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The Organism as a Unit of Life Cellular Structure (cell = unit of life)…one or many! Metabolism = Homeostasis (PSN, Resp, N2fix, ferment, etc.) Growth = irreversible change in size Movement…includes internal, limbs, locomotion Reproduction…failure = extinction Acclimatization-short term responses = behavior Adaptation-long term responses = evolution

Biology is multidimensional Ecosystem Community Population Organism Organ System Organ Tissue Cell This array is an example of what dimension? Levels of Organization What fields of biology are at each extreme? Biophysics and Biochemistry In this course our focus will be upon… The Organism! This level of organization is also… Hierarchial / Multidimensional!

Swedish Botanist, Physician, and Zoologist Carolus Linnaeus (aka Carl von Linné) Swedish Botanist, Physician, and Zoologist 1707 - 1778 Developed a hierarchial classification scheme that we use to this day! http://upload.wikimedia.org/wikipedia/commons/6/68/Carl_von_Linné.jpg

Taxonomy is also Hierarchial! The Organisms are Diverse: Taxonomy 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

Not chimps, gorillas, etc. Figure 1-5 Page 7 of 3rd edition of your book (deleted from current edition) KINGDOM Not plants, fungi, etc. (Animalia) PHYLUM Not invertebrates (Chordata) CLASS Not birds, reptiles, etc. (Mammalia) ORDER Not bison, etc. (Primates) FAMILY Not lemurs, monkeys etc. (Hominidae) GENUS Not chimps, gorillas, etc. (Homo) SPECIES Not H. neanderthalensis, H. floresiensis, etc. (Homo sapiens)

√ Homo sapiens There are many Homo sapiens in class. Learn your own Latin binomial. Our genus means “self” not gender identity Our epithet: we think that we think! Our epithet always ends in ‘s’: One Homo sapiens is the instructor. There are many Homo sapiens in class. Print in italics, underscore in manuscript. I am a Homo sapiens. √

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)

How many organisms are there? What is a species? Animal species concept… if offspring are fertile then same species… does not apply to species of other kingdoms: Prokaryotes (no sex) Allopolyploidy in plants

X Horse: Equus caballus Donkey: Equus asinus Mule: Sterile Hybrid http://www.fotosearch.com/comp/JNB/JNB002/00099924.jpg http://www.explorecrete.com/albums/album19/donkey.jpg http://www.muleranch.com/Clients/RedPeak-JerryHeitzlerMule.gif Mule: Sterile Hybrid

X X Fertile Hybrids! Coyote Canis latrans Wolf Canis lupus German Shepherd Dog Canis familiaris X X http://museum.utep.edu/chih/theland/animals/mammals/clatrans.jpeg http://www.ecores.uzhgorod.ua/Fotogalereya/fauna/Canis_lupus_01.JPG http://www.dog.com/breed/docgrafx/germshep.jpg http://www.city.west-lafayette.in.us/wlpd/coyredw.jpg Coydog http://www.leerburg.com/Photos/wolfdog-05.jpg Wolfdog Fertile Hybrids!

What is a Species? The Case of Bread Wheat AA (diploid wheat) x DD (diploid grass) Triticum urartu Aegilops tauschii AD (sterile diploid) similar to mule! colchicine or spontaneous AADD (fertile tetraploid) BB (diploid grass) Aegilops speltoides BBAADD Fertile hexaploid Bread Wheat Triticum aestivum colchicine or spontaneous BAD (sterile triploid) Bread Wheat Created 7500 BC with spontaneous doubling of DNA Levy A. A. and M. Feldman. 2002. The impact of polyploidy on grass genome evolution. Plant Physiol. 130: 1587-1593.

How many kingdoms are there? Good Question! The relationships among known organisms are not completely understood. Are you a lumper or a splitter? Newer information appears to back up the taxonomic decisions of splitters! Historical shifts from 2, to 3, to 4, to 5, to 6 and now to many more in just the last 40 years!

Multicellular Animals Shifting Kingdoms Lumpers Splitters 2 3 5 6 8 Bacteria Archaea Archezoans Euglenoids Chrysophytes Green Algae Brown Algae Red algae Slime Molds True Fungi Bryophytes Tracheophytes Protozoans Myxozoans Multicellular Animals

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

DOMAIN BACTERIA DOMAIN ARCHAEA DOMAIN EUKARYA 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

How Many Kingdoms? Extant 8 5 3 First Eukaryote! Extinct 2 1 Multicellular Animals Myxozoans Protozoans Tracheophytes Bryophytes True Fungi Slime Molds Red algae Brown Algae Green Algae Chrysophytes Euglenoids Archezoans Archaea Bacteria 8 5 3 First Eukaryote! Extinct 2 1 Long Time with Prokaryotes only Original Cell

How Many Kingdoms? Extant 8 5 3 First Eukaryote! Extinct 2 1 Multicellular Animals Myxozoans Protozoans Tracheophytes Bryophytes True Fungi Slime Molds Red algae Brown Algae Green Algae Chrysophytes Euglenoids Archezoans Archaea Bacteria 8 5 3 First Eukaryote! Extinct 2 1 Long Time with Prokaryotes only Original Cell

Here is a phylogeny that covers some of the animals: http://thehurricanes.deviantart.com/gallery/ http://thehurricanes.deviantart.com/art/Phylogeny-with-Spongebob-156909686

Figure 1-9 Page 10 of 3rd Edition Plants, fungi, and animals are small branch tips on the tree of life This node represents the common ancestor of archaea and eukaryotes This node represents the common ancestor of all organisms alive today

In which direction is the axis of time shown? Page 7 Figure 1.5 In spite of this graphic image, and the highlighted point on the lower right, your book, like most others, is organized as if there were only two kingdoms (Plantae and Animalia), as if nothing happened since Linnaeus! DOMAIN BACTERIA Mycoplasma How is this graphic from your book the same, and how is it different from the other depictions of the “Tree of Life” you have seen so far? 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

David Hillis’ tree of life based on total genome sequences (at the time) Eukaryotes Archaeons How many twigs would be on this diagram if ALL the extant organisms were shown? ? Prokaryotes Time Dimension? http://upload.wikimedia.org/wikipedia/commons/1/11/Tree_of_life_SVG.svg

Because this analysis is easier/faster, more species can be included! David Hillis’ tree of life based on rRNA sequence analysis (at press time) Rhodophyta Because this analysis is easier/faster, more species can be included! origin Stramenopila http://www.zo.utexas.edu/faculty/antisense/tree.pdf

Why did the five-kingdom system of classification fall out of favor? It was too complex—the original two-kingdom system of Linnaeus was more useful. Many organisms were difficult to classify because they had characteristics of more than one kingdom. There were too many prokaryotes to be included in a single kingdom. It did not reflect the actual evolutionary relationships among organisms very well. Answer: D

Summary Points for Taxonomic/Phylogenetic Classification Linnaean Classification is hierarchical: Kingdom, Phylum, Class, Order, Family, Genus, Species Organisms have names: Common names are redundant and multiple, Latin binomials are universal and almost unique Species of organisms have a recognized binomial: Genus name and specific epithet There are more than a million species of organisms on our planet--most are arthropods Many species on Earth are unknown or virtually unstudied Organisms are grouped into a few kingdoms The number of kingdoms has increased over time on the planet, and in biology over time too Phylogenic Cladistics relates organisms based on evolutionary pathways rather than on taxa All organisms on this planet evolved from a single ancestor and so are a clade Most of the recognized Kingdoms are close to natural groupings based on shared ancestry Kingdom Protista needs further dissection to become a natural grouping

For Figuring Biological Data This Week! Bring your Biologist at Work Worksheet (completed?) Bring your Figuring Biological Data Worksheet (read!) Bring your Laptop with Excel installed…if you have one Bring your Flash Drive if you do not have a laptop Download the Course Data file from the course website: To your Laptop with Excel…OR To your Flash Drive