Evolution and Population Genetics Flashcards
History of Evolution, Variation, Inheritance, Hardy-Weinberg, Malthus, Mendel, Population Genetics, Selection and Fitness.
Evolution
a change in allele (gene) frequencies in a population over time.
4 Rules of Evolution
- Variations exist in the population (via mutations) BEFORE any selection
- Populations evolve, NOT individuals
- Selection is NOT random
- Changes (i.e. evolution) happens across generations, not within a generation
Genotype
all the genetic characteristics that determine the structure and functioning of a organism
Genotype governs reproductive output and affects competitive ability
Determining genotype may be complicated because:
- Phenotype may be similar for different genotypes - Environmental effects may interfere with expression
- Multiple genes may be implicated in a single phenotype
Phenotype or trait
the physical expression in an organism of the interaction between its genotype and its environment
Population
the group of organisms of a particular species that inhabit a particular area~ often arbitrary
antibiotic resistance
What happened? Evolution by natural selection
4 Agents of Evolution
- Mutation
- Genetic Drift = Random events
- Gene Flow = Movement = Migration
- Natural Selection = Adaptive evolution (including sexual selection)
What is NOT biological evolution?
- Individual Development
- Ecosystem Change
- Cultural Evolution
Individual Development
Changes in form, physiology, behavior as an individual grows. These changes occur within individuals, not within populations or species (within generations, not across generations).
Example: metamorphosis
Ecosystem Change
Changes in species composition and abundances.These changes occur within ecosystems, not within populations or species.
Cultural evolution
Changes in ethics, politics, economics, technology, ideas; ideas transmitted through learning, not genetic change
- e.g., the “evolution” of evolutionary theory is not biological evolution
Example of Cultural Evolution
Japanese macaques
Researchers in 1950’s left sweet potatoes on beaches to lure macaques out of the forest. One young macaque discovered that she could wash sand off potatoes by rinsing them in water (new behavior). Her siblings and mother soon learned the behavior, and over time the entire macaque population gradually learned to wash potatoes by imitation. Macaques also learned how to “season” potatoes with saltwater, use water to sort wheat from sand, bathe in hot springs, and even make snowballs for fun! This is cultural evolution by learning, not biological evolution (in which change occurs because heritable traits are passed from parents to offspring).
Why is Evolution Important?
The central unifying theory of modern biology
Theodosius Dobzhansky
“Nothing in biology makes sense except in the light of evolution.”
–Theodosius Dobzhansky (1973)
Dobzhansky was a Evolutionary biologist, key figure of the Modern Synthesis with his “Genetics and the Origin of Species” (1937)
Quoting the French philosopher Pierre Teilhard de Chardin in his essay:
“Evolution is a general postulate to which all theories, all hypotheses, all systems must hence forward bow and which they must satisfy in order to be thinkable and true. Evolution is a light which illuminates all facts, a trajectory which all lines of thought must follow – this is what evolution is.”
Why study evolution?
- To understand the diversity of life…
- Conservation biology
- Fisheries management…
- Agriculture
- Medicine…
- Forensics and paternity analysis…
Conservation biology
a. Identify genetically distinct lineages that warrant conservation status.
Example: Achatinella mustelina - a single species of land snail endemic to the “big island” of Hawaii. Polymorphic for shell color along distinct geographical zones
ESU’s = Evolutionarily significant units
b. Population size, inbreeding depression, and genetic variation.
Inbreeding Depression
Relatives more likely to mate in small populations (= inbreeding). Relatives more likely to share copies of deleterious alleles.Produces offspring with 2 copies of deleterious allele.Inbred European viper populations have more birth defects and stillborn young (= inbreeding depression).
Low Genetic Variation
Genetic variation accumulates via mutation and recombination.
After population crashes, population size may recover quickly BUT…
Genetic variation remains low because mutation and recombination require more time.
Consequence: Populations with low genetic variation cannot evolve in response to changing environments.
Example: Cheetahs
Fisheries Management
Removing large fish selects for slower growth rate:
Fish populations evolve in response to fishing “selection”Fishing not only depletes populations, it can change their life history
Common practice is to harvest large fish
Experiment by Conover & Munch shows that harvesting fish causes an evolutionary response - alteration of their life history (attempt to maximize reproduction and survival)
Management recommendation: set both lower and upper limits on size in order to offset effects of selection
Agriculture and Evolution
Artificial selection has produced or enhanced most of our important agricultural crops and livestock.
Escape of genetically modified (GM) genes into wild populations
Genetically engineered crops developed as a means to facilitate weed and pest control…
Pest species evolve resistance to pesticides. The more we use pesticides, the more we select for resistant pests… (ex: canola and wild mustard)
Increase in pesticide-resistant species
Antibiotic Resistance
Bacteria have short generation times, lots of variation, and easily pickup “pieces” of DNA which
allow bacteria populations to evolve quickly.
Bacteria evolve resistance to antibiotics The more we use antibiotics, the more we select for resistant bacteria… People often think that the patient is becoming physiologically “desensitized” or developing a tolerance to the antibiotic drug.What is actually happening is that the antibiotics are killing vulnerable bacteria, which selects for any mutations that produce resistant bacteria.In other words, the patient is not changing, the bacteria are evolving.
Viruses also evolve rapidly (HIV-AIDS, influenza, hepatitis). Evolutionary trees help us understand where a virus came from, how it may have evolved, and how to treat various “strains.”
Strains are derived from single lineages
Huntington’s Chorea
disrupts nerve function, loss of control over body and mind, then death.
Symptoms do not occur until late in life (after reproduction).Disease “invisible” to selection. Although the disease is “invisible” to natural selection, genes for Huntington’s Chorea can now be detected by genetic analysis so that carriers can decide whether or not to have children.
Many severe genetic disorders are maintained in human populations.Shouldn’t natural selection remove genetic defects from the population?
Screening for diseases
Determine pathways and proteins impacted by gene
Look for correlations between diseases and presence of allele
Forensics and paternity analysis…
DNA fingerprinting can identify criminals and determine child paternity. “Non-coding” sections of the genome are “invisible” to natural selection, so they rapidly accumulate mutations that can distinguish between individuals.
Noncoding regions are not constrained by having to create specific proteins
Often consist of repeating sequences (created by errors in recombination)
Essentialism
- The physical world and its life forms are fixed
- All members of a class share unchanging properties that define the class
- Attributed to Greek philosopher Aristotle (384-322 BC)
Is color adaptive?
sometimes, depending on …..
Adaptations MUST
• Improve fitness such that organisms WITH the trait have higher fitness than those without
(All other things being equal)
• Show correlation between the presence of the
feature and the hypothesized selective pressure
Does it enhance fitness?
Does its presence correspond to a
specific selective regime?
Types of Adaptions
Feeding specializations
Crypsis
Mate attraction or competition
Adaptation
specialized features that enhance fitness
Adaptation (v) is the process by which features that enhance fitness are fixed in a population or species.
Scala Naturae
- The “great chain of being”
- Life arranged hierarchically, culminating in divinity
Carolus Linnaeus
(Swedish,1707-1778)
- Carl von Linné, botanist, father of modern taxonomy
- Systema Naturae (1735) – binomial nomenclature - Hierarchical taxonomy embodied Scala Naturae - Still used today, but reflects evolutionary relationships
Old thought
Chair and chairness
The physical world and its life forms are fixed – most controversial aspect of what Darwin proposed, was that species were NOT fixed in form (fixed as unchanging)
All members of a class share unchanging properties that define the class
Evolutionary thinkers existed but they lacked mechanisms to drive evolution
George-Louis Leclerc
a.k.a. Buffon
(French,1707-1788)
- Recognized that differences between
related species living in different parts
of the world reflect the different
environments they inhabit - After migrating, organisms must somehow
change to suit their new environment
Jean-Baptiste Lamarck
(French, 1744-1829)
- Philosophie Zoologique (1809)
- First explicit scientific treatment of evolution
Lamark proposed a mechanism, now shown to be incorrect:
“internal force” (unknown) that causes parents to produce offspring slightly different from itself = accumulates changes over time, so species transform into another one.
No extinction and no branching
Transformism
Inheritance of acquired characters
- Individuals change during development
- If changes are beneficial, parents transmit
these acquired characters to their offspring
- Famous discussion of giraffe’s neck
Transformism
- Lineages persist forever, but change in form
- Vague mechanism of “internal force”
- No extinction or branching of lineages
Georges Cuvier
(French, 1769-1832)
- Paleontologist and comparative anatomist
- Strong critic of Lamarck’s ideas
- favored essentialism. Disputed Lamarck’s claim that forms change gradually over time
Extinction
- First to firmly establish extinction as fact
- Rigorously reconstructed and classified fossils of mastodons and many other extinct organisms
- attributed extinction to discrete catastrophic events
Essentialism
- Disputed Lamarck’s claim that forms change gradually over time
- Correlation of parts – organisms are so integrated in form and function that any changes would lead to death (“irreducible complexity”)
The Geologists
James Hutton and Charles Lyell
Charles Lyell
(British 1797-1875)
- Uniformitarianism Historical changes result from uniform geological processes that still occur today (e.g., erosion, sedimentation, volcanism)
- supplanted geological catastrophism
Earth is very old and is always slowly changing.Past can inform the present, and vice versa.
Lyell’s ideas profoundly influenced Darwin.Could species also change gradually along with these changes to their environment?
Gradualism
James Hutton, (Scottish 1726-1797)
- Gradualism Earth’s physical features gradually changed due to slow geological processes
Uniformitarianism
Historical changes result from uniform geological processes that still occur today (e.g., erosion, sedimentation, volcanism)
Changing views of earth’s history
Earth has had a complex history during which it has changed significantly in terms of its geology, topography, and inhabitants.
The complexity of the Earth’s history can be explained in terms of the processes that are observed today —erosion, volcanism, etc
Implications:
Earth is very old and is always slowly changing.
Past can inform the present, and vice versa.
setting the stage for Darwin
Essentialism is dominant
- Most people, including most biologists, still thought that species do not change, in part because of influential essentialists like Cuvier or Linnaeus
No satisfactory theory for biological diversity
- Those who favored evolution (Lamarck) had incorrect views of the process (transformism) and the mechanism (inheritance of acquired characters)
Extinction and Branching
- Cuvier demonstrates that extinction happens
- Even those who favored “evolution” did not think species could “split”
Uniformitarianism is promoted
- Geologists (Hutton and Lyell) argue that the Earth is old and constantly changing, not static and unchanging as thought by essentialists
- Could species also be gradually changing with their environment?
Darwin
Did not invent the idea of evolution: he explained observations – came up with hypothesis
Only later did hypo became a theory: Science is “organized skepticism”.
Scientific Theories are constantly evaluated and updated: DATA
Scientists would discard the Theory of Evolution if it were inconsistent with observations
New discoveries (DATA) in biology continue to validate the Theory of Evolution
SO FAR….no tested hypotheses or observations have negated the Theory of Evolution
He proposed a mechanism for evolution:
Natural selection
Descent with modification is the outcome of evolution
Came up with a hypothesis to explain evolution
Catalog of evidence supporting decent with modification:
(THE FACT OF EVOLUTION)
Proposed natural selection :
(MECHANISM OF EVOLUTION)
The Beagle arrived at the Galapagos in 1835.
What led to his ideas about evolution?
Modern species, in at least some cases, resemble fossils
Modern domesticated animals can be made to vary through intentional selection (artificial selection)
The creatures in archipelagos vary from island to island
Organisms may have very complex modifications that are necessary for their survival
General observations about domesticated varieties
Unlike wild species, most varieties are freely inter-fertile
Closely related varieties show more pronounced morphological differences than closely related wild species
Common opinion among animal and plant breeders held that domesticated varieties arose from wild ancestors that had the same or similar characteristics as the domesticated variety
In other words, each variety is descended from a unique ancestral species.
Domesticated pigeons resembled only one wild species …
Artificial selection
new varieties arise by preferentially breeding individuals showing specific desirable traits.
Traits arise as random “sports” that are then selectively bred.
This process occurs over many generations, not in a single step
“Improvement” of breeds is a continual process, resulting in the accumulation of fairly significant modifications in a relatively short period of time
Galapagos
The Beagle arrived at the Galapagos in 1835.
Darwin did not pay much attention to the finches after leaving the Galapagos.The following year (in 1837), the ornithologist John Gould made a descriptive account of the Galapagos collections, with the surprising opinion that the finches belonged to the SAME family.
Close observation showed a wide range of variation in the size and shape of the beaks; These differences correlated with feeding preferences
Each feeding type has a characteristic range of beak shapes. The 13 species of finches found on the Galapagos comprise the same number of feeding types as 9 FAMILIES of birds in South America.
The Galapagos Islands have a harsh, arid climate, characterized by extended periods of severe drought. Annual cycles: hot, wet winters, cooler, dry summers. Multi-year cycles of extreme droughts (ENSO).
Thomas Robert Malthus
(1766-1894)
“An Essay on the Principle of Population, as It Affects the Future Improvement of Society, with Some Remarks on the Speculations of Mr. Godwin, M. Condorcet, and other Writers.”
(1798, published anonymously)
Usually referred to as the “Essay on Population”
Premise: Left unchecked, human reproduction rates will rapidly outpace resource production, leading ultimately to “crime, disease, war, and vice.” (these being “natural” checks on population growth)
Struggle for existence
Thomas Robert Malthus
Reproductive potential AND reproductive effort GREATLY exceed requirements of reproductive replacement
At the point where population size outstrips resource production, there are only two alternatives: find the means to expand the resource pool, or DIE.
WHICH organisms survive has to do with interactions among organisms, and between organisms and their environment
Finches and the “Malthusian dilemma”
In periods of drought, favorable resources (e.g. soft buds and seeds) are quickly depleted, leaving only less favorable food (hard, tough seeds, etc.)
Only those birds with beaks capable of breaking these tough food items can survive.
Death of “unfavorable” birds readjusts population size to the available resource pool.
“Favorable” beak morphologies are passed on to offspring
Very small morphological changes
accumulate over a long period of time,
leading to eventual (morphological)
divergence of populations
Widely differing morphologies
gradually become reproductively
incompatible
“Seeing this gradation and diversity of structure in one small, intimately related group of birds, one might really fancy that from an original paucity of birds in this archipelago, one species had been taken and modified for different ends.”
C. Darwin
“The Voyage of the Beagle” (1845)
The 4 postulates of natural selection
Variation: “Individuals within species are variable.”
Inheritance: “Some of these variations are passed on to offspring.”
Differential survival: “In every generation, more offspring are produced than can survive.”
Extinction: “The survival and reproduction of individuals is not random. Individuals who survive and reproduce are those with the most favorable variation…”
Darwin proposes more than natural selection
Common descent
Gradualness of change over time
Population differentiation
Natural selection
Common descent
All living things part of a community of descent.
Organisms that are more closely related (have a more recent common ancestor) more similar than those that are more distantly related
Gradualness of change over time
Differences among organisms have accumulated in small increments over a long time
Outgrowth of his “uniformitarianist” perspective
Population differentiation
Changes in species reflect changes in the proportion of individuals in a population bearing certain hereditary traits
Changes in species take place at the level of individuals within population
Talking here about variation among individuals
Not a sudden origin of new species, or transformation of individuals
VARIATION, NOT TRANSFORMATION
Natural Selection
Population differentiation caused by differential reproductive success of individuals bearing particular traits
Individuals that have more success are those better able to use resources in a particular habitat
Same principles independently derived by Alfred Wallace during his work in Malaysia
Alfred Russell Wallace
Professional “curiosity” collector
Wrote a paper on natural selection in 1858 and sent it to Darwin.
A year later Darwin published “Origin of the Species”
We cannot talk about the history of Darwin without mentioning his nemesis,
Into this historical setting there stepped a man whose role in the history of biology is enigmatic and often under appreciated, Alfred Russell Wallace. Wallace was a poor man of limited education who had to struggle just to get by. He earned his living by voyaging to places like South America and the Far East and collecting many
Maybe he didn’t want to arouse controversy. Maybe he was afraid to offend many peoples religious sensibilities.
Anyway, what happened next is a fascinating story. Wallace, racked with a high fever in the tropics of Southeast Asia came up with the concept of natural selection. The idea that all organisms were engaged in a struggle for existence, and the survivors were those that went on to populate the world. Those that tended to survive and give rise to future generations were more fit or better adapted to the environment than those that didn’t make it. Thus, the earth’s flora and fauna changed through time. After Wallace recovered from his fever, he wrote a paper on this topic and sent it to Charles Darwin whom he didn’t know but had heard of, asking him to present it at a prestigious English scientific meeting. The year was 1858.
Darwin, upon receiving the manuscript, went into a state of shock. Here was someone who had come up with what he thought was his idea alone. He realized the scope of all those years of work and thought during which he had not published. Then, Darwin went feverishly went to work writing. He first took Wallace’s paper and added to it a long section of his own. He added his name to the paper as a co-author and then he included a letter signed by 2 famous scientists of the day describing how he had been thinking of these ideas long before Wallace, and then the paper was read at the meeting and published, while Wallace was in Asia.
A year letter, “On the Origin of Species by Means of Natural Selection or the Preservation of Favored Groups in the Struggle for Existence was Published”. What is typically referred to as Darwin’s Origin of the Species. Darwin received almost all of the credit for the idea of Natural Selection described in the book and he also received the credit for convincing people that evolution by common descent had occurred.
The moral is, never ask somebody you don’t know to read something to an audience when you can’t make it there. The interesting things is that Wallace and Darwin became friends. Wallace was very magnanimous, that is, he didn’t feel like he didn’t need to get credit, or he was very stupid. Basically he appreciated the fact that Darwin gave him any credit at all. In those days, if you were poor in England you had little prospect for success, and Darwin’s money and prestige made it easier for him to obtain most of the credit at the expense of Wallace, but also, I think, made the idea more palatable to the general public who could understand how a rich, well known gentleman scientist could come up with a great idea but would sadly probably not be able to understand how some poor unknown came up with a great idea.
It’s sad, but things still can work like this in science. In the end, it might be hypocritical to fault Darwin. How many of us, in the face of seeing 18 years of work down the tubes, when given the opportunity to obtain credit for an idea wouldn’t have done what he did. In the end, it’s best to view Darwin like any other great thinker. He was human and therefore flawed. Those who came before him had created an atmosphere in which ideas on evolution could be accepted. He was smart, and in the right place at the right time, which sure beats being in the wrong place at the wrong time.
Darwin’s Reception
The general idea of evolution
- Controversial among the general public
- Scientists generally accepted evolution per se
Darwin’s particular concept of evolution
- Controversial among scientists, most of whom envisioned “progressive” change
- Darwinian evolution based on lineage splitting, NOT inherently “progressive” towards higher forms
Darwin’s Mechanism of Natural Selection
- Generally rejected by scientists
- One important flaw was the lack of a mechanism for heredity
At this point, however, there are still two serious gaps in our knowledge:
By what mechanism does inheritance occur?
How is variability generated in populations?
A big flaw in Darwin’s theory
Darwin lacked a theory of inheritance
For lack of a better alternative, Darwin favored blending inheritance:
New variant arises and is favored by natural selection. Offspring are intermediate. Trait spreads, but is further diluted. After many
generations, trait is prevalent but blended away.
There are naturally existing differences in a population (=variation)
• More offspring are produced than can survive
• Organisms with favorable variation will be preserved (i.e., will leave more offspring)
• Accumulation of differences over time leads to adaptive radiation
Darwin’s Main Interest….
• Establishing Natural Selection as the mechanism for Evolution (On the Origin of Species by Means of
Natural Selection,or the Preservation of Favored Races in the Struggle for Existence)
Without variation, there can be no evolution!
True or False?
TRUE!
Variation
Variation is the raw material for evolution by natural selection
Natural selection is a sorting process of differential survival & reproduction
Without variation, there can be no evolution!
Genetics and environment both contribute to variation.
Four postulates of natural selection expanded on
Variation: “Individuals within species are variable.”
Inheritance: “Some of these variations are passed on to offspring.”
Differential survival: “In every generation, more offspring are produced than can survive.”
Extinction: “The survival and reproduction of individuals is not random. Individuals who survive and reproduce are those with the most favorable variation…”
Discrete Variation
Multiple forms within a species
(ex: polymorphism)
