Lecture 6: Adaptation and Comparative Method

Phylogenetic trees are used to study…

the evolution of phenotypic characteristics (traits) of organisms

True or false: One major thing that we do with phylogenies is study adaptation

True

Adaptation

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

• A process of genetic change within a population, because of natural selection, by which the average value of a character becomes improved with respect to a specific function.

Darwinian fitness

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

Tails of male peacocks are..

excluded by most biologists as an adaptation because this feature evolved by sexual selection

What is a result of natural selection in producing an adaptation?

Organisms evolve to become better at doing particular things, such as resisting the cold, finding food, and avoiding predation

Adaptation can be perceived at various levels, from gene to population corresponding to selection at any of these levels

• Gene selection

• Individual (natural selection)

• Group selection

• Kin selection

  • Intragenomic selection

Physiological adaptation

individual’s phenotypic adjustment to environmental conditions occurring during ontogeny, as in acclimation, physical conditioning (learning, sensitization, habituation, recalibration of reward system, addiction)

True or false: With physiological adaptation, individuals do not evolve since there is no change in DNA sequence within an individual that is passed onto their offspring

True

Epigenetic mechanisms

Genetic material of an individual, including within its gametes, can be modified and can affect offspring (even for more than one generation)

• Ex: DNA methylation, histone modification

True or false: The ability to adapt physiologically to changing conditions is itself adaptive in the evolutionary sense

True

The extent of “phenotypic plasticity” varies among…

organisms

Traits within organisms vary in plasticity. What is an example?

• Muscle is more plastic than the lung. Muscle can change more in response to environmental stimuli.

How common is evolutionary adaptation?

Adaptations are expected to be exceedingly common

Selection is always occurring, so all aspects of the phenotype are constantly evolving towards state of better adaptation.

The major directive force in evolution

natural selection

• because it is inevitable by phenotypic variation, variation affecting Darwinian fitness, and heritability of traits

How has studying adaptation used different methods than the common scientific method?

Biologists first assume that all traits are adaptive and show how they are adaptive.

• Usually, the null hypothesis is that the trait is not an adaptation + alternative hypothesis

Burden of proof

should be on demonstrating adaptation

In addition to natural selection, the main factors that affect phenotypic variation are..

1. Random mutation and genetic drift

2. Immigration/ emigration and gene flow

3. Sexual selection

These factors work to counter natural selection (by decreasing the value of one trait)

What does it mean when variation in some aspects of a phenotype are neutral?

It doesn’t matter with respect to natural selection.

• Ex. The amount of hair on the back of your fingers does not affect your Darwinian fitness

True or false: Selection and adaptation should probably be considered “innocent until proven guilty”

True. Do not assume everything is an adaptation

How can we recognize adaptions? Demonstrating adaptations involves…

1. Specifying the selective agent or agents (ex. predators) that favor a trait

2. Showing that the trait in question has evolved via this assumed natural selection by origin (historical) or maintenance (current function)

3. Elucidating the components of, and the sequence of steps to, the final (complex) adaptive state

True or false: Adaptations can be defined based on current function and utility and/or historical origin

True

Preadaptation

Possession of the necessary properties to permit a shift into a new ecological niche or habitat (with evolution of a new function)

T/F: A structure is preadapted for a new function if it can assume that function without evolutionary modification

T

T/F: Lobe-finned fishes were preadapted for walking on land

T

How are reptiles preadapted for arid conditions?

• Low evaporative water loss because of impermeable skin and low metabolic rate

• Produce uric acid (low water lsos)

  • Cleidoic (amniotic) eggs can be laid away from waterT

Teolology

the explanation of phenomena in terms of the purpose they serve rather than of the cause by which they arise.

Four general approaches to studying adaptation

1. Comparisons of Species (or populations)/ Comparative Method - show what has happened in past evolution

2. Biology of natural populations - natural selection in action caused by extent of individual variation (repeatability), heritability and genetic correlation , and natural and sexual selection

3. Selection Experiments and Experimental Evolution - shows, experimentally, what might happen during future evolution. Tests evolutionary selection.

4. Comparison of Real Organisms with Predictions of Theoretical Models - shows how close selection can get to producing optimal solutions

What are the four problems with/ limitations of 2-species comparative studies?

1. Independent variable is confounded with species (lineage) membership

2. Species almost always will differ

3. Degrees of freedom for correlating trait with environment = N-2 = 0

4. Comparison of only two species would not allow inference concerning which state was ancestral.

Comparing Multiple Species: General Procedure

1. Develop questions or hypothesis

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

3. Characterize environmental features that should indicate variation in the “selective regime”

4. a. Relate phenotypic to environmental variation: evidence for adaptation?

   b. Relate traits to each other: evidence of sexual selection?
   c. Relate traits to each other: elucidate functional relations, trade-offs, etc

Interspecific (multiple species_ comparative studies are very useful, but they face a basic statistical problem:

related species tend to resemble each other, so they do not necessarily represent independent pieces of evidence

Statistical Consequences of Ignoring Phylogenetic Relatedness

• Type I error rates: will be inflated if species are treated as independent: null hypothesis will be rejected too often

• Power: (ability to detect relationships) will be affected

• Estimates: of correlations, slopes or group differences will be inaccurate

Phylogenetically Based Analytical Methods Allow One to:

1. Avoid statistical problems caused by non-independence

2. Learn more from the data, eg;

   a. infer ancestral states

   b. compare rates of evolution (phylogenetic liability) across lineages or across traits

   c. test for “outlier” species

   1. Make better choices as to which species should be compared

Phylogenetic pseudoreplication

a statistical error that occurs when data points are treated as independent when they are not

Phylogenetically Independent Contrasts (Felsenstein 1985)

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

• Applicable to essentially all types of statistical analyses

• Can cope with incomplete phylogenetic information, including arbitrary branch lengths, various types of character evolution

When computing phylogenetically independent contrasts the general sequence of procedures is as..

1. Identify the independent contrasts

2. Compute the raw contrasts (differences in trait values)

3. Compute the standard deviation of contrasts

4. Divide the raw contrasts by their standard deviations.