BIOL-3305 Spring 2025 Exam III Study Guide

Flashcards covering key concepts for the BIOL-3305 Spring 2025 Exam III, focusing on Neutral Theory, Quantitative Genetics, Sexual Selection, Life History Evolution, Speciation, and Human Evolution.

What is the neutral theory of molecular evolution?

The neutral theory of molecular evolution claims that most fixed substitutions between species and polymorphisms within species are caused by evolutionary forces.

Why does neutral theory predict a molecular clock?

Neutral theory predicts a molecular clock because substitution rates vary less than replacement rates.

What does it mean that the NTME is an explicative theory and a null hypothesis?

The NTME is an explicative theory and a null hypothesis, meaning there are functional constraints in the rates of molecular evolution.

What is the Ka/Ks ratio and what does it tell us about selection?

The Ka/Ks ratio tells us about selection; a ratio greater than 1 indicates positive selection.

What was the key finding of McDonald and Kreitman's comparison of the Adh gene?

McDonald and Kreitman's comparison of the Adh gene showed evidence of selection by comparing sequences between and within species.

When does genetic hitch-hiking happen and what is a selective sweep?

Genetic hitch-hiking happens when a gene increases in frequency due to its linkage to a positively selected gene; a selective sweep is the reduction or elimination of variation among the nucleotides near a mutation in DNA

Distinguish between quantitative and discrete phenotypes. Define pleiotropic and polygenic effects.

Quantitative phenotypes are continuous, while discrete phenotypes are categorical. Pleiotropic effects are when one gene affects multiple traits, and polygenic effects are when multiple genes affect one trait.

What are the components of variance of a quantitative trait?

Components of variance of a quantitative trait include genetic and environmental variance. Heritability can be estimated by parent-offspring regression, where the slope represents the heritability.

What is a selection differential and what do we mean by response to selection?

The selection differential is the difference between the mean trait value of the selected individuals and the mean trait value of the entire population. Response to selection is the change in the mean trait value in the next generation.

What are the modes of selection on phenotypic traits?

Directional selection favors one extreme, stabilizing selection favors the average, and disruptive selection favors both extremes.

What does the heritability of a trait tell us about the causes of differences in mean phenotype between populations?

The heritability of a trait tells us about the proportion of phenotypic variation due to genetic variation. A heritability of zero means there is no genetic variation.

Differentiate between Recombination, Reproduction and Gender.

Recombination is the exchange of genetic material, reproduction is the production of offspring, and gender is the classification of organisms based on their reproductive roles.

What are the advantages and disadvantages of sexual reproduction?

Advantages of sex include faster evolution, new genotype combinations, and avoidance of Muller’s ratchet. Disadvantages include the two-fold cost of sex, genome dilution, and energy cost.

Anisogamy vs isogamy; disruptive selection and the origin of Anisogamy.

Anisogamy is when gametes are different sizes, while isogamy is when they are the same size. Disruptive selection is believed to be the origin of Anisogamy

What is sexual dimorphism? Compare and contrast natural selection and sexual selection.

Sexual dimorphism is the difference in appearance between males and females. Sexual selection is a form of natural selection driven by competition for mates.

Explain Bateman’s principle and the asymmetries in sexual reproduction.

Bateman’s principle suggests that male reproductive success is typically limited by access to females, while female reproductive success is limited by resources, leading to asymmetries in sexual selection.

What is intrasexual selection? intersexual selection?

Intrasexual selection is competition within the same sex, while intersexual selection is mate choice.

In what ways can male-male competition be expressed?

Male-male competition can be expressed through direct combat, sperm competition, or alternative mating strategies.

What do we mean by good genes or the “sexy_son” hypotheses in the context of female choice?

"Good genes" and "sexy son" are hypothesis to explain why females might choose certain males - where "good genes" is that the male has genes beneficial to offspring survival, and "sexy son" is to create male offpring attractive to other females, continuing the gene line.

What is runaway sexual selection, and how does it work?

Runaway sexual selection is a positive feedback loop where selection for a male trait and female preference for that trait reinforce each other; eventually leading to maladaptive traits.

What does Life History Evolution Theory explain?

Life History Evolution Theory explains the evolution of life history traits.

What causes life histories to evolve?

Life histories evolve due to extrinsic factors (e.g., predation) and intrinsic factors (e.g., genetics).

What are life history traits? What does the net reproductive rate (R) measure?

Life history traits are traits related to reproduction, survival, and growth. The net reproductive rate (R) measures the average number of offspring produced by an individual during its lifetime.

Explain the Y-model for resource acquisition and allocation.

The Y-model explains that resources are allocated among survival, growth, and reproduction, creating trade-offs.

Senescence and ageing. What are the differences among these concepts.

Senescence is the decline in function with age, while ageing is the process of getting older.

What is the rate of living hypothesis for senescence?

The rate of living hypothesis suggests that senescence is due to physical wear and tear.

What are the evolutionary theories of senescence?

Evolutionary theories suggest that the force of natural selection lessens with advancing age, leading to mutation accumulation and antagonistic pleiotropy.

Species are the fundamental unit of evolution. Origins of Biodiversity.

Species are the fundamental unit of evolution. The study of the origins of biodiversity is process of speciation.

Most species concepts try to define the genetic cohesion of sets of populations

Most species concepts try to define the genetic cohesion of sets of populations, such as Morphospecies, Biological, Phylogenetic, Genealogical Species Concept vs. General lineage species concept

A common theme is trying to describe the independence of populations

A common theme is trying to describe the independence of populations and the absence of gene flow between species.

What are the steps of speciation

Typically speciation has a 3-step process 1) isolation of populations (reduce gene flow); geography of speciation (allopatric, peripatric, parapatric, sympatric) 2) divergence of populations (selection/drift); Two kinds of divergence of interest: divergence that has no effect on ability to interbreed, and divergence that does. Drift; Local adaptation (natural selection in varying environments) sexual selection. Divergence is typically a slow process of accumulating differences (Dobzhansky-Muller incompatibilities) 3) evolution of reproductive barriers

What is Reinforcement?

Reinforcement is the process by which selection acts to reduce interbreeding by assortative mating to decrease the formation of hybrids; prezygotic isolating mechanisms evolve faster in sympatric species than allopatric species

What are the origins of Humans?

Humans are within apes, with our closest relatives being the chimp (chimps + bonobos) clade.

What are the origins of Modern Humans?

Modern humans (Modern Human Sapiens – MHS) are descended from an African population(s) of archaic H. sapiens.

Hominids are characterized by mosaic evolution

Hominids are characterized by mosaic evolution, with bipedality evolving long before large brains and tool use, and an unknown time before language.

What makes humans unique?

Humans are characterized by: an added life-cycle stage allows for more, high quality babies, we have a higher metabolism, often associated with maintaining energetically expensive tissue (bigger brains) allows learning; often associated with prepared and social learning (cultural intelligence hypothesis). Our bodies are better at accumulating fat(remember the “thrifty phenotype” hypothesis); Also, we are only animals that can cooperate both flexibly and in very large numbers; great imagination - we believe the stories we tell ourselves.

What is Additive genetic variance?

Additive genetic variance is the portion of the genetic variance that is due to the additive effects of genes.

What is Allopatric speciation?

Allopatric speciation is speciation that occurs when populations are geographically separated.

What is Anisogamy?

Anisogamy is the condition in which a species has two types of gametes that differ in size.

What is Heritability?

Heritability is the proportion of phenotypic variation in a population that is due to genetic variation.

What is Recombination?

Recombination is the exchange of genetic material between homologous chromosomes during meiosis.

What is Response to selection?

Response to selection is the change in the mean phenotype value in a population that results from selection.

What is Runaway sexual selection?

Runaway sexual selection is a form of sexual selection in which selection for a male trait and selection for a female preference for that trait reinforce each other

What is Senescence?

Senescence is the decline in function with age

What is Sexual selection?

Sexual selection is a form of natural selection driven by competition for mates.

What is Sympatric speciation?

Sympatric speciation is speciation that occurs when populations are in the same geographic area.

What is Two-fold cost of sex?

Two-fold cost of sex refers to the cost of sexual reproduction compared to asexual reproduction.

Who are humans most closely related to among the apes?

humans are most closely related to chimpanzees and bonobos. Phylogenetic analyses of genetic data show that humans share a more recent common ancestor with chimps and bonobos than with gorillas or orangutans.

What are the key points in understanding primate origins and relationships?

Primate origins trace back to early arboreal mammals. The book explains that primates evolved traits like forward-facing eyes, grasping hands, and enhanced vision. These adaptations supported life in trees and laid the groundwork for later divergence into monkeys, apes, and eventually humans. Relationships are reconstructed using both fossil records and molecular data, which help establish when key divergences occurred in primate evolution.

What evidence supports relationships among primates and great apes?

• Morphological traits (skull shape, dental patterns)

• Genetic sequences (DNA )

• Molecular clocks estimating divergence times
  Together, these show that great apes (including gorillas, chimps, and humans) share common ancestry.

What does the molecular clock estimate in great ape evolution?

The molecular clock method uses mutation rates in DNA to estimate how long ago species diverged. According to the textbook, this method suggests that humans and chimpanzees diverged from a common ancestor about 6 million years ago, while the divergence between humans and gorillas occurred around 8–10 million years ago. These estimates help refine the timeline of hominid evolution.

Why are humans described as the lone survivors of a once diverse hominid clade?

Humans are the only surviving members of a once diverse group of bipedal, large-brained hominins that included species like Australopithecus, Paranthropus, Homo habilis, and Homo erectus. Fossil evidence shows many hominin species coexisted in Africa, especially during periods of environmental change. Over time, all other lineages went extinct, leaving Homo sapiens as the sole survivor.

How did climate change influence early human evolution?

human evolution as being deeply influenced by Miocene cooling and the shifting African tectonic plates, which led to more open and variable environments. These changes likely favored traits such as bipedality, tool use, and cognitive flexibility, as hominins had to adapt to increasingly fragmented and unpredictable habitats.

What is the evidence for multiple early sympatric lineages?

The fossil record reveals that multiple early hominin species lived at the same time and in the same regions (sympatry). For example, fossils of Australopithecus afarensis and Kenyanthropus platyops overlap in both time and geography. This suggests a bush-like evolutionary tree rather than a linear one, with many branches developing simultaneously.

What is the evidence for multiple late sympatric lineages?

Later in human evolution, Homo sapiens shared time and space with species such as Neanderthals, Denisovans, and potentially Homo floresiensis. Genetic evidence supports this: modern human genomes include Neanderthal and Denisovan DNA, showing interbreeding occurred, and that multiple hominin species coexisted in Eurasia before modern humans became globally dominant

Why are modern humans called children of climate change?

Modern Homo sapiens evolved during a period of major climate fluctuations, especially over the last 200,000 years. These rapid environmental changes in Africa likely drove the evolution of our species’ large brains, cultural complexity, and adaptability. The book emphasizes that climate instability favored flexible, social, and inventive humans—traits that are hallmarks of modern behavior

What is mosaic evolution and how does it apply to hominids?

Mosaic evolution refers to the idea that different traits evolve at different rates and times. In hominids, bipedality evolved millions of years before large brains and advanced tool use. For instance, Australopithecus afarensis (“Lucy”) was a biped but still had a small brain. Language and symbolic thinking likely came even later. This staggered timeline shows how human evolution didn’t proceed in a single step, but in a piecemeal, trait-by-trait fashion.

What are the three waves of human migration "Out of Africa"?

there were three major waves of human migration from Africa:

1. Homo erectus (~1.8 million years ago):

   • First hominin to leave Africa.

   • Reached parts of Asia and Europe, used fire and tools, but eventually went extinct.

2. Ancestors of Neanderthals and Denisovans (~500,000 years ago):

   • These groups split from the human lineage after H. erectus.

   • Neanderthals spread into Europe; Denisovans into parts of Asia.

3. Modern Homo sapiens (~60,000–70,000 years ago):

   • Left Africa and rapidly colonized the globe.

   • Replaced or interbred with other hominin groups (e.g., Neanderthals, Denisovans).

What does molecular evidence say about the origins of modern humans?

Molecular data confirms that all living humans are descended from a small population of archaic Homo sapiens that lived in Africa. This supports the “Out of Africa” model. As modern humans migrated, they experienced serial founder effects and genetic bottlenecks, which reduced genetic diversity the farther from Africa they traveled. This is why most genetic variation is found within African populations today, and why non-African populations carry fewer genetic variants overall.

What are the characteristics of Neanderthals and Denisovans, and where were they found?

Neanderthals lived across Europe and western Asia. They were robust, with large brow ridges, a wide nose, and powerful builds suited to cold climates. They made tools, used fire, buried their dead, and may have had basic symbolic culture.
Denisovans were discovered from DNA extracted from fossils found in Denisova Cave (Siberia). They are genetically distinct from Neanderthals and modern humans, though few physical remains exist. Their DNA reveals they were a sister group to Neanderthals.

What genomic exchanges occurred between Neanderthals, Denisovans, and modern humans?

Modern humans interbred with both Neanderthals and Denisovans. Non-African human populations carry ~1–4% Neanderthal DNA, while some Southeast Asian and Oceanian populations carry up to 5% Denisovan DNA. This genomic exchange occurred when Homo sapiens encountered these groups after migrating out of Africa. These ancient gene flows contributed to traits such as immune function and adaptation to cold or high-altitude environments.

What happened to the Neanderthals?

Neanderthals went extinct about 40,000 years ago. The exact reason is unclear, but theories include:

• Competition with modern humans for resources

• Climate fluctuations that stressed populations

• Genetic swamping through interbreeding
  Emlen & Zimmer suggest that modern humans may have had cognitive or social advantages that helped them outcompete Neanderthals—effectively becoming the “top of the food pyramid.”

Who were the “Hobbits” (Homo floresiensis and Homo luzonensis), and what do we know about Denisovans?

Homo floresiensis (nicknamed “Hobbits”) was a small-bodied hominin species found on Flores Island, Indonesia, standing about 3.5 feet tall. They had a small brain but made tools and likely hunted. Homo luzonensis was found in the Philippines and had a mix of modern and archaic traits. These island species likely evolved through island dwarfism and show that hominin diversity persisted in isolated regions even after the emergence of Homo sapiens. Denisovans, by contrast, are mostly known from DNA and limited fossil evidence, but they too reflect the broad geographic and genetic diversity of archaic humans

What makes us human?

• An added childhood life stage

• High metabolism

• Social and cultural learning

• Fat accumulation ability

• Cooperation and imagination

Speciation

The process by which new biological species arise, often through mechanisms such as geographic isolation, genetic divergence, and reproductive isolation.

Extrinsic Properties

Qualities or characteristics of an organism or system that are influenced by external factors or environmental conditions rather than being inherent to the organism itself

Intrinsic Properties

Characteristics inherent to an organism or system, independent of external influences or interactions

How many living species are on Earth?

Estimates vary, but scientists suggest there are 8–10 million species on Earth, though only about 1.5–2 million have been formally described. New species continue to be discovered, especially in marine environments, tropical forests, and among microorganisms.

Are species real?

Yes. While definitions vary, species are real biological entities that represent evolutionarily distinct lineages. They can be identified as clusters of individuals that share traits and gene flow, distinct from other clusters.

Why don’t species clusters fuse?

Species clusters do not fuse because of reproductive isolation. Barriers such as geographic separation, behavioral differences, or genetic incompatibility prevent interbreeding, preserving species boundaries.

Does everything have to belong to a species?

While species are a fundamental unit of biological classification, not all organisms fit neatly into this concept—especially asexual organisms or microbes. The species concept is a useful tool, but it has limitations, particularly in lineages without clear reproductive boundaries.

What are the two axes of divergence used to describe species diversity?

Speciation is studied through:

• Phenotypic divergence: visible traits shaped by adaptive evolution (e.g., beak size, color).

• Genotypic divergence: genetic differences due to neutral mutations and drift.
  These axes help researchers explore different routes to speciation in what’s called “process space.”

What are the major species concepts, and how do they differ?

Different species concepts define species in different ways:

• Morphospecies Concept: Identifies species based on distinct physical traits.

• Biological Species Concept: Defines species as groups that can interbreed and are reproductively isolated from others.

• Phylogenetic Species Concept: Species are the smallest monophyletic groups on a phylogenetic tree.

• Genealogical Species Concept: Uses shared ancestry and descent patterns from genetic data.

• General Lineage Species Concept (De Queiroz): Defines species as evolving metapopulation lineages that maintain identity over time and space.

All attempt to describe genetic cohesion within species, but emphasize different evidence or criteria.

What are species criteria and how are species recognized?

Species criteria are the observable or measurable features used to identify and separate species. These include:

• Morphology (body form and structure)

• Genetics (DNA sequences and variation)

• Geography (where populations are found)

• Breeding tests (whether two groups can produce fertile offspring

What is the species problem?

The “species problem” refers to the lack of a universally accepted definition of a species. This confusion arises because different species concepts emphasize different aspects of biology (e.g., morphology, genetics, interbreeding). As a result, biologists disagree on how to define and delimit species, especially in microbes, hybrids, and asexual organisms.

How do different species concepts view the speciation process?

Process-based species concepts (like the Biological Species Concept) define speciation as the evolution of reproductive barriers—traits that prevent gene flow between populations. In contrast, pattern-based concepts (like the Phylogenetic Species Concept) define speciation as the point at which a clade splits, forming two lineages with shared ancestry but independent futures.

What happens when populations are isolated from each other?

Isolated populations experience reduced gene flow. Over time, they accumulate genetic differences due to genetic drift and natural selection, leading to divergence. This can eventually result in reproductive isolation and speciation, especially if environmental pressures differ across populations.

What is reinforcement in the context of speciation?

Reinforcement occurs when hybrids between diverging populations have lower fitness. In response, natural selection favors individuals that mate only with members of their own group—this is called assortative mating. Reinforcement strengthens reproductive barriers and accelerates the completion of speciation when previously separated populations come into contact again.

How is gene flow between species prevented?

Gene flow is blocked by reproductive isolating mechanisms, which fall into two categories:

• Prezygotic barriers: Prevent mating or fertilization. These include differences in mating behavior, timing, habitat, or gamete compatibility.

• Postzygotic barriers: Occur after fertilization and reduce hybrid fitness. Examples include hybrid sterility or inviability.

Together, these barriers help maintain species boundaries even when populations come into contact.

Can speciation ever happen quickly?

Yes. While speciation is usually gradual, some processes can lead to rapid or even instantaneous speciation. A clear example is polyploidy—common in plants—where an error in meiosis creates offspring with extra chromosome sets. These individuals are instantly reproductively isolated from the parent population, resulting in instant speciation.

What are the three main steps in the speciation process?

• Isolation of populations – Gene flow is reduced or cut off (via allopatric, peripatric, parapatric, or sympatric mechanisms).

• Divergence of traits – Through genetic drift, natural selection, or sexual selection, populations accumulate differences. Sometimes divergence is neutral; sometimes it's adaptive.

• Evolution of reproductive barriers – Isolation becomes permanent as prezygotic or postzygotic barriers prevent interbreeding.

What is the role of geographic isolation in speciation?

Geographic isolation (especially allopatry) is a common first step in speciation. It physically separates populations, blocking gene flow and allowing independent evolutionary trajectories through drift or selection.

What types of divergence occur between populations?

There are two key types:

• Neutral divergence – Differences accumulate but don’t affect interbreeding.

• Reproductive divergence – Differences lead to mating barriers, preventing gene flow.

These differences can arise from drift, environmental adaptation, or sexual selection, often slowly through mechanisms like Dobzhansky-Muller incompatibilities.

What types of reproductive isolation exist?

• Premating barriers – Prevent mating attempts (e.g., behavioral, habitat, or mechanical isolation).

• Postmating prezygotic barriers – Mating occurs, but no zygote forms.

• Postzygotic barriers – Hybrids are produced but are unfit or sterile, as seen in Haldane’s Rule (e.g., heterogametic sex is more often sterile).

What is reinforcement in speciation?

Reinforcement is natural selection against hybridization. When hybrids have low fitness, selection favors individuals who mate with their own kind (assortative mating), increasing reproductive isolation—especially common in sympatric populations.

How quickly do isolating mechanisms evolve?

Prezygotic barriers often evolve faster in sympatric species because selection directly acts against unfit hybrids. In allopatric species, isolation arises more slowly without such direct pressure.

Can reproductive isolation happen instantly?

Yes—in some cases. Speciation can occur almost instantaneously through:

• Chromosomal rearrangements

• Polyploidy (especially in plants)

• Hybridization, which can produce new species in a single generation if the hybrid is reproductively isolated

What are Dobzhansky-Muller incompatibilities?

They are genetic incompatibilities that arise when two populations evolve separately. When these populations interbreed, their hybrid offspring may have harmful gene interactions, leading to reduced fitness or sterility, which helps drive postzygotic reproductive isolation.

What is Life History Theory (LHT)?

explains how natural selection shapes the timing and allocation of resources to key life events like growth, reproduction, and survival.
It helps us understand why organisms differ in traits like lifespan, number of offspring, age at maturity, and parental care—based on trade-offs in how energy is spent.

What are life history strategies?

patterns in how organisms allocate resources to growth, reproduction, and survival—like when to reproduce, how many offspring to have, and how long to live.

What is a life history table and what does R measure?

tracks survival and reproduction rates across ages.
Net reproductive rate (R) measures the average number of offspring a female produces in her lifetime. If R > 1, the population grows.

Why don’t we see "Darwinian demons"

Because of trade-offs. The Y-model explains that resources are limited—energy used for one function (like reproduction) reduces energy for others (like survival). No organism can maximize everything.

How does predation affect life history? (Guppy example)

High predation risk favors early reproduction and more offspring (fast strategy). In low-predation environments, guppies evolve slower life histories with fewer, larger offspring and delayed reproduction.

What are the main theories of senescence and aging?

Rate of Living Hypothesis (ROLH) and Evolutionary Theories of Aging (EVT)

What is the Rate of Living Hypothesis (ROLH)?

suggests aging (senescence) is caused by accumulated damage from metabolism—a result of physical wear and tear.
It predicts:

• Little genetic variation in aging rates (if natural selection already optimized lifespan)

• A negative correlation between metabolic rate and lifespan
  But evidence from data across mammals does not fully support these predictio

What are the Evolutionary Theories of Aging (EVT)?

explain aging as a consequence of weakened natural selection with age.
Key components:

• Mutation accumulation: Late-acting harmful mutations build up because selection is weak late in life.

• Antagonistic pleiotropy: Genes that help early in life (e.g., boost reproduction) may be favored—even if they harm later-life fitness.

What are the costs of sexual reproduction?

• Twofold cost of sex (males don’t directly reproduce)

• Energy cost of finding mates

• Genome dilution (offspring only get half your genes)

• Risk of sexually transmitted infections

What are the benefits of sexual reproduction?

• Faster evolution via recombination

• Purging of harmful mutations (Muller’s ratchet)

• Creation of novel genotype combinations (Red Queen effect)

What is anisogamy and why is it important?

Evolution of gametes of unequal size (large eggs, small sperm).
It leads to reproductive asymmetry: females invest more per gamete, which underpins sexual selection—males compete, females choose.

What is sexual dimorphism?

differences in appearance or behavior between sexes.
It evolves via sexual selection, especially when one sex (usually males) competes for access to mates. Natural selection shapes traits for survival; sexual selection shapes traits for mating success (e.g. size, coloration, displays).