Comparative Approach: Estimating Tree of Life with Molecules and Morphology, Study notes of Botany and Agronomy

Download Comparative Approach: Estimating Tree of Life with Molecules and Morphology and more Study notes Botany and Agronomy in PDF only on Docsity! 1 Molecular Systematics . . . Macromolecules, Morphology, and Trees . . . Phylogenetic Tree of Life Ernst Haeckel’s 1866 “Tree of Life” Tree of Life 140 Years Later? http://tolweb.org/tree/phylogeny.html Thousands of phylogenetic “tests” confirm the hypothesis of common ancestry as fact. “Nothing in biology makes sense except in the light of evolution” Theodosius Dobzhansky 2 Phylogeny Development Genetics Taxonomy Cytology Ecology Biogeography Morphology “Nothing in evolution makes sense except in the light of molecular systematics ?” Molecules vs. Morphology? How do you best “estimate” this tree of life? Morphology, field studies, herbarium? Macromolecules? Molecules vs. Morphology? Is the use of morphology suspect? 5 merous Oenothera mutant CA 4 CO 4 A 4,8 G (4) __ • placental and marsupial mammals each exhibit divergence (of homologous parts) when moving into new selection pressure • but convergence (of analogous parts) relative to each other under similar selection pressure Molecules vs. Morphology? Is the use of morphology suspect? 5 Phylogenetic analysis Parsimony Likelihood Bayesian Systematic interpretation Classification Character evolution Biogeography phylogenetic tree Molecular Systematics - in brief 3. “Gene trees” = “Species trees” all the time (homology issue)/ Sectional relationships of Clarkia • relationships based on morphology and chromosome structure by Harlan Lewis • duplicated pgi protein discovered in some sections in late 1970s by Les Gottlieb • Gottlieb argued that duplications are rare and that these 4 sections are related Issues in Molecular Systematics 3. “Gene trees” = “Species trees” all the time (homology issue)/ Modified sectional relationships • note: sections with single pgi have different molecular weights (59.0 vs. 60.4) • Gottlieb argued that hybridization and chromosomal translocation gave rise to the pgi duplication in early ancestor Issues in Molecular Systematics • new phylogeny proposed by Lewis C affinis C cylindrica C lewisii C rostrata C epilobioides C similis C delicata C calientensis C springvillensis C tembloriensis C unguiculata C biloba C lingulata C modesta C dudleyana C heterandra C bottae C xantiana C imbricata C purpurea C williamsonii C speciosa C tenella C amoena C gracilis C franciscana C rubicunda C mildrediae C rhomboidea C virgata C arcuata C lassenensis C breweri C concinna C pulchella Gayophytum 100 91 71 94 59 87 93100 52 72 98 72 79 67 Strict consensus of 36 MP trees 696 steps, CI= 0.72, RI = 0.73 3. “Gene trees” = “Species trees” all the time (homology issue) • DNA sequences from chloroplasts say no! • duplicated pgi protein occurred once but is ancestral! • multiple losses of one or the other duplicated protein • how can this hypothesis be tested? DNA tree loss 60.4 loss 60.4 loss 5 .0 loss 59.0 Issues in Molecular Systematics 6 3. “Gene trees” = “Species trees” all the time (homology issue) Issues in Molecular Systematics confirms this hypothesis! 3. “Gene trees” = “Species trees” all the time (homology issue) •compare “orthologous” gene copies, not “paralogous” copies • big issue in molecular systematics of all organisms • but, get information from 2 genes! Issues in Molecular Systematics Using gene duplications to one’s advantage How do you resolve the base of the “tree of life”? What outgroup do you use? ? Issues in Molecular Systematics Bacteria Archaea Eukaryota Where is the root of life? Using gene duplications to one’s advantage Issues in Molecular Systematics ? ? ? 7 Archaea Archaea Bacteria Bacteria Eukaryota EukaryotaGene A Gene A2 Gene A1 Using gene duplications to one’s advantage: each copy acts as the outgroup for the other! Issues in Molecular Systematics 4. Hybridization/introgression - many examples P. alba P. nigra P. tristis - Eurasian balsam poplar Issues in Molecular Systematics 4. Hybridization/introgression • nuclear DNA indicates European white and black poplars and Asian balsam P. tristis are unrelated Issues in Molecular Systematics 4. Hybridization/introgression • cpDNA indicates European white and black poplars are sister taxa and balsam P. tristis is identical to black poplar! Issues in Molecular Systematics 10 5. Genome rearrangements Issues in Molecular Systematics • all Asteraceae except Barnadesia and relatives have derived cpDNA inversion 5. Genome rearrangements Issues in Molecular Systematics • Barnadesia as first diverging lineage in Asteraceae is supported by sequence data as well 6. Sampling issues Issues in Molecular Systematics • gene sampling too little: homoplasy levels • taxa sampling too little: placeholder issues • isolated taxa: long branch attraction • all have been issues in basal angiosperm phylogenetics Issues in Molecular Systematics • single gene (rbcL) rooted angiosperms on long branch (Ceratophyllum) correct root • use of exemplars for larger lineages generated long branches and rooting on these nodes Sytsma & Baum 1996 (Flowering Plant Origin, Evolution & Phylogeny) 11 “Nothing in evolution makes sense except in the light of molecular systematics ?” Phylogeny Development Genetics Taxonomy Cytology Ecology Biogeography Morphology Yes, in part Morphology Development Genetics Taxonomy Cytology Ecology Biogeography Phylogeny But, it is a two-way interaction Paleontologist Phil Gingerich with 40 my old Basilosaurus with small hind legs in Egypt • a wealth of Cetacean fossils showing transitional forms from a putative ancestral Mesonychid type to modern whales has been uncovered Early stages were clearly terrestrial Molecules and Morphology Morphology places Cetaceans as sister to the living Artiodactyla - a lineage of hoofed ungulates - with these two related to the extinct Mesonychids Molecules and Morphology The whale lineage has the double pully-type astragalus seen only in Artiodactyl hoofed mammals present on land today Astragalus: the highest bone in the ankle on which the foot rotates Modern pronghorn in middle with 2 fossil Cetaceans on the sides Molecules and Morphology 12 However, Artiodactyls have specialized cranial and dental features not seen in Cetaceans or the extinct Mesonychids Molecules and Morphology Recent molecular data surprisingly places the whale lineage within the Artiodactyla and closest to the hippo Molecules and Morphology The two phylogenetic hypotheses are similar but different - is this just a “whale of a tale”? “Why are these two independent data sets saying something similar but yet different?” Molecules and Morphology morphology molecules Have Cetaceans secondarily lost the cranial/dentition features of modern Artiodactyla? or . . . does DNA evolution have some other underlying process going on causing incorrect placement? Molecules and Morphology morphology molecules