Studied by 11 people
tree of life
refers to the concept that all living organisms are related to one another through a shared ancestry
phylogeny
a unifying principal: all organisms are linked to one another through their shared evolutionary history
tree
a simplified model of the genealogy of life
taxon
any organism, or species, or group of species that we designate or name
taxa
what is the plural of taxon
speciation
the process whereby one species gives rise to two descendent species
speciation events
Phylogenies are the result of multiple what?
internal node
1
root node
3
internal branches
2
Terminal node
4
bifurcating trees
these are trees in which each internal node gives rise to two descendent branches, the photo is an example of one
polytomy
Trees with nodes that have three or more descendent branches, they usually reflect uncertainty about phylogenetic relationships
monophyletic group
a group of organisms consisting of the MCRA and all its descendants
clade
a monophyletic group
polyphyletic group
a group of organisms that excludes the MCRA
paraphyletic group
a group of organisms consisting of their MCRA but excluding some of it’s descendants
Synapomorphies
Monophyletic groups (clades) can often be recognized by special features or characteristics called _______________, which are unique to (or especially characteristic of) that group. They arrive from the MCRA of that clade.
homologous traits
those that are inherited from a common ancestor, an example would be hair, milk and mammary glands in mammals
classification
the naming of taxa and their placement in a hierarchical arrangement
genus and family
when naming a species, the names of the what are included?
sister groups
two clades or species that are each other’s closest relatives (the two descendants of a single node)
in-group
the group of taxa under study
outgrip
one or more taxa (usually closely related to the in-group) that are not members of the in-group
cladogram
only the relative branching order is depicted, no meaning to branch lengths
phylogram
branch length is proportional to the amount of character change
chronogram
branch length is proportional to time
parsimony
if we apply this principal, then we search for a tree that requires the least amount of change in character states
outgroup method
in this method you use one or more outgroups to estimate the ancestral character states (the character states in the MCRA of the group)
unrooted trees
trees that have been removed and relationships among taxa are more ambiguous, shows splitting events but tells us nothing about the sequence
parsimony uninformative
invariant characters (TTTT) and one taxon different, but other three the same (ATTT)
parsimony informative
in the case of the four taxa, only those characters where two taxa have one state and two have a second state are this, like (ATAT)
phylogenetic relatedness
the --------------- ---------------- of two taxa is a function of how recently they last shared a common ancestor
float freely
unrooted trees can ------------------- ----------------- and the branches of the trees can rotate around internal nodes without changing the meaning
internal branches
unrooted trees are the same if their -------------- -------------- separate the same subsets (bipartitions ) of taxa
maximum likelihood
an example of a model-based approach to estimating phylogenies
transitions
changes from one purine to another purine (A<→G) or from one pyrimidine to another pyrimidine (C<→T)
transversions
changes from one purine to a pyrimidine or vice-versa (A<→C, A<→T, G<→C, G<→T)
transitions
what is more likely to occur, transitions or transversions?
self-incompatible
can not self fertilize
self-compatible
have the ability to self fertilize
mutualism
each organism benefits, examples are corals and symbiotic algae
parasitism
one organism benefits to the detriment of the other, examples are birds and lice or mammals and tapeworms
strict coevolution
if there has been ---------- -------------, then the phylogeny of one set of organisms should match that of the other
biogeography
the study of the geographical distribution of organisms
dispersal and geographical events
historical biogeographers are particularly interested in the roles of ------------- and --------------- ---------
molecular clock
the greater the genetic difference between taxa the older the MCRA also defined as if rates of DNA coveolition are roughly constant then we can estimate the divergence time between two taxa on the basis of their degree of genetic divergence
2 million years
two sister species are 6% divergent in their DNA. The DNA diverges 1.5% per million year. How long ago did these two species split?
calibrated
the relationship between genetic difference and time since divergence can be --------------- with known times from the fossil record or from geographical events
medicine and conservations
two uses for phylogenies are …
bacteria, archaea and eukarya
what are the three domains of life?
eukarya
what domain of the life has the smallest branch on the tree on life (there is the least of them)?
The Great Chain of Being
what was a common idea before 1500’s, was created by Aristotle
Ernest Haeckel
who put together the three kingdom tree, 1866
Robert Whittaker
who put together the five kingdom tree, 1969
microsporidium
characteristics of this organism include: unicellular parasite, infects arthropods and vertebrates, has no mitochondria, but has a nucleus and makes spores to allow for dormancy outside the host, they are fungi
mitochondria
there are many Eukaryotes that lack a _____________ or have a highly reduced one
universal homologies
characteristic found in all animals
last universal common ancestor
LUCA stands for what?
ribosomal RNA
everyone has it, contains both highly conserved and variable regions, not laterally transferred between organisms, large and growing database
Carl Woese
made the very first tree based on molecular data, in 1987
eocyte tree
a tree that has two domains, eukarya came from Archaea
paraphyletic
in the oocyte tree the prokaryotic bacteria are considered to be
prokaryotes
a group that combines bacteria and archaea, they are paraphyletic and they have a nucleoid, and they have a petidoglycan layer, they’re unicellular, have no cytoskeleton, lack a nucleus and have no membrane enclosed organelles, DNA molecules often circular and they may only have one chromosome
nucleoid
blob of DNA that is not surrounded by a membrane
peptidoglycan layer
a mesh like structure that prevents a cell from exploding, this region is often targeted by antibiotics
false
true or false, you can get infected by an archaea
antibiotics
what was discovered by Alexander Fleming in 1928?
antibiotic resistance
what started occurring pretty soon after the development of antibiotics?
antibiotic crisis
we are facing an --------------- --------, as vert fews antibiotics are being developed and the medicines that get through don’t last
binary fission
the primary form of cell division and reproduction in prokaryotes is known as what?
binary fission
asexual reproduction, gives riser to clones, rapid can divide in 20-50 minus, produces two identical daughter cells and there is a strong environmental influence
genetic variation
mutations and selection, plasmids and lateral gene transfer are three ways to introduce what?
plasmid
extra chromosomal DNA, small circular molecules, automatically replace in the host cell (via the organ of replication), are passed during bacterial multiplication
conjugation
one cell is connected to another cell
transformation
they are able to uptake DNA from the environment, only portions of genome transferred
transduction
virus infects cell and when in the cell, it captures DNA from the cell and then injects that DNA into other cells, which causes resistance
gene transfer
what complicates phylogenies?
morphology
------------- does not predict physiology, phylogeny or ecology
gram positive
have a thick peptidoglycan layer
gram negative
have a thin peptidoglycan layer
ether
what is stronger an ether linkage or an ester linkage in extreme environments ?
anaerobes
do not and may even be killed by oxygen
aerotolerant anaerobes
can tolerate the presence of oxygen, even though they cannot use it
facultative
this type of organisms can live with or without oxygen
aerobes
require oxygen to live
microaerophiles
aerobes that can use oxygen only when it is present at levels reduced from that of air
D
what test tube contains microaerophiles?
photo
energy source = light
auto
carbon source = carbon dioxide
chemo
energy source = inorganic substance or organic compounds
hetero
carbon source = organic compounds
microbes
what started photosynthesis, control elemental cycles, decompose, help with agriculture and are everywhere
extremophiles
group of organisms that can live everywhere
temperature
thermophile and psychrophile
salt
halophile
radiation
radiophile
pressure
barophile
desiccation
xerophile
pH
alkaphile and acidophile
Note
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