Phylogeny Fig Overview: Inves8ga8ng the Tree of Life Phylogeny Systema8cs

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1 Ch. 26 Phylogeny BIOL 22 Fig. Fig Overview: Inves8ga8ng the Tree of Life Phylogeny evoluonary history of a species or group of related species Systema8cs classifies organisms and determines their evoluonary relaonships Systemasts use fossil, molecular, and genec data to infer evoluonary relaonships

2 Fig Carolus Linnaeus 8th century published a system of taxonomy based on resemblances Binomial Nomenclature Two key features of his system remain useful today two part names for species Binomial nomenclature hierarchical classificaon binomial Binomial Nomenclature two part scienfic name of a species genus first part of the name specific epithet second part Unique for each species within the genus The first leker of the genus is capitalized and the enre species name is italicized Both parts together name the species not the specific epithet alone

3 Hierarchical Classifica8on Linnaeus introduced a system for grouping species in increasingly broad categories domain, kingdom, phylum, class, order, family, genus, species Top down taxon Taxonomic unit at any level of hierarchy Fig Species: Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora Class: Mammalia Phylum: Chordata Kingdom: Animalia Bacteria Domain: Eukarya Archaea Linking Classifica8on and Phylogeny phylogene8c trees Used by systemasts to depict evoluonary relaonships Order Family Genus Species Carnivora Felidae Mustelidae Canidae Panthera Taxidea Lutra Canis Panthera pardus Taxidea taxus Lutra lutra Canis latrans Canis lupus

4 Linking Classifica8on and Phylogeny Linnaean classificaon and phylogeny can differ from each other Systemasts have proposed the PhyloCode which recognizes only groups that include a common ancestor and all its descendents Linking Classifica8on and Phylogeny A phylogenec tree represents a hypothesis about evoluonary relaonships Each branch point represents the divergence of two species Sister taxa Order Family Genus Carnivora Felidae Mustelidae Canidae Panthera Taxidea Lutra Canis Species Panthera pardus Taxidea taxus Lutra lutra Canis latrans Canis lupus are groups that share an immediate common ancestor A rooted tree includes a branch to represent the last common ancestor of all taxa in the tree A polytomy Linking Classifica8on and Phylogeny is a branch from which more than two groups emerge ANCESTRAL LINEAGE Common ancestor of taxa A F Branch point (node) Polytomy Taxon A Taxon B Taxon C Taxon D Taxon E Taxon F Sister taxa

5 What Can and Can t Learn from Phylogene8c Trees t Learn from Phylogene8c Trees Phylogenec trees do show pakerns of descent do not indicate when species evolved or how much genec change occurred in a lineage It shouldn t be assumed that a taxon evolved from the taxon next to it Sor8ng Homology from Analogy Organisms with similar morphologies or DNA sequences are likely to be more closely related Homology than organisms with different structures or sequences similarity due to shared ancestry Analogy similarity due to convergent evoluon Fig. 26 7

6 Bat and bird wings are homologous as forelimbs, but analogous as funconal wings Homoplasies Analogous structures or molecular sequences Homology Sor8ng Homology from Analogy that evolved independently can be disnguished 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 Cladis8cs Cladis8cs groups organisms by common descent Clade group of species that includes an ancestral species and all its descendants can be nested in larger clades but not all groupings of organisms qualify as clades A valid clade is monophyle8c signifying that it consists of the ancestor species and all its descendants Fig. 26 A A A B Group I B B C C C D D D E E Group II E F F F Group III G G G (a) Monophyletic group (clade) (b) Paraphyletic group (c) Polyphyletic group

7 Shared Ancestral and Shared Derived Characters Compared to an ancestor an organism has both shared and different characteriscs shared ancestral character originated in an ancestor of the taxon shared derived character evoluonary novelty unique to a parcular clade A character can be both ancestral and derived depending on the context Inferring Phylogenies Using Derived Characters When inferring evoluonary relaonships it is useful to know in which clade a shared derived character first appeared Lancelet (outgroup) Lamprey Tuna TAXA Salamander Turtle Leopard Lancelet (outgroup) Lamprey CHARACTERS Vertebral column (backbone) Hinged jaws Four walking legs Amniotic (shelled) egg Vertebral column Hinged jaws Four walking legs Tuna Salamander Turtle Hair Amniotic egg Hair Leopard (a) Character table (b) Phylogenetic tree Inferring Phylogenies Using Derived Characters outgroup species or group of species that is closely related to the Ingroup Systemasts the various species being studied compare each ingroup species with the outgroup to differenate between shared derived and shared ancestral characteriscs

8 Phylo Trees with Propor8onal Branch Lengths In some trees Branch length can reflect the number of genec changes that have taken place in a parcular DNA sequence in that lineage Drosophila Lancelet Zebrafish Frog Chicken Human Mouse Phylo Trees with Time Scale In other trees branch length can represent chronological me branching points can be determined from the fossil record Drosophila Lancelet Zebrafish Frog Chicken Human Mouse PALEOZOIC MESOZOIC CENOZOIC Millions of years ago 65.5 Present Maximum Parsimony and Maximum Likelihood Systemasts can never be sure of finding the best tree in a large data set narrow possibilies by applying the principles of maximum parsimony and maximum likelihood Maximum parsimony the tree that requires the fewest evoluonary events (appearances of shared derived characters) is the most likely Maximum likelihood given certain rules about how DNA changes over me a tree can be found that reflects the most likely sequence of evoluonary events

9 Fig Human Mushroom Tulip Human 3% 4% Mushroom 4% Tulip (a) Percentage differences between sequences 5% 5% 5% 5% 5% % 2% 25% Tree : More likely (b) Comparison of possible trees Tree 2: Less likely Phylogene8c Trees as Hypotheses The best hypotheses for phylogenec trees fit the most data: morphological, molecular, and fossil Phylogene8c bracke8ng allows us to predict features of an ancestor from features of its descendents Lizards and snakes Crocodilians Common ancestor of crocodilians, dinosaurs, and birds Ornithischian dinosaurs Saurischian dinosaurs Birds Fig Front limb Hind limb Eggs (a) Fossil remains of Oviraptor and eggs (b) Artist s reconstruction of the dinosaur s posture

10 evolu8onary history in the genome the genome Comparing nucleic acids or other molecules to infer relatedness is a valuable tool for tracing organisms evoluonary history DNA that codes for rrna changes relavely slowly and is useful for invesgang branching points hundreds of millions of years ago mtdna evolves rapidly can be used to explore recent evoluonary events Gene duplicaon Gene Duplica8ons and Gene Families increases the number of genes in the genome providing more opportunies for evoluonary changes Like homologous genes duplicated genes can be traced to a common ancestor Orthologous genes found in a single copy in the genome homologous between species can diverge only a\er speciaon occurs Gene Duplica8ons and Gene Families Paralogous genes result from gene duplicaon so are found in more than one copy in the genome can diverge within the clade that carries them and o\en evolve new funcons

11 Fig Ancestral gene Ancestral species Speciation with divergence of gene Species A (a) Orthologous genes Orthologous genes Species B Species A Gene duplication and divergence (b) Paralogous genes Paralogous genes Species A after many generations Orthologous genes Genome Evolu8on are widespread and extend across many widely varied species Gene number and the complexity of an organism are not strongly linked Genes in complex organisms appear to be very versale and each gene can perform many funcons Molecular clock Molecular Clocks uses constant rates of evoluon in some genes to esmate the absolute me of evoluonary change In orthologous genes nucleode substuons are proporonal to the me since they last shared a common ancestor In paralogous genes nucleode substuons are proporonal to the me since the genes became duplicated

12 Molecular Clocks Molecular clocks are calibrated against branches whose dates are known from the fossil record Number of mutations Divergence time (millions of years) 2 Neutral Theory Neutral theory states that much evoluonary change in genes and proteins has no effect on fitness and therefore is not influenced by Darwinian selecon the rate of molecular change in these genes and proteins should be regular like a clock The molecular clock Difficul8es with Molecular Clocks does not run as smoothly as neutral theory predicts Irregularies result from natural selecon in which some DNA changes are favored over others Esmates of evoluonary divergences older than the fossil record have a high degree of uncertainty The use of mulple genes may improve esmates

13 Fig Index of base changes between HIV sequences Computer model of HIV Range Year 98 2 From Two Kingdoms to Three Domains Early taxonomists classified all species as either plants or animals Later, five kingdoms were recognized Monera (prokaryotes), Prosta, Plantae, Fungi, and Animalia More recently the three domain system has been adopted Bacteria, Archaea, and Eukarya The three domain system is supported by data from many sequenced genomes Fig EUKARYA Land plants Dinoflagellates Green algae Forams Ciliates Diatoms Red algae Amoebas Cellular slime molds Animals Fungi Euglena Trypanosomes Leishmania Thermophiles Sulfolobus Green nonsulfur bacteria (Mitochondrion) Halophiles Methanobacterium ARCHAEA COMMON ANCESTOR OF ALL LIFE Spirochetes Chlamydia Green sulfur bacteria BACTERIA Cyanobacteria (Plastids, including chloroplasts)

14 From Two Kingdoms to Three Domains There have been substanal interchanges of genes between organisms in different domains Horizontal gene transfer movement of genes from one genome to another Very common in prokaryotes Viruses and eukaryotes do it too complicates efforts to build a tree of life Fig Bacteria Eukarya Archaea Billions of years ago Some researchers suggest that eukaryotes arose as an endosymbiosis between a bacterium and archaean Ring of Life? If so, early evoluonary relaonships might be beker depicted by a ring of life instead of a tree of life

15 Fig Eukarya Bacteria Archaea You should now be able to:. Explain the jusficaon for taxonomy based on a PhyloCode 2. Explain the importance of disnguishing between homology and analogy 3. Disnguish between the following terms: monophylec, paraphylec, and polyphylec groups; shared ancestral and shared derived characters; orthologous and paralogous genes 4. Define horizontal gene transfer and explain how it complicates phylogenec trees 5. Explain molecular clocks and discuss their limitaons