Classification and Phylogeny

Learning Objectives At the end of this unit, a student should be able to… Justify the use of scientific binomials for species Arrange the Linnaean categories from most to least inclusive Distinguish between homologous and analogous characteristics and how they are applied to resolving phylogenies Distinguish between ancestral and derived characteristics and how they are applied to resolving phylogenies Interpret a cladogram and describe the relationships among organisms using proper phylogenetic terminology Distinguish among monophyletic, paraphyletic, and polyphyletic groups Distinguish ingroup and outgroups Apply the principle of parsimony to the construction of a cladogram

Classification of Life The grouping and naming of organisms goes by different, interrelated names Systematics Classification of organisms Cladistics Classification of organisms according to measurable characteristics they have in common Phylogenetics Classification of organisms according to measurable characteristics they have in common based on evolutionary history Taxonomy Application of names for organisms and groups Classification based on evolutionary relationships (common decent) is a)taxonomy b)Linnaean c)phylogeny d) divisions e)none of these The aspect of classification concerning the application of names to groups of organisms A scientist involved with the classification of organisms a)systematist b)taxonomist c)phylogeneticist d)all these e)none of these

Classification Our classification hierarchy and taxonomic system was introduced by Carl von Linné aka Carl Linnaeus, Carolus Linnaeus ~ 1750 C.E. Like all classification, it is a human construction to better understand the world around us Domain Kingdom Phylum Class Order Family Genus Species (this one is “new”)

Classification Domain Kingdom Phylum Class Order Family Genus Species Our classification hierarchy is arranged from large groups that are broadly defined, to smaller groups that are more narrowly defined

Largest (broadly defined) Smallest (narrowly defined) DOMAIN Largest (broadly defined) Eukarya KINGDOM Animalia PHYLUM Chordata Figure 1.10: Classification of the chimpanzee (Pan troglodytes). CLASS Mammalia ORDER Primates FAMILY Pongidae Smallest (narrowly defined) GENUS Pan SPECIES Pan troglodytes

Catamount, mountain lion, panther, puma, SXU mascot Classification Domain Kingdom Phylum Class Order Family Genus Species Eukarya Animalia Chordata Mammalia Carnivora Felidae Puma Puma concolor Cougar (Common name) Catamount, mountain lion, panther, puma, SXU mascot Each species has only one scientific name or “binomial”, consisting of the genus and the specific epithet (Many common names!)

Classification and Relationships Domain Kingdom Phylum Class Order Family Genus Species Eukarya Animalia Chordata Mammalia Carnivora Felidae Puma Puma concolor Eukarya Animalia Chordata Mammalia Carnivora Felidae Panthera Panthera tigris Eukarya Animalia Chordata Mammalia Carnivora Felidae Panthera Panthera pardus Eukarya Animalia Chordata Mammalia Carnivora Felidae Panthera Panthera leo Cougar Tiger Leopard Lion

Biological species concept Ecological species concept What is a species? Whatever we say it is. Lions and Tigers could be considered the same species based on which species concept? biological b) ecological c) typological d) all these e)none of these Example: Biological species concept vs. Ecological species concept

Species Biological species concept Ecological species concept if two individuals can produce viable offspring, then they are the same species. What about asexual organisms like bacteria? Ecological species concept same as BSC, except individuals must occupy a similar ecological niche

Tigers and Lions Panthera tigris Panthera leo

Liger ♀ ♂ Panthera tigris Panthera leo

Tiglon ♂ ♀ Panthera tigris Panthera leo

naming branches and defining branch points in an evolutionary tree Classification Phylogenetics Reconstructing the evolutionary relationships of organisms Classification based on common descent “Tree of Life” naming branches and defining branch points in an evolutionary tree

Classification Domain Kingdom Phylum Class Order Family Genus Species Today, systematists do their best to taxonomic names to the actual evolutionary history The individual most responsible for our current classification system is a) Louis Pasteur b)Anton Van Leeuwenhoek c)Carl Linnaeus d) Kanye West e) none of these Other scientists propose a new classification system, more like a barcode for each branch “The Phylocode”

Phylogeny Reconstructing evolutionary history Terminology (learn the definitions) homologous, analogous clade (monophyletic, paraphyletic, polyphyletic) parsimony ingroup, outgroup branch, node cladogram, phylogram

Amniote Evolution

Amniote Evolution Vertebrate “ingroup” non-vertebrate “outgroup” The organism that is defined as a close relative that doesn’t belong to the organisms of interest is called an a) monophyly b) ingroup c) outgroup d) paraphyly e) all these

Data matrix Lancelet A Chimpanzee P Sunfish Lizard Frog Bear Lamprey jaws amniotic egg tetrapod opposable thumb mammary glands vertebrae upright posture Lancelet A Chimpanzee P Sunfish Lizard Frog Bear Lamprey Human

Data matrix Lancelet A Lamprey P Sunfish Frog Lizard Bear Chimpanzee vertebrae jaws tetrapod amniotic egg mammary glands opposable thumb upright posture Lancelet A Lamprey P Sunfish Frog Lizard Bear Chimpanzee Human

Data matrix Vertebrate “ingroup” Lancelet A Lamprey P Sunfish Frog vertebrae jaws tetrapod amniotic egg mammary glands opposable thumb upright posture Lancelet A Lamprey P Sunfish Frog Lizard Bear Chimpanzee Human Vertebrate “ingroup”

Data matrix non-vertebrate “outgroup” Lancelet A Lamprey P Sunfish vertebrae jaws tetrapod amniotic egg mammary glands opposable thumb upright posture Lancelet A Lamprey P Sunfish Frog Lizard Bear Chimpanzee Human non-vertebrate “outgroup”

Trees and Clades Taxon “H” Taxon “G” Taxon “F” Taxon “E” Taxon “D” Taxon “C” Taxon “B” Taxon “A”

Trees and Clades clade branch node Taxon “H” Taxon “G” Taxon “F” Taxon “E” Taxon “D” Taxon “C” Taxon “B” Taxon “A” clade branch node

Amniote Evolution clade node

Amniote Evolution Limbs

Amniote Evolution Amniotic egg

Amniote Evolution Nodes are defined by shared derived characters A clade in an evolutionary (phylogenetic) tree is defined by one or more a) analogies b) plesiomorphies c) synapomorphies d) paramorphies Nodes are defined by shared derived characters “synapomorphies” Amniotic egg

(Branch lengths are not meaningful) Trees and Clades clade Taxon “A” node Taxon “B” Taxon “C” branch Taxon “D” In an evolutionary tree, organisms grouped together after one branch point are a a) clade b) node c) taxon d) phylogram e) cladogram In an evolutionary tree, a shared derived character typically defines a a) paraphyly b) cladogram c) phylogram d) plant e) clade In an evolutionary tree, a shared common ancestor is depicted by a a) cladogram b) node c) phylogram d) tree e) clade Taxon “E” Taxon “F” Taxon “G” Taxon “H” Outgroup Taxon Cladogram (Branch lengths are not meaningful)

Homology

Homology Vestigial characters A homologous characteristic that has been reduced or non-functional is a) analogous b) not evolved c) vestigial d) paraphyletic e) none of these Vestigial characters

Convergent evolution Similarities exist between distantly related taxa because of selective forces Homoplasy: non homologous similarity Similarities between distantly related organisms can arise from a) convergent evolution b) will power c) co-evolution d) parsimony e) none of these