Organellar Genomes Organellar Genomes and Genetic Markersand Genetic Markers

Level 3 Molecular Evolution and Level 3 Molecular Evolution and BioinformaticsBioinformatics

Jim ProvanJim Provan

Organellar variationOrganellar variation

DiploidDiploid HaploidHaploid HaploidHaploid

BiparentalBiparental Uniparental:Uniparental:Angiosperms (M)Angiosperms (M)Gymnosperms (P)Gymnosperms (P)

MaternalMaternal

NucleusNucleus ChloroplastChloroplast MitochondrionMitochondrion

PloidyPloidy

RecombinationRecombination

InheritanceInheritance

Variation at drift/mutation Variation at drift/mutation equilibriumequilibrium

Nuclear (diploid)Nuclear (diploid)

44NµNµ

(4(4NµNµ + 1) + 1)

Organellar (haploid)Organellar (haploid)

22NµNµ

(2(2NµNµ + 1) + 1)

0.00010.0001 0.0010.001 0.010.01 0.10.1 11 1010 100100 10001000

NµNµ

1.01.0

0.80.8

0.60.6

0.40.4

0.20.2

0.00.0

DiploidDiploid

HaploidHaploid

Selective sweepsSelective sweeps

AA

11

BB

11

CC

22

AA

33 AA

33

AA

33

AA

33

Plant organelle genomes - Plant organelle genomes - implications for markersimplications for markers

Generally lower diversity due to:Generally lower diversity due to:Haploid genomeHaploid genome

Lower mutation ratesLower mutation rates

Lack of recombination - selective sweepsLack of recombination - selective sweeps

Lack of intraspecific variation Lack of intraspecific variation species specific species specific markersmarkers

Detection of intraspecific variation Detection of intraspecific variation variable regions variable regionsNon-coding regionsNon-coding regions

Tandemly-duplicated genesTandemly-duplicated genes

Mononucleotide microsatellitesMononucleotide microsatellites

Very little mitochondrial variationVery little mitochondrial variation

Genetic change during Genetic change during fragmentationfragmentation

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

Maternal markers useful for Maternal markers useful for recording historical eventsrecording historical events

Ratios of pollen:seed flowRatios of pollen:seed flow

Combined analysis of nuclear and organellar Combined analysis of nuclear and organellar markers can give information on relative markers can give information on relative importance of seed and pollen flowimportance of seed and pollen flowImportant for:Important for:

Dynamics of natural populationsDynamics of natural populationsTransgene movementTransgene movement

WindWindInsectInsectWindWind

BirdBirdRuminantRuminant

WindWind

DispersalDispersalPollenPollen SeedSeed

Pollen:SeedPollen:SeedRatioRatioSpeciesSpecies

QuercusQuercusArganiaArganiaPinusPinus

1961962.52.51818

Animal mitochondrial DNA in Animal mitochondrial DNA in population geneticspopulation genetics

Maternal inheritance and relatively rapid rate Maternal inheritance and relatively rapid rate of evolution have led to widespread use in of evolution have led to widespread use in studies of matrilineal gene flowstudies of matrilineal gene flow

Sensitive indicator of:Sensitive indicator of:Female-mediated gene flow (maternal inheritance)Female-mediated gene flow (maternal inheritance)Founder events (haploid genome)Founder events (haploid genome)

Comparisons of spatial distribution of nuclear Comparisons of spatial distribution of nuclear and mitochondrial markers provides and mitochondrial markers provides information on sexual bias in dispersalinformation on sexual bias in dispersal

Geographical structuring with Geographical structuring with sedentary femalessedentary females

Offspring from each Offspring from each mother will have maternal mother will have maternal mtDNA genotype and half mtDNA genotype and half paternal nuclear genotypepaternal nuclear genotype

If mothers have different If mothers have different mtDNA genotypes, groups mtDNA genotypes, groups of offspring will be:of offspring will be:

Completely different for Completely different for mitochondrial markersmitochondrial markers

At least 50% similar for At least 50% similar for nuclear markersnuclear markers

The “Mitochondrial Eve” The “Mitochondrial Eve” hypothesishypothesis

Studies suggested that Studies suggested that between 140,000 and between 140,000 and 360,000 years ago, a 360,000 years ago, a single mtDNA haplotype single mtDNA haplotype existed!existed!Theoretical studies Theoretical studies dispute this:dispute this:

Rate of extinction of Rate of extinction of maternal lineages is highmaternal lineages is highEven if several thousand Even if several thousand mtDNAs were present, mtDNAs were present, high probability that only high probability that only one would have survivedone would have survived

Chloroplast DNA Chloroplast DNA phylogeography of phylogeography of Alnus Alnus

glutinosaglutinosa (L.) Gaertn. (L.) Gaertn.

R. Andrew King and Colin FerrisR. Andrew King and Colin Ferris

Molecular Ecology Molecular Ecology (1998) (1998) 77: 1151-1161: 1151-1161

IntroductionIntroduction

Until recently, fossil pollen mapping was the only Until recently, fossil pollen mapping was the only way to study history of plant populationsway to study history of plant populations

Studies in various trees have shown that after Studies in various trees have shown that after the last (Würrm) glaciation, Europe was the last (Würrm) glaciation, Europe was recolonised from at least three separate refugia:recolonised from at least three separate refugia:

Southern SpainSouthern Spain

Southern ItalySouthern Italy

Balkan peninsulaBalkan peninsula

Use of chloroplast-specific markers should give Use of chloroplast-specific markers should give new insights into post-glacial histories of plant new insights into post-glacial histories of plant speciesspecies

Chloroplast haplotype Chloroplast haplotype distribution in alder (distribution in alder (Alnus)Alnus)

Post-glacial history of Post-glacial history of AlnusAlnus

Obvious high levels of genetic variation below Obvious high levels of genetic variation below the southern limit of the ice during the last the southern limit of the ice during the last glaciationglaciation

Two dominant haplotypes found throughout Two dominant haplotypes found throughout northern Europenorthern Europe

Majority of Europe colonised from single Majority of Europe colonised from single refugium in the Balkansrefugium in the Balkans

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

European European Pinus sylvestris Pinus sylvestris populationspopulations

Nicole Soranzo, Ricardo Alia, Jim Provan Nicole Soranzo, Ricardo Alia, Jim Provan and Wayne Powelland Wayne Powell

Molecular Ecology Molecular Ecology (2000) (2000) 99: 1205-1211: 1205-1211

Maternal markers in conifersMaternal markers in conifers

In virtually all embryophytes (seed plants), the In virtually all embryophytes (seed plants), the mitochondrial genome is inherited maternally mitochondrial genome is inherited maternally i.e. via the seedi.e. via the seedChloroplast genome inherited in a different Chloroplast genome inherited in a different manner in angiosperms and gymnosperms:manner in angiosperms and gymnosperms:

In angiosperms, chloroplast genome is also mostly In angiosperms, chloroplast genome is also mostly inherited maternally inherited maternally In gymnosperms, chloroplast genome is inherited In gymnosperms, chloroplast genome is inherited paternally i.e. via both pollen and seedpaternally i.e. via both pollen and seed

In conifers, mitochondrial markers will be good In conifers, mitochondrial markers will be good indicators of historical eventsindicators of historical events

Mitochondrial variation in Scots Mitochondrial variation in Scots pine in Spainpine in Spain

Two haplotypes found Two haplotypes found in mitochondrial in mitochondrial nadnadI I regionregionGeneral NE / SW split in General NE / SW split in haplotype distributionhaplotype distribution

Only one (dark) haplotype Only one (dark) haplotype found in rest of Europefound in rest of Europe

Distribution of variation in Distribution of variation in Spanish Spanish Pinus sylvestrisPinus sylvestris

BetweenBetweenpopulationspopulations

(60%)(60%)

WithinWithinpopulationspopulations

(40%)(40%)

Mitochondrial variation in Mitochondrial variation in European European P. sylvestrisP. sylvestris

Levels of population differentiation revealed using Levels of population differentiation revealed using mitochondrial markers were 10- to 30-fold higher mitochondrial markers were 10- to 30-fold higher than in previous studies using nuclear and than in previous studies using nuclear and chloroplast markerschloroplast markersLow degree of variation in non-Spanish populations Low degree of variation in non-Spanish populations probably due to post-glacial recolonisation from a probably due to post-glacial recolonisation from a common refugiumcommon refugiumSpanish populations below southern limit of Spanish populations below southern limit of glaciation:glaciation:

Not subjected to glaciation - represent ancient gene poolsNot subjected to glaciation - represent ancient gene poolsPhysical isolation of populations on different mountain Physical isolation of populations on different mountain ranges accounts for high levels of between-population ranges accounts for high levels of between-population differentiationdifferentiation

rbcrbcL sequences reveal multiple L sequences reveal multiple cryptic introductions of the cryptic introductions of the

Japanese red alga Japanese red alga Polysiphonia Polysiphonia harveyiiharveyii

Lynne McIvor, Christine Maggs, Jim Lynne McIvor, Christine Maggs, Jim Provan and Michael StanhopeProvan and Michael Stanhope

Molecular Ecology Molecular Ecology (2001) (2001) 1010: 911-919: 911-919

Introductions of Introductions of Polysiphonia Polysiphonia harveyii harveyii from Japanfrom Japan

Aim: to test whether Aim: to test whether global populations of global populations of P. P. harveyii harveyii had arisen from a had arisen from a single or multiple single or multiple introductionsintroductionsMethodology:Methodology:

Sequence Sequence rbcrbcL geneL geneAlign sequencesAlign sequencesConstruct phylogenetic tree Construct phylogenetic tree showing relationships showing relationships between observed between observed genotypesgenotypesCompare with geographic Compare with geographic distributiondistribution

Minimum-spanning phylogenetic Minimum-spanning phylogenetic networknetwork

XX YY ZZ

FF AA

DD

EE

CC

BB

ChoshiChoshiChoshiChoshi

ShimodaShimodaShimodaShimoda OshoroOshoroOshoroOshoro

AkkeshiAkkeshiAkkeshiAkkeshi

HOKKAIDOHOKKAIDOHOKKAIDOHOKKAIDO

HONSH

U

HONSH

U

HONSH

U

HONSH

U

North CarolinaNorth CarolinaNew ZealandNew Zealand

MontereyMonterey

North CarolinaNorth CarolinaNew ZealandNew Zealand

MontereyMonterey

EuropeEuropeNova ScotiaNova Scotia

EuropeEuropeNova ScotiaNova Scotia

Multiple introductions of Multiple introductions of P. P. harveyiiharveyii

Multiple hypothetical ancestral genotypes present Multiple hypothetical ancestral genotypes present which were not observed:which were not observed:

Consistent with Japan being the centre of diversity of Consistent with Japan being the centre of diversity of P. P. harveyiiharveyiiMost likely not observed due to limited sampling, rather Most likely not observed due to limited sampling, rather than extinctionthan extinction

Non-Japanese populations of Non-Japanese populations of P. harveyii P. harveyii represented by two divergent genotypes:represented by two divergent genotypes:

One possibly linked to Honshu genotypesOne possibly linked to Honshu genotypesOne possibly linked to Hokkaido genotypesOne possibly linked to Hokkaido genotypes

Most likely represent at least two separate Most likely represent at least two separate introductions from original centre of diversity in introductions from original centre of diversity in JapanJapan

MitochondrialMitochondrialNuclearNuclear

Nuclear and mitochondrial Nuclear and mitochondrial variation in Scots pine in variation in Scots pine in

SwedenSweden

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

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

Mitochondrial markers Mitochondrial markers show definite boundary show definite boundary at 60°N, even after ~50 at 60°N, even after ~50 generations of contactgenerations of contact