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Comparative methods wrapup and some thoughts on the future of systematics

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Comparative methods wrap-up and some thoughts on the future of systematics ... Implemented in SimMap (brahms.ucsd.edu/simmap.html) Other uses of phylogenies ... – PowerPoint PPT presentation

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Title: Comparative methods wrapup and some thoughts on the future of systematics


1
Comparative methods wrap-up and some thoughts on
the future of systematics
2
The study of character evolution
  • Many methods allow one to study the evolution of
    single traits or pairs of potentially correlated
    traits, given a phylogeny
  • What do we do about phylogenetic uncertainty?

3
One approach
  • Repeat the analysis over a number of plausible
    trees and see if the results are robust to
    phylogenetic uncertainty

4
A better approach
  • Treat the phylogeny as a nuisance parameter
  • E.g., estimate the posterior probability of two
    traits being correlated, given the trait data,
    some sequence data for the same species, a model
    for the evolution of traits and sequences, and
    priors on all the parameters

5
Stochastic mappingHuelsenbeck et al. (2004)
Syst. Biol.
  • Use a posterior distribution of trees
  • Simulate evolution up each tree (only keeping
    simulations that arrive at the observed data)
  • Look at the simulations to see if they show
    evidence of directionality, correlated evolution,
    etc.
  • Implemented in SimMap (brahms.ucsd.edu/simmap.html
    )

6
Other uses of phylogenies
  • Estimating dN/dS ratios (and how they differ from
    lineage to lineage)
  • Studying community assembly in ecology
  • Quantifying phylogenetic diversity for
    conservation biology
  • Look for evidence of changed rates of
    diversification

7
Detecting changes in the rate of species
accumulation
  • Under a constant rate of speciation (with no
    extinction), which of the following trees is more
    likely?

8
Explanation
What is the probability that the next speciation
event will be on the A side?
B
A
9
Explanation
Now what is the probability that the next
speciation event will be on the A side?
B
A
10
The counterintuitive result
  • All basal splits equally likely e.g., for 100
    taxa, a 199 basal split is as likely as a 5050
    split
  • What can we learn?

11
How can one study changes in diversification rate?
  • Take account of time if the delay until the
    second speciation (t) is long, then acceleration
    in the ingroup is implied (Sanderson and Donoghue
    1994 Science)

t
t
12
How can one study changes in diversification rate?
  • Look for a repeated pattern that trait x
    correlates with clades that are bigger than their
    non-x sister groups
  • Provides evidence that the character is a key
    innovation

13
Trends in Phylogenetics
  • The field has matured from one driven by
    algorithmic approaches to ones based on explicit
    statistical approaches
  • Phenetics-gt Parsimony-gt Likelihood-gt Bayesian
    phylogenetics

14
What can we hope for in the future? - empirical
  • Easier data collection - data sets with more
    sequences and more species
  • Phyloinformatics resources to collate the results
    of phylogenetic studies and build a comprehensive
    tree of life

15
What can we hope for in the future? - theoretical
  • More sophisticated (and realistic models) of
    molecular evolution
  • Simultaneous alignment and phylogenetic inference
  • Methods that do not assume a singe true tree for
    the whole genome
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