Species Concepts and Microbial Diversity

Question 1

What is morphological diversity

Answer 1

The diversity of shape, colour, and size

Question 2

What is genetic diversity

Answer 2

The diversity of genetic information

Question 3

What is metabolic diversity

Answer 3

The diversity of kinds of metabolism

Question 4

What is a species

Answer 4

The species is the basic unit of ecology no ecosystem can be fully understood until it has been dissected into its component species and until the mutual interactions of these species are understood.

Question 5

What is the biological species concept

Answer 5

Groups of interbreeding or potentially interbreeding natural populations that reproductively isolated from other such groups.

Question 6

What is the error in the biological species concept

Answer 6

This assumes that sex is the mechanism of reproduction, so this definition is a problem

Question 7

What is the pragmatic/operational definition of a species

Answer 7

Prokaryotic strains be allocated to species when they are at least approximately 70% identical base pair sequence (DNA similarity) and a difference in the melting point of DNA/DNA homoduplexes and heteroduplexes of less than 5 degrees Celsius

Question 8

What is the phylogenetic species concept

Answer 8

There are species that exist because they are evolutionarily more similar. The evolution process leads to groups and they are biologically relevant to one another.

Question 9

What is the problem with phylogenetic species concept

Answer 9

We don’t know what level of species we want to be looking for or if different approaches to phylogeny are possible that we haven’t tested yet.

Question 10

During Speedy speciation in bacterial microcosm, what is the null model

Answer 10

All strains have the same fitness and ecotype. Only one in the article has this situation will fit this model

Question 11

During Speedy speciation in bacterial microcosm, what is the single ecotype community model

Answer 11

One strain will become the more dominant strain in an attempt to push out the other from the community. 2 situations fit this model situation, so there must not have been some sort of speciation event.

Question 12

During Speedy speciation in bacterial microcosm, what is the multiple-ecotype community model

Answer 12

The strains will experience speciation and two species will develop. 7 situations fit this model, so there must have some sort of speciation event.

Question 13

During Speedy speciation in bacterial microcosm, how did they test the different ecotypes to prove or disprove it

Answer 13

The colony morphology was checked to see if they were different which they were. There was competition experiments to see what would change and every single time there wasn’t an ecotype that went extinct so they must be different.

Question 14

During Speedy speciation in bacterial microcosm, what are the main takeaways of the article

Answer 14

Speciation appears to be “easy.” Speciation seems to happen as often as slow “improvements” over time. Can be “cryptic” species.

Question 15

During Speedy speciation in bacterial microcosm, what are the problems

Answer 15

There is no horizontal gene transfer and if we were to replicate this in a stable environment instead of in a controlled one would we have seen this or would these ecotypes have not survived.

Question 16

What are instantaneous speciation

Answer 16

There is single mutations and chromosomal mutations these can create new species

Question 17

What is geographic speciation

Answer 17

Physical or chemical separation leading to accumulation of mutations goes until speciation and this is a gradual and slow process.

Question 18

What are the auxiliary genes

Answer 18

These are the genes that don’t keep the cell alive and can be transferred within the same generation. This is can be traits such as antibiotic resistance, and any sort of trait that will make it better for functionality.

Question 19

What are core genes

Answer 19

Core genes are the housekeeping genes that are necessary to keeping the cell alive and are necessary to biology. They are typically stuff like rRNA, DNA enzymes and other functional trait. This will be passed down through vertical gene transfer.

Question 20

What is novel acquisition of lateral gene transfer

Answer 20

Gene X is inserted to do X function, and this leads to a novel adaptation in the microorganism

Question 21

What is loss and regain in lateral gene transfer

Answer 21

X gene is no longer required so X gene is lost. X function is required so X function is supplied by X’ gene.

Question 22

What is homologous replacement in lateral gene transfer

Answer 22

There is X gene that has X function. An antibiotic-resistant form of X is found. Possible recombination occurs with the microorganism. The original X gene is lost.

Question 23

What is analogous replacement in lateral gene transfer

Answer 23

X gene has X function in a microorganism. Y gene has a function introduced to the microorganism. The two genes experience recombination. X gene is lost and Y gene sticks around

Question 24

What is species richness

Answer 24

Total number of species

Question 25

What is species evenness

Answer 25

Relative abundance of species

Question 26

What is species dominance

Answer 26

The most abundant species

Question 27

What is the operational taxonomic unit

Answer 27

Unit of diversity defined by method rather than species concept. The operation is defined by the available data. This circumvents the traditional species definition as a unity of diversity.

Question 28

What is operational taxonomic unit that is used in culture-based data

Answer 28

Colony morphology, phase variation, and distant relatives with similar colony morphology

Question 29

What is operational taxonomic unit with target core genes

Answer 29

Measurement of diversity. Identifying community members through comparison of sequence to sequence database.

Question 30

What are the problems with operational taxonomic units

Answer 30

Organisms with the same genome may not have the same niche. Lateral and horizontal gene transfer. Similar proteins with similar functions can have very low sequence similarity.

Question 31

What is amplicon sequence variant

Answer 31

This is a one nucleotide difference in sequence. Possible because we understand sequence error and can determine where sequences are real or not.

Question 32

What are rarefaction curves

Answer 32

Counts Operational Taxonomic Unit as a function of sampling effort. Can compare the richness of samples from habitat for ecology and treatment for the experimental system. Sampling effort can vary between samples and we must reach a plateau

Question 33

What is DNA Hybridization

Answer 33

Rate of DNA-DNA hybridization is inversely proportional to diversity. Lower sequence similarity between distantly related organisms/genomes. It is extremely rare to due technical difficulty. This is done through simultaneous culturing effort, hybridize culture isolates DNA and eDNA and then gave birth to the idea that we cultivate less than 1% of bacteria.

Question 34

What is parametric methods

Answer 34

Parametric methods assume a log-normal distribution of species-abundance distribution

Question 35

What is non-parametric estimations

Answer 35

Uses mark-and-recapture probabilities to interpret species representations, so there is less assumptions and less likely to be wrong.

Question 36

What do diversity indices tell us

Answer 36

How many species are in a sample? Their distribution or evenness of species within the community. Discovery of new species.

Question 37

What does higher diversity allow for

Answer 37

Higher diversity makes a system productive, so competition will drive selection and selection leads to optimization and innovation. Higher diversity systems are thought to be robust to disturbance and permanent change due to genetic redundancy.

Question 38

What does phylogenetic trees allow for

Answer 38

They graphically depict diversity. Places DNA sequence in a tree so that it is compared to known sequences and other sequences from the sample. Branch length and branch structure information. New methods allow trees to be compared so that the sequence phylogeny of a group of individuals can be compared to other groups.