Evolutionary Biology Lecturer: Chaolun Allen Chen Lab. Evolutionary Ecology and Genetics of the Coral Reefs Research Centre for Biodiversity, Academia Sinica, Taiwan

Textbook: Futuyma (2005), EVOLUTION, Sinauer Chapters of my lectures: Ch.1 Evolutionary Biology (Feb. 21) Ch.2 The Tree of Life: Classification and Phylogeny (Mar. 7) Ch.3 Pattern of Evolution (Mar.7/ 14) Ch.6 The Geography of Evolution (Mar. 14) Ch.7 The Evolution of Biodiversity (Mar. 21/ 28) Ch. 13 Evolution of Phenotypic Traits (Mar. 28) Ch. 14 Conflict and Cooperation (Apr.??) Problems and Discussion topics Group discussion and take-home questions Group leader has to Hand-in by next lecture through Will posted in my website:

21st Century---Age of Biology-- WHY?

21st Century---Age of Biology--Challenges! –Climate Change –Habitat Conversion –Pollutants –Emerging Diseases –Introduction of Exotics –Loss of Biodiversity

21st Century---Age of Biology-- New Technologies, New Integrated Approaches –Genomics, Molecular, Evolutionary, and Computational –Remote Environmental Sensing –Nanotechnology

A new era of biology began on November 24, 1859 ?

Chapter 1 Opener: The peacock, Pavo cristatus Why?

Genetic variation in populations –Contributes to evolution Cuban Tree Snails

1.1 A tuberculosis ward at a U.S. Army base hospital in France during World War I

1.2 Development of drug resistance

The Evolution of Drug-Resistant HIV In humans, the use of drugs –Selects for pathogens that through chance mutations are resistant to the drugs’ effects Natural selection is a cause of adaptive evolution

Researchers have developed numerous drugs to combat HIV –But using these medications selects for viruses resistant to the drugs

The ability of bacteria and viruses to evolve rapidly –Poses a challenge to our society

CDC HEALTH ALERT CDC Recommends against the Use of Amantadine and Rimantadine for the Treatment or Prophylaxis of Influenza in the United States during the 2005–06 Influenza Season Recent evidence indicates that a high proportion of currently circulating Influenza A viruses in this country are resistant to these medications Distributed via Health Alert Network January 14, 2006, 3:25 PM EST

Carolus Linnaeus –Interpreted organismal adaptations as evidence that the Creator had designed each species for a specific purpose –Was a founder of taxonomy, classifying life’s diversity “for the greater glory of God”

Lamarck’s Theory of Evolution Lamarck hypothesized that species evolve –Through use and disuse and the inheritance of acquired traits –But the mechanisms he proposed are unsupported by evidence

1.3(1) Lamarck’s theory of organic progression

1.3(2) Darwin’s theory of descent with modification

1.4 A contrast between transformational and variational theories of evolutionary change

November 24, 1859 –The day Charles Darwin published On the Origin of Species by Means of Natural Selection and –Introduces a Revolutionary Theory

Why was it important? 1 ST consistent, unified and scientific theory of evolution Primary concept: descent with modification Unity of life –diversification from common ancestor = common origin Rhythm of evolution is gradual Mechanism of evolution is natural selection

Why a Revolution? –Earth is likely older than 6,000 years –Species can change –Fundamental Question How did all this diversity arise? Common mechanism(s) can explain diversity.

The Origin of Species –Focused biologists’ attention on the great diversity of organisms

Darwin made two major points in his book –Presented evidence that the many species presently inhabiting the Earth are descendants of ancestral species –Proposed a mechanism for the evolutionary process, natural selection

The Darwinian revolution challenged traditional views of a young Earth inhabited by unchanging species To understand why Darwin’s ideas were revolutionary –We need to examine his views in the context of other Western ideas about Earth and its life

The historical context of Darwin’s life and ideas Linnaeus (classification) Hutton (gradual geologic change) Lamarck (species can change) Malthus (population limits) Cuvier (fossils, extinction) Lyell (modern geology) Darwin (evolution, natural selection) Mendel (inheritance) Wallace (evolution, natural selection) 1750 American RevolutionFrench Revolution U.S. Civil War Hutton proposes his theory of gradualism Malthus publishes “Essay on the Principle of Population.” 1809 Lamarck publishes his theory of evolution Lyell publishes Principles of Geology. 1831–1836 Darwin travels around the world on HMS Beagle. Darwin begins his notebooks on the origin of species Darwin writes his essay on the origin of species Wallace sends his theory to Darwin The Origin of Species is published Mendel publishes inheritance papers. 1865

Resistance to the Idea of Evolution The Origin of Species –Shook the deepest roots of Western culture –Challenged a worldview that had been prevalent for centuries

The Scale of Nature and Classification of Species The Greek philosopher Aristotle –Viewed species as fixed and unchanging The Old Testament of the Bible –Holds that species were individually designed by God and therefore perfect

Fossils, Cuvier, and Catastrophism The study of fossils –Helped to lay the groundwork for Darwin’s ideas Fossils are remains or traces of organisms from the past –Usually found in sedimentary rock, which appears in layers or strata

Paleontology, the study of fossils –Was largely developed by French scientist Georges Cuvier Cuvier opposed the idea of gradual evolutionary change –And instead advocated catastrophism, speculating that each boundary between strata represents a catastrophe

Theories of Gradualism Gradualism –Is the idea that profound change can take place through the cumulative effect of slow but continuous processes

Geologists Hutton and Lyell –Perceived that changes in Earth’s surface can result from slow continuous actions still operating today (uniformitarianism) –Exerted a strong influence on Darwin’s thinking

As the 19th century dawned –It was generally believed that species had remained unchanged since their creation, but Darwin (and others) challenged this thinking In The Origin of Species in 1859, Darwin proposed that species change through natural selection Evolution--change over time in the genetic composition of populations

Darwin’s Research As a boy and into adulthood, Charles Darwin –Had a consuming interest in nature Soon after Darwin received his B.A. degree –He was accepted on board the HMS Beagle, which was about to embark on a voyage around the world

Darwin’s interest in the geographic distribution of species –Was kindled by the Beagle’s stop at the Galápagos Islands near the equator west of South America England EUROPE NORTH AMERICA Galápagos Islands Darwin in 1840, after his return SOUTH AMERICA Cape of Good Hope Cape Horn Tierra del Fuego AFRICA HMS Beagle in port AUSTRALIA Tasmania New Zealand PACIFIC OCEAN Andes ATLANTIC OCEAN

The Voyage of the Beagle During his travels on the Beagle –Darwin observed and collected many specimens of South American plants and animals Darwin observed various adaptations of plants and animals –That inhabited many diverse environments

Darwin’s Focus on Adaptation As Darwin reassessed all that he had observed during the voyage of the Beagle –He began to perceive adaptation to the environment and the origin of new species as closely related processes

From studies made years after Darwin’s voyage –Biologists have concluded that this is indeed what happened to the Galápagos finches (a) Cactus eater. The long, sharp beak of the cactus ground finch (Geospiza scandens) helps it tear and eat cactus flowers and pulp. (c) Seed eater. The large ground finch (Geospiza magnirostris) has a large beak adapted for cracking seeds that fall from plants to the ground. (b) Insect eater. The green warbler finch (Certhidea olivacea) uses its narrow, pointed beak to grasp insects.

In 1844, Darwin wrote a long essay on the origin of species and natural selection –But he was reluctant to introduce his theory publicly, anticipating the uproar it would cause In June 1858 Darwin received a manuscript from Alfred Russell Wallace –Who had developed a theory of natural selection similar to Darwin’s Darwin quickly finished The Origin of Species –And published it the next year

The Origin of Species Darwin developed two main ideas –Evolution explains life’s unity and diversity –Natural selection is a cause of adaptive evolution

Descent with Modification The phrase descent with modification –Summarized Darwin’s perception of the unity of life –States that all organisms are related through descent from an ancestor that lived in the remote past

In the Darwinian view, the history of life is like a tree –With multiple branches from a common trunk to the tips of the youngest twigs that represent the diversity of living organisms Figure 22.7 Hyracoidea (Hyraxes) Sirenia (Manatees and relatives) Years ago Millions of years ago Deinotherium Mammut Stegodon Mammuthus Platybelodon Barytherium Moeritherium Elephas maximus (Asia) Loxodonta africana (Africa) Loxodonta cyclotis (Africa)

Natural Selection and Adaptation Evolutionary biologist Ernst Mayr –Has dissected the logic of Darwin’s theory into three inferences based on five observations

Observation #1: For any species, population sizes would increase exponentially –If all individuals that are born reproduced successfully

Observation #2: Nonetheless, populations tend to be stable in size –Except for seasonal fluctuations Observation #3: Resources are limited Inference #1: Production of more individuals than the environment can support –Leads to a struggle for existence among individuals of a population, with only a fraction of their offspring surviving

Observation #4: Members of a population vary extensively in their characteristics –No two individuals are exactly alike

Observation #5: Much of this variation is heritable Inference #2: Survival depends in part on inherited traits –Individuals whose inherited traits give them a high probability of surviving and reproducing are likely to leave more offspring than other individuals

Inference #3: This unequal ability of individuals to survive and reproduce –Will lead to a gradual change in a population, with favorable characteristics accumulating over generations

Artificial Selection In the process of artificial selection –Humans have modified other species over many generations by selecting and breeding individuals that possess desired traits

Summary of Natural Selection Natural selection is differential success in reproduction –That results from the interaction between individuals that vary in heritable traits and their environment

Population genetics provides a foundation for studying evolution Microevolution –Is change in the genetic makeup of a population from generation to generation Bent grass on heavy metal tailings

Rediscovery of Genetics ca Apparent contradiction between gradualism and particulate inheritance Mutationism of de Vries and Goldschmidt

The Modern Synthesis Population genetics –Is the study of how populations change genetically over time –Reconciled Darwin’s and Mendel’s ideas p t -> evolution happens -> p t+1

The modern synthesis –Integrates Mendelian genetics with the Darwinian theory of evolution by natural selection –Focuses on populations as units of evolution

Modern Synthesis (Neodarwinsim) Formal models of Fisher, Wright, and Haldane Dobzhansky: chance variation and balanced polymorphisms Mayr: Systematics, species, speciation, selection, genotype and phenotype Simpson: Paleontology--fossil record shows gradual change and impact of continental drift Genes mutate, organisms are selected, and populations (species) evolve

Ronald Fisher Ernst Mayr JBS Haldane George Gaylord Simpson Theodosuis Dobzhansky

Challenges to the Modern Synthesis Horizontal Expansion –Neutral Theory of Molecular Evolution Motoo Kimura Vertical Expansion –Criticism of Gradualism: Model of Punctuated Equilibrium-Gould and Eldredge –What is an individual: processes of evolution at distinct levels, interactions between levels Junk DNA, selfish genes Species selection

1972 Eldredge and Gould--Punctuated Equilibrium 1968 Kimura: Neutral Theory of Molecular Evolution 1953 Watson-Crick Double Helix Modern Synthesis 1900 Mendel Rediscovered

Motoo Kimura and family Stephen J. Gould

A Few Other Important Developments (of many) Phylogenies (trees) become the explicit mark of evolutionary studies Interface between comparative embryology and developmental genetics (evo-devo)-- same basic set of genes are redeployed in different ways produce dramatically different results

Evolution is the unifying theory of biology