BIOL105 LECTURE 6: Adaptive and the Comparative Method

adaptation

• a feature which has evolved via natural selection because it enhances darwinian fitness in a given environment

darwinian fitness

the ability of organisms to survive and/or reproduce = lifetime reproductive success

T/F: individuals do not evolve

TRUE

• no change that happens in the DNA sequence within an individual is passed on to their offspring

• genetic material of an individual including within its gametes can be modified by epigenetic mechanisms

burden of proof

• selection and adaptation should be considered “innocent until proven guilty”

preadaptation

• possession of the new necessary properties to permit a shift into a new ecological niche or habitat

4 general approaches to study adaptation

1. comparisons of species

2. biology of natural populations

3. selection experiments and experimental evolution

4. comparison of real organisms with predictions of theoretical models

1. comparison of species (or populations)

• the comparative method

• shows what has happened in past evolution

2. biology of natural populations

• extent of individual variation (repeatability)

• heritability and genetic correlation

• natural and sexual selection

• field manipulations and introduction

• shows present evolution in action

3. selection experiments and experimental evolution

• shows experimentally what might happen during further evolution

• allows direct tests of evolutionary hypotheses

• used by darwin

4. comparisons of real organisms with predictions of theoretical models

• shows how close selection can get to producing optimal solutions

steps to the comparative method

1. obtain phylogeny from independent sources (ex: DNA seq)

2. obtain data on one or more phenotypic traits of interest

3. A- map traits onto tree and use maximum parsimony to infer how many changes have occurred and where on the tree
   B- compare species and/or traits by the use of statistical methods that incorporate phylogenetic information

sampling schemes for comparing species

1. do two species differ in the predicted direction? (not adequate, not enough data)

2. do multiple sets of species pairs differ in the prediction direction? (fine, doesn’t use all the data)

3. does the expected relationship hold across many species? (requires phylogenetically informed statistical methods)

limitations of two-species comparative studies

• the species may differ in many ways and for many reasons, in addition to the one that is of interest

• the species almost always will differ (due to drift, different environmental conditions, speciation)

  degrees of freedom for correlating traits with environment is N-2=0 (can’t do statistical test)

• comparison of only two species would mot allow for inference concerning which state was ancestral

steps to compare multiple species

1. develop question/hypotheses

2. measure several species (and/or populations for some phenotypic trait(s); calculate means

3. characterize environmental features that should indicate variation in the ‘selective regime’

4. relate phenotypic to environmental variation: evidence for adaptations(sexual selection, functional relations, trade-offs)

statistical consequences of ignoring phylogenetic relatedness

1. type 1 errors (inflated if species are treated as independent, null hypothesis rejected too often)

2. power (ability to direct relationships is affected)

3. estimates of correlations, slopes, or group differences will be inaccurate

phylogenetically based analytical methods allow one to:

• avoid statistical problems caused by non-independence

• learn from data (infer ancestral states, compare rates of evolution across lineages or across traits)

• test for “outlier” species

phylogenetic independent constrats (felsenstein)

• first fully phylogenetic method; can use any topology and branch lengths

• applicable to all types of statistical analyses (correlation, regression, pca, etc)

• compe with incomplete phylogenetic info, including arbitray branch length, various types of trait ev

phylogenetic signal

• tendency of related species to resemble each other