Systematics, Taxonomy, & Phylogenetics David L Systematics, Taxonomy, & Phylogenetics David L. Reed, Mammalogy Class August 27, 2002

Systematics is …. Systematics is the study of the diversity of organisms and the relationships among these organisms. It provides the framework for studies of biological diversity & evolution

Systematics comprises: Classification - ordering of organisms into groups (pigeon-holing) Nomenclature - the naming of organisms Identification- placement of a new organism into a previously described group

Linnaeus’ Binomial Nomenclature Domain, Kingdom, Phylum, Class, Order, Family, Genus, and Species Latin binomial (Genus species) Hierarchical structure Very flexible when changes need to be made Book outlining all the rules for nomenclature Work an example

Classifications Phenetic Phylogenetic Based on overall similarity (Phenetic) Pros-- easy to see similarity, intuitive Cons--doesn’t account for evolutionary history Phylogenetic Based on shared derived characters Pros--contains evolutionary history Cons--computationally harder

Phenetic Classification: Phenetic classification (grade-level classification) is based upon overall similarity (Numerical Taxomony) Phenogram: a branching diagram (tree) that links taxa by estimates of overall similarity

Phenetic Groupings Kangaroos with kangaroo mice (jumping legs) Sugar gliders with flying squirrels (gliding membrane) Bats with birds (wings) House cat Mountain Lion Domestic dog Grey Fox Bobcat Grey Wolf African Lion

Downfall of Phenetics Overall similarity misled biologists into putting things in non-natural groups (i.e. Ungulata-Artiodactyls + Perrisodactyls) Better to use characters that are evolutionarily shared among group members (synapomorphic characters)

Phylogenetic classification (cladistics): Based upon evolutionary relationships (i.e. upon common ancestry) Would put all marsupials together because of the synapomorphic pouch Separates birds and bats because they have unique evolutionary origins for their wings

Diagrams for Cladistic Analyses Cladogram is a tree diagram which depicts a hypothesised evolutionary history A Phylogram is a tree which indicates by branch length the degree of change believed to have occurred along each lineage

Cladograms and phylograms Bacteria 1 Bacteria 2 Cladograms show branching order - branch lengths are meaningless Bacteria 3 Eukaryote 1 Eukaryote 2 Eukaryote 3 Eukaryote 4 Phylograms show branch order and branch lengths Bacteria 1 Bacteria 2 Bacteria 3 Eukaryote 1 Eukaryote 2 Eukaryote 3 Eukaryote 4

Character Matrix Characters Taxa 1 2 3 4 5 A B C D

Unrooted Cladogram C A B D

Character Matrix Characters Taxa 1 2 3 4 5 A (out) B C D

Rooted Tree (requires additional information) B C D 5 (0-1) Characters Time 4 (0-1) Taxa 1 2 3 4 5 A (out) B C D 3 (0-1) 2 (0-1) 1 (0-1)

Character Matrix Characters Taxa 1 2 3 4 5 A (out) B C D E

Rooted topology D B C A E 5 5 3 2 4 1 (0-1) Taxa 1 2 3 4 5 A (out) B C B C D E

Taxa No. of Possible Unrooted Trees 4 3 5 15 6 105 7 945 8 10,395 9 135,135 10 2,027,025 11 34,459,425 12 654,729,075 13 13,749,310,575 14 316,234,143,225 7,905,853,580,625 16 213,458,046,676,875 17 6,190,283,353,629,375 18 191,898,783,962,510,625 19 6,332,659,870,762,850,625 20 221,643,095,476,699,771,875 21 8,200,794,532,637,891,559,375 <-------(2.5 Billion years to compute!!!!!!!!!!!!!)

What about Fossils? Fossils often have far fewer characters to measure DNA sequencing usually isn’t possible Result is that paleontology still uses phenetic classification, sometimes However, phylogenetic analyses can still be done when data are available

Phylogenetic systematics Uses tree diagrams to portray relationships based upon common ancestry Monophyletic groups (clades) - contain species which are more closely related to each other than to any outside of the group

Monophyletic groups monophyletic groups (clades) Rodent outgroup Fox Wolf Coyote Cougar Bobcat Domestic Cat Lion

Paraphyly and Polyphyly Rodent outgroup Wolf Coyote Canidae (polyphyletic) Fox Dog Bobcat Domestic Cat Felidae (paraphyletic) Cougar

What can we use phylogenies for? Character evolution Host-parasite evolution Systematics and Taxonomy Evolutionary history Comparative biology

Character Evolution - Amniota Rayfinned fish Rayfinned fish salamaders crocodiles mammals salamaders mammals crocodiles turtles lungfish lizards snakes lungfish turtles lizards snakes frogs birds frogs birds amnion absent present 3 steps 1 step

Comparative Analyses

Comparative Analyses