1. Species tree phylogenetics of a clade of Cuban Anoles Seth Rudman

2. Introduction to Anolis Anolis sagrei, one of Cuba's most common species; Anolis vermiculatus, an aquatic species from western Cuba; Anolis barbatus, a strange Cuban species that feeds on snails; Anolis allisoni, another Cuban species; Anolis bartschi, a spectacular rock- dweller that lacks a dewlap; Anolis distichus, from Hispaniola; Anolis aliniger, a montane species from Hispaniola (center).

3. Introduction to Anolis Anolis sagrei, one of Cuba's most common species; Anolis vermiculatus, an aquatic species from western Cuba; Anolis barbatus, a strange Cuban species that feeds on snails; Anolis allisoni, another Cuban species; Anolis bartschi, a spectacular rock- dweller that lacks a dewlap; Anolis distichus, from Hispaniola; Anolis aliniger, a montane species from Hispaniola (center).

4. Ecomorphs

17. Anolis sagrei

18. Phylogenetics basics: a quick review

19. Making a Gene Tree 1) Collect tissue 2) Extract DNA and Sequence 1 mtDNA marker and 2 common nDNA markers

20. 3) Align sequences and make a tree

21. Difficulties of Phylogenetics Conflicting gene histories Gene A reconstructs this topologyGene B reconstructs this topology

22. Difficulties of Phylogenetics Short distances between nodes

23. Problems encountered by my early trees…

24. Species Trees Helpful to imagine a gene tree as a tree contained within the true phylogeny. Think of a species tree as an aggregate of all gene trees.

25. What I’m doing now Re-sample characters to form smaller datasets and determine the importance of sampling many nuclear loci.