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N. Ivalú Cacho & David A. Baum 2009
Your NAME: _______________________
Due: Friday February 27, 2009 @ 11:59pm. Email to nicacho@wisc.edu
Phylogenetic Analysis of Molecular Data (Botany 563)
Computer Lab 05: Integrative parsimony analysis
Learning objective: Apply what has been learned to this point about parsimony analysis.
Study case: Cactus life form evolution? (based on Edwards E. et al. AJB 93(7): 1177-1188)
The Cactaceae contain 1500 –1800 species renowned for their remarkable morphological and
physiological adaptations to drought. They are conspicuous components of the New World’s arid regions
and represent one of the world’s most spectacular desert radiations. The great majority of cactus diversity
is found in two major lineages, the Opuntioideae and Cactoideae. Most members of these groups are what
might be regarded as ‘‘typical’’ cacti: stem succulents with vestigial or ephemeral leaves, a welldeveloped photosynthetic stem cortex (stomata are present in stem) with CAM carbon metabolism,
specialized ‘‘collapsable’’ xylem cells that aid in water storage, deeply recessed inferior ovaries, and
specialized short shoots (areoles) with very reduced internodes that produce spines, new long shoots,
glochids (in Opuntioideae), and flowers. The remaining cacti consist of two small genera, Pereskia
(Pereskioideae) and Maihuenia (Maihueniodeae).
Multiple phylogenetic studies support the monophyly of the opuntioid and cactoid subfamilies, but their
relationships to Maihuenia and Pereskia have remained unresolved. This is due both to limited sampling
of Pereskia as well as an inability of the molecular data to resolve basal cactus nodes. To date, no studies
have confirmed or rejected the monophyly of Pereskia. Pereskia species are often interpreted as
‘‘relictual cacti,’’ and are used as a general model of the ancestral condition from which the highly
specialized morphology and physiology of the core cacti arose. Pereskia species are widely distributed in
the Caribbean and Central and South America. They have superior to inferior ovaries; broad, flattened
leaves with C3 photosynthesis; areoles with leaf production; dense, fibrous wood; a simple stem cortex
without stomata and poorly developed stem dermal layers; non-succulent tissues; and, inhabit relatively
mesic environments. This generalized depiction of Pereskia species has led botanists to believe that the
stem succulent cacti are derived from woody, nonsucculent trees with C3 photosynthesis, as opposed to
other growth forms (e.g., an herbaceous, succulent CAM plant).
While the ‘‘Pereskia model’’ has been useful, but it also down plays some potentially important ways in
which Pereskia species differ from one another. An alternative perspective of Pereskia is supported by
other studies that have emphasized the substantial ecological, morphological, and anatomical diversity
found within Pereskia.
Our ability to infer early events in the evolutionary history of the cacti rests squarely on resolving two
outstanding problems in cactus phylogeny: (1) whether Pereskia is monophyletic, and (2) how Pereskia
species are related to the rest of the cacti.
DNA sequences were obtained from representatives of Opuntioideae, Cactoideae, all species of Pereskia
and Maihuenia, and selected Portulacaceae to incorporate as outgroups. Five gene regions were
sequenced representing the three plant genomes: the nuclear gene phytochrome C; rbcL, trnK/matK, and
psbA-trnH from the chloroplast genome, and the mitochondrial gene cox3. It might be worth keeping in
mind that chloroplast and mitochondria are maternally inherited, and that the nuclear genome inheritance
is biparental.
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N. Ivalú Cacho & David A. Baum 2009
Datasets: pereskia2.nex, pereskia2.morpho.nex
Matrix dimensions and character diagnostics:
a) Number of taxa: ______; number of characters: ________
b) Parsimony informative characters: ______; Total variable characters: _______
c) How many named character sets does this data have?____________
d) List the character sets from (c):__________________________________________________
Task 1. Data diagnostics. Is there any phylogenetic signal in the data?
Report:
a) test(s) you performed
b) why did you performed such test(s)
c) null hypothesis being tested; mention the alternative hypothesis as well
d) relevant p-value or statistic
e) your conclusion(s)
f) what would your approach be your conclusion(s) had been the opposite
Task 2. Is there evidence against combining the data that suggests they should be analysed separately?
Report:
a) test(s) you performed
b) why did you performed such test(s)
c) null hypothesis being tested; mention the alternative hypothesis as well
d) specific commands (character partition, constraint, character exclusion, character weighting, etc.)
you used, and why you used them
e) relevant p-value or statistic
f) your conclusion(s)
g) what would your approach be your conclusion(s) had been the opposite
Task 3. Do the data support the monophyly of Pereskia?
Report:
a) analysis and/or test(s) performed (characters included and why, kind of searches or analysis and
parameters!)
b) why did you performed such analysis/test(s)
c) in the case of tests, the null hypothesis being tested and alternative hypothesis
d) specific commands you used (character partition(s), constraint(s), character exclusion, character
weighting, etc.), and why you used them
e) relevant result(s), p-value, or statistic. When doing searches, remember to report number of trees
found and their length. Paste relevant figure(s).
f) your conclusion(s); make reference to your figure(s) as necessary.
Task 4. Answer the following questions in the light of your results.
a) Where did stem succulent cacti most likely diversified giving rise to Opuntioide and Cactoideae?
b) Do the data support/rule out a single origin of inferior ovary in the Cactaceae?
c) Are stem stomata and delayed bark formation likely to be associated with the transition to stembased photosynthesis?
d) Are there portions of your phylogeny that remain unresolved or weakly supported (be explicit)? If
so, explain how would you proceed to increase resolution/support.
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