AN INTRODUCTION TO EVOLUTIONARY BIOLOGYAcadec Super Quiz 2008-2009

Table of Contents What is Evolution?

History and Development of a Unifying Discipline

Latin America and Evolutionary Biology Taxonomy, Classification, and Species Mechanisms of Genetic Variation and

Earth’s Diversity Select Topics in Evolutionary Biology

What is Evolution?

In this section:o Evolution and the Nature

of Scienceo The Rise of Evolutionary

Biologyo The Development of

Evolutionary Theoryo Modern Synthesis

Evidence for Evolution

Paleontologists study fossils that give clues to evolutionary processes

Tiktaalik is one such fossil (early tetrapod)

Many other scientific fields support the theory of evolution

Evolution and Biology

• Evolution provides an explanation for the diversity of life

• The passing down of traits is now explained by both evolution and genetics

• Mutations and natural selection change populations across multiple generations

Small and Large Evolutionary Changes

Evolution produces small-scale changes over short periods of time Example: Bacteria with antibiotic resistance

Large-scale changes occur over longer periods of time (speciation)

Speciation and other large-scale changes can help organisms inhabit new environments Example: The amniotic egg

Transitions like these, both large and small, can be found in the fossil record

Evolution in Various Fields

Medicine: genetic analysis of SARS virus

Agriculture: artificially selecting wheat for preferred traits

Industry: selecting molecules for preferred traits

Accepting Evidence of Evolution

Science relies on natural phenomena and testable explanations

Some see the differing natures of science and religion as being in conflict

Many scientists and theologians find no conflict They can reconcile the two explanations of

the world Evolution is still considered a theory, but

has been widely accepted as a fact

Descent with Modification

• Dobzhansky says, “nothing in biology makes sense except in the light of evolution”

• Evolution means change between generations, or “descent with modification”

• A lineage is dependent on an ancestor-descendent relationship

Adaptation

Adaptation is “design” in living things

Adaptation allows organisms to survive and reproduce

Examples include the woodpecker’s beak and camouflage

Evolution Before Darwin

Jean-Baptiste Lamarck wrote Philosophic Zoologique in 1809

Lamarck argued that animals “strived” to adapt (in place to natural selection)

Others before Darwin believed in species fixity The idea that species never

change

Charles Darwin’s Arrival and Reception

After his voyage on the Beagle (1832-37), Darwin failed to reconcile all current theories with the concept of adaptation

Darwin created his own theory, which included the concept of natural selection; Alfred Wallace also arrived at this conclusion on his own

Darwin and Wallace presented their findings in 1858

The theory seemed to contradict the Bible and was controversial among laymen, but was somewhat less so among scientists

Flaws in the Theory of Evolution

• Darwin’s theory of evolution lacked a means of heredity, meaning that there was no mechanism to explain the passing down of traits

• Natural selection insufficiently explained intermediate forms in evolution (like proto-wings), which were seen as better explained by directed variation

Mendelian Genetics

Gregor Mendel explained how traits were passed down from one generation to the next

His pea plant experiments (1856-63) explored concepts of hybridization, and dominant and recessive phenotypes

Mendel mailed his findings to Darwin, who never looked at them

A rediscovery of Mendelian inheritance in the early 1900s led to a marriage between that theory and Darwin’s theory of evolution

The Modern Synthesis

• Fisher, Haldane, and Wright all published materials supporting a connection between Darwinian evolution and Mendelian genetics

• Combined with natural selection, Mendelian inheritance answered all the questions initially raised in 1858

Further Development of Evolutionary Biology

Dobzhansky, Ford, Kettlewell, Mayr, Huxley, and many others published materials on genetics and evolution

The concepts of genotypes and gene pools were incorporated into the new way of thinking

Pre-Darwinian Evolutionary Thought

• Ancient Greeks had theories on evolution

• James Ussher calculated the earth’s age to be roughly 6,000 years old according to Genesis

• Hutton, Lyell, Linnaeus, Buffon, E. Darwin, W. Smith, Werner, Cuvier, and Lamarck all contributed to evolutionary theory

Darwin and the Wallace-Darwin Theory

1. Adaptation2. Variation3. Over-

reproduction4. Natural

selection

1. Variability in traits2. Over-reproduction3. Variability in fitness4. Fitness determines

success5. Heritable traits and

change between generations

Darwin’s Theory The Wallace-Darwin Theory

Concepts in the Modern Synthesis

Genetic definition of evolution: “changes in allele frequencies within populations”

Alleles are different versions of the same gene

Sources of these changes include genetic drift (random changes), gene flow (exchanges between populations), mutation pressure (copying errors in genetic replication), and natural selection (“survival of the fittest”)

Darwin and the Galapagos

In this section:o The Voyage of the HMS

Beagleo Chapter XVII: Galapagos

Archipelago (excerpt from Darwin’s journal)

o Adaptive Radiation of Darwin’s Finches

Darwin’s Background

Raised in the Anglican Church

Loved science, went to medical school (1825)

Dropped out after witnessing surgery on a child with no anesthesia

Joined Christ’s College at Cambridge to study religion and pursue science in his spare time

Before, During, and After the Beagle Two watershed events for Darwin: he re-read his

grandfather’s book and later witnessed his professor, Adam Sedgwick, making a scientific error

Professor Henslow recommended Darwin for the Beagle

Darwin got along with Captain FitzRoy most of the time

During the voyage, Darwin collected many specimens of flora and fauna

Back in England, he married and had 10 children Darwin returned in poor health and stayed that way

until his death in 1882

The Voyage of the Beagle

Darwin’s Journal: Introduction

The text in the guide has been condensed

He gives credit to Owen, Waterhouse, Gould, Jenyns, and Bell for influencing his work

He thanks several colleagues, especially Professor John Henslow, who helped him (from London) during the voyage

The Galapagos

September 15th-23rd

There are ten Galapagos islands, all south of the Equator, spotted with many craters, and volcanic in origin

Chatham Island had relatively few plants, only giant tortoises and some dull-colored birds

Charles Island had been frequented by buccaneers and whalers, now inhabited by political exiles and others

September 29th

Darwin visited Albemarle Island and Narborough Island

Both were covered with black lava formations and much of the islands was sterile

There were black lizards on Albemarle, as well as yellow-brown ones

October 8th – James Island

Darwin came across a group of Spaniards, as well as other small groups

Darwin learned that tortoise meat can be prepared a number of ways, and also visited a salina

Measured the temperature in various instances: the sand was at least 137º F

Mice, Land Birds, and Water Birds

Mus Galapagoensis was the only indigenous terrestrial mammal (and mouse)

Darwin caught 26 land birds, 25 of which were unique to the archipelago

He also caught 11 water birds, only 3 of which were new species

Reptiles – the Tortoise

Darwin discovered snakes, lizards, tortoises, and sea turtles

He was surprised to find no toads or frogs at all, even though the environment seemed ideal for them (perhaps egg differences?)

Tortoises travel to water sources, sometimes four miles a day

The inhabitants believed the tortoises to be deaf

Galapagos Lizards

Aquatic: lives on rocky sea beaches

About a yard long Eats only seaweed When frightened, it will

allow itself to be captured rather than jump in the ocean

When thrown in, it will come out and return to the previous spot

Terrestrial: lives in burrows

Confined to the central islands

Smaller than the aquatic ones

Eats cactus and other vegetation

Will fight another lizard if held next to it

Amblyrhynchus cristatus Amblyrhynchus Demarlii

Shells, Insects, and Plants

Darwin collected 90 shells, of which 47 were previously unknown

Also collected several insects, most of which were new species, but was surprised by how few there were

Collected 100 new species of flowering plants Was extremely surprised that fewer American

species of flora had not arrived at the islands through natural means, given the short distance between the two locations

The Tameness of Birds

Darwin noted that birds were not afraid of humans

The birds could be killed from close range even after other birds had been killed nearby

Darwin believed this to mean that an instinct to avoid humans would have to be passed down through multiple generations

Adaptive Radiation

Adaptive radiation is the diversification of populations into ecological niches

Four key concepts:1. Origins2. Speciation3. Diversity4. Disparity

Finches and Speciation

Darwin’s finches are unique because of their rapid diversification and relative youth (3 MYA)

Allopatric speciation: geographic separation

Sympatry can lead to interbreeding with or without fitness loss or no interbreeding

Environmental Factors

Sympatry is not required for speciation Not all islands might have existed when

speciation began A changing environment has significant effects

on adaptive radiation

Adaptation and Reproductive Isolation 1977 drought:

populations of small finches decreased (no small seeds)

c. 1987 drought: populations of large finches decreased (no large seeds)

Dynamic equilibrium Medium ground finches respond to cues

from their own species even when genetically able to hybridize

Finch Songs

Songs are learned traits passed down from parent to offspring

Songs are particular to populations, not necessarily entire species

Changes in environment can lead to natural selection of different songs than those of a parent species Some changes to songs are by chance, not

natural selection alone

Adaptive Landscapes

Genotype and phenotype frequencies can be plotted on a 3D landscape to determine fitness

Areas of best fitness are known as peaks

Adaptive Landscape and the River of Life

Genotype and phenotype frequencies can be plotted on a 3D landscape to determine fitness

Areas of best fitness are known as peaks

The river of life is a visual metaphor that may replace the tree of life (accuracy)

Taxonomy, Classification, and Species

In this section:o Classificationo Taxonomy

Taxonomy, Traditional Classification, and Cladograms

Aristotle, John Ray, Carolus Linnaeus, and Robert Whittaker all made significant contributions to taxonomy

Classifications from largest to smallest: Kingdom, Phylum, Class, Order, Family, Genus, Species

Traditional classification focuses on common ancestry and amount of divergence (major characters)

Cladograms focus on derived characteristics and incorporate parsimony

Cladistics vs. Phenetics

Uses one or more derived characters

Focuses on lineages and common ancestry

Does not include overall similarity

Uses algorithms to determine similarity

Mathematical and objective

Not used very often, but helpful in objective studies

Cladistics Phenetics

Nomenclature

According to the International Code of Botanical Nomenclature:1) All taxa belong to a higher taxonomic

group2) The first name for a new species to be

published is considered valid (the “dibs” rule)

3) All new taxa must have an author

Definition of a Species

Unlike all other categories (e.g. Kingdom), species are not an artificial construct, and actually exist in nature

Reproductive compatibility typically defines a species (can these two animals have fertile offspring?)

Asexual reproduction and grey areas make this definition imperfect

Nomenclature and Classification

Taxonomic keys help scientists determine which species an organism is

Evolution and lineages determine the closeness of relationships in classifying multiple organisms

Example of Dichotomous Key

Dichotomous keys use technical language in simple steps to help classification

Methods of Classification

Phenetics (numerical taxonomy) uses algorithms for an objective classification

Cladistics is the most popular and focuses on lineages

Evolutionary taxonomy is a combination of the two, but considered arbitrary by most scientists

Kingdom Systems

Kingdoms, ranging in number from three to thirteen in some systems, are the largest taxonomic group

The most common is a five kingdom system, but it is being replaced by a six kingdom model

Mechanisms of Genetic Variationand Earth’s Diversity

In this section: The Evidence for Biological

Evolution Evolutionary Mechanisms Introduction to Evolutionary

Biology On the Many Origins of

Species Speciation Standing in Place

Contributions From Other Areas

Paleontology: fossils

Genetics: DNA Astrophysics and

geology: age of the earth

Physics and chemistry: dating methods

Anthropology: human origins

Origins of the Universe and Earth

Georges Lemaitre: the Big Bang theory

Background radiation and distances allow for dating of the universe

Universe: 14 BYA Earth: 4.6 BYA Moon: 4.4-4.5 BYA

Life’s Formation on Earth

Life is at least 3.5 billion years old

Life required three conditions to form: self-reproducing molecules (RNA?), enough molecules for variation, and heritable variations

Protocells with variations led to natural selection

The Fossil Record

Newer sediment deposits are closer to the surface (and those fossils resemble modern organisms)

540 MYA: hard-bodied organisms begin to dominate the fossil record

Tiktaalik is a transitional form

Archaeopteryx: dinosaur-bird?

Homologous and Analogous Structures

Homologous structures are morphological characteristics in multiple organisms that come from a single ancestral lineage (like human arms and dog forelimbs)

Analogous structures look similar but do not come from a common ancestral origin (like a dolphin’s and shark’s front fins/flippers)

Evolution and Geographical Distribution

Evolution and Geographical Distribution

Organisms live in so many different places because evolution (via adaptive radiation) produces a variety of life forms suited to ecological niches

Variations in precipitation levels, elevations, soils, and other factors lead to rapid speciation in colonizing species

The Impact of DNA

DNA provides clues to past genetic changes According to genetic information, humans are closely

related to chimpanzees, but increasingly far from gorillas, mice, chickens, and puffer fish

DNA shows how much all life on Earth has in common

The Impact of DNA

DNA provides clues to past genetic changes According to genetic information, humans are closely

related to chimpanzees, but increasingly far from gorillas, mice, chickens, and puffer fish

DNA shows how much all life on Earth has in common

Humans and Chimps

Humans are 98% genetically identical to chimpanzees

In the case of one gene, all of the differences between humans and chimps (only 5 out of 250 nucleotides) could be matched on one side by gorilla DNA

Human Evolution Timeline

Evolutionary Mechanisms

Mutation, recombination, and gene flow increase genetic variation

Mutations can be beneficial, deleterious, or neutral

Genetic drift and natural selection decrease genetic variation

Natural selection can be directional, stabilizing, or disruptive

Case Study: Manchester Moths

The Evolutionary Process

Gene mutation leads to individuals being selected which leads to population evolution

Microevolution: gene mutations, small changes

Macroevolution: speciation, big changes

Abiogenesis is the theory of how living things first appeared (this is NOT evolution)

Misconceptions

Morphological change and evolution are not always bound to one another

Tiny changes might be the environment acting on an organism, and not really evolution

Organisms act on the environment just as much as the environment acts on organisms

Genetic Variation

Mutation types: deletion, duplication, inversion, insertion, translocation

Most animals are diploid (two alleles for every gene at each locus)

Homozygous: same alleles Heterozygous: two different

alleles Linkage disequilibrium alters

allele frequency

Mating

Assortative mating creates a non-random distribution of alleles at a given locus

Non-random mating disrupts the Hardy-Weinberg equilibrium (allele frequencies)

Humans tend to mate with individuals of the same race, meaning there are fewer heterozygotes than predicted in the Hardy-Weinberg equilibrium

Natural Selection

Sometimes heterozygotes are more fit than either homozygotes (malaria)

Reproductive success: direct, indirect, and inclusive fitness

Traits can end up used for something other than their original purpose This process is called

exaptation

Sexual Selection

Fitness is not always related to being big, fast, or strong; reproductive success is more important

Females often select males based on secondary characteristics (peacock’s tail, flashes in fireflies)

These characteristics may reveal “good genes” or other desirable qualities in males

Genetic Drift

Genetic drift is a random sampling error that occurs naturally in all sexually-reproducing populations

Mutations and genetic drift generally balance each other (mutations adding and drift subtracting)

Fisher and Wright disagreed on the importance of drift: Fisher said it had a negligible effect on large populations, while Wright said it was important in all populations

Unlike drift, the founder effect represents the remaining genetic material after a population “crash”

Mutation and New Alleles

Most mutant alleles are neutral Some are harmful The smallest proportion are beneficial

Most new mutations are lost from the gene pool within one generation

Neutral mutations lost due to random drift, deleterious ones often selected against, and beneficial ones selected for (but still often lost)

Beneficial mutations happen less frequently but thrive most often

Recombination and Gene Flow

Recombination is the mixing of maternal and paternal alleles during cell replication

It increases variation by shuffling genetic material

Gene flow is the addition of new genes via population mixing

Gene flow between distantly related species is horizontal transfer Horizontal transfer is rare

Evolutionary Mechanisms – More

Genetic variation in a population is determined by the balance of mechanisms Natural selection can be positive or negative Genetic drift is random, so it cannot be positive or

negative Recurrent mutation of a beneficial allele will help it

reach fixation An allele that “catches a ride” with a beneficial allele

is a hitchhiker

Evolutionary Theory and Genetics

Lamarck’s theory and Darwin’s studies are two early contributions to the new field

Mendel mailed Darwin his paper but Darwin never opened it

Mendel’s work was not accepted early on because he only studied discrete traits

Fisher’s Fundamental Theorem of Natural Selection states that adaptive change in a given population is proportional to the genetic variation present

DNA and RNA

DNA nucleotides: adenine, guanine, cytosine, thymine

RNA: uracil instead of thymine; used in transcription

Introns do not code, exons do

Silent and replacement sites evolve at different rates

Evolution and Development

Vestigial structures are traces of ancestry in modern animals Example: the human

appendix Common descent and

macroevolution are supported by the organization of traits (nested patterns of evolution)

Speciation

Allopatric speciation occurs with geographic separation (most common)

Sympatric speciation (sometimes called microallopatric speciation) occurs without geographic separation

Extinction

Normal extinction occurs for many reasons Competition, disappearing habitat, loss of

food source, etc. Mass extinction follows large-scale

events Asteroid impact, climate change, humans

Mass extinction is followed by huge periods of adaptive radiation because there are empty niches to fill Largest mass extinction: end of the Permian Most famous mass extinction: Cretaceous-

Tertiary boundary

Punctuated Equilibrium

Punctuated equilibrium theory states that evolution is not a steady process Instead, long periods of

relatively little evolution and change are broken up by bursts of rapid change

Proposed by Stephen Jay Gould and Niles Eldredge

Evolution’s Importance

Evolution unites disparate fields of biology

It explains the distribution of traits across multiple lineages and the variation of life on Earth

It helps explain how modern species came to be

Rhagoletis: A Case Study

The apple maggot Rhagoletis is diverging into two species Speciation began without

geographic separation Cause appears to be mating

habitat preference (apple and hawthorn plants)

Studied first by Benjamin Walsh, then by Guy Bush

Diversity in the Amazon

Speciation in the Amazon was originally thought to occur according to river separations

Research revealed that ancient ridges were responsible for some speciation

Mitochondrial DNA helped separate the two causes

Sympatric Speciation and Frequency

Sympatric speciation is an explanation for speciation that occurs with no apparent physical separation Has occurred with other flies, fish, butterflies The theory is established; now the focus is on

how and why

Sympatric Speciation Examples

Indigobirds – prefer mates that know the same song

Cichlids – exist at different depths within one lake

Palm Trees – initially separated by soil differences, now kept apart by flowering timing

Sympatry: How Significant?

Some argue that the examples are still allopatric on a small scale

Others argue that sympatry exists but is very minor in the big picture of evolution

Some “clear cut” cases of allopatry are now attributed to sympatry

Select Topics in Evolutionary Biology

In this section:o Jurassic

Genomeo Turn On: A

Revolution in the Field of Evolution?

o Evolution and Tinkering

Genome Sizes

Big genomes are found in animals with big bone cells

Small genomes are found in animals with small bone cells

Junk DNA: non-coding material (98.5% of human DNA)

Fossils and Genomes

Birds evolved from theropods, which had relatively small genomes This contradicted the assumption that

small genomes evolved with flight Genome sizes may be affected by

natural selection

Embryos and Evolution

Recapitulation: “ontogeny recapitulates phylogeny”

Two kinds of change Through a lifetime Through a lineage

Is embryonic development a small-scale model of evolution?

Evo Devo’s Findings

Evo Devo is short for evolutionary developmental biology

All animals are built from essentially the same genes (including Hox genes)

Differences in animals are caused by the same genes expressed at different times and places

Evolution is mostly a matter of “throwing switches”

“Throwing Switches”

Gene expression, not gene presence, is the guiding force of evolution

Secret to this might lie in the non-coding or “junk” DNA This may explain the

wide variation of life with so few genes

Evo Devo: A Revolution?

Evo devo may be more of a paradigm shift than a revolution

Darwin’s theory of evolution and Mendel’s theory of inheritance were revolutions

Evo devo is not quite as significant a breakthrough, but still important

The Nature of Science Science follows a

method Hypotheses have to

be testable Science gives

provisional answers to limited questions

Religion and mythology can offer comprehensive answers

Hierarchy of Objects and Constraints

Sciences can be arranged in order of complexity (physics to psychosociology)

Successive integrations in nature: analyzing complex objects at all levels and determining predictability

Constraints and history dictate evolutionary systems

Natural Selection

Natural selection is the result of two constraints Reproduction Ongoing interaction with the

environment Natural selection gives direction to

changes

Natural Selection as a Tinkerer

Natural selection is not an engineer Engineers use specific tools to achieve a

planned result with an ideal outcome in mind

It is a tinkerer It does the best it can with what is

available Some evolutionary changes appear to be

constant, small-scale improvements (not long term “projects”)

Results of Tinkering

Human females spontaneously abort nearly all malformed fetuses before the first 3 weeks of pregnancy

Humans have developed an association between pleasure and sex to spur them to reproduce

Tinkering and the Human Brain

New structures superimposed over old ones

Conflicts between the “visceral” brain and the logical brain occur because of these additional structures and connections

Conclusions

Darwin, Wallace, and many others represent the foundation of the unifying theory of evolution

Theories about evolution are shifting because of new genetic information and breakthroughs in other fields

Though most scientists agree evolution is a fact, there are still questions about types of evolution (sympatric vs. allopatric), its speed, and how exactly it occurs

Developing fields like genetics and evo devo are uncovering new information and raising even more questions