Chapter 26: Phylogeny and the Tree of Life

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1 Chapter 26: Phylogeny and the Tree of Life 1. Key Concepts Pertaining to Phylogeny 2. Determining Phylogenies 3. Evolutionary History Revealed in Genomes

2 1. Key Concepts Pertaining to Phylogeny

3 PHYLOGENY the evolutionary history of species or group Cell division error Species: Panthera pardus TAXONOMY system by which organisms are named and classified based on morphological and molecular (DNA, proteins) data Genus: Panthera Family: Felidae 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-18 th century and still used today Domain: Bacteria Kingdom: Animalia Domain: Eukarya Phylum: Chordata Domain: Archaea

4 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

5 Order Family Genus Species Phylogenetic Trees Carnivora 1 Felidae Mustelidae Canidae Panthera Taxidea Lutra Canis 2 Panthera pardus (leopard) Taxidea taxus (American badger) Lutra lutra (European otter) Canis latrans (coyote) Canis lupus (gray wolf) A PHYLOGENITIC TREE is a branching diagram representing a hypothesis of evolutionary relationships each branch point indicates divergence from a common ancestor shows patterns of descent, NOT morphological similarity SISTER TAXA groups that share an immediate common ancestor (e.g., wolf and coyote)

6 BASAL TAXON earliest lineage to diverge from the remainder of a group ROOTED if all taxa in a group have the same common ancestor they are said to be rooted Branch point: where lineages diverge ANCESTRAL LINEAGE Taxon A Taxon B Taxon C Taxon D Taxon E Taxon F Sister taxa POLYTOMY more than two lineages diverge from a single branch point (due to uncertain divergence) This branch point represents the common ancestor of taxa A G. Taxon G This branch point forms a polytomy: an unresolved pattern of divergence. Basal taxon

7 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) Australian marsupial mole analogous structures that arise independently are referred to as homoplasies North American eutherian mole

8 2. Determining Phylogenies

9 All available information, molecular, morphological and physiological, are used in determining phylogenetic relationships. Geckos ANCESTRAL LIZARD (with limbs) No limbs Snakes Iguanas When molecular and morphological data contradict, molecular data takes precedence. No limbs Monitor lizard Eastern glass lizard

10 Cell A G division errora G 1 C C A T C A G T 2 C C A T C A G T C C C C Using DNA Homology to Construct Phylogenies 1 2 C C A T C A G A G C C A T C A G A G T G T A Insertion Deletion T C C 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 o computers are used to find the best alignment accounting for deletions, insertions, etc 1 C C A T C A A G T C C 2 C C A T G T A C A G A G 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 2 C C A T G T A C A G A A G G T T C C C C NOTE: Random chance would result in 25% homology between sequences, so true homology must be >25%.

11 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 clades are a monophyletic groups 1 A B Group I SHARED ANCESTRAL CHARACTERS (SAC) characters that originated before the clade C D E SHARED DERIVED CHARACTERS (SDC) F characters found only within the clade G

12 PARAPHYLETIC group consists of a single common ancestor and some (not all) of its descendants (b) Paraphyletic group A (c) Polyphyletic group A Common ancestor of even-toed ungulates Paraphyletic group Other even-toed ungulates Hippopotamuses 2 B C D E F Group II 3 B C D E F Group III Cetaceans Seals G G Bears POLYPHYLETIC group consists of organisms with more than 1 common ancestor Polyphyletic group Other carnivores

13 CHARACTERS Lancelet (outgroup) Lamprey Bass Frog Turtle Leopard 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 TAXA Lancelet (outgroup) Lamprey Vertebral column (backbone) Hinged jaws 4 walking legs Amnion Vertebral column Hinged jaws Four walking legs Bass Frog Turtle Hair Amnion Hair Leopard (a) Character table (b) Phylogenetic tree

14 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

15 Technique 3 1/C I 1/C I III Species I Species II Species III II III 1/C III II 1/C 1/C II I 1 Three phylogenetic hypotheses: I I III 4 2/T 3/A I 3/A 2/T I 4/C 3/A III II III III II II I 4/C 3/A 4/C II III 2/T 4/C 4/C III II 2/T 2/T 3/A II I 2 Species I Species II Site C C T T A T T C Results I II I III III II Species III Ancestral sequence A A G G A T C T III II I 6 events 7 events 7 events

16 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 Common ancestor of crocodilians, dinosaurs, and birds Lizards and snakes Crocodilians Ornithischian dinosaurs Saurischian dinosaurs Birds

17 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

18 Phylogenetic Branch Lengths can be used to Indicate the Degree of Genetic Differences Drosophila Lancelet Zebrafish Frog Chicken Human Mouse

19 Phylogenetic Branches can also Indicate Time Drosophila Lancelet Zebrafish Frog Chicken Human Mouse PALEOZOIC MESOZOIC CENO- ZOIC Present Millions of years ago

20 3. Evolutionary History Revealed in Genomes

21 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 species Speciation with divergence of gene Formation of paralogous genes: within a species Ancestral gene Species C Gene duplication and divergence Gene families result from repeated duplication of an original gene followed by subsequent mutation. Species A Orthologous genes Species B Paralogous genes Species C after many generations

22 Number of mutations 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. For example, the number sequence differences (i.e., nucleotide substitutions) in orthologous genes can reveal: Divergence time (millions of years) the amount of time that has passed since 2 species diverged from a common ancestor the amount of time that has passed since the gene was duplicated This is best determined with neutral mutations (mutations that are neither selected for or against).

23 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.

24 Cell division error Euglenozoans Forams Diatoms Current Model of the Tree of Life COMMON ANCESTOR OF ALL LIFE Ciliates Red algae Green algae Land plants Amoebas Fungi Animals Nanoarchaeotes Methanogens Thermophiles Proteobacteria (Mitochondria)* Chlamydias Spirochetes Gram-positive bacteria Cyanobacteria (Chloroplasts)* Domain Eukarya Domain Archaea Domain Bacteria 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

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