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2/9/2015 Chapter 26: Phylogeny and the Tree of Life 1. Key Concepts Pertaining to Phylogeny 2. Determining Phylogenies 3. Evolutionary History Revealed in Genomes 1. Key Concepts Pertaining to Phylogeny Cell division error PHYLOGENY – the evolutionary history of species or group Species: Panthera pardus Genus: Panthera TAXONOMY – system by which organisms are named and classified Family: Felidae • based on morphological and molecular (DNA, proteins) data Order: Carnivora • not necessarily based on evolutionary history, though it can be Class: Mammalia TAXONOMIC HIERARCHY – series of nested groupings used to categorize organisms • developed by Carolus Linnaeus of Sweden in the mid-18th century and still used today Phylum: Chordata Domain: Bacteria Kingdom: Animalia Domain: Archaea Domain: Eukarya 1 2/9/2015 TAXON – a specific category or level in the taxonomic hierarchy (e.g., “class” or “family”) BINOMIAL NOMENCLATURE – how organisms are named • genus & specific epithet (e.g., Homo sapiens, Escherichia coli, Tyrannosaurus rex) o both terms are “latinized” and written in italics o the specific epithet is an adjective and is not capitalized o the genus is a noun and is capitalized • also developed by Carolus Linnaeus Order Family Genus Phylogenetic Trees Species Felidae Panthera Panthera pardus (leopard) Taxidea taxus (American badger) Lutra lutra (European otter) Lutra Mustelidae Taxidea Carnivora A PHYLOGENITIC TREE is a branching diagram representing a hypothesis of evolutionary relationships 1 Canis Canidae 2 • each branch point indicates divergence from a common ancestor • shows patterns of descent, NOT morphological similarity Canis latrans (coyote) SISTER TAXA – groups that share an immediate common ancestor (e.g., wolf and coyote) Canis lupus (gray wolf) BASAL TAXON – earliest lineage to diverge from the remainder of a group Branch point: where lineages diverge Taxon A 3 Taxon B 4 Taxon C ROOTED – if all taxa in a group have the same common ancestor they are said to be “rooted” POLYTOMY – more than two lineages diverge from a single branch point (due to uncertain divergence) Sister taxa 2 Taxon D ANCESTRAL LINEAGE 1 5 Taxon E Taxon F Taxon G This branch point represents the common ancestor of taxa A–G. Basal taxon This branch point forms a polytomy: an unresolved pattern of divergence. 2 2/9/2015 Homology vs Analogy HOMOLOGY – similarities due to common ancestry • Molecular Homology – similarity in DNA, protein sequences • Morphological Homology – skeletal & fossil similarities ANALOGY – morphological similarity due to convergent evolution (e.g., bird vs bat wings) • analogous structures that arise independently are referred to as homoplasies Australian marsupial “mole” North American eutherian mole 2. Determining Phylogenies All available information, molecular, morphological and physiological, are used in determining phylogenetic relationships. Geckos ANCESTRAL LIZARD (with limbs) No limbs Snakes Iguanas Monitor lizard When molecular and morphological data contradict, molecular data takes precedence. Eastern glass lizard No limbs 3 2/9/2015 Using DNA Homology to Construct Phylogenies Cell 1 C C A T C AG AG T C C division 2 C C A T C A G AG T C C error Deletion 1 C C A T C AG AG T C C 2 C C A T C AG AG T C C Sequences in non-conserved regions of DNA (i.e., sequences not subject to Natural Selection) are aligned since they are presumably free to mutate G T A Insertion o computers are used to find the best alignment accounting for deletions, insertions, etc 1 C C A T C AAG T C C 2 C C A T G TA C AG AG T C C The degree of homology in similar regions can be used to construct a phylogeny o greater homology = more recent common ancestor 1 C C A T C A AG T C C NOTE: Random chance would result in 25% homology between sequences, so true homology must be >25%. 2 C C A T G TA C AG AG T C C Using Cladistics to Construct Phylogenies CLADE – an ancestral species and all descendants • all descendants have a single common ancestor (a) Monophyletic group (clade) • all members of clade have unique shared derived characters A 1 • clades are a monophyletic groups B Group I C SHARED ANCESTRAL CHARACTERS (SAC) D • characters that originated before the clade E SHARED DERIVED CHARACTERS (SDC) F • characters found only within the clade PARAPHYLETIC group – consists of a single common ancestor and some (not all) of its descendants (b) Paraphyletic group G Paraphyletic group Common ancestor of even-toed ungulates Other even-toed ungulates (c) Polyphyletic group Hippopotamuses A A B B C D 2 Group III Cetaceans C 3 D E Group II E F F G G Seals Bears POLYPHYLETIC group – consists of organisms with more than 1 common ancestor Polyphyletic group Other carnivores 4 2/9/2015 Constructing phylogenies based on shared derived characters (SDCs): • start with an outgroup (group that diverged before the lineage of interest) and construct the phylogeny based on multiple SDCs • a character table can be used to identify successive branch points, each being due to a SDC found in successively fewer members of the phylogeny Bass Frog Turtle Leopard Lancelet (outgroup) Lamprey CHARACTERS Lancelet (outgroup) TAXA Vertebral column (backbone) 0 1 1 1 1 1 Hinged jaws 0 0 1 1 1 1 4 walking legs 0 0 0 1 1 1 Amnion 0 0 0 0 1 1 Hair 0 0 0 0 0 1 Lamprey Bass Vertebral column Hinged jaws Frog Turtle Four walking legs Amnion Leopard Hair (b) Phylogenetic tree (a) Character table Using the Principle of “Maximum Parsimony” to Construct Phylogenies A phylogeny should be constructed based on maximum parsimony, i.e., the simplest solution that is consistent with the facts. • this is the principle of “Occam’s Razor” in which the hypothesis with the fewest assumptions is favored Applying the principle of maximum likelihood to phylogenies based on DNA sequences: • the hypothesis that requires the least number of mutational events is favored Technique 3 1/C I 1/C I II III III II III II 1/C I 1/C Species I 1 Species II Three phylogenetic hypotheses: I I 4 III II III II III II I 1 Site 2 3 Species I C T A T Species II C T T C Species III Ancestral sequence A G A C G T T 2 A 1/C Species III 4 3/A 2/T I 2/T 3/A II 4/C III II II I 2/T 3/A I I II III III III 2/T 2/T 4/C 6 events 3/A 4/C III 4/C 3/A 4/C Results I II 7 events III II I 7 events 5 2/9/2015 Phylogenetic Bracketing Phylogenetic bracketing is the process of inferring unknown characters in extinct species based on the principle of maximum parsimony: • in this example the shared characters of crocodiles and birds are also attributed to 2 groups of dinosaurs • this example of phylogenetic bracketing exhibits maximum parsimony since the simplest explanation for these shared characters would be a single common ancestor from which all 4 groups evolved Lizards and snakes Crocodilians Ornithischian dinosaurs Common ancestor of crocodilians, dinosaurs, and birds Saurischian dinosaurs Birds Evidence Supporting a Case of Phylogenetic Bracketing Front limb Hind limb This fossil supports a prediction based on phylogenetic bracketing – that dinosaurs, like crocodiles and birds, engaged in brooding, the bodily warming of eggs. Eggs (a) Fossil remains of Oviraptor and eggs (b) Artist’s reconstruction of the dinosaur’s posture based on the fossil findings Phylogenetic Branch Lengths can be used to Indicate the Degree of Genetic Differences… Drosophila Lancelet Zebrafish Frog Chicken Human Mouse 6 2/9/2015 Phylogenetic Branches can also Indicate Time Drosophila Lancelet Zebrafish Frog Chicken Human Mouse 542 CENOZOIC MESOZOIC PALEOZOIC 251 Millions of years ago 65.5 Present 3. Evolutionary History Revealed in Genomes Orthologous vs Paralogous Genes ORTHOLOGOUS GENES – homologous genes in different species PARALOGOUS GENES – homology between different genes in the same species due to duplication Formation of orthologous genes: a product of speciation Ancestral gene Ancestral gene Ancestral species Species C Speciation with divergence of gene Gene duplication and divergence Orthologous genes Species A Formation of paralogous genes: within a species Species B Gene families result from repeated duplication of an original gene followed by subsequent mutation. Paralogous genes Species C after many generations 7 2/9/2015 Molecular Clocks Certain genes or other regions of genomes tend to change (i.e., evolve) at a constant rate and thus serve as a molecular clock. Number of mutations For example, the number sequence differences (i.e., nucleotide substitutions) in orthologous genes can reveal: • the amount of time that has passed since 2 species diverged from a common ancestor 90 60 • the amount of time that has passed since the gene was duplicated 30 0 0 60 90 30 Divergence time (millions of years) 120 This is best determined with neutral mutations (mutations that are neither selected for or against). Problems with Molecular Clocks A molecular clock will not give accurate predictions if the rate of mutation is not constant which will be the case if: • there is natural selection (i.e., a mutation is not neutral) • changes in selective factors over time (i.e., under some conditions a mutation may be neutral and under other conditions it may not be) • for these or other reasons the mutation rate may change over time One can increase the number of genes and taxa analyzed as molecular clocks to dilute any inaccuracies associated with any particular gene, however the problems indicated above can never be entirely eliminated. Cell division error Euglenozoans Forams Diatoms Red algae Green algae Land plants Domain Eukarya Ciliates Amoebas Fungi Animals Methanogens COMMON ANCESTOR OF ALL LIFE Thermophiles Domain Archaea Nanoarchaeotes Proteobacteria Chlamydias Spirochetes Gram-positive bacteria Cyanobacteria (Chloroplasts)* Domain Bacteria (Mitochondria)* Current Model of the “Tree of Life” • this model, as with previous models, will no doubt change over time as more information pertaining to current and extinct species becomes available • as new information becomes available, we get closer and closer to the true evolutionary relationships among all species, both past and present 8