BIS2C LEC

Questão	Responda
what is the main point behind the tree of life?	all organisms are related and share a common ancestry
what is the size of the mrca of all turtles? how do we know this? explain the evolution of gigantism	small medium, by the most parsimonious method we know turtle converged to have larger size on islands that select for that body type
list the non-monophyletic groups in the tree of life	archaea + bacteria- exclude eukaryotes, so they're paraphyletic
list the monophyletic groups in the tree of life	plant animals and fungi
list the functions of a phylogenetic tree	1. allow us to trace history of evolutionary changes in orgs 2. common ancestors of morphologically similar orgs 3. help us predict similarities, differences
what does a tree tell us about lineage?	The lineage has diverged separating completely
define taxon (taxa)	any org or group at an unspecified level that we designate with a name. Can be species, domain, phyla.
speciation	one homologous group diverges into differing groups due to reproductive isolation
what are phlyo trees unable to show us?	-time it took for each taxa to speciate - exact time at which they diverged - sequence of divergence of sister taxa
why are the internal nodes of a tree not counted as taxa?	once the group diverges, that homologous group at the int. node no longer exists- speciated.
monophyletic groups	include MRCA and all descendant taxa
paraphyletic groups	include MRCA, exclude some of the descendant taxa
polyphyletic groups	include descendant taxa, but exclude their MRCA
how was it determined that the L. bicolor were separate species?	ancestral character state reconstruction or trait mapping determined these new relationships and taxanomic categories- they were fooled b/c they converged at the same time
bifurcating vs polytomic trees	2 species diverge from one internal node vs 3+ species from one node
what do polytomies indicate about the tree?	there is uncertainty in the phylo relationships of those taxa- results from equally parsimonious trees
what do the # of internal nodes tell us about a tree?	the # of monophyletic groups in the tree - minus those mono groups made up by the terminal taxa
why were reptiles ever paraphyletic?	they excluded a group of desc.- birds
why are reptiles considered to be monophyletic now?	they include all the desc. groups including birds
why are bacteria and archaea non monophyletic?	exclude euks
what type of group are bacteria and archaea?	paraphyletic
what do clades have that other group types do not	synamorphies shared within group from common ancestor not shared with other groups
synapomorphies vs homologous traits	* synapomorphies are not present in the ancestral group. shared derived traits that distinguish one group from another vs same characteristics from the same common ancestor
when a trait evolves independently in 2+ separate groups or taxa	convergence or conv. evol.
is the 4 chamber heart of birds homologous or analogous with mammals?	it is analogous, this is because the trait independently evolved in birds and not seen in the mrca of the birds that it shares with the other taxa in its group
explain how a trait by looking at a tree would be homologous or homoplasious/ analogous	homo if present in the common ancestor of the two groups or taxa, if not then it is analogous/ homoplasious
homology vs homoplasy/ analogy	1. similar characteristics, share common ancestor 2. similar characteristics, DO NOT share common ancestor
the main points in using phylo trees in conservation	identify hidden diversity, reveal major lienages and emphasize the older ancestral groups- overall you must conserve the greatest diversity of the lineage
how you can discern species name from names of higher groups	species names are binomial and all groups above species are unomial
why can't non-monophyletic groups be characterized?	they are historically artificial groups that cannot be characterized by synamorphies that arose in a common ancestor
how do you identify a sister group?	the group that diverged from a lineage at the same time as the other
what is the importance of sister groups	they're used to contrast between taxa with different traits
at what point does a derived trait appear on a tree?	when you start splitting up into the in groups
what kind of traits do the out groups share with the ancestor?	ancestral traits
what does a cladogram tell us	branching order: which taxa came along first
importance of a phylogram	branch length= amount of character change
importance of chronogram	branch length= how long taxa took to speciating
what must be true about traits to build a phylogenic tree	there must be variation= discrete traits
steps to estimating phylogeny	1. look for varying traits and similar ones among organisms 2. then you assign codes to the character states 3. form a data matrix with these codes 4. look for similarities 5. find most parsimonious tree
what does an unrooted tree tell us	sequence of branching events and relationships but no temporal sequences
how many unrooted trees are possible for 4 taxa	3 (3 different taxa can be adjacent to reference taxa)
how many different rooted trees are possible for a 4 taxa unrooted tree?	5= the # of segments
which characters are the parsimony uninformative ones?	the traits that don't change or only change once which get scores 0 and 1
which characters in a matrix are parsimony informative?	the ones that involve 2 possible changes or more
name a type of parsimony uninformative character	invariant characters
what type of group are unicellular eukaryotes?	non- monophyletic, paraphyletic
describe character state changes at the molecular level. How long does this take?	nucleotide substitution at different dna sites that occur over generations at the population level
what are the three things we can look at to build a phylo tree?	morphology, ecology and behavior or orgs
list the possible causes of changes in character states in a phylo tree	dna substitutions, LGT, convergent evolution, mutations
why are many flowers self incompatible?	genetic variation would increase the fitness of the flower
in the example of the Linanthus phlox flowers, which trait evolved? how many times	self-compatibility, can self fertilize. evolved 3 times.
what is character conflict on a tree?	when there are different characters that only experience 1 change on diff trees : char. 1&3 on one tree and 2 on another- the same characters on 2 diff trees have diff #s of changes
what is a model based approach for tree building	taking into account the probability of rates of change for diff nucleotide subs
what types of nucleotide subs can occur	transitions: C<->T, A<->G and transversions: A<->C, G<->T, C<->G, A<-> T
which is more likely between transitions and transversions?	transitions- therefore they hold less weight when they differ slightly
how do trees with close to the same # of transitions compare	they are approximately as likely since it is common- transversions are taken into account more
T or F: a tree with a transversion may have a higher likelihood.	yes b/c they are rare-- but why though?!
how can we use models to find the ML tree?	relative frequencies of transition rates vs transversion rates
list several ways to find likelihood of trees in a model based approach	1. freq of transitions vs transversion rates 2. synonymous and non syn 3. subs at different codons
synonymous vs non synonymous	nuc sub causes no change in AA nuc sub causes a change in the AA it codes for
list applications of phylogeny	1. method/rate of character changes 2. coevolution: how when clades evolve 3. biogeography- org distribution 4. community- ecology 5. conservation priorities
how phylogeny is used in conservation	*save the older lineage and maintain diversity- identify unsuspected diversity, reveals major lineages of a clade, emphasizes conservation of the older lineages
the african cichlid fish study	by looking at the phylo tree, we can better understand how to conserve greater diversity of the lineage b/c we see what other pops of cichlids we should conserve in order to promote diversity and include the mrca
what is the purpose behind using phylo trees for conservation?	preserving the sets of species that best capture the evol history of the group from mrca
steps to finding where an event occurred on the phylo tree	1. use characters like DNA to build the tree 2. see how other traits evolved on this tree by looking at morph, behav, ecological
3 ways to look at the evo of traits on a phylo tree	1. most parsimony 2. outgroup method 3. probability of state changes
which is more likely: a plant becomes self compatible or incompatible?	self incompatible- increases the genetic diversity of the flower in most cases
in the case of the linanthus phlox flowers, which trait evolved by convergent evolution?	self compatibility converged
how many times did tortoises evolve gigantism	twice: convergent evolution- b/c these separate taxa both got that same trait and evolved at the same time
why were the L. bicolor flowers of the phlox family thought to be the same species?	they had similar morphology but through a phylo tree they realized they are different- by reduced petal size
is large size in tortoises analogous or homologous?	analogous- arose from convergence
are the L. bicolor traits analogous or homologous?	analogous
why do we compare sister taxa to find why one group has more species than another?	we use time as a control b/c we know they speciated at the same time from the same lineage so we can look at other factors such as ecology and behavioral
what is net diversification?	the # of extant taxa, used in contrasting sister species
what 2 things determine net diversification?	speciation and extinction rates
conclusion of the study about clade diversification rates - plants with canals (rubber or resin)	the clades with the canals were more diverse than those without. these evolved by convergence.
conclusion of case study of biogeography in horses	used an area phylogeny (locations replaced names on the tree) + fossils, horses originated in North America
what type of tree is used for biogeography in phylogenetics? ex in horse study	chronogram: tells us how long ago taxa have bee speciated
how do we find out when an event occured on a tree?	use dna and use # of mutations as indicator of time (mutation rate) as a molecular clock, and calibrate that clock with other data like a fossil
to say that 2 sister taxa are 10% divergent is to say that ...	they are each 5% diveregent, so with mutation rate we can date back to when it split from the mrca
how long ago did humans start wearing clothes?	100,000
how lice tells us how long ago human started wearing clothes	speciate when the new ecological niche for lice arose when human started wearing clothes (became body lice), so use that as a basis
how was the tree in the body lice study calibrated	out group method by a head louse in a chimp b/c we know that branch point in time
function of gene annotation in phylogenomics	what does a gene do
steps in gene annotation	1. identify homologs in sequence 2. align them 3. add additional sequences- this allows you to see what resulted from mere substitutions and deletions
what does sequence similarity indicate in gene annotation?	which gene is closest to the one in question by which sequence would undergo the fewest changes to be like our one in question
how we find gene function with gene annotation and parsimony	most parsimonious function for our gene would be the one with the fewest # changes to get the that function
why are microbes difficult to sort into a phylogenic tree?	lacks informative traits, many homologies- morph, ambiguous evo relationships leading to polytomies, lack nucleus, unculturable,
why is RNA used to infer phylogeny?	all cellular organisms have them in common, they infer homologies and are phylogenetically informative
prokaryotes vs eukaryotes	proks: lack nucleus and cytoskeleton, do not divide by mitosis but binary fission, lack membrane bound organelles, and has circular chromosomes
if it has a peptidoglycan cell wall, it must be...	bacteria
what groups are nitrogen fixators?	bacteria and archaea
in the eocyte tree, are the archaea mono or non mono? 3 domains tree?	in the eocyte tree, the archaea are a paraphyletic group because they exclude euks, 3 domains tree they are mono
brief overview of the history of antibiotics	used in the 40s, Golden Age in the 50s, focus on resistance after that
how mutations quickly spread in a bacterial pop	since they are haploid and have a short speciation/extinction rate, mutation moves quickly
vertical transmission of genes in bacteria	genes are cloned by binary fission as mother and daughter cells are formed
conjugation	dna exchange between bacteria via pilus , can occur intra or interspecies, only some or parts of genome passed along
bacterial plasmid	not needed for growth or reproduction, that is why it can be removed to lose pathogenicity
LGT vs sexual reproduction	LGT can occur across different species and domains, does not involve the transfer of the entire genome, has multiple mechanisms, not linked to reproduction (swap and go like conjugation)
functions of plasmids	metabolic: allow them to find niche, fertility: controls formation of fertility factors, resistance to antibiotics and toxins, virulence: presence determines pathogenicity
what establishes new pops in microbes?	lateral gene transfer followed by vertical gene transfer (bunnies)
transformation:	the dna of lysed, foreign bacterial cell is taken in by another cell and added by recombination
transformation vs transduction	1. genotype of cell is altered by the uptake of foreign dna from its environment 2. viruses carry prok. genes from one cell to another
case study of a. tumefaciens	bacteria that causes tumor in plants via transformation, used in biotech to grow plants by LGT
list the bacterial traits introduced by LGT	virulence, antibiotic resistance, metabolism
how do we know if it is convergent evolution occurring rather than lgt?	distantly related taxa have adaptations that require a change in not just one gene but the whole genome, like thermophily, then its conv.
how can you tell if it is lgt or maybe convergence?	distantly related orgs have the same genes needed to alter metabolic process (more simple) like antibiotic resistance
list the possible sources of antibiotic resistant bacteria	1. free living soil bacteria with resistance, 2. non pathogenic human bacteria with antib resistance 3. antibiotic producing bacteria 4. other pathogens that produce resistance and are found in animals/ humans
what is xanthan gum and its uses?	bacteria used as a thickener in many foods due to its polysach capsule it forms around each bacterium
the roles of microbes	-food industry - plant symbionts -enzymes -bioproducts -medicine -probiotic -pathogen -global cycle -biodiversity -bioremediation
ways that prokaryotes differ	1. form/morph: shape, gram + or - 2.functional: 3. phylogenetic diversity
key features of biofilms	polysach matrix, heterogeneic structure, adhere to liquid air interfaces, soft tissues and solid surfaces, has genetic diversity
stages in biofilm production	attachment/aggregation matrix production communication heterogeneity
quorum sensing is a system of communication between ...	intra and interspecies bacteria
virus group type	polyphyletic
structure shared by all viruses	capsid, nucleic acid
virus hosts are mostly	bacteria
where many viruses are found	ocean-water
what type of life cycles can plants have?	alternation of generations
list the types of eukaryotic life cycles	alternation of generations, haplontic and diplontic
do all land plants form a monophyletic group?	yes
mosses, liverworts and hornworts make what type of group?	non-monophyletic group- they are paraphyletic
which hypothesis is correct for turtle gigantism?	gigantism evolved separately on the galapagos and aldabra islands by the most parsimonious method
the case studies showing how to find where an event occured on a phylo tree	the phlox bicolor flowers and the gigantism in tortoises
how we compare clade diversification rates	we look at the net diversification of many different sister taxa with different # of extant species to control for time
case study of clade diversification rates	plant defense by use of canals- which ended up having higher net diversification (higher speciation rates) due to it aiding in defense against herbivores
give an example of tree applications in biogeography	horses: tells geo history and the dispersal pattern of the horses: used an area phylo tree
where the ancestral horses originated	1. przelwaski's horses from central asia then they dispersed to Africa then Europe and N Americ: East to west
where did horses speciate?	as they moved from central asia to africa
where did the speciation of zebras take place? which species has lead to the modern horses?	only in africa przewalski's horse
how do we find out "when" an event occured on a phylo tree?	# of mutations of dna on the tree and use mutation rates as molecular clocks to say how many years ago something happened- model approach + phylogram = cladogram;must calibrate with fossil or ancient thing
to say 2 sister taxa are n% divergent, it means they are .5n% divergent from common ancestor	use this value of time to find when the 2 speciated by the molecular clock method= called a DIVERGENCE TIME ESTIMATE
molecular clock assumptions and caveats	-rates of dna changes are constant - the generation times are the same - the dna sites are assumed neutral and not like sex linked or some other
molecular clock case study	when did humans start wearing clothes
human clothing case study	body lice speciation time conforms to the est time in which humans started wearing clothes because they evolve as their niches do ~100,000 years ago
what was used to calibrate the tree in the molecular clock study?	head lice sequence dna from a chimp b/c they diverged 5.5 mya like we did - we use this as an outgroup to date the emergence of the body lice we have
genome sequencing case study	phylogenetics: dna sequence to annotate genes in a genome
steps in the gene annotation	you get a known gene and align the gene sequnces so you can see the homologs and insertion and deletions between them, add more sequences to find more alignments, most parsimonious is the one w/ fewest steps back to original sequence in question
microbes are what type of group?	monophyletic?
in which major branches in the tree of life are the microbes found?	all 3: euks, proks, archaea
the problems with classifying microbes	- morphology varies - many cannot be cultured - homologous and analogous traits indistinguishable -no phylo informative traits to infer a phylo tree
universal homologies shared by yeast, humans bacteria and archaea	dna, protiens, codons
the importance of the rRNA in systematics	they are perfect for building trees because they all have them but * * rRNA is PHYLOGENETICALLY INFORMATIVE. they vary in protein synthesis allowing us to classify and place on the tree
How do prokaryotic cells divide	not by mitosis (differentiation)- lack cytoskeleton and nucleus- binary fission
do archaea divide by mitosis?	no they lack a cytoskeleton and nucleus
differences of prokaryotes vs euks	proks: binary fission or schizogeny, nucleiod, no membrane bound organelles or cytoskeleton, circular dna plasmids, 1 chromosome. euks opposite
how archaea are unique to the euks and bacteria	ether linked cell walls, some are methanogens and none conduct chlorophyll based photosynthesis
unique characteristics of bacteria to euks and arch	peptidoglycan in cell wall, ribosomes denatured by streptomycin and not effected by diptheria toxin
how does the eocyte tree differ from the 3 domains tree of life?	archaea are a paraphyletic group vs 3 domains where they are monophyletic
when did antibiotic resistance arise?	pharmacologic era 1960s
steps in binary fission	elongation of plasma membrane, doubling of the chromosome, cleaving of the cell then cytokinesis producing clones
vertical transmission of genes	parents pass directly to offspring
an example of vertical gene transmission	binary fission
what is the ploidy of bacterial cells?	haploid
how does genetic recombination occur in LGT?	crossing over with dna fragments of new cell and plasmid of recipient cell followed by cell division
how bacteria exchange plasmids	via conjugation tube where the plasmids of one flows to the other then the tube is retracted
convergence or LGT? how you can tell	LGT can't transfer entire genomes so if a distance relative gets thermophilic traits, it convergence
how to tell traits arise via LGT or convergence	simple transfer not requiring the entire genome: virulence, metabolism, resistance- can be LGT or convergence
explain which type of bacteria would be most affected by penecillin	gram positive- penicillin binds to peptidoglycan layer- + has more peptido.
effects of penicillin on bacteria- how it kills it	binds to enzymes holding peptid. layer, cell wall weakens, leads to cell death can't divide
biofilm: who can make it?	all domains: archaea bacteria protists fungi algae
characteristics of a mature biofilm	has more than one species of bacteria- intraspecies communication
bacteria: uni or multicellular?	uni cellular until they are part of a mature biofilm colony which then becomes multicellular
positive types of biofilms	bioremediation, protect against pathogens, nutrient cycling and part of food chain
negative biofilm examples	pathogenicity, dental plaque, corrosion of pipes on boats
metabolic diversity in bacteria	aerobes and anaerobes
is oxygen toxic to all anaerobes?	only the obligate anaerobes. Facultative switches between oxygen and none, and the aerotolerant don't use it but aren't hurt by it
photoautotrophs: where they're found, energy and C source	all domains, light energy, CO2
photoheterotrophs	some bacteria: light energy, organic compounds
chemolithotrophs	some bacteria and most archaea: inorganic compounds, CO2
chemoheterotrophs	all domains, organic compounds and organic compounds
metabolic types found in all domains	chemoheterotrophs and photoautotrophs
metabolic types with same carbon sources	photoautotrophs with chemolithotrophs, photoheterotrophs with chemohetertrophs
metabolic types with same energy sources	photoautotroph and photoheterotroph
list functional diversity in prokaryotes	interactions with other orgs, global nutrient cycles, industrial and agricultural uses and shaping earth's history
global cycles microbes aid	C, N, P, S and cations
# of bacteria in the soil, mL of water, and in the world	40million, 1 million, and 5x10^30 (5 nonillion)
extremophiles	anaerobes, thermophiles, psychrophiles, halophiles, barophiles, xerophiles, alkaphiles, acidophiles, radiophiles
example of a mesophile	e.coli
heat adaptations of thermophiles	decrease fluidity/fluid content of membranes; make proteins more stable prevent denaturing with different amino acids and salt bridges; slow down enzyme rate since heat increases it
relationships between thermophilic species	closely related by lineage not thermophilic capabilities
how we study microbes	uptake of CO2, decomposition rates,
why it's hard to study microbes	convergence leads to similarities not from homology, few character traits to refer to, rapid divergence, difficult to culture
benefits of culturing samples	determine process and properties of single org, rRNA sequence analysis, morph, produce large volumes, genetics and genomics
what is the result of the great plate culture anomaly	more can be observed via microscope than cultured
metagenomics	*you don't culture the sample, this is what makes it different from other analyses. dna sample of the entire microbial community in the environment and you sequence them to infer functions and compare to other communities
blood falls	red due to Fe cycling microbes underneath surface
culturable bacteria	proteobacteria, cyanobacteria and firmicutes
cyanobacteria:	photosynthetic w/ chlorophyll A, membrane system for photosyn, developed from endosymbiosis, some toxic, nitrogen fixation in heterocysts
what is the largest group of bacteria	proteobacteria
proteobacteria	gram negative, N fixing rhizobium, largest group, most diversity, e. coli- human pathogen, cholera, plague and gi issues, formed from endosym with mitochondria
firmicutes	low gc/ta ratios, gram +, produce endospores to endure harsh env, agents of disease like staph strep tetanus; include small mycoplasmas
bacteria vs archaea	archaea have no peptidoglycan cell wall, have etherlinked membrane, are the only methanogens, do not conduct photosynthesis, and none are pathogenic.
what group holds the only know methanogens?	euryarcheota
2 clades of archaea	crenacrchaota and euryarcheota
crenarchaota	thermophilic and acidophilic- some are mesophiles, not all are extremophiles
euryarchaeota	methanogens that use chemautotrophy to reduce co2 and make ch4, found in animal guts,
methanogen habitat	deep sea thermal vents and guts of grazers
pink euryarcheaota in basic alkaline environment	halophiles
bacteriosrodohpsin	uses light to make atp- not photosynthetic though?
extreme halophiles	monophyletic group of euryarcheoata that have square cells only
methanogen group type	paraphyletic/non mono
halotolerant, halophilic and non halophilic growth rate comparison to ion concentration	non- e.coli: lower conc., halotolerant like staph: mid range, halophile like vibrio fischeri: high
most archaea have what metabolic type	chemolithotroph
steps to pcr for phylo analysis	dna extraction -- pcr - rna sequence -
fourth domain hypothesis	rna polymerase II mapped and showed 4th domain of viruses
T or F: Archaea perform photosynthesis	yes- but not chlorophyll based!
which prokaryotes perform nitrogen fixation	some in bacteria and archaea
define virus	NONCELLULAR infectious agents that replicate only in host cell and makes cell syn virions to tranfer infection and make more bacteriophages
virus definition	intracellular parasites with nucleic acids capable of replication and lacking own cells
are viruses alive?	argue for: replicate mutate experience natural selection evolve against: noncellular don't replicate by division and have no metabolism
components of virion	nucleic acid capsid sometimes an envelope
capsid function	contains dna needed to inject into the host cell for replication
genomic diversity in viruses	dna and rna, shape, strandedness, + and - sense
describe the central dogma of molecular biology	replication transcription and translation by dna rna and proteins- viruses don't follow this path!
viruse genomes location	rna, not dna
virus types with most diverse host cell types	double stranded +/- retroid
features of tobacco mosaic virus	helical virions codes for 4 genes
what is the largest virus?	mimivirus codes for 1000 genes larger than mycoplasmas- largest bacteria
viruses be like...	1. 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.
virus replication cycle	1. attachment to host cell membrane - 2. penetration of host cell membrane by: endocytosis, mechanical penetration, inject genome 3. uncoating 4. replication and assembly 5. find new cell host
2 stages of virus replication cycle	lytic: cell lyses releasing viruses and lysogenic: the prophage is apart of the bacterial chromosome as the cell replicates and is noninfective
how viruses hijack host cells	mRNA proteins block transcription of host cell, uses host rna polymerase to transcribe its own cells
what type of phylo group are viruses?	polyphyletic
are there more microbes or viruses on earth?	viruses- 1x10^31
viruses effecting plants-	stunt growth, discolored and reduced biomass: cassava mosaic, citrus tristeza,
biomass and abundance in proks euks and viruses	proks= most biomass virus= most abundant 94
are viruses only parasitic?	yes
are all parasites pathogenic?	some may be, some not
define parasite	live in or on another org getting nutrients from it and may or not be pathogenic
define pathogen	biological agent causing disease to host; can be bacteria or virus. can be harmful or not.
infectious diseases are caused by...	pathogens
non infectious diseases are caused by ...	environmental or host factors
indicator for disease	symptoms
examples of infectious and non infectious diseases	inf: rabies noninf: heart disease
which are there more of in rich countries: infectious or non diseases?	non infectious - 93%
more infectious disease deaths in rich or poor?	poor countries- 64% deaths
what are the sources for human disease?	animal diseases became human diseases
zoonotic disease: define and examples	animal disease goes to humans or vice versa like rabies lyme plague- complete life cycle in the host
zoonotic disease stages	stage 5: comes from humans only- HIV stage 4: human mostly and animals- dengue stage 3: some human and animals- ebola stage 2: only from animals-rabies stage 1: only in animals-
a human only disease is what zoonotic stage?	5
factors driving zoonotic disease emergence	human wildlife interactions
nipah virus	high fatal rate: bats-fruit-pigs-humans
symbiotic relationships effects on host	parasitism: - or +, commensalism: 0 mutualism: +
# of bacterial species on the stomach	40,000
most abundant cell type in human body	microbial, fewer human cells
human microbe key points	varies person to person, but person's own microbiome is constant, microbiomes are similar among body parts of others, microbiomes classification of species differ greatly between people, microbiomes similar if classified by function
gut microbe functions	digestions, vitamin synthesis, drug metabolism, pathogen resistance, immune response, gut epo cells, odor appearance, cardiac size and behavior
changes in human ecology effecting microbes	population density, weather/climate, technology
diseases caused by microbial changes	asthma, crohns disease, allergies autism obesity
group type for mrca of all eukaryotes	polytomy
microbial eukaryotes phyly type	paraphyletic
how euk microbes differ	reproduction morphology symbioses ecological importance metabolism locomotion morph: unicellular/cellular reprod: sexual/asexual; many groups, strictly or both; diploid vs haploid loco: flagella, cilia, pseudopods metab: auto;/heterotrophs, an/aerobic symb: endosymbiosis, parasites
are euk microbes uni or multicellular?	they can be either
what is the cellular ancestral state for euk microbes?	unicellular, then later became multi by convergence
asexual repro types in euk microbes	binary fission schizogeny budding spores
sexual reprod in euk microbes	alternation of generations
locomotion in euk microbes	due to pseudopods, cilia and flagella
land plant metabolism can be...	photosynthetic pathogenic parasitic
metabolic types in microbial euks	auto/heterotrophs an/aerobes
likelihood of LGT in euks vs proks	more likely in proks- not as common in euks but happens
where euks lack ability to acquire new metabolic processes...	they are awesome at symbiosis with other domains of life
mutualist symbioses in euks	digestive defensive behavioral autotrophic and nutritional
an example of defensive symbiosis	biofilms
sister taxa of brown algae	diatoms!
brown algae and diatoms found in which clade	chromoalveolates
how chromoalveolates were made	secondary symbiosis with red algae in a flagellate
plastid loss	cilliates and oomycites
photosynthetic chromoalveolate	dinoflagellates
apicomplexans	all parasites of animals- like malaria. organelles at tip for transfer.
function of apicoplast	no photosynthesis but involved in lipid protein syn for malaria transfer
apicomplexans life cycle	completed in 2 different hosts
toxoplasma life cycle	can only reproduce in the host cell- cat. virus must find way back
photosynthetic sister taxa to apicomplexans	dinoflagellates
dinoflagellates	primary producers in marine env- endosymb with coral- when they die cloral bleaching occurs
alveolate clade	ciliates dinoflags and apicomplexans
straminopile clade	oomycetes diatoms brown algae slime nets: all have synapomorphy- hairs on longer of 2 flagella
straminopile synapomorphy	hairs on longer of the 2 flagella
diatom features	photosynthetic producers in marine and fresh h2o unicellular and filamentous store oil in vacuole- so oil source
brown algae and oomycetes	brown algae multicellular marine exclusive oomycetes multcellular non photsynth, absorptive heterotrophs
irish potato famine and sudden oak death	oomycetes did it
feature of unikont clade	single flagella
amoebozoan groups locomotion/ feeding	loboseans, slime molds pseudopods phagocytosis or parastism
plasmodial slime modes	mitosis and no cytokinesis: single cells form multinucleate plasmodium feeds by phago forms fruiting bodys to repro
cellular slime molds	indiv. cells eat by phago and form multicellular fruiting bodies
slime mold life cycles	sexual: single. aggregate, fruiting body, spores released, start over sexual: zygote from agreggation, karygamy, zygote -meiosis - amoeba born
hypothesis for virus origins?	?
sexual reproduction	2 steps: haploid gametes fuse to form diploid zygote and diploid zygote undergoes meiosis making haploid gametes
sexual reproduction steps	diploid zygote- meiosis- haploid gametes- syngamy- fusion of gametes- forms zygote
multicellular orgs repro cycles: which is multicellular?	haploid stage diploid or both
3 variations of reprod cycle:	diplontic haplontic and alt of generations
diplontic life cycle	expansion of diploid phase, gametes are the only haploid cells
haplontic life cycle	expanded haploid phase only diploid cell is zygote
alternation of generations	A diploid spore-forming organism gives rise to a haploid gamete-forming organism ! When haploid gametes fuse a diploid zygote is formed. ! Both stages multicellular and undergo mitosis, meiosis forms spores H
evidence of endosymb in mitochondria and chloroplasts	membrane components more like that of bacteria than of other euks morph resembles bacteria contain own genomes components resemble bacterias
do all euks have mitochondria?	most- not all, diplomonads
how we know mitochondria came from endosymbiosis	pcr and phylogenetic analysis of dna in mitochondria linked it single endosym event with a proteobacterium
conclusions of mitochondria phylo analysis	1 endosym with proteobacterium, mitochondria presence is a homologous trait in euks, derived trait- not present before endosymb
ancestral and derived features of euks	ancestral: cell wall membrane dna derived: cytoskeleton cell wall lost membrane bound dna phagocytosis
mitochondria endosymbiosis type	primary endosymbiosis - proteobacteria in cell
method to find origin of chloroplasts	phylo analysis of dna plastids in genomes traced plastids that derived from endosymb event with cyanobacterium
primary symbiosis of chloroplasts	three genomes in one cells: host mitochon and chlroplast phagocytosis then double membrane
why chloroplasts are scattered about	endosymb of chloroplasts happened in the plantae ancestor only- those who formed endosymbiotic relationship with this group got it
secondary symbiosis gave rise to	euk host cells with plant symbionts with chloroplasts
which plantae was the endosymbiont leading to chloroplasts	euglenid
primary vs secondary endosymbiosis	1. bacteria engulfed for mitochondria or chloroplasts 2. a eukaryotic symbiont is engulfed and already contains chloroplast/ mito
results of secondary endosymbiosis	diatoms-red algae apicomplexans, dinoflag and amoebozoans
# of nuclei present in tertiary endosymbiosis	3 (host, symbiont w/ own nuc + that of cyanobacterium)- photosynth euk symbiont engulfed by nucleus having host
tertiary endosymbiosis resulted in...	photosynthetic properties of dinoflaggs and brown algae
transitions vs transversions: which requires the fewest steps?	transitions are generally more common than transversions B. if the character in the tree undergoes the minimum amount of change it will involve a transversion C. if the character in the tree undergoes multiple changes it could involve both transitions and transversions E. the character exhibits homoplasy on this tree
cladogram relationships	closer within immediate clade than with outgroup
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.	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)	Primary: symbiosis between a cell that engulfed either a mitochondria or a chloroplast. Should have 3 genomes, if you count organelles and nuclear DNA separately, 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) *

Próximo

Descrição

Resumo de Recurso

Semelhante

	Criado por jsmwilliams quase 11 anos atrás