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Last Lecture Linnaeus' Species Plantarum, 1753 • Binomial Nomenclature • Hierarchical • Artificial Classi

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Last Lecture Linnaeus' Species Plantarum, 1753 • Binomial Nomenclature • Hierarchical • Artificial Classi Last lecture Linnaeus’ Species Plantarum, 1753 •binomial nomenclature •hierarchical •artificial classification system Phylogenetic Classification A “good” classification system should have power of prediction. Ever since Darwin, the goal of classification has been a “natural” classification that reflects evolutionary relationships. Phylogeny = the pattern of evolutionary relationships among species; a branching evolutionary tree of life. Today our goal is phylogenetic classification = a hierarchical ordering of taxa according to phylogenetic relationships consisting of a nested set of ever more inclusive groups. Phylogeny Phylogeny is often presented as a diagram (a phylogenetic tree). http://media-2.web.britannica.com/eb-media/98/5598-004.gif http://www.sp.uconn.edu/~terry/DHE/Mione1.jpg Phylogenetic tree Ingroup Outgroup Group 2 Group 1 H G F E D C B A Terminal branch Node = most recent common ancestor Internal branch = ancestral species Root = common ancestor time Ingroup = the study group. Sister group = the group that is most closely related to the ingroup; closest outgroup. Outgroup = a more distantly related group. The “tree thinking challenge” Sister relationships are reciprocal relationships! (Baum et al. 2005) Topology = pattern of branching of a phylogenetic tree. The “tree thinking challenge” cont. (Baum et al. 2005) The “tree thinking challenge” cont. (Baum et al. 2005) Monophyletic groups H G F E D C B A Monophyletic group (or clade) = a group composed of a common ancestor and all of its descendents. [mono = one, phylum = tribe] Paraphyletic groups H G F E D C B A Paraphyletic group = a group containing a common ancestor and some, but not all, of its descendents. [para = near, “not quite”, phylum = tribe] Polyphyletic groups H G F E D C B A Polyphyletic group = a group that does not include the common ancestor of its members. [poly = many, phylum = tribe] Phylogenetic classification Phylogenetic classification = a hierarchical ordering of taxa according to phylogenetic relationships consisting of a nested set of ever more inclusive groups. Or, in a more concise way, the use of phylogeny to produce the classification taxon (plural – taxa) = any named group at any hierarchical level (could be a species, genus, family, etc.). Goal of phylogenetic classification: recognize monophyletic groups only! In other words, identify a nested, hierarchical set of monophyletic groups. Phylogenetic classification http://www.wpclipart.com/food/fruit/tomato/tomato.png Before: Lycopersicon esculentum Now: Solanum lycopersicum Phylogenetic classification has more power of prediction (Spooner et al., 1993) Phylogenetic reconstruction Phylogenetic reconstruction (cladistics) in systematics = the process by which we determine or estimate relationships (from the present diversity to the pattern of evolutionary relationships). It’s a hypothetical reconstruction of the sequence of evolutionary events. Phylogenetic hypotheses are subject to further evaluation when new data become available. BUT HOW DO WE RECONSTRUCT PHYLOGENY? Phylogenetic reconstruction We look for comparable similarities (characters). “The characters which naturalists consider as showing true affinity between any two or more species, are those which have been inherited from a common parent, all true classification being genealogical.” (Charles Darwin 1859) Character = a variable trait of an organism or group. Character states = alternate forms of a character. Homology Homology = similarity due to inheritance of a feature from a common ancestor. A character that arose with the evolution of a group and is shared due to common ancestry is homologous. Homologous character: wing of all birds. Non-homologous character: wing of birds, bats, and insects. Two components of homology: When we talk about homology as evidence for relationship, we must refer both to a trait (character) and a group of organisms. Synapomorphy Synapomorphy = shared, derived character. (from Gr. syn—together (shared) + apo—away + morph—form) A character in two or more groups that can be traced back to the same feature in the common ancestor of those groups, and not found in other organisms. Synapomorphies diagnose monophyletic groups. Example: feathers on birds. Symplesiomorphy Symplesiomorphy = shared, ancestral character. (from Gr. syn—together (shared) + plesio—near + morph—form) An ancestral trait that is shared by two or more modern groups and can be traced back to their common ancestor, but is not found among all descendants of this ancestor. Symplesiomorphies diagnose paraphyletic groups. Example: keratin scales on reptiles. Convergent character Convergent character is NOT homologous! (from Latin: con—together + vergere—to incline together) A trait due to evolution in parallel in two different organisms, i.e., convergent evolution or parallel evolution, and not due to common ancestry. Convergent characters diagnose polyphyletic groups. Example: wings on birds, bats, and insects. Determining whether a character is derived or ancestral Polarity = direction of evolutionary change. Most commonly used method to determine polarity: Outgroup comparison = inference from distribution of character states in sister group. For a variable character with two or more states, the state occurring in the outgroup is ancestral. Phylogenetic reconstruction = grouping species by shared derived states of characters. Phylogenetic reconstruction from characters Parsimony = the principle that the explanation requiring the least change is preferred. Characters Taxa a b c outgrp 0 0 0 1 0 1 0 2 1 0 1 3 1 1 1 out 1 2 3 out 1 3 2 out 1 2 3 c b c b a c a c b c a a a b b 4 steps 5 steps 6 steps Sources of character data Actual phylogenetic inferences often use many taxa and a large number of characters. Sources of data = any comparative data. morphology cytology behavior DNA sequences etc. Inferring phylogenies using DNA sequences Real example with DNA sequence data (nucleotide sites). Green plants Green plants Land plants Bryophytes Tracheophytes (vascular plants) Seed plants “Green algae” Gymnosperms Angiosperms Mosses Hornworts Liverworts Ferns Lycophytes Conifers (Stefanovic et al. 1998) Conifers (Gernandt et al. 2008) .
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