Lecture 13-14 Flashcards
What is genomics
Genomics is the study of the “entire hereditary information” in an organism, which is mostly encoded in the genome.
What is a genome
The genome is the sequence of all the DNA in a single cell.
What are the subsets and products of the genome
mitogenome (the mitochondrial genome)
exome (all the exons that could potentially be expressed)
transcriptome (the expressed genes (expressed exons) in a particular tissue or set of tissues that you are studying)
proteome (the proteins), metabolome (other metabolic products)
How to assemble a genome with shotgun sequencing
Collect the organism and extract a lot of high-quality DNA (long strands) break into fragments read the fragments with a high-throughput sequencer (currently Illumina and PacBio machines are dominant) piece together the fragments recognise the genes (annotation
What good are genomes
(Try) to find all the genes involved in a phenotype,
not just one or two
To reconstruct deep phylogenies (phylogenomics)
Cancer genomics
Natural product prospecting and marker assisted selection
What is it called when we compare individuals within a single species
resequencing
What is biogeography
It is the study of the patterns and causes of the
distribution of living things.
What is vicariance
Vicariance is the splitting of distributions, such as when
ancient landmasses split and separate due to continental drift,
or when mountain ranges divide lowland populations.
What is dispersal
Dispersal is movement of organisms or their propagules (such
as seeds).
What is phylogeography
Phylogeography is the study of the genetic and geographic structure of populations and species.
What does phylogeography use
generally uses genetic information to examine
genealogical history and patterning within species and populations.
What is coalescent theory
The tracing of allelic ancestries back to their
most recent common ancestor
• mtDNA lineages will coalesce on average 4
fold faster than recombining nuclear markers
• With nuclear DNA sequences, recombination
is possible within and between alleles
• The number of potential ancestors of an
individual doubles with each generation back
What type of markers are used in phylogeography
Mitochondrial (mtDNA) or chloroplast (cpDNA) vs genomic markers
advantages of mtDNA
• Effectively neutral markers
• High mutation rate means that variation will
usually be present
• High copy number allows for ease of
amplification from limited or archived samples
• Effective population size ¼ of diploid nuclear
genes so genetic drift occurs faster
• No recombination so each uniparentally
inherited haplotype has only one ancestor in
previous generation
What are disadvantages to using mtDNA is phlyogeography
Uniparentally inherited so if there are differences between sexes then no information about one sex
In plants mtDNA is less variable and recombines
cp (chloroplast) DNA variation higher, but not as high as animal mtDNA.
