Lecture 1

BIOL 3306 – Evolutionary Biology(1) Why study evolution?

Ricardo Azevedo

August 23, 2011

Outline

General information

What is evolution?

Evolution is both a theory and a fact

Why study evolution?

Tree thinking

General informationInstructors

� Ricardo Azevedo August 23 – October [email protected]

Office hours: Thursdays, 11:30 AM – 12:30 PM

� Diane Wiernasz October 11 – December [email protected]

General informationMeeting information

� Tue/Thu, 10:00 – 11:30 AM SEC 101

� Tue/Thu, 5:30 – 7:00 PM SEC 203

General informationPrerequisites

BIOL 3301 Genetics (enforced)

General informationWebsites

� General http://BIOL3306F11.blogspot.com/

� Testing https://www.casa.uh.edu/

General informationCourse blog

General informationCASA

General informationTextbook

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

General informationExams

� Exam 1: Thu, September 22� Exam 2: Thu, October 27� Exam 3: Thu, December 1

� Final (optional): Tue, December 13

No midterms will be dropped

General informationClickers

� Quick, simple questions about material justcovered (10 pts total)

� “Homework” questions (15 pts total)

� Opinion/feedback questions (not for credit)

∼ 20% “free” questions

General informationClickers

� Clicker questions will begin next Tuesday

� You can only answer these questions witha clicker

� Buy it at the UH bookstore or from anotherstudent

� Set it to channel 48 (press: Ch – 48 – Ch)

General informationTesting

� Midterms (3×): 25 pts each

� Final (optional): averaged into midterms

� Clickers: 25 pts

General informationGrading

� A 85 – 100 points

� B 70 – 84

� C 50 – 69

� D 40 – 49

� F 0 – 39

No curving

General informationRecipe for success

� 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 office hours

What is evolution?Minimal definition (general)

Change over time

Examples:

biology evolution, development, cancerphysics solar system, stars, galaxiesculture language, knowledge, fashiontechnology airplane, computer, communications

What is evolution?Moore’s law — transistors in integrated circuits

What is evolution?Minimal definition (biological)

Change in the heritable properties

of populations of organisms

over several generations

Examples: pesticide resistance in insects, HIV disease progression,E. coli evolution in the laboratory, origin of birds from reptilian ancestor

What is evolution?HIV-1 from a single patient (gp120 gene)

Metzker et al. (2002)

Patient Victim Controls

Phylogeny of gp120 sequences

Evolution

HIV-1 from a single patient

Human-chimp DNA

sequence divergence

F&H: p 19

F&H p 19





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

What is evolution?Tasmanian devil facial tumor disease

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





Individual organisms do not evolve





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

What is evolution?Mean height of conscripts in Italy (1854–1963)

Growing up with good nutrition: first 20 years 319

This sexual dimorphism in the height trend is striking,and has not been observed elsewhere. It was greater before1940 than after, and was still present when expressed inpercentage terms. Among parents born before 1905 fatherswere 6·9 % taller than mothers, whereas in the 1958 cohortmen were 9·3 % taller than women.

Kuh et al. (1991) point out that, in general, growth inboys is believed to be more responsive (or plastic) than ingirls to changes in the environment, so that in good timesboys grow relatively faster, but when times get hard theirgrowth is more affected. Eveleth & Tanner (1990) in theirdiscussion of environmental influences on growth make thesame point. However, Kuh et al. (1991) find the evidencefor male plasticity unconvincing, and look for otherexplanations.

Whatever the causation, the sexual dimorphism in heighttrend highlights an interesting contradiction. Francis Galton(1886) in his famous paper on regression to the mean inhereditary stature assumed an 8 % sex difference in heightwhen he adjusted for sex differences in the heights of thefamily offspring, and the same value of 8 % is seen in manypopulations today (Cole, 2000). However Cole (2000), likeKuh et al. (1991), found that the percentage differenceincreased with time. Thus, men have either remainedconsistently 8 % taller than women over the last 110 years,or they have been getting progressively taller. The twoobservations are incompatible.

The simplest explanation is to do with the families thatGalton (1886) studied. If they were relatively advantaged(as they presumably were), the percentage difference inparental heights could have been greater than that for thegeneral population at that time, which would bring it nearerto the current value of 8 %.

Child heightThe size of the secular height trend in childhood varies withthe age of the child. Dutch infants at 1 year of age wereconsistently shorter in 1997 than they were in 1965 (Table1), while at ages 8 and 21 years they were appreciably taller.Takaishi (1995) published height data from birth to 17 years

for Japanese children between 1940 and 1990, during whichtime there has been a dramatic increase in height at mostages. Fig. 2 plots the secular trend between 1950 and 1990by age and sex, showing little effect before 2 years, like theDutch pattern in Table 1. Subsequently the trend increasesto a peak at age 11 years in girls and 14 years in boys, andthen falls back to a value in adulthood similar to that seen atage 2 years, at least in girls. The boys’ curve is still falling atage 17 years, and probably returns to the age 2 years level byage 20 years.

Thus the secular trend in childhood can be viewed inthree distinct periods: before age 2 years, where there isvery little trend; from age 2 years to puberty, where theincreasing trend is clearly related to the pubertal growthspurt; post-puberty where the trend falls to match that foradults. The dramatic increase in trend at puberty is due to anincreased growth tempo, with children growing faster andmaturing earlier, and this transiently magnifies the trend atthe age of peak height velocity. However, after it has passed,Fig. 2 shows that the increase in final height (mm) hasalready been achieved by the age of 2 years.

To try to understand the basis of the secular trend, twoprocesses need to be distinguished: trends in size in earlylife up to age 2 years, which are carried through toadulthood, and trends in maturation, as exemplified by theage of menarche.

WeightAlong with secular changes in height there are alsoconcomitant changes in weight, both in adults and inchildren. As an example, changes since 1920 in height andweight of 8–18-year-old Oslo schoolgirls show clearupward trends over the period, steeper before the SecondWorld War than after, and with a sharp downturn duringwartime which was most marked at age 12 years (Liestøl &Rosenberg, 1995). Although height has largely stabilizedsince 1975, weight has continued to increase, reflecting thegrowing epidemic of obesity throughout the Western world.Obesity is often documented using the BMI (weight/height2)rather than weight. The increase in obesity has been most

Fig. 1. Mean height in Italian conscripts from 1854 to 1963. (FromHermanussen et al. 1995)

Fig. 2. Secular trends in height by sex for Japanese childrenbetween 1950 and 1990. (1), Boys; (0), girls. (From Takaishi,1995)

Cole (2000) Secular trends in growth. Proc Nutr Soc 59: 317–24.

Evolution is both a theory and a factTerms used to describe the nature of science

Fact: In science, an observation that has been repeatedly

confirmed, and for all practical purposes, is accepted as

“true”. Truth in science, however, is never final, and what is

accepted as a fact today may be modified or even

discarded tomorrow.

Hypothesis: A tentative statement about the natural world

leading to deductions that can be tested. If the deductions

are verified, it becomes more probable that the hypothesis

is correct. If the deductions are incorrect, the original

hypothesis can be abandoned or modified. Hypotheses can

be used to build more complex inferences and explanations.

Science and Creationism: A View from the National Academy of Sciences (1999)


Law: A descriptive generalization about how some aspect

of the natural world behaves under stated circumstances.

Theory: In science, a well-substantiated explanation of

some aspect of the natural world that can incorporate facts,

laws, inferences, and tested hypotheses.



The contention that evolution should be taught as a “theory,

not as a fact” confuses the common use of these words

with the scientific 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

reflection.


Evolution is both a theory and a factSummary 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.

� Evolution as such

� Speciation

� Natural selection

� Gradualism

� Common ancestry

� Other mechanisms

F&H pp 38–40









� Speciation


� Gradualism

� Common ancestry


F&H pp 38–40









� Speciation


� Gradualism

� Common ancestry










� Speciation


� Gradualism

� Common ancestry










� Speciation


� Gradualism

� Common ancestry










� Speciation


� Gradualism

� Common ancestry










� Speciation


� Gradualism

� Common ancestry


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

� 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 thechimpanzee genome and comparison with the human genome. Nature 437: 69–87.

F&H pp 756–763

Why study evolution?Apes have already risen...

Primate Phylogeny

PLoS Genetics | www.plosgenetics.org 3 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

PLoS Genetics | www.plosgenetics.org 3 March 2011 | Volume 7 | Issue 3 | e1001342

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

Why study evolution?Two types of explanations in biology

� Proximate “How?” questions functional biology

� Ultimate “Why?” questions evolutionary biology

Why study evolution?Respiration — Proximate explanations

� Metabolism� glycolysis� pyruvate decarboxylation� Krebs cycle� oxidative phosphorylation

� Cell biology� mitochondria

Why study evolution?Respiration — Ultimate explanations

� ∼ 2.4 billion years ago, thelevel of oxygen in the Earth’satmosphere began to rise

� Mitochondria evolved froman α-proteobacterium-likeendosymbiont

F&H pp 585–588

Tree thinking

Darwin (1837)

Tree thinking

On the Origin of Species

Charles Darwin (1859)

Evolution

! Continental islands sit on a continental shelf

(e.g., Greenland, Great Britain, Ireland, Sicily,

Barbados, Trinidad, Sumatra, Java, Tasmania)

! Oceanic islands do not sit on a continental shelf

and have a volcanic origin

(e.g., Galapagos, Azores, Cape Verde, Aleutian Islands,

Hawaii Islands, Mariana Islands, Mauritius)

Biogeography

Islands

Biogeography

Many oceanic islands appear over volcanic hotspots

! Impoverished and unbalanced(e.g. radiations of finches in Galapagos, or Drosophila in Hawaii)

! Relatively rich in highly mobile organisms(e.g. birds, insects, bats, aquatic mammals, seed plants)

! Relatively poor in less mobile organisms(e.g. freshwater fish, land mammals, reptiles and amphibians)

! Species similar to those in closest mainland

Biogeography

Flora and fauna of oceanic islands(in comparison with continental islands)

Tree thinkingEvidence for evolution

That species can be classified easily according to a

hierarchical system is a consequence of evolution.

Tree thinkingSummary of the theory of evolution








� Speciation


� Gradualism

� Common ancestry


Tree thinkingTime

z

GorillaPan Homo

y

xw

Pongo Hylobates � Time advances from thebottom (root) to the top (tips)

� The top of the tree representsthe most recent time (typicallythe present)

F&H pp 50–53

Tree thinkingBranching

z

GorillaPan Homo

y

xw

Pongo Hylobates � The tips of the tree (•) representspecies

� The nodes of the tree (•, w–z)represent ancestral speciesundergoing speciation

F&H pp 50–53

Tree thinkingAncestors and descendants

z

GorillaPan Homo

y

xw

Pongo Hylobates

� x speciated before y

� y is the most recent commonancestor of Pan and Gorilla

F&H pp 50–53

Tree thinkingRelationships

z

GorillaPan Homo

y

xw

Pongo Hylobates� Pan is more closely related to

Homo than it is to Gorilla

� Both Pan and Homo are equallyclosely related to Gorilla

F&H pp 756–763

Tree thinking

z

GorillaPan Homo

y

xw

Pongo Hylobatesz

Gorilla

Pan

Homoy

x

wPongo

Hylobates

Changing the orientation does not change the tree

Tree thinking

z

GorillaPan Homo

y

xw

Pongo Hylobates

z

Gorilla PanHomo

y

xw

Pongo Hylobates

Rotating clades around a node does not change the tree

Next Lecture

Evidence for evolution (continued)

F&H chpt 2

Lecture 1

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Transcript of Lecture 1