Lecture 4: Phylogeny and the Tree of Life Campbell: Chapter 26

All life is interconnected by descent Humans Rattlesnake Pine tree Amoeba Bacterium How to determine the pattern of descent?

Systematics - field of biology dealing with diversity and evolutionary history of life Includes Taxonomy: DINC Description Identification Nomenclature Classification Goal: Determine Evolutionary History (Phylogeny) of Life

Description = assign features Character = a feature (e.g., “petal color”) Character states = two or more forms of a character (e.g., “red,” “white”).

Identification = associate an unknown with a known How? One way: Taxonomic Key, e.g., Tree Leaves simple …….………………………… Species A Leaves pinnate …….………..…..…..…… Species B Herb Flowers red …….…………………………… Species C Flowers white …….…………………..…… Species D

Nomenclature Naming, according to a formal system. Binomial: Species are two names (Linnaeus): E.g., Homo sapiens Homo = genus name sapiens = specific epithet Homo sapiens = species name

Nomenclature Hierarchical Ranks: Domain Kingdom Phylum Class Order Family Genus Species

Classification Placing objects, e.g., life, into some type of order. Taxon = a taxonomic group (plural = taxa).

How to classify life Phenetic classification Based on overall similarity Those organisms most similar are classified more “closely” together.

Problem with phenetic classification: Can be arbitrary, e.g., classify these:

Phylogenetic classification Based on known (inferred) evolutionary history. Advantage: Classification reflects pattern of evolution Classification not ambiguous

= representation of the history of life

Ingroup – group studied Outgroup – group not part of ingroup, used to “root” tree

Branch point (node) Taxon A Taxon B Sister taxa Taxon C ANCESTRAL Fig. 26-5 Branch point (node) Taxon A Taxon B Sister taxa Taxon C ANCESTRAL LINEAGE Taxon D Taxon E Taxon F Common ancestor of taxa A–F Polytomy

Apomorphy (derived trait) = a new, derived feature E.g., for this evolutionary transformation scales --------> feathers (ancestral feature) (derived feature) Presence of feathers is an apomorphy for birds.

Taxa are grouped by apomorphies Apomorphies are the result of evolution. Taxa sharing apomorphies underwent same evolutionary history should be grouped together.

Principle of Parsimony That cladogram (tree) having the fewest number of “steps” (evolutionary changes) is the one accepted. Okham’s razor: the simplest explanation, with fewest number of “ad hoc” hypotheses, is accepted.

Other methods of phylogeny reconstruction: Maximum Likelihood or Bayesian analysis Uses probabilities Advantage: can use evolutionary models.

Sequentially group taxa by shared derived character states (apomorphies) Lancelet (outgroup) (outgroup) Lancelet Salamander Lamprey Leopard Lamprey Tuna Turtle Vertebral column (backbone) Tuna 1 1 1 1 1 Vertebral column Hinged jaws 1 1 1 1 Salamander Hinged jaws CHARACTERS Four walking legs 1 1 1 Turtle Four walking legs Amniotic (shelled) egg 1 1 Amniotic egg Leopard Hair 1 Hair (a) Character table (b) Phylogenetic tree Fig. 26-11

DNA sequence data – most important type of data 1 Deletion 2 Insertion Fig. 26-8a

DNA sequence data - alignment 3 Fig. 26-8b 4 Each nucleotide position = Character Character states = specific nucleotide

Homology Similarity resulting from common ancestry. E.g., the forelimb bones of a bird, bat, and cat.

Homoplasy (analogy) Similarity not due to common ancestry Reversal – loss of new (apomorphic) feature, resembles ancestral (old) feature. Convergence (parallelism) – gain of new, similar features independently.

Convergent evolution: spines of cacti & euphorbs Cactus Euphorb

Convergent evolution: spines of cacti & euphorbs euphorb spines cactus spines

* * Leg-less lizards Snake Both examples of reversal within Tetrapods: loss of a derived feature – forelimbs. legged lizards leg-less lizards snakes * * Example of convergence relative to one another! Independently evolved. *= loss of legs gain of legs (Tetrapods)

Convergent evolution: wings of some animals evolved independently

Convergent evolution: Australian “mole” and N. Am. “mole” Fig. 26-7 Convergent evolution: Australian “mole” and N. Am. “mole”

Orthology – genes homologous Gene Duplication can occur! Ancestral gene Ancestral species Speciation with divergence of gene Orthology – genes homologous Orthologous genes Species A Species B (a) Orthologous genes Species A Gene duplication and divergence Paralogy – genes not homologous Paralogous genes Species A after many generations (b) Paralogous genes Fig. 26-18

Monophyletic Group a group consisting of: a common ancestor + all descendents of that common ancestor

C B F E D A Cladograms can be “flipped” at nodes, show same relationships

One can date divergence times with molecular clock and fossils Fig. 26-13 One can date divergence times with molecular clock and fossils Drosophila Lancelet Zebrafish Frog Chicken Human Mouse PALEOZOIC MESOZOIC CENOZOIC 542 251 65.5 Present Millions of years ago

Relationship = recency of common ancestry i.e., taxa sharing a common ancestor more recent in time are more closely related than those sharing common ancestors more distant in time.

Example: Are fish more closely related to sharks or to humans?

Example: Are crocodyles more closely related to lizards or to birds?

Lizards & Turtles Snakes Crocodiles Birds

Lizards & Turtles Snakes Crocodiles Birds

Is “E” more closely related to “D” or to “F”? Is “E” more closely related to “B” or to “A”? Is “E” more closely related to “B” or to “C”? C B F E D A

Is “E” more closely related to “D” or to “F”? Is “E” more closely related to “B” or to “A”? Is “E” more closely related to “B” or to “C”? C B F E D A Answers: F, B, neither (equally to “B” & “C”)

Paraphyletic group Consist of common ancestor but not all descendents Paraphyletic groups are unnatural, distort evolutionary history, and should not be recognized.

Lizards & Turtles Snakes Crocodiles Birds

“Reptilia” here paraphyletic Lizards & Turtles Snakes Crocodiles Birds

Re-defined Reptilia monophyletic Lizards & Turtles Snakes Crocodiles Birds

Dinosaurs Lizards & Turtles Snakes Crocodiles Birds

Did humans evolve from apes? Importance of a name: Did humans evolve from apes?

Orangutan Gorilla Chimpanzees Humans

Pongidae “Great Apes” Hominidae Orangutan Gorilla Chimpanzees Humans

Pongidae “Great Apes” Pongidae or Hominidae Orangutan Gorilla Chimpanzees Humans

Pongidae or Hominidae Orangutan Gorilla Chimpanzees Humans

Pongidae or Hominidae Orangutan Gorilla Chimpanzees Humans

We are human, but we are also apes. We share unique human features. We also share features with other apes (and with other animals, plants, fungi, bacteria, etc.). Humans didn’t evolve from apes, humans are apes.

All of life is interconnected by descent.

There are no “higher” or “lower” species.

Importance of systematics & evolution: 1) Foundation of biology - study of biodiversity 2) Basis for classification of life 3) Gives insight into biological processes: speciation processes adaptation to environment 4) Can be aesthetically/intellectually pleasing!