Center for Learning In Retirement Drawing Darwin’s Diagram: University of Connecticut Storrs, CT January 10, 2017 Drawing Darwin’s Diagram: Creating Cladograms Ross Koning, PhD Professor of Biology Eastern Connecticut State University Willimantic, CT

Swedish Botanist, Physician, and Zoologist Carolus Linnaeus (aka Carl von Linné) Swedish Botanist, Physician, and Zoologist 1707 - 1778 Developed a hierarchial classification scheme do deal with all these organisms, and we use to this day (though we are moving away from it a little bit)! http://upload.wikimedia.org/wikipedia/commons/6/68/Carl_von_Linné.jpg

Taxonomy is Hierarchial! The Organisms are Diverse Domain Bacteria Archaea Eukarya Kingdom Eubacteria Gram + Protista (Chromista) Plantae Fungi Animalia Phylum Proteobacteria Eury-archaeota Phaeophyta Anthophyta Magnolio-phyta Basidio-mycota Chordata Class Gamma-proteobacteria -- Phaeo-phyceae Dicoty-ledonae Hymeno-mycetes Mammalia Order Entero-bacteriales Halo-bacteriales Fucales Rosales Agaricales Primates Family Entero-bacteriaceae Halo-bacteriaceae Fucaceae Rosaceae Agaricaceae Hominidae Genus Escherichia Halo-bacterium Fucus Rosa Agaricus Homo Species E. coli H. salinarum F. distichus R. multiflora A. bisporus H. sapiens Common DH5 Halophytic archaeon Rockweed Wild Rose Mushroom Human

How many organisms are there? Good Question! Let’s exclude extinct species! Many extant are unknown so we estimate! Bacteria: 10,000 Archaea: 1,000 Protista: 20,000 (includes Stramenopila and Rhodophyta) Plantae: 285,000 (mostly flowering) Fungi: 110,000 Animalia: 1,400,000 (mostly arthropods)

Descent with Modification http://www2.biologie.uni-halle.de/zool/mol_ecol/Bilder/DarwinBild.jpg Charles Darwin - British Naturalist Formal Studies: Medicine and Theology 1809 - 1882 http://upload.wikimedia.org/wikipedia/en/3/3e/Charles_Darwin_1854.jpg Descent with Modification 1880 The Power of Movement in Plants 1871 Descent of Man 1859 Origin of Species Species evolved from generation to generation over time 1831-1836 HMS Beagle Voyage http://www.omniscopic.com/blog/uploaded_images/darwin-791061.jpg

Notice the very large number of extinctions! Darwin’s Tree of Life (1859) the only figure in: On the Origin of Species future time present The Roman numerals each represent 1000 generations many more many more past time The letters A-L represent hypothetical progenitor species within a single genus Notice the very large number of extinctions! http://upload.wikimedia.org/wikipedia/commons/f/f4/Darwins_tree_of_life_1859.gif

A VERY simple Tree of Life! Question 14 Page 15 before nucleus true nucleus Turn back to the tree of life shown in Figure 1.5. Note that Bacteria and Archaea are prokaryotes, while Eukarya are eukaryotes. On the simplified tree below, draw an arrow that points to the branch where the structure called the nucleus originated. Explain your reasoning. DOMAIN BACTERIA DOMAIN ARCHAEA DOMAIN EUKARYA A VERY simple Tree of Life! the origin of life

Which dimension shows the progression of time? Figure 25.19 Bacteria Which dimension shows the progression of time? Archaea Last universal common ancestor (LUCA) Flowering plants Mosses Figure 25.19 Evolution Produces a Tree of Life, Not a Progressive Ladder of Life. Tapeworms The branches on the tree represent the relatedness of populations. All of the species have evolved from a common ancestor. None is “higher” than any other Vertebrates Fungi 8

Page 7 Figure 1.5 DOMAIN BACTERIA Mycoplasma There are many depictions of the tree of life that differ in various ways. How is this graphic from a textbook the same, and how is it different from the other depictions of the “Tree of Life”? In which direction is the axis of time shown? The long list of organisms down the right are __? Firmicutes Cyanobacteria Actinobacteria Spirochaetes Chlamydiae Bacteriodetes -Proteobacteria -Proteobacteria -Proteobacteria This node represents the common ancestor of all organisms alive today -Proteobacteria -Proteobacteria DOMAIN ARCHAEA Thaumarchaeota Crenarchaeota Korarchaeota This node represents the common ancestor of archaea and eukaryotes Euryarchaeota DOMAIN EUKARYA Slime molds Fungi Animals Choanoflagellates Fungi, animals, and plants are small branch tips on the tree of life Euglenids Parabasilids The three twigs highlighted on the tree are showing which level of modern Linnean taxonomy? Diplomonads Red algae Green algae Land plants Foraminiferans Ciliates Dinoflagellates Apicomplexans Water molds Diatoms Brown algae

Here is a phylogeny that only covers some of the animals: ( with a nod to Sponge Bob Square Pants! ) Steps in the pathways of evolution are shown http://thehurricanes.deviantart.com/gallery/ http://thehurricanes.deviantart.com/art/Phylogeny-with-Spongebob-156909686

How do we make a tree of life? Extant Multicellular Animals Myxozoans Protozoans Tracheophytes Bryophytes True Fungi Slime Molds Red algae Brown Algae Green Algae Chrysophytes Euglenoids Archezoans Archaea Bacteria 0.5 Land! Animals 1 Multicellular 2 First Eukaryotes Extinct 3 Cyanobacterial Oxygen Long Time with Prokaryotes only 4 BYBP Origin of Life Original Cell

Emil Hans (Willi) Hennig German entomologist Hennig developed a mechanism (cladistics) to find the pathways of evolution among related organisms. It is based not only on what one sees, but on many kinds of evidence, including molecular sequences. The pathways are determined by virtue of shared derived characteristics (synapomorphies). Rather than putting organisms into Linnean taxonomic “boxes,” the cladistics process shows the pathway of evolution. Emil Hans (Willi) Hennig German entomologist 1913-1976 http://scienceblogs.com/evolvingthoughts/upload/2007/04/Willi_Hennig2.jpg

Evidence Categories History - clearer recently, more obscure anciently Fossils - stratigraphic depth, isotope decay, etc. Chemical - metabolic products such as O2, Ss Molecular - DNA sequence alterations, etc. Developmental sequences - onto- phylo- geny Biogeography - Pangea, Gondwana & Laurasia

How do we find the Evolution Pathway? Phylogenetic Systematics Inferences from comparison of extant organisms Characters-Attributes of the organism Anatomy Morphology Development Physiology Macromolecule Sequences Polarizing Character States Plesiomorphies-Ancient, shared by descendants Apomorphies-More-recent derivatives Synapomorphy-Shared among related organisms Autapomorphy-Found only in one organism Use of outgroup to compare to ingroup

CLADE CRITTERS! Time to have some fun creating our own cladogram! What do those 18 year-olds do with this topic in freshman biology? This activity was NOT offered in the biology courses in my days at University of Michigan in Ann Arbor (1971-1981). In fact, even at Eastern, I introduced this activity in the late 1980s, but it was only in my “modernized” section of Organismal Biology. We will work with hypothetical organisms I like to call CLADE CRITTERS!

Page 7 Clade Critters Lacking Antennae OG A B C D E Plesiomorphies are features so anciently evolved that they are found in all of the organisms including OG.

Page 7 Clade Critters Lacking Antennae OG A B C D E Apomorphies are features modern enough to have evolved among the members of the in-group; i.e. not observed in OG.

Page 7 Clade Critters Lacking Antennae OG A B C D E Synapomorphies are features shared among the members of the in-group indicating closer relatedness, establishing branching.

Page 7 Clade Critters Lacking Antennae OG A B C D E Autapomorphies are features evolved so recently they are observed only in one member of the in-group.

Now we fill out a data matrix to direct our cladogram construction B C D E Large Black Wide Long Thick 1 1 1 1 1 2 1 3 5

Lights ON, Please!

Time to make the cladogram on Page 2: B A D C -- 2 black eye -- 3 wide neck -- 7 long wing CD -- 8 long leg -- 5 dark body BE ACD -- 1 large eye -- 9 thick leg -- 4 wide body BE Comma separation at one step might be clearer! -- 6 wide wing -- 10 long stinger

The diagram you produced on Page 2: OG E B A D C -- black eye -- long wing -- wide neck -- long leg -- dark body -- large eye -- thick leg -- wide body The differences in the in-group are explained in 10 steps! -- wide wing -- long stinger

This diagram is based on the same clade critter data… But is not the result of cladistic analysis: OG E B A D C 25 Steps!! <-- black eye <-- long leg <-- dark body <-- wide neck <-- thick leg <-- wide body <-- long wing <-- large eye <-- wide wing <-- long stinger What concept was used to make this diagram? Scientists reject this diagram because of parsimony…why?

This is likely your cladogram from Page 2 of Cladistics OG E B A D C -- 2 black eye -- 3 wide neck -- 7 long wing -- 8 long leg -- 5 dark body -- 1 large eye -- 9 thick leg -- 4 wide body -- 6 wide wing -- 10 long stinger

What do we do with the newly-discovered Clade Critter (page 3)? OG E B A D C -- black eye OG -- long wing -- wide neck -- long leg -- dark body -- large eye -- thick leg -- wide body F -- wide wing -- long stinger

Is it easier to evolve or to lose a characteristic? There are two possible explanations— which is most parsimonious? OG F E B A D C dark -- body -- dark bodyR -- black eye -- long wing Two Forward Evolutions -- wide neck -- dark bodyR -- long leg -- dark body F -- large eye A homoplasy of parallelism or… convergence -- thick leg -- wide body A single evolution But two reversals -- dark body -- wide wing -- long stinger Is it easier to evolve or to lose a characteristic?

Is dark body a complex characteristic? There are two possible explanations— which is most parsimonious? OG F E B A D C dark -- body -- dark bodyR -- black eye -- long wing Two Forward Evolutions -- wide neck -- dark bodyR -- long leg -- dark body F -- large eye A homoplasy of parallelism or… convergence -- thick leg -- wide body A single evolution But two reversals -- dark body -- wide wing -- long stinger Is dark body a complex characteristic? Maybe one enzyme!

And one fewer step! Maybe one enzyme! There are two possible explanations— which is most parsimonious? OG F E B A D C dark -- body -- black eye -- long wing Two Forward Evolutions -- wide neck -- long leg -- dark body F -- large eye A homoplasy of parallelism or… convergence -- thick leg -- wide body And one fewer step! -- wide wing -- long stinger Maybe one enzyme!

Keep Calm and Keep Learning In Retirement! Happy New Year!