CHAPTER 26 Phylogeny and The Tree of Life

Learning Targets

Focus Questions 1. What is binomial nomenclature? And why is it useful? 2. What are the taxanomic groups from domain to species? 3. Why must scientists sort homologies from analogies when making phylogenetic trees? 4. What are the three domains of life and how are they related to each other? 5. What problems are there with the old 5 kingdom system of classification?

FIGURE 26.3 Species: Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora Class: Mammalia Phylum: Chordata Domain: Bacteria Kingdom: Animalia Domain: Archaea Domain: Eukarya

5 kingdom system is no longer valid…Why?

FIGURE 26.7 Are they related? How would you know? What would you look for?

DNA USED AS INDICATOR OF RELATEDNESS… How is this done?

FIGURE

FIGURE Deletion Insertion

FIGURE Deletion Insertion

FIGURE Deletion Insertion Alignment is awesome!

FIGURE 26.9 Even non-homologous chromosomes share ~ 25% of the genome

FIGURE TAXA Lancelet (outgroup) Lamprey Bass Frog Turtle Leopard Vertebral column (backbone) Four walking legs Hinged jaws Amnion Hair Vertebral column Hinged jaws Four walking legs Amnion Hair (a) Character table (b) Phylogenetic tree CHARACTERS Lancelet (outgroup) Lamprey Bass Frog Turtle Leopard Making a Cladogram…

FIGURE 26.UN07

FIGURE Archaea Bacteria Eukarya COMMON ANCESTOR OF ALL LIFE Land plants Green algae Red algae Forams Ciliates Dinoflagellates Cellular slime molds Amoebas Animals Fungi Euglena Trypanosomes Leishmania Sulfolobus Thermophiles Halophiles Methanobacterium Green nonsulfur bacteria (Mitochondrion) Spirochetes Chlamydia Cyanobacteria Green sulfur bacteria (Plastids, including chloroplasts) Diatoms Look closely…which domains are more related to each other? A branching tree?

FIGURE Bacteria Eukarya Archaea Billions of years ago Horizontal Gene transfer mitochondrion chloroplast

FIGURE Archaea Eukarya Bacteria

Focus Questions 1. What is the difference between monophyletic, polyphyletic and paraphyletic groups? 2. What is the difference between orthologous and paralogous genes, why are they important? 3. What is the difference between shared derived characteristics and shared ancestral characteristics? 4. What is a molecular clock, how is it used?

FIGURE (a) Monophyletic group (clade) (b) Paraphyletic group (c) Polyphyletic group Group  Group  Group  A B C D E F G A B C D E F G A B C D E F G Which is the correct way to classify?

Branch point: where lineages diverge ANCESTRAL LINEAGE This branch point represents the common ancestor of taxa A–G. This branch point forms a polytomy: an unresolved pattern of divergence. Sister taxa Basal taxon Taxon A Taxon B Taxon C Taxon D Taxon E Taxon F Taxon G How to Read a phylogenetic Tree

Determine shared bases Compute possibilities and apply maximum parsimony

Sometimes the results are surprising

FIGURE Formation of orthologous genes: a product of speciation Formation of paralogous genes: within a species Ancestral gene Ancestral species Species C Speciation with divergence of gene Gene duplication and divergence Orthologous genes Paralogous genes Species A Species B Species C after many generations

Not all molecular clocks run at the same rate Mammalian Molecular Clock