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what is the main point behind the tree of life?
what is the size of the mrca of all turtles? how do we know this? explain the evolution of gigantism
list the non-monophyletic groups in the tree of life
list the monophyletic groups in the tree of life
list the functions of a phylogenetic tree
what does a tree tell us about lineage?
define taxon (taxa)
speciation
what are phlyo trees unable to show us?
why are the internal nodes of a tree not counted as taxa?
monophyletic groups
paraphyletic groups
polyphyletic groups
how was it determined that the L. bicolor were separate species?
bifurcating vs polytomic trees
what do polytomies indicate about the tree?
what do the # of internal nodes tell us about a tree?
why were reptiles ever paraphyletic?
why are reptiles considered to be monophyletic now?
why are bacteria and archaea non monophyletic?
what type of group are bacteria and archaea?
what do clades have that other group types do not
synapomorphies vs homologous traits
when a trait evolves independently in 2+ separate groups or taxa
is the 4 chamber heart of birds homologous or analogous with mammals?
explain how a trait by looking at a tree would be homologous or homoplasious/ analogous
homology vs homoplasy/ analogy
the main points in using phylo trees in conservation
how you can discern species name from names of higher groups
why can't non-monophyletic groups be characterized?
how do you identify a sister group?
what is the importance of sister groups
at what point does a derived trait appear on a tree?
what kind of traits do the out groups share with the ancestor?
what does a cladogram tell us
importance of a phylogram
importance of chronogram
what must be true about traits to build a phylogenic tree
steps to estimating phylogeny
what does an unrooted tree tell us
how many unrooted trees are possible for 4 taxa
how many different rooted trees are possible for a 4 taxa unrooted tree?
which characters are the parsimony uninformative ones?
which characters in a matrix are parsimony informative?
name a type of parsimony uninformative character
what type of group are unicellular eukaryotes?
describe character state changes at the molecular level. How long does this take?
what are the three things we can look at to build a phylo tree?
list the possible causes of changes in character states in a phylo tree
why are many flowers self incompatible?
in the example of the Linanthus phlox flowers, which trait evolved? how many times
what is character conflict on a tree?
what is a model based approach for tree building
what types of nucleotide subs can occur
which is more likely between transitions and transversions?
how do trees with close to the same # of transitions compare
T or F: a tree with a transversion may have a higher likelihood.
how can we use models to find the ML tree?
list several ways to find likelihood of trees in a model based approach
synonymous vs non synonymous
list applications of phylogeny
how phylogeny is used in conservation
the african cichlid fish study
what is the purpose behind using phylo trees for conservation?
steps to finding where an event occurred on the phylo tree
3 ways to look at the evo of traits on a phylo tree
which is more likely: a plant becomes self compatible or incompatible?
in the case of the linanthus phlox flowers, which trait evolved by convergent evolution?
how many times did tortoises evolve gigantism
why were the L. bicolor flowers of the phlox family thought to be the same species?
is large size in tortoises analogous or homologous?
are the L. bicolor traits analogous or homologous?
why do we compare sister taxa to find why one group has more species than another?
what is net diversification?
what 2 things determine net diversification?
conclusion of the study about clade diversification rates - plants with canals (rubber or resin)
conclusion of case study of biogeography in horses
what type of tree is used for biogeography in phylogenetics? ex in horse study
how do we find out when an event occured on a tree?
to say that 2 sister taxa are 10% divergent is to say that ...
how long ago did humans start wearing clothes?
how lice tells us how long ago human started wearing clothes
how was the tree in the body lice study calibrated
function of gene annotation in phylogenomics
steps in gene annotation
what does sequence similarity indicate in gene annotation?
how we find gene function with gene annotation and parsimony
why are microbes difficult to sort into a phylogenic tree?
why is RNA used to infer phylogeny?
prokaryotes vs eukaryotes
if it has a peptidoglycan cell wall, it must be...
what groups are nitrogen fixators?
in the eocyte tree, are the archaea mono or non mono? 3 domains tree?
brief overview of the history of antibiotics
how mutations quickly spread in a bacterial pop
vertical transmission of genes in bacteria
conjugation
bacterial plasmid
LGT vs sexual reproduction
functions of plasmids
what establishes new pops in microbes?
transformation:
transformation vs transduction
case study of a. tumefaciens
list the bacterial traits introduced by LGT
how do we know if it is convergent evolution occurring rather than lgt?
how can you tell if it is lgt or maybe convergence?
list the possible sources of antibiotic resistant bacteria
what is xanthan gum and its uses?
the roles of microbes
ways that prokaryotes differ
key features of biofilms
stages in biofilm production
quorum sensing is a system of communication between ...
virus group type
structure shared by all viruses
virus hosts are mostly
where many viruses are found
what type of life cycles can plants have?
list the types of eukaryotic life cycles
do all land plants form a monophyletic group?
mosses, liverworts and hornworts make what type of group?
which hypothesis is correct for turtle gigantism?
the case studies showing how to find where an event occured on a phylo tree
how we compare clade diversification rates
case study of clade diversification rates
give an example of tree applications in biogeography
where the ancestral horses originated
where did horses speciate?
where did the speciation of zebras take place?
which species has lead to the modern horses?
how do we find out "when" an event occured on a phylo tree?
to say 2 sister taxa are n% divergent, it means they are .5n% divergent from common ancestor
molecular clock assumptions and caveats
molecular clock case study
human clothing case study
what was used to calibrate the tree in the molecular clock study?
genome sequencing case study
steps in the gene annotation
microbes are what type of group?
in which major branches in the tree of life are the microbes found?
the problems with classifying microbes
universal homologies shared by yeast, humans bacteria and archaea
the importance of the rRNA in systematics
How do prokaryotic cells divide
do archaea divide by mitosis?
differences of prokaryotes vs euks
how archaea are unique to the euks and bacteria
unique characteristics of bacteria to euks and arch
how does the eocyte tree differ from the 3 domains tree of life?
when did antibiotic resistance arise?
steps in binary fission
vertical transmission of genes
an example of vertical gene transmission
what is the ploidy of bacterial cells?
how does genetic recombination occur in LGT?
how bacteria exchange plasmids
convergence or LGT? how you can tell
how to tell traits arise via LGT or convergence
explain which type of bacteria would be most affected by penecillin
effects of penicillin on bacteria- how it kills it
biofilm: who can make it?
characteristics of a mature biofilm
bacteria: uni or multicellular?
positive types of biofilms
negative biofilm examples
metabolic diversity in bacteria
is oxygen toxic to all anaerobes?
photoautotrophs: where they're found, energy and C source
photoheterotrophs
chemolithotrophs
chemoheterotrophs
metabolic types found in all domains
metabolic types with same carbon sources
metabolic types with same energy sources
list functional diversity in prokaryotes
global cycles microbes aid
# of bacteria in the soil, mL of water, and in the world
extremophiles
example of a mesophile
heat adaptations of thermophiles
relationships between thermophilic species
how we study microbes
why it's hard to study microbes
benefits of culturing samples
what is the result of the great plate culture anomaly
metagenomics
blood falls
culturable bacteria
cyanobacteria:
what is the largest group of bacteria
proteobacteria
firmicutes
bacteria vs archaea
what group holds the only know methanogens?
2 clades of archaea
crenarchaota
euryarchaeota
methanogen habitat
pink euryarcheaota in basic alkaline environment
bacteriosrodohpsin
extreme halophiles
methanogen group type
halotolerant, halophilic and non halophilic growth rate comparison to ion concentration
most archaea have what metabolic type
steps to pcr for phylo analysis
fourth domain hypothesis
T or F: Archaea perform photosynthesis
which prokaryotes perform nitrogen fixation
define virus
virus definition
are viruses alive?
components of virion
capsid function
genomic diversity in viruses
describe the central dogma of molecular biology
viruse genomes location
virus types with most diverse host cell types
features of tobacco mosaic virus
what is the largest virus?
viruses be like...
virus replication cycle
2 stages of virus replication cycle
how viruses hijack host cells
what type of phylo group are viruses?
are there more microbes or viruses on earth?
viruses effecting plants-
biomass and abundance in proks euks and viruses
are viruses only parasitic?
are all parasites pathogenic?
define parasite
define pathogen
infectious diseases are caused by...
non infectious diseases are caused by ...
indicator for disease
examples of infectious and non infectious diseases
which are there more of in rich countries: infectious or non diseases?
more infectious disease deaths in rich or poor?
what are the sources for human disease?
zoonotic disease: define and examples
zoonotic disease stages
a human only disease is what zoonotic stage?
factors driving zoonotic disease emergence
nipah virus
symbiotic relationships effects on host
# of bacterial species on the stomach
most abundant cell type in human body
human microbe key points
gut microbe functions
changes in human ecology effecting microbes
diseases caused by microbial changes
group type for mrca of all eukaryotes
microbial eukaryotes phyly type
how euk microbes differ
are euk microbes uni or multicellular?
what is the cellular ancestral state for euk microbes?
asexual repro types in euk microbes
sexual reprod in euk microbes
locomotion in euk microbes
land plant metabolism can be...
metabolic types in microbial euks
likelihood of LGT in euks vs proks
where euks lack ability to acquire new metabolic processes...
mutualist symbioses in euks
an example of defensive symbiosis
sister taxa of brown algae
brown algae and diatoms found in which clade
how chromoalveolates were made
plastid loss
photosynthetic chromoalveolate
apicomplexans
function of apicoplast
apicomplexans life cycle
toxoplasma life cycle
photosynthetic sister taxa to apicomplexans
dinoflagellates
alveolate clade
straminopile clade
straminopile synapomorphy
diatom features
brown algae
and oomycetes
irish potato famine and sudden oak death
feature of unikont clade
amoebozoan groups locomotion/ feeding
plasmodial slime modes
cellular slime molds
slime mold life cycles
hypothesis for virus origins?
sexual reproduction
sexual reproduction steps
multicellular orgs repro cycles: which is multicellular?
3 variations of reprod cycle:
diplontic life cycle
haplontic life cycle
alternation of generations
evidence of endosymb in mitochondria and chloroplasts
do all euks have mitochondria?
how we know mitochondria came from endosymbiosis
conclusions of mitochondria phylo analysis
ancestral and derived features of euks
mitochondria endosymbiosis type
method to find origin of chloroplasts
primary symbiosis of chloroplasts
why chloroplasts are scattered about
secondary symbiosis gave rise to
which plantae was the endosymbiont leading to chloroplasts
primary vs secondary endosymbiosis
results of secondary endosymbiosis
# of nuclei present in tertiary endosymbiosis
tertiary endosymbiosis resulted in...
transitions vs transversions: which requires the fewest steps?
cladogram relationships
Viruses to survive they must be able to do 3 things
o Get into a susceptible host. Attachment to host cell membrane. Not in plant, fungal and bacterial viruses. Penetration of host cell membrane: endocytosis, mechanical penetration with plant and fungal viruses. Inject genome with some bacterial viruses
o Must be able to replicate and make more virus. Uncoating. Replication. Self-assembly of virus particles
o Most have some mechanism to move the newly made viruses to new susceptible host.
Primary: symbiosis between a cell that engulfed either a mitochondria or a chloroplast.
Should have 3 genomes, if you count organelles (1) and nuclear DNA separately (2), in the end (one nuclear genome, one mitochondrial genome, one chloroplast genome) *
Secondary: engulfing one cell/organism that has a chloroplast/mitochondria from primary endosymbiosis.
Should have 5 genomes, if you count organelles and nuclear DNA separately, in the end (3 from primary + 1 nuclear genome + 1 mitochondrial genome) *
Tertiary: engulfing an organism that is already secondary endosymbiont. Thus, acquiring their mitochondria and/or chloroplasts. Should have 7 genomes, if you count organelles and nuclear DNA separately, in the end (5 from secondary + 1 mitochondrial and 1 nuclear genome)
