Ge104: Introduction to Geobiologyto geobiology, and (c) makes a breakthrough, however small, in...

Ge104: Introduction to Geobiology

Professor:Woody FischerOffice: 107 N. Mudd [x6790][email protected] hours: by appt.

Meeting Time:Lecture: TT 7-8:30pm 267 ArmsNo Lab. No Section.

Website:http://web.gps.caltech.edu/classes/ge104/ . Look here for lecture slides and exercise materials.

TA:Jena JohnsonOffice: 102 N. [email protected] hours: TBD

Sunday, September 30, 2012

mailto:[email protected]


http://web.gps.caltech.edu/classes/ge104/

http://web.gps.caltech.edu/classes/ge104/



Performance assessment:Quizzes 05%Writing (5x) 40%Midterm exam 20%Final exam 35%


Exams:There are two exams, midterm and final. Both are take home and closed book. The midterm will be 1 hour and cumulative. The final will be 3 hours and cumulative, but weighted to topics covered in the second half of the course. Important exam dates: midterm Nov. 1, final Dec. 14. Note that the final date may change depending on how we arrange the schedule at the end of the course to accommodate students attending the Fall AGU meeting.

Quizzes:There will be two short quizzes, administered in class, to test your understanding of the geological timescale [ http://www.geosociety.org/science/timescale/ ]. Tue 10/9, and Thu 11/8.


http://www.geosociety.org/science/timescale/




Writing (News & Views): This is an opportunity to practice and hone your critical reading and writing skills in the context of learning about geobiology. Every two weeks you will write a short perspective piece on a recently published study broadly related to the geobiology subdiscipline. The goal is to emulate the style, feeling, and intent of a Nature "News & Views" article. These articles are limited to 1000 words (excluding figure caption and references). They should have more than 5 but less than 12 references, and one original color figure that helps explain the interesting aspects of the study being discussed (e.g. - problem, data, methods, results, interpretation). Make it visually appealing. Choose a paper that (a) was published in the past month, (b) is on a topic of interest to you and broadly related to geobiology, and (c) makes a breakthrough, however small, in understanding an important geobiological process or event. You will need to read through a number of papers to find one that is suitable. Attached in the appendix is a list of some common journals for geobiology research. Try browsing the most recent issues or articles in press. And just because a paper already has a published perspective piece (either in Nature or Science Magazine) you can still use it for your N&V, particularly if you disagree with the perspective or see the importance of the study differently. Your N&V are due at the beginning of class on the due date. Please compile your articles into pdf format and embed your figure and caption in the text, and submit them electronically via email to Sebastian and I. At the beginning of class on the day N&Vs are due, you will be expected to give a very brief (3 minute) review of your paper to the class and field questions arising from quick discussion. N&V due dates: Oct. 9, Oct. 23, Nov. 6, Nov. 20, Dec. 4 [date may change due to AGU].


Some questions you can ask to get started: What problem is this paper addressing, and why is it important? What approach did the authors bring to bear on this problem (e.g., new methods, inverse modeling, statistical reanalysis, new observations, new theory)? Can you reconstruct the logic of the argument? How were the data interpreted? How could the data be interpreted? What did the study do right? What did it do wrong? What is the next step?


Collaboration Policy:You are expected to abide by the Caltech honor code. Present your own work. You can consult with classmates for thoughts on your News & Views exercises, but not on quizzes or exams. When researching and writing your News & Views papers, cite only references from the primary published literature.

Late Work Policy:Students are responsible for handing in work on time. Worked turned in one day late will be marked down by 25%. Work turned in thereafter (and until the final day of class) will be marked down by 50%. No late work will be accepted after the final day of class.


Goal: decipher, understand, and appreciate the interplay between life and environments

The history of the Earth is inseparable from the history of life on Earth

Fundamental Duality: process and history


The greatest contribution of Earth scientists to Science is the discovery of time.


How do we know time?

We are fortunate that Earth has recorded its history


Walker, J.D., and Geissman, J.W., compilers, 2009, Geologic Time Scale: Geological Society of America, doi: 10.1130/2009.CTS004R2C. ©2009 The Geological Society of America.

235

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

2009 GEOLOGIC TIME SCALEPALEOZOIC

PER

MIA

ND

EVO

NIA

NO

RD

OVI

CIA

NSI

LUR

IAN

MISSIS-SIPPIAN

PENNSYL-VANIAN

CAM

BRIA

N*

CAR

BON

IFER

OU

S

AGE(Ma) EPOCH AGE PICKS

(Ma)PERIOD

251

260

254

266268271276

284

297

304306

299.0

318

326

345

359

374

385

392

398

407411416419421

428426

436439

423

444446

455

461

472468

479

488

496501503507

492

510 517521

535 542

GZELIANKASIMOVIANMOSCOVIAN

BASHKIRIAN

SERPUKHOVIAN

VISEAN

TOURNAISIAN

FAMENNIAN

FRASNIAN

GIVETIAN

EIFELIANEMSIAN

PRAGHIANLOCKHOVIAN

312

PRECAMBRIAN

PR

OT

ER

OZ

OIC

AR

CH

EA

N

AGE(Ma)

EON ERABDY.

AGES(Ma)

1000

1200

1800

2050

2300

1400

1600

2500

2800

3200

3600

3850

L

M

M

E

E

E

E

Furon-gian

Series 3

Series 2

Terre-neuvian

L

L

L

M

M

542

630

850

MESOZOIC

TR

IAS

SIC

JUR

AS

SIC

CR

ETA

CE

OU

S


(Ma)

MAGNETICPOLARITY

PERIOD PERIOD

HIS

T.

AN

OM

.

CH

RO

N.

LATE

EARLY

LATE

EARLY

MIDDLE

LATE

EARLY

MIDDLE

MAASTRICHTIAN65.5

70.6

83.585.8

89.3

93.5

99.6

112

125

130

136

140

145.5

151

156

165

161

CAMPANIAN

SANTONIANCONIACIAN

TURONIAN

CENOMANIAN

ALBIAN

APTIAN

BARREMIAN

HAUTERIVIAN

VALANGINIAN

BERRIASIAN

TITHONIAN

KIMMERIDGIAN

OXFORDIAN

CALLOVIANBATHONIANBAJOCIANAALENIAN

TOARCIAN

PLIENSBACHIAN

SINEMURIAN

HETTANGIAN

NORIAN

RHAETIAN

CARNIAN

LADINIAN

ANISIANOLENEKIAN

INDUAN

C31

C32

C33

31

32

33

M0rM1

M5

M10

M12M14M16M18M20

M22

M25

M29

M3

168172

176

197

190

201.6204

241

228

251.0250

245

RA

PID

PO

LAR

ITY

CH

AN

GE

S

30 C30

C3434

CENOZOICAGE(Ma) EPOCH AGE PICKS

(Ma)

MAGNETICPOLARITY

PERIOD

HIS

T.

AN

OM

.

CH

RO

N.

QUATER-NARY PLEISTOCENE

MIO

CE

NE

OLI

GO

CE

NE

EO

CE

NE

PALE

OC

EN

EPLIOCENE

PIACENZIAN

0.011.8

3.6

5.3

7.2

11.6

13.8

16.0

20.4

23.0

28.4

33.9

37.2

40.4

48.6

55.8

58.7

61.7

65.5

L

E

L

M

E

L

M

M

E

E

L

ZANCLEAN

MESSINIAN

TORTONIAN

SERRAVALLIAN

LANGHIAN

BURDIGALIAN

AQUITANIAN

CHATTIAN

RUPELIAN

PRIABONIAN

BARTONIAN

LUTETIAN

YPRESIAN

DANIAN

THANETIAN

SELANDIAN

CALABRIANHOLOCENE

TE

RT

IAR

YPA

LEO

GE

NE

NE

OG

EN

E1 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

GELASIAN 2.6

183

CHANGHSINGIAN

WORDIANROADIAN

WUCHIAPINGIAN

CAPITANIAN

KUNGURIAN

ASSELIAN

SAKMARIAN

ARTINSKIAN

PRIDOLIANLUDFORDIAN

GORSTIANHOMERIAN

RHUDDANIAN

TELYCHIANAERONIAN

SHEINWOODIAN

HIRNANTIAN

SANDBIANKATIAN

DARRIWILIANDAPINGIAN

STAGE 10STAGE 9PAIBIAN

GUZHANGIANDRUMIANSTAGE 5STAGE 4STAGE 3

STAGE 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

*International ages have not been fully established. These are current names as reported by the International Commission on Stratigraphy.

Sources for nomenclature and ages are primarily from Gradstein, F., Ogg, J., Smith, A., et al., 2004, A Geologic Time Scale 2004: Cambridge University Press, 589 p. Modifications to the Triassic after: Furin, S., Preto, N., Rigo, M., Roghi, G., Gianolla, P., Crowley, J.L., and Bowring, S.A., 2006, High-precision U-Pb zircon age from the Triassic of Italy: Implications for the Triassic time scale and the Carnian origin of calcareous nannoplankton and dinosaurs: Geology, v. 34, p. 1009–1012, doi: 10.1130/G22967A.1; and Kent, D.V., and Olsen, P.E., 2008, Early Jurassic magnetostratigraphy and paleolatitudes from the Hartford continental rift basin (eastern North America): Testing for polarity bias and abrupt polar wander in association with the central Atlantic magmatic province: Journal of Geophysical Research, v. 113, B06105, doi: 10.1029/2007JB005407.


Nicholas Steno (1638 - 1686)

Steno’s Laws of Stratigraphy:• Law of Superposition• Law of Original Horizontality• Law of Lateral Continuity

...then he converted to Catholicism and became a priest.


!"#$%&%"'$(%)*+,%-./0%$*"$',%$-1)2$-%)1-($(*&*(%3$

4.-',$,*3'1-#$*"'1$',-%%$+.-'35

670'*+0%$%&%"'3$1/3%-&./0%$*"$.$3*"80%$3%)'*1"$91-:$

',%$/.3*3$19$.$-%0.'*&%$'*:%$3).0%5

;,.'$*3$',%$,*3'1-*).0$3%<7%")%$19$%&%"'3$*"$',*3$

)-133=3%)'*1">

J

IH

J

IH

F

E

D

C

B

E

D

C

B

G

A

DE

F

CB

A

What’s the sequence of events in this cross-section?

Relative timescales

Field relationships


Relative timescales

Relative timescales can be constructed locally from rocks in contact with one another, but how can we construct relative timescales across large distances (e.g. Colorado and South China)?

Find a phenomenon global in scope and preservable in rocks that changes systematic through time!


Relative timescalesBiostratigraphy

William Smith (1815)

...then he died in a debtor’s prison.He made the first geological map...


Relative timescales

Biostratigraphy

Time

Evolution

Taxa useful for biostratigraphy• widespread environmentally and geographically• limited time span• easily fossilized• easily identified

Limitations• Facies/ecology• Paleogeography/Provincialism• FAD and LAD ≠ evolution


Absolute timescales

Radiometric


Absolute timescales

Radiometric

!"#$%&'( )%*+,-.

(",#/+,(.0%1+,%'

2/+.3'41,%'(.

5678"9%"(


Absolute timescales

Radiometric

543+/-1 Ma


Absolute timescales

Radiometric



235

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


PER

MIA

ND

EVO

NIA

NO

RD

OVI

CIA

NSI

LUR

IAN

MISSIS-SIPPIAN

PENNSYL-VANIAN

CAM

BRIA

N*

CAR

BON

IFER

OU

S


(Ma)PERIOD

251

260

254

266268271276

284

297

304306

299.0

318

326

345

359

374

385

392

398

407411416419421

428426

436439

423

444446

455

461

472468

479

488

496501503507

492

510 517521

535 542


BASHKIRIAN

SERPUKHOVIAN

VISEAN

TOURNAISIAN

FAMENNIAN

FRASNIAN

GIVETIAN

EIFELIANEMSIAN

PRAGHIANLOCKHOVIAN

312

PRECAMBRIAN

PR

OT

ER

OZ

OIC

AR

CH

EA

N

AGE(Ma)

EON ERABDY.

AGES(Ma)

1000

1200

1800

2050

2300

1400

1600

2500

2800

3200

3600

3850

L

M

M

E

E

E

E

Furon-gian

Series 3

Series 2

Terre-neuvian

L

L

L

M

M

542

630

850

MESOZOIC

TR

IAS

SIC

JUR

AS

SIC

CR

ETA

CE

OU

S


(Ma)

MAGNETICPOLARITY

PERIOD PERIOD

HIS

T.

AN

OM

.

CH

RO

N.

LATE

EARLY

LATE

EARLY

MIDDLE

LATE

EARLY

MIDDLE

MAASTRICHTIAN65.5

70.6

83.585.8

89.3

93.5

99.6

112

125

130

136

140

145.5

151

156

165

161

CAMPANIAN

SANTONIANCONIACIAN

TURONIAN

CENOMANIAN

ALBIAN

APTIAN

BARREMIAN

HAUTERIVIAN

VALANGINIAN

BERRIASIAN

TITHONIAN

KIMMERIDGIAN

OXFORDIAN


TOARCIAN

PLIENSBACHIAN

SINEMURIAN

HETTANGIAN

NORIAN

RHAETIAN

CARNIAN

LADINIAN

ANISIANOLENEKIAN

INDUAN

C31

C32

C33

31

32

33

M0rM1

M5

M10

M12M14M16M18M20

M22

M25

M29

M3

168172

176

197

190

201.6204

241

228

251.0250

245

RA

PID

PO

LAR

ITY

CH

AN

GE

S

30 C30

C3434


(Ma)

MAGNETICPOLARITY

PERIOD

HIS

T.

AN

OM

.

CH

RO

N.


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

28.4

33.9

37.2

40.4

48.6

55.8

58.7

61.7

65.5

L

E

L

M

E

L

M

M

E

E

L

ZANCLEAN

MESSINIAN

TORTONIAN

SERRAVALLIAN

LANGHIAN

BURDIGALIAN

AQUITANIAN

CHATTIAN

RUPELIAN

PRIABONIAN

BARTONIAN

LUTETIAN

YPRESIAN

DANIAN

THANETIAN

SELANDIAN

CALABRIANHOLOCENE

TE

RT

IAR

YPA

LEO

GE

NE

NE

OG

EN

E

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

GELASIAN 2.6

183

CHANGHSINGIAN

WORDIANROADIAN

WUCHIAPINGIAN

CAPITANIAN

KUNGURIAN

ASSELIAN

SAKMARIAN

ARTINSKIAN

PRIDOLIANLUDFORDIAN

GORSTIANHOMERIAN

RHUDDANIAN

TELYCHIANAERONIAN

SHEINWOODIAN

HIRNANTIAN

SANDBIANKATIAN




STAGE 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



Relative timescales

Magnetostratigraphy


Relative timescales

Event stratigraphy

Examples:• Volcanic eruption• Tsunami• Bollide impact


Relative timescales

Chemostratigraphy

D. DePaulo


!"#$%

&'(#)#*#$

&+,$-.Relative timescales

Chemostratigraphy

Shuram C isotope excursion


NATURE GEOSCIENCE | VOL 4 | MAY 2011 | www.nature.com/naturegeoscience 285

The global carbon cycle is the biogeochemical engine at the heart of acid–base and redox processes in the oceans and atmosphere. It constitutes the most fundamental way in which

the biosphere shapes the chemistry of our planet. Studying the behaviour of the carbon cycle during times past, however, presents unique challenges. On geological timescales, the CO2 emitted from volcanoes and the weathering of sedimentary rocks departs the !uid Earth in two primary sinks — carbonate minerals, and organic car-bon; the burial of organic carbon can be linked stoichiometrically to !uxes of O2 to the atmosphere. Owing to biases intrinsic to the sedi-mentary record, it is not possible to directly measure the amount of organic carbon buried as a function of time. Instead, geobiologists use carbon isotope ratios in carbonate rocks to constrain the pro-portional organic carbon burial !ux (for example, ref."1), creating time series data by measuring many samples collected in a strati-graphic section according to height (for example, ref."2). Ultimately, carbon isotope ratios can provide a measure of the global carbon cycle at the geological instant of sedimentation.

#e history of the carbon cycle is recorded in carbonate miner-als and organic compounds found in sediments and sedimentary rocks of modern to Archean age3–10. Over the past several decades studies of the chemostratigraphic variation of isotopic carbon have enabled reconstructions of ancient seawater composition including the variation of alkalinity, oxygen, and !uxes of carbon2,8,11–15. #e behaviour of the carbon cycle varies over geologic time, marked by di$erent steady states punctuated by brief intervals of anomalous dynamics16–22. #ese anomalies o%en signify special events in the history of life, such as the rise of macroscopic and skeletonized ani-mals, as well as mass extinctions2,8,16,23–26.

#e secular variability of marine carbon isotope ratios in carbon-ate-rich sedimentary successions also provides a basis for global cor-relation18. Owing to the lack of robust biostratigraphic constraints, construction of ‘carbon isotope curves’ has seen widespread applica-tion to correlate poorly fossiliferous Precambrian strata, particularly those of the Neoproterozoic era17. Carbon isotopic data typically are

Enigmatic origin of the largest-known carbon isotope excursion in Earth’s historyJohn P. Grotzinger1*, David A. Fike2 and Woodward W. Fischer1

Carbonate rocks from the Middle Ediacaran period in locations all over the globe record the largest excursion in carbon isotopic compositions in Earth history. This finding suggests a dramatic reorganization of Earth’s carbon cycle. Named the Shuram excursion for its original discovery in the Shuram Formation, Oman, the anomaly closely precedes impressive events in evolution, including the rise of large metazoans and the origin of biomineralization in animals. Instead of a true record of the carbon cycle at the time of sedimentation, the carbon isotope signature recorded in the Shuram excursion could be caused by alteration following deposition of the carbonate sediments, a scenario supported by several geochemical indicators. However, such secondary processes are intrinsically local, which makes it di!cult to explain the coincident occurrence of carbon isotope anomalies in numerous records around the globe. Both possibilities are intriguing: if the Shuram excursion preserves a genuine record of ancient seawater chemistry, it reflects a perturbation to the carbon cycle that is stronger than any known perturbations of the modern Earth. If, however, it represents secondary alteration during burial of sediments, then marine sediments must have been globally preconditioned in a unique way, to allow ordinary and local processes to produce an extraordinary and widespread response.

plotted as a function of stratigraphic position12,24,27–31 to highlight secular changes in seawater chemistry through time.

As the evaluation of Neoproterozoic chemostratigraphy devel-oped, an extraordinary excursion was discovered in the Ediacaran Shuram Formation, Oman28. Now known as the ‘Shuram excur-sion’ (SE), it constitutes one of the most impressive carbon isotopic excursions in Earth history32,33. Plotting, by rank order, the sign and magnitude of carbon isotope excursions recorded over the past 1,000"million years (Myr) shows that the largest anomalies are nega-tive in sign and found in Neoproterozoic strata (Fig."1). #e SE is

1Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California 91125, USA, 2Earth and Planetary Sciences, Washington University, St. Louis, Missouri 63130, USA. *e-mail: [email protected]

–15

–10

–5

0

5

10NeoproterozoicPalaeozoicMesozoicCenozoic

Rank order

Shuram

Mag

nitu

de (!

)

Figure 1 | Historical variability of carbon isotopic composition of sedimentary rocks. Rank order of carbon isotope excursions greater than 2 ‰ over the past 1,000 Myr is shown in terms of sign and magnitude. Negative excursions are common in the Neoproterozoic stratigraphic record. The SE is the largest of these; such a distribution of isotope excursions through time provides clear evidence for large-scale change in the operation of the global carbon cycle over geologic history. Data from ref.!18.

REVIEW ARTICLEPUBLISHED ONLINE: 17 APRIL 2011!|!DOI: 10.1038/NGEO1138

© 2011 Macmillan Publishers Limited. All rights reserved


and high negative d13C values havenot been reported (Fig. 6). However,the succession is siliciclastic-rich andonly sporadic data points are avail-able. Other sections such as the KrolGroup in India (Jiang et al., 2002)show repetitive low-amplitude negat-ive excursions, with no apparent shiftcomparable with that preserved in theShuram Formation. The recentlydocumented Zhuinska Group of Cen-tral Siberia (Pokrovsky and Melez-hik, 2005), on the other hand, tendsto support a similar long-lived andvery negative d13C trend.Worldwide correlations of Ediaca-

ran strata su!er from a lack of absoluteages and incompleteness of the chem-ostratigraphic record (Fig. 6). Di!er-ent age brackets for the Shuram and

equivalent excursions are suggested,based on U–Pb age data defining theend of the excursion (Condon et al.,2005), subsidence analysis (Sayloret al., 1998) or more comprehensivecorrelations (Halverson et al., 2005).However, the time lines proposed inthis paper combined with a continuousd13C record allow the Oman successionto serve as a chemostratigraphic refer-ence for the Ediacaran period (Fig. 6).

Implications for Neoproterozoic iceages

Improvements in the geochronologicalconstraints on glaciation now suggestat least three glacial epochs for theNeoproterozoic (Ho!mann et al.,2004). The best-constrained glacial

event of the Ediacaran is the Gaskiersof Newfoundland, which is dated at c.580 Ma and is thought to have lastedaround 1 Myr (Bowring et al., 2003;Fig. 6). Possible coeval glacial depositsexist (Halverson et al., 2005) but su!erfrom poorer time constraints. How-ever, theEdiacaran (Gaskiers) glacial isthought to be a non-global, localizedevent (Halverson et al., 2005) and didnot leave any recognizable imprint intheNafun stratigraphic record (Fig. 2).The Oman succession shows that

the carbon isotopic record is una!ec-ted by any glaciations taking place onthe Ediacaran-age Earth, as opposedto the Sturtian and Marinoan glacia-tions, which are recorded by bothglacigenic deposits and negative car-bon isotopic excursions in associated

Namibia

–6 0 6

ama

N

635.

5 ±

1.2M

a3

548.

8 ±

1Ma4

551.

1 ±

0. 7

Ma5

635.

2 ±

0. 6

Ma5

–12 0 6

yennoB

ooreynuB

anihcarB

bem usT

aneelaccuN

yelsnwa

RC

BA

akonoW

Adelaiderift complex

586 ± 301

Acramanejecta

Marinoan Glacial

Yangtze platform South China

–6 0 6

A

B

C

D

gniygneD

Nantuo

Siliciclastics

Ediacaran fauna

Shelly fossil

LimestonesDolostones

Unconformities

Marinoan glacials

13C

13C

13C

13C

13C

–10 0 5

gnilritS

einnhoJyadnoo

N

Death valley

580 ± 7 MaCorrelated

incision age onthe Brown’s

Hole Fm2

Wildrose

Bänninger(2003)

Shu

ram

Bua

hK

hufa

i

M

asira

h ba

yar

A

–12 0 6

hsadaH

Oman (composite)

545055

565075

575085

585095

595006

506016

51 6026

526036

5 36555

065

Fiq

Gaskiers

?

Ghaub

–10 0 10

Canada

Stelfox

)aM( e

miT

.C do o

W

Ingt

aB

luef

low

erliarte

maG

debp eehS

Ris

ky

13C (‰)

500 m

Fig. 6 The d13C and strontium isotope composite profile from Oman, plotted against time, shows a major negative excursion andlong recovery in the time period c. 600–550 Ma. The Oman section is compared with other successions plotted on a thickness scale:The post-Marinoan Windermere Supergroup of NW Canada (Narbonne et al., 1994; James et al., 2001), the Johnnie Formation ofDeath Valley (Banninger, 2003; Corsetti and Kaufman, 2003, 2005), the Doushantuo Formation of the Yangtze Platform (Yanget al., 1999; Jiang et al., 2003a,b; Condon et al., 2005), the Wonoka Formation of the Adelaide rift complex (Calver, 2000; Walteret al., 2000; Foden et al., 2001) and the Nama and Tsumeb groups of Namibia (Kaufman et al., 1993; Grotzinger et al., 1995;Saylor et al., 1998). Isotopic age references are 1Preiss (1987); 2Schaefer and Burgess (2003); 3Ho!mann et al. (2004); 4Grotzingeret al. (1995); 5Condon et al. (2005).

Terra Nova, Vol 18, No. 2, 147–153 E. Le Guerroue et al. • 50 Myr isotopic recovery in the Ediacaran ocean.............................................................................................................................................................

! 2006 Blackwell Publishing Ltd 151


Relative timescales

Phylogeny

PLoS Biology | www.plosbiology.org 1899

Essay

November 2006 | Volume 4 | Issue 11 | e352

Genome analyses are delivering unprecedented amounts of data from an abundance of

organisms, raising expectations that in the near future, resolving the tree of life (TOL) will simply be a matter of data collection. However, recent analyses of some key clades in life’s history have produced bushes and not resolved trees. The patterns observed in these clades are both important signals of biological history and symptoms of fundamental challenges that must be confronted. Here we examine how the combination of the spacing of cladogenetic events and the high frequency of independently evolved characters (homoplasy) limit the resolution of ancient divergences. Because some histories may not be resolvable by even vast increases in amounts of conventional data, the identifi cation of new molecular characters will be crucial to future progress.

“… there is, after all, one true tree of life, the unique pattern of evolutionary branchings that actually happened. It exists. It is in principle knowable. We don’t know it all yet. By 2050 we should – or if we do not, we shall have been defeated only at the terminal twigs, by the sheer number of species.”

Richard Dawkins [1]

Who are tetrapods’ closest living relatives? Which is the earliest-branching animal phylum? Answers to such fundamental questions would be easy if the historical connections among all living organisms in the TOL were known. Obtaining an accurate depiction of the evolutionary history of all living organisms has been and remains one of biology’s great challenges.

The discipline primarily responsible for assembling the TOL—molecular systematics—has produced many new insights by illuminating episodes in life’s history, posing new hypotheses,

as well as providing the evolutionary framework within which new discoveries can be interpreted [2]. Molecular systematics has surmounted the confusion stemming from comparisons of morphologically disparate species to reveal unexpected evolutionary relationships such as the Afrotheria, a clade composed of strikingly different mammals including elephants, aardvarks, manatees, and golden moles [3]. It has also aided the placement of the history of life in a temporal framework, shedding light on key evolutionary events independently of—and in many cases well before—the availability of fossil or biogeographic evidence. A notable example is the discovery that the Hawaiian drosophilid lineage predates by many million years the oldest extant Hawaiian island, having originated on islands now submerged [4].

With such powers in mind, for the casual reader of the phylogenetics literature, the contents table of the May 2005 issue of Molecular Biology and

Evolution may be somewhat bewildering. Two articles only a few pages apart paradoxically provide evidence for both rejecting [5] and corroborating [6] the existence of Ecdysozoa, a metazoan

Bushes in the Tree of LifeAntonis Rokas*, Sean B. Carroll

Citation: Rokas A, Carroll SB (2006) Bushes in the tree of life. PLoS Biol 4(11): e352. DOI: 10.1371/journal.pbio.0040352

DOI: 10.1371/journal.pbio.0040352

Copyright: © 2006 Rokas and Carroll. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Abbreviations: TOL, tree of life; PIC, parsimony-informative character; RGC, rare genomic change

Antonis Rokas is Research Scientist at The Broad Institute of MIT and Harvard, Microbial Genome Analysis and Annotation, Cambridge, Massachusetts, United States of America. Sean B. Carroll is Investigator at the Howard Hughes Medical Institute and Professor at the University of Wisconsin Madison, R. M. Bock Laboratories, Madison, Wisconsin, United States of America.

* To whom correspondence should be addressed. E-mail: [email protected]

DOI: 10.1371/journal.pbio.0040352.g001

Figure 1. The Shape of a Clade Infl uences its Resolvability(A) Early in a clade’s history (gray box), the number of cladogenetic events is smaller and the length of stems larger in tree-like (left) relative to bush-like clades (right). (B) In the absence of homoplasy, the number of PICs for a stem is proportional to its time span; many PICs (rectangles) accumulated on the long stem x (left), whereas few PICs accumulated on the short stem y (right). (C) When the stem time span is long, the effect of homoplastic characters (crosses supporting a clade of species A and C and bullets supporting a clade of species B and C) is not suffi cient to obscure the true signal (left). In contrast, the same number of homoplastic characters is suffi cient to mislead reconstruction of short stems (right), because the number of homoplastic characters shared between species A and C (three crosses in each of the two species) is larger than the number of true PICs (two rectangles).

Essays articulate a specifi c perspective on a topic of broad interest to scientists.

Rokas & Carroll 2006


for the diversity of the living biota [2,15–21], althoughthere is concern that methodological bias might accountfor some of the observed negative g values [22,23].

Decreasing rates of diversification have been primarilymodeled assuming diversity-dependent diversification(i.e. logistic growth) [16,17,21]. Under this framework,decreasing rates of diversification can be detected ina molecular phylogeny only if there is diversity-depend-ent speciation (Box 2 Figure Ia and c); diversity-depend-ent extinction (Box 2 Figure Ib) alone is insufficient toleave a signature of decreasing diversification on a phy-logeny [17]. Initial modeling results suggested thatextinction must also be zero to observe decreasing diver-sification rates in molecular phylogenies [17]. However,further computer simulations showed that the signal of

decreasing diversification rates can be preserved in mol-ecular phylogenies if initial rates of speciation are highcompared with the extinction rate (captured by theLiMe ratio) [21].

Box 1. Detecting decreases in diversification rates

At the heart of most methods developed for extracting the diversitydynamics from molecular phylogenies is the conversion of thephylogeny to a chronogram (a time-calibrated phylogeny; see [36–38]) which can be visually represented by a Lineage Through Time(LTT) plot (Figure I). Once the chronogram has been constructed, adecrease in the net diversification rate can be assessed bydetermining if the nodes are concentrated deeper in the tree thanexpected by a pure birth process. This can be determined with the gstatistic [12], which measures how far the center of mass of thechronogram differs from the center of mass expected under a purebirth model. For a complete phylogeny (one where all the specieshave been included), the null hypothesis of a constant rate ofdiversification is rejected at a 5% level if g is less than –1.645 [12].This critical value must be adjusted if the sampling of the clade isincomplete [12]; incomplete sampling leads to more negativegamma values.

[(Box_1)TD$FIG]

Figure I. Lineage through time (LTT) plots expected under differentdiversification models. The chronogram in the upper left was simulatedusing a pure birth model, whereas the one in the upper right was simulatedwith a diversity-dependent model of diversification in which speciation wasdiversity-dependent and extinction was constant. The corresponding LTT plotsand their g values are shown in the lower panels. The model of a constant rateof diversification is rejected for the diversification process shown in the upperright panel.

Box 2. Models of diversity-dependent diversification

Two fundamental models have been proposed to describe long-term diversity dynamics. The first class of models, the exponentialmodels, suggest that diversity is not limited at all (e.g. [39],[40]) or, ifit is, that the biosphere is so far from the equilibrium diversity thatwe can effectively ignore it. The second class of models (followingMcArthur and Wilson [41]) proposes the existence of a carryingcapacity that caps the maximum diversity each portion of the biotacan achieve [42–45], whereas variants of these models assess theimpact of extinction on the extent to which the carrying capacity isrealized [46]. At present, there is no consensus as to which model isbest. At the heart of the logistic models is the notion of diversity-dependent diversification in which competition for limited resourcesretards diversification as species numbers increase. That is, speciesinteractions have a negative feedback on diversification. Here wepresent three simple diversity-dependent models that have beenused to simulate and describe the decrease in diversification ratesseen in real clades.

[(Box_2)TD$FIG]

Figure I. Different models of diversity-dependent diversification. In the firstmodel (a), only the speciation rate decreases as a function of the number ofspecies while the extinction rate is constant (SP_VAR). In the second model (b),the speciation rate is constant but the extinction rate is diversity-dependent(EX_VAR). In the third model (c), the speciation and extinction rates arediversity-dependent (BOTH_VAR). Initial speciation rate ! lo ; speciation rate atequilibrium ! l; initial extinction rate ! mo ; extinction rate at equilibrium ! m.Note that the diversification process enters a state of species turnover whenthe clade reaches the equilibrium diversity of 75 species. After this point,speciation and extinction rates are, on average, equal.

Opinion Trends in Ecology and Evolution Vol.25 No.8

435

for the diversity of the living biota [2,15–21], althoughthere is concern that methodological bias might accountfor some of the observed negative g values [22,23].

Decreasing rates of diversification have been primarilymodeled assuming diversity-dependent diversification(i.e. logistic growth) [16,17,21]. Under this framework,decreasing rates of diversification can be detected ina molecular phylogeny only if there is diversity-depend-ent speciation (Box 2 Figure Ia and c); diversity-depend-ent extinction (Box 2 Figure Ib) alone is insufficient toleave a signature of decreasing diversification on a phy-logeny [17]. Initial modeling results suggested thatextinction must also be zero to observe decreasing diver-sification rates in molecular phylogenies [17]. However,further computer simulations showed that the signal of

decreasing diversification rates can be preserved in mol-ecular phylogenies if initial rates of speciation are highcompared with the extinction rate (captured by theLiMe ratio) [21].

Box 1. Detecting decreases in diversification rates

At the heart of most methods developed for extracting the diversitydynamics from molecular phylogenies is the conversion of thephylogeny to a chronogram (a time-calibrated phylogeny; see [36–38]) which can be visually represented by a Lineage Through Time(LTT) plot (Figure I). Once the chronogram has been constructed, adecrease in the net diversification rate can be assessed bydetermining if the nodes are concentrated deeper in the tree thanexpected by a pure birth process. This can be determined with the gstatistic [12], which measures how far the center of mass of thechronogram differs from the center of mass expected under a purebirth model. For a complete phylogeny (one where all the specieshave been included), the null hypothesis of a constant rate ofdiversification is rejected at a 5% level if g is less than –1.645 [12].This critical value must be adjusted if the sampling of the clade isincomplete [12]; incomplete sampling leads to more negativegamma values.

[(Box_1)TD$FIG]

Figure I. Lineage through time (LTT) plots expected under differentdiversification models. The chronogram in the upper left was simulatedusing a pure birth model, whereas the one in the upper right was simulatedwith a diversity-dependent model of diversification in which speciation wasdiversity-dependent and extinction was constant. The corresponding LTT plotsand their g values are shown in the lower panels. The model of a constant rateof diversification is rejected for the diversification process shown in the upperright panel.

Box 2. Models of diversity-dependent diversification

Two fundamental models have been proposed to describe long-term diversity dynamics. The first class of models, the exponentialmodels, suggest that diversity is not limited at all (e.g. [39],[40]) or, ifit is, that the biosphere is so far from the equilibrium diversity thatwe can effectively ignore it. The second class of models (followingMcArthur and Wilson [41]) proposes the existence of a carryingcapacity that caps the maximum diversity each portion of the biotacan achieve [42–45], whereas variants of these models assess theimpact of extinction on the extent to which the carrying capacity isrealized [46]. At present, there is no consensus as to which model isbest. At the heart of the logistic models is the notion of diversity-dependent diversification in which competition for limited resourcesretards diversification as species numbers increase. That is, speciesinteractions have a negative feedback on diversification. Here wepresent three simple diversity-dependent models that have beenused to simulate and describe the decrease in diversification ratesseen in real clades.

[(Box_2)TD$FIG]

Figure I. Different models of diversity-dependent diversification. In the firstmodel (a), only the speciation rate decreases as a function of the number ofspecies while the extinction rate is constant (SP_VAR). In the second model (b),the speciation rate is constant but the extinction rate is diversity-dependent(EX_VAR). In the third model (c), the speciation and extinction rates arediversity-dependent (BOTH_VAR). Initial speciation rate ! lo ; speciation rate atequilibrium ! l; initial extinction rate ! mo ; extinction rate at equilibrium ! m.Note that the diversification process enters a state of species turnover whenthe clade reaches the equilibrium diversity of 75 species. After this point,speciation and extinction rates are, on average, equal.


435

Number of species0 25 7550

How accurate is comparative biology alone?

birth rate

death rate


2 Whale evolution

(c)

(a)

(b)

Fig. 1. Comparison of skeletons showing the morphology of (a) a model ancestral land mammal (Elomeryx; skeleton is about2 m or 6 ft in length); (b) a semiaquatic middle Eocene protocetid (Rodhocetus; 3 m or 10 ft in length); and (c) a fully aquaticmiddle-to-late Eocene basilosaurid (Dorudon; 6 m or 18 ft in length). All are standardized to approximately the same head andthorax size. Note that the archaeocete whales Rodhocetus and Dorudon have longer skulls and shorter necks, progressivelyshorter forelimbs, and progressively longer tails and more reduced hindlimbs compared with land-dwelling Elomeryx.

teeth and high-frequency sonar to aid in feeding onfish (odontocetes) or by developing baleen to strainplankton from seawater directly, bypassing fish in thefood chain altogether (mysticetes).

Fossil record. Whales have large bones, makingthem relatively easy to find as fossils. Whales are bydefinition water-dwelling animals, and watery envi-ronments are generally ideal for preserving bonesas fossils. Whales thrive in shallow marine environ-ments on the margins of continents, and the Ceno-zoic Era when whales lived is represented in thegeological record by widespread shallow marine de-posits. However, since whales reside at or near thetop of the food chain (that is, they are rare comparedwith other animals), they have a good, but not yetgreat, fossil record. The fossil record is sufficientlydense and continuous, though, that broad lineagescan be traced up and down through successive strata,moving forward and backward through earth historyand evolutionary time.

The most interesting whales, in some respects, arethose that document the transition from land to sea,and here an archaic whale from the Eocene namedRodhocetus, classified in the family Protocetidae, iscrucially important. Rodhocetus is similar in some

respects to the later Eocene basilosaurid Dorudon(Fig. 1). Both are known from nearly complete skele-tons. Similarities include long tapering skulls withpointed incisors and canine teeth, complex punctur-ing and shearing premolar and molar teeth, necks ofmedium length, a narrow and deep chest or thorax,and mobile forelimbs modified to some degree forswimming. Dorudon is similar, in turn, to primitivemysticete and odontocete whales known from thesubsequent Oligocene Epoch. Comparison betweenRodhocetus and Dorudon shows a reduction of theneural spines rising above the thoracic vertebrae,great elongation of the vertebral column with addi-tion of lumbar vertebrae, and great reduction of thehindlimbs in Dorudon.

Skeletons of primitive archaeocete whales with as-sociated forelimbs and hindlimbs were discoveredin 2000. The most complete of these, Rodhocetus,is important in showing that primitive archaeoceteshad morphological characteristics of land mammalsin general, and of the anthracotheriid group of artio-dactyls in particular. Artiodactyls are hoofed animalswith even numbers of toes; anthracotheriids are agroup of artiodactyls that lived in the Eocene andOligocene and are thought to have given rise to living

An example from whales


2009 STEEMAN ET AL.—CETACEAN EVOLUTION 7

FIGURE 3. (Continued)

Cetacean phylogeny from comparative molecular biology

Time (myr)






Time (myr)



FIGURE 1. Coastline maps indicating the timing of opening and closure of oceanic gateways. By 30 Ma, the Drake Passage and the TasmanianSeaway had opened enough for the Antarctic Circumpolar Current to be established. At 12 Ma, the 3 major equatorial oceanic gateways, theTethys Seaway, the IndoPacific Seaway, and the Central American Seaway, were still open. Between then and the present, these 3 equatorialgateways have been closed or restricted, inhibiting significant equatorial exchange between the Pacific, Atlantic, and Indian oceans. Maps areavailable from http://jan.ucc.nau.edu/!rcb7/ with permission.

Following a discarded burn-in of 30,000,000 steps, sam-ples from the Markov chain were taken every 1000steps. Parameters were checked for acceptable mixingand convergence to the stationary distribution with theprogram Tracer 1.4 (Rambaut and Drummond 2007).The posterior sample of trees was analyzed using thediagnostic software AWTY (Nylander et al. 2008), and

convergence of topological split frequencies was foundto be satisfactory. A maximum clade-credibility treewas obtained from the set of trees sampled from theposterior.

Second, divergence time estimation was carried outusing a relaxed molecular clock approach, as imple-mented in r8s 1.7 (Sanderson 2002). Date estimates were


















Time (myr)


record is !54–59% complete. Similarly, the FreqRatmethod of Foote and Raup [32] (which uses only fossildata) indicates that the fossil record of genera is !52%complete at the stage level. It would appear that the real

diversity in the past was almost twice the observed fossildiversity.

A more refined estimate of the true diversity of ceta-ceans over time can be made. The boundary-crossermethod is conservative because it takes the fossil recordliterally, and because it ignores taxa found in only onestratigraphic interval [33]. The true diversity was probablymuch higher. To put an upper limit on how much higher,we counted the number of taxa present in each strati-graphic interval (the sampled in bin method), and thencorrected that number by an estimate of the preservationpotential of each interval (see Box 3), which ranged from0.22 to 0.85. When the observed diversity in the fossilrecord is corrected using this approach (Figure 2b, upperdiversity curves), it would appear that the Cetacea had anall-time high diversity in the late Miocene, and that therehas been a long-term trend of decrease in diversity eversince. In the late Miocene (Tortonian), there are 67 namedfossil cetacean genera. Once we compensate for the incom-pleteness of the fossil record, it appears that there mayhave been as many as !130 genera, compared with the 41today. If we assume there were 2.2 species/genus as thereare today, there may have been !270 species in the lateMiocene compared with 89 today. Even if the fossil generawere all monospecific, it appears that there were morespecies in the late-Miocene (!130) than there are speciesalive today (the 89 described species).

However, these estimates probably overestimate thetrue cetacean diversity because the sampled in bin methodassumes that all taxa in an interval co-existed, whereas itis likely that at least some of the taxa last seen in aninterval had become extinct before some of those first seenin the interval had originated (a motivation for theboundary-crosser method was to circumvent this problem).Given this caveat, a measured reading of the fossil recordindicates that cetacean diversity has been at least slightlydeclining (and perhaps plummeting) over the last !12million years.

Box 3. Estimating true diversities from the fossil record

Compensating for the incompleteness of the fossil record is not atrivial task, in part because fossil preservation varies with time andspace [47]. However, the development of analytical tools [48–53] hasgreatly improved our ability to compensate for the incompletenessof the fossil record. The most commonly used approach foraccommodating non-homogeneous sampling in the fossil recordis the use of sub-sampling methods (e.g., [48–50]). However, sub-sampling discards data and therefore is not useful if one isinterested in absolute diversity trajectories. An alternative approachis to try to directly quantify the incompleteness of the fossil record.This can be done by first calculating the preservation potential foreach stratigraphic interval, i.e. the probability of finding a taxon inthe interval. This is estimated by first counting the number of taxathat range through the interval, i.e. that are known before and afterthe interval. The preservation potential is simply the proportion ofrange through taxa present in the interval [54,55]. The total diversityin an interval is then estimated by dividing the number of taxaactually sampled in the interval by its preservation potential.However, this may overestimate the total standing diversity becausenot all taxa found in an interval may have co-existed (some mayhave become extinct before others had originated). More sophisti-cated methods exist for estimating preservation potentials ofstratigraphic intervals, for example see Alroy [56], but they aremore demanding of the data and were not used here.

[(Figure_2)TD$FIG]

Figure 2. Cetacean diversification viewed through the eyes of a molecularphylogeny and the fossil record. (a) The lineage through time (LTT) plot is basedon the most recently published Cetacean molecular phylogeny published bySteeman et al. [27]. The g value is consistent with a model of constantdiversification rate. (b) Fossil-based diversity curve at the genus and specieslevels. The lower boundaries of the envelopes represent the most conservativeestimate of cetacean diversity, which uses the boundary-crosser method ofcounting taxa and assumes that the fossil record is complete. The upper boundaryof the estimated diversity curve uses the sampled in bin (SIB) method of countingdiversity, and includes a correction for the incompleteness of the fossil record andassumes that all taxa in an interval co-existed (Box 3). The raw data used were thenumber of fossil genera; the number of species was estimated by applying thespecies/genus ratio of the living taxa (2.2) to the fossil genus diversity curve. (c)Fossil-based diversification rate plot at the genus level calculated using theboundary-crosser rate method [57]. There are insufficient data to estimate ratesprior to the late Oligocene. Steeman et al. [27] suggest increases in the netdiversification rate during times of ocean restructuring, the most important ofwhich is shown by the red box. The fossil record shows that cetacean diversity hasprobably been dropping since the mid-Miocene and that the current netdiversification rate is negative. Fossil data are from Uhen and Pyenson [28] andwere analyzed through the Paleobiology Database. All three panels share the sametimescale. The stratigraphic intervals sampled are indicated by the small un-named boxes at the top of the timescale.


438

From Steeman et al. (2009) (i.e. - molecules)

From PaleoBiology database (i.e. - fossil record)

A time of oceans restructuring


record is !54–59% complete. Similarly, the FreqRatmethod of Foote and Raup [32] (which uses only fossildata) indicates that the fossil record of genera is !52%complete at the stage level. It would appear that the real

diversity in the past was almost twice the observed fossildiversity.

A more refined estimate of the true diversity of ceta-ceans over time can be made. The boundary-crossermethod is conservative because it takes the fossil recordliterally, and because it ignores taxa found in only onestratigraphic interval [33]. The true diversity was probablymuch higher. To put an upper limit on how much higher,we counted the number of taxa present in each strati-graphic interval (the sampled in bin method), and thencorrected that number by an estimate of the preservationpotential of each interval (see Box 3), which ranged from0.22 to 0.85. When the observed diversity in the fossilrecord is corrected using this approach (Figure 2b, upperdiversity curves), it would appear that the Cetacea had anall-time high diversity in the late Miocene, and that therehas been a long-term trend of decrease in diversity eversince. In the late Miocene (Tortonian), there are 67 namedfossil cetacean genera. Once we compensate for the incom-pleteness of the fossil record, it appears that there mayhave been as many as !130 genera, compared with the 41today. If we assume there were 2.2 species/genus as thereare today, there may have been !270 species in the lateMiocene compared with 89 today. Even if the fossil generawere all monospecific, it appears that there were morespecies in the late-Miocene (!130) than there are speciesalive today (the 89 described species).

However, these estimates probably overestimate thetrue cetacean diversity because the sampled in bin methodassumes that all taxa in an interval co-existed, whereas itis likely that at least some of the taxa last seen in aninterval had become extinct before some of those first seenin the interval had originated (a motivation for theboundary-crosser method was to circumvent this problem).Given this caveat, a measured reading of the fossil recordindicates that cetacean diversity has been at least slightlydeclining (and perhaps plummeting) over the last !12million years.

Box 3. Estimating true diversities from the fossil record

Compensating for the incompleteness of the fossil record is not atrivial task, in part because fossil preservation varies with time andspace [47]. However, the development of analytical tools [48–53] hasgreatly improved our ability to compensate for the incompletenessof the fossil record. The most commonly used approach foraccommodating non-homogeneous sampling in the fossil recordis the use of sub-sampling methods (e.g., [48–50]). However, sub-sampling discards data and therefore is not useful if one isinterested in absolute diversity trajectories. An alternative approachis to try to directly quantify the incompleteness of the fossil record.This can be done by first calculating the preservation potential foreach stratigraphic interval, i.e. the probability of finding a taxon inthe interval. This is estimated by first counting the number of taxathat range through the interval, i.e. that are known before and afterthe interval. The preservation potential is simply the proportion ofrange through taxa present in the interval [54,55]. The total diversityin an interval is then estimated by dividing the number of taxaactually sampled in the interval by its preservation potential.However, this may overestimate the total standing diversity becausenot all taxa found in an interval may have co-existed (some mayhave become extinct before others had originated). More sophisti-cated methods exist for estimating preservation potentials ofstratigraphic intervals, for example see Alroy [56], but they aremore demanding of the data and were not used here.

[(Figure_2)TD$FIG]

Figure 2. Cetacean diversification viewed through the eyes of a molecularphylogeny and the fossil record. (a) The lineage through time (LTT) plot is basedon the most recently published Cetacean molecular phylogeny published bySteeman et al. [27]. The g value is consistent with a model of constantdiversification rate. (b) Fossil-based diversity curve at the genus and specieslevels. The lower boundaries of the envelopes represent the most conservativeestimate of cetacean diversity, which uses the boundary-crosser method ofcounting taxa and assumes that the fossil record is complete. The upper boundaryof the estimated diversity curve uses the sampled in bin (SIB) method of countingdiversity, and includes a correction for the incompleteness of the fossil record andassumes that all taxa in an interval co-existed (Box 3). The raw data used were thenumber of fossil genera; the number of species was estimated by applying thespecies/genus ratio of the living taxa (2.2) to the fossil genus diversity curve. (c)Fossil-based diversification rate plot at the genus level calculated using theboundary-crosser rate method [57]. There are insufficient data to estimate ratesprior to the late Oligocene. Steeman et al. [27] suggest increases in the netdiversification rate during times of ocean restructuring, the most important ofwhich is shown by the red box. The fossil record shows that cetacean diversity hasprobably been dropping since the mid-Miocene and that the current netdiversification rate is negative. Fossil data are from Uhen and Pyenson [28] andwere analyzed through the Paleobiology Database. All three panels share the sametimescale. The stratigraphic intervals sampled are indicated by the small un-named boxes at the top of the timescale.


438

From Steeman et al. (2009) (i.e. - molecules)

From PaleoBiology database (i.e. - fossil record)

A time of oceans restructuring


Timescale Quiz next Tuesday


235

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


PER

MIA

ND

EVO

NIA

NO

RD

OVI

CIA

NSI

LUR

IAN

MISSIS-SIPPIAN

PENNSYL-VANIAN

CAM

BRIA

N*

CAR

BON

IFER

OU

S


(Ma)PERIOD

251

260

254

266268271276

284

297

304306

299.0

318

326

345

359

374

385

392

398

407411416419421

428426

436439

423

444446

455

461

472468

479

488

496501503507

492

510 517521

535 542


BASHKIRIAN

SERPUKHOVIAN

VISEAN

TOURNAISIAN

FAMENNIAN

FRASNIAN

GIVETIAN

EIFELIANEMSIAN

PRAGHIANLOCKHOVIAN

312

PRECAMBRIAN

PR

OT

ER

OZ

OIC

AR

CH

EA

N

AGE(Ma)

EON ERABDY.

AGES(Ma)

1000

1200

1800

2050

2300

1400

1600

2500

2800

3200

3600

3850

L

M

M

E

E

E

E

Furon-gian

Series 3

Series 2

Terre-neuvian

L

L

L

M

M

542

630

850

MESOZOIC

TR

IAS

SIC

JUR

AS

SIC

CR

ETA

CE

OU

S


(Ma)

MAGNETICPOLARITY

PERIOD PERIOD

HIS

T.

AN

OM

.

CH

RO

N.

LATE

EARLY

LATE

EARLY

MIDDLE

LATE

EARLY

MIDDLE

MAASTRICHTIAN65.5

70.6

83.585.8

89.3

93.5

99.6

112

125

130

136

140

145.5

151

156

165

161

CAMPANIAN

SANTONIANCONIACIAN

TURONIAN

CENOMANIAN

ALBIAN

APTIAN

BARREMIAN

HAUTERIVIAN

VALANGINIAN

BERRIASIAN

TITHONIAN

KIMMERIDGIAN

OXFORDIAN


TOARCIAN

PLIENSBACHIAN

SINEMURIAN

HETTANGIAN

NORIAN

RHAETIAN

CARNIAN

LADINIAN

ANISIANOLENEKIAN

INDUAN

C31

C32

C33

31

32

33

M0rM1

M5

M10

M12M14M16M18M20

M22

M25

M29

M3

168172

176

197

190

201.6204

241

228

251.0250

245

RA

PID

PO

LAR

ITY

CH

AN

GE

S

30 C30

C3434


(Ma)

MAGNETICPOLARITY

PERIOD

HIS

T.

AN

OM

.

CH

RO

N.


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

28.4

33.9

37.2

40.4

48.6

55.8

58.7

61.7

65.5

L

E

L

M

E

L

M

M

E

E

L

ZANCLEAN

MESSINIAN

TORTONIAN

SERRAVALLIAN

LANGHIAN

BURDIGALIAN

AQUITANIAN

CHATTIAN

RUPELIAN

PRIABONIAN

BARTONIAN

LUTETIAN

YPRESIAN

DANIAN

THANETIAN

SELANDIAN

CALABRIANHOLOCENE

TE

RT

IAR

YPA

LEO

GE

NE

NE

OG

EN

E

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

GELASIAN 2.6

183

CHANGHSINGIAN

WORDIANROADIAN

WUCHIAPINGIAN

CAPITANIAN

KUNGURIAN

ASSELIAN

SAKMARIAN

ARTINSKIAN

PRIDOLIANLUDFORDIAN

GORSTIANHOMERIAN

RHUDDANIAN

TELYCHIANAERONIAN

SHEINWOODIAN

HIRNANTIAN

SANDBIANKATIAN




STAGE 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



Know the following intervals:• Hadean (4.55Ga - 3.850Ga)• Archean (3.85Ga - 2500Ma)• Proterozoic (2500Ma - 542Ma)

• Paleoproterozoic (2500Ma - 1600Ma)• Mesoproterozoic (1600Ma - 1000Ma)• Neoproterozoic (1000Ma - 542Ma)

• Ediacaran (635Ma - 542Ma)

EonEra

Period


Date post:	27-Jun-2020
Category:	Documents
Upload:	others
View:	0 times
Download:	0 times

Ge104: Introduction to Geobiologyto geobiology, and (c) makes a breakthrough, however small, in...

Documents