Post on 15-Dec-2015
BioQUEST Evolution Modules
Frank PriceScholar in Residence, Hamilton College
fprice@hamilton.edu(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 (fprice@hamilton.edu)
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 M Adult 132.0 73.5 46.0 21.015.5 8.3 7.5 8.510.5
Camarhynchus heliobates M Adult 128.0 72.0 47.0 23.015.0 8.0 7.0 8.010.0
Camarhynchus heliobates M Adult 127.0 71.0 49.0 22.015.0 8.0 7.0 9.010.5
Camarhynchus heliobates F Adult 130.0 70.5 40.5 21.515.0 8.3 7.0 9.510.0
Camarhynchus heliobates F Adult 157.0 71.0 40.5 20.515.5 8.0 7.0 8.510.5
Camarhynchus heliobates F Adult 133.0 73.0 53.0 23.015.3 8.0 7.0 9.011.0
Camarhynchus heliobates M Adult 123.0 72.0 48.5 21.515.0 8.0 6.5 9.010.3
Camarhynchus heliobates M Adult 126.0 70.0 48.5 21.515.0 8.0 7.0 8.011.0
Camarhynchus heliobates M Adult 133.0 71.5 45.0 23.515.5 8.5 6.5 8.010.5
Camarhynchus heliobates M Adult 127.0 69.0 39.0 21.515.0 8.0 6.5 8.010.5
Camarhynchus heliobates M Adult 122.0 71.0 42.0 21.515.0 7.5 6.7 8.310.0
Camarhynchus heliobates M Adult 128.0 72.0 43.0 21.515.0 8.0 6.5 8.710.0
Camarhynchus heliobates M Adult 125.0 73.0 43.0 22.015.0 7.7 7.0 9.010.0
Camarhynchus heliobates M Adult 129.0 74.0 45.5 22.315.0 7.7 7.0 8.59.5
Camarhynchus heliobates M Adult 128.0 73.0 50.0 23.015.0 8.0 6.7 8.310.0
Camarhynchus heliobates F Adult 137.0 67.5 46.0 20.015.5 8.0 7.0 8.010.5
Camarhynchus heliobates F Adult 132.0 69.5 42.5 22.015.3 7.5 6.7 8.010.0
Camarhynchus heliobates F Adult 138.0 71.0 44.0 22.515.0 9.0 7.0 9.011.5
Camarhynchus heliobates F Adult 112.0 70.0 42.0 21.014.5 8.0 6.7 7.710.0
Camarhynchus heliobates F Adult 142.0 70.0 42.5 21.715.0 8.7 6.7 8.011.0
Camarhynchus heliobates F Adult 136.0 68.0 41.5 21.015.0 8.5 6.0 7.510.0
Camarhynchus heliobates F Adult 120.0 70.0 45.0 22.014.0 8.0 7.0 8.710.0
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
Example of Exported Data
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
Example of Exported Data
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
Example of Exported Data
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
Each PairStudent's t 0.05
BeakH By No.Finches
7
8
9
10
1 2 3 4 6 7 8 9 10 11
No.Finches
Each PairStudent's t 0.05
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
Each PairStudent's t 0.05