BIS 2C Midterm 1

tree of life

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