Finish phylogenetic inference

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Lecture 15

• Finish phylogenetic inference
• Review
• Species identification
• Cryptic species
• Hybridization
• Mid-term exam

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Tree Building Methods

• Distance based
• Calculate distance between OTUs
• Construct tree
• Advantages
• Computationally efficient
• Can use more characters
• Can include biases
• Base composition bias
• Transitions / transversions
• Codon position bias
• Disadvantage
• Information loss
• reduced to distance
• Examples
• UPGMA
• Neighbor-joining
• Minimum Evolution

• Character based
• Use ind. characters to construct trees
• Advantages
• Fewer assumptions
• Direct use of data
• No loss of information
• Disadvantages
• Computationally intensive
• Can only use shared derived characters
• Examples
• Maximum Parsimony
• Maximum Likelihood

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Types of characters

• Informative for Maximum Parsimony and distance
  methods
• Synapomorphies
• Informative for distance methods
• Autapomorphies
• Uninformative
• Symplesiomorphies

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Genetic distance trees
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Maximum Parsimony

• Parsimony
• Simplest explanation is the best
• Choose tree which can be explained by fewest
  steps
• For example lungs and swim bladders

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Maximum Parsimony
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Bootstrap analysis

• Resampling of characters
• With replacement
• Characters may be sampled several times
• Repeat 1000 times
• Reconstruct phylogeny
• 1000 trees
• Construct consensus tree
• Indicate how often specific groups occur

Second replicate
First replicate
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Bootstrap analysis
Indicates how well a tree is supported by data
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Key Concepts and Review

• Phylogenetic Inference
• Genealogies ? species trees
• How to read a tree
• Parts of a tree
• Rotation
• Rooting
• Reconstruction
• Lots of possible trees
• Alignment

• Tree building methods
• Distance based
• UPGMA, Neighbor Joining, Minimum Evolution
• Character based
• Maximum parsimony, Maximum likelihood
• Types of characters
• Synapomorphies
• Autapomorphies
• Symplesiomorphies
• Potential problems
• Homoplasy and saturation
• Bootstrapping

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Species identification, cryptic species and
hybridization

• Species identification
• Cryptic species
• Hybridization

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Rockfish species identification

• Fillets
• Done in lab
• RFLP
• Generally important
• Often included in guides
• Isoelectric focussing of proteins
• Pacific Ocean Perch, Sebastes alutus
• http//www.cfsan.fda.gov/frf/rfe0.html
• Larvae
• Difficult to identify morphologically
• Molecular identification of larvae
• Allozymes, RFLP or PCR presence/absence
• Problem?

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Species ID using matching techniques

• May not detect species differences
• Depends on
• number of loci
• Number of restriction enzymes
• E.g. Sebastes carnatus S. chrysomelas
• Not distinguishable with allozymes
• May not cover all intraspecific variation
• Reference samples only local
• Significant population structure
• E.g. Pacific Ocean Perch, Sebastes alutus
• Population structure around Vancouver Island
• Have to be careful with interpretation
• Better in a phylogenetic context

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Identification of whale meat

• IWC ban on whaling
• Whaling continued for scientific purposes
• Japanese reports mainly show minke whales
• Molecular study
• Baker Palumbi 1994
• CITES restrictions on export of whale products
• PCR in portable lab in hotel room
• Removed template DNA
• No whale product exported
• Sequenced D-loop
• Most variable region

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Identification of whale meat

• Well resolved phylogeny
• High bootstrap values
• IWC reports of southern hemisphere minke whales
• Most samples
• Some from northern hemisphere
• Hunted only by Norway
• Export restrictions
• Some samples fin whales
• Not hunted since 1989
• Humpback whales
• Hunt prohibited since 1966
• Unambiguous demonstration of illegal hunting /
  import
• Usable because of observation of CITES rules

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Noninvasive species ID from shed material

• Possible from
• Feces
• Producing species
• Food species
• Hairs
• Bones
• Important for conservation issues
• E.g otter in Denmark
• Scat difficult to identify
• Molecular identification
• mtDNA cyt b
• Surprises in distribution of otter and mink

European otter (endangered)
North American mink (introduced)
Polecat
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Parasite diagnosis

• Dog heartworm
• Major dog disease in US
• Caused by filarial worm
• Mosquito intermediate hosts
• Difficult to find larvae in mosquitoes
• Amplification of 16S rRNA gene
• Species specific primers
• Very sensitive assay
• Potential problem?

Watts et al. (1999)
Parasites 10 5 1 0 pos.
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Identification of parasites

• Cestode parasites
• Live in guts of fish
• Cyathocephalus truncatus
• Life history stages
• eggs
• Procercoid
• Cysticercoid
• difficult to identify
• Sequencing of 18S rDNA
• Identified procercoids in amphipod
• Established intermediate host

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Cryptic species

• Cryptic species
• Morphologically very similar
• Still different species
• No interbreeding
• Bonefishes
• Circumtropical distribution
• mtDNA cyt b
• Three known species collected
• Poss. 5 additional species
• Important for
• Management
• Conservation
• Evolutionary biology

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Hybridization

• Evolutionary significance
• Interactions between selection and gene flow
• Possibly speciation
• Conservation significance
• Protection of threatened species
• Introduced species
• May lead to introgression
• Continued hybridization and back crosses
• Hybrid zones
• Steep clines in
• allele frequencies
• Morphological characters

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Hybrid Zones

• European toads
• Steep cline
• Allozyme loci
• Morphological characters
• Lower fitness of hybrids
• tension zone
• Genomic incompatibility
• Some migration across hybrid zone

Futuyma 1998
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Hybrid zone in European house mice

• Two species in central Europe
• Tight hybrid zone N-S
• Free interbreeding
• Asymmetrical introgression
• domesticus ? musculus
• Discordance between nuclear and mtDNA pattern
• Influx of females
• Continued backcrossing to M musculus males
• Higher parasite susceptibility of hybrids
• Lower fitness

Avise 1994
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Hybridization as speciation mechanism?

• Generally accepted in plants
• Not so much in animals
• Recent evidence
• Lake Tanganyika cichlids
• N marunguensis have mtDNA haplotypes from both
  parental species
• Now separate species
• Also in rockfish
• NW Atlantic

Neolambrologus olivaceus
Neolambrologus helianthus
Neolambrologus marunguensis
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Key Concepts

• Species identification
• Matching markers
• RFLP, allozymes
• Potential problems
• Identification in phylogenetic context
• Whale meat
• Parasite and disease diagnosis
• Detection of infection
• Identification of intermediate hosts
• Identification of cryptic species

• Hybridization
• Significance
• Evolutionary biology
• Conservation
• Introgression
• Hybrid Zones
• Hybrid fitness
• Asymmetrical introgression
• mtDNA vs nuclear DNA
• Speciation by hybridization
• Mainly plants
• Also animals

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Mid-term exam

• Distribution
• Reading
• Chapter of new book by Trevor Beebee (UK)
• Please provide feedback
• Understandable
• Covers the subject
• Anything else
• Homepage
• Grading key for term paper
• Handout on writing