BIS 2C midterm

What is a thermophile?

optimum growth at 45-80 degrees celsius

What is hyperthermophile?

optimum growth at >80 degrees celsius

What is a mesophile?

optimum growth at moderate temperatures

What are the different kinds of electron donors?

organo (organic) and litho (inorganic)

What are obligate anaerobes?

oxygen is toxic

What is heredity?

passing on traits from parent to offspring *also known as linear or vertical inheritance (passing on traits from parent to offspring)

What are the different types of energy sources?

photo (sunlight) and chemo (breaking chemical bonds)

What is Occam's razor?

prefer the competing hypothesis that minimizes the number of ad hoc assumptions *principle of parsimony

What do microbes that live in extreme environments provide?

provide insights into potential biotechnology and exobiology

What are some features of the genetic code?

redundant and conserved across life

What is unique trait?

same number of character changes for all possible trees

What is an ingroup?

set of species that you want to estimate evolutionary relationships

What did antibiotic resistance evolve from?

short generation time and mutations

What does the lipoprotein cell membrane show?

shows all life is cellular

what are terminal nodes?

species or groups of species

For a given number of species, N, there are many more rooted than unrooted trees

specifically (2N-3) times more trees

What are unnatural groupings?

specify groups of species that contradict their phylogenetic relationships

What are terminal branches?

subtend tips of the tree

what is another word for shared derived state?

synapomorphies

What can't be determine from unrooted trees?

synapomorphies or unrooted trees

What is a data matrix?

table of trait information *species in rows *traits in columns

What is a conserved feature across life?

the central dogma

What invention aided in the study of microbes?

the microscope

What is speciation?

the process of species formation

What is special about nodes of a tree?

they can be swiveled *tree topological information (set of common ancestry relationships) is not affected by swiveling of nodes

How are all living organisms related to one another?

through shared ancestry

What is invariant?

total number of changes on any tree is 0

What is parsimony uninformative?

traits that have the same optimal parsimony score for all possbile trees

What are sister groups?

two groups that are each others closest relatives

What is reflected in polytomies?

uncertainty in the estimated phylogeny *generally assume that the true underlying tree is dichotomous

How do animals recolonize their microbiota?

use coprophagy

How can some cyanobacteria both fix atmospheric nitrogen and photosynthesize?

use folded membranes

what are outgroups?

used to objectively choose the correct rooting

Are microbes motile?

yes

Can both eukaryotes and prokaryotes be multicellular?

yes

Can prokaryotes make new genetic recombinants?

yes *but not through sex

Can both euakryotes and prokaryotes photosynthesize?

yes *cyanobacteria and plants

What are the characteristics of Low G-C gram positive (firmicutes)?

- Low G+C/A+T ratio in DNA -some produce endospores which are resistant "seeds" that germinate when conditions are good -many agents of diseases

What are the three different classes of symbiosis?

- mutualism (+,+) -commensalism (+, 0) -parasitism (+, -)

How do prokaryotes make new genetic recombinants?

-DNA is passed through cells regardless of their genetic history -new DNA can be mixed with the DNA in recipient cell and passed on -exchange of DNA across lineage is called lateral or horizontal gene transfer

What are the major groups of bacteria??

-Spirochetes -Chlamydias -High G-C gram positive -Low G-C gram positive (firmicute) -cyanobacteria -proteobacteria

What is likelihood?

-a score that measures the fit of the data to the model *measures the probability of observing the data under a fully specified model

How do biofilms act as a form of communication?

-act as a means of communication between prokaryotic cells *enables them to function like a multicellular organism

What are the characteristics of mitosis?

-also asexual -DOES have a cell cycle -DOES have membrane bound organelles

What is culturing?

-also called cultivation -growth of microorganisms in controlled or defined conditions

Among what species is body morphology often associated w/ the type of locomotion?

-among microbial eukaryote *Ciliate *Amoeboid *Flagellate

What allows archaea to live in extreme environments?

-archaea fatty acid chain is different -> branched so changes chemistry

How are most microbes beneficial?

-are key players in ecosystem/organism processes *nitrogen *carbon *animals

What are the characteristics of binary fission?

-asexual, rapid division -no cell cycle -no membrane-bound organelles

What is the difference between archaea, bacteria, and eukaryotes in terms of metabolism?

-bacteria and archaea are diverse in how they obtain nutrition -eukaryotes are metabolically limited -bacteria and archaea utilize every type of trophy

What happens to rooted and unrooted trees as the number of species increases?

-both increase *number of rooted trees increases more rapidly than unrooted trees

What information do cladograms convey?

-branch lengths are arbitrary -> only topological information

What information do phylograms convey?

-branch lengths reflect the amount of character change

How can some microbes be harmful?

-can be causative agents of highly infectious and lethal human diseases

What are some complications w/ eukaryotic genomes?

-central assumption of phylogenetics is linear inheritance (not always the case) -genes have histories too (congruent vs. conflict) -eukaryotes are chimeric -> multiple histories are present within a single genome *there are interconnections that must be taken into account in trees -mitochondria have their own genome and other unusual features

what should classification reflect?

-classification should reflect phylogeny *but beware of unwarranted assumptions *even if two groups are monophyletic and have been assigned the same taxonomic rank (Ex: family), they are not equivalent in any meaningful way *can differ in age, species diversity, or morphological diversity

What are biofilms?

-composed of groups of bacteria that secrete an extracellular polymer that binds cells together (slime) *slime is polysaccharide *can happen on solid surfaces or soft tissue of organisms

What do unrooted trees do?

-constrains (but does not completely specify) the possible set of ancestor-descendant relationships

What do bacteria cell membranes contain?

-contain peptidoglycan (special polymer of amino sugars)

What are the major groups of archaea?

-crenarchaeota -euryarchaeota (methanogens) -euryarchaeota (halophiles)

What is metagenomics?

-culture independent studies

What are the unusual features of chloroplast?

-deep genetic history of mitochondria -chloroplast different from cell

How do microbes differ in regards to oxygen?

-differ in their use and tolerance of oxygen *aerobes -> requires oxygen *anaerobes -> vary in their tolerance/use of oxygen

What traits are usually used for phylogeny estimation?

-discrete

What are the characteristics of multicellularity?

-division of labor -some cells give up reproduction *in construction of fruiting body -> some cells make reproductive cells and others make stalk or supporting structure -> some cells not involved in reproduction

What are the complications of pure culture?

-easier for contamination -some may need to be together -hard to replicate some conditions

What kind of linkages does archaea have?

-ether linkages *lipids w/ fatty acids linked to glycerol

How do microbiomes affect infants?

-evidence that diet has effect and it is established in infants even before birth *both quality and quantity -also difference in microbiomes w/ different forms of delivery

Why does LGT complicate phylogeny?

-exchange of genes among unrelated organisms erases phylogenetic history

What do trees typically exclude? what do they include?

-exclude *fossil species -includes *only include a fraction of extant (living) species

What is Quorum Sensing?

-expression of group behavior genes as a result of density dependent interactions *some genes turn on in the presence of certain organisms

How are extremophiles characterized?

-extremophility is relative -halophiles -> extremely salty environments -thermophiles -> Extremely hot and extremely cold

What happens in mainstream commercial livestock industries?

-feed continuous stream of low dose antibiotics to animals as prophylaxis (action taken to prevent disease) *causes pressure on populations of bacteria to get resistant genes *mutations tend to be small -> antibiotic resistance encoded by more than a few things

Why are we currently facing an antibiotic crisis?

-few new antibiotics are being developed and the medicines that get through don't last

What are the two possible arrangements of peptidoglycan in bacteria?

-gram + (peptidoglycan outside) - gram - (peptidoglycan inside, thinner)

What are the characteristics of chlamydias?

-gram negative -cocci or rod shaped -extremely small -live only as intracellular parasites *small because of this

What are the characteristics of spirochetes?

-gram negative -motile -axial filaments (modified flagella) -many are pathogens and others are free living

What are the characteristics of proteobacteria?

-gram negative, largest group -E. coli -mitochondria evolved from this group -includes many human and animal pathogens

What is the great plate count anomaly?

-great mystery in microbiology -many more cells are present in the environment than can be grown in lab cultures

What results did the study of obesity and microbiomes suggest?

-gut microbiota are diverse and metabolically active *our proportion of gut microbiota is very similar to that of mice *gut microbiomes affected by obesity *both wildtype (++) and heterozygous stay lean lean mice -> proportion of 2 most dominant groups are the same in obese -> proportions are different *in study took obese mice and fed western diet *no microbiome -> gradual growth mice w/ (ob, ob) microbiome -> greater increase in weight *showed that microbiome affect weight gain even if diet is the same *presence or absence of microbes also affect activity

Are halophiles monophyletic? Are hyperthermophiles monophyletic?

-halophiles are monophyletic -hyperthermophiles are NOT monphyletic

Why is the cell membrane of archaea unique?

-has ether linkages *bacteria and eukaryotes have ester linkages

What are some unusual features of mitochondria?

-have their own genome -circular DNA that replicates on its own

What traits are relevant for phylogeny estimation?

-heritable -discrete -fixed within species -potentially variable within species

What are the characteristics of High G-C gram positive?

-high G+C/A+T ratio in DNA -elaborate branching -decomposers, root symbionts -most bacterially derived antibiotics from this group -causative agents of diseases like tuberculosis and leprosy -many originally misclassified as fungi

What is pure culture?

-ideal -in which only one type of microbe is present

What is maximum likelihood estimation?

-identifies the optimal parameter values *it is the value of the model parameter(s) for which the data are most likely to be observed under the model

How does peptidoglycan influence morphology?

-if moved around in cell then it gets completely different morphologies *different morphologies resulted from small rearrangement in peptidoglycan in machinery *mapping these morphologies w/ insights from the cellular machinery provides a better picture of morphological evolution

What was the problem w/ the first trees developed?

-ignorance in pattern and process of evolution -assume teleological evolutionary process *teleological -> think everything has certain design or purpose -human-centric view

What are the limits of lateral gene transfer?

-large, complex sets of genes are less likely to be transferred -only portions of the genome are transferred

What are the characteristics of euryarchaeota (halophiles)?

-live in most salty, alkaline enivronments on earth -many are photoheterotrophs

Has the microbiome of humans changed?

-looked at human hunter gatherer cultures *compared Hadza to western culture *found that Hadza had many different species but US didn't have much diversity

Who was Carl Woese?

-looked at the molecular machinery of cells to build a tree of life based on data *used data based on universal homology (ribosome) *sampled different environments -> organisms grown in culture and unusual habitats *extracted ribosomal RNA and sequenced it *used data and put it into data matrix *used reference taxa that were known and then added unknowns *analyzed data and produced trees *it was clear that there was a group that corresponded to eukaryotes that were known and same for bacteria *there was also an entirely new branch in the tree of life

In what ways are euakryotes limited in regards to metabolism?

-metabolically limited in capabilities relative to archaea and bacteria *euakryotes do form transduction sometimes called transvection -less able to "acquire" metabolic processes from other species via lateral gene transfer -adept to acquiring capabilities by engaging in symbiosis w/ archaea and bacteria

What is a parameter?

-model comprised of one or more parameters *these elements of the model can assume different values

What terms should not be used when referring to clades?

-more advanced, more highly derived -more ancestral, more primitive

What do bacteria use to move around?

-move using multiple flagella *flagella of bacteria, archaea, and eukaryotes are not homologous

What are the characteristics of prokaryotic cells?

-no nucleus -circular DNA -haploid -no membrane-enclosed organelles -no cytoskeleton -binary fission (not mitosis)

What is a microbe?

-not referring to monophyletic group *encompasses organisms from all three domains and represents the bulk of biodiversity

What are the characteristics of eukaryotic cells?

-nucleus present -linear DNA -haploid or diploid or more -membrane-enclosed organelles present -cytoskeleton -mitosis

What are the characteristics of euryarchaeota (methanogens)?

-only known methanogens *produce methane by reducing CO2 (form of chemoautotrophy)

What do terms such as basal refer to?

-only properly refer to internal nodes of a tree *even then it's a relative statement

What are some of the reasons for antibiotic resistance?

-overuse of antibiotics (feeding animals antibiotics w/out being sick) -reproduce fast -can spread through populations -can exchange genes between one another

What are the 2 types of unnatural groups?

-paraphyletic -polyphyletic

What is linear inheritance?

-passed from ancestor to descendants

What are gram stains?

-peptidoglycan is sensitive to staining agents *some antibiotics work by affecting the peptidoglycan layer and thus cell wall synthesis *gram + stains, gram - doesn't

What are the characteristics of cyanobacteria?

-photolithoautotrophic -many can fix nitrogen -contain internal membrane system for photosynthesis -chloroplasts derived from endosymbiotic cyanobacteria

What do phylogenies have? What do unrooted trees have?

-phylogenies *have root node *completely specify evolutionary relationships *at least partially specify a temporal direction -unrooted trees *lack a root node *constrain but do not completely specify evolutionary relationships *do not specify a temporal direction

How do microbes run carbon and nitrogen cycling?

-really bacteria and only a few archaea are capable of fixing nitrogen

How old is antibiotic resistance?

-realtively ancient *found antibiotic resistance in ice cores *resistance -> a way a species interacts, competition

What is homoplasy?

-similarity in a trait among different organisms that has evolved independently

What is homology?

-similarity in a trait among different organisms that is due to inheritance from a common ancestor

How do bacteria feed?

-some bacteria feed singularly -some congregate to form multicellular fruiting bodies and show evidence of cooperative feeding

What is the eocyte hypothesis?

-some recent analysis suggests that there may be only two domains *suggests eukaryotes are sister to some but not all archaea

What are the three morphologies common between archaea and bacteria (prokaryote morphology)?

-sphere or coccus, occurs singularly or in plates, blocks, or clusters -rod or bacillus -helical or spiral

What information do chronograms convey?

-the branch lengths reflect temporal information (time)

What are the three domains tree?

-the current hypothesis has archaea and eukarya as sister groups *tree is root based on ancestral gene duplications

What is the root node?

-the most inclusive internal node -MRCA of the entire tree

Why do phylogenies also have a temporal dimension?

-they partially specify the relative ordering of events

How can eukaryotes create new recombinants?

-through sex *requires meiosis (prokaryotes are already 1n) and fertilization

What are some universal characters?

-use of DNA as genetic material -use of ACTG in DNA (ACUG in RNA) -three letter genetic code -central dogma (DNA -> RNA -> protein) -lipoprotein cell membrane -20 core amino acids in protein -ribosomal proteins and RNA -RNA polymerase proteins

What type of series do we use to estimate phylogeny?

-use series of nested loops *outer loop is set of all possible unrooted trees for the N study species *inner loop is set of characters of study species recorder in data *innermost loop is set of ancestral state assignments

Describe the Linnaean classification system

-uses single (unomial) names and are placed in a ranked hierarchy of increasingly more inclusive groups *genus family order class phylum kingdom

What are the effects of fecal transplants?

-very high success rate for some infections

Can morphology be used for prokaryote phylogeny?

-w/ limited morphology and lots of species, convergence is rampant *can have same morphology but doesn't mean they're related

How was penecillin discovered?

-was a lab accident *although antibiotic effects of some fungi (and bacteria) were known *discovered that near fungi bacteria died *where bacteria dying -> inhibition zone

What does parsimony mean?

-we prefer the history that minimizes number of evolutionary changes

What are the differences between LGT and sexual reproduction?

1) LGT typically involved part of the genome 2) LGT not reproduction 3) LGT has multiple mechanisms 4) LGT can occur over large phylogenetic distances

What are the hypotheses for viruses?

1) They are a fourth domain 2) they are of a separate origin 3) independent origin within other domains 4) all of the above?

What are the similarities between LGT and sexual reproduction?

1) both create new genetic combinations 2) both may involved recombination

What are the three ways lateral gene transfer can happen?

1) conjugation -> bacteria and archaea directly exchange parts of their genomes *part that's exchanged are plasmids (small, circular independent collection of genes) 2) transformation -> bacteria and archaea can pick up DNA from their environment 3) transduction -> viruses can trasmit DNA between hosts

What are the key features of biofilm?

1) extracellular polysaccharide matrix 2) surface attachment *solid surface or soft tissue in living organisms 3) structural heterogeneity AND diversity

What are the six steps of parsimony-based estimation of phylogeny?

1) making list of all possible unrooted trees for N species and visit the first tree on the list 2) for the first character, identify minimum number of changes on current tree and add this to score 3) repeat step 2 for remaining characters, and record the score for the current tree as sum of changes 4) repeat steps 2 and 3 for each of the remaining unrooted trees on the list 5) the unrooted tree(s) with the smallest score is (are) the optimal solution 6) use outgroup to root the optimal unrooted tree(s)

What are the advantages of model based inference?

1) models make our assumptions about the evolutionary process explicit 2) rather than making arbitrary assumptions about the cost/probability of various changes, these features can be estimated directly from the data 3) we can objectively compare competing models / test alternative hypotheses according to their relative ability to explain the observed data 4) we can assess the degree of uncertainty in estimates of phylogeny, and accommodate this uncertainty in our inferences about evolutionary history

What are the problems with parsimony?

1) under parsimony, probability (cost) of a character is the same for every branch *this assumption if biologically implausible and causes bias in estimates of phylogeny 2) probability (cost) of a character change is the same between all states *strong assumption that is difficult to justify 3) the probability (cost) of a character change is the same for all characters *ex: loss or gain of eyes similar to change in eye color *biologically implausible and known to cause bias 4) parsimony doesn't allow use to assess uncertainty in our estimates *can't quantify uncertainty

What two questions can metagenomics help answer?

1) which microbial species live in an environment *instead of attempting pure culture, go directly to environment and rely on rRNA sequencing or genomes (use universal homologies) *go to where you have some known taxa 2) how do they function (metabolically) in the environment *targeting genes of known function can give understanding of what microbes are doing *take sample and extract DNA *use probes that look for genes associated w/ certain characters *won't know who has them but they're there

What does a phylogeny specify?

COMPLETELY specifies the set of ancestor-descendant relationships among taxa

Archaea are always extremophiles

FALSE

Are archaea things that exclusively live in extreme environments

False

Are all microbes invisible to the naked eye?

NO

Does archaea have peptidoglycan?

NO

Are all microbes small?

NO *some of the largest cells are visible to the naked eye *many others are multicellular w/ complex internal structure

Are microbiomes the same in all parts of our bodies?

NO *different microbiomes in different parts of the body *so different it can be used in forensics

Do some microbes have a nucleus?

True

Most bacteria and archaea haven't been cultured in lab setting

True

Vast majority of microbes remain uncultured

True

No bacteria or archaea have chloroplast or mitochondria

True *b/c they are the chloroplast and mitochondria

Can LGT happen in eukaryotes?

YES

What is a model?

a mathematical description of a process *intended to describe process that gave rise to our observed data

What does tree topology specify?

a nested set of common-ancestry relationships (indicating who is more likely related to whom)

Where does character change happen?

along the branches of a tree

Among what species are capable of movement?

among bacteria and archaea

What is binary fission?

an asexual process that results in exact duplicates (clones)

What is symbiosis?

an association between at least two different organisms in which at least one of them benefits

What attacks peptidoglycan?

antibiotics can attack peptidoglycan

What does the eocyte hypothesis argue?

argues for paraphyletic archaea *eukaryotes are only related to some but not all archaea

How are species assigned?

assigned compound (binomial) names, consisting of the genus name and the species name, both italicized

What are the different kinds of carbon sources?

auto and hetero

What organisms have peptidoglycan?

bacteria

What organisms are capable of fixing atmospheric nitrogen?

bacteria and only a few archaea

What determines how bacteria move around?

based on lifestyle *different forms of motility

What is a trend for parsimony informative characters?

both states occur in 2 or more species *traits (potentially) have different minimum number of changes between trees using parsimony score

What are aerotolerant anaerobes?

can't use oxygen but are not damaged by it

Character histories are....

character histories are estimated, not observed *can only directly observe data from extant species

What are universal homologies?

characters found in all living organisms *b/c all life is related and connected by a pattern of ancestry and descent

To which level of trophy does the giant shipworm belong?

chemolithoautotroph

What do internal branches do?

connect two speciation events

What does phylogeny typically ignore?

details of the population level processes

What do unrooted trees not have?

don't have root node

what are facultative anaerobes?

don't need oxygen but use it when available

What kind of linkages do bacteria and eukaryotes have?

ester linkages

What are phylogenies?

estimates of geneological (evolutionary) relationships

How do we evaluate the possible character histories?

evaluate all possible state assignments to the two internal nodes (state to the power of 2)

What is polyphyletic?

exclude the most recent common ancestor of the included species

What is the field of systematics focused on?

focused on organizing biological diversity *involved identifying and arranging them in a hierarchical classification scheme

What can terms like ancestral, primitive, or advanced be used for?

for describing character states

Where do all novelties ultimately arise from?

from a mutation in a single organism

What is paraphyletic?

groups include some but not all descendants of a given common ancestor

What is gram positive?

has a thick layer of peptidoglycan on the outside, and a thin plasma membrane

What is gram negative?

has layer of peptidoglycan in between two plasma membranes

What do most organisms have living on and around them?

have a "cloud" of microbes *have more archaeal and bacterial cells in body than human cells *affect health and possibly psychology

What do internal nodes indicate?

indicate speciation events

What aspect of the ribosome is conserved across life?

its structure and function

What's LUCA?

last universal common ancestor

What does having the same site pattern in character states mean?

means they must have the same score

What are natural groupings called?

monophlyetic groups or clades

What are the characteristics of crenarchaeota?

mostly thermophilic and acidophilic

Is all microbial life unicellular?

no *archaea and bacteria is not always unicellular

What is the discovery void of antibiotics?

no new antibiotics discovered for a long time

Are speciation and character evolution related?

no, they are independent

Why is parsimony an obsolete method?

non-statistical inference method that is being used for phylogeny estimation, which is a statistical problem

What are traits?

observable features of an organism *strictly concerned w/ strictly heritable (not acquired) states *traits can be discrete or continuous