Chapter 25: Phylogeny and Systematics

1. Valuable Information Can Be Derived From Classifying Organisms • A parasitic flatworm, Schistosoma, causes a blood infection in over 200 million people in S. America, Africa, China, Japan and Southeast Asia. • This flatworm inhabits two organisms during its lifecycle. • a freshwater snail for one part • people for another part. The larvae swim from the snail and penetrate the skin when a person is contact with infected water. The flatworm matures and lives in the abdominal blood vessels. It causes a slow death. Chapter 25: Phylogeny and Systematics

2. Intro: Schistosoma • For most of the 20th century only one species was known to infect humans, Schistosoma japonicum, transmitted by a single species of snail with the genus Oncomelania. • In the 1970’s, a different snail was discovered to be transmitting the parasite to human in the Mekong River in Laos. • Additional research into the types of snails in SE Asia lead to the conclusion that S. japonicum was actually a cluster of at least 6 species. • They found that the evolutionary diversification from an ancestor produced these modern snails. Three of these could host the Schistosoma. Ten have a genetic trait that allows them to resist invasion by the parasite.

3. Intro: Schistosoma • So biologists use this information to determine whether or not a newly discovered species is likely to be a host for the parasite. • Controlling the presence of just these types of snails and not all freshwater snails would then be undertaken. • Systematics, the process of inferring evolutionary relationships among organisms, allows us to: • determine the evolutionary relationships among the snails that are hosts. • determine the number of times the genes resisting infection in the snails arose.

4. How Are Phylogenetic Trees Reconstructed? • Evolutionary Agents Have Been At Work • Mutations • Migration of alleles or genetic drift • Natural Selection • Bottleneck Effect and Founder Effect • Phylogeny is the history of descent of a group of organisms from a common ancestor. • Through the process of speciation, we organize lineages of organisms as branching “trees.” • These phylogenetic trees show us the order in which lineages split.

5. Phylogeny • The phylogenetic trees are based on evolutionary changes in the traits of organisms. • Darwin noticed that closely related species, those that shared a common ancestor, were very similar. That is, they would share many characteristics that they inherited from the common ancestor. • Systematists expect traits inherited from a common ancestor in the distant pass to be shared by a large number of species. • The sharing of traits by a group of species indicates that they MAY be descendents of a common ancestor.

6. All present-day taxa descending from a common ancestor are shown at the right Phylogeny — Most Ancient Ancestor + Ancestor Snail The distance between branches means nothing — + Species that can transmit Schistosoma are shown as (+) + A split indicates a division of a population into two, forming new species. The red inhibit icons indicate evolution of genes blocking the transmission of Schistosoma to humans. — — — — The curves indicate nothing about evolution — — But the positions of the branches on the time axis tells us the order in which populations split. — —

7. Phylogeny • Homologous Traits • any two features descended from a common ancestral feature. • These features could be anatomical structures, behavior patterns, nucleotides in a DNA sequence • Traits that are shared by most or all organisms in any lineage being studied are likely to have been inherited relatively unchanged from an ancestor that lived very long ago. • All vertebrates have a vertebral column and fossil ancestral vertebrates also had one. Therefore it is homologous.

8. Phylogeny • Derived Traits • Derived traits differ from their ancestral form. • Evolutionists infer the state of the trait in some ancestor and then determine how it has been modified. This is not easy because: • Similar features may evolve similarly due to similar environmental pressures (Convergent Evolution). Wings of bats, birds evolved independently. • Similar developmental processes occurred in distantly related organisms. (Parallel Evolution). Wing development in butterflies and moths produce similar patterns on their wings. • Sometimes a character will revert from a derived state back to the ancestral one. (Evolutionary Reversals). Most frogs lack teeth on their lower jaw, but ancestors of frogs had teeth. One frog genus has re-evolved teeth in its lower jaw.

9. Phylogeny • Identifying Ancestral Traits • This is difficult because traits can become so different from the ancestral type. • One way to distinguish the ancestral trait from a derived trait is that the ancestral trait is not only in the group you are studying (focal group) but also in an outgroup, a lineage that branched off from the focal group below its base on an evolutionary tree. • Traits found only in the focal group then must be derived traits.

10. Phylogeny Reconstructing a Simple Phylogeny Derived Trait

11. Phylogeny • Hagfish are considered from distantly related to the other vertebrates than the other vertebrates are to each other. Hagfish will therefore be our outgroup. • Derived traits are those that have been acquired by other members since their separation from the hagfish. • Forming the Phylogenetic Tree • The chimpanzee and the mouse share two characteristics. These are absent in the outgroup and other species. Therefore we infer they are derived characteristics from a common ancestor. Fur; mammary glands Mouse Chimpanzee

12. Phylogeny • The pigeon has one unique trait- feathers. Crocodiles, pigeons, mice and chimpanzees all have 4-chambered hearts. So this evolved before the feathers. Crocodile 4-chambered heart Pigeon Feathers Fur; mammary glands Mouse Chimpanzee

13. Phylogeny • Claws and Nails are shared by lizards, crocodiles, pigeons, mice and chimpanzees so this structure was present in an ancestor of all of these organisms. Since lizards do not have 4-chambered hearts they diverged along a different lineage. lizards Claws/nails Crocodile 4-chambered heart Pigeon Feathers Fur; mammary glands Mouse Chimpanzee

14. Phylogeny • Lungs are common between salamander, lizards, crocs, pigeons, mice and chimps so lungs developed prior to these organisms. But the salamander does not have claws or nails. salamanders Lungs lizards Claws/nails Crocodile 4-chambered heart Pigeon Feathers Fur; mammary glands Mouse Chimpanzee

15. Phylogeny • Jaws are common between perch, salamander, lizards, crocs, pigeons, mice and chimps so lungs developed prior to these organisms. But the perch does not have lungs so it must have branched off. perch Jaws salamanders Lungs lizards Claws/nails Crocodile 4-chambered heart Pigeon Feathers Fur; mammary glands Mouse Chimpanzee

16. Phylogeny • Common ancestor had a vertebral column and the hagfish has no derived traits. Common Ancestor hagfish perch Jaws salamanders Lungs lizards Claws/nails Crocodile 4-chambered heart Pigeon Feathers Fur; mammary glands Mouse A particular trait appears after each branch point. Chimpanzee Feathers arose after the lineage leading to birds and crocodiles separated.

17. Phylogeny • Various Methods of Reconstructing Phylogenetic Trees • Parsimony Principle • The simplest hypothesis is preferred to explain the known facts. • This minimizes the number of evolutionary changes that need to be assumed for all the traits in a tree. • “The best hypothesis is the one that requires the fewest explanations using of :” • Convergent Evolution • Parallel Evolution • Evolutionary Reversals

18. Phylogeny • Various Methods of Reconstructing Phylogenetic Trees • 2. Maximum Likelihood Method • This uses molecular data • It uses computer programs to analyze mutation frequencies.

19. Traits Used in Reconstructing Phylogenies • Morphology and Development • Use the size and shape of body parts • Fossil record helps to differentiate between ancestral and derived traits. • Early developmental stages of many organisms are similar. • Sea squirts have a rod of tissue, the notochord, during their larval stage but it disappears when they are adults. Vertebrates also have this same rod of tissue so this supports the belief that sea squirts are more closely related to vertebrates than would be expected by examination of the adults alone.

20. Traits Used in Reconstructing Phylogenies (cont’d) • 2. Molecular Traits • Protein Structure • Determine the number of amino acids for a particular protein that have changed since the lineages have diverged. • DNA Base Sequences • Chloroplast genes are used extensively in the phylogenetic relationships among plants • Medina is used with animals. • 10,000 base pairs of nuclear DNA were sequenced of a nonfunctional sequence formed in early primate evolution by duplication of a hemoglobin gene. This revealed a new genus

21. A Phylogeny of Anthropoid Primates 622 Common Ancestor Spider Monkey (Ateles) 457 128 Rhesus monkey 199 Orangutan 150 94 70 Gorilla 92 14 Chimpanzee 76 Humans Numbers indicate the number of base-pair changes in the globin region of DNA. So humans and chimps share a more recent ancestor with each other than they do with gorillas.

22. Each taxonomic level is more general than the one below it. • Carolus Linnaeus devisedthis system to assign species to particular groups but he did not have an evolutionary theme in mind. Figure 25.7 Hierarchical classification • Taxon: simply a grouping of organisms at a given level. So a species is a taxon; so is a genus or a phylum.

23. Biological Classification and Evolutionary Relationships • Current Biological Classifications Reflect Evolutionary Relationships • Taxonomic groups should be monophyletic. • A monophyletic group is also called a clade which contains all the descendants of a particular ancestor and no other organisms. • A clade is a group of organisms that can be removed from a phylogenetic tree by one “cut” in the tree. Common Ancestor Common ancestor to D, E, F D E Common ancestor to E, F F

24. Biological Classification and Evolutionary Relationships • Polyphletic: A taxon consisting of members with more than one recent common ancestor. (B, C and D) A Common Ancestor B C D Common ancestor to A, B and C Common ancestor to B and C

25. Biological Classification and Evolutionary Relationships • Paraphyletic taxon includes some but not all descendants of a single ancestor A Common Ancestor B Common ancestor to A, B and C Common ancestor to B and C

26. Figure 25.9 Monophyletic versus paraphyletic and polyphyletic groups