Schools of Systematics Schools of Systematics What Is Evolutionary

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

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

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

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.