Download Biodiversity - National Center for Case Study Teaching in Science

Learning Outcomes:
1. Define biodiversity and discuss its importance in ecosystems.
2. Explain several species concepts, and analyze the difficulties
with identifying species.
3. Discuss factors involved in the evolution of DNA sequences and
the choice of a gene for a barcoding study, and interpret a gene
tree to make inferences about sequence evolution in that
gene.
4. Define barcode gap and discuss the utility of DNA barcoding for
species discovery and identification.
5. Discuss various ways that biodiversity is valued, and use this
concept to evaluate the significance of cryptic biodiversity.
2
John and Marie are biology students who are
traveling to the Area de Conservación Guanacaste
in Costa Rica on a spring break trip to conduct a
biodiversity survey with their Principles of Biology
class.
3
CQ1: Which measure would be a good way for John
and Marie to assess biodiversity in Costa Rica?
A.
B.
C.
D.
Count the number of species
Count the number of different ecosystems there
Analyze genetic diversity within a few species
All of the above
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Species richness: one aspect of biodiversity
• The number of species total, or in a particular
group
• For discussion within your group:
1 minute
• Brainstorm all the ways you can think of that
John and Marie might be able to count all the
species of insects in the rainforest.
• What are some difficulties you could anticipate
as John and Marie attempt to count all the
insect species?
End
5
They decide to study species richness of butterflies,
and they find many different types, including the
neotropical skipper butterfly (Astraptes fulgerator).
• Described in 1775
• Ranges from southern U.S. to
northern Argentina
• Near desert to deep rain forest
• Lowlands to middle elevations
• Urban to pristine habitats
• Large variety of plant food sources
Let’s take a look at some larvae…
6
CQ2: Are these two caterpillars the same species?
A. Yes
B. No
C. We need more information
7
CQ3: Which species concept would you be using if you
were attempting to classify these two caterpillars
according to the information given here (their
appearance)?
A.
B.
C.
D.
Biological species concept
Morphological species concept
Phylogenetic and evolutionary species concepts
Any of the above
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Discuss in your groups: What additional
information would help you decide if these
two caterpillars belong to the same species?
1 minute
End
9
You were looking at
these 2 before!
10 different caterpillars within A.
fulgerator complex, labeled with
preferred food source; for example:
• TRIGO eats plants of the Trigonia genus
• CELT eats Celtis iguanaea
Adults all look much more similar
10names
Fig. 2. Last-instar caterpillars of 10 species in the A. fulgerator complex from the ACG. Interim
reflect the primary larval food plant and, in some cases, a color character of the adult. (Hebert et al. 2004)
Discuss in your groups:
Could it be scientifically reasonable to
classify these 10 caterpillars as one
species, if their adult butterflies all
look virtually indistinguishable?
1 minute
End
11names
Fig. 2. Last-instar caterpillars of 10 species in the A. fulgerator complex from the ACG. Interim
reflect the primary larval food plant and, in some cases, a color character of the adult. (Hebert et al. 2004)
CQ4: John and Marie do a DNA barcoding study of the caterpillars
they have collected. They use the mitochondrial gene cytochrome c
oxidase I (COI). For this gene, butterflies in the same genus (but
different species) have average sequence divergence of 6.5%, while
butterflies within the same species have average sequence
divergence of only 0.25%. If two organisms have COI sequence
divergence of 6.2%, what is the most likely conclusion?
A.
B.
C.
D.
They belong to the same species.
They belong to different species within the same genus.
They belong to different genera (genus, plural).
It cannot be determined with this information.
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The “barcode gap:” small differences among
individuals of the same species, larger differences
among different species
Species 1
Individual 1
Individual 2
Individual 3
Individual 4
Individual 5
0-1%
Genus 1
about 2-7%
Species 2
Individual 6
Individual 7
0-1%
Individual 8
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Barcoding genes:
• Chosen because they have very little difference in sequences
within species, but high enough between species to generate
a barcode gap
• Differ depending on taxonomic group:
• Fish and invertebrates: COI (mitochondrial gene
cytochrome c oxidase I)
• Plants: rbcL (a chloroplast gene)
• Fungi: ITS (internal transcribed spacer region)
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CQ5: What is probably true about the COI gene
used for barcoding, given what you know about
sequence evolution?
A. Substantial mutations to the gene probably have no consequence to
survival of the organism, and thus very frequently persist in the
lineage.
B. Substantial mutations to the gene probably have negative
consequences to survival of the organism, and thus persist only
infrequently in the lineage.
C. This gene never mutates, so all versions of this gene among organisms
are identical.
D. We could not make an inference about evolution of the COI gene.
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CQ6: If a gene with a more rapid rate of evolution
was used for barcoding, rather than COI, what
could be the result?
A. There might not be enough differences among species to build a gene
tree.
B. There might be too many differences, even within species, to build a
gene tree.
C. The gene tree would be the same, regardless of which gene was used
to make it.
D. There’s no way to predict with this information what the result would
be.
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CQ7: Which of the following could be a gene tree for these 4
individuals who represent typical barcodes for their species,
based on partial sequences for their COI genes?
Individual 1: ….AGTCGTCGTGAGATCGTCGTGA....
Individual 2: ….AGTCGTCGTGAAATCGTCGTGA....
Individual 3: ….AGTCGTCGTGAAATCTTCGGGA....
Individual 4: ….AGTCGTCGTGAAATCTTCGCGA....
A
1
2
3
4
B
1
1
2
3
4
C
2
3
4
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In your groups: Propose a mechanism by which
the sequences could have evolved in this scenario,
explaining at which point a nucleotide mutation
occurred in the gene evolution.
Species 1: ….AGTCGTCGTGAGATCGTCGTGA....
Species 2: ….AGTCGTCGTGAAATCGTCGTGA....
Species 3: ….AGTCGTCGTGAAATCTTCGGGA....
Species 4: ….AGTCGTCGTGAAATCTTCGCGA....
1
2
3
4
1 minute
End
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Sample sizes in parentheses
>10 identical sequences in black
Caricatures of caterpillar color patterns
Fig. 3 (from Hebert et al. 2004). Tree showing distances for COI DNA
sequences for individuals from the A. fulgerator complex.
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TRIGO diverges from others
in the complex by 5.4%
CELT diverges from others in
the complex by 3.4%
Fig. 3 (partial, from Hebert et al. 2004). Tree
showing distances for COI DNA sequences for
individuals from the A. fulgerator complex.
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CQ8: After their investigation, John and Marie can
consider these to be two different species because
TRIGO
CELT
A. They look different
B. Their DNA barcodes are too different to consider them
the same species
C. They eat different foods
D. All of the above
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CQ9: In order to consider all the caterpillar types in this
complex to be a single species, what level of DNA
barcode divergence would we have to find among them?
A.
B.
C.
D.
0%
0-1%
1-3%
>4%
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John and Marie found several different groups of
COI barcodes for their A. fulgerator caterpillars.
• Groundbreaking 2004 study that revealed “cryptic” (hidden) biodiversity
(Hebert et al. 2004):
• Cryptic species are 2 or more distinct but morphologically similar species that were
previously classified as a single species.
• Hypothesis was challenged by Brower (2006), who suggested we need more
information but there are 3-7 species in the complex.
• Other studies have revealed previously unknown biodiversity and are
working to reveal more, for example:
• Scorched mussel complex contains 4 cryptic species (Lee & Foighil 2004).
• At least 3 cryptic species of snapping shrimp (Mathews 2006).
• Numerous examples from many taxa.
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CQ 10: Cryptic species are an example of species that are
hard to identify using the morphological species concept.
Which species concept would utilize gene trees
constructed from DNA barcodes to identify species
boundaries?
A.
B.
C.
D.
Biological species concept
Morphological species concept
Phylogenetic and evolutionary species concepts
Any of the above
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CQ 11: When cryptic species are discovered, our
understanding of which aspect of biodiversity has
increased?
A.
B.
C.
D.
Species diversity/richness
Ecological diversity
Genetic diversity
Morphological diversity
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CQ12: What proportion of Earth’s total biodiversity
do you think we have already identified?
A.
B.
C.
D.
E.
0-5%
5-25%
26-50%
51-90%
90-100%
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Does cryptic biodiversity such as that discovered
in A. fulgerator matter?
Imagine that your group is a research team that has presented a proposal to a scientific
funding agency. Your group is requesting $1,000,000 to conduct a DNA barcoding
expedition that could potentially uncover more cryptic biodiversity.
4 minutes
Your proposal made it through the first round of reviews, but some reviewers commented
that your rationale for why cryptic biodiversity is important needs more support.
Specifically, they cite this butterfly example, noting that in this case, the additional species
that were discovered are still quite morphologically and ecologically similar to each other,
so an argument could be made that this sort of biodiversity is not significant to our
understanding of how ecosystems and life on Earth function.
What points can you make to counter this reasoning, and strengthen your argument that
cryptic biodiversity is important and you should get funding to find it?
End
***You may wish to consider the video you watched before class regarding the value of
nature/biodiversity to help you formulate your argument.***
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DNA barcodes can be used in several ways:
1) Species discovery:
• To reveal cryptic biodiversity, as in the case of A. fulgerator.
• To reveal previously undescribed species through large scale
sampling efforts.
• Efforts by Barcode of Life are establishing barcode libraries and
documenting new species through global sampling efforts
(http://www.barcodeoflife.org/content/community/projects).
2) Species identification: To identify an unknown individual to
species level, if a barcode for that species has been documented
• Identifying unknown foods, such as fish in restaurants (Willette et al.
2017).
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CQ13: To use barcodes to identify individuals to the
species level, what must be true?
A. There must be 0% sequence divergence between that
individual and the species to which it is assigned.
B. There must be 0-1% sequence divergence between that
individual and the species to which it is assigned.
C. There must be 5-7% sequence divergence between that
individual and the species to which it is assigned.
D. There must be 100% sequence divergence between that
individual and the species to which it is assigned.
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CQ14: An individual with barcode sequence …
AGTCGTCGTGAAATCTTCGGGT... is analyzed. To which species does it
likely belong?
Individual from species 1: ….AGTCGTCGTGAGATCGTCGTGA....
Individual from species 2: ….AGTCGTCGTGAAATCGTCGTGA....
Individual from species 3: ….AGTCGTCGTGAAATCTTCGGGA....
Individual from species 4: ….AGTCGTCGTGAAATCTTCGCGA....
A.
B.
C.
D.
E.
1
2
3
4
Cannot be determined
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One-minute paper:
• In 1-3 sentences, summarize and evaluate the way that DNA
barcodes have changed the way biologists view and analyze
biodiversity.
1 minute
End
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References:
Brower, A.V.Z. 2006. Problems with DNA barcodes for species delimitation: “Ten species” of
Astraptes fulgerator reassessed (Lepidoptera: Hesperiidae). Systematics and Biodiversity 4(2):
127–132.
Hebert, P.D., E.H. Penton, J.M. Burns, D.H. Janzen, and W. Hallwachs. 2004. Ten species in
one: DNA barcoding reveals cryptic species in the Neotropical skipper butterfly Astraptes
fulgerator. PNAS 101(41): 14812–14817.
Lee, T., and D.O. Foigil. 2004. Hidden Floridian biodiversity: mitochondrial and nuclear gene
trees reveal four cryptic species within the scorches mussel, Brachidontes exustus , species
complex. Molecular Ecology 13(11): 3527–3542.
Mathews, L.M. 2006. Cryptic biodiversity and phylogeographical patterns in a snapping
shrimp species complex. Molecular Ecology 15(13): 4049–4063.
Willette, D.A, S.E. Simmonds, S.H. Cheng, S. Esteves, T.L. Kane, H. Nuetzel, N. Pilaud, R.
Rachmawati, and P.H. Barber. 2017. Using DNA barcoding to track seafood mislabeling in Los
Angeles restaurants. Conservation Biology, doi: 10.1111/cobi.12888.
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