Biology Exam 2

o What are the two major concepts that make up Darwinian evolution?

1. Descent with modification from a common ancestor

2. Natural selection

The five major lines of evidence for descent from a common ancestor are:

1. Fossil record — shows transitional forms and gradual changes over time.

2. Homology — similarities in structure, development, or genetics due to shared ancestry.

3. Biogeography — geographic distribution of species that reflects patterns of common descent.

4. Hierarchical organization of life — life is organized into nested groups based on shared characteristics.

5. Vestigial organs — reduced or unused structures inherited from ancestors.

How homology relates to the other four:

• Fossil record:

Reveals gradual changes in homologous structures across time.

• Biogeography:

Species in certain areas share homologous traits due to common ancestors specific to that region.

• Hierarchical organization of life:

Classification systems are based on groups sharing homologous features.

• Vestigial organs:

These are homologous structures that have lost their function but remain as evolutionary leftovers.

Fossil

is the preserved remains or traces of an ancient organism.

What type of rocks are fossils typically found in?

Fossils are typically found in sedimentary rocks.

Strata

are layers of sedimentary rock where fossils are found.

How do strata relate to geologic time?

Strata shows the relative age of fossils, with older layers beneath younger ones, helping scientists understand the sequence of life and place organisms in Earth's geologic timeline.

Origination

- the process by which new species arise

Extinction

- the process by which species disappear

Why the shared genetic code of all life on earth is a homology

— a homology because it indicates common ancestry; all living organisms inherited this code from a single ancestral life form.

"Hierarchical" organization of life on earth

— The structured arrangement of living things from the smallest building blocks to the entire biosphere. Each level is composed of the elements from the level below it.

- If life on earth was not organized in a hierarchy, the relationships and interactions between organisms wouldn't be based on dominance or power. Evolution would follow less linear paths, and there would be no more "survival of the fittest."

Why descent from a common ancestor predicts that organisms from a certain region will be closely related?

If species evolved in a particular geographic area, they are more likely to have shared a recent common ancestor with other species in that same region, leading to similar traits due to limited gene flow.

o

Vestigial structure

- feature of an organism that is a historical remnant of a structure that served a function in its ancestors

Fitness

— an organism's ability to survive and reproduce in its environment.

FITNESS

Relationship to genes, traits, phenotypes, survival & reproduction

— variations in genes can lead to different traits, which can affect an organism's fitness. Phenotypes are observable physical traits, which directly impact their fitness. An organism must survive to reproductive age to pass on its genes. Reproduction is the most important aspect of fitness since it directly determines the number of offspring an organism produces and contributes to the gene pool.

Adaptation

— traits that benefit an organism in a particular environment. Directly improves fitness.

Three conditions for natural selection to occur

1) Organisms vary in their characteristics

2) That variation is heritable

3) That variation affects survival and reproduction

Acclimation

— individual organism's short-term, reversible adjustment.

Adaptation

— long-term, heritable change in a population's genetic makeup that occurs over generations.

Adaptations are specific to a particular environment

— the traits or behaviors that help an organism survive and reproduce are uniquely suited to the specific conditions of that environment and might not be beneficial in a different environment.

Example:

Adaptations are specific to a particular environment

-being a sickle cell carrier can be beneficial in areas with high rates of malaria since being a carrier can increase malaria resistance.

Role of mutation in new traits

— mutations are the ultimate source of new traits and genetic variation, serving as the raw material for evolution by introducing new alleles that can be passed on.

Biological species concept

— defines a species as a group of organisms that can interbreed and produce fertile offspring.

Allopatric speciation

— the disruption of gene flow because of a geographic barrier. It causes the isolated groups to evolve independently over time, eventually leading to the development of distinct species that can no longer interbreed due to genetic divergence and reproductive isolation.

Adaptive radiation

— species diverge into many new species, each adapted to fill a specific role in their ecosystem.

Example: Darwin’s finches.

Role of sexual selection in trait evolution

— certain characteristics increase chances of finding a mate, which means some traits that are not beneficial for survival still occur because they increase reproductive success.

Evolutionary trade-offs

— improving one trait may come at the expense of another, meaning an organism can’t optimize all traits simultaneously. Example: wild Soay sheep with large horns have higher reproductive success, but those with small horns have increased survival rates.

Explain how a phylogenetic tree represents a hypothesis about evolutionary history.

Visualizes the branching pattern of evolutionary descent from a common ancestor

o Explain how both phylogenetic trees and Linnean hierarchy group species by relatedness.

Mastery level: Can a phylogenetic tree differ from Linnean hierarchy? Are all Linnean groupings monophyletic?

— phylogenetic trees depict evolutionary history visually, while Linnaean hierarchy groups organisms into increasingly broad categories. Phylogenetic trees and the Linnaean hierarchy can differ. Not all Linnaean groups are monophyletic.

Nodes on a phylogeny

— indicate the most recent common ancestors.

Branching points on a phylogeny

— represent a lineage splitting into two or more distinct species. Each species can interbreed and is reproductively isolated from other groups, relating to the biological species concept.

o

Homology:

shared traits due to common ancestry

Analogy:

similar traits from independent evolution, often due to similar environmental pressures (convergence)

Homoplasy:

all similarities that are NOT due to shared ancestry

o Describe how homologies are used to generate phylogenetic trees. Explain how this relates to the principle of parsimony.

Homologies

- help scientists determine which organisms share a more recent common ancestor

o Describe how homologies are used to generate phylogenetic trees. Explain how this relates to the principle of parsimony.

Parsimony:

the most likely evolutionary tree is the one that requires the fewest evolutionary changes to explain observed data

o Given a phylogenetic tree, be able to:

· Find the most recent common ancestor of a set of taxa

· Determine which taxa are more closely related (sister taxa)

· Identify the outgroup/basal taxon if shown (taxon at the base)

· Recognize monophyletic groups (aka clades or 'natural groups'), paraphyletic groups, and polyphyletic groups

· Find any polytomies and explain what they mean with respect to taxon-relatedness (2+ lineages diverge from 1 node, indicating uncertainty about evolutionary relationships among those taxa)

· If the tree also shows evolutionary events (tick marks showing new traits, e.g. 'amniotic egg'), be able to describe the characteristics of a given tip or node

· If the tree also shows evolutionary events, be able to identify examples of convergent evolution (traits appear on separate branches that are not directly connected)

Find the most recent common ancestor

— locate the node where the set of taxa branch from.

Determine which taxa are more closely related (sister taxa)

— sister taxa share the most recent common ancestor and are connected by the same node.

Identify the outgroup/basal taxon

— the taxon shown at the base of the tree, branching off before all others.

Monophyletic group (clade)

— includes an ancestor and all of its descendants.

Paraphyletic group

— includes an ancestor and some, but not all, of its descendants.

Polyphyletic group

— group of organisms without a shared recent common ancestor.

Polytomy

— when two or more lineages diverge from one node, indicating uncertainty about evolutionary relationships among those taxa.

Describing characteristics at a given tip or node

— use tick marks that show evolutionary events (such as 'amniotic egg') to describe traits that define that taxon or node.

Convergent evolution

— occurs when traits appear on separate branches that are not directly connected, showing that similar features evolved independently.

o Given one or more phylogenetic trees + a character data matrix, be able to:

· Determine which trees show the same evolutionary relationships

· Map where evolutionary events (trait changes) occur using tick marks

· Determine which tree(s) is/are the most parsimonious by mapping evolutionary events.

Determine which trees show the same evolutionary relationships

— compare the branching patterns to see if the same taxa share the same most recent common ancestors and branch order.

Map where evolutionary events occur

— place tick marks on branches where trait changes (evolutionary events) occur, based on the character data matrix.

Most parsimonious tree

— the tree with the fewest total evolutionary changes (least number of tick marks needed to explain all trait changes).

2 reasons for using many characters when building a phylogenetic tree

1. Minimizes the effects of convergence, reducing the chance that similar traits evolved independently and misleading the tree.

2. Provides a more complete picture of evolutionary relationships, making the tree more accurate and reliable.

Mastery: How are mutation rates and fossil ages important for calibrating a molecular clock? What are some assumptions used when applying a molecular clock?

Mutation rates

— clock based on the assumption that mutations accumulate at a constant rate over time.

Mastery: How are mutation rates and fossil ages important for calibrating a molecular clock? What are some assumptions used when applying a molecular clock?

Fossil ages

— known age of a fossil can calibrate a point on the clock, and then be used as a reference point to determine time of divergence.

Mastery: What might happen if one or more of these assumptions of molecular clock are violated, How would that affect our interpretations of branching patterns (topology) or Branch lengths?

If assumptions are violated

— it can lead to incorrect estimates of divergence times, misinterpret branching patterns (topology), and distort branch lengths, making the tree less accurate in showing true evolutionary relationships.

• Incorrect branching patterns (topology):

The order of divergence might be misrepresented, making species appear more or less closely related than they really are.

• Distorted branch lengths:

Branch lengths, which represent evolutionary time or the amount of change, may become inaccurate — some branches might appear too long or too short relative to others.

• Misleading divergence times:

The molecular clock could give the wrong estimates for when two species diverged, leading to errors in reconstructing evolutionary history.

This is why careful calibration and testing of assumptions (such as checking rate consistency) are critical when using molecular clocks.

Domain more closely related to Domain Eukarya

— Domain Archaea is more closely related to Domain Eukarya.

Outgroup — Domain Bacteria is the outgroup.

Genetic material in the most ancient organisms

— RNA, since it can store genetic information and catalyze chemical reactions.

What energy and carbon sources are used by prokaryotes?

Photoautotrophs

Chemoautotrophs

Photoheterotrophs

Chemoheterotrophs

Photoautotrophs

— use light as an energy source and CO₂ (inorganic carbon) as a carbon source.

Chemoautotrophs

— use inorganic chemicals as an energy source and CO₂ (inorganic carbon) as a carbon source.

Photoheterotrophs

— use light as an energy source and organic compounds as a carbon source.

Chemoheterotrophs

— use organic compounds as both the energy source and carbon source.

Photosynthesis

likely evolved in bacteria 3.4 billion years ago

The increase in oxygen levels changed the composition of Earth's atmosphere and paved the way for evolution and diversification of life

Conjugation

- transfer of genetic material through direct cell-to-cell contact, allows for the rapid spread of genetic information

Transformation

- the uptake of free DNA from the surrounding environment, allows bacteria to acquire new genetic traits

Transduction

- transfer of genetic material via a bacteriophage, drives genetic diversity

Domain Eukarya

all organisms with a nucleus in their cells

Are protists eukaryotic or prokaryotic organisms?

Eukaryotic

What was the role of endosymbiosis in the rise of the eukaryotes?

Eukaryotic cells

evolved from prokaryotic cells through a series of endosymbiotic events. The prokaryotic cells were engulfed by other cells, but instead of being digested, they established symbiotic relationships

Plants, animals, and fungi

are not sister taxon to protists because "protist" is a paraphyletic grouping, meaning it doesn't form a natural clade.

Complex multicellularity

arose several times among the eukaryotes, across various lineages.

Kingdom Fungi:

diverse group of eukaryotic organisms, characterized by heterotrophic nutrition and cell walls made of chitin

Ascomycota:

form spores in sacs called asci during sexual reproduction

Basidiomycota:

form club-shaped structures called basidia, which bear spores

Are fungi more closely related to plants or animals?

Animals

The nutritional mode of fungi

Is chemoheterotrophy, meaning they obtain both energy and carbon by absorbing organic compounds from other organisms.

-Fungi are heterotrophic. They cannot make their own food and instead absorb nutrients from other organic material, often by secreting enzymes to break it down first.

Fungal hyphae

Its role is to form a network called mycelium that helps fungi absorb nutrients, grow, and reproduce

Fungi Reproduction

Both sexually and asexually

Plasmogamy:

fusion of the cytoplasm of 2 cells during sexual reproduction

Karyogamy:

subsequent fusion of the 2 nuclei within that fused cell

Why are fungi important in ecosystems?

1. They are decomposers, nutrient recyclers, and mutualists.

2. Maintain healthy soils, support plant growth, facilitate carbon and nutrient cycles.

Lichens:

composed of fungus and algae

Mycorrhizae:

composed of fungus and plant root

Kingdom Animalia

— multicellular, eukaryotic, consume organic material, breathe oxygen, reproduce sexually, grow from blastula.

Metazoa

— encompasses all animals.

Eumetazoa

— all animals with true tissues (not sponges or placozoa).

Bilaterians

— animals with bilateral symmetry during embryonic development.

Deuterostomes

— bilaterian animals whose anus forms before the mouth during embryonic development.

Chordates

— bilaterian animals that at some point possess a notochord, dorsal hollow nerve cord, pharyngeal slits, post-anal tail, and thyroid gland.

Vertebrates

— animals with a vertebral column and skull.

Amniotes

— vertebrate animals whose embryo develops in an amnion and chorion and has an allantois.

Mammals

— amniotes with milk-producing mammary glands, hair/fur, and warm-blooded.

Monotremes

— mammals that lay eggs.

Marsupials

— mammals that give birth to relatively undeveloped young who continue development in an external pouch.

Eutherians/Placentals

— mammals that give birth to live, developed young.