Bio182 Chapter 26 Phylogeny and Tree of Life PDF

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Summary

This lecture with Jaime Kontaske is about how phylogeny came around and how we all started at one ancestor and have slowly made a tree with how different species have evolved....

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Chapter 3: Phylogeny and Tree of Life ★ Investigating the Tree of Life ○ Phylogeny: the evolutionary history of a species or group of related species. Shows evolutionary relationships ■ Taxonomy: is the ordered division and naming of organisms. ■ Uses scientific names instead of common names ● Common names cause confusion ● Different languages use different words for the same organism

★ Binomial Nomenclature ○ In the 18th century, Carolus Linneaus published a system of taxonomy based on resemblances ■ Two key features in his, that remain used today: ● Two part names for species (binomial) ● Hierarchical classification ■ The first part of the name is the genus ■ The second part is called the specific epithet, and is unique for each species within the genus ■ The first letter of the genus is capitalized and the entire species name is iticalized. ● Example: H. sapiens or Homo sapiens ● In print, the name is underlined ○ Linneaus proposed using a two part Latin scientific name ○ Therefore the name's the same in all countries no matter what language ○ New organisms names are Latinized (add Latin endings) ○ More than 11,000 names he came up with are still being used today -including Homo sapiens which means wise man

★ Hierarchical classification ○ Linnaeus introduced the idea of classifying animals in increasingly broad categories ○ The taxonomic groups from broad to narrow are: ■ Domain ■ Kingdom ■ Phylum ■ Class ■ Order ■ Family ■ Genus

■ Species ○ A taxonomic unit at any level of hierarchy is called taxon ○ Ways to help you remember order: ■ Did King Phillip Cry Out For Goodness Sakes ■ Dear Karen Please Come Over For Great Spaghetti

★ Linking Classification and Phylogeny ○ The discipline of systematics classifies organisms and determines their evolutionary relationships ○ Systematists use fossil , molecular and genetic data to infer evolutionary relationships. ○ They are depicted as branching phylogenetic trees

★ What We Can and Cannot Learn From Phylogenetic Trees ○ They show patterns of descent not phenotypic similarity ○ Do not indicate when species evolved or how much change occurred in each lineage ○ Should not be assumed that a taxon evolved from the taxon next to it. ○ Represents a hypothesis about evolutionary relationships ○ A rooted tree includes a branch to represent the last common ancestor of all related taxa in that tree ○ Each branch point represents the divergence of two species ○ Sister taxa are groups of that share an immediate common ancestor

★ Applying Phylogenies ○ Provide important information about similar characteristics in closely related species ○ Corn is the 2nd most important food source in the world ○ Based on DNA corn phylogeny has been established that wheat and wild grass are closely related to corn. ○ These grasses may be the closest living relative of corn and provide useful reservoirs of beneficial genes that can be transferred to corn by breeding and genetic engineering. ○ Also led to the ID of the gene responsible for corn ○ Comparison of DNA and mtDNA can help identify whale meat and ivory that may have been poached.

★ Phylogenies are inferred from morphological and molecular data ○ To be able to infer these, systematics gather info about morphologies, genes, and biochemistry or living organisms ○ Organisms w/ similar morphologies or DNA sequences are likely to be more closely related than organisms with different structures or sequences.

★ Sorting Homology from Analogy ○ Systematics need to distinguish between these two ways when setting up a

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phylogenetic tree Homology is similarity due to ancestry Analogy is similarity due to convergent evolution Austrailian moles are marsupials while American moles are placental mammals. Also very similar looking externally ■ Internally, they are different by anatomy, physiology, and reproductive systems Fossils showed their most common ancestor lived about 1400 MYA Bats and birds wings are homologous as forelimbs, but analogous as functional wings Homology can be distinguished from analogy by comparing fossil evidence and the degree of complexity The more complex two similar structures are, the more likely it is that they are homologous

★ Homology or Analogy? ○ Quills of a porcupine and a cactus spine? Analogous ○ Cat paw and human hand? Homologous as forelimbs, but analogous as functionality ○ Owl wing and hornet wing? Analogous

★ Evaluating Molecular Homologies ○ Systematics use computer programs and mathematical tools when analyzing comparable DNA segments from different organisms.

★ Cladistics ○ Cladistics: groups of organisms by common descent ○ Clade: a group of species that includes an ancestral species and all its descendants ○ Clades can be nestled into larger clades, but not all groupings of organisms qualify as clades. ○ A valid clade is monophyletic, signifying that it includes the ancestor species and all its descendants

★ Shared Ancestral and Shared Derived Traits ○ In comparison with its ancestor an organism has both shared and different characteristics ■ A shared ancestral trait, is a character that originated in an ancestor of the taxon ■ A shared derived trait, is an evolutionary novelty unique to a particular clade. ○ A characteristics can be ancestral and derived, depending on the context. ■ Backbone is a shared ancestral character from vertebrates ■ When distinguishing vertebrates from invertebrates, the backbone

is a derived trait.

★ Phylogenetic trees with proportional branch lengths ○ In some trees the length of branch lengths can represent evolutionary time is ○ The length of a branch can represent the number of genetic changes that have taken place in a particular DNA sequence in that lineage. ★ Phylogenetic trees with branches that indicate time ○ In other trees, branch can represent chronological time and branching points can be determined from the fossil record

★ Phylogenetic Trees as Hypotheses ○ The best hypotheses for phylogenetic trees fit the most data: morphological, molecular and fossil ○ Phylogenetic bracketing, allows us to predict features of an ancestor from features of its descendants.

★ An organism’s evolutionary history is recorded in its genome ○ Comparing nucleic acids or other molecules to infer relatedness is a valuable tool for tracing organisms’ evolutionary history. ○ Compare gene duplications and gene families

★ From Two Kingdoms to Three Domains ○ Early taxonomists classified all species as either plants or animals ○ Later 5 kingdoms were recognized: Monera (prokaryotes), Protista, Plantae, Fungi, and Animalia ○ More recently the three domain system has been adopted: Bacteria, Archaea, and Eukarya ■ This three-domain system is widely supported by data from many sequenced genomes

★ A Simple Tree of All Life ○ The tree of life suggest that the domains of Eukarya and Archaea are more closely related than to Bacteria ○ The Tree of Life is based largely on rNA genes, as they have evolved slowly.

★ Horizontal Gene Transfer ○ There have been substantial interchange of genes between organisms in different domains ○ Horizontal gene transfer: the movement of genes from one genome to another...