Tree Thinking: How to Read a Phylogenetic Tree - Biology Lecture Notes

Tree thinking: How to read a phylogenetic tree Class objectives Learn the parts of a phylogenetic tree Learn how to read a phylogenetic tree Learn the differences between clades shown in a phylogenetic tree Learn the different types of phylogenetic trees  Classification, taxonomy,...

Tree thinking: How to read a phylogenetic tree Class objectives Learn the parts of a phylogenetic tree Learn how to read a phylogenetic tree Learn the differences between clades shown in a phylogenetic tree Learn the different types of phylogenetic trees  Classification, taxonomy, and nomenclature Classification (Systematics): System of grouping species in a hierarchical classification of groups nested within larger groups. Taxon (plural taxa): group of organisms assigned to any of the Linnean system Taxonomy: Discipline in charge of naming Taxa. Nomenclature: Rules to name taxa. Evolution Change – Time How do we represent this? “Drawing” evolution In a phylogenetic tree… we only know the “tips”  A phylogenetic tree “History of events by which species or other taxa have successively arisen from common ancestors” Anagenesis: Changes within a species Cladogenesis: Branching of a lineage into two or more descendants Not only species… Gene trees or gene phylogenies Not only species… Gene trees or gene phylogenies Population phylogenies (“phylogeography”)  life has a history tps://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_03 Phylogenetic tree Cladogram - topology Model-based tree Phylogenetic tree Cladogram - topology Model-based tree Dated tree Card et al. 2014 What’s in a Phylogenetic tree? Page & Holmes (2004)  Monophyly Paraphyly Polyphyly  Monophyly Paraphyly Polyphyly  Monophyly Paraphyly Polyphyly Page & Holmes (2004) Page & Holmes (2004) Page & Holmes (2004) How do we build phylogenies? (For later) Data = Morphology, behavior, molecular Homology = Orthology Method – Parsimony vs Model-based phylogeny Homology and homoplasy as a continuum Zina Deretsky Let’s run an example Let’s run an example Let’s run an example  Phylogenetic tree = A hypothesis of the evolution of taxa. We use these phylogenies to support our biological classification. Monophyletic group = Contains all the descendants from the Most Recent Common Ancestor (MRCA). Paraphyletic group = A group that doesn’t This Photo by Unknown Author is licensed under CC BY-NC-  Cladogram = Depicts only relationships Additive tree = branch length indicates evolutionary distance Dated tree = Branch length indicates time of divergence This Photo by Unknown Author is licensed under CC BY-NC-