BIOL 322 Midterm
What are the 10 taxonomic ranks? - answer Life
Domain
Kingdom (not in bacteria or archaea)
Phylum
Class
Order
Family
Genus
Species
Subspecies
What are infraspecific designations? - answer Words used to differentiate between
strains of a species (Biovar, Serovar, Pathovar, Phagovar, Morphovar)
What type of strains are given the designation Biovar? - answerstrains with special
biochemical properties
What type of strains are given the designation Serovar? - answer strains with distinctive
antigenic properties
What type of strains are given the designation Pathovar? - answerstrains with
pathogenic properties
What type of strains are given the designation Morphovar? - answerstrains with special
morphological features
What is a species concept? - answerPhilosophical framework used to understand why
organisms can be sorted into species
What is species definition? - answerMathematical and more practical outline of how to
assign organisms to a species
What are the 3 ways to look at species concept? - answerBiological
Ecological
Phylogenitic
What is the biological species concept? - answerspecies are groups of interbreeding
natural populations that are reproductively isolated from other such groups (LGT in
bacteria)
,What is the ecological species concept? - answerdefines a species in terms of its
ecological niche
What is the phylogenetic species concept? - answerdefines a species as the smallest
group of individuals that share a common ancestor, forming one branch on the tree of
life
What are the 9 ways to look at species definition? - answerMorphospecies
Taxospecies
Genomospecies (DDH)
16s rRNA Sequencing
Multi-locus Sequencing (MLST & MLSA)
Whole Genome Sequencing
Average Nucleotide Identity (ANI)
Core Genome Phylogeny
Gene Composition Sequencing (GCS)
What is the morphospecies species definition? - answerSpecies are defined strictly by
morphology
What is the taxospecies species definition? - answerSpecies are defined by biochemical
properties (metabolism, enzymes etc.)
Not really used anymore because it's easily confused by LGT.
What is genomospecies species definition? - answerOrganisms are defined as being
the same species if the DNA-DNA Hybridization (DDH) test shows >70% relatedness
How is a DDH test performed? - answerDNA of 2 organisms are melted into individual
strands.
DNA is cooled, and one strand from each organism comes together to form a new
double stranded helix
The % of the genes that are able to hybridize together determines their relatedness
What is the 16s rRNA sequencing species definition? - answerOrganisms can possibly
be the same species if the sequence of their 16s rRNA's are >97% the same.
The only way to be sure is by then proving that their DDH is >70% as well
What are the properties of 16s rRNA that make it good for sequencing? -
answerUniversal
Functionally conserved
Abundant
Encodes for RNA molecule, not protein
, What is the multi-locus sequencing species definition? - answerUses 7 genes spread
out evenly around the genome to increase resolution without sequencing entire genome
What are the 2 types of multi-locus sequencing? - answerMulti-locus sequence typing
(MLST)
Multi-locus sequence analysis (MLSA)
What does MLST do? - answerUses allelic mismatches to recognize strains within a
species.
Uses tables to show relatedness, and from these can determine recombination:mutation
ratio.
What does MLSA do? - answerUses protein coding genes to characterize a more
diverse group.
Uses phylogenetic trees to show relatedness
What is a Burst Diagram? - answeridentifies mutually exclusive related groups in a
population, then identifies the founding genotype of each group
Larger the dot = more common the sequence type
lines radiating from dot = single locus variants
What is the whole genome sequencing species definition? - answerEntire gene is
sequenced.
What is a core genome? - answerThe stable bacterial genome shared by all members
of a species
What is an auxiliary set? - answerThe variable bacterial genome that is susceptible to
LGT.
What is the average nucleotide identity species definition? - answercompares all of the
protein coding genes in the core genomes of 2 bacterial organisms
>95% ANI is equivalent to it being >70% DDH (they are the same species)
What is the core genome phylogeny species definition? - answerMakes a long chain of
all protein coding genes in a bacterial core genome, then align it with one from another
organism and compare.
What is the genome composition sequencing species definition? - answerConserved
DNA
What are the 10 taxonomic ranks? - answer Life
Domain
Kingdom (not in bacteria or archaea)
Phylum
Class
Order
Family
Genus
Species
Subspecies
What are infraspecific designations? - answer Words used to differentiate between
strains of a species (Biovar, Serovar, Pathovar, Phagovar, Morphovar)
What type of strains are given the designation Biovar? - answerstrains with special
biochemical properties
What type of strains are given the designation Serovar? - answer strains with distinctive
antigenic properties
What type of strains are given the designation Pathovar? - answerstrains with
pathogenic properties
What type of strains are given the designation Morphovar? - answerstrains with special
morphological features
What is a species concept? - answerPhilosophical framework used to understand why
organisms can be sorted into species
What is species definition? - answerMathematical and more practical outline of how to
assign organisms to a species
What are the 3 ways to look at species concept? - answerBiological
Ecological
Phylogenitic
What is the biological species concept? - answerspecies are groups of interbreeding
natural populations that are reproductively isolated from other such groups (LGT in
bacteria)
,What is the ecological species concept? - answerdefines a species in terms of its
ecological niche
What is the phylogenetic species concept? - answerdefines a species as the smallest
group of individuals that share a common ancestor, forming one branch on the tree of
life
What are the 9 ways to look at species definition? - answerMorphospecies
Taxospecies
Genomospecies (DDH)
16s rRNA Sequencing
Multi-locus Sequencing (MLST & MLSA)
Whole Genome Sequencing
Average Nucleotide Identity (ANI)
Core Genome Phylogeny
Gene Composition Sequencing (GCS)
What is the morphospecies species definition? - answerSpecies are defined strictly by
morphology
What is the taxospecies species definition? - answerSpecies are defined by biochemical
properties (metabolism, enzymes etc.)
Not really used anymore because it's easily confused by LGT.
What is genomospecies species definition? - answerOrganisms are defined as being
the same species if the DNA-DNA Hybridization (DDH) test shows >70% relatedness
How is a DDH test performed? - answerDNA of 2 organisms are melted into individual
strands.
DNA is cooled, and one strand from each organism comes together to form a new
double stranded helix
The % of the genes that are able to hybridize together determines their relatedness
What is the 16s rRNA sequencing species definition? - answerOrganisms can possibly
be the same species if the sequence of their 16s rRNA's are >97% the same.
The only way to be sure is by then proving that their DDH is >70% as well
What are the properties of 16s rRNA that make it good for sequencing? -
answerUniversal
Functionally conserved
Abundant
Encodes for RNA molecule, not protein
, What is the multi-locus sequencing species definition? - answerUses 7 genes spread
out evenly around the genome to increase resolution without sequencing entire genome
What are the 2 types of multi-locus sequencing? - answerMulti-locus sequence typing
(MLST)
Multi-locus sequence analysis (MLSA)
What does MLST do? - answerUses allelic mismatches to recognize strains within a
species.
Uses tables to show relatedness, and from these can determine recombination:mutation
ratio.
What does MLSA do? - answerUses protein coding genes to characterize a more
diverse group.
Uses phylogenetic trees to show relatedness
What is a Burst Diagram? - answeridentifies mutually exclusive related groups in a
population, then identifies the founding genotype of each group
Larger the dot = more common the sequence type
lines radiating from dot = single locus variants
What is the whole genome sequencing species definition? - answerEntire gene is
sequenced.
What is a core genome? - answerThe stable bacterial genome shared by all members
of a species
What is an auxiliary set? - answerThe variable bacterial genome that is susceptible to
LGT.
What is the average nucleotide identity species definition? - answercompares all of the
protein coding genes in the core genomes of 2 bacterial organisms
>95% ANI is equivalent to it being >70% DDH (they are the same species)
What is the core genome phylogeny species definition? - answerMakes a long chain of
all protein coding genes in a bacterial core genome, then align it with one from another
organism and compare.
What is the genome composition sequencing species definition? - answerConserved
DNA
