Exam 1 BIO 122 Flashcards
, Confirmation Bias
When someone finds/accepts evidence that supports their hypothesis (or opinion) and doesn’t test it or look at alternatives. Cherry picking data.
Who’s a scientist who is unaware of their confirmation bias?
Rats fed diet with genetically modified corn, the herbicide roundup, or both. Died earlier than control rats fed GMO free diet.
Used 200 rats, 20 control. 9/10 chance a rat would die from the treatment pool than the control pool.
Charles Walcott Lipalian geological interval.
Lipalian Interval was a time where animals gradually evolved from single celled organisms through progressively more complex forms into the animals found in the burgess shale, yet geological conditions prevented their fossilization.
Life is diverse, how can we describe it?
Taxonomy - use a hierarchical naming system to classify organisms based on similarity.
Cladistics/systematics/phylogenetics - Builds hypothetical trees to show evolutionary relationships between organisms - Phylogenies.
What does taxonomy do?
Places organisms into hierarchical groups.
Morphological Species Concept
Groups organisms based on their physical similarities.
What are all the hierarchical groups?
Domain, kingdom, phylum, class, order, family, genus, species.
Does classification via taxonomy reflect evolutionary history
Not necessarily
Binomial System
Genus species, devised by Carlos Linnaeus (1700s)
Why do evolutionary relationships not always resemble a branching tree?
Beacuse of endosymbiosis and horizontal gene transfer
What do phylogenies show?
Hypothesized evolutionary history and relationships.
Branching patterns show hypothesized speciation events from a common ancestor.
Parsimony
The phylogeny with the least amount of evolution needed is most likely correct. (Not always correct but a good starting point)
Why is it that the closer related two organisms are the more similar they should be?
Less time to accumulate differences since diverging from their common ancestor.
Occam’s Razor and how it relates to phylogenetics.
Among competing hypotheses, the one with the fewest assumptions is more likely to be correct.
Regarding phylogenetics, the assumption of parsimony requires one to construct a phylogeny with the fewest evolutionary events.
What do phylogenies show?
Relationships between taxa, the branching order shows speciation events relative to each other. Can show time, genetic difference, or morphological difference but most dont.
What is a node?
A branching point, shows the common ancestor of all the organisms branching after it.
What is a clade?
All the descendants from a node
How does one build a phylogeny?
Compile a list of characteristcs
Score each organism for the presence or absence of a characteristics
Shared Ancestral Characters
Characteristics that are shared by all of the organisms.
Shared Derived Characters
Characters that only a subset of organism’s posses.
Convergence vs Homology
Homologous meaning determining if the characteristics used were derived from a common ancestor.
Convergence meaning the same characteristic evolved independently.
Example of homologous vs convergence:
Forelimbs of birds and bats are homologous (their common ancestor had a humerus, radius, ulna, etc.)
However, their use as “wings” is convergent (their common ancestor had legs, not wings).
Paraphyletic vs Polyphyletic
l——— X
l —— Y
–l—l
l —— Z
l —— A
l—l
—— B
If you were to make a phylogeny with just X and Y it would be paraphyletic because it leaves out Z.
If you were to make a phylogeny with just Z and A it would be polyphyletic because it groups distantly related species together (and leaves out their close relatives).
Can phylogenies be constructed from morphological or molecular data or both?
Both or either or
Morphological data requires that researchers define characters and character states (open to human bias).
Molecular data can be gene sequence similarity, presence or absence of genes or gene families, sequence of siRNA.
Can phylogenies differ based on morphological to molecular data?
Yes, they can differ.
Lateral gene transfer/horizontal gene transfer
Molecular phylogenies reveal that DNA is sometimes passed between organisms, and not solely passed from one generation to the next.
What does lateral gene transfer allow?
One group to gain new traits from another group.
Is lateral gene transfer common among microorganisms and viruses?
somewhat
Is a phylogenic tree more or less parsimonious with the least amount of evolutionary events.
more
Lateral Gene transfer mechanisms:
Transformation, Transduction, Conjugation,
Transduction
Retroviruses occasionally incorporate host genes, and incorporate into host lineages.
Genetic material is transferred between bacteria by a bacteriophage, a virus that infects and carries bacterial DNA from one host cell to another.
Conjugation
Plasmids (fragments of DNA) can be passed between species of bacteria.
How did eukaryotes originate?
When archaea endosymbiosed aerobically respiring bacteria (branches of each domain merged and made a new domain).
What do archaea and eukarya share?
Characteristics related to packaging/organizing DNA, and gene expression.
Are bacteria and archaea all entirely single celled?
Do they have nuclei?
What are they called?
Yes, No, Prokaryotes.
Do prokaryotes reproduce rapidly?
yes
How do prokaryotes get energy?
Either from the sun or from a wide range of chemicals (photo vs chemo)
Oxidation of molecules vs light
How do prokaryotes get carbon?
Either from CO2 or other organisms (auto vs hetero)
How do bacteria get “virtually everywhere”?
In the absence of an essential nutrient, most bacteria can form an endospore which is dehydrated and metabolically inactive but can be revived centuries later to form new cells.
The cell wall of many bacteria is made out of what?
Peptidoglycan
What is the minimal morphological diversity in prokaryotes?
Envelope, capsule, wall
What are the three biggest groups of living things? Three domains?
Bacteria, Archaea, Eukarya
Where did the origin of Eukarya likely come from?
Mitochondria (archaea)
In bacteria, how did flagella like evolve?
From proteins that enable secretion of materials through the cell membrane.
Can bacteria fix carbon from co2 into organic molecules? Can some bacteria produce oxygen?
Some can
yes
Do bacteria fix nitrogen? If so, into what? Do some generate N2?
Yes, into organic molecules..
Some also generate N2 that goes back into the environment.
All nitrogen in living things has passed through ____.
Prokaryotes
What largely explains the changes in temperature over millions of years?
Changes in atmospheric CO2.
What can alter atmospheric CO2?
Increases or decreases in photosynthesis, decomposition, sedimentation, and volcanic activity.
What are the 5 super groups that contain most of the diversity in domain bacteria?
Proteobacteria (most diverse), chlamydias, spirochetes, cyanobacteria, gram-positive bacteria.
The major divisions in bacterial phylogeny are recognized mostly on ______.
Molecular data.
Chlamydias
Genus of bacteria
Require animal hosts to reproduce (cant make their own atp), most well known member causes the STD.
Spirochetes
Heterotrophs that spiral through their environment.
Cyanobacteria
Generate O2 via plant-like photosynthesis, and are the likely group that chloroplasts are derived from.
Gram-Positive Bacteria
2 very diverse phyla, most members contain thick peptidoglycan cell wall that can be stained.
The first archaea that were well known exist in ____.
Extremely hot or saline environments.
Thermophile
Archaea are common in geological hot springs such as this one in Yellowstone national park. Archaea are also common in hydrothermal vents in water up to 121 celcius.
Halophile
Archaea that contain red pigments used in capturing light energy.
Live in extremely salty environments.
They do this by pumping K+ into their cells to prevent water loss via osmosis.
Mesophiles
Most archaea. They live in more ordinary conditions (oil, ocean water, animal, and plant microbiomes).
Thermal diversity archaea
Most archaea require normal temperature. Some require 90+C to survive and thrive above boiling. Others thrive at -20C.
Metabolic diversity archaea
Archaea use many metabolic pathways found in bacteria. Only known domain to produce methane as a waste product. Some species can use light for energy but do not release oxygen.
How did eukaryotic cells evolve?
Archaea endosymbiosis with aerobic bacteria 2 billion years ago. (resulting in mitochondria)
Lokiarchaeota
An archaea group with many eukaryote specific genes including those involved in building and modulating the cytoskeleton.
Examples of endosymbiosis
Corals: Cnidarian (jellyfish) with dinoflagellate (protist). Dinoflagellates are acquired by each host independently.
Squid select bioluminescent bacteria (vibrio) to grow in them, which alters the development of the squids light organs.
Eukaryotes that are not plants, animals, or fungi are ____.
Protists
Supergroups of eukaryotes:
SAR, Excavata, Archaeplastida, Unikonta
Is Eukaryote phylogeny resolved, if so, why?
No, due to significant amount of morphological and molecular diversity, convergence, endosymbiosis, and horizontal gene transfer.
Clonal Species
Where cells work together but are not dependent on each other.
Amoeba
Each super group has independently evolved amoeba cell lineages. Predatory single cellular eukaryotes.
Some differentiating factors between Eukarya, Bacteria, and Archaea.
Eukarya - Nuclear Envelope
Bacteria - Peptidoglycan in cell wall
Archaea - Membrane lipids with some branched hydrocarbons (eukarya and bacteria have unbranched hydrocarbons)
What does SAR stand for and what is it
Stremenophiles, Alveolates, Rhizarians. 3 diverse lineages that were found to form a monophyletic group based on molecular similarity.
Are there photosynthetic SAR species? If so, how?
Many SAR species are photosynthetic due to secondary endosymbiosis of an archaeplastid over 1 billion years ago.
What are diatoms?
Diatoms are photosynthetic phytoplankton that make silicon glass wall as protection against predators. They play a major role as aquatic photosynthesizers.
What are archaeplastids?
A super-group of eukaryotes. Archaeplastids are a monophyletic group that originated through endosymbiosis of a cyanobacterium.
Are all archaeplastids photosynthetic?
Yes
How did plants arise?
Through archaeplastids.
What is volvox?
A genus of fresh water green algae that form spherical colonies.
How are Fungi related to Eukaryotes?
Fungi are one kingdom of Eukaryotes.
Heterotrophs that feed by absorption.
What is yeasts?
Single celled fungi
What are hyphae
Multicellular fungi are long strips of cells that are only 1 cell thick.
Maximizes surface area of fungus.
Mycelium
The body of a fungus (mass of a hyphae).
How do fungi absorb organic matter and nutrients around them?
They secrete digestive enzymes to their surroundings, and then absorb the hydrolyzed organic molecules.
What are most fungal hyphae’s cell walls made of?
Chitin
Cell structure of fungal hyphae…
Can have septa that separate each cell, or can be continuous (essentially one giant cell with many nuclei).
How do multicellular fungi move and why are they well adapted to absorb nutrition from the environment?
They move by growing hyphae towards nutrient rich areas. They’re well adapted because they maximize surface area.
What’s special about hyphae with septa in terms of moving toward nutrients?
Most hyphae with septa have pores that allow cytoplasm, nutrients, and even nuclei to move from cell to cell. This allows them to leave behind cell walls and move all other resources towards nutrient areas.
How do fungi reproduce?
Both sexually and asexually.
Two fungi of different mating types (+ or -) can exchange nuclei. This results in mycelia that have haploid nuclei from two individuals (heterokaryotic/dikaryotic).
What are Cryptomycetes and Microsporidians?
Basal fungi
Cryptomycetes - 30 identifiable species but probably are much more. Most known species are parasites.
Microsporidians - Unicellular parasites.
Chitrids, Zoopagomycetes, and Mucoromycetes
Chitrid - Mostly aquatic. Frequent parasites of fish and amphibians. Basal Fungi.
Zoopagomycetes - Crown fungi (doesn’t make flagellated spores). Cordyceps fungi, can infect insects and change their behavior.
Mucoromycetes - Mold that acts as a decomposer, many species form symbiotic relationships with plant roots.
What are the crown fungi?
Ascomycetes and Basidiomycetes
Fungi play many negative ecological roles
Some fungi are predatory and capture animals and digest them.
Many fungi are parasites on plants and animals, they digest living tissue.
What are mycorrhizal fungi?
Fungi receive carbohydrates and other nurtients from the plant, which provides minerals and ions that would’ve never been provided.
What is particularly susceptible to fungi parasites?
Amphibians
What are some positive ecological roles that fungi play?
Decompose organic material and help produce soil from plant material.
Decomposition allows for nutrient cycling.
What is lichens relationship with fungi and a photosynthetic organism?
Lichens are mutualisms between fungi and a photosynthetic organism.
