PHYOGENY & THE Tree of life

1. PHYOGENY & THE Tree of life Campbell and Reece, Chapter 26

2. definitions Phylogeny Systematics • The evolutionary history of a species or group of species • Discipline focused on classifying organisms & determining their evolutionary relationships

3. Taxonomy • how organisms are classified and named • each step called a taxon(plural: taxa)

4. BINOMIAL NOMENCLATURE Man’s Genus species: Homo sapiens • used to avoid ambiguity • the Latin scientific name for each individual species • is the Genus species portion of taxonomy

5. 3 DOMAINS • DOMAIN ARCHAEA • Prokaryotes • many live in Earth’s extreme environments • as molecularly close to eukaryotes as Domain Bacteria • includes multiple kingdoms

6. (notice position of domain Archaea)

7. Domain Archaea methanogen thermophile

8. Domain Bacteria • Prokaryotic • very diverse group • use every major mode of nutrition & metabolism • beneficial: photoautotrophs, alcoholic fermentation, Vit K production • pathologic: strep throat, flesh-eating disease, ulcers, Rheumatic fever

9. Domain Bacteria Gram Positive Bacteria Stretococcus Gram Negative Bacteria Legionellapneumophilia

10. Domain Bacteria Spirochetes

11. Domain Eukarya • Eukaryotic cells • more complex, become specialized • able to form multicellular organisms • greatest diversity

12. Domain Eukarya Plants Fungi

13. Domain Eukarya Animal Protozoa

14. Domain Eukarya Algae Cells Algae

15. Linnean Classification

16. PHYLOGENETIC TREES • show the evolutionary history of a group of organisms • represented by a branching diagram • each branch point represents the divergence of 2 evolutionary lineages from a common ancestor

17. Phylogenetic Trees Branch Point

18. sister taxa • basal taxa

19. What you cannot learn Phylogenetic Trees What you can learn • patterns of descent • common ancestors • does not show phenotypic similarity • cannot tell ages of species based on where branches are in the “tree” • Sister taxa did not evolve from each other; they have a common ancestor (that could be extinct)

20. Uses of Phylogenetic Tree If “close” relatives found they could be source of beneficial alleles that could be transferred to hardier taxa via genetic engineering 2. Using DNA samples are now able to differentiate legal species from illegal species of whale, tuna

21. Phylogenies are inferred from morphological & molecular data • Homology: similarity in characteristics resulting from a shared ancestry

22. Homologous Chromosomes in same species • When chromosomes duplicate in S Phase of Cell Cycle see genes in same loci of each sister chromatid

23. Homologous Chromosomes across Species with Common Ancestor • Genes or certain DNA sequences can also be homologous if they descended from sequences carried by a common ancestor

24. Organisms that share very similar morphologies or DNA sequences are likely to be more closely related than organisms with vastly different structures • There are examples of organisms that look very different but have very similar DNA sequences because species underwent adaptive radiation.

25. Homology vs. Analogy • Analogy is similarity due to convergent evolution: occurs when similar environmental pressures & natural selection produce similar (analogous) adaptations even though organisms have different ancestors.

26. homoplasies: analogous structures that arose independently (Greek: to mold in same way) • Examples: • bird & bat wing: their common ancestor did not fly

27. The more complex the structure found in 2 species the more likely it is that they have a shared ancestor

28. Molecular Evidence of Evolutionary Relationships • DNA sequence similaritieshave been documented among prokaryotes & eukaryotes: (comparative genomics) • High degree of sequence similarity noted in some eukaryotic nuclear genes to Archaea & mitochondrial genes are similar to Bacteria

29. Using DNA to map an organism’s evolutionary history • The more recently 2 species have branched from a common ancestor, the more similar their DNA sequences should be • The longer ago 2 species have been on separate evolutionary paths, the more their DNA should have diverged

30. Different genes evolve at different rates Nuclear DNA Mitochondrial DNA • changes slowly • useful for investigating relationships between taxa that diverged hundreds of millions of yrs ago • evolves rapidly • useful to investigate more recent evolutionary events

31. Eukaryotic genes consist of numerous coding regions (exons) that are separated by noncoding regions (introns) • Both are transcribed into pre-mRNA and then intron sequences are removed

32. In humans 90% of the exons are homologous to exons found in Drosophila & Caenorhabditis (nematode worms

33. Puffer Fish is vertebrate with smallest known genome (1/7th human genome) & yet has all exons present in humans • In chromosomes “homologous” means sequences are so similar that they are not likely due to chance so are considered the result of common ancestry

34. Duplication in human genome • both of genes & chromosome segments

35. Based on these duplications & new combinations of exons it seems that • the vertebrate evolution has required very few new proteins • evolutionary change involves making new genes by rearranging functional domains into novel combinations (called “exon shuffling”)

36. Exon Shuffling • Important source of genetic variation (in addition to mutations & crossing over) • Still investigating mechanism

37. Homologous Genes • 60% of human genes that encode proteins are homologous to genes from other organisms • The high degree of conservation of both genes & exons among widely diverse organisms from all 3 Domains is strong evidence for their common ancestry

38. Nonfunctional Sequences • Another bit of strong evidence for relatedness among diverse organisms is the similarity in DNA sequences that have no apparent function. • One category of these are pseudogenes

39. Pseudogenes 2 kinds: • 1. arises from DNA replication  mutations  STOP codons in one of duplicates; other no mutation • 2. Processed Pseudogenes: arise during transcription or translation: lack a promoter sequence so cannot be transcribed

40. To date, 2909 pseudogenes in human genome

41. Other functionless DNA LINEs SINEs • Long Interspersed Nucleotide Element • Families: 1,2,3 • Are retrotransposons • Short Interspersed Nucleotide Element • Also 3 families in humans • Specific LINEs & SINEs found only in cloven-hooved mammals & whales

42. Retroviruses • RNA virus • Infects cell and turns its single strand  double strand which inserts into host genome

43. RetrovirusRetrotransposon • Retrovirus inserts self into host genome but somewhere along the way genes for capsids lost • If LINEs in different species are homologous it is considered to be strong evidence that these 2 species share a common ancestor where that particular LINE first became established

45. Review: • Phylogeny can be inferred from • –the fossil record, • –morphological homologies, and • –molecular homologies

46. Phylogenetic trees are used to depict hypotheses about the evolutionary history of a species • Shared characters are used to construct phylogenetic trees • Shared ancestral characters group organisms into clades • Shared derived characters distinguish clades & form branching points in the tree of life

47. Shared Characteristics are used to Construct Phylogenetic Trees • Cladistics: an approach to systematics in which organisms are placed into groups based primarily on common descent • Clades: groups organisms are placed in • 1 clade will include ancestor & all its descendants • 3 types:

48. 1. Monophyletic Group • equivalent to a clade • ancestral species & all its descendants

49. 2. Paraphyletic Group • consists of an ancestral species & some of its descendants

50. 3. Polyphyletic Group • Some members of this group will have different ancestors