Download Teaching deep time through macroevolution and

Teaching about time
a biologists perspective
Biochemistry
Physiology
Ecology
Evolution
Origins of biodiversity and estimates of divergence times
10-6s
TIME
109
years
Integrative Courses
Vertebrate or Invertebrate Zoolgy
Comparative Anatomy
Biogeography
*not drawn to scale
Biologist’s general modus operandus
• We had no training on how to teach about deep time
other than memorizing the chart
• We focus on teaching biological processes, not so
much the time scales during which they proceed
• We make modest attempts to talk about deep time
(give out handouts)
• We give our geology/paleontology colleagues
absolute authority to provide dates of events (with no
discussion of error, methods, etc.)
• We do not assess whether students grasp time
concepts within evolution
• We avoid confrontations with students who challenge
us with biblical timelines of events
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Teaching deep time through
macroevolution and phylogenetics
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Stories of evolution through phylogenies of many topologies
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Biomedcentral.com
Genetic diversity/no morphological diversity
Plethodontid salamanders
3.1 mya (Pliocene)
mt DNA sequence
P. hubrichti
RM 1
N1
RM 2
BM 1
BM 2
DG VA 1
GF 1
N2
GF 2
WT VA1
DG VA 2
WT VA 2
SI 1
SI 2
S1
CW 1
CW 2
RBB 1
RBB 2
BR 1
CM 1
CM 2
BR 2
S2
PG 1
SM. 1
SM. 2
PG 2
ML 1
ML 2
CD 1
S3
CD 2
Desmognathus wrighti
N1
(pygmy salamander)
N2
S3
S2
S1
Combination mtDNA and allozyme
Genetic variation among Indian groups of peoples
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BMC Genetics 2004, 5:23
Phylogeography of Drosophila in Hawaii
(Bromham and Penny, 2003)
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Molecular clocks
Zuckerkandl and Pauling 1962
• Implicitly used when choosing a
region to assay for variation
given the expected evolutionary
distance of interest
• Explicitly used when attempting
to date divergence times
• Need to calibrate divergence
times estimated with DNA
variation with historical
geological dates/events
• Lots of debate and criticism
about the use of molecular
clocks
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Inquiry-based integrated
instructional unit:
Phylogenetic analysis of the bony fishes:
Morphological and mtDNA sequence
3-4 week module
Comparative Anatomy
Evolution
Genetics
Molecular Biology
Ichthyology, etc
Introductory Biology
What are the phylogenetic relationships
among orders of Actinopterygii?
150 mya
200 mya
250 mya
300 mya
Learning activities
1. Students assign traits to a set of sea shells and generate a
“tree” based on the similarity of characters--this is done
by hand. [cladograms are visual representations of
calculated relationships]
2. Students create character matrix and extract DNA/
sequence the 28s rRNA gene. [scaled up repetition, base
pair differences are empirically determined]
3. Students align sequences, calculate the number of
differences among taxa and use a computer program to
generate a phylogenetic tree [more complex iteration of
initial exercise; introduces bioinformatics]
4. Students download cytb sequence and generate another
tree for the same taxa [repeat tree making skills]
Assessment
Exam questions:
“What is a molecular clock, and how is it relevant to
phylogenetic analysis?”
“Compare the cytb tree to the tree you constructed from the 28S
rRNA gene you made earlier in the week. Which gave a more
robust hypothesis (and why), and what are the reasons why
the two genes resolved different hypotheses?”
….but that’s it.
Goals of this workshop (for me)
1. Learn more formal pedagogy behind teaching deep time
2. Learn how to integrate cognitive science in pedagogy of
phylogenetics
• Analogy
• Diagram reasoning (“tree thinking” Catley and Novick,2009)
3. Form collaborations with geoscientists to generate a working
group interested in integrating teaching methods of deep time
from geoscience and evolutionary biology perspectives.
Molecular clocks
When is a molecule not appropriate?
Questions to ask yourself
Do molecular clocks tick evenly through time?
Is there a geological or climatic date/event for
calibration?
Are geological calibrations accurate?
Molecules can evolve at different rates than
organisms (or other molecules)!
Is the clock ticking at different rates among lineages?
Deuterostome phylogeny: Morphology
Morphological Analysis
no
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no
MTR
1
WHI
2
BUT
3
TRO
4
Body form
1
lateral compression
0
lat assym body
0
Head shape
2
# dorsal fins
0
dorsal fin spike
0
hard fin rays (Y/n)
1
dorsal ray type
1
fleshy dorsal fin
0
adipose fin
0
# anal fins
1
Caudal fin type
2
Caudal fin shape
0
pectoral fin shape
0
pectoral fin ratio
1
pelvic fin ratio
2
pelvic fin (yes/no)
0
Muscular fin
0
loc pelvic fin
1
scale type
3
loss of scales
0
scale distribution
0
scale shape
2
# nostril pairs
1
Deviated nostrils (yes/no)0
nostril position
1
eye location in skull
2
eye placement
0
jaw type
2
Jaw protrusion
2
Jaw hinge type
1
teeth
1
teeth pointed/blunt
0
>1 teeth row
0
Fleshy lips
1
mouth position
2
elongate rostrum
0
Gular plate (yes/no)
0
peduncle:tail ratio
1
Lateral line coloration
0
0
2
0
3
0
0
1
1
1
0
1
2
2
2
1
2
0
0
1
2
0
1
3
0
1
1
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0
1
1
0
0
0
1
0
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0
0
1
1
2
1
0
2
1
1
0
0
0
0
2
2
0
0
1
?
1
0
?
2
1
0
3
0
0
1
1
0
2
2
1
1
1
1
0
1
0
1
1
0
1
1
0
2
0
1
0
1
0
1
1
2
3
0
0
1
0
0
0
2
0
0
3
0
0
1
0
0
2
2
1
0
0
1
0
2
0
0
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0
2
1
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1
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0
0
0
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0
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0
1
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0
0
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1
0
0
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0
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0
2
1
1
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1
1
0
1
2
0
0
1
1
0
0
1
3
0
0
2
0
0
1
1
0
1
2
0
0
1
0
1
2
0
0
1
1
Character
2
3
4
5
6
Character
1
FLO POR LUN
5
6
7
CIC
8
SUN
9
0
2
0
1
1
1
0
0
1
0
2
2
1
2
1
0
0
1
0
3
0
1
3
0
1
1
2
0
2
1
1
1
1
0
1
2
0
0
?
0
1
2
0
1
1
1
1
1
0
0
1
2
1
0
0
2
0
0
1
3
0
1
2
0
1
1
2
0
2
1
1
1
0
0
0
2
0
0
2
0
0
1
0
1
1
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1
1
0
0
1
2
1
0
1
1
0
0
1
3
0
0
2
1
0
1
1
0
2
2
1
0
0
0
1
2
0
0
1
0
0
0
0
2
0
0
1
1
1
0
1
2
0
0
0
2
0
0
1
?
1
1
3
0
1
1
1
0
1
1
0
0
0
1
0
2
0
0
0
1
1
2
0
1
1
1
0
1
0
0
1
1
1
1
1
1
0
0
0
2
0
1
2
0
1
1
2
0
2
2
1
0
0
0
0
2
0
1
2
0
7
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MAC BOW GAR
10
11
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GOL
13
SHK
14
0
2
0
1
1
1
1
1
0
0
1
1
1
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1
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0
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0
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0
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1
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0
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1
1
2
0
1
2
1
0
1
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
12
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Genomic/mt DNA
extraction
PCR target gene sequence
DNA sequence
Alignment
gi|38154450|gb|AY452491.1|
gi|1144505|gb|U34341.1|OMU3434
gi|1144500|gb|U34340.1|ABU3434
GTGAGCTCTCGCTGGCCCTTGAAAATCCGGGGGAGAAGGTGTAAATCTCG
GTGAGCTCTCGCTGGCCCTTGAAAATCCGGGGGAGAGGGTGTAAATCTCG
GTGAGCTCTCGCTGGTCCTTGAAAATCCGGGGGAGAAGGTGTAAATCTCG
*************** ******************** *************
gi|38154450|gb|AY452491.1|
gi|1144505|gb|U34341.1|OMU3434
gi|1144500|gb|U34340.1|ABU3434
CGCCAGGCCGTACCCATATCCGCAGCAGGTCTCCAAGGTGAACAGCCTCT
CGCCGGGCCGTACCCATATCCGCAGCAGGTCTCCAAGGTGAACAGCCTCT
CGCCGGGCCGTACCCATATCCGCAGCAGGTCTCCAAGGTGAACAGCCTCT
**** *********************************************
 REV PRIMER
GGCATGTTAGATCAAGGTAGATAAGGGAAGTCGGCAAATCAGATCCGTAA
GGCATGTTAGAACAATGTATGTAAGGGAAGTCGGCAAGTCAGATCCGTAA
GGCATGTTAGAACAATGTAGGTAAGGGAAGTCGGCAAGTCAGATCCGTAA
*********** *** *** **************** ************
gi|38154450|gb|AY452491.1|
gi|1144505|gb|U34341.1|OMU3434
gi|1144500|gb|U34340.1|ABU3434
Phylogenetic analysis
gi|38154450|gb|AY452491.1|
gi|1144505|gb|U34341.1|OMU3434
gi|1144500|gb|U34340.1|ABU3434
CTTCGGGATAAGGATTGGCTCTAAGGGCTGGGTCGGTCGGGCTGGAGTGC
CTTCGGGATAAGGATTGGCTCTAAGGGCTGGGTCGGTCGGGCTGGGGTGC
CTTCGGGATAAGGATTGGCTCTAAGGGCTGGGTCGGTCGGGCTGGGGTGC
********************************************* ****
gi|38154450|gb|AY452491.1|
gi|1144505|gb|U34341.1|OMU3434
gi|1144500|gb|U34340.1|ABU3434
GAAGCGGGGCTGGGCTCGTGCCGCGGCTGGGGGAGCAGTCGCCCCGTCGC
GAAGCGGGGCTGGGCTCGAGCCGCGGCTGGGGGAGCAGTTGCTCCGCCTC
GAAGCGGGGCTGGGCACGCGCCGCGGCTGGACGAG-----GCGTCGCCT*************** ** *********** ***
** ** *
Variation in mutation rates among genomic regions
Hartl & Clark, Principles of Population Genetics
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Biological factors that affect molecular clocks
Neutral Theory
Limitations:
1. Gene to gene variation in rates of mutation
2. Lineage to lineage variation in rates of mutation
3. Variation if portions of genome under selection (vs. neutral)
Molecular clocks
When is a molecule not appropriate?
Saturation
(homoplasy)