Evolutionary applications #6 Flashcards
What are the main forms of sequencing technology?
The main forms of sequencing technology are Sanger sequencing, Next generation sequencing, Third generation sequencing, and now Fourth generation sequencing.
What factors determine which sequencing method to use?
The factors that determine which sequencing method to use include the biological question, sensitivity, specificity, cost, amount of data required, and genomic resources available.
What is a Fastq file?
A Fastq file is a text-based format for storing biological sequence data and its corresponding quality scores. It uses ASCII characters and has four lines per sequence.
What are quality scores and how are they calculated?
Quality scores are based on the probability of a base call being correct. They are calculated using the formula Q = -10 log10 p, where p is the probability of an incorrect base call. For example, Q10 means there is a 1 in 10 chance of an incorrect base call.
What are the common next steps after sequencing data is produced?
The common next steps after sequencing data is produced include assembly (reconstructing the original DNA sequences) and alignment (finding the location of reads in the genome).
What are the applications of sequencing data?
The applications of sequencing data include understanding individuals or populations (population genomics), understanding species (comparative genomics), and understanding ecosystems (metagenomics and eDNA).
How can sequencing data inform conservation decisions?
Sequencing data can inform conservation decisions by identifying genetic structure and evolutionarily significant units (ESUs) of a population, as well as identifying unique genes and functions.
What is an example of using sequencing data to inform conservation decisions?
An example of using sequencing data to inform conservation decisions is the translocation of kākāpō to predator-free islands in the 1980s. Genome sequencing and population analysis showed differences between mainland and Stewart Island populations, leading to conservation strategies that prevent pairings between related individuals and favor matings with “mainland heritage.”
How can sequencing data be used to understand species?
Sequencing data can be used to understand species by identifying conserved genes and unique genes/functions, as well as gene gain and loss.
What is an example of using sequencing data to understand species?
An example of using sequencing data to understand species is the identification of the loss of the L-gulonolactone oxidase (GULO1) gene in Haplorhini primates, which depend on vitamin C in their diets. This gene is non-functional in humans and other Haplorhini primates, suggesting a mutation in the last common ancestor.
How can sequencing data be used to understand ecosystems?
Sequencing data can be used to understand ecosystems by analyzing temporal and spatial variability in a particular ecosystem, such as wetlands, and identifying dominant species and their impact.
