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CLADISTICS: UNRAVELING EVOLUTION Major groups of organisms: Prokaryotes (Bacteria, Archaea)—no nucleus, unicellular and simple multicellular Protists—eukaryotes, ±multicellularity, ±motility, ±photosynthesis, various life cycles Plants—eukaryotes, photosynthetic, sporic life cycles Fungi—eukaryotes, simple multicellular, non-motile, zygotic life cycles Animals—eukaryotes, consumers, gametic life cycles How are these organisms related? What was the path of evolution to each? What did the ancestors look like? How do we figure out the answers? Contrast terms: Adaptation/natural selection: change in the distribution of characters of a population Speciation/divergence: emergence of two (or more?) species from one ancestor species Phylogeny: "origin of groups", groups=species, genera, families, etc., the pattern of evolution; formation of evolutionary "trees" (based on shared characteristics, assuming lines of inheritance of the genes for the characteristics) Taxonomy: classification of organisms into groups Phylogenetic systematics: taxonomy to follow/illuminate phylogeny Cladistics: mathematical system for phylogenetic systematics Assumptions of phylogeny Common ancestors Inheritance of traits Speciation events lead to divergence of genes, traits Thus finding traits that are similar implies a common ancestor; traits that are different implies a speciation event For some "character," E,F,G share a "character state" different from that of A,B,C,D (e.g., character = vascular system, character states = secondary growth (EFG) and no secondary growth (ABCD)) (e.g. character = organization of genes; character states = nucleus, no nucleus) Problems in recognizing phylogeny Variable character states (environmental, not hereditary) Convergence of character states (convergent adaptation) Hybridization (anastomosis of genetic lines) Examples: desert plants Ocotillo: has leaves, but only in the rainy season (environmentally determined character state) Cactus vs euphorbes: adaptation to different deserts (convergent evolution) The most confusing anastomosis: early evolution of photosynthetic eukaryotes by endosymbiosis endosymbiosis green algae brown algae red algae chloroxybacteria cyanobacteria . green algae brown algae red algae chloroxybacteria cyanobacteria How can we "unravel" the path of evolution? Traditional solutions: use lots of traits (“characters”), judgment (ignore some traits: human, rattlesnake Hb); geographical location (cactus vs euphorbes) New solution: use molecular (gene sequence) evidence, cladistics Molecular evidence = lots of characters (each base position in a gene), so convergence can be discounted on a statistical basis Cladistics: find most parsimonious trees (least changes) (See "Do a cladistic analysis" in Rost et al.) Step 1: Identify conserved regions: Step 2: Align conserved regions: Step 3: Identify new conserved regions: Step 5: Use non-conserved regions to build "character matrix": Step 6: Construct all possible cladograms (there are 15 possibilities for this matrix): Step 7: Identify the base sequence changes needed for each cladogram; choose the one with the least: Step 8: Use an "outgroup" to "root" the cladogram and show phylogeny: Cladistic methods can also be applied to protein sequences: (These are the amino acid sequences of cytochrome c) Summary •Speciation events can be used to suggest the course of evolution •Cladistics is a method for determining relationship trees and infer speciation events •Cladistic methods can be applied to DNA sequences, protein sequences (and traditional character matrixes)