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N. Ivalú Cacho & David A. Baum 2009 Your NAME: _______________________ Due: Friday February 27, 2009 @ 11:59pm. Email to [email protected] 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. 1 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. 2