Phylogenetics Phylogenetics The affinities of all the beings of the same class have sometimes been represented by a great tree As buds give rise by growth to fresh buds and these if vigorous branch out and overtop on all sides many a feebler branch so by generation I believe it has been with the great Tree of Life Life which fills with its dead and broken branches the crust of the earth and covers the surface with its ever branching and beautiful ramifications Charles Darwin 1859 Phylogenetics What exactly is phylogenetics and how is done Phylogenetics Building trees trees showing how branches branches or clades clades are connected to each other Phylogenetics Phylogenetics But We only have extant species the leaves leaves and so we must estimate how the branches branches once connected the leaves leaves Thus Phylogenetics is the estimation of the tree tree through time time knowing only the leaves leaves Phylogenetics However the leaves leaves are scattered over space space Some areas have related leaves leaves others have unrelated leaves leaves Thus phylogenetics is compounded by issues of both time time and space space Phylogenetics Additionally many related leaves leaves diverge in form form while other unrelated leaves leaves converge in form form Thus phylogenetics is compounded by issues of time time and space space and form form Phylogenetics In natural and phylogenetic systems of classification characters are selected a posteriori for their value in correlating with other characters to form hierarchical structure of groups Phylogenetics What characters are selected or even considered has been very subjective Consider Cronquist and Dalghren with mustard oil families Phylogenetics Phylogenetics Do you rely on morphological or chemical characters or both These first phylogenetic classifications are phyletic phyletic involve a subjective selection of characters for classification Phylogenetics Phylogenetics Two main groups of systematists became dissatisfied with the phyletic approach and developed more objective methods phenetic and cladistic Phenetics vs Cladistics Phenetics Principles Principles of Numerical Taxonomy 1963 by Peter Sneath and Robert Sokal Cladistics Phylogenetic Systematics 1966 by Willi Hennig all out war in the 1960s and 1970s With the rise of molecular phylogenetics additional approaches are now invoked ML Bayesian far more of a continuum of models are now seen Phenetics vs Cladistics W Hennig R Sokal Phenetics uses overall similarity similarity all characters used distance distance approaches Phenetics vs Cladistics Phenetics vs Cladistics only informative cladogram Phenetics uses overall similarity similarity all characters used distance distance approaches Cladistics uses only phylogenetically informative characters Graphical representation is called a phenogram dendrogram network Derived state is shared by 2 but not all taxa shared derived character states states apocarpy sympetaly epipetaly trees epigyny beetle poll tepals bicarpellate heterostyly Phenetics vessels Phenetics vs Cladistics 1 Magnolia 2 Nymphaea 3 Rosa 4 Primula 5 Gentiana 6 Aster Data Matrix taxa characters cladogram phenogram states Phenetics UPGMA cluster analysis UPGMA cluster analysis convert data matrix into pair wise matrix based on overall similarity convert data matrix into pair wise matrix based on overall similarity 2 Nymphaea 3 Rosa 4 Primula 5 Gentiana 6 Aster Phenetics identify most similar pair of taxa and cluster them Aster 1 Magnolia Gentiana 90 Phenetics reduce overall similarity matrix by clustering together Magnolia and Nymphaea and recalculate similarity values identify most similar pair of taxa and cluster them identify most similar pair of taxa and cluster them Magnolia 80 Primula reduce overall similarity matrix by clustering together Gentiana and Aster and recalculate similarity values Gentiana UPGMA cluster analysis Nymphaea UPGMA cluster analysis Aster Data Matrix Phenetics 75 Phenetics Phenetics UPGMA cluster analysis UPGMA cluster analysis cluster together Gentiana Aster and Primula and recalculate values cluster together Magnolia Nymphaea and Rosa and recalculate values Rosa Nymphaea Magnolia identify most similar pair of taxa and cluster them cluster the two remaining larger groups at 42 5 to make final phenogram 70 Phenetics apocarpy sympetaly epipetaly trees epigyny beetle poll tepals bicarpellate heterostyly How do you analyze this same data based on cladistics shared derived character states states vessels many different methods based on similarity or differences including multiple components ordination etc Cladistics 1 Magnolia 2 Nymphaea 3 Rosa 4 Primula 5 Gentiana 6 Aster in lab you will be using Neighbor joining using a computer program PAUP Cladistics Issue 1 ordering or polarizing character states Cladistics Issue 1 ordering or polarizing character states plesiomorph primitive state apomorph derived state use outgroups Cladistics apocarpy sympetaly epipetaly trees epigyny beetle poll tepals bicarpellate heterostyly Add in Amborella as sister outgroup to rest of angiosperms vessels Issue 1 ordering or polarizing character states Cladistics 1 Magnolia 2 Nymphaea 3 Rosa 4 Primula 5 Gentiana 6 Aster Blue flowers synapomorph shared derived state sister group heterostyly Amborella 1 Magnolia 2 Nymphaea 3 Rosa 4 Primula 5 Gentiana 6 Aster 0 0 0 0 0 1 Magnolia 0 0 0 0 0 0 2 Nymphaea 0 0 0 0 1 0 0 0 0 0 3 Rosa 1 0 0 0 1 0 1 1 0 0 4 Primula 1 1 1 1 1 0 1 1 0 1 5 Gentiana 1 1 1 1 1 0 1 1 1 0 6 Aster 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 2 Nymphaea 0 0 0 0 1 0 0 0 0 0 3 Rosa 1 0 0 0 1 0 1 1 0 0 4 Primula 1 1 1 1 1 0 1 1 0 1 5 Gentiana 1 1 1 1 1 0 1 1 1 0 6 Aster 1 1 1 1 1 1 1 1 1 0 Hypogyny epigyny Polypetaly sympetaly 0 Amborella Trees herbs Apocarpy syncarpy Homostyly heterostyly Cladistics 1 Magnolia Note 2 uniformative characters 1 Hypogyny epigyny 0 0 Apomorph Trees herbs 0 0 Various carpels bicarpellate 0 0 Tepals sepals peals 0 1 beetle poll other poll 0 No vessels vessels Free stamens epipetaly Cladistics Homostyly heterostyly bicarpellate Various carpels bicarpellate tepals Tepals sepals peals beetle poll beetle poll other poll epigyny Free stamens epipetaly trees Polypetaly sympetaly epipetaly Amborella Apocarpy syncarpy sympetaly Plesiomorph 0 No vessels vessels Convert data matrix to 0 1 apocarpy Cladistics vessels Cladistics Issue 2 how do you select the best best tree estimation procedure from vast number of possible