Topic 3: Systematics II Schools of Systematics What are the schools of thought of systematics? • Systematics – The clustering of groups or organisms based on a unifying set of principles (evolutionary, or otherwise) How does one make a cladogram? • If the system is based on evolution, then it is What are higher taxa & ranks? phylogenetic How should they be used in this course? • These underlying principles are typically Applying phylogenies – Evolution and evolution and parsimony homoplasy in Anolis Schools of Systematics What is Evolutionary Systematics? Evolutionary ______________ Oldest approach to reconstructing phylogeny Systematics Phenetics ______________ __________________ Cladistics ______________ Model-based ______________ Often ______ objective – “Anything goes” approaches No explicit procedure to reconstructing phylogeny The scientist’s opinions about character weighting and relationships are important What is Evolutionary Systematics? What is Evolutionary Systematics? An evolutionary tree Clustering is based on both _____________ and Note: ancestors, time, and anagenesis ________________ features Evolutionary trees are produced Ancestors occur and time is recognized Anagenesis is recognized Basal Archosaur Both monophyletic and ______________ groups Basal Diapsid are recognized Time No longer used Basal Sauropsid Basal Amniote 1 What is Phenetics? What is Phenetics? A response to the lack of objectivity of By looking at gross similarity, the analysis can be Evolutionary Systematics confounded by _______________ and __________________ Not necessarily __________________ Modern uses: ‘True’ evolutionary relationships are not knowable Low taxonomic levels Measures overall ______________ among taxa Morphometrics and some immunological data Does not differentiate between ancestral and derived (characters are not polarized) Explicit quantitative procedure What is Cladistics? What is Phenetics? Also called Phylogenetic Systematics A ______________________ is produced Note confounding effects of anagenesis and Originated in the 1950s by Hennig, convergence popularized in the 1960s, further developed after that Response to the need for a ______________ system that was ________________ and _________________ Therefore, phylogenetic Evolutionary Tree Phenogram What is Cladistics? What is Cladistics? Also called Phylogenetic Systematics Also called Phylogenetic Systematics Only ____________________ are used Used extensively from the 1960s to to cluster taxa hierarchically present day __________________, not anagenesis, Used to reconstruct phylogeny and is the focus of cladistics study character evolution Premise that little is known about Well implemented in computer character evolution algorithms Not explicitly model-based Parsimony is the guiding principle 2 Cladistics: How to make a cladogram _______________ Timeless and without (OG (A (B (C, D)))) ancestors A representation of character state distribution An hypothesis of relationship _______ an evolutionary tree Cladistics: How to make a cladogram ABCD E How do these “Caminacules” differ from one another? Cladistics: How to make a cladogram ABCD E Code each of the characters (columns) in a table (taxa in rows) 1. Single or close together hind limbs (0), OR 2 separate hind limbs (1) 2. Front limbs are short (0), OR lengthened (1) 3. Abdomen is unpatterned (0), OR patterned (1) 4. Abdomen is flat (0), OR bulbous (1) 5. Two (0) front limbs, OR four (1) 6. One or no eyes (0), OR two laterally-directed eyes (1) 1 Cladistics: How to make a cladogram Taxon 1 2 3 4 5 6 A B C D E Cladistics: How to make a cladogram ABCD E 1 Cladistics: How to make a cladogram What is the likelihood approach? However, with many taxa, finding the best topology is computationally intensive Developed in the 1960s to present Places phylogenetic reconstruction in an With m taxa, then number of rooted explicitly ____________________ framework topologies, n, is: Realization that we do know things about 2( m − 3)! character evolution, particularly DNA n = 2m−2 (m − 2)! Find the tree with the greatest likelihood: If m = 5, then n = 7!/(8 x 6) = 105 L ∝ P(Data | Tree) Maximum parsimony __________ ___________________________ ___________________________ What is Bayesian Inference? Why are model-based approaches so powerful? Both likelihood and Bayesian approaches are Developed in 1764 by Thomas Bayes computationally intensive Applied to phylogenetics in 1996 Builds on likelihood approaches by also allowing Allow us to use knowledge of character evolution in for the incorporation of ___________________ reconstructing phylogeny, which parsimony doesn’t Allows calculation of the actual probability of a really do tree: Primarily applied to DNA sequence data, but L recently, even morphological data can by used P(data | tree)P(tree) P(tree | data) = P(data) Why are model-based approaches so powerful? What do we know about DNA evolution? (More in other classes) 1 What are higher taxa and ranks? What are higher taxa and ranks? What do they mean? • Erected to recognize diversity in Archae, Domain Ranks Domain Eubacteria, Eukarya • Major divisions within Eukarya (Plantae, Kingdom What do they mean? Kingdom Animalia, Fungi, etc.) Are they real? Phylum Phylum • Distinct body plans within Animalia (Plantae Are they comparable? and Fungi use Divisions) Class Class How should they be used? Order Order Hierarchical framework of • Some sub-groupings Family classification Family Genus Genus Species Species • ____________________________________ Subspecies Subspecies • Some distinct group within a species? What are higher taxa and ranks? What are higher taxa and ranks? Are they real? Are they comparable? Families of Urodela (Salamanders): • 3 domains are monophyletic, no evidence Domain Domain that a Domain is something biologically real • Most are monophyletic, no evidence of Kingdom Kingdom biological reality Phylum • Recent evidence suggests that evolution of Phylum developmental genetic “kernels” defined Class Class __________ before the Cambrian explosion* Order Order Family • _________________ of biological reality Family Genus Genus Species Species • Most scientists agree that species are actual Subspecies Subspecies ___________________________ • Little evidence for biological reality Fig. 3-1: Pough et al. 2004. * Davidson & Erwin. 2006. Science 311:796. What are higher taxa and ranks? An Example – Evolution & Homoplasy in Anolis • Approximately 400 species of Anolis, ~125 of which Domain How should they be used? occur in the Caribbean Most don’t have a specific meaning, Kingdom are not biological entities, and aren’t Phylum comparable to other groups of the same rank Class Trend to not use ranks Order Including this course! Family Use monophyletic groups (clades) to Genus refer to higher taxa Species _________________ are obviously Subspecies useful, maybe _____________ as well Photos © AS Munoz, G White, J Hance, PJ Bergmann 1 An Example – Evolution & Homoplasy in Anolis Anolis Ecomorphs • Many species occur in the Caribbean • On the Greater Antilles, “___________” have evolved Twig giant © J. Losos • The same ______________, with similar morphology Crown giant and ecology, have evolved on each of the four big Trunk-crown islands Trunk-crown dwarf © Auburn Herp Soc Cuba Haiti/Dominican Rep. Trunk-ground Jamaica Puerto Rico Powell and Russell, 1992. © Reptilien-Center.de Homoplasy in Anolis – different phylogenetic signal from different datasets Replicate Evolution in Anolis Locomotor Morphology mtDNA Anolis ecomorphs evolved in a ______________ Sequences ______________ on each of the Greater Antilles From Jackman et al., 2000. From Jackman et al., 2000. 2.