BIS 2C M1 locked

True or False: Branch lengths on a phylogram correspond to the degree of relatedness between taxa.

False

Branch lengths correspond to the proportion of genetic change

True or False: Universal homologies are invariant characters and thus not informative in determining relationships on the tree of life.

True

Because these features are shared among all organisms, they will not help determine relationships among them

True or False: Recombination only occurs via sexual reproduction

False

Lateral gene transfer may also result in recombinant DNA

True or False: The primary difference between binary fission and mitosis is that during binary fission, the ploidy of the cell is reduced (haploid)

False

Both binary fission and mitosis maintain the same number of chromosomes as the original cell. Meiosis is the process by which chromosome number is reduced

True or False: Multicellularity is homologous on the tree of life

False

Multicellularity has evolved multiple times, including in bacteria

True or False: The human microbiome varies on a fine enough scale to allow for forensic identification

True

True or False: Unrooted trees completely specify evolutionary relationships

False

Relationships on unrooted trees are not defined until a root has been placed. Note, however, that some possibilities are excluded

True or False: Polytomies are internal nodes with three or more descendant lineages

True

Polytomies have three or more descendant lineages arising from a single node (MRCA)

True or False: A synapomorphy of Bacteria is peptidoglycan

True

Only bacteria have peptidoglycan

True or False: In a colonial organism, some, but not all, cells are capable of sexual reproduction

False

In colonial organisms, all cells retain the ability to reproduce

When building phylogenies, how do we know which species to use as the outgroup?

It is identified using independent evidence

Outgroups are defined by prior knowledge, usually by a previous phylogenetic analysis

Bats, pterodactyls, and birds all have wings. What can we conclude about their evolution?

The bones in the wings are homologous and the evolution of flight is homoplasious

Since these animals are all tetrapods, they do share the same bones although they are modified for flight. Additionally, flight evolved 4 separate times in animals (insects, bats, birds, and pterosaurs).

The two competing hypotheses (three-domains and eocyte) for the Tree of Life discussed in class differ in...?

Whether or not archaea are monophyletic

The main difference between the three-domains tree and the eocyte hypothesis is that Eukaryotes are related to some, but not all Archaea. This makes Archaea paraphyletic

Clostridium tetani are an endospore-forming bacterium in the Firmicutes. The small white circles are the endospores. What is the function of the endospores?

They allow the bacterium to survive harsh conditions

Endospores are highly resistant to harsh environmental conditions

What is the name of the process in which bacteria and archaea can directly exchange parts of their genome?

Conjugation

The sex pilus forms between two cells and allows transfer of genetic material

You are on an expedition studying microbes in the Sargasso Sea. You discover a new microbe, but you are not sure of its identity. What morphological feature or capability would help you positively identify the organism as Archaea?

Ether-linked membrane lipids

Only Archaea have ether linkages

Lateral Gene Transfer (LGT) and sexual reproduction in eukaryotes are similar in that they both...?

Create new genetic combinations

Although LGT is not reproduction, it does result in new genetic combinations

The great plate count anomaly refers to the inability of all microbes observed in an environment to be grown in pure culture. Which of the methods described below has been used by scientists to overcome this problem?

Direct DNA sequencing of environmental samples

These are culture-independent studies that involve direct sequencing of environmental samples (metagenomics, employed by Carl Woese)

Biofilms are composed of a community of microbes embedded in a polysaccharide matrix. Another feature of mature biofilms is that they are...?

Structurally heterogeneous

What are the key steps in quorum sensing?

Attachment to substrate → Signal Producing Protein → Signal Receptor Protein → Group Behavior Genes

Some microbial adaptations (e.g. hyperthermophily) require changes to be made in most or all genes in the genome. In such cases, when one sees distantly related groups with this adaptation, it is most likely the result of...?

Convergent evolution

As a microbiologist, you are brought a microorganism to identify. It has a distinct cell wall, is gram-negative, extremely small (0.5 μm), and is growing as a parasite inside an animal cell. It cannot be grown outside of the host cell. The specimen is most likely a...?

Chlamydia

Lateral gene transfer is problematic in phylogenetic reconstruction because...?

Distantly related species will appear to be each other's closest relatives

You were asked to read the recent article, "Scientists Unveil a New Tree of Life." As discussed in lecture, how does this study contrast with the original three-domains study by Carl Woese (1977)?

The recent study used whole genomes as opposed to ribosomal RNA

In a specimen from the dissection of Azolla water ferns (from lab), there is a cell that looks like a chain of beads. They are symbiotic cyanobacteria. What is the function of the large, circular cell in the middle?

Nitrogen fixation

Purple sulfur bacteria are photolithoautotrophs. Which of the following compounds do they use as an electron donor?

H2S

Building phylogenetic trees using statistical methods (as opposed to parsimony) allows phylogeneticists to correct for...?

Transition vs. transversion rates

True or False: A data matrix summarizes characters and character states for taxa prior to phylogenetic analysis

True

True or False: Binary fission and meiosis both involve a reduction in ploidy

False

True or False: All photosynthetic bacteria lack chloroplasts

True

True or False: When using parsimony, the cost of change between character states is assumed to be the same

True

True or False: DNA, mitochondria, and ribosomes are universal homologies

False

True or False: Recent studies argue that LUCA originated in hot, acidic springs

False

True or False: Oxygenic photosynthesis evolved before anoxygenic photosynthesis

False

True or False: The coccus body form is homologous in Bacteria and Archaea

False

True or False: The plasma membrane of a eukaryotic cell is structurally/chemically more similar to that of an archaeon than to that of a bacterium

False

True or False: Nodes on a phylogeny represent the most recent common ancestor (MRCA) of two or more descendant lineages

True

Bacillus antracis (Firmicutes) cause a deadly disease: anthrax. What feature of anthrax makes it so dangerous?

The ability to produce endospores

Why do we consider Stigmatella to be a case of multicellularity in bacteria?

Some, but not all, cells form the reproductive structures

You are a doctor treatinga patient for a mystery illness. You send out a blood sample and the microbes shown at the right are discovered. If you plan on treating the patient with penicillin, what else do you need to know in order to determine whether or not the treatment will be effective?

Presence/absence of peptidoglycan and a gram stain

What feature is an adaptation of thermophilic Archaea that allows for life at high temperatures?

Lipid Monolayer

The evolution of mitochondria and plastids from bacterial endosymbionts were ancient events. Recently, spheroid bodies, which have their own genome and can fix gaseous nitrogen (N2), were discovered in unicellular eukaryotes called diatoms. If the spheroid body evolved by endosymbiosis, how would you discover which bacterial lineage was the original partner in this endosymbiosis?

Discover which bacteria can fix nitrogen and sample their genes; do a phylogenetic analysis with the spheroid genome and genes from bacterial candidates

bifurcating

splitting into 2

sister group

2 clades or species that are each other's closest relatives

ingroup

set of taxa under study

outgroup

taxa that fall phylogenetically outside of group under study

derived

trait that is modified in the ingroup

ancestral

features present in common ancestor (starting conditions)

phylogeny

evolutionary relationships among taxa

classification

naming of taxa & placement in hierarchal arrangement

binomial

pair of descriptive names for species

genera

plural for genus

Linnaean classification

species -> genus -> family -> order -> class -> phylum

phyla

plural for phylum

taxon

group of organisms at any level of classification

higher taxa

more inclusive taxa

monophyletic

unique common ancestor & all of its subsequent descendants

synapomorphies

shared derived traits used to distinguish taxa

paraphyletic

contains MRCA, but not ALL descendants

polyphyletic

group of organisms that excludes MRCA

homoplasious characters

similarities arose independently (not inherited by common ancestor)

cladogram

depicts relative branching order (no meaning to branch length)

phylogram

branch length proportional to amount of character change

chronogram

branch length proportional to time

unrooted tree

relationships among taxa more ambiguous, position of root unknown

principle of parsimony

the simplest of 2 (or more) competing theories is preferred

invariant

TTTT, AAAA (all same)

parsimony-uniformative

one taxon different, others same (TCTT, CCCT)

parsimony-informative

2 taxa have one state, 2 taxa have second state (GAGA, CCAA)

congruent characters

consistent, "telling the same story"

characters in conflict

telling different story

transitions

A --> G, C--> T

tranversions

A,G --> C,T

molecular time clock

calibrating divergence time estimates on molecular phylogenies

Carl Woese

father of Archaea, took phylogenetic taxonomy of 16S ribosomal RNA

homology

sharing of traits via a common ancestry

rRNA

led to diversification of bacteria & archaea

negative-sense single stranded RNA viruses

measles, rabies, H5N1

positive-sense single stranded RNA viruses

causes disease in agriculture

RNA retroviruses

HIV

double-stranded RNA viruses

plant & human diseases (diarrhea)

DNA viruses

smallpox, herpes

virus

acellular, small genome, need host for reproduction, capsids

common features of the 3 domains

glycolysis

replicated DNA conservatively

DNA encodes peptides

produce peptides by transcription & translation

plasma membranes & ribosomes

prokaryote features

no cytoskeleton

circular DNA

no nucleus

binary fission

LGT

no organelles

microbe

single celled organisms too small to be seen with the unaided eye

microbe studies

model systems

causative agents of disease

agricultural & industrial importance

biotechnology

mitochondria & chloroplast of eukaryotes

medical research

bacteria & forensic science

coccus

sphere shaped bacteria

cocci

plural for coccus

rod-bacillus

long chain/cluster shaped bacteria

helical

elongated, thin shaped bacteria

gram-positive

bacteria with thick layer of peptidoglycan outside the plasma membrane

gram-negative

bacteria with thin layer of peptidoglycan & a distinct outer membrane (periplasmic space)

archaea & eukaryote similarities

DNA packed by histone-like proteins

DNA not completely "naked"

presence of TATA box

RNA pol similar

S-LAYER

monomolecular layer of proteins or glycoproteins found in Archaea

archaea features

ether linkages

S-LAYER

lipid monolayer

quorum sensing

communication between prokaryotes via chemical signals

synthetic ecology

exchange genes in order to survive

biofilm

thin, slimy film of bacteria that adheres to a surface

anaerobes

require no oxygen