BI2CV1 Lecture 2 - Tree Thinking PDF

Tree thinking BI2CV1 Comparative Vertebrate Biology Dr Manabu Sakamoto [email protected] Recap: What is the tree of life (phylogeny)? A representation (often graphical) of the evolutionary history (evolutionary relationships) of a group of organisms. Tree-like b...

Tree thinking BI2CV1 Comparative Vertebrate Biology Dr Manabu Sakamoto [email protected] Recap: What is the tree of life (phylogeny)? A representation (often graphical) of the evolutionary history (evolutionary relationships) of a group of organisms. Tree-like branching structure. Shows descendants splitting from common ancestors. Darwin 1837 Phylogeny: phylogenetic Tree or coral of life? Corals might be better analogies of phylogeny than trees. Trees: Roots, trunk, branches, leaves are all alive Corals: Only living bits are the tips Built on top of dead ‘ancestors’ Tree of life Nonetheless, trees adequately capture the essence of phylogeny. New species splitting from ancestors = branching. Evolutionary history of species lineages = branches Branches split but (usually) don’t fuse. Why is phylogeny important? Why phylogeny is important “Nothing in Biology Makes Wings of flying Sense Except in the Light vertebrates are of Evolution” not homologous Theodosius Dobzhansky Phylogeny is a record of Evolved separately from evolutionary history terrestrial ancestors. Any study taking a comparative framework …but share requires “tree-thinking” common ancestry in terms of the structures, i.e., forelimbs Why is phylogeny important? Directly comparing pairs assumes all comparisons are equal. Why is phylogeny important? Phylogenetic statement made with such a comparison is that all taxa are independent of each other. Star phylogeny Why is phylogeny important? In reality, some species are more closely related to each other than they are to others. Phylogenetic structure in comparisons Tree thinking underlies all comparative biology! Toxicology Pharmacology Tree thinking in biology Toxicology You know that rat poison is potentially more harmful to you than insecticides, and even more so than weed killers! Pharmocology Testing drugs on mammal systems, not other vertebrates, let alone invertebrates or plants! How to read a phylogenetic tree Basic components of a phylogenetic tree Terminal Edges (branches) branch alal (tip, leaf) = species Internal Hypothetical ancestral lineage Nodes Internal Splits/branching events branch Hypothetical ancestors Clades Groups of species sharing a common ancestor Root Origin Terminal branches Terminal Terminal branches are the branch lineages directly leading up to the observed species, both living and extinct. They represent the independent evolutionary history of each species. Internal branches Internal branches represent ancestral or extinct lineages that gave rise to descendant Internal lineages. branch They form part of the shared evolutionary history between the descendant lineages and species. Nodes Hypothetical ancestors from which descendants split off. Descendants could include hypothetical ancestors of further descendants. Clades Clades are groups of species sharing a common ancestor. A phylogenetic tree is also a clade. Clades can be as small as two species as long as they share a common ancestor. Humans (Homo), and chimps + bonobos (Pan) form a clade (Tribe, Hominini). Root The root is just a special node. Like other nodes, the root is also a hypothetical ancestor, but one for the whole tree. Phylogenetic evolutionary history observed The evolutionary history of planktic foraminifera (single- celled eukaryotes) can be observed in fossils and represented as a phylogenetic tree. Pearson and Penny 2021. PLOS ONE 16: e0249113 Phylogeny and comparative biology Shared evolutionary history Some species are more closely related to each other than either are to the other species on a tree. This means that apparent similarities in closely Perforated Rotary related species may be acetabulu ankle because of shared Erect m joint ancestry (they all inheritedhindlimb Single- it from a common hinge ancestor). ankle joint Shared evolutionary history Shared evolutionary history can be represented as a A B C D pairwise matrix. Diagonal 2 2 Root-tip evolutionary Time Phylogenetic matrix 1 3 history A B C D 4 Off-diagonals A 4 2 1 0 1 Pairwise shared B 2 4 1 0 evolutionary history C 1 1 4 0 Shared Independe nt evolutionar D 0 0 0 4 y history evolutionar y history Comparative biology is phylogenetic! Taxonomy Who are they? Adaptatio Adaptatio n n What do they look Form Selectio like? n What are they Function doing? Selectio Selectio n n What do they need Ecology to do? Where do they …this is a Environment live? phylogene tic process! Adaptation and natural selection Adaptatio Adaptatio n n Selectio n Selectio Selectio n n