Lecture 13-14 Flashcards Preview

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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



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.


Why is nuclear DNA used in phylogeography

• unlinked nuclear genetic markers can capture a genome-wide picture of the population
• Nuclear DNA markers are recombining and
can be under selection
• More complete but far more complicated