BIOL 3306 Evolutionary Biology (1) Why study evolution?

Ricardo Azevedo
August 23, 2011

Outline

General information
Instructors

General information What is evolution? Evolution is both a theory and a fact Why study evolution? Tree thinking

Ricardo Azevedo razevedo@uh.edu Ofce hours: Diane Wiernasz dwiernasz@uh.edu

August 23 October 6 Thursdays, 11:30 AM 12:30 PM October 11 December 1

General information
Meeting information

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Prerequisites

Tue/Thu, 10:00 11:30 AM Tue/Thu, 5:30 7:00 PM

SEC 101 SEC 203

BIOL 3301 Genetics (enforced)

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Websites

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Course blog

General Testing

http://BIOL3306F11.blogspot.com/ https://www.casa.uh.edu/

General information
CASA

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Textbook

Freeman & Herron (2007) Evolutionary Analysis. 4th ed. Prentice Hall.

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Exams

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Clickers

Exam 1: Exam 2: Exam 3: Final (optional):

Thu, September 22 Thu, October 27 Thu, December 1 Tue, December 13

Quick, simple questions about material just covered (10 pts total) Homework questions (15 pts total)

Opinion/feedback questions (not for credit) 20% free questions

No midterms will be dropped

General information
Clickers

General information
Testing

Clicker questions will begin next Tuesday You can only answer these questions with a clicker Buy it at the UH bookstore or from another student Set it to channel 48 (press: Ch 48 Ch)

Midterms (3): Final (optional): Clickers:

25 pts each averaged into midterms 25 pts

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Grading

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Recipe for success

A B C D F

85 100 points 70 84 50 69 40 49 0 39

Come to class and take notes Read the textbook regularly, both before and after class Do well in clicker questions Remember that topics are closely interrelated Study in groups Ask questions in class, in the blog and/or in ofce hours

No curving

What is evolution?
Minimal denition (general)

What is evolution?
Moores law transistors in integrated circuits

Change over time

Examples: biology physics culture technology evolution, development, cancer solar system, stars, galaxies language, knowledge, fashion airplane, computer, communications

What is evolution?
Minimal denition (biological) Patient
Victim Controls

What is evolution?

HIV-1 from a single patient (gp120 gene)

Evolution

HIV-1 from a single patient

Change in the heritable properties of populations of organisms over several generations

Examples:

pesticide resistance in insects, HIV disease progression,

Human-chimp DNA sequence divergence

E. coli evolution in the laboratory, origin of birds from reptilian ancestor

Phylogeny of gp120 sequences

Metzker et al. (2002) F&H: p 19

F&H p 19

What is evolution?
Minimal denition (biological)

What is evolution?
Tasmanian devil facial tumor disease

Change in the heritable properties of populations of organisms over several generations

Excludes development of an organism (ontogeny) Includes development or cancer from the point of view of the cells

McCallum & Jones (2006) To lose both would look like carelessness: Tasmanian Devil facial tumour disease. PLoS Biol 4:e342.

What is evolution?
Minimal denition (biological)

Change in the heritable properties of populations of organisms over several generations

Individual organisms do not evolve

What is evolution?
Minimal denition (biological)

What is evolution?
Mean height of conscripts in Italy (18541963)
Growing up with good nutrition: first 20 years

Change in the heritable properties of populations of organisms over several generations

Excludes direct effects of changes in the environment (e.g., the secular increase in human height)

Fig. 1. Mean height in Italian conscripts from 1854 to 1963. (From Cole (2000) Secular trends in growth. Proc Nutr Soc 59: 31724. Hermanussen et al. 1995)

Fig. 2. Secular trends between 1950 and 199 1995)

Evolution is both a theory and a fact

Terms used to describe the nature of science

Fact: In science, an observation that has been repeatedly conrmed, and for all practical purposes, is accepted as true. Truth in science, however, is never nal, and what is accepted as a fact today may be modied or even discarded tomorrow. Hypothesis: A tentative statement about the natural world leading to deductions that can be tested. If the deductions are veried, it becomes more probable that the hypothesis is correct. If the deductions are incorrect, the original hypothesis can be abandoned or modied. Hypotheses can be used to build more complex inferences and explanations.
Science and Creationism: A View from the National Academy of Sciences (1999)

This sexual dimorphism in the height trend is striking, and has not been observed elsewhere. It was greater before 1940 than after, and was still present when expressed in percentage terms. Among parents born before 1905 fathers Evolutionwerebothtaller than mothers, whereas in the 1958 cohort is 69 % a theory and a fact Terms used men were 93 % taller than women. to describe the nature of science Kuh et al. (1991) point out that, in general, growth in boys is believed to be more responsive (or plastic) than in girls to changes in the environment, so that in good times boys grow relatively faster, but when times get hard their growth is more affected. Eveleth & Tanner (1990) in their discussion of environmental influences on growth make the Law: A descriptive generalization (1991) find the evidence same point. However, Kuh et al. about how some aspect for male world behaves under and circumstances. of the natural plasticity unconvincing,stated look for other explanations. Theory: In science, a well-substantiated explanation of Whatever the causation, the sexual dimorphism in height some aspect of the natural world that can incorporate facts, trend highlights an interesting contradiction. Francis Galton (1886) in his and tested on regression laws, inferences,famous paperhypotheses. to the mean in hereditary stature assumed an 8 % sex difference in height when he adjusted for sex differences in the heights of the Science and Creationism: A View from the National Academy of Sciences family offspring, and the same value of 8 % is seen in(1999) many populations today (Cole, 2000). However Cole (2000), like Kuh et al. (1991), found that the percentage difference increased with time. Thus, men have either remained consistently 8 % taller than women over the last 110 years, or they have been getting progressively taller. The two observations are incompatible. The simplest explanation is to do with the families that Galton (1886) studied. If they were relatively advantaged (as they presumably were), the percentage difference in parental heights could have been greater than that for the general population at that time, which would bring it nearer

for Japanese children time there has been ages. Fig. 2 plots the by age and sex, show Dutch pattern in Tab to a peak at age 11 y then falls back to a v age 2 years, at least i age 17 years, and pro age 20 years. Thus the secular three distinct period very little trend; fro increasing trend is spurt; post-puberty w adults. The dramatic increased growth tem maturing earlier, and the age of peak heigh Fig. 2 shows that t already been achieve To try to underst processes need to b life up to age 2 adulthood, and trend age of menarche.

Along with secula concomitant change children. As an exam

Evolution is both a theory and a fact

Terms used to describe the nature of science

Evolution is both a theory and a fact

Summary of the theory of evolution

The contention that evolution should be taught as a theory, not as a fact confuses the common use of these words with the scientic use. In science, theories do not turn into facts through the accumulation of evidence. Rather, theories are the end points of science. They are understandings that develop from extensive observation, experimentation, and creative reection.
Science and Creationism: A View from the National Academy of Sciences (1999)

Life on earth evolved gradually beginning with one primitive species perhaps a self-replicating molecule that lived more than 3.5 billion years ago; it then branched out over time, throwing off many new and diverse species; and the mechanism for most (but not all) of evolutionary change is natural selection.
Coyne (2009) Why Evolution is True.

Evolution as such Speciation Natural selection

Gradualism Common ancestry Other mechanisms

F&H pp 3840

Evolution is both a theory and a fact

Summary of the theory of evolution

Evolution is both a theory and a fact

Summary of the theory of evolution

Life on earth evolved gradually beginning with one primitive species perhaps a self-replicating molecule that lived more than 3.5 billion years ago; it then branched out over time, throwing off many new and diverse species; and the mechanism for most (but not all) of evolutionary change is natural selection.
Coyne (2009) Why Evolution is True.

Life on earth evolved gradually beginning with one primitive species perhaps a self-replicating molecule that lived more than 3.5 billion years ago; it then branched out over time, throwing off many new and diverse species; and the mechanism for most (but not all) of evolutionary change is natural selection.
Coyne (2009) Why Evolution is True.

Evolution as such Speciation Natural selection

Gradualism Common ancestry Other mechanisms

F&H pp 3840

Evolution as such Speciation Natural selection

Gradualism Common ancestry Other mechanisms

Evolution is both a theory and a fact

Summary of the theory of evolution

Evolution is both a theory and a fact

Summary of the theory of evolution

Life on earth evolved gradually beginning with one primitive species perhaps a self-replicating molecule that lived more than 3.5 billion years ago; it then branched out over time, throwing off many new and diverse species; and the mechanism for most (but not all) of evolutionary change is natural selection.
Coyne (2009) Why Evolution is True.

Life on earth evolved gradually beginning with one primitive species perhaps a self-replicating molecule that lived more than 3.5 billion years ago; it then branched out over time, throwing off many new and diverse species; and the mechanism for most (but not all) of evolutionary change is natural selection.
Coyne (2009) Why Evolution is True.

Evolution as such Speciation Natural selection

Gradualism Common ancestry Other mechanisms

Evolution as such Speciation Natural selection

Gradualism Common ancestry Other mechanisms

Evolution is both a theory and a fact

Summary of the theory of evolution

Evolution is both a theory and a fact

Summary of the theory of evolution

Life on earth evolved gradually beginning with one primitive species perhaps a self-replicating molecule that lived more than 3.5 billion years ago; it then branched out over time, throwing off many new and diverse species; and the mechanism for most (but not all) of evolutionary change is natural selection.
Coyne (2009) Why Evolution is True.

Life on earth evolved gradually beginning with one primitive species perhaps a self-replicating molecule that lived more than 3.5 billion years ago; it then branched out over time, throwing off many new and diverse species; and the mechanism for most (but not all) of evolutionary change is natural selection.
Coyne (2009) Why Evolution is True.

Evolution as such Speciation Natural selection

Gradualism Common ancestry Other mechanisms

Evolution as such Speciation Natural selection

Gradualism Common ancestry Other mechanisms

Why study evolution?

Nothing in biology makes sense except in the light of evolution . . . Without that light it becomes a pile of sundry facts some of them interesting or curious but making no meaningful picture as a whole. Dobzhansky (1973)

Why study evolution?

Human / chimpanzee genome sequence comparison

Why study evolution?

Apes have already risen...
Primate Phylogeny

3% genome-wide nucleotide insertion / deletion differences 1.2% genome-wide nucleotide sequence substitution differences 29% proteins have exactly the same amino acid sequence proteins differ on average in only 2 amino acids

The Chimpanzee Sequencing and Analysis Consortium (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 6987.

F&H pp 756763

PLoS Genetics | www.plosgenetics.org

March 2011 | Volume 7 | Issue 3 | e1001342

Perelman et al. (2011) A molecular phylogeny of living primates. PLoS Genet 7:e1001342.

Why study evolution?

Apes have already risen...
Primate Phylogeny

Why study evolution?

Two types of explanations in biology

Proximate Ultimate

How? questions Why? questions

functional biology evolutionary biology

Perelman et al. (2011) A molecular phylogeny of living primates. PLoS Genet 7:e1001342.

Why study evolution?

Respiration Proximate explanations

Why study evolution?

Respiration Ultimate explanations

Metabolism

glycolysis pyruvate decarboxylation Krebs cycle oxidative phosphorylation

2.4 billion years ago, the level of oxygen in the Earths atmosphere began to rise Mitochondria evolved from an -proteobacterium-like endosymbiont

Cell biology

mitochondria

PLoS Genetics | www.plosgenetics.org

March 2011 | Volume 7 | Issue 3 | e1001342

F&H pp 585588

Tree thinking

Tree thinking

Evolution

On the Origin of Species Charles Darwin (1859)

Darwin (1837)

Tree thinking
Evidence for evolution

Tree thinking

Biogeography

Summary of the theory of evolution Many oceanic islands appear over volcanic hotspots

That species can be classied easily according to a hierarchical system is a consequence of evolution.

Life on earth evolved gradually beginning with one primitive species perhaps a self-replicating molecule that lived more than 3.5 billion years ago; it then branched out over time, throwing off many new and diverse species; and the mechanism for most (but not all) of evolutionary change is natural selection.
Coyne (2009) Why Evolution is True.

Evolution as such Speciation Natural selection

Gradualism Common ancestry Other mechanisms

Tree thinking
Time

Tree thinking
Branching

Pan

Homo

Gorilla

Pongo Hylobates

Time advances from the bottom (root) to the top (tips) The top of the tree represents the most recent time (typically the present)

Pan

Homo

Gorilla

Pongo Hylobates

The tips of the tree () represent species The nodes of the tree (, wz) represent ancestral species undergoing speciation

z y

z y

x w

x w

F&H pp 5053

F&H pp 5053

Tree thinking
Ancestors and descendants

Tree thinking
Relationships

Pan

Homo

Gorilla

Pongo Hylobates

Pan

Homo

Gorilla

Pongo Hylobates

z y

x speciated before y y is the most recent common ancestor of Pan and Gorilla
z y

Pan is more closely related to Homo than it is to Gorilla Both Pan and Homo are equally closely related to Gorilla

x w

F&H pp 5053

F&H pp 756763

Tree thinking

Tree thinking

Pan Pan Homo Gorilla Pongo Hylobates y z y z Homo z x Gorilla y y z Pan Homo Gorilla Pongo Hylobates Gorilla Homo Pan Pongo Hylobates

x w

Pongo

x w

x w

Hylobates

Rotating clades around a node does not change the tree Changing the orientation does not change the tree

Next Lecture

Evidence for evolution (continued)

F&H chpt 2