Evolution Exam 4 (Final)

How to Calculate Indirect Fitness

(# of offspring)(r) = indirect fitness Suppose a young female meerkat can either have her own litter of pups or help raise her mother's pups. >her mother has a litter of four pups that reach adulthood. >Her mother's pups are the young meerkat's siblings and half siblings (0.5 and 0.25) >The coefficient of relatedness, r, for this mixed situation equals 0.32 If the young meerkat attempts to have her own litter the first year she is sexually mature, she will produce no pups that reach adulthood >2nd year = 1 pup >3rd year = 3 pups >4th year = 4 pups The coefficient of relatedness between a parent and pup is 0.5. Using Hamilton's equation, calculate the indirect fitness of the young meerkat for a single year in which she helps raise her mother's pups. Provide the value of indirect fitness to two decimal places. year 1 (4 of moms pups)(0.32)= 1.28 (0 own pups)(0.5)= 0 indirect fitness to help mom year 2 (4 of moms pups)(0.32)= 1.28 (1 pup)(0.5) = 0.5 still better indirect fitness to help mom year 3 (4 of moms pups)(0.32)= 1.28 (3 pups)(0.5)= 1.5 better to have own pups by 3rd year of sexual maturity

3. What is its adaptive value?

-ultimate -how does variation in song structure affect fitness?

4. How did it evolve?

-ultimate -how has song structure changed over evolutionary time?

Newt vs. Garden Snake

--> the garden snake eats the newt --> newt develops skin toxin --> snake becomes resistant to toxin level of newt --> newt evolves to create more toxin --> snake becomes even more resistant --> big circle! now the newt is SUPER toxic to everything except snakes BUT snake is more susceptible to its own predators (cost of evolving to eat newt)

1. How does it work?

-proximate -how do neurons produce the necessary muscle contractions to produce song?

2. How does it develop?

-proximate -how do young bird's acquire songs from older individuals?

Can behavior evolve?

1. Is there variation in a behavioral trait in a population? 2. Does that variation have a heritable component? 3. Do individuals with different behaviors have different reproductive success?

Modern medicine has dramatically decreased mortality

1918 flu pandemic >>>>> HIV/AIDS

Sticklebacks

2 Buckets 1. a Stickleback fish from a lake 2. a Stickleback fish from a marine environment fake fish were arranged in a circle on a wire to simulate a school of fish 1. fish from the lake did not follow the school 2. fish from marine environment followed the school (behavioral predator defense) Other Traits -marine sticklebacks have more armor plates (tough to eat)

Coevolutionary Arms Race

A coevolutionary arms race occurs when species interact antagonistically in a way that results in each species exerting reciprocal directional selection on the other. What would we expect to occur if there was heritable variation for antagonistic traits in only one of the two interacting species? -the coevolutionary arms race would break down, wouldn't happen

Evolution of Antibiotic Resistance

>Antibiotics, and other treatments, exert extremely strong selection for resistance. >Bacteria are capable of acquiring mutations through both vertical and horizontal gene transfer - speeding up the evolution of resistance. >Prevalence of antibiotic usage results in pervasive selection for resistance. >This can occur not only on a large scale, but within a single patient

In which era did the first humans evolve?

>Cenozoic (66 mya - present) >Molecular clocks indicate that the most recent common ancestor of all primates lived ~66-69 mya. >Oldest primate fossil - 55 mya

Evolution of Ebola: 2013-2016 Epidemic

>Ebola outbreaks occur due to zoonotic transmission. >The 2013-2016 Ebola epidemic was by far the largest outbreak in history - with lots of human to human transmission. >Ebola is highly virulent with poor transmission. >How did Ebola evolve during this outbreak?

Hopi Hoekstra: Deer Mice

>Focus: how genes control complicated behavior >She takes a cast of a deer mouse burrow, and since each species (she studied two sister species) has its own characteristic burrow, these lumpy molds embody inherited behaviors. >Length, volume and shape are easily measured. >That data, partly drawn from the field and partly from the lab, once combined with crossbreeding and advanced DNA analysis allowed Dr. Hoekstra to trace the architecture of a mouse burrow right back to the genes. They identified four regions of DNA that help control burrow design: three for length and one for the presence or absence of an escape tunnel.

Difference between humans and apes:

>Fully bipedal, adaptions for running and walking >Shorter fingers and longer, more opposable, thumb >Smaller teeth and flatter face >Enormous brain - relative to body size, our brain is 3X the size of other primate brains. >More extensive tool use.

Evidence of Interbreeding with Neanderthals

>Humans diverged from Neanderthals and Denisovans about 530,000 years ago. >1 - 6% of the genomes of non-African modern humans comes from interbreeding with Neanderthals and Denisovans >If an allele is present in both humans and Neanderthals, but not in West-Africans

Mitochondria

>Mitochondria are derived from free-living bacteria >Mitochondria produce energy in eukaryotic cells • Two membranes • Their own genome • Maternally inherited >DNA sequence similarity shows the mitochondria is more similar to bacteria >Mitochondria have been associated with eukaryotic cells for 2 billion years - maybe first even as ATP parasites.

Molecular (DNA) Evidence

>Molecular phylogenies unequivocally place humans in the primate clade. >Molecular clocks allow us to date splits in the branches of the primate phylogeny.

Learning can Evolve

>Offered fruit flies a choice between orange and pineapple jelly. >One of the jellies was laced with bitter-tasting quinine. >Flies learned to avoid the jelly that tasted bad. >Some flies learned more quickly than others. >Ability to learn quickly was heritable.

Darwin recognized that humans, apes, monkeys, & lemurs shared a common ancestor.

>On the Origin of Species does not mention this evolutionary relationship (1859). > He was afraid that delving into the evolutionary relationship between humans and primates might prejudice readers against evolution. >Published The Descent of Man in 1871. -In The Descent of Man, Darwin pointed out that many similarities between humans and apes are best explained as homologies. -coccyx/true tail -5 fingers and thumb

QTL Analysis of Foxes

>QTL analysis identified candidate genes. >Anna Kukekova used a QTL analysis to identify candidate genes for tameness in foxes. >Using what we have learned about QTL analysis, how do you think she designed her experiment? -More recently, researchers have looked at difference in gene expression in the brains of tame and aggressive foxes. -They identified 177 with significantly different expression levels, 30 of which are in located in the QTLs identified in Kukekova's study.

Domestication of the Dog

>Studies of dog fossils and genes indicate that they were domesticated from gray wolves about 25,000 years ago in Eurasia. >Early domestication appears to have been primarily on behavior.

3. New Adaptations DO NOT Evolve from Scratch.

>They are modifications of previously existing structures, pathways, or other traits. >Complex adaptations are not perfect. -Because complex adaptations are modifications of previously existing structures their evolutionary history can constrain the "perfection of the adaptation"

Phenotypic Plasticity

A single genotype produces multiple phenotypes depending on the environment.

The Out-of-Africa hypothesis makes predictions that are testable using molecular phylogenetics approaches:

All major ethnic groups of humans are derived from recent African ancestry. A group of scientists identified patterns of genetic variation at 1327 loci in 121 African populations, 4 African-America populations, and 60 non-African populations. The constructed a phylogenetic tree using the neighbor joining method.

Antagonistic Pleiotropy: number of cervical vertebrae

Almost all mammals have seven cervical vertebrae. Why? >Mutations that change the number of cervical vertebrae have detrimental effects on other traits. >Human children born with abnormal number of cervical vertebrae are 120 times more likely to develop pediatric cancer.

Hamilton's Rule

Altruistic behavior can evolve if the benefit to the recipient, weighted by the relatedness of the recipient, exceeds the cost of the donor. rB > C

Ancestors of Homo neanderthalensis started expanding out of Africa starting around _________________

Ancestors of Homo neanderthalensis started expanding out of Africa starting around 600 thousand years ago.

Types of Behavior

Animals with a nervous system display two types of behavior: 1. innate 2. learned

Brain Size

Brain size increased gradually over evolutionary time.

Why did hominins shift from moving in trees to walking on the ground?

Changes in climate lead to expansions of woodlands and grassland where there was once tropical forests in Africa.

Coevolution requires heritable genetic variation

Coevolved adaptations arise from the same mechanisms that give rise to the adaptations we have previously discussed. • Parasitoid wasps lay their eggs inside of aphids. • The eggs hatch and feed on the aphid's internal organs. • Aphid's immune cells coat the larvae and can suffocate them.

Belyaev Experiment

Dmitri Belyaev -1959 -Began an experiment to study the process of domestication in real time -He was especially keen on understanding the domestication of wolves to dogs, but rather than use wolves, he used silver foxes as his subjects. >The domesticated silver fox is a form of the silver fox which has been domesticated - to some extent - under laboratory conditions. >The silver fox is a melanistic form of the wild red fox. Domesticated silver foxes are the result of an experiment which was designed to demonstrate the power of selective breeding to transform species, as described by Charles Darwin in On the Origin of Species. >The experiment explored whether selection for behaviour rather than morphology may have been the process that had produced dogs from wolves 1. Staring when the foxes were one month old, the scientists would approach the cage with food. 2. They repeated these tests over several months and measured each fox's behavioral response. 3. They gave each animal a 'tameness score'. 4. By recording the changes in foxes when in each generation only the most tame foxes were allowed to breed. >Many of the descendant foxes became both tamer and more dog-like in morphology, including displaying mottled or spotted coloured fur and floppy ears *Variation in Fox Behavior is Heritable*

Importance of Diversity in Medical Research

Drug effectiveness and the nature of side effects can vary between people of different ancestry.

1. Laws of Physics Constrain Evolution

During the carboniferous period - oxygen levels were much higher - and much larger insects existed. insects rely on diffusion of oxygen through the skin for respiration

Earliest fossil of our own genus (Homo) dates to ______

Earliest fossil of our own genus (Homo) dates to 3 million years ago. Homo habilis ("handy man") made stone tools.

Endosymbionts

Endosymbionts are mutualists that live within another organism -Aster leafhoppers are nutritionally-dependent on two bacterial endosymbionts. -The bacterial species have lost most of the genes they need survive outside of their hosts. -Bacterial endosymbionts synthesize amino acids that they provide to the insects. -Allows them to feed on nutrient-poor plant sap.

Endosymbionts can span _____ evoutionary time spans.

Endosymbionts can span long evolutionary time spans The endosymbionts found in aster leafhoppers today descend from ancient bacteria that were taken up by insects 280 million years ago.

Why haven't flies evolved to be 'smarter'?

Evolutionary Constraints 1. Laws of Physics 2. Antagonistic Pleiotrophy 3. New adaptations do not evolve from scratch

Improper Use of Antibiotics

For antibiotics to work effectively, they must kill all the bacteria causing an infection before the evolution of resistance. Improper Use: • Prescribing antibiotics to patients without bacterial infections. • Not taking the entire prescribed course of antibiotics • Feeding livestock low levels of antibiotics to increase growth.

Rare fossils can provide lots of information:

Fossils of earliest hominins are scarce. But, they indicate that upright posture (bipedalism) was one of the very first steps in the evolution of our lineage.

Game Theory

Game theory is a mathematical approach to studying behavior that solves for the optimal decision in strategic situations where the payoff of a particular choice depends on the choice of others. An evolutionary stable strategy is a behavior, which if adopted by a population in a given environment, cannot be invaded by any alternative behavioral strategy.

Human Variation & Medicine

Growing realization that genetic variation among humans has widespread implications for medicine. • Alleles that cause genetic diseases vary in frequency in different populations. • Different alleles can result in the same disease phenotype. • As a result, optimal treatment may differ between individuals.

Hominins

Hominins include humans as well as all species more closely related to humans than chimpanzees. >Hominins originated in Africa and were restricted to that continent for about 5 million years. >Humans are the only surviving hominin species >Not all of these species are in our direct lineage. >Earliest hominids are known from rare fossils: -Sahelanthropus

Homo erectus started expanding out of Africa starting around _____________

Homo erectus started expanding out of Africa starting around 2.1 million years ago.

Out-of-Africa Model

In the 1980's, a competing hypothesis was proposed. The Out-of-Africa model proposed that Homo sapiens evolved in Africa and that some populations expanded to other continents much later. Evidence: • Earliest fossils with clearly modern traits were found in Africa. • The fossil record of humans outside of Africa begins 100,00 years ago and only gets strong 50,000 years ago.

Inclusive Fitness

Inclusive fitness describes an individual's combined fitness, including its own reproduction as well as any increase in the reproduction of its relatives due specifically to its own actions. A diploid animal shares: • 50% of its alleles with offspring • ~25% of its alleles with nieces and nephews • ~12.5% of its alleles with its cousins Kin selection is selection arising from the indirect fitness benefits of helping relatives.

Individual vs. Group Selection

Individual selection describes selection arising from variation in fitness among individuals. Group selection is selection arising from variation in fitness among groups. What happens when group selection and individual selection oppose each other? -when an individual has the best phenotype it spreads through the group -traits evolve for the good of the individual and then it evolves for the good of the group -a lot of evolutionists say individual selection is most important Cellular Slime Mold: individuals group together stalk: die fruiting body: reproduce and live -certain mutations allow some of the mold cells to live in the fruiting body -why? game theory

Innate Behavior

Innate behaviors are not learned or practiced. • Organisms will preform a behavior the first time it is exposed to the proper stimulus.

Learned Behavior

Learning allows animals to modify their behavior to adapt to changes in their environment. Synaptic plasticity

Where and when did our species evolve?

Multi-regional model vs. Out-of-Africa Model

Evolving Pathogens

Natural selection favors mutations that allow pathogens to: • Evade the immune system • Copy themselves more efficiently • Resist antibiotic (bacterial pathogens) Pathogens can evolve faster than their hosts: >Pathogens can evolve within a single host. >Pathogens have potential for very rapid evolution: • Short generation time • High mutation rate

Neanderthals had _________ brains than humans.

Neanderthals had larger brains than humans.

Tinbergen's Four Questions:

Nikolaas Tinbergen (1907 - 1988) developed the conceptual foundations for the modern study of behavior: 1. How does it work? 2. How does it develop? 3. What is its adaptive value? 4. How did it evolve?

Oldest Human Fossils

Oldest known Homo sapien (human) fossil (300,000 years old)

Natural Selection of Cancer

Once cells start to divide uncontrollably, they begin to evolve by natural selection inside our body.

Humans coexisted with other Homo species

Other species in our genes went extinct recently. • Neanderthals (40,000 ya) • Denisovan (30 - 50,000 ya) Fossils are young enough that we can sequence their DNA.

Adaptation to the Human Immune System

Our immune system also exerts strong selection on pathogens. Example: • New strains of flu are constantly evolving, requiring new vaccines each year.

Origin of New Diseases

Phylogenetics reveals the evolutionary history of pathogens. • Some pathogens have coevolved with our ancestors for millions of years. • Evidence for frequent origin of new diseases via host shifts (zoonotic transmission) Examples of zoonotic transmission: • Influenza strains - birds, pigs • HIV - primates • West Nile Virus - crows, horses • SARS - palm civets • MERS - camels • Ebola - bats? >Pathogens are poorly adapted to new hosts

Plant Behavior

Plant behavior occurs through communication between cells and gene expression changes within cells. >Stimuli include chemicals, heat, light, touch, and gravity >Tropism: The growth or movement of a plant toward or away from a stimulus. +Positive tropism is growth toward a stimulus -Negative tropism is growth away from a stimulus -Heliotropism: a form of tropism, is the diurnal motion or seasonal motion of plant parts (flowers or leaves) in response to the direction of the sun -Phototropism: growth toward light in general (sun or laboratory light) -Thigmotropism: a form of tropism, is a directional growth movement which occurs as a mechanosensory response to a touch stimulus -Gravitropism: their roots respond positively, growing down, into the soil, and their stems respond negatively, growing upward, to reach the sunlight

2. Antagonistic Pleiotropy

Pleiotropy occurs when one gene influences two or more seemingly unrelated traits. Antagonistic pleiotropy occurs when a mutation with beneficial effects for one trait also causes detrimental effects on other traits.

Public health policies influence this trade-off:

Policies that reduce transmission can lead to the evolution of lower virulence: • Frequent hand washing, vaccinations, etc. Policies that increase transmission can lead to the evolution of greater virulence: • Crowding in prisons/refugee camps, poor hygiene following natural disasters, air travel, etc.

Species Can Evolve a Range of Relationships with Other Species

Positive + Negative: Antagonistic Coevolution Positive + Neutral Positive + Positive: Mutualism

NIH Precision Medicine Initiative

Precision medicine is "an emerging approach for disease treatment and prevention that takes into account individual variability in genes, environment, and lifestyle for each person." Pharmacogenomics is the study of how genes affect a person's response to particular drugs. • Part of precision medicine

Somatic Mutations Cause Cancer

Proto-oncogenes are normal genes whose function, when altered by mutation, have the potential to cause cancer. • Oncogenes are mutated versions of proto-oncogenes. • Gain of function Tumor suppressor genes are genes that suppress cell growth and proliferation. • Mutations to these genes can increase cancer risk. • Loss of function

Coevolution

Reciprocal evolutionary change between interacting species, driven by natural selection >Species exist in a web of interactions

Evolution of Social Behavior

Social behavior describes behavioral interactions between individuals of the same species. Sociality is the degree to which individuals in a population tend to associate in social groups.

Is there heritable variation for behavioral traits in the wild?

Sticklebacks Hopi Hoekstra and her mice

Humans are still evolving!

The basic ingredients required for evolution still apply to humans: • Genetic Variation, Heritability, Differential Reproductive Success We live in a very different environment than our ancestors. • New selection pressures Evidence of recent adaptions: Evolutionary genomics has uncovered many instances of recent adaptations in human populations. -lactase persistence -skin pigmentation -height -high altitude -arctic environment -trypanosome resistance -high fat diet -malaria -thick hair -toxic arsenic-rich environments -starchy food -increased BMI

Evolution & Cancer

The evolution of multicellular life: • Cooperation between cells allowed organisms to occupy new environments and take advantage of new resources. • Loss of individuality • Regulation of growth and cell division • Cancer occurs due to uncontrolled cellular proliferation. ❖ Knowledge of genetic variation within cancer can increase efficacy of treatment. ❖ Understanding evolution is fundamentally important for identifying effective cancer treatments.

The most recent common ancestor of humans and chimps lived about ____ mya

The most recent common ancestor of humans and chimps lived about 7 mya Humans and chimps differ by less than 2% in the DNA sequences of our protein-coding genes.

Multi-Regional Model

Until the 1980's, scientists only had access to morphological data in the fossil record. Based upon this evidence, a number of paleontologists argued that Homo sapiens had evolved gradually across Africa, Asia and Europe from an older hominin species over the past 1 million years. This hypothesis is known as the multi-regional model of human evolution.

Phenotype

a measurable aspect of an organism, such as morphology, physiology, and behavior.

Behavior

an internally generated response to external stimulus. >Stimulus can be biotic or abiotic. -food sources -sunlight -other organisms >Behavior is part of an organism's phenotype >Can organism's behave without a brain? Organisms were behaving billions of years before the evolution of the brain.

Dinosaurs

dominated the ecosystem until a mass extinction- 65mya

Synaptic Plasticity

occurs when the number or strength of synaptic connections between neurons is altered in response to stimuli.

Altruism

occurs whenever a helping individual behaves in a way that benefits another individual at a cost to its own fitness. Why do individuals display altruistic behaviors? -Hamilton's Rule

Sahelanthropus

oldest known bipedal hominid (~7 million years old)

Trade-off between virulence and transmission

stronger selection for competition within hosts favors rapid replication and increased virulence stronger selection for movement across hosts favors reduced virulence

Virulence

the ability of a pathogen to cause disease • Driven by the pathogen's use of host resources to replicate.

Human Microbiome

the complete collection of microorganisms in the human body's ecosystem

Evolutionary Medicine

the integrated study of evolution and medicine to improve scientific understanding of the reasons for disease and the actions that can be taken to improve health.

Transmission

the passage of a pathogen from one host to another • Pathogens vary in their mode of transmission.

Proximate vs. Ultimate Causes and Tinbergen's Four Questions

• Proximate Cause - How? • Ultimate Cause - Why? 1. How does it work? (Proximate) 2. How does it develop? (Proximate) 3. What is its adaptive value? (Ultimate) 4. How did it evolve? (Ultimate)