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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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recall evolutionary relationships are depicted in phylogenetic trees

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

a phylogenetic tree represents a hypothesis about evolutionary relationships
A phylogenetic tree represents a hypothesis about evolutionary relationships
  • Recall: how are trees constructed?
  • Trees are built using information from
    • Fossils
    • Morphology
    • Sequences
slide9

Relationships are inferred from the tips

    • One method is grouping by shared derived characteristics
slide10

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...
slide12

Each branch meets at a common ancestor

    • Why is it not correct to say humans evolved from chimps?
rooting trees
“Rooting” trees
  • Unrooted trees don’t give any information about the order of divergence
tree branch lengths can also reflect the amount of change on each branch
Tree branch lengths can also reflect the amount of change on each branch
  • DNA sequences accumulate mutations at a constant rate
recall sometimes morphological and sequence trees differ
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

morphological characteristics don t always reflect evolutionary relationships
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

slide19

Distantly related organisms can look similar

    • Morphology can be independently evolved

homology analogy

sequences can be problematic too
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

the problem with coi
The problem with COI
  • Not a neutral gene (violates assumption of ML method)
the problem with coi1
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

the problem with coi2
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/

slide27

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

why is phylogenetics important
Why is phylogenetics important?
  • Information about evolutionary relationships is necessary for all other research about evolution
tigriopus californicus a model for speciation
Tigriopuscalifornicus, a model for speciation

What is a species?

How do species come about?

recall independent reassortment and recombination occurs during meiosis
Recall: Independent reassortment and recombination occurs during meiosis

AAxBB

25% AA

50% AB

25% BB

slide34
Testing hypotheses about the evolution of hybrid breakdown: Mitochondria-nuclear incompatibilities should arise faster