<p>&lt;p&gt;&amp;lt;p&amp;gt;Introduction to Phylogenetic Systematics Mark Fishbein Dept. Biological Sciences Mississippi State University 13 October 2003 Which of these critters are most closely related? gopher tortoise purple gallinule alligator gila monster kingsnake ? Phylogeny ? Branching history of evolutionary lineages ? New branches arise via speciation ? Speciation occurs when gene flow is severed between populations ? Phylogenetic relationships depicted as a tree W. S. Judd, et al., Plant Systematics W. S. Judd, et al., Plant Systematics Phylogenetic data ? Morphology ? Secondary chemistry ? Cytology ? Allele frequencies ? Protein sequences ? Restriction sites ? DNA sequences “Molecular” data Molecular (genetic) data ? Proteins Serology (immunoassay) Isozymes (electrophoretic variants) Amino acid sequences ? DNA Structural (translocations, inversions, duplications) Restriction sites DNA sequences ? Substitutions ? Insertions/Deletions From Raven et al. (1999), Biology of Plants What are genes? Genomes ? All of the genes within a cell are the genome ? Genes located in the nucleus are the nuclear genome ? Other genomes (organellar) Mitochondrion: mitochondrial genome Chloroplast: plastid genome From Raven et al., 1999, Biology of Plants nucleus chloroplast mitochondrion Comparison of Genomes NuclearMitochondrialPlastid SizeLargeSmallSmall NumberMultipleSingleSingle Shape of Chromosomes LinearCircularCircular PloidyDiploidHaploidHaploid InheritanceBiparentalUniparentalUniparental From Freeman and Herron (1998), Evolutionary Analysis Inversion Crossing over, duplication, and loss Structural rearrangements Chemistry of Genes ? DNA ? Parallel strands linked together ? Linear array of units called nucleotides Phosphate Sugar: deoxyribose One of four bases ? Adenine (“A”) ? Cytosine (“C”) ? Guanine (“G”) ? Thymine (“T”) From Raven et al. (1999), Biology of Plants DNA structure ? Paired strands are linked by bases A must bond with T G must bond with C ? Each link is composed of a purine and a pyrimidine A entire mtDNA sequences (15,000 bp) in animals ? 2004: ? The Large Data Set Headache ? Problem: the large number of sequences, not the size of sequences ? Application of phylogenetic optimality criteria requires evaluation of all possible trees ? Algorithms guaranteed to find optimal solutions have limited applicability The Problem of Finding Optimal Trees ? There are too many trees to evaluate! ? The number of possible topologies increases very rapidly with the number of taxa/samples ? There are (2m - 5)! / 2m-3(m-3)! unrooted trees , where m = number of taxa From Hillis et al. (1996), Applications of Molecular Systematics TaxaTrees 3 1 4 3 5 15 7945 9 135,135 stars in the universe atoms in the universe Heuristic Methods ? Starting trees followed by rearrangement Starting trees sample “tree space” Rearrangements search for local optima ? How to get starting trees? ? How to rearrange trees? ? These methods are prone to getting trapped on local optima Cutting-edge Methods ? Ratchet Temporarily “warps” the character space ? Annealing algorithms Accept suboptimal trees and gradual movement towards optima ? Genetic algorithms Analogous to evolution by natural selection Using Phylogenies Why are birds so different than their closest relatives? Is the rate of molecular evolution in birds especially high? What genes are involved in the origin of novel traits (like wings)? &amp;lt;/p&amp;gt;&lt;/p&gt;</p>