B6A2SystematicsF10 - Biological Classification What’s in...

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Unformatted text preview: Biological Classification What’s in a name? Biological Classification “Bears” • Taxonomy: naming & classifying organisms • Systematics: studying relationships among taxonomic groups North America Australia Systems of Systematics I. Anthrocentric II. Ecological III. Hierarchical IV. Phylogenetic I. Anthrocentric Systems Aristotle, 384–322 BCE – Scalae Naturae (“ladder of nature”) • “advanced” = more human-like • “primitive” = less human-like * Archaic, prejudicial expressions: Any organism successfully surviving is not “primitive”! * Better terms: “generalized” vs. “specialized” or “derived” Heyer I. Anthrocentric Systems • “human-centered” — Classified based on their relevance or usefulness to humans – Edible / inedible / medicinal – Wild vs. domestic – Crops vs. weeds • Still basis for political policies – “Biological resources” – Commercially harvested vs. recreationally harvested vs. non-targeted (trash, by-catch) species II. Ecological Systems • Classified based on their habitat, niche or behavior – “Plant” (planted in place / sessile) vs. “Animal” (animated / motile) – “beasts of the field” / “beasts of the air” / “beasts of the sea” (fish) • Useful for studying ecological relationships and effects of environment on body forms – Vegetation types: herb / shrub / tree – Aquatic life: plankton / nekton / benthos – Assemblages of organisms in a specific community • Oak woodland biota; coral reef biota; etc. 1 Biological Classification III. Hierarchical Systems Carolus Linnaeus (Carl von Linné), 1707–1778 —“Father of modern taxonomy & systematics” • Classified based on their relative similarities of body form Carolus Linnaeus (Carl von Linné), 1707–1778 —“Father of modern taxonomy & systematics” Carl von Linné, 1775 III. Hierarchical Systems • Develop a standard hierarchy of similarities ii. “…finish the work of Adam.” • Identify, name, and categorize all forms of life on earth. • Develop a standard “universal” naming practice (“scientific name”) Taxonomy & Linnaean Hierarchy • For taxa with high diversity and large number of species, (esp., arthropods) additional levels may be added by using prefixes super-, sub-, or infra• E.g., d) Order e) Family • may be expanded to d) Order d’) Suborder d”) Infraorder d”’) Superfamily e) Family Heyer Taxonomy & Linnaean Hierarchy • Levels called taxa (sing., taxon: “classification”) – The more similar two organisms are, the more levels they have in common a) b) c) d) e) f) g) p” ou ” S nd d Sa oo n G ee or G r rF e ve F i n O e On am s C hes lip C hi y P la gP in g s “K in “K • Classified based on their relative similarities of body form Carolus Linnaeus (Carl von Linné), 1707–1778 —“Father of modern taxonomy & systematics” i. Recognize “patterns in creation” • Swedish botanist, zoologist, physician, linguist, poet, & educator. Degree in Medicine; professor of medicine & botany - Uppsala University. • Also one of the fathers of modern ecology. One of the most influential intellectuals of the 18th century. • Students from all over Europe ( esp . England) came to study under him. Then went out to join numerous exploratory expeditions around the world (e.g., with James Cook) and join faculties of major universities. • Linnaeus also corresponded with collectors and naturalists around the world who sent him exotic specimens. Kingdom Phylum (Division)* Class Order Family* Genus Species *not in the original Linnaean hierarchy Carl Linné, 1737 Biological Kingdoms Classification of Life on Earth • Classical two-kingdom model – Plants – Animals Worked well for macroscopic terrestrial life. But became inadequate once microbial and oceanic ecosystems were explored • Expanded five-kingdom model (Whittaker 1960s) Cells are the basic unit of life, so define types of life by the types of their cells – Monera – Protista – Fungi – Plantae – Animalia 2 Biological Classification Linnaean Taxonomy Some rules: Since all scientific and academic work in Linnaeus’ time was conducted in Latin or Greek, • all taxonomic names are written in Latin or Greek … – – – – – rosa: “rose” homo : “human ” canis : “dog” porifera: “pore bearing” brevispinus: “short-spined” Linnaean Taxonomy Some rules: • Names of families always end in “-idae” [animals] or “-aceae” [plants & fungi] – Hominidae – Can idae – Rosacea • Names of genera must be unique I.e., not given to any other genus – Homo – Canis – Rosa • … or in Latinized/Hellenized derivations of proper names – ricketsia: [in honor of Ed] Rickets – californicus: [discovered in] California • A species is a group of organisms similar enough to interbreed Classification of some edible shellfish Linnaean Taxonomy The universal “scientific name ” for a species : • Binomial nomenclature (“two-name naming”) The universal name for a species is its gener ic name with a specific epithet, i.e., its genus + species names American Lobster Market Squid Blue Mussel Virginia Oyster European Oyster Kingdom Animalia Animalia Animalia Animalia Animalia Phylum Arthropoda Mollusca Mollusca Mollusca Mollusca Class Malacostraca Cephalopoda Bivalvia Bivalvia Bivalvia Order Decapoda Decapoda Mytiloida Pterioida Pterioida • The two names must be unique to one species. Family Nephropidae Loliginidae Mytilidae Ostreidae Ostreidae • The genus name must be capitalized; the species name all lower case — even if it’s in a title. Genus Homarus Loligo Mytilus Crassostrea Ostrea Species americanus opalescens edulis virginica edulis – Homo sapiens – Canis familiaris • The scientific name is always printed (type-set; word processed) in italics . If handwritten, it must be underlined . • The species name must include the genus. Note: some names are duplicated for taxa other than genus! – Homo sapiens or H. sapiens , but never just sapiens Linnaean Taxonomy The Law of Priority : • If more than one name has been assigned to organisms later decided to be all one species, the first published name becomes the name for the combined group. • The specimen originally used to the describe the newly named species is the type specimen. – The type specimen is carefully archived in a certified museum collection available for subsequent studies. • If a group of organisms originally classified as a single species becomes divided into multiple species, the original scientific name belongs to the new group that includes the type species. “The Linnaean Enterprise” • Identify, name, and categorize all forms of life on earth. • Systema Naturae – 1735 (first edition) – By 1758 (tenth ed.) • Included 4400 animal spp. & 7700 plant spp. • First consistent use of binomial nomenclature 1760 edition Heyer 3 Biological Classification “The Linnaean Enterprise” • Still lots to do! • Present — ~1.8 million species named (~70% of them are insects) Only ~ 1% studied significantly Estimated ~10 million spp. yet to be named IV. Phylogenetic Systems 1. Classical (authoritative) phylogenetics 2. Phenetics 3. Cladistics 4. Synthetic systematics – Try to incorporate bits of all of the above A phylogenetic “tree” • Aristotle’s philosophy in a Darwinian context Heyer IV. Phylogenetic Systems • Classified based on presumed common ancestry • Usually still use Linnaean hierarchy, but now more levels in common suggests a more recent divergence from a common ancestor. • But since we don’t actually know the ancestry above the level of genus or maybe family, still dependent upon degrees of similarity. – Comparative morphology & anatomy – Comparative embryology – Comparative biochemistry — proteins & DNA • Much disagreement may be debated regarding which similarities and which differences are most phylogenetically significant! 1. Classical phylogenetics • “Traditional evolutionary taxonomy” (TET) • Authoritative — Influential “experts” on each taxon pick which characters are most significant – Create “trees” (dendrograms) – Often arbitrary and contradictory – Certain popular trees get perpetuated when published in textbooks 2. Phenetics • Morphometrics — carefully measure all dimensions of body form • Phenogram (taxonomic cluster) — mathematic programs calculate degrees of similarity (cluster analysis — advent of available computers) • TET purists argue that all body forms are not dependent upon ancestry, \ should not be included – Homology vs. analogy • Pheneticists counter that since no one actually knows ancestry, at least metric methods are less arbitrary than TET. 4 Biological Classification Problem: Divergence vs. Convergence — Homology vs. Analogy Similarity due to convergence is analogy . (Similar adaptations to similar environments; not shared ancestry.) 3. Cladistics More vocabulary: • A true clade must be monophyletic – must include an ancestor and all of the known descendants of that ancestor. – A grouping that only includes an ancestor and some of its descendants is paraphyletic. – A grouping that includes organisms from different ancestries is polyphyletic. • Derived apomorphic characters shared by members of a clade are synapomorphic. • Ancestral characteristics inherited prior to the branching of a clade are plesiomorphic. Building Cladograms Each bifurcation of the branch is based upon the state (presence/absence) of an apomorphic character Heyer 3. Cladistics • Traditional phylogeneticists get to have computer programs too! • Clade (“branch”) — replace traditional taxon – Groups of organisms presumed to be derived from a common ancestor are organized by bifurcating (two-way splitting) of a branch – Each bifurcation is based upon the acquisition of a new, unique character (apomorphy). • Maximum parsimony: the branch pattern that can be created with the fewest required steps is most likely the most correct. Building Cladograms Major assumptions: Assemble a table of character states 1. The group of organisms is monophyletic 2. The outgroup (used for comparison) is closely related to, but separate from your group 3. You can tell which character states are homologous or analogous. Cladograms Monophyletic clades 5 Biological Classification Cladograms Paraphyletic grouping Cladograms Polyphyletic grouping Cladograms Cladograms Rule of Parsimony: Rule of Parsimony: The simplest explanation is the most likely explanation. The simplest explanation is the most likely explanation. But not always! Heyer 6 Biological Classification Synthetic Systematics Correlating clades with hierarchal taxa Hylobatidae Model based upon morphometrics — paraphyletic Pongidae? New Family? Model based upon some molecular biology — is this really better? clades Chordate Systematics ‹TET classes Both systems have valid uses Heyer 6B Biological Classification Biological Kingdoms Biological Kingdoms Cellular characteristics for the five-kingdom model: • Organelles: specialized compartments within the cells Classification of Life on Earth – Prokaryote: no nucleus or other membranous organelles – Eukaryote: nucleus & other organelles present • Classical two-kingdom model – Plants – Animals Worked well for macroscopic terrestrial life. But became inadequate once microbial and oceanic ecosystems were explored • – Autotrophic ( “self feeding ”) • photosynthetic • chemosynthetic • Expanded five-kingdom model (Whittaker 1960s) Cells are the basic unit of life, so define types of life by the types of their cells – Monera – Protista – Fungi – Plantae – Animalia Monera - bacteria • No true nucleus • Small, single prokaryotic cells Energy source – Heterotrophic ( “feed on others ”) • Intracellular digestion • Extracellular / external digestion and/or absorption • Extracellular / ingestion • Cell wall — rigid surrounding structure outside of the cell • Tissues – Present or absent – Chemical structure – Unicellular or generalized colonies – Differentiated into specialized tissue types Protista • single celled eukaryotic organisms • i.e.: – Amoeba – algae – slime molds Fungi • • • • Eukaryotic Multicellular (most) Cell wall — chitin Heterotrophic (cannot make own food) – External digestion • i.e. yeast, mushrooms Heyer Plants • Eukaryotic • Multicellular • Photosynthetic – chloroplasts • Cell wall – cellulose • i.e. Trees, mosses, ferns 7 Biological Classification Splitting a Kingdom Animals • • • • Eukaryotic Multicellular, motile No cell walls Heterotrophic – ingestion • i.e. worms, insects, vertebrates, “us” • • 1970s, Woese , et al Structure of ribosomes (molecular machines necessary for translating DNA instructions to build proteins) among two groups of Monera very different • Differences sufficient to separate Monera into two distinct kingdoms – Eubacteria - “typical” bacteria – Archaebacteria “extremophile ” bacteria rRNA phylogeny • • 1990s, Woese , et al, proposed that archaebacteria were as different from eubacteria as from eukaryotic kingdoms. Grouped the kingdoms into three domains – Bacteria - Eubacteria – Archaea - Archaebacteria – Eukarya - Protista , Fungi, Plantae , & Animalia Fig. 1: A speculatively rooted tree for rRNA genes (NASA Astrobiology Institute) Revisions of the concept of Kingdoms of Life Biological Kingdoms Linnaeus 1735 Haeckel 1866 Chatton 1937 Copeland 1956 Whittaker 1969 Woese et al. 1977 Woese et al. 1990 2 kingdoms 3 kingdoms 2 empires 4 kingdoms 5 kingdoms 6 kingdoms Prokaryota Monera Monera Eubacteria Bacteria Archae bacteria Archaea Protista Protista Eukarya (not treated) Protista Eukaryota Protista Fungi Plantae Plantae Plantae Plantae Animalia Animalia Animalia Animalia Animalia Currently: 6 Kingdoms into 3 Domains Fungi Vegetabilia Heyer Previously: 5 Kingdom system 3 domains The future? 8 ...
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