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Phylogenetics and classification

Phylogenetics and classification. Taxonomy: the classification of living organisms. Historically, classification was hierarchical. Phylogeny: Classification using evolutionary relationships. Species. Order. Family. Genus.

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Phylogenetics and classification

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  1. Phylogenetics and classification

  2. Taxonomy: the classification of living organisms

  3. Historically, classification was hierarchical

  4. Phylogeny: Classification using evolutionary relationships

  5. Species Order Family Genus Recall: Evolutionary relationships are depicted in phylogenetic trees Pantherapardus Panthera Felidae Taxidea taxus Taxidea Carnivora Mustelidae Lutra lutra Lutra Canis latrans Canidae Canis Canis lupus Figure 26.4

  6. Different ways of depicting trees

  7. A phylogenetic tree represents a hypothesis about evolutionary relationships • Recall: how are trees constructed? • Trees are built using information from • Fossils • Morphology • Sequences

  8. Relationships are inferred from the tips • One method is grouping by shared derived characteristics

  9. Statistical methods • Maximum parsimony • What is the least number of steps needed to map all derived characters onto a tree? • Maximum likelihood • Given what we know about how sequences evolve, a tree can be found that reflects the most likely sequence of evolutionary events • Bayesian Inference, UPGMA, Neighbor-joining, etc...

  10. Parts of a phylogenetic tree

  11. Each branch meets at a common ancestor • Why is it not correct to say humans evolved from chimps?

  12. A monophyletic group of species includes an ancestral species and ALL of its descendents

  13. “Rooting” trees • Unrooted trees don’t give any information about the order of divergence

  14. Tree branch lengths can also reflect the amount of change on each branch • DNA sequences accumulate mutations at a constant rate

  15. Recall: Sometimes morphological and sequence trees differ Morphology-based phylogeny indicates two bilaterian clades: deuterostomes and protostomes Molecular phylogeny Indicates 3 bilaterian clades: Deuterostomia, Lophotrochozoa , Ecdysozoa **Based on nucleotide sequences of small subunit ribosomal RNA

  16. Trees are hypotheses (best guess given the current information)

  17. Morphological characteristics don’t always reflect evolutionary relationships • Closely related organisms can look different • Small changes in genes can lead to large morphological changes http://www.nature.com/hdy/journal/v97/n3/full/6800872a.html

  18. Distantly related organisms can look similar • Morphology can be independently evolved homology analogy

  19. Sequences can be problematic too • Incomplete lineage sorting http://sciblogs.co.nz/the-atavism/2012/03/15/chimps-are-our-closest-relatives-but-not-for-all-of-our-genes/ http://www.nature.com/nature/journal/v483/n7388/full/nature10842.html

  20. Sequences can mutate “back”

  21. Case study: Mitochondrial COI, a barcode for species identification

  22. The problem with COI • Not a neutral gene (violates assumption of ML method)

  23. The problem with COI • Too conserved for some taxa (not enough information to resolve relationships) http://www.poriferabrasil.mn.ufrj.br/iss/09-book/pdf/Heim%20et%20al%20-%20Molecular%20markers%20for%20species%20discrimination%20in%20poriferans.pdf

  24. The problem with COI • mtDNA is “leaky” between species http://whyevolutionistrue.wordpress.com/2012/07/24/a-new-study-of-polar-bears-underlines-the-dangers-of-reconstructing-evolution-from-mitochondrial-dna/

  25. Multiple genes are needed to reconstruct evolutionary relationships

  26. Trees are hypotheses (best guess given the current information)But hypothesis can be repeatedly tested and the best ones have support from multiple lines of evidence

  27. Why is phylogenetics important? • Information about evolutionary relationships is necessary for all other research about evolution

  28. Tigriopuscalifornicus, a model for speciation What is a species? How do species come about?

  29. Hybrid incompatibility arises when genes accumulate mutations in isolation

  30. Recall: Independent reassortment and recombination occurs during meiosis AAxBB 25% AA 50% AB 25% BB

  31. Genetics underlying hybrid incompatibility – the search for “speciation genes”

  32. Testing hypotheses about the evolution of hybrid breakdown: Mitochondria-nuclear incompatibilities should arise faster

  33. Snowball theory: speciation rate increases with divergence

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