/5/4 LETURE PRESENTTIONS For MPELL IOLOY, NINTH EITION Jane. Reece, Lisa. Urry, Michael L. ain, Steven. Wasserman, Peter V. Minorsky, Robert. Jackson hapter 6 Phylogeny and the Tree of Life Overview: Investigating the Tree of Life Legless lizards have evolved independently in several different groups Lectures by Erin arley Kathleen Fitzpatrick Figure 6. Phylogeny is the evolutionary history of a species or group of related species The discipline of systematics classifies organisms and determines their evolutionary relationships Systematists use fossil, molecular, and genetic data to infer evolutionary relationships Figure 6. Figure 6.a
/5/4 Figure 6.b Figure 6.c oncept 6.: Phylogenies show evolutionary relationships Taxonomy is the ordered division and naming of organisms inomial Nomenclature In the 8th century, arolus Linnaeus published a system of taxonomy based on resemblances Two key features of his system remain useful today: two-part names for species and hierarchical classification Hierarchical lassification The two-part scientific name of a species is called a binomial The first part of the name is the genus The second part, called the specific epithet, is unique for each species within the genus The first letter of the genus is capitalized, and the entire species name is italicized oth parts together name the species (not the specific epithet alone) Linnaeus introduced a system for grouping species in increasingly broad categories The taxonomic groups from broad to narrow are domain, kingdom, phylum, class, order, family, genus, and species taxonomic unit at any level of hierarchy is called a taxon The broader taxa are not comparable between lineages For example, an order of snails has less genetic diversity than an order of mammals
/5/4 Figure 6.3 Species: Panthera pardus enus: Panthera Family: Felidae Order: arnivora Linking lassification and Phylogeny Systematists depict evolutionary relationships in branching phylogenetic trees lass: Mammalia Phylum: hordata omain: acteria Kingdom: nimalia omain: Eukarya omain: rchaea Figure 6.4 Order Family enus Species arnivora Felidae Mustelidae Panthera Taxidea Lutra Panthera pardus (leopard) Taxidea taxus (merican badger) Lutra lutra (European otter) Linnaean classification and phylogeny can differ from each other Systematists have proposed the Phyloode, which recognizes only groups that include a common ancestor and all its descendants anidae anis anis latrans (coyote) anis lupus (gray wolf) phylogenetic tree represents a hypothesis about evolutionary relationships Each branch point represents the divergence of two species Sister taxa are groups that share an immediate common ancestor rooted tree includes a branch to represent the last common ancestor of all taxa in the tree basal taxon diverges early in the history of a group and originates near the common ancestor of the group polytomy is a branch from which more than two groups emerge 3
/5/4 Figure 6.5 ranch point: where lineages diverge NESTRL LINEE This branch point represents the common ancestor of taxa. Taxon Taxon Taxon Taxon Taxon E Taxon F Taxon This branch point forms a polytomy: an unresolved pattern of divergence. Sister taxa asal taxon What We an and annot Learn from Phylogenetic Trees Phylogenetic trees show patterns of descent, not phenotypic similarity Phylogenetic trees do not indicate when species evolved or how much change occurred in a lineage It should not be assumed that a taxon evolved from the taxon next to it pplying Phylogenies Phylogeny provides important information about similar characteristics in closely related species phylogeny was used to identify the species of whale from which whale meat originated Figure 6.6 RESULTS Minke (Southern Hemisphere) Unknowns #a,, 3, 4, 5, 6, 7, 8 Minke (North tlantic) Unknown #9 Humpback (North tlantic) Humpback (North Pacific) Unknown #b ray lue Unknowns #,, Unknown #3 Fin (Mediterranean) Fin (Iceland) oncept 6.: Phylogenies are inferred from morphological and molecular data To infer phylogenies, systematists gather information about morphologies, genes, and biochemistry of living organisms Morphological and Molecular Homologies Phenotypic and genetic similarities due to shared ancestry are called homologies Organisms with similar morphologies or N sequences are likely to be more closely related than organisms with different structures or sequences 4
/5/4 Sorting Homology from nalogy When constructing a phylogeny, systematists need to distinguish whether a similarity is the result of homology or analogy Homology is similarity due to shared ancestry nalogy is similarity due to convergent evolution onvergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages Figure 6.7 at and bird wings are homologous as forelimbs, but analogous as functional wings nalogous structures or molecular sequences that evolved independently are also called homoplasies 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 Evaluating Molecular Homologies Figure 6.8- Systematists use computer programs and mathematical tools when analyzing comparable N segments from different organisms 5
/5/4 Figure 6.8- Figure 6.8-3 eletion eletion Insertion Insertion 3 Figure 6.8-4 3 Insertion eletion It is also important to distinguish homology from analogy in molecular similarities Mathematical tools help to identify molecular homoplasies, or coincidences Molecular systematics uses N and other molecular data to determine evolutionary relationships 4 Figure 6.9 oncept 6.3: Shared characters are used to construct phylogenetic trees Once homologous characters have been identified, they can be used to infer a phylogeny 6
/5/4 ladistics ladistics groups organisms by common descent clade is a group of species that includes an ancestral species and all its descendants lades can be nested in larger clades, but not all groupings of organisms qualify as clades valid clade is monophyletic, signifying that it consists of the ancestor species and all its descendants Figure 6. Figure 6.a (a) Monophyletic group (clade) (a) Monophyletic group (clade) (b) Paraphyletic group (c) Polyphyletic group roup roup roup E E roup E F F F E F Figure 6.b (b) Paraphyletic group paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants E roup F 7
/5/4 Figure 6.c (c) Polyphyletic group polyphyletic grouping consists of various species with different ancestors E F roup Shared ncestral and Shared erived haracters In comparison with its ancestor, an organism has both shared and different characteristics shared ancestral character is a character that originated in an ancestor of the taxon shared derived character is an evolutionary novelty unique to a particular clade character can be both ancestral and derived, depending on the context Figure 6. Inferring Phylogenies Using erived haracters When inferring evolutionary relationships, it is useful to know in which clade a shared derived character first appeared HRTERS Vertebral column (backbone) Hinged jaws Four walking legs mnion TX Lancelet (outgroup) Lamprey ass Frog Turtle Leopard Vertebral column Hinged jaws Four walking legs Lancelet (outgroup) Lamprey ass Frog Turtle Hair mnion Hair Leopard (a) haracter table (b) Phylogenetic tree 8
/5/4 Figure 6.a HRTERS Vertebral column (backbone) Hinged jaws Four walking legs mnion Lancelet (outgroup) Lamprey TX ass Frog Turtle Leopard Figure 6.b Vertebral column Hinged jaws Four walking legs Lancelet (outgroup) Lamprey ass Frog Turtle Hair mnion Hair Leopard (a) haracter table (b) Phylogenetic tree n outgroup is a species or group of species that is closely related to the ingroup, the various species being studied The outgroup is a group that has diverged before the ingroup Systematists compare each ingroup species with the outgroup to differentiate between shared derived and shared ancestral characteristics haracters shared by the outgroup and ingroup are ancestral characters that predate the divergence of both groups from a common ancestor Phylogenetic Trees with Proportional ranch Lengths In some trees, the length of a branch can reflect the number of genetic changes that have taken place in a particular N sequence in that lineage Figure 6. rosophila Lancelet Zebrafish Frog hicken Human Mouse 9
/5/4 Figure 6.3 In other trees, branch length can represent chronological time, and branching points can be determined from the fossil record rosophila Lancelet Zebrafish Frog hicken Human PLEOZOI MESOZOI 54 5 65.5 Millions of years ago ENOZOI Present Mouse Maximum Parsimony and Maximum Likelihood Systematists can never be sure of finding the best tree in a large data set They narrow possibilities by applying the principles of maximum parsimony and maximum likelihood Maximum parsimony assumes that the tree that requires the fewest evolutionary events (appearances of shared derived characters) is the most likely The principle of maximum likelihood states that, given certain rules about how N changes over time, a tree can be found that reflects the most likely sequence of evolutionary events Figure 6.4 Human Mushroom Tulip Figure 6.4a Human 3% 4% Mushroom Tulip 4% Human Mushroom Tulip (a) Percentage differences between sequences Human 3% 4% 5% 5% Mushroom 4% 5% 5% 5% Tulip % (a) Percentage differences between sequences % 5% Tree : More likely (b) omparison of possible trees Tree : Less likely
/5/4 Figure 6.4b 5% 5% omputer programs are used to search for trees that are parsimonious and likely 5% 5% 5% % % 5% Tree : More likely (b) omparison of possible trees Tree : Less likely Figure 6.5 TEHNIQUE Figure 6.5a TEHNIQUE Species Species Species Three phylogenetic hypotheses: Site 3 4 Species T T Species T T Species ncestral sequence T T 3 4 RESULTS / 3/ /T 4/ 3/ 4/ / / /T 3/ 4/ /T 4/ / / 3/ 4/ /T /T 3/ Species Species Species Three phylogenetic hypotheses: 6 events 7 events 7 events Figure 6.5b Figure 6.5c TEHNIQUE 3 / / TEHNIQUE Species Species Species ncestral sequence Site 3 4 T T T T T T 4 RESULTS 3/ /T 4/ 3/ 4/ / /T 3/ 4/ /T 4/ / / 3/ 4/ /T /T 3/ 6 events 7 events 7 events
/5/4 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 For example, phylogenetic bracketing allows us to infer characteristics of dinosaurs Figure 6.6 ommon ancestor of crocodilians, dinosaurs, and birds Lizards and snakes rocodilians Ornithischian dinosaurs Saurischian dinosaurs irds Figure 6.7 irds and crocodiles share several features: four-chambered hearts, song, nest building, and brooding These characteristics likely evolved in a common ancestor and were shared by all of its descendants, including dinosaurs The fossil record supports nest building and brooding in dinosaurs Front limb Eggs Hind limb (a) Fossil remains of Oviraptor and eggs (b) rtist s reconstruction of the dinosaur s posture based on the fossil findings nimation: The eologic Record Figure 6.7a Figure 6.7b Front limb Hind limb Eggs (a) Fossil remains of Oviraptor and eggs (b) rtist s reconstruction of the dinosaur s posture based on the fossil findings
/5/4 oncept 6.4: n organism s evolutionary history is documented in its genome omparing nucleic acids or other molecules to infer relatedness is a valuable approach for tracing organisms evolutionary history N that codes for rrn changes relatively slowly and is useful for investigating branching points hundreds of millions of years ago mtn evolves rapidly and can be used to explore recent evolutionary events ene uplications and ene Families ene duplication increases the number of genes in the genome, providing more opportunities for evolutionary changes Repeated gene duplications result in gene families Like homologous genes, duplicated genes can be traced to a common ancestor Figure 6.8 Orthologous genes are found in a single copy in the genome and are homologous between species They can diverge only after speciation occurs Formation of orthologous genes: a product of speciation ncestral gene ncestral species Formation of paralogous genes: within a species ncestral gene Species Speciation with divergence of gene ene duplication and divergence Orthologous genes Paralogous genes Species Species Species after many generations Figure 6.8a Formation of orthologous genes: a product of speciation ncestral gene ncestral species Paralogous genes result from gene duplication, so are found in more than one copy in the genome They can diverge within the clade that carries them and often evolve new functions Speciation with divergence of gene Species Orthologous genes Species 3
/5/4 Figure 6.8b Formation of paralogous genes: within a species ncestral gene Species ene duplication and divergence enome Evolution Orthologous genes are widespread and extend across many widely varied species For example, humans and mice diverged about 65 million years ago, and 99% of our genes are orthologous Paralogous genes Species after many generations ene number and the complexity of an organism are not strongly linked For example, humans have only four times as many genes as yeast, a single-celled eukaryote enes in complex organisms appear to be very versatile, and each gene can perform many functions oncept 6.5: Molecular clocks help track evolutionary time To extend molecular phylogenies beyond the fossil record, we must make an assumption about how change occurs over time Molecular locks molecular clock uses constant rates of evolution in some genes to estimate the absolute time of evolutionary change In orthologous genes, nucleotide substitutions are proportional to the time since they last shared a common ancestor In paralogous genes, nucleotide substitutions are proportional to the time since the genes became duplicated Molecular clocks are calibrated against branches whose dates are known from the fossil record Individual genes vary in how clocklike they are 4
/5/4 Figure 6.9 Number of mutations 9 6 3 Neutral Theory Neutral theory states that much evolutionary change in genes and proteins has no effect on fitness and is not influenced by natural selection It states that the rate of molecular change in these genes and proteins should be regular like a clock 3 6 9 ivergence time (millions of years) Problems with Molecular locks The molecular clock does not run as smoothly as neutral theory predicts Irregularities result from natural selection in which some N changes are favored over others Estimates of evolutionary divergences older than the fossil record have a high degree of uncertainty The use of multiple genes may improve estimates pplying a Molecular lock: The Origin of HIV Phylogenetic analysis shows that HIV is descended from viruses that infect chimpanzees and other primates HIV spread to humans more than once omparison of HIV samples shows that the virus evolved in a very clocklike way pplication of a molecular clock to one strain of HIV suggests that that strain spread to humans during the 93s Figure 6. Index of base changes between HIV gene sequences..5..5 HIV Range djusted best-fit line (accounts for uncertain dates of HIV sequences) oncept 6.6: New information continues to revise our understanding of the tree of life Recently, we have gained insight into the very deepest branches of the tree of life through molecular systematics 9 9 94 96 98 Year 5
/5/4 From Two Kingdoms to Three omains Early taxonomists classified all species as either plants or animals Later, five kingdoms were recognized: Monera (prokaryotes), Protista, Plantae, Fungi, and nimalia More recently, the three-domain system has been adopted: acteria, rchaea, and Eukarya The three-domain system is supported by data from many sequenced genomes nimation: lassification Schemes Figure 6. Eukarya Land plants inoflagellates reen algae Forams iliates iatoms Red algae ellular slime molds moebas Euglena Trypanosomes nimals Leishmania Fungi Sulfolobus Thermophiles Halophiles OMMON NESTOR OF LL LIFE Methanobacterium rchaea reen nonsulfur bacteria (Mitochondrion) Spirochetes hlamydia reen sulfur bacteria yanobacteria (Plastids, including chloroplasts) acteria Figure 6.a Figure 6.b reen nonsulfur bacteria (Mitochondrion) Thermophiles Sulfolobus OMMON NESTOR OF LL LIFE Spirochetes reen sulfur bacteria hlamydia yanobacteria (Plastids, including chloroplasts) acteria Halophiles Methanobacterium rchaea Figure 6.c Eukarya Land plants inoflagellates reen algae Forams iliates iatoms Red algae ellular slime molds moebas nimals Fungi Euglena Trypanosomes Leishmania Simple Tree of ll Life The tree of life suggests that eukaryotes and archaea are more closely related to each other than to bacteria The tree of life is based largely on rrn genes, as these have evolved slowly 6
/5/4 Figure 6. There have been substantial interchanges of genes between organisms in different domains Horizontal gene transfer is the movement of genes from one genome to another Horizontal gene transfer occurs by exchange of transposable elements and plasmids, viral infection, and fusion of organisms Horizontal gene transfer complicates efforts to build a tree of life acteria Eukarya rchaea 4 3 illions of years ago Figure 6.3 Is the Tree of Life Really a Ring? Some researchers suggest that eukaryotes arose as a fusion between a bacterium and archaean If so, early evolutionary relationships might be better depicted by a ring of life instead of a tree of life rchaea Eukarya acteria Figure 6.UN Figure 6.UN ranch point Taxon Most recent common ancestor Taxon Taxon Sister taxa Taxon (a) (b) (c) Polytomy Taxon E Taxon F Taxon asal taxon 7
/5/4 Figure 6.UN3 Figure 6.UN4 Monophyletic group Polyphyletic group Salamander Lizard E E E oat F F F Human Paraphyletic group Figure 6.UN5 Figure 6.UN6 Figure 6.UN7 Figure 6.UN8 8
/5/4 Figure 6.UN9 Figure 6.UN Figure 6.UN 9