Phylogenetic Trees - Lecture Notes

Lecture: Phylogenetic trees Development of Phylogenetics: ● Darwin, The Origin of Species, 1859 (publication date) ○ ● ● ● First phylogenetic tree → Macroevolution: evolution on a scale at or above the level of species Microevolution: smaller evolutionary changes of allele frequencies within a species or population Species diversion: accumulation of differences between closely related populations within a species, leading to speciation Tree of Life ● Phylogeny: the study of the evolutionary history and relationships among individuals or groups of organisms ○ Generally thought of as diagrammatic depictions of organisms that are connected through common descent ● Domains: ○ Archaea ○ Bacteria ○ Eukarya ■ Protista ■ Fungi ■ Plantae ■ Animalia ● Based on DNA sequences ● Hierarchical in structure ● Some relatedness to OG Linnaean system 1) Tree Structure and Terminology of Phylogenies ● ● Anagenesis: the gradual evolution of a species that continues to exist as an interbreeding population ○ The evolutionary change of features within a single lineage (branch) ○ Occurs on all branches Cladogenesis: which occurs when there is branching or splitting, leading to two or more lineages and resulting in separate species ● ● ● ● ● ● ● ○ The branching of a lineage into 2+ descendant lineages ○ Depicting divergence (when it splits into 2) Phylogenetic tree = phylogeny = evolutionary tree ○ Diagrammatic depiction of organisms that are connected through common descent ○ show the evolutionary history of organisms, and are not just a way of grouping of organisms ○ Vocab: ■ Terminal nodes (“tips”) or taxa: end of the tree; species, family, or class ■ Sister taxa: originated from a common ancestor ■ Internal nodes: ancestors ■ Root: bottom of tree/organization ■ Branch: connection between internal nodes and taxa Phylogeny portrays relationship (common ancestry), not similarity There are many ways of drawing the same tree ○ What is important is maintaining the evolutionary relationship & relationship b/w taxa Taxa are more closely related to each other when they have a more recent common ancestor Monophyletic Group ○ Group that contains the ancestor and all of its descendants ■ Humans, mice & lizards Paraphyletic group ○ Group that contains ancestor and some but not all of its descendants ■ Ex. Fish Polyphyletic group ○ Group of descendants that does not contain the most recent common ancestor ■ Ex. Warm-blooded animals form a polyphyletic group Mono Para Poly 2) Inferring phylogenies ● Key Terms: ○ Homologous traits: traits that have been inherited from common ancestors ○ Character: a trait used to infer a phylogeny (e.g. number of fingers) ○ Character states: possible values of the character (e.g. 2, 3, 4, ...) ○ Outgroup: a more distantly related group of organisms that serves as a reference group when determining the evolutionary relationships of the ingroup ● Confidence in individual branches of a phylogeny can be assessed through bootstrapping methods ○ Leave out some character data, and determine which (if any) of the branches in the most parsimonious tree differ from those in the tree that was inferred using all the data Other approaches (besides parsimony) are also available and currently more commonly used ○ e.g. maximum likelihood, Bayesian inference methods ● ● Parsimony ○ the principle that the simplest tree is the best and most likely one ○ So many possible trees & not all can be evaluated in practice ○ The parsimony principle is basic to all science and tells us to choose the simplest scientific explanation that fits the evidence. In terms of tree-building, that means that, all other things being equal, the best hypothesis is the one that requires the fewest evolutionary changes ● Using DNA sequences to infer phylogenies ○ Much of phylogenetics is driven by DNA sequences ■ Uninformative sites: locations where the nucleotides are all the same ■ Informative sites: where the nucleotide is different/ consistently diff. In that one site ○ Introgression ■ can lead to different trees for different genes ■ Introgression: the transfer of genetic information b/w species ■ (i) hybrid speciation ● hybrid speciation: hybridization between two different species leads to a new species ○ Ex. Influenza virus ■ (ii) Horizontal gene transfer ● HGT: the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction) 3) What good is a phylogeny? ● I. Inferring the history of character evolution through ancestral state reconstruction ○ Ex. Humans evolved a non-opposable big toe! ○ How many times were dogs domesticated? ■ Using just mitochondrial DNA (which evolves more rapidly than nuclear DNA) a phylogeny was created ■ Dogs do not form a single monophyletic group; some dogs are more closely related to some wolves, and other dogs to other wolves A) Inferring spatial transmission dynamics from phylogenies ■ Genomic epidemiology ● Studies the susceptibility to disease, & movement over space & time ■ Ex. Ebola case study ● External nodes were the geographic location ○ B) Inferring transmission of a virus between multiple hosts II. Estimating time of divergence ○ “molecular clock”: is a figurative term for a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged ■ variation in the molecular clock rate, due to: ● Differences in generation time ● Differences in evolutionary constraints ○ (e.g. vector borne viruses vs. directly transmitted viruses) ○ For viruses, often times we are interested in time of divergence to figure out what events may have driven viral spread. ■ You don’t need a “fossil” record for estimating time of divergence for viruses (just sequences sampled at different times!) ● Ex. Zika ○ ● ● III. Understanding patterns of evolution ○ i. Most features of organisms have been modified from pre-existing features ○ ii. Evolution of characters and morphological traits is often gradual ○ iii. Rates of character evolution differ ■ mosaic evolution: evolution of different characters at different rates within a lineage ● Each species is a mosaic of ancestral characters and derived characters ● hence, it is inaccurate to say that one living species is more ‘advanced’ than another ○ iv. Homoplasy is common ■ Homoplasy– the independent evolution of a character or character state in different taxa ● Homoplasy most commonly arises due to convergent evolution ■ Corollary: Traits that are under strong selection are bad choices for creating phylogenetic trees ● Want to use only homologous traits! ○ Ex. bird and bats both evolved wings/flight but not one from the other