AN INTRODUCTION TO EVOLUTIONARY BIOLOGY Acadec Super Quiz

AN INTRODUCTION TO EVOLUTIONARY BIOLOGY Acadec 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 o Evolution and the Nature of Science The Rise of Evolutionary Biology The Development of Evolutionary Theory 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 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 1900 s 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 Darwin’s Theory 1. 2. 3. 4. Adaptation Variation Over-reproduction Natural selection The Wallace-Darwin Theory 1. 2. 3. 4. 5. Variability in traits Over-reproduction Variability in fitness Fitness determines success Heritable traits and change between generations

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 Beagle o 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 Fitz. Roy 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 15 th-23 rd 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 29 th Darwin visited Albemarle Island 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 8 th – 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 Amblyrhynchus cristatus Aquatic: lives on rocky sea beaches Amblyrhynchus Demarlii Terrestrial: lives in burrows Confined to the central islands Smaller than the aquatic ones 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 Eats cactus and other vegetation Will fight another lizard if held next to it

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. 2. 3. 4. Origins Speciation Diversity 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 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 3 D 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 3 D 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 Classification o 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 Cladistics Uses one or more derived characters Focuses on lineages and common ancestry Does not include overall similarity Phenetics Uses algorithms to determine similarity Mathematical and objective Not used very often, but helpful in objective studies

Nomenclature According to the International Code of Botanical Nomenclature: 1) All taxa belong to a higher taxonomic group 2) 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 Variation and Earth’s Diversity In this section: The Evidence for Biological 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: selfreproducing 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 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 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 6 -7 MYA last common ancestor of humans and chimps 4. 1 MYA Australopithecus afarensis (southern ape) 2. 3 MYA Homo habilis (skillful man) 1. 8 MYA Homo erectus (upright man) 200, 000 years ago Homo sapiens (wise man)

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

Soot covered the birch trees Rapid natural selection occurred Soon after 1848 Biston betularia moths were mainly lightcolored The Industrial Revolution Before 1848 Case Study: Manchester Moths The moths were primarily darkcolored

The Evolutionary Process Gene mutation leads to individuals being selected which leads to population evolution Microevolution: gene mutations, small changes Macroevolution: speciation, big changes Abiogenesisis 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 effectrepresents 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 Mass extinction follows large-scale events Competition, disappearing habitat, loss of food source, etc. 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 o o Jurassic Genome Turn On: A Revolution in the Field of Evolution? 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 smallscale 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 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