Phylogenetics: Building Evolutionary Trees from Scattered Species, Study notes of Botany and Agronomy

Download Phylogenetics: Building Evolutionary Trees from Scattered Species and more Study notes Botany and Agronomy in PDF only on Docsity! 1 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, 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” - showing how “branches” or “clades” are connected to each other Phylogenetics 2 But . . . We only have extant species - the “leaves” Phylogenetics - and so we must estimate how the “branches” once connected the “leaves” ? Thus . . . Phylogenetics is the estimation of the “tree” through “time” knowing only the “leaves” Phylogenetics However, the “leaves” are scattered over “space”. Some areas have related “leaves”, others have unrelated “leaves”. Thus, phylogenetics is compounded by issues of both “time” and “space”. Phylogenetics Additionally, many related “leaves” diverge in “form”, while other unrelated “leaves” converge in “form”. Thus, phylogenetics is compounded by issues of “time” and “space” and “form”. Phylogenetics 5 Phenetics vs. Cladistics • Phenetics uses “overall similarity” - all used! • Graphical representation is called a phenogram, dendrogram, network Phenetics vs. Cladistics • Cladistics uses only phylogenetically informative characters • Derived state is shared by 2 but not all taxa - “shared derived character states” only informative cladogram Phenetics vs. Cladistics cladogram phenogram=/ Phenetics Data Matrix 1. Magnolia 2. Nymphaea 3. Rosa 4. Primula 5. Gentiana 6. Aster taxa ap oc ar py sy m pe ta ly ep ip et al y tr ee s ep ig yn y be et le p ol l. te pa ls he te ro st yl y bi ca rp el la te ve ss el s characters + + - + - -+ - +- - + - + - -- - +- + + - - - -- - -- + - + - - +- - -+ + - + - + -- - -+ + - + - + -- + -+ states 6 1. Magnolia 2. Nymphaea 3. Rosa 4. Primula 5. Gentiana 6. Aster + + - + - -+ - +- - + - + - -- - +- + + - - - -- - -- + - + - - +- - -+ + - + - + -- - -+ + - + - + -- + -+ Phenetics Data Matrix • convert data matrix into pair-wise matrix based on overall similarity UPGMA cluster analysis Phenetics • convert data matrix into pair-wise matrix based on overall similarity UPGMA cluster analysis • identify most similar pair of taxa and cluster them G en tia na As te r 90% Phenetics • reduce overall similarity matrix by clustering together Gentiana and Aster and recalculate similarity values UPGMA cluster analysis • identify most similar pair of taxa and cluster them N ym ph ae a M ag no lia 80% Phenetics • reduce overall similarity matrix by clustering together Magnolia and Nymphaea and recalculate similarity values UPGMA cluster analysis • identify most similar pair of taxa and cluster them G en tia na As te r 75% Pr im ul a 7 Phenetics • cluster together Gentiana, Aster, and Primula and recalculate values UPGMA cluster analysis • identify most similar pair of taxa and cluster them M ag no lia N ym ph ae a 70% Ro sa Phenetics • cluster together Magnolia, Nymphaea, and Rosa and recalculate values UPGMA cluster analysis • cluster the two remaining larger groups at 42.5% to make final phenogram Phenetics • many different methods based on similarity or differences (including multiple components, ordination, etc.) • in lab you will be using Neighbor-joining using a computer program PAUP 1. Magnolia 2. Nymphaea 3. Rosa 4. Primula 5. Gentiana 6. Aster ap oc ar py sy m pe ta ly ep ip et al y tr ee s ep ig yn y be et le p ol l. te pa ls he te ro st yl y bi ca rp el la te ve ss el s + + - + - -+ - +- - + - + - -- - +- + + - - - -- - -- + - + - - +- - -+ + - + - + -- - -+ + - + - + -- + -+ Cladistics How do you analyze this same data based on cladistics - “shared derived character states”? 10 Cladistics Issue #2 - how do you select the “best” tree? • often uses the optimality criterion of “parsimony” • in the context of evolution, parsimony = choosing the tree that requires the fewest number of evolutionary changes (apomorphies) • choose the shortest, simplest, most efficient tree • choose the tree with the least amount of homoplasy - convergences or reversals or character conflict 1. Magnolia 2. Nymphaea 3. Rosa 4. Primula 5. Gentiana 6. Aster A po ca rp y - sy nc ar py Po ly pe ta ly - sy m pe ta ly Fr ee s ta m en s - ep ip et al y T re es - he rb s H yp og yn y - ep ig yn y be et le p ol l. - ot he r po ll. T ep al s - se pa ls + p ea ls H om os ty ly - he te ro st yl y V ar io us c ar pe ls - bi ca rp el la te N o ve ss el s - ve ss el s 1 0 0 0 0 00 0 00 0 0 0 0 0 01 0 00 1 0 0 1 0 01 0 10 1 1 1 1 0 11 0 11 1 1 1 1 1 01 0 11 1 1 1 1 1 01 1 11 Cladistics 0 0 0 0 0 00 0 00 Amborella 2 characters conflict! Cladistics • two trees are equally parsimonious • with character conflict, each is 11 steps long and not the expected 10 Consistency Index = 0.91 # changes minimally expected # changes occurred on tree Cladistics • tree 1 has vessels as synapomorphy for all taxa except outgroup + Nymphaea ⇒ herbs ⇒ vessels ⇒ trees Tree 1 • habit is homoplasious (“messy”) with an origin to herb and then reversal back to tree 11 Cladistics • tree 2 has herbs as synapomorphy for all taxa except outgroup + Magnolia ⇒ vessels ⇒ herbs ⇒ no vessels Tree 2 • vessels is homoplasious (“messy”) with an origin to vessels and then reversal back to vessel-less Cladistics • a consensus tree depicts the maximum information possible from all most parsimonious trees Cladistics Issue #3 - how do you construct a classification? • most cladists advocate monophyletic groupings only - stressing primacy of descent • a different group, evolutionary taxonomists, allow for paraphyletic grouping - stressing both descent and modification Cladistics Milkweeds are a highly derived lineage from within the dogbane family - Apocynaceae • recognizing Asclepiadaceae makes the Apocynaceae paraphyletic • some agree since Aslepiadaceae are so divergent Issue #3 - how do you construct a classification? 12 Cladistics Issue #3 - how do you construct a classification? peripheral isolates: new species forms at edge of retained ancestral species Lisianthius in central Panamanian cloud forests Recognize paraphyletic species? • island or peripheral geographic speciation is a common model in plants • ancestral species becomes paraphyletic, new species monophyletic Cladistics Paraphyletic species - 3 options: 1. Recognize both the derived (apo) species and the paraphyletic ancestral (plesio) species - 2 species Cladistics Paraphyletic species - 3 options: 2. Recognize the derived (apo) species and monophyletic units from the ancestral (plesio) species Cladistics Paraphyletic species - 3 options: 3. Recognize only one monophyletic species