Welcome to

Introductory Biology II

Organismic and Evolutionary Biology

(BIOL 202)

Comparative Genomics helps elucidate ancestor/descendent relationships among major lineages of mammals, from the primordial mammal, with an early divergence of montremes, then marsupials, then placentals, including primates and their close relatives the bats.

Lecture Topics in Unit I: Evolutionary Processes

•History, Science and Life

•How populations evolve

•What species are and how they arise

•Macroevolution; patterns and process

•How to determine evolutionary relationships

•How molecules and genomes evolve

Today’s Topics:

•Descent with modification; development of evolutionary thinking

•History of Life on Earth

•Classification

•Scientific Inquiry

Fossils of the large (15-30 cm) soft-bodied organisms Pteridinum simplex are locally abundant in sandstone beds of the terminal Proterozoic (~550 my old) Nama group in Namibia. New insights from paleontology, geochemistry and molecular genetics are collectively illuminating the pattern, developmental basis, and environmental context of early animal evolution

Lecture 1:

History, Life and Science

What Darwin and Wallace Figured Out

•Evolution happens; species’ characters (traits) change over time and indeed such evolutionary change may result in origin of new species from existing ones

•Natural selection drives evolution; evolution is a consequence

•Diversity of life on earth is the consequence of evolution, and all organisms, ultimately, share a common ancestry

A young Charles Darwin, and a reproduction of the HMS Beagle

Prevailing Ideas about Life, Change and Evolution arose in Ancient Greece

•Scientific inquiry arose with the Ancient Materialists of Greece and Her Colonies (5th, 6th century BC)

•Methodically applied observation and logic to problem solving

•(eg, Anaximander, Empedocles)

•Classical Traditionalists of Greece and her Colonies (4th and 3rd century BC) departed from the “scientific approach” of their predecessors.

•Culminated in writings of Plato and Arisotle

• Plato’s Theory of Forms (Eidos)

• Aristotle

• Father of Modern Biology

• Applied Plato’s theory of forms to living things

• Developed important, unifying, enduring biological concept; Scala naturae

•Aristotle’s non-evolutionary concepts, including immutability of species and “Scala Naturae” that were incorporated in Christian Theology and remained the principal model of biological thought for 2000 years – until the 18th century

Emergence of Scientific Thinking Arose with the Breakdown of Classical Tradition -- in the1500’s

Contributing factors to that breakdown

•Renaissance

•Global Exploration

•Protestant Reformation

Important contributors to “new” approaches to Knowledge

•Gutenberg

•Copernicus

•Thomas Aquinas

•Francis Bacon

•RediWorld exploration, the renaissance, the protestant reformation…all contributed to a new intellectual atmosphere that led to the advance of scientific empiricism and rationalistic thinking

Intellectual Climate of Darwin’s Era (late 1700’s-Origin)

•William Paley and others develop and promote Natural Theology, which pervades European and American Science

•Carolus Linnaeus establishes huge intellectual model; Systema naturae

•Inception of modern systematics, built on Aristotelian Scala naturae; non-evolutionary

•New Sciences of Geology and Paleontology are strong intellectual influences

•Catastrophism and progressionism prevailed in many early cultures and were incorporated in Geology – toppled by theories of gradualism and uniformitarianism of Hutton and Lyell

•Growing knowledge of geological processes leads to questions regarding age of earth

19th Century England: The Intellectual Context in which Darwin Developed His Ideas

Important concepts, publications that strongly influenced early 19th century scientific thinking

-Botanist Carolus Linneaus Systema Naturae -Reverend William Paley Natural Theology-Ettiene George St. Hillaire Environmentalism-Cuvier Catastrophism

Radical 19th century geological concepts about the nature and pace of geological processes –age of earth- that influenced Darwin’s thinking during the voyage

-Geologist Hutton Gradualism -Geologist Lyell Uniformitarianism

Concept that influenced Darwin’s thinking after the voyage

-Thomas Malthus An Essay on Population

The Voyage of the Beagle

Course of the HMS Beagle’s World Journey

Continental comparisons of floras and faunas

Taxa showed continental affinities --even to the point that plants and animals from temperate South America showed a stronger affinity to those of tropical South America than those of temperate Europe

Within-continent comparisons of fossil and living taxa

Found fossils of extinct taxa that appeared to be ancestral to living taxa found there – i.e., distinct resemblances to living South American taxa

Unique “species groups” with curious distributions on the Galapagos Islands

Found that most species were “endemic”, yet bore resemblance to South American taxa

with unique distribution on the archipelago

From the Beagle to “Origin”

Darwin turned his “post-Beagle” attention to:

•Artificial Selection

•Population Theory of Thomas Malthus

Published “Origins” some 20 years after his voyage

•Central Thesis of Origins: Descent with modification results in a branching tree of species, in which related species share common ancestry

Darwin studied domestic pigeons, which were subjected to artificial selection by pigeon fanciers to such an extent that the various races produced showed levels of differentiation that one might expect among species

The mathematical model on which Thomas Malthus based his hypothesis; food production is arithmetic, population growth is geometric (An Essay on the Principal of Population, 1778)

Darwin’s Line of Reasoning in Support of Descent with Modification (Evolution through Natural Selection)

Observation 1. All species have potential fertility for exponential population growth

Observation 2. Populations tend to remain stable in size

Observation 3. Environmental resources are limited

Inference 1: More individuals are produced than can survive; struggle for existence leads to survival of a fraction of offspring each generation; differential survival

Observation 4: Individuals within a population vary extensively in their characteristics

Observation 5. Much variation is heritable

Inference 2. Survival is not random; depends in part on hereditary makeup; individuals with inherited traits best fit to the environment are likely to have more offspring than others; differential reproduction

Inference 3. Unequal survival and reproduction will lead to gradual change in a population, with favorable characteristics accumulating over generations

Darwin developed his idea of Evolution, of descent with modification, on five ideas that are each now regarded as theories (well-supported ideas with broad explanatory power)

1.Perpetual Change. Life is very old and life forms undergo perpetual inter-generational change in form and diversity

2.Common Descent. All life forms share a common ancestry.

3.Multiplication of Species. New species arise from pre-existing species

4.Gradualism. Large differences in form among species is due to incremental accumulation of many small differences over long periods of time

5.Natural Selection. Organisms in a population experience differential survival and reproduction as a consequence of variability in heritable traits.

Continental Drift. Earth’s crust consists of moving plates some 40 km thick, suspend on a molten, fluid mantle

History of Life on Earth

•Earth is more than 5 billion years old

•Life originated some 3.5 billion years ago

•Diversification of life has ensued only in the last 10% of Earth’s existence

•That 600 million years includes the Paleozoic, Mesozoic and Cenozoic Eras

Much of our knowledge on the history of life on Earth is based on interpretation of fossils -- the

Fossil Record

1000

2000

3000

4000

5000

Earth Cools

Photosynthesis evolves

Earth forms 5+ billion years ago

Oldest Eukaryotic fossils

Accum. of atmospheric. O2

and evolution of aerobic respiration

Origin of life - anaerobic

Oldest prokaryotic fossils

Mil

lion

s of

Yea

rs A

go (

mya

)History of Earth and

Life

~ 2 billion years of a strictly prokaryotic world!!

RNA sequence data shows Bacteria and Archaea diverged early, about 3 billion years ago

1000

2000

3000

4000

5000

Earth Cools

Photosynthesis evolves

Earth forms

Oldest Eukaryotic fossils

Substantial atmospheric O2

Origin of life

Oldest prokaryotic fossils

Beginning of Paleozoic EraM

illi

ons

of Y

ears

Ago

(m

ya)

History of Earth and

Life

Symbiotic theory of origin of Eukaryotes

Paleozoic Era

Mesozoic Era

Cenozoic Era

~250 mya

~65 mya

Pangea

Laurasia

Gondwana

Eras are bounded by major faunal turnovers that are thought to be related to cataclysmic phenomena of global dimensions

A thin band rich in iridium marks the boundary between rocks deposited in the Cretaceous and the Tertiary Periods

H C

Paleozoic Era

Mesozoic Era

Cenozoic Era

Periods of cold climates and glaciations have punctuated Earth’s history

~600 mya ~250 mya ~65 mya

Paleozoic Mesozoic Cenozoic

Today

Phanerozoic Eon (Time of “visible” life)

Paleozoic Era (Time of “Old Animals”)

Mesozoic Era (Time of “Middle Animals”)

Cenozoic Era (Time of “New Animals”)

Paleozoic Era

Precambrian Cambrian

•The Cambrian Period is the oldest geological period from which fossils of relatively complex organisms are represented

•Most of the extant (currently living) phyla are represented in the Cambrian, but not before.

~600 mya ~500 mya ~250 mya

PreCambrian Paleozoic Mesozoic Cenozoic

Evolutionary tree of vertebrate animals and close relatives

Width of the track indicates relative species abundance of each group through geological time

Mass Extinctions and the Geological Time Scale

A Mass Extinction is the widespread extinction of many taxa, globally, that occurs in a relatively brief period of geologic time.

Many of the periods between periods, and between eras, are demarcated by mass extinctions

Two important mass extinctions to be aware of, now, are the:

•Permian Extinctions (“ended” the Paleozoic Era)

•K/T Extinctions (“ended the Mesozoic Era)

Changes in numbers of families of marine invertebrate and vertebrate animals; five major extinctions since the Cambrian Explosion

Along the coast of Tethys, an ancient warm ocean that stretched from Spain to Indonesia, an undulating Basilosaurus catches fish with its four-foot long jaws and battery of sharp teeth

(Valkenburgh. Natural History. April 1994)

Evolutionary patterns in the rocks; Ambulocetus natans is an important find and a useful case study

Fossil formation in sedimentary deposits

Edinburgh Scotland

Dating Fossils

•Relative Dating

Absolute Dating of Fossils and Rocks:

Radiometric Dating

Radiometric Dating; Using decay rates of radioisotopes to accurately estimate age of a fossils and rocks

Radioactive isotopes can be detected and their amounts measured by the radiation they emit as they decompose to more stable atoms.

•Paleontologists use the clocklike decay of radioactive isotopes to date fossils and rocks

Emergence of Scientific Thinking Arose with the Breakdown of Classical Tradition -- in the1500’s

•Renaissance

•Global Exploration

•Protestant Reformation

Intellectual Climate of Darwins Era (late 1700’s-Origin)

Natural Theology, ala William Paley, pervades European and American Science

Carolus Linnaeus establishes huge intellectual model; ________

_____________

Intellectual Climate of Darwins Era (late 1700’s-Origin)

William Paley and others develop and promote Natural Theology, which pervades European and American Science

Carolus Linnaeus establishes huge intellectual model; Systema naturae

•Inception of modern systematics, built on Aristotelian Scala naturae; non-evolutionary

New Sciences of Geology and Paleontology are strong intellectual influences…

•Catastrophism of Georges Cuvier

•Gradualism of Hutton

•Uniformitarianism of Lyell

•Environmental Determinism

Charles Darwin (1809-1882) and Darwinism

Charles Darwin

…Rich kid; natural-born naturalist and observationist; graduated Cambridge having studied religion and medicine

...Credited with figuring out that “natural selection” imposes character changes (adaptations) on populatons over time, one outcome being “speciation”, such that “diversity” is the consequence of a “species branching process”

...collected and synthesized a compelling body of information to back it up -- voyage of the Beagle (1831-1836)

•published it -- Origin of Species 1859

Voyage of the Beagle

•Cape Verde Island

•Brazil to Tierra del Fuego

•The Galapagos Islands

From the Beagle to Origin

•Artificial Selection

•Population Theory of Thomas Malthus

•Central Thesis of Origins: Descent with modification results in a branching tree of species, in which related species share common ancestry

Ernst Mayr’s formalization of Darwin’s Theory

(stated as inferences based on observations)

Scientific Inquiry

Scientific enterprise

•Describe natural systems (recognize patterns, phenomena)

•Develop causal explanations (figure out underlying processes)

Scientific Inquiry

Scientific enterprise

•Describe natural systems (recognize patterns, phenomena)

•Develop causal explanations (figure out underlying processes)

Hypothesis-testing (hypothetico-deductive reasoning)

•Identifiy problem/question

•Conceive an explanation (hypothesis)

•Conceive (deduce) a falsifiable prediction

•Test prediction (if false)

Causal Explanations Lie at Two Levels

•Proximate Explanations

•the mechanistic “how” explanations

•answers tend to be rooted in cell-, tissue- and organ-level physiological processes

•often amenable to experimental approaches of hypothesis testing

•Ultimate Explanations

•the evolutionary “why” explanations

•often amenable to experimental approaches, but also often best approached with comparative methods

Strength of Inference

•Generally speaking, experimental approach is considered a stronger form of inference. Why?

Strength of Inference

•Generally speaking, experimental approach is considered a stronger form of inference. Why?

•One can control all but a single variable in an experiment, ruling out alternative competing explanations

•Causation is more firmly established (than in comparative work), because manipulation, tweaking, of one variable has a specific effect that is predicatable in space and time

Strength of Inference

•Generally speaking, comparative approach is considered a weaker form of inference. Why?

•One can’t control all but a single variable

•The results are often lead to correlations that fall short of making a compelling case for causation (one variable actually “causing” the change in another variable)

Scientific Inquiry

Scientific enterprise

•Describe natural systems (recognize patterns, phenomena)

•Develop causal explanations (figure out underlying processes)

Hypothesis-testing (hypothetico-deductive reasoning)

•Identifiy problem/question

•Conceive an explanation (hypothesis)

•Conceive (deduce) a falsifiable prediction

New Sciences of Geology and Paleontology are strong intellectual influences…

•Catastrophism of Georges Cuvier

•Gradualism of Hutton

•Uniformitarianism of Lyell

•Environmental Determinism

Pre-Origins Ideas about Evolution

•Inheritance of Acquired Characteristics of Lamarck

Continental Drift:

Earths land masses existed as a “super continent” 250 million years ago

How does “evolution” happen at the population level?

…mutation, migration, non-random mating, genetic drift…

and natural selection

What is “natural selection”?

…differential reproduction and mortality

What is “fitness”?

…relative reproductive contribution to subsequent generations

•a. the exponential decline in radioactivity of carbon 14. This siotope has a half-life of 5600 yrs; half the c14 in a specimen will be gone in 5600, half of the remainder will be gone in another 5600 years, half the remainder will be gone in another 5600, etc

•Use of C14 dating to determin age of a fossilized clam shell. Because the half life of C14 is relativel short, this isotope is only reliable for dating fossils less than about 50,000 yrs old. To date older fossils, paleontologists use radioactive isotopes with longer half lives. Radiometric dating has an error factor of less than 10%.