Microbial Evolution exam 1

what is evolution?

• change in genetic composition of a population with the passage of each generation

• changes in allelic frequency in populations over time

time + generation + genetic composition =

Microevolution

small divergence

adaptation

ex/ bacteria changing to become resistant

Macroevolution

Big divergence

Speciation

ex/ beak shape

Sources of Genetic Diversity

1. Mutation

2. Gene flow

3. Genetic drift

4. Selection (natural and artificial)

Characteristics of all living things (organisms)

• metabolism

• organization (cells)

• reproduction

• growth/develop (more than one stage of life)

• Adaptation

• Homeostatsis

Asexual Reproduction

the organism is producing more of itself without the assistance of any other organism

ex/ bacteria and microbes

Sexual Reproduction

there are two types (male and female) of an organism that come together in some way and produce another organism like themselves

Viruses

• a NON-living thing that is able to grow inside another organism and form more of itself

• it can not grow without the help of living organism

• acellular microorganisms, extremely small

What are microbes when is comes to the domains of life?

everything but plants and animals plus viruses

LUCA

Late Universal Common Ancestor

Eukaryotic vs Prokaryotic

Comparison of a few traits of bacteria, archaea, and eukarya

Know the arrow and highlighted parts

Microorganisms

mostly exist as single cells, clusters of cells that can independently carry on all of the necessary processes of life to grow and divide

Biomass

weight after water is removed

Subsurface bacteria

no oxygen, lots of pressure, cold, and dark

vast majority of bacteria are thought to be subsurface (over 80%)

Microbial Diversity

• Morphological Diversity

• Genetics Diversity

• Functional Diversity

• Habitat Diversity

Grouping of Organisms/Microbes

life→domain→kingdom→phylum→class→order→family→genus→species

Species

Operational taxonomic unit that has an ANI (Average Nucleotide Identity) of less than 3% or (5%) different at the DNA level in the conserved genes

Population genetics

field of biology that studies allele frequencies in populations and how they change overtime

Population

group of organisms of the same species that are found in the same area and can interbreed

gene pool

a population consists of all copies (alleles) of all the genes in that population

allele frequency

how common an allele is in a population

Mutation

a heritable change in the nucleotide sequence of an organism’s genome

if a mutation is evolution a change must occur

sexual reproduction is the most important driver for different mutations (crossing over)

Mutation: Deletion

Mutation: Duplication

Mutation: Inversion

Mutation: Insertion

Mutation: Translocation

Point Mutations

Gene flow

the movement of alleles into, or out of, a population as a result of immigration or emigration

Gene Flow in bacteria

genetic transfer processes like horizontal gene transfer, allow DNA to pass between organisms without the need for sexual reproduction

Horizontal Gene Transfer (HGT)

the movement of genetic information across normal mating barriers, between more or less distantly related organisms (no new generation)

Genetic Drift

change in the composition of a gene pool as a result of chance or random events

Natural Selection

which more advantages traits are likely to be passed down

Three Requirements:

• different individuals in a population have different traits

• traits are heritable

• some traits help individuals that possess them survive and reproduce better than other traits

doesn’t cause mutations or adaptions- they arise randomly, and it selects beneficial ones

fitness

an individual’s ability to produce viable offspring

Genetic Drift vs. Natural Selection

Bottlenecks effect

an event reduces population size by an order of magnitude

surviving population has less genetic variability than before

The newly developing gene pool will be divergent from the original

Founder Effect

when a small group breaks away from a larger population to colonize a new territory

differs from bottleneck in that original population remains largely intact

Systematics

study of the diversity of life, with focus on relationships between organisms

taxonomy

science of classifying organisms

for microbes, based on phenotype, genotype, and phylogeny

Phylogeny

study of evolutionary relationships between organisms

study using molecular sequence comparsions

Phylogenetic tree

shows evolutionary relationships between organism/classes of organisms

Homologous genes

originated from common ancestor

Orthologs

homologs with same functions

Paralogs

homologs with different function

rooted tree

shows branch/node for last common ancestor of all organisms on the tree

unrooted tree

doesn’t show last common ancestor

Microbial species (commonly accepted definition)

group of strains with similar genetics and characteristics that share a recent common ancestor

core genome

genes all strains of that species have

pan genome

genes that only one or some strains of that species have

Two main kinds of information inherent to any tree

1. topology

2. branch lengths

chronogram

allows you to look at chronology

how long in the past they separated

can treat a genetic distance that is larger as the same as one that is smaller

Phylogram

focuses on genetic distance

branch lengths all directly correlate to genetic distance

visually less pretty

Taxon

an organism that exists as a distinct population

Operational taxonomic unit (OTU)

branch

branch length is very important

if branch length is set to match the change, it can tell you the genetic distance visually (not in a chronogram)

Unscaled vs Scaled branches

bifurcating vs multifurcating

monophyletic

consists of a common ancestor and all its descendants

Clade ABF- A and B are descendants of F

Outgroup

more distantly related used as a reference point

formula for possible arrangements

2^N-1

tree growth

tree anatomy

Homoplasy

similarity due to parallel evolution, convergent evolution or secondary loss

Homology

similarity due to common ancestry

Parallel evolution

independent evolution of same character from same ancestral state

Convergent evolution

independent evolution of same character from different ancestral states

Secondary loss

Reversion to ancestral state

this is your reminder to look at substation matrices (ppt 4 slides 19-32)

YOU’VE GOT THIS

PAM

Point Accepted Mutations (ppt 5 slides 6-13)

BLOSUM

blocks amino acid substitution matrices (ppt 5 slides 14-18)

PAM vs BLOSUM