Species Concepts and Microbial Diversity Flashcards
What is morphological diversity
The diversity of shape, colour, and size
What is genetic diversity
The diversity of genetic information
What is metabolic diversity
The diversity of kinds of metabolism
What is a species
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.
What is the biological species concept
Groups of interbreeding or potentially interbreeding natural populations that reproductively isolated from other such groups.
What is the error in the biological species concept
This assumes that sex is the mechanism of reproduction, so this definition is a problem
What is the pragmatic/operational definition of a species
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
What is the phylogenetic species concept
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.
What is the problem with phylogenetic species concept
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.
During Speedy speciation in bacterial microcosm, what is the null model
All strains have the same fitness and ecotype. Only one in the article has this situation will fit this model
During Speedy speciation in bacterial microcosm, what is the single ecotype community model
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.
During Speedy speciation in bacterial microcosm, what is the multiple-ecotype community model
The strains will experience speciation and two species will develop. 7 situations fit this model, so there must have some sort of speciation event.
During Speedy speciation in bacterial microcosm, how did they test the different ecotypes to prove or disprove it
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.
During Speedy speciation in bacterial microcosm, what are the main takeaways of the article
Speciation appears to be “easy.” Speciation seems to happen as often as slow “improvements” over time. Can be “cryptic” species.
During Speedy speciation in bacterial microcosm, what are the problems
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.
What are instantaneous speciation
There is single mutations and chromosomal mutations these can create new species
What is geographic speciation
Physical or chemical separation leading to accumulation of mutations goes until speciation and this is a gradual and slow process.
What are the auxiliary genes
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.
What are core genes
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.
What is novel acquisition of lateral gene transfer
Gene X is inserted to do X function, and this leads to a novel adaptation in the microorganism
What is loss and regain in lateral gene transfer
X gene is no longer required so X gene is lost. X function is required so X function is supplied by X’ gene.
What is homologous replacement in lateral gene transfer
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.
What is analogous replacement in lateral gene transfer
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
What is species richness
Total number of species
What is species evenness
Relative abundance of species
What is species dominance
The most abundant species
What is the operational taxonomic unit
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.
What is operational taxonomic unit that is used in culture-based data
Colony morphology, phase variation, and distant relatives with similar colony morphology
What is operational taxonomic unit with target core genes
Measurement of diversity. Identifying community members through comparison of sequence to sequence database.
What are the problems with operational taxonomic units
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.
What is amplicon sequence variant
This is a one nucleotide difference in sequence. Possible because we understand sequence error and can determine where sequences are real or not.
What are rarefaction curves
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
What is DNA Hybridization
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.
What is parametric methods
Parametric methods assume a log-normal distribution of species-abundance distribution
What is non-parametric estimations
Uses mark-and-recapture probabilities to interpret species representations, so there is less assumptions and less likely to be wrong.
What do diversity indices tell us
How many species are in a sample? Their distribution or evenness of species within the community. Discovery of new species.
What does higher diversity allow for
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.
What does phylogenetic trees allow for
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.
