Transcript Title goes here

BioQUEST Evolution Modules
Frank Price
Scholar 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
* 24 Funded NSF grants cite
BioQUEST Library resources
• Previous :
– Annenberg/CPB
– Foundation for Microbiology
– Beloit College
– University of Chicago
– Center for Biology
Education, UW - Madison
– Apple Computer
– Pew Midstates Science &
Mathematics Consortium
BioQUEST Modules: Disciplines
• Background &
Pedagogy
• Behavior
• Biomathematics
• Botany
• Cell Biology
• Development
• Ecology
• Evolution
• 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
•
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•
BIRDD
EVOLVE
Biology Student Workbench
MacClade 2.1
Phylogenetic Investigator
BeeVisit
BGuILE: Galapagos Finches
BGuILE: TB Lab
Bumpus
Caminicules
Dendrograminaceae
Data Library
(Mac, Win)
Simulation: microevolution
(Mac)
Analytical tool
(Mac, Win)
Analytical tool
(Mac)
Instructional tool
(Mac)
Simulation: pollination
(Win)
Simulation: ecology, selection
(Mac)
Simulation : antibiotic selection (Mac)
Numeric Dataset
(Mac, Win)
Visual dataset
(Mac, Win)
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
Beagle Investigations Return Darwinian Data:
About
BIRDD
The Darwin's F inch Data Resource (DFDR)
Main Table of Contents
(versio n 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,
or
Select Go to Main Table of Contents
under the Script menu
Introduction to BIRDD,
Database Notes
How To
Navigate
Around
BIRDD
Finch Morphology
Data
DNA Sequence
Data
Species
Data
Vocalization
Data
Protein Data
Island
Data
Weather
Data
Pictures &
Panoramas
Quit
Print All
"How To" Pages
Skeletal Data
Bibliography
Tourist
Data
For technical support, comments and suggestions,
contact Frank Price by phone (315) 853-5233 or by e-mail ([email protected])
• Digital library of raw data:
– Realistic
– Accessible
– Exportable
• Open–ended
• Instructional Support:
– Getting Started
– Classroom Examples
– Teaching Evolutionary Biology
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.
Data Resources:
Islands
Galápagos Archipelago: Islands
Land Area
Darwin (Culpe pper)
Cocos Isl.
8000 km
.
Wolf (Wen man)
Pinta (Abi ngdo n)
Gal ápagos
Length
NW -SE
Genovesa(Tower)
430 km
Roca Redonda
Marchena (Bind loe)
Length
SW -NE
Bartolomé (Barth olom ew)
220 km
Santiago
Bainbridge Rock s
(Ja mes)
Daphne Major & Minor
Seymour
Distance
to Mainland
Cow ley
1000 km
Beagle
Guy
Fa wke s
Rábida
(Jervis)
Fernandina
Santa Cruz
(Ind efatigab le)
Ede n
(Narboro ugh)
(N. Sey mour)
Baltra (S. Se ym our)
Pinzón
Plaza Norte , Pla za Sur
(Duncan)
Isabela
• Area
• Max. Elevation
• Age
• Vegetation zones
• Topographic map
• Breeding status of each finch
species
Santa Fe
(Alb emarl e)
Sin Nombre
Los Hermanos
(Barrin gton )
(Nameless)
(Crossman)
San Cristóbal
Tortuga
(Brattle)
Campéon (Champion)
Enderby
Caldwell
(Chath am)
Española
(Hood)
Floreana
Gardne r
(Charle s, Sa nta Ma ria)
Healey et al. (1996)
FileName Islands Clone.fp3
Number of species of:
---------------------------------------------------------------------------------------
• Ferns
• Flowering plants
• Land birds
• Darwin’s finches
Gardne r
Watson
Map_Source Scanned from Harris, M. (1982), modifications & changes from Grant, P. (1986), US Defense Mapping Agency (1985),
Archipelago maps
& displays of island
information.
page 1
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
Display of a
GenBank
sequence.
Sequence Name
No. Sequences
---------------------------------------------------------------------------------------------------------------------------------------------------------------
--------------------------------------------------------
• 16S Ribosomal RNA gene (partial)
• Mitochondrial Control Region (short)
• Microsatellite Repeat Region
• Cytochrome b protein
• Cytochrome b gene (partial)
• Mitochondrial Control Region (partial)
• Major Histocompatibility C Class II gene
16
12
16
33
40
56
40
Data Resources:
Specimen Morphology
Measurements Used by Sources
Upper Beak Length, or "Culmen"
(Lack's method)
(method of Snodgrass &
Heller, Sulloway, Swarth)
Nostril-Upper
Beak Length
Beak
Height
Tarsus
Length
Wing
Length
Middle
Toe &
Claw
Length
Beak
Width
Lower Beak
Length
(Gonys)
Filename:
Dfmorph.brd
page 1
Help screen showing measurements.
Snodgrass
Lack & Heller Sulloway Swarth
-----------------------
No. specimens
6,758
Island, sex, orig. &
modern taxon name 
Plumage

Beak height

Beak width
Upper beak length

-------------------------------------
----------------------------------
-----------------------------
549
51
75











Table of Raw Measurements in All Data
Beak
Data Resources:
Specimen Morphology
(cont.)
Taxon.L69
Age
Body
Wing
Tail
Camarhynchus heliobates
M
Adult
137.0
69.5
44.5
15.5
8.5
11.0
7.0
9.3
21.5
Camarhynchus heliobates
M
Adult
132.0
73.5
46.0
15.5
8.3
10.5
7.5
8.5
21.0
Camarhynchus heliobates
M
Adult
128.0
72.0
47.0
15.0
8.0
10.0
7.0
8.0
23.0
Camarhynchus heliobates
M
Adult
127.0
71.0
49.0
15.0
8.0
10.5
7.0
9.0
22.0
Camarhynchus heliobates
F
Adult
130.0
70.5
40.5
15.0
8.3
10.0
7.0
9.5
21.5
Camarhynchus heliobates
F
Adult
157.0
71.0
40.5
15.5
8.0
10.5
7.0
8.5
20.5
Camarhynchus heliobates
F
Adult
133.0
73.0
53.0
15.3
8.0
11.0
7.0
9.0
23.0
Camarhynchus heliobates
M
Adult
123.0
72.0
48.5
15.0
8.0
10.3
6.5
9.0
21.5
Camarhynchus heliobates
M
Adult
126.0
70.0
48.5
15.0
8.0
11.0
7.0
8.0
21.5
Camarhynchus heliobates
M
Adult
133.0
71.5
45.0
15.5
8.5
10.5
6.5
8.0
23.5
Camarhynchus heliobates
M
Adult
127.0
69.0
39.0
15.0
8.0
10.5
6.5
8.0
21.5
Camarhynchus heliobates
M
Adult
122.0
71.0
42.0
15.0
7.5
10.0
6.7
8.3
21.5
Camarhynchus heliobates
M
Adult
128.0
72.0
43.0
15.0
8.0
10.0
6.5
8.7
21.5
Camarhynchus heliobates
M
Adult
125.0
73.0
43.0
15.0
7.7
10.0
7.0
9.0
22.0
Camarhynchus heliobates
M
Adult
129.0
74.0
45.5
15.0
7.7
9.5
7.0
8.5
22.3
Camarhynchus heliobates
M
Adult
128.0
73.0
50.0
15.0
8.0
10.0
6.7
8.3
23.0
Camarhynchus heliobates
F
Adult
137.0
67.5
46.0
15.5
8.0
10.5
7.0
8.0
20.0
Camarhynchus heliobates
F
Adult
132.0
69.5
42.5
15.3
7.5
10.0
6.7
8.0
22.0
Camarhynchus heliobates
F
Adult
138.0
71.0
44.0
15.0
9.0
11.5
7.0
9.0
22.5
Camarhynchus heliobates
F
Adult
112.0
70.0
42.0
14.5
8.0
10.0
6.7
7.7
21.0
Camarhynchus heliobates
F
Adult
142.0
70.0
42.5
15.0
8.7
11.0
6.7
8.0
21.7
Camarhynchus heliobates
F
Adult
136.0
68.0
41.5
15.0
8.5
10.0
6.0
7.5
21.0
Camarhynchus heliobates
F
Adult
120.0
70.0
45.0
14.0
8.0
10.0
7.0
8.7
22.0
Filename:
Sex
Upper Lower Nost.-U
Width Height
Tarsus
Dfmorph.brd
Mdl. Toe
& Claw
page 1
Display of measurements.
Snodgrass
Lack & Heller Sulloway Swarth
-----------------------
Nostril–upper beak l.
Lower beak length
Body length
Tail length
Wing length
Tarsus length
Middle toe & claw l.

-------------------------------------





----------------------------------
-----------------------------







Data Resources:
Vocalizations
Help screen describing graphic display of a vocalization
13 vocalizations
---------------------------------------------------------------------
• Playable sounds
• Sonograms
• Waveform diagrams
• Species descriptions
Display of a vocalization (upper left),
with expanded views of its components.
Data Resources:
Weather
• Island, station location
• Elevation
Monthly Averages (11 stations)
---------------------------------------------------------------------------------------------------------------------------
• Precipitation
• Maximum temperature
• Sea temperature
• Temperature
• Minimum temperature
• Hours of sunlight
Monthly Data (one station, 1950–1989)
----------------------------------------------------------------------------------------------------------------------------------------------------------
• Year
• Total precipitation
• Month
Data Resources:
Bibliography
• 320 References, searchable by
• Author
• Title
• Citation
• Type of reference (8 types)
Data Resources:
Pictures & Panoramas
Image of an organism.
• 12 Habitat panoramas (all major habitat types)
• 16 Organisms/scenes
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
70 00
60 00
50 00
N.Touris
ts
40 00
30 00
20 00
10 00
19 80
19 90
Ye ar
Archipelago Map
Darwin (Culpepper)
Cocos Isl.
.
Wolf (Wenman)
Pinta (Abingdon)
Galá pagos
Genovesa (Tower)
Marchena (Bindloe)
Santiago
(James)
Daphne Major & Minor
Baltra (S. Seymour)
Rábida
(Jerv is )
Santa Cruz
(Indefatigable)
Fernandina
(Narborough)
Pinzón
(Dunc an)
Isabela
Santa Fe
(Albemarle)
(Barrington)
San Cristóbal
(Chatham)
Española
(Hood)
Floreana
(Charles, Santa Maria)
BIRDD’s Main Table of Contents
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
Scatterplots: Lack Species
18
18
21
16
16
14
12
10
16
N-UBkL
BeakH
N-UBkL
14
10
11
8
8
6
6
6
18
11
16
BeakH
6
50
21
60
G. coni
n = 350
G. scan
n = 587
70
W ingL
80
90
50
60
70
W ingL
80
90
G. magn
18
G. magn
21
16
16
12
G. for t n = 1272
10
G. for t
G. coni
G. fuli
G. diff
6
11
16
BeakH
21
G. diff
8
G. fuli (n = 1374)
6
G. coni
G. for t
G. scan
8
6
12
10
11
G. diff n = 374
G. scan
14
16
N-UBkL
G. magn
n = 375
BeakH
14
N-UBkL
12
50
60
70
W ingL
80
G. fuli
6
90
50
60
70
W ingL
80
90
Geospiza: Sample Densities
G. magn
18
G. magn
G. magn
18
21
16
16
14
12
G. for t
10
16
N-UBkL
BeakH
N-UBkL
14
G. for t
10
11
8
G. fuli
8
G. fuli
6
6
6
11
16
BeakH
21
G. for t
12
G. fuli
6
50
60
70
W ingL
80
90
50
60
70
W ingL
80
90
G. coni
18
18
G. scan
21
16
16
12
10
16
G. coni
G. diff
8
8
G. diff
6
6
6
11
16
BeakH
21
G. coni
12
10
G. scan
11
N-UBkL
14
G. coni
BeakH
N-UBkL
14
G. scan
G. diff
6
50
60
70
W ingL
80
90
50
60
70
W ingL
80
90
Example of Exported Data
G. difficilis: Density Contour Plot for each Island
11.0
Drw n_Clp G. diff
11.0
(n = 92)
10.5
10.0
10.0
9.5
9.5
9.0
9.0
BeakH
10.5
BeakH
Darwin, Wolf
8.5
8.0
7.5
7.5
7.0
7.0
6.5
60
70
W ingL
Snti_Jams G. diff
(n = 62)
10.0
9.5
9.5
9.0
9.0
BeakH
10.5
10.0
8.5
8.0
7.5
7.5
7.0
7.0
70
W ingL
Pnt_Abng G. diff
(n = 27)
60
11.0
10.5
10.0
10.0
9.5
9.5
9.0
9.0
BeakH
10.5
BeakH
(n = 40)
6.5
60
Pinta, Genoveas
70
W ingL
SCru_Inde G. diff
8.5
8.0
6.5
11.0
60
11.0
10.5
BeakH
Santiago, St. Cruz
(n = 92)
8.5
8.0
6.5
11.0
W lf_W nm G. diff
8.5
(n = 71)
8.5
8.0
8.0
7.5
7.5
7.0
7.0
6.5
70
W ingL
Gnov_Twr G. diff
6.5
60
70
W ingL
60
70
W ingL
Example of Exported Data
G. difficilis: Density Contour Plot for Samples
All Islands
12.0
12.0
11.0
10.0
N-UBkL
N-UBkL
11.0
9.0
7.0
7.5
8.0
8.5 9.0
BeakH
9.5
10.0
10.0
9.0
7.0
7.5
8.0
8.5
9.0
BeakH
9.5
10.0
Example of Exported Data
G. fuliginosa: Morphology Measures by
Number of Species per Island