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history of genetic markers used to assess diversity

  • allozymes - first widely used genetic markers
  • DNA cloning + sequencing - sanger
  • PCR - mullis
  • fragment analyses - moritz
  • comparative/functional genomics
  • metagenomics/non-model organisms - venter

allozymes

  • data are enzyme banding patterns
  • each band assumed to reflect a different allele
  • work out allele frequency by counting N alleles in each genotype + dividing N by copies
  • phenotypes so may be under selection

allele frequencies

  • used to compare diversity within + differentiation between populations
  • frequency of alleles homogenised across pops. by gene flow + differentiate by pop. structure
  • neutral variation assumed to predict how genetic variation relates to connectivity + demographic patterns

PCR

can use regions of genome predicted to evolve neutrally for estimation of pop. structure

PCR - microsatellites

  • repeats added/lost frequently
  • can compare many loci within individuals + many individuals at once
  • genotypes can be used to calculate degree of inbreeding + how different individuals are from each other

microsatellite allele frequency

  • count alleles across individuals within a pop. to calculate pop. allele frequencies or compare number of alleles
  • calculate genetic distance among pops. or pop. genetics analyses of differentiation based on multiple loci

genetic distance analysis

  • distance matrix-based on shared characters or similarity of allele-frequencies
  • can visualise in a 'haplotype' network

genetic distance analyses - haplotype network

  • visually compare how different alleles are from each other + relative frequency
  • circles are individual haplotypes
  • size of circle shows frequency across all individuals (relative abundance)
  • colours indicate different populations
  • cant use to estimate relative abundance

structure analyses

  • how much diversity is there within vs between pops.
  • what are the genetically distinct clusters
  • for each sampled individual, what is the probability of belonging to each of these clusters
  • can be calculated from multi-locus allele freqs.
  • cant be used to estimate how different things are from one another or relative abundance

diversity - how many things

  • structure analysis
  • haplotype network

diversity - how different are the things

  • genetic distance
  • haplotype network

diversity - how abundant is each thing

  • allele + genotype frequencies
  • haplotype network

diversity - how are things structured in time and space

  • genetic distances
  • haplotype networks
  • structure analysis

DNA sequencing

  • sequence alignment to detect variable sites (polymorphism)
  • next generation sequencing

DNA sequence variation

allele-frequency based approaches but nucleotide diversity more informative because more power to quantify how different things are from one another

nucleotide diversity

average number of pairwise differences between SNPs divided by length of sequence compared

metagenomics

  • study of genetic material recovered directly from environmental samples
  • diversity in sampled of unknown communities

what can you do with comparitive sequence data

  • genetic data analyses
  • population genetic analyses - connectivity, selection, inbreeding
  • phylogenetic analyses - historical relatedness