Organellar Genomes and Genetic Markers

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Organellar Genomes and Genetic Markers

• Level 3 Molecular Evolution and Bioinformatics
• Jim Provan

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Organellar variation
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Variation at drift/mutation equilibrium
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Selective sweeps
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Plant organelle genomes - implications for markers

• Generally lower diversity due to
• Haploid genome
• Lower mutation rates
• Lack of recombination - selective sweeps
• Lack of intraspecific variation ? species
  specific markers
• Detection of intraspecific variation ? variable
  regions
• Non-coding regions
• Tandemly-duplicated genes
• Mononucleotide microsatellites
• Very little mitochondrial variation

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Genetic change during fragmentation

• In fragmented populations, differentiaton due to
  drift will be more marked in haploid organellar
  genomes
• Maternally inherited markers travel via seed ?
  organellar gene flow less substantial

• Maternal markers useful for recording historical
  events

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Ratios of pollenseed flow

• Combined analysis of nuclear and organellar
  markers can give information on relative
  importance of seed and pollen flow
• Important for
• Dynamics of natural populations
• Transgene movement

Wind
Bird
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Insect
Ruminant
2.5
Wind
Wind
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Animal mitochondrial DNA in population genetics

• Maternal inheritance and relatively rapid rate of
  evolution have led to widespread use in studies
  of matrilineal gene flow
• Sensitive indicator of
• Female-mediated gene flow (maternal inheritance)
• Founder events (haploid genome)
• Comparisons of spatial distribution of nuclear
  and mitochondrial markers provides information on
  sexual bias in dispersal

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Geographical structuring with sedentary females

• Offspring from each mother will have maternal
  mtDNA genotype and half paternal nuclear genotype
• If mothers have different mtDNA genotypes, groups
  of offspring will be
• Completely different for mitochondrial markers
• At least 50 similar for nuclear markers

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The Mitochondrial Eve hypothesis

• Studies suggested that between 140,000 and
  360,000 years ago, a single mtDNA haplotype
  existed!
• Theoretical studies dispute this
• Rate of extinction of maternal lineages is high
• Even if several thousand mtDNAs were present,
  high probability that only one would have survived

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Chloroplast DNA phylogeography of Alnus glutinosa
(L.) Gaertn.

• R. Andrew King and Colin Ferris
• Molecular Ecology (1998) 7 1151-1161

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Introduction

• Until recently, fossil pollen mapping was the
  only way to study history of plant populations
• Studies in various trees have shown that after
  the last (Würrm) glaciation, Europe was
  recolonised from at least three separate refugia
• Southern Spain
• Southern Italy
• Balkan peninsula
• Use of chloroplast-specific markers should give
  new insights into post-glacial histories of plant
  species

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Chloroplast haplotype distribution in alder
(Alnus)
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Post-glacial history of Alnus

• Obvious high levels of genetic variation below
  the southern limit of the ice during the last
  glaciation
• Two dominant haplotypes found throughout northern
  Europe
• Majority of Europe colonised from single refugium
  in the Balkans

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Patterns of variation at a mitochondrial
sequence-tagged-site locus provides new insights
into the postglacial history of European Pinus
sylvestris populations

• Nicole Soranzo, Ricardo Alia, Jim Provan and
  Wayne Powell
• Molecular Ecology (2000) 9 1205-1211

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Maternal markers in conifers

• In virtually all embryophytes (seed plants), the
  mitochondrial genome is inherited maternally i.e.
  via the seed
• Chloroplast genome inherited in a different
  manner in angiosperms and gymnosperms
• In angiosperms, chloroplast genome is also mostly
  inherited maternally
• In gymnosperms, chloroplast genome is inherited
  paternally i.e. via both pollen and seed
• In conifers, mitochondrial markers will be good
  indicators of historical events

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Mitochondrial variation in Scots pine in Spain

• Two haplotypes found in mitochondrial nadI region

• General NE / SW split in haplotype distribution
• Only one (dark) haplotype found in rest of Europe

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Distribution of variation in Spanish Pinus
sylvestris
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Mitochondrial variation in European P. sylvestris

• Levels of population differentiation revealed
  using mitochondrial markers were 10- to 30-fold
  higher than in previous studies using nuclear and
  chloroplast markers
• Low degree of variation in non-Spanish
  populations probably due to post-glacial
  recolonisation from a common refugium
• Spanish populations below southern limit of
  glaciation
• Not subjected to glaciation - represent ancient
  gene pools
• Physical isolation of populations on different
  mountain ranges accounts for high levels of
  between-population differentiation

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rbcL sequences reveal multiple cryptic
introductions of the Japanese red alga
Polysiphonia harveyii

• Lynne McIvor, Christine Maggs, Jim Provan and
  Michael Stanhope
• Molecular Ecology (2001) 10 911-919

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Introductions of Polysiphonia harveyii from Japan

• Aim to test whether global populations of P.
  harveyii had arisen from a single or multiple
  introductions
• Methodology
• Sequence rbcL gene
• Align sequences
• Construct phylogenetic tree showing relationships
  between observed genotypes
• Compare with geographic distribution

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Minimum-spanning phylogenetic network
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Multiple introductions of P. harveyii

• Multiple hypothetical ancestral genotypes present
  which were not observed
• Consistent with Japan being the centre of
  diversity of P. harveyii
• Most likely not observed due to limited sampling,
  rather than extinction
• Non-Japanese populations of P. harveyii
  represented by two divergent genotypes
• One possibly linked to Honshu genotypes
• One possibly linked to Hokkaido genotypes
• Most likely represent at least two separate
  introductions from original centre of diversity
  in Japan

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Nuclear and mitochondrial variation in Scots pine
in Sweden

• Scots pine believed to have recolonised Sweden
  from both North and South after glaciation

• Nuclear (monoterpene) markers suggest clinal
  variation but not definite

• Mitochondrial markers show definite boundary at
  60N, even after 50 generations of contact