BioQUEST Evolution Modules Frank Price Scholar in Residence, Hamilton College [email protected] (315) 853–5233 in collaboration with other members of

BioQUEST Evolution Modules

Frank PriceScholar in Residence, Hamilton College

[email protected](315) 853–5233

in collaboration with other members of the BioQUEST Curriculum Consortium

BioQUEST: Biology Quality Undergraduate Educational Simulations & Tools• Consortium of ≈150 active members & ≈5,000 fellow-travelers

• Dedicated to Biology Curriculum Reform

BioQUEST Philosophy• 3 Peas:

– Problem Posing

– Problem Solving

– Peer Persuasion

• Students need to do what professionals do:– Ask their own questions.– Find appropriate data.– Analyze data with appropriate professional tools.– Answer their questions.– Persuade peers of the value of their answers.

• They need opportunities to work in the context of the discipline

BioQUEST Philosophy• Inquiry–oriented approach

– Goals, assumptions, models, history become explicit– Promote interpretation of data– Effect-to-cause reasoning– Encourages multivariate approaches

• Encourage collaboration– Advantages of collaborative learning– Multiple modes of learning, – Multiple skills

• De-emphasize “content” relative to skills

• Emphasize Information Technology as a tool– Supplement, not replace, actual lab/field work

BioQUEST Funding• Active

– Howard Hughes Medical Institute,

– National Science Foundation*, Division of Undergraduate Education

– Partnership for Advanced Computing Infrastructure

• Previous :– Annenberg/CPB

– Foundation for Microbiology

– Beloit College

– University of Chicago

– Center for Biology Education, UW - Madison

– Apple Computer

– Pew Midstates Science & Mathematics Consortium* 24 Funded NSF grants cite

BioQUEST Library resources

BioQUEST Modules: Disciplines• Background & Pedagogy

• Behavior• Biomathematics• Botany• Cell Biology• Development• Ecology• EvolutionEvolution• General Biology• Genetics

• Microbiology• Molecular Biology• Molecular Visualization

• Mycology• Zoology• Physiology• Statistics• Tools• Zoology

The Problems With Evolution Educaton:

• Evolution is widely misunderstood– We don’t teach it well

• Lack of Labs– Time and space– Variety of data & methods– Pedagogical models

• Lack of Data

Key Pedagogical Points:Goals for Students• Understanding of products of evolutionary biology (state of the art)– Theory– History

• Learn assumptions that frame thinking

• Practice methods

Key Pedagogical Points: Evolutionary Biology

• Goals of Evolutionary Inquiry– Theory: models of processes/phenomena– History: phylogenies as historical hypotheses

• Shared assumptions, e.g.:– Species as gene pool w/ genetic variation– New variation continuous, random– Evolution: statistical change of population – Historical contingency

• Methodologies & Tools– Various

BioQUEST Modules: Evolution• BIRDD Data Library (Mac, Win)

• EVOLVE Simulation: microevolution (Mac)

• Biology Student Workbench Analytical tool (Mac, Win)

• MacClade 2.1 Analytical tool (Mac)

• Phylogenetic Investigator Instructional tool (Mac)

• BeeVisit Simulation: pollination (Win)

• BGuILE: Galapagos Finches Simulation: ecology, selection (Mac)

• BGuILE: TB Lab Simulation : antibiotic selection(Mac)

• Bumpus Numeric Dataset (Mac, Win)

• Caminicules Visual dataset (Mac, Win)

• Dendrograminaceae Visual dataset (Mac, Win)

On–Line Info:

• BioQUEST Curriculum Consortium: http://bioquest.org/

• BioQUEST Liberary purchase:http://www.apnet.com/bioquest/(Academic Press)

Our Solution: BIRDD

• Digital library of raw data:– Realistic– Accessible– Exportable

• Open–ended

• Instructional Support:– Getting Started– Classroom Examples– Teaching Evolutionary Biology

Beagle Investigations Return Darwinian Data:

The Darwin's Finch Data Resource (DFDR)

Main Table of Contents (version 2.0)

+ Click buttons to go to information or data sets.(boldface buttons are functional)

+ To return to this location from anywhere in BIRDD,Click a Return to Main Table of Contents button,

orSelect Go to Main Table of Contents

under the Script menu

IslandData

SpeciesData

Introduction to BIRDD,Database Notes

How ToNavigateAroundBIRDD

Quit

Print All"How To" Pages

AboutBIRDD

WeatherData

Pictures &Panoramas

Finch MorphologyData

Skeletal Data

Protein Data

DNA SequenceData

VocalizationData

For technical support, comments and suggestions,contact Frank Price by phone (315) 853-5233 or by e-mail ([email protected])

Bibliography

TouristData

Opportunities

• For students– Senior Projects– Database development (possible summer stipend)– Student teaching

• For faculty– Material for labs

• Evolution, Ecology, Intro. Biol., animal morphology, Statistics, etc.

– Opportunities for student projects• In courses• Database development

– “Publish” your data

BIRDD Has Been Tested At:

• Beloit College (small, liberal arts):– Zoology: non–major’s intro. (Paul Whittaker)– Biological Issues, Making Sense of Evolutionary

Explanations: non–major’s (Sam Donovan)– Evolution: major’s (John Jungck)

• U. WI, Madison– Introductory Zoology: major’s intro., > 800

students/semester (Jean Heitz)

Jean Heitz’ Approach to Using BIRDD: Grant Proposals ( Used in Introductory Zoology, UWI, Madison)

• Week 1:– Acquaint students w/ BIRDD, Galapagos, finches– Find some preliminary questions

• Week 2:– Present ideas to whole lab for critique– Revise, develop preliminary answers– More thorough analysis of data,

• Week 3:– Present 2nd proposal draft to whole lab for critique– Write final propsal

• Week 4: Turn in proposal

Availability:

• BioQUEST Library CD–ROM indiv: $99*

ISBN: 0-12-099470-4 Site: $650 U/C*

• Macintosh: $350 HS

– System 7, System 7.1+ suggested, 4 MB available RAM

• Windows: Windows 3.1+, Windows 95 + suggested, 8 MB available RAM.

• Both: 180 MB of free hard disk space, color monitor with 800 x 600+ resolution, QuickTime® 3+ to play panorama & sound files.

Galápagos Archipelago: Islands

Isabela(Albemarle)

Pinta (Abingdon)

Marchena (Bindloe)

Genovesa (Tower)

San Cristóbal(Chatham)

Española(Hood)

Floreana(Charles, Santa Maria)

Santa Fe(Barrington)

Fernandina(Narborough)

Santa Cruz(Indefatigable)

Santiago(James)

Tortuga(Brattle)

Darwin (Culpepper)

Wolf (Wenman)

Seymour (N. Seymour)

Baltra (S. Seymour)

Daphne Major & Minor

Los Hermanos (Crossman)

Pinzón(Duncan)

Bartolomé (Bartholomew)

Roca Redonda

Sin Nombre (Nameless)

Watson

Campéon (Champion)

EnderbyCaldwell

GardnerGardner

Rábida(Jervis)

Beagle

Eden

GuyFawkes

Cowley

Cocos Isl..

Bainbridge Rocks

Plaza Norte, Plaza Sur

Galápagos

Land Area

8000 km

LengthNW-SE

430 km

LengthSW-NE

220 km

Distanceto Mainland

1000 km

Scanned from Harris, M. (1982), modifications & changes from Grant, P. (1986), US Defense Mapping Agency (1985),Healey et al. (1996)

Map_Source

page 1Islands Clone.fp3FileName

Data Resources:Islands

• Area• Max. Elevation• Age• Vegetation zones• Topographic map • Breeding status of each finch species

Number of species of:---------------------------------------------------------------------------------------

• Ferns• Flowering plants• Land birds• Darwin’s finches

Archipelago maps & displays of island

information.

Data Resources:Darwin’s Finch Species Information

• Pictures• Plumage descriptions• Foraging method• Foraging habitat• Breeding habitat• Breeding status on islands

Diagrams of-------------------------------------------------

• Lateral view of skull, musculature• Ventral views of skull, musculature• Hard palate• Beak cross–section

Display of a species’

information.

Data Resources:Molecular Sequences

Sequence Name No. Sequences--------------------------------------------------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------

• 16S Ribosomal RNA gene (partial) 16• Mitochondrial Control Region (short) 12• Microsatellite Repeat Region 16• Cytochrome b protein 33• Cytochrome b gene (partial) 40• Mitochondrial Control Region (partial) 56• Major Histocompatibility C Class II gene 40

Display of a GenBank sequence.

Data Resources:Specimen Morphology

Snodgrass Lack & Heller Sulloway Swarth

----------------------- ------------------------------------- ---------------------------------- -----------------------------

No. specimens 6,758 549 51 75Island, sex, orig. &

modern taxon name Plumage Beak height Beak width Upper beak length

Help screen showing measurements.

Measurements Used by Sources

Upper Beak Length, or "Culmen"

TarsusLength

MiddleToe &ClawLength

Nostril-UpperBeak Length

Lower BeakLength(Gonys)

BeakWidth

BeakHeight

(method of Snodgrass & Heller, Sulloway, Swarth)

(Lack's method)

WingLength

page 1Dfmorph.brdFilename:

Data Resources:Specimen Morphology (cont.)

Snodgrass Lack & Heller Sulloway Swarth

----------------------- ------------------------------------- ---------------------------------- -----------------------------

Nostril–upper beak l. Lower beak length Body length Tail length Wing length Tarsus length Middle toe & claw l.

Taxon.L69 Sex Age Body Wing TailMdl. Toe& ClawTarsus

Table of Raw Measurements in All Data

Upper Lower Width HeightNost.-U

Beak

Camarhynchus heliobates M Adult 137.0 69.5 44.5 21.515.5 8.5 7.0 9.311.0




Camarhynchus heliobates F Adult 130.0 70.5 40.5 21.515.0 8.3 7.0 9.510.0



















page 1Dfmorph.brdFilename:

Display of measurements.

13 vocalizations---------------------------------------------------------------------

• Playable sounds• Sonograms• Waveform diagrams• Species descriptions

Data Resources:Vocalizations

Help screen describing graphic display of a vocalization

Displays of Each Vocalization & Expanded Components

The basic Song: tur-tur-tur—tur

Isabela/AlbemarleCamarhynchus heliobates Mangrove F.

The two Whistles

The two soft chips

Basic Song, whistles & chirps.tur-tur-tur, ... whistle. tur-tur-tur—tur, ... tur-tur-tur—tur, chip,

Full Record File: Component 2 File:

Component 3 File:Component 1 File:

DFFILES > E_Sounds >Chel.mov DFFILES > E_Sounds >Chel_Wh.mov

DFFILES > E_Sounds >Chel_ch.movDFFILES > E_Sounds >Chel_So.mov

DFVOCAL.BRD

File Name: p. 1

Display of a vocalization (upper left), with expanded views of its components.

Data Resources:Weather

• Island, station location • Elevation

Monthly Averages (11 stations)---------------------------------------------------------------------------------------------------------------------------

• Precipitation • Temperature• Maximum temperature • Minimum temperature• Sea temperature • Hours of sunlight

Monthly Data (one station, 1950–1989)----------------------------------------------------------------------------------------------------------------------------------------------------------

• Year • Month• Total precipitation

Data Resources:Bibliography

• 320 References, searchable by• Author• Title• Citation• Type of reference (8 types)

Data Resources:Pictures & Panoramas

• 12 Habitat panoramas (all major habitat types)• 16 Organisms/scenes

Image of an organism.

Panorama of a habitat. Help screen describing panorama displays and their controls.

Data Resources:Tourist Visits (1979–1997)

• Year• Month• Number of tourists

No. Tourists per Month 1979-1997

1000

2000

3000

4000

5000

6000

7000

1980 1990

Year

Archipelago Map

Isabela(Albemarle)

Pinta (Abingdon)

Marchena (Bindloe)

Genovesa (Tower)

San Cristóbal(Chatham)

Española(Hood)

Floreana(Charles, Santa Maria)

Santa Fe(Barrington)

Fernandina(Narborough)

Santa Cruz(Indefatigable)

Santiago(James)

Darwin (Culpepper)

Wolf (Wenman)

Baltra (S. Seymour)

Daphne Major & Minor

Pinzón(Duncan)

Rábida(Jervis)

Cocos Isl..

Galápagos

BIRDD’s Main Table of Contents

Navigating Around BIRDD:Tables of Contents

Click forinformationabout BIRDD,includingcontactinformation

Click to print allof these notesfor reference

A click herebrought you tothese notesClick for

documentationabout the database

Click boldfacebuttons to go to

named databases

Click to leave BIRDD

All BIRDD databases have a Table of Contents similar to this one forBIRDD Itself:

Plain buttonsare not yetfunctional

page 1DFMAIN.BRDFileName

This is one of BIRDD’s help screen and describes the main table of contents.

Sample Help Screen

Example of Exported Data

Opened with a Statistics Program


Scatterplot Matrix: All Species, All Islands

Scatterplot Matrix: All Species, All Measurements

Red = G. fuligiginosa Green = G. fortis, Blue = G. magnirostris

Correlations

Scatterplot Matrix

50

60

70

80

90

369

1215182124

101214161820222426

79

111315

1719

0.70.9

1.2

1.51.7

2.0

2.3

WingL

50 60 70 80 90

BeakH

3 5 7 911 14 17 2023

UBeakL

10 1315 1820 2325

N-UBkL

78910 12 14 16 18

BkN-TipL/BkH

.7 .91.11.41.72.02.3

Scatterplots: Lack Species

6

8

10

12

14

16

18

6 11 16 21BeakH

66

BeakH

G. magnn = 375

G. for t n = 1272

G. fuli (n = 1374)

G. diff n = 374

G. conin = 350G. scan

n = 587

6

8

10

12

14

16

18

6 11 16 21BeakH

66

BeakH

6

11

16

21

50 60 70 80 90WingL

650

WingL

G. magn

G. for t

G. fuli

G. diff

G. coni

G. scan

6

11

16

21

50 60 70 80 90WingL

650

WingL

6

8

10

12

14

16

18

50 60 70 80 90WingL

650

WingL

G. magn

G. for t

G. fuli

G. diff

G. coni

G. scan

6

8

10

12

14

16

18

50 60 70 80 90WingL

650

WingL

Geospiza: Sample Densities

G. coni

6

11

16

21

50 60 70 80 90WingL

650

WingL

G. magn

650

WingL

G. fuli

G. for t

650

WingL

6

8

10

12

14

16

18

50 60 70 80 90WingL

G. magn

650

WingL

650

WingL

G. fuli

650

WingL

G. for t

6

8

10

12

14

16

18

50 60 70 80 90WingL

650

WingL

G. diff

650

WingL

G. coni

650

WingL

G. scan

6

11

16

21

50 60 70 80 90WingL

650

WingL

G. diff

650

WingL

G. coni

650

WingL

G. scan

6

8

10

12

14

16

18

6 11 16 21BeakH

66

BeakH

G. diff

66

BeakH

G. coni

66

BeakH

G. scan

6

8

10

12

14

16

18

6 11 16 21BeakH

66

BeakH

G. magn

66

BeakH

66

BeakH

G. for t

G. fuli

Example of Exported DataG. difficilis: Density Contour Plot for each Island

6.5

7.0

7.5

8.0

8.5

9.0

9.5

10.0

10.5

11.0

60 70WingL

6.5

WingL

Drwn_Clp G. diff (n = 92)

6.5

7.0

7.5

8.0

8.5

9.0

9.5

10.0

10.5

11.0

60 70WingL

Wlf_Wnm G. diff (n = 92)

6.5

WingL

Darwin, Wolf

6.5

7.0

7.5

8.0

8.5

9.0

9.5

10.0

10.5

11.0

60 70WingL

Snti_Jams G. diff (n = 62)

6.5

WingL

6.5

7.0

7.5

8.0

8.5

9.0

9.5

10.0

10.5

11.0

60 70WingL

6.5

WingL

SCru_Inde G. diff (n = 40)Santiago, St. Cruz

6.5

7.0

7.5

8.0

8.5

9.0

9.5

10.0

10.5

11.0

60 70WingL

Pnt_Abng G. diff (n = 27)

6.5

WingL

6.5

7.0

7.5

8.0

8.5

9.0

9.5

10.0

10.5

11.0

60 70WingL

Gnov_Twr G. diff (n = 71)

6.5

WingL

Pinta, Genoveas


G. difficilis: Density Contour Plot for Samples

N-UBkL

9.0

10.0

11.0

12.0

7.0 7.5 8.0 8.5 9.0 9.5 10.0BeakH

All Islands

N-UBkL

9.0

10.0

11.0

12.0

7.0 7.5 8.0 8.5 9.0 9.5 10.0

BeakH


G. fuliginosa: Morphology Measures by Number of Species per Island

WingL By No.Finches

5456586062

64666870

1 2 3 4 6 7 8 9 10 11

No.Finches

Each PairStudent's t 0.05

N-UBkL By No.Finches

7

8

9

10

1 2 3 4 6 7 8 9 10 11

No.Finches


BeakH By No.Finches

7

8

9

10

1 2 3 4 6 7 8 9 10 11

No.Finches


BkL/H Ratio By No.Finches

0.8

0.9

1.0

1.1

1 2 3 4 6 7 8 9 10 11

No.Finches


Documents

BioQUEST Evolution Modules Frank Price Scholar in Residence, Hamilton College [email protected] (315) 853–5233 in collaboration with other members of