Population Genomic Approaches
What is Metagenomics and what are the primary organisms studied?
The sequencing and analysis of DNA from environmental or gut samples. Microbial Communities.
What advantages from other techniques does RAD capture (“Rapture”) combine?
*Bonus (100 points)*: What is the shared family of the two species from the example (in this paragraph)?
Combines the DNA library creation from DNAseq with the ability to target highly specific loci from targeted sequence capture.
Bonus answer: Salmonidae
What are the two types of techniques used to describe the locations of loci within a givin genome?
Physical and linkage mapping
What does bioinformatics analyze?
DNA, RNA, and protein sequence datasets
In the RAD capture example about lake and rainbow trout, the study used a capture array to target how many loci?
500 loci
What type of application studies the genomes from specimens excavated from caves, permafrost, or ice cores?
Paleogenomics
What does RADseq stand for? And why was it a breakthrough?
Restriction site-associated DNA sequencing. Allows for discovery and genotyping of thousands of SNPs at once.
What is the biggest difference between physical and linkage maps?
A physical map is a genome sequence whereas a linkage map describes the gene order between loci along chromosomes.
Why do researchers need to get better at recognizing the limitations of some genomics methods?
False recognition of positive selection can occur when background selection has reduced genetic variation. (And other factors that lead to false positives or low gene flow, recombination etc)
What does the figure and graph tell us about what kind of phenotype the RXFP2 gene affect?
Affect the size of the horns.
What factors do Epigenetic mechanisms and epigenomic variation significantly contributed to know that we have seen a major increases in evidence?
Phenotypes, abiotic and biotic stress response, disease conditions, adaptation to habitat and range distributions in various organisms.
What type of sequencing can be used for genotyping degraded DNA? (EX: historic or fecal)
Targeted Sequence Capture
What does significant GD influence and detect?
Footprints of natural selection and the ability to map contributing to phenotypic variations.
What is one reason mentioned in the paper the advancement of genomics study techniques is so “exciting”?
Improved understanding of inbreeding depression and genetic rescue
With the reconstruction of ancient adaptive phenotypes and inferences scientist were able to find out what about the species Mammuthus primigenius?
They were able to find out extinction causes.
Population Proteomics being the study of proteins within and among populations, what kind of key insights can population proteomics provide for population geonomics?
Functional and metapopulation ecology, adaptation, and acclimation processes under various climate and environment conditions.
Why is genome assembly from sequencing hard for some organisms, such as plants?
They have repetitive elements (retrotransposons) in more than 50% of the genome.
What does the recombination rate affect and why is it important to know how the recombination rate varies across a genome?
Gametic Disequilibrium and it is important for interpreting genomic patterns of genetic diversity and differentiation.
What are the four main steps of bioinformatics?
1) sequence read filtering
2) assign reads to loci
3) genotype calling
4) filter for problematic loci (don’t meet biological expectations)
The first published genome of this species only had 50% of the sequences ordered into chromosomes:
Rainbow Trout
What application investigates gene expression profiles and which different genese are expressed in different environments or conditions?
Bonus (100pt): When this application is combined with metagenomics, what can they provide?
Metatranscriptomics.
Bonus: They can provide entire transcriptome and genome repertoires through sequencing total DNA/RNA samples.
The study of transcriptome data to compare the gene expressions within populations and understand mechanisms of evolutionary change is called?
Population Transcriptomics
Why is the combination of the 2 mapping techniques the most ideal approach to Population Genomics?
Bonus (100pts): When these two techniques are combined what key factor can be estimated and mapped across a genome?
Because they complement each other, and the linkage map improves the accuracy of the physical.
Bonus: The Recombination Rate
What is the downfall of the ability to access entire genomes and so many SNPs for bioinformatics mentioned in the text?
Large datasets present challenges for filtering loci (outliers) that could lead to incorrect results or conclusions.
If wild-born steelhead trout with one hatchery parent have a lower reproductive rate in the wild, what would this suggest?
adaptation to captivity leads to the transmission of maladaptive gene expression to wild-born offspring.