Cladistics. I. Terms & Concepts. I. Terms & Concepts. A. Phylogeny vs. Cladogram. B. Phylogeny vs. Tokogeny

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1 Cladistics Reading for this topic: Worobey et al Contaminated polio vaccine theory refuted. Nature 428: 820. [note: when requesting this, request a color copy] I. Terms & Concepts A. Phylogeny vs. Cladogram I. Terms & Concepts B. Phylogeny vs. Tokogeny 1

2 I. Terms & Concepts C. Clades & Monophyletic groups I. Terms & Concepts D. Sister groups I. Terms & Concepts E. Phylogenetic Evidence 1. Characters & Character states Morphological Characters e.g., Phyllotaxy: 0 = alternate; 1 = opposite; 2 = whorled. e.g., Carpel Presence: 0 = absent; 1 = present. 2

3 I. Terms & Concepts E. Phylogenetic Evidence 1. Characters & Character states Molecular Characters (e.g., DNA sequence characters) Protein coding genes (e.g., cox1 or rbcl) Structural RNA genes (e.g., 18S or 26S rdna) I. Terms & Concepts E. Phylogenetic Evidence 1. Characters & Character states Molecular Characters (e.g., DNA sequence characters) Protein coding genes (e.g., cox1 or rbcl) Structural RNA genes (e.g., 18S or 26S rdna) e.g., Position 36 in rbcl gene: 0 = A; 1 = G; 2 = C; 3 = T. or e.g., Position 36 in rbcl gene: A; G; C; T. I. Terms & Concepts E. Phylogenetic Evidence 1. Characters & Character states Molecular Characters (e.g., amino acid sequence characters) e.g., Position 5 in rubisco: 0 = glutamine; 1 = proline; etc. 3

4 I. Terms & Concepts E. Phylogenetic Evidence 2. Apomorphies vs. plesiomorphies a. autapomophy vs. synapomorphy b. synapomorphy vs. symplesiomorphy c. hashmarks I. Terms & Concepts E. Phylogenetic Evidence 3. Homology, analogy, and homoplasy I. Terms & Concepts E. Phylogenetic Evidence 3. Homology, analogy, and homoplasy Homology = similarity due to common descent e.g., plicate leaves in Cocos and Serenoa e.g., petals in Magnolia and Liriodendron e.g., 5 stamens in Solanum and Capsicum e.g., flippers in whales and arms (forelimbs) in terrestrial mammals. e.g., lack of vertebrae in bacteria, plants, snails 4

5 I. Terms & Concepts E. Phylogenetic Evidence 3. Homology, analogy, and homoplasy Analogy = similarity due to similar function (usually only superficial) e.g., wings in birds and bats and insects e.g., reduced to absence petals in Poaceae and Fagaceae e.g., succulence in Aloe and Crassula leaves e.g., tendrils in grapes and bean plants I. Terms & Concepts E. Phylogenetic Evidence 3. Homology, analogy, and homoplasy Homoplasy = confounds phylogenetic inference b/c it creates similarity that is not homologous e.g., reversals e.g., convergence I. Terms & Concepts E. Phylogenetic Evidence 3. Homology, analogy, and homoplasy Primary Homology Assessment (during character coding and scoring) e.g., PETAL COLOR: 0 = red; 1 = blue 5

6 I. Terms & Concepts E. Phylogenetic Evidence 3. Homology, analogy, and homoplasy Secondary Homology Assessment (read from cladogram) Sp. A Red Sp. B Red Sp. D Blue Sp. E Blue Sp. F Blue Sp. C Red I. Terms & Concepts E. Phylogenetic Evidence 3. Homology, analogy, and homoplasy Secondary Homology Assessment (read from cladogram) Sp. A Red Sp. B Red Sp. C Red Sp. D Blue Sp. E Blue Sp. F Blue II. Cladogram Construction A. Scope Ingroup vs. outgroup Leaf shape IG Sp. A cordate IG Sp. B cordate IG Sp. C elliptic IG Sp. D elliptic A B 1 step on this unrooted network C D 6

7 II. Cladogram Construction A. Scope Ingroup vs. outgroup A C Leaf shape IG Sp. A cordate IG Sp. B cordate IG Sp. C elliptic IG Sp. D elliptic Root here? B Root here? D II. Cladogram Construction A. Scope Ingroup vs. outgroup A B C D Leaf shape IG Sp. A cordate IG Sp. B cordate IG Sp. C elliptic IG Sp. D elliptic 1 step on this rooted network Problem: These are equally parsimonious A 1 step on this B C D rooted network II. Cladogram Construction A. Scope Ingroup vs. outgroup Leaf shape IG Sp. A cordate IG Sp. B cordate IG Sp. C elliptic IG Sp. D elliptic Problem: These are equally parsimonious 1 step on this rooted network D C A B A 1 step on this B C D rooted network 7

8 II. Cladogram Construction A. Scope Ingroup vs. outgroup Leaf shape IG Sp. A cordate IG Sp. B cordate 1steponthis this IG Sp. C elliptic rooted network IG Sp. D elliptic OG Sp. elliptic OG A B C D OG D C A B OG A B C D 2 steps on this rooted tree, either way II. Cladogram Construction B. Data Matrix II. Cladogram Construction C. Parsimony to cladogram construction / phylogenetic inference 1. For one character at a time 8

9 How to infer a phylogeny Or How to build a cladogram: Synapomorphies Snail Hagfish Perch Salamander Lizard Mouse Chimp Human Snail Hagfish Perch Salamander Lizard Mouse Chimp Human Evidences for relationships? Shared derived character states. 9

10 How to infer a phylogeny Or How to build a cladogram: Synapomorphies How to infer a phylogeny Or How to build a cladogram: Synapomorphies How to infer a phylogeny Or How to build a cladogram: Synapomorphies 10

11 How to infer a phylogeny Or How to build a cladogram: Synapomorphies How to infer a phylogeny Or How to build a cladogram: Synapomorphies How to infer a phylogeny Or How to build a cladogram: Synapomorphies Fur; mammary glands 11

12 How to infer a phylogeny Or How to build a cladogram: Synapomorphies Loss of tail Fur; mammary glands II. Cladogram Construction C. Parsimony to cladogram construction / phylogenetic inference 1. For one character at a time (e.g., Tutorial 1) II. Cladogram Construction Simple when all characters yield compatible results i.e., no homoplasy, where one character does not contradict another Examples of homoplasy: reversal and parallelism/convergence 12

13 II. Cladogram Construction e.g., adding snake would introduce a reversal regarding absence of legs. II. Cladogram Construction e.g., adding pedalism as a character would introduce a parallelism / convergence regarding bipedalism. II. Cladogram Construction C. Application of Parsimony to cladogram construction / phylogenetic inference 2. For multiple characters at a time (e.g., Tutorial 2, but below is different) a. Start with all possible ingroup topologies 13

14 II. Cladogram Construction C. Application of Parsimony to cladogram construction / phylogenetic inference 2. For multiple characters at a time (e.g., Tutorial 2) b. Use parsimony to map characters II. Cladogram Construction C. Application of Parsimony to cladogram construction / phylogenetic inference 2. For multiple characters at a time (e.g., Tutorial 2) c. Choose cladogram with fewer steps 10 steps Loss of tail Fur; mammary glands 14

15 How to evaluate an alternative cladogram? Parsimony (number of steps) How to evaluate an alternative cladogram? Parsimony (number of steps) How to evaluate an alternative cladogram? Parsimony (number of steps) 15

16 How to evaluate an alternative cladogram? Parsimony (number of steps) How to evaluate an alternative cladogram? Parsimony (number of steps) How to evaluate an alternative cladogram? Parsimony (number of steps) Fur; mamm Fur; mammary glands 16

17 How to evaluate an alternative cladogram? Parsimony (number of steps) Fur; mamm Fur; mammary glands tail How to evaluate an alternative cladogram? Parsimony (number of steps) 17 steps Fur; mamm Fur; mammary glands tail How to evaluate an alternative cladogram? Parsimony (number of steps) 18 steps karate Fur; mamm Fur; mammary glands tail 17

18 III. Uses of Cladograms A. Taxonomies (Classifications) 1. Revision of Existing Classification Schemes (e.g., angiosperms) III. Uses of Cladograms Angiosperms are monophyletic: therefore, we could recognize as a taxon (e.g., Magnoliophyta or Magnoliopsida) Review synapomorphies from Taxonomic Overview lectures nymphaeids (water-lilies & friends) magnoliids monocots Ranunculids & other primitive eudicots rosids caryophyllids asterids But what about classic subdivision into monocots & dicots? e.g., Cronquist (1981) Which of Cronquist s classes is not monophyletic (i.e., which is paraphyletic)? Magnoliophyta (angiosperms) Magnoliopsida (dicots) Liliopsida (monocots) nymphaeids (water-lilies & friends) magnoliids monocots Ranunculids & other primitive eudicots rosids caryophyllids asterids 18

19 But what about classic subdivision into monocots & dicots? e.g., Cronquist (1981) Which of Cronquist s classes is not monophyletic (i.e., which is paraphyletic)? Magnoliophyta (angiosperms) Magnoliopsida (dicots) Liliopsida (monocots) nymphaeids (water-lilies & friends) magnoliids monocots Ranunculids & other primitive eudicots rosids caryophyllids asterids Analogous to situation with birds, dinosaurs and reptiles: Birds evolved from theropod dinosaurs and dinosaurs evolved from reptiles. Thus, the old classification of Reptilia and Aves as classes violates cladistic principles of classification. More: Cronquist s Magnoliidae included water-lilies, Magnoliids, and some primitive eudicots. nymphaeids nymphaeids (water-lilies & friends) (water-lilies & friends) magnoliids monocots Ranunculids & other primitive eudicots rosids caryophyllids asterids 19

20 Dr. Hardy s classifications of angiosperms: Magnoliopsida (angiosperms) Various monophyletic subclasses. Nymphaeidae Magnoliidae Liliidae Ranunculidae Proteidae Rosidae Caryophyllidae Asteridae III. Uses of Cladograms A. Taxonomies (Classifications) 2. Construction of new classification schemes (e.g., cycads) 20

21 1. Most parsimonious cladogram from Stevenson (1992). 2. Classification based on cladogram. III. Uses of Cladograms A. Taxonomies (Classifications) 3. How to recognize new taxa within existing shemes (e.g., spiderworts) e.g., recognition of new genus, Plowmanianthus, in Commelinaceae (2004). Timeline: Strange Commelinaceae discovered at Field Museum Herbarium- were misplaced in Gesneriaceae indet folders 2. Herbarium search turns up several more 3. Ca Tim Plowman returns from S America w/ living plant 4. C-some counts, flower point to relationship with Cochliostema... 21

22 Timeline (Continued): : Fieldwork in S America reveals new discoveries that further support affinity w/ Cochliostema cm Summary of Biogeography & character states uniting & differentiating Cochliostema and these new undescribed species. Cochliostema 1. NW South America. 2. n = Epiphytic in trees. 4. Fringed petals. 5. Reduction to 3 stamens. 6. Filaments basally fused. 7. Anthers concealed by fused filament hairs. 8. Anthers spirally coiled Undescribed spp. 1. NW South America. 2. n= Semi-terrestrial: rooting only in leaf litter. 4. Fringed petals. 5. Reduction to 3 stamens. 6. Filaments basally fused. 7. Anthers concealed by unfused filament hairs. 8. Anthers strongly curved, but not spirally coiled Cladistic analysis of Hardy (2001) provided support for the recognition of two genera, with the undescribed species comprising the second genus, Plowmanianthus. Which of the following three cladograms match the one obtained by Hardy? Hint: remember Hennig s principle that only monophyletic groups should be named. Hint 2: Hennig said that clades (and taxa) are recognized based on synapomorphies, not symplesiomorphies. A B C 22

23 III. Uses of Cladograms B. Disease Origins & Disease Forensics HIV origins Table 1. A comparison of species (strains) of Human Immunodeficiency Virus (HIV). Species Virulence Transmittability Prevalence Purported origin HIV-1 High High Global Common Chimp HIV-2 Lower Low West Africa Sooty Mangabey e.g., HIV origins 1992: Rolling Stone, Tom Curtis: HIV-1 (human immunodeficiency virus type 1) may have jumped into humans via OPV Chimps have related Simian IV (SIVcpz) Human HIV is clearly derived from SIVcpz Certain population of chimps in DR Congo were allegedly used to prepare OPV by Hilary Koprowski in the 1950 s. Rolling stone retracts story. 1999: The River: A Journey to the Source of HIV and AIDS by Edward Hooper. 7 yrs journalistic research. His conclusion: Good evidence for OPV-origin. Map of the Democratic Republic of the Congo 23

24 Worobey et al Contaminated polio vaccine theory refuted. Nature 428: 820. Map of chimp subspecies Pan troglodytes troglodytes (green) and P. t. schweinfurthii (red) Cladogram showing phylogenetic relation of HIV-1 types to SIV found in Ptt. HIV transmission (disease forensics) CDC Teams Up with Systematists: 1990 s: Florida dentist was suspected of transmitting HIV to several of his patients. Several of his patients were indeed infected, but some had other risk factors as well. Conclusions? Which patients were infected by dentist, which were not? 24

25 III. Uses of Cladograms C. Conservation Strategic Planning Conservation Strategies / Prioritization One park to be designated, two possible locations of equal area: Area 1: includes 100 species from lineages 4 and 5 Area 2: includes 90 species from lineages 1 and 4. III. Uses of Cladograms D. Ancestor Reconstruction III. Uses of Cladograms Hardy CR, HP Linder Phylogeny and historical ecology of Rhodocoma (Restionaceae) from the Cape Floristic Region. Aliso 23:

26 III. Uses of Cladograms III. Uses of Cladograms E. Testing Adaptational Hypotheses Euphorbia (Euphorbiaceae) Cereus (Cactaceae) Which cladogram provides the stronger evidence for succulence (s) as an adaptation to desert (xeric) environments? NS (mesic) NS (mesic) S (xeric) NS (mesic) NS (mesic) S (xeric) NS (mesic) NS (mesic) S (xeric) NS (mesic) NS (mesic) NS (mesic) NS (mesic) NS (mesic) NS (mesic) S (xeric) S (xeric) S (xeric) 26