ma) for the pre-Cenomanian, and rounded to one decimal place (100 ka) for the Cenomanian to Pleistocene interval. The numbered epochs and ages of the Cambrian are provisional.REFERENCES CITED Cohen, K.M., Finney, S., and Gibbard, P.L., 2012, International Chronostratigraphic Chart: International Commission on Stratigraphy, www.stratigraphy.org (last accessed May 2012). (Chart reproduced for the 34th International Geological Congress, Brisbane, Australia, 5–10 August 2012.) Gradstein, F.M, Ogg, J.G., Schmitz, M.D., et al., 2012, The Geologic Time Scale 2012: Boston, USA, Elsevier, DOI: 10.1016/B978-0-444-59425-9.00004-4.

GSA GEOLOGIC TIME SCALE v. 4.0

1

Evolutionary trends patterns of directional change over time Cope’s rule-mammals get larger the longer they exist passive: constraint on size active: selection for size

Evolutionary trends Active trends through parallel change or species selection

11

Phyletic Gradualism

New species arise through gradual transformation of ancestral species Darwin accepted gradualism as the primary means for species diversification -’gaps’ in the fossil record were confounding

11

Phyletic Gradualism

New species arise through gradual transformation of ancestral species

11

Punctuated Equilibria Niles Eldredge and Stephen J. Gould (1972) Prolonged stasis of well-adapted ‘forms’ (not to exclusion of less well-adapted ‘forms’) interrupted by rapid shifts from one state to another. May explain rapid evolutionary changes observed during Cambrian explosion

11

Punctuated Equilibria Niles Eldredge and Stephen J. Gould (1972) Prolonged stasis of well-adapted ‘forms’ (not to exclusion of less well-adapted ‘forms’) interrupted by rapid shifts from one state to another. Punctuated anagenesis: loss of ancestral state

Punctuated Equilibrium

• Pattern of change in the fossil record

– Long periods of little or no change (stasis) followed by rapid change – Stasis is punctuated by rapid change

• A hypothesis about the evolutionary process

– Evolutionary change accompanied speciation which occurred “off stage” in small (allopatric) populations (i.e., subpopulations of a species).

10