2 MPELL IOLOGY IN FOUS URRY IN WSSERMN MINORSKY REEE What kind of organism is this? Phylogeny Lecture Presentations by Kathleen Fitzpatrick and Nicole Tunbridge, Simon Fraser University SEON EITION onvergent evolution of limbless bodies No limbs Eastern glass lizard Phylogeny of lizards and Snakes No limbs Eastern glass lizard Monitor lizard Monitor lizard Iguanas NESTRL Iguanas Legless lizard known as the eastern glass lizard LIZR (with limbs) No limbs Snakes Geckos NESTRL LIZR (with limbs) No limbs Snakes Geckos oth eastern glass lizard and snakes both evolved from different lineages of lizards with legs Investigating the Tree of Life 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 oncept 2.: Phylogenies show evolutionary relationships Organisms share many characteristics because of common ancestry 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: twopart names for species and hierarchical classification
inomial Nomenclature 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) Linnaean classification. omain: acteria Species: Panthera pardus Genus: Panthera Family: Felidae Order: arnivora lass: Mammalia Phylum: hordata Kingdom: nimalia omain: rchaea omain: Eukarya Hierarchical lassification 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 Ex. Panthera is a taxon at the genus level Linking lassification and Phylogeny Systematics is the study of biological diversity and the evolutionary relationships among organisms, both extinct and modern Systematists depict evolutionary relationships in branching phylogenetic trees Linnaean classification and phylogeny can differ from each other Systematists have proposed that classification be based entirely on evolutionary relationships onnection between classification & phylogeny is the most recent common ancestor of all members of the weasel (Mustelidae) and dog (anidae). 2 is the most recent common ancestor of coyotes and gray wolves. ranch point: where lineages diverge NESTRL LINEGE How to read a phylogenetic tree This branch point represents the common ancestor of taxa G. Taxon Taxon Taxon Taxon Taxon E Taxon F Taxon G This branch point forms a polytomy: an unresolved pattern of divergence. Sister taxa asal taxon 2
How to read a phylogenetic tree phylogenetic tree represents a hypothesis about evolutionary relationships Each branch point represents the divergence of two taxa from a common ancestor Sister taxa are groups that share an immediate common ancestor rooted tree includes a branch to represent the most recent 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 How to read a phylogenetic tree polytomy is a branch from which more than two groups emerge rooted tree includes a branch to represent the most recent 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 oncept heck This cladogram represents an imaginary group of organisms,,,, and E. common ancestor for species and E would be at which position number? oncept heck This cladogram represents an imaginary group of organisms,,,, and E. common ancestor for species and E would be at which position number?.. 2. 3. 4.... 2.. 3. 4. E... 2. 3. 4.... 2.. 3. 4. E. 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 Figure 2.6 Results What is the species identity of food being sold as whale meat? Minke (Southern Hemisphere) mtn Unknown mtn #a, 2, 3, 4, 5, 6, 7, 8 Minke (North tlantic) mtn Unknown mtn #9 Humpback mtn Unknown mtn #b lue mtn Unknown mtn #,, 2, 3 Fin mtn 3
pplying Phylogenies Phylogeny provides important information about similar characteristics in closely related species Phylogenetic trees based on N sequences can be used to infer species identities For example: phylogeny was used to identify the species of whale from which whale meat originated When anthrax spores were sent to a politicians and journalists in fall 2, researchers used phylogenetic trees based on N data to identify the strain of bacterium. Which of the trees shown below depicts a different evolutionary history for taxa -? () () () Which of the trees shown below depicts a different evolutionary history for taxa -? oncept 2.2: Phylogenies are inferred from morphological and molecular data To infer phylogeny, systematists gather information about morphologies, genes, and biochemistry of the relevant organisms The similarities used to infer phylogenies must result from shared ancestry () () () 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 oncept heck phylogenetic tree is a:. hypothesis about the evolutionary history of a species.. guess about the evolutionary history of a species.. factual representation of the evolutionary history of a species. detailed timeline of a species evolutionary history. E. None of the above. 4
oncept heck phylogenetic tree is a:. hypothesis about the evolutionary history of a species.. guess about the evolutionary history of a species.. factual representation of the evolutionary history of a species. detailed timeline of a species evolutionary history. E. None of the above. Sorting Homology and nalogy Homology is phenotypic and genotypic similarity due to shared ancestry nalogy is similarity due to convergent evolution When two organisms from different evolutionary lineages experience similar environmental pressures, natural selection may result in convergent evolution Figure 2.7 onvergent evolution of analogous borrowing characteristics onvergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages ustralian marsupial mole North merican eutherian mole istinguishing homology from analogy oth birds and bats have adaptations that allow them to fly. at s wing shows a greater similarity to a cat s forelimb than to a bird s wing. Fossil evidence shows that bat and bird wings arose independently from walking forelimbs of different ancestors. at and bird wings are homologous as forelimbs, but analogous as functional wings Evaluating Molecular Homologies Molecular homologies are determined based on the degree of similarity in nucleotide sequence between taxa Systematists use computer programs when analyzing comparable N segments from different organisms Figure 2.8-s T G G T 5
Figure 2.8-s2 T G G T Figure 2.8-s3 T G G T eletion T G G T eletion T G G T G T Insertion G T Insertion T G T 2 T G T G G T Figure 2.8-s4 T G G T eletion T G G T G T Insertion T G T 2 T G T G G T. Homologous N segments in species and 2 2. eletion and insertion mutations appear in both species 3. Two shaded regions do not align because of mutations 4. omputer programs adds gaps in sequence to align similar sequences. T G T 2 T G T G G T Figure 2.9 Shared bases in nucleotide sequences that are otherwise very dissimilar are called molecular homoplasies G G T G T T G G T T G G G T T T T G T G oncept 2.3: Shared characters are used to construct phylogenetic trees Once homologous characters have been identified, they can be used to infer a phylogeny ladistics ladistics classifies organisms by common descent clade is a group of species that includes an ancestral species and all its descendants lades can be nested within larger clades, but not all groupings of organisms qualify as clades 6
HRTERS (outgroup) Lamprey ass Turtle Leopard Monophyletic (single tribe) consists of the ancestral species and all its descendants Figure 2.-2 Paraphyletic (besides the tribe) consists of an ancestral species and some but not all of its descendants Figure 26.c Polyphyletic (besides the tribe) consist of various species with different ancestors ommon ancestor of even-toed ungulates Paraphyletic group Other even-toed ungulates Hippopotamuses etaceans Seals ears Polyphyletic group Other carnivores Shared ncestral and Shared erived haracters In comparison with its ancestor, an organism has both shared and different characteristics Using derived characters to infer phylogeny TX shared ancestral character is a character that originated in an ancestor of the taxon ackbone in mammals shared derived character is an evolutionary novelty unique to a particular clade Hair in mammals When inferring evolutionary relationships, it is useful to know in which clade a shared derived character first appeared Vertebral column (backbone) Hinged jaws Four limbs mnion Hair (a) haracter table 7
HRTERS (outgroup) Lamprey ass Turtle Leopard Using derived characters to infer phylogeny Vertebral column Hinged jaws Four limbs (b) Phylogenetic tree mnion Hair (outgroup) Lamprey ass Turtle Leopard Figure 2.2 When inferring evolutionary relationships, it is useful to know in which clade a shared derived character first appeared Vertebral column (backbone) Hinged jaws Four limbs mnion Hair (a) haracter table TX Vertebral column Hinged jaws Four limbs mnion (b) Phylogenetic tree Hair (outgroup) Lamprey ass Turtle Leopard onsider the phylogeny below: 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 Phylogenetic Tree Species M has green toes, and species L has red toes. If species H and K have green toes, what can we conclude about the evolution of red toes?. It occurred in the common ancestor of M, H, K, and L.. It occurred in the common ancestor of H, K, and L.. It occurred in the lineage leading to L after that lineage diverged from the common ancestor of H and K. Figure 2.3 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 hicken Human Zebrafish rosophila Figure 2.4 ranch length can represent chronological time, and branching points can be determined from the fossil record rosophila Zebrafish hicken Human Mouse Mouse 5 4 3 2 Millions of years ago Present 8
Maximum Parsimony and Maximum Likelihood Systematists can never be sure of finding the best tree in a large data set 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 Phylogenetic Trees as Hypotheses Phylogenetic bracketing allows us to predict that, features shared by two groups of closely related organisms are present in ancestors and all of its descendants For example, phylogenetic bracketing allows us to infer characteristics of dinosaurs based on shared characters in modern birds and crocodiles ommon ancestor of crocodilians, dinosaurs, and birds Lizards and snakes rocodilians Ornithischian dinosaurs Saurischian dinosaurs other than birds irds irds and crocodiles share several features: four-chambered hearts, song, nest building, and egg 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 oncept 2.5: New information continues to revise our understanding of evolutionary history Recently, systematists have gained insight into the very deepest branches of the tree of life through analysis of N sequence data 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 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 The three domains of life OMMON NESTOR OF LL LIFE Euglenozoans Forams iatoms iliates Red algae Green algae Plants moebas Fungi nimals Nanoarchaeotes Euryarcheotes renarcheotes Proteobacteria (Mitochondria)* hlamydias Spirochetes Gram-positive bacteria yanobacteria (hloroplasts)* omain Eukarya omain rchaea omain acteria 9
The three-domain system highlights the importance of single-celled organisms in the history of life omains acteria and rchaea are single-celled prokaryotes omains Eukarya are single-celled or multicellular eukaryotes Only three lineages in the domain Eukarya are dominated by multicellular organisms, as kingdoms Plantae, Fungi, and nimalia The Important Role of Horizontal Gene Transfer 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, which have evolved slowly, allowing detection of homologies between distantly related organisms Other genes indicate different evolutionary relationships 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 Horizontal Gene Transfer tangled web of life ncestral cell populations Plantae Methanogens Thermophiles yanobacteria Proteobacteria omain Eukarya omain rchaea omain acteria You should now be able to:. efine Phylogeny, Taxonomy, Systematics, 2. Know the correct hierarchy of the Linnaean system of classification 3. Know the difference between homology and analogy 4. Know the importance of phylogenetic trees 5. efine lade, Monophyletic, Paraphyletic, and Polyphyletic 6. Know the modern classification system. What modern criterion is used for its construction?