1Classification and PhylogenyThe diversity of life is great. To communicate about it, there must be a scheme for organization.There are many species that would be difficult to organize without a scheme based on consistent criteria.Classification - an organized scheme for grouping organisms - a tool for communication -Taxonomy - the practice of naming and classifying organisms.Linnaeus developed the classification scheme we use todaySpecies have binomial names (Genus species) and are arranged in a hierarchical classification - Linnaeus saw a genus as a general kind of organism and a species as a more specific kind of organism. Linnaeus grouped organisms by their degree of similarity (as he saw it). “God creates, Linnaeus organizes”Hierarchical - a series of successive and inclusive rankingsThe major categories used in our current hierarchical classification are Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species - many intermediate subcategories are necessary for organizing the diversity within groups with many species2Evolution through anagenesis and cladogenesis has produced the diversity of living things today, which can be represented as a treeThe currently used classification has 3 Domains - two prokaryotic and one eukaryotic.3A tree that represents the pattern of cladogenesis (but not necessarily the amount of anagenesis) is called a cladogram.A phylogeny is a representation of the hypothetical evolutionary history of a group of organisms that may be a cladogram, but may also include information about the amount of evolution in each lineage.Darwin pictured the process of evolution with variable rates of anagenesis and cladogenesis and many extinctionsThe process of developing an estimate of the evolutionary history of a group of organisms is called phylogenetic inference.The unit of data used in phylogenetic inference in the character. Characters are any physical characteristics of a group of organisms They can be anatomical (morphological) behavioralorganisms. They can be anatomical (morphological), behavioral, physiological, biochemical, molecular.Characters may be useful for phylogenetic inference if they come in alternate character states - different shapes of the same bone, enzymes that differ in their amino acid sequence, genes that differ in their nucleotide sequence, etc.4The states of a character may represent evolutionary changes. For any two states of a character one may have originated earlier in the evolutionary history of the group and one may have originated later. Character states that originated earlier in the evolutionary history ofCharacter states that originated earlier in the evolutionary history of a group can be called primitive or ancestral or plesiomorphic.Character states that originated later are called advanced or derived or apomorphic.Derived states of a character provide information about the degree of relatedness of two or more species. A derived state that is shared pby two or more species is called a synapomorphy. Synapomorphies allow species to be grouped and organized into a phylogeny.In this example0 = ancestral state1 = derived stateLungs are a synapomorphy that allow all vertebrates with four legs to be grouped together. A synapomorphy can identify a monophyletic group - all the descendants of the single common ancestor. The common ancestor possessed the derived state of the character.5A character state matrixPhylogenetic inference - using character states to develop an estimate of evolutionary relationshipCharacterSpeciesabcdefghij10011100000The task is determine the relatedness of a group of 100111000002 00100111103 00100110014(outgroup)1100000000ancestor 0000000000species in the “ingroup.” An outgroup - a group that is related to the ingroup, but clearly not a member of the ingroup, provides orientation.Th t f thThe common ancestor of the whole group is hypothesized to have had the ancestral state of all characteristics.CharacterSpeciesabcdefghij1 00111000002 001001111030010011001A simple example - a constant rate of evolution with no evolutionary reversals or multiple origins of the derived state300100110014(outgroup)1100000000ancestor 0000000000A derived state that has evolved only once isonly once is called homologous in all the species that share it.6CharacterSpeciesabcdefghi j1 00110000002 00101111113 00101100004 (outgroup)1100000000An example with variable rates of evolution among branches.Overall sp. 1 & sp. 3 are most similarancestor0000000000Synapomorphies and not overall similarity reflect evolutionary historyCharacter a b c d e f g h i j Species 1 0 1 1 0 0 0 1 1 0 1 2 0 1 1 1 1 1 0 1 0 0 30111111011An example with evolutionary reversals and multiple origins of the derived state of some characters.3 0 1 1 1 1 110114 (outgroup) 1 0 0 0 0 0 0 0 0 0 ancestor 0 0 0 0 0 0 0 0 0 0 Character states that arise more than once are called homoplasious. The derived state of characters g and h evolvedcharacters g and h evolved twice - they are examples of convergent evolution.The ancestral state of character j is present in species 2. This is an evolutionary reversal.7How can the ancestral and derived states of a character be identified?Outgroup comparison is the most commonly used method. The state of a character found in species outside the group being analyzed is the ancestral state.analyzed is the ancestral state. For example - among tetrapods (vertebrates with four limbs –amphibians, reptiles, birds, and mammals) there are those with amniotic development (the embryo forms and develops within an amniotic sac) and those without. The tetrapods themselves provide no information about the direction of evolution because the amnion could have been gained or lost during evolution Thethe amnion could have been gained or lost during evolution. The outgroup, all other vertebrates (the fishes), does not have amniotic development. Therefore, it is most likely that amniotic development is the derived state in tetrapods. The derived state (having amniotic development) can then be used as a potential synapomorphy and used in constructing a phylogeny.Synapomorphies are the basis for modern classifications. Organisms that share the derived state of a characteristic that evolved only once can be classified as belonging to the same group. Ancestral states do not provide information about evolutionary relatednessevolutionary relatedness and are usually not used for classifying organisms.8Convergent