the complex hybrid origins of the root knot nematodes
DESCRIPTION
Talk given UK Population Genetics Group at Popgroup47 in Bath January 2014TRANSCRIPT
COMPLEX HYBRID ORIGINS OF ROOT KNOT NEMATODES
Dave LuntEvolutionary Biology Group, University of Hull
Institute of Evolutionary Biology, University of Edinburgh
Georgios KoutsovoulosMark Blaxter
Sujai Kumar
COMPLEX HYBRID ORIGINS OF ROOT KNOT NEMATODES
AcknowledgementsAfrica Gómez, Richard Ennos, Amir Szitenberg, Karim Gharbi, Chris Mitchell, Steve Moss, Tom Powers, Janete Brito, Etienne Danchin, Marian
Thomson & GenePool
FundingNERC, BBSRC, Yorkshire Agricultural Society,
Nuffield Foundation, University of Hull, University of Edinburgh
COMPLEX HYBRID ORIGINS OF ROOT KNOT NEMATODES
Dave LuntEvolutionary Biology Group, University of Hull
http://www.slideshare.net/davelunt/presentations
davelunt.net
@davelunt
@EvoHull +EvoHull
+davelunt
http://www.github.com/davelunt
davelunt.net
@davelunt
@EvoHull +EvoHull
+davelunt
http://www.github.com/davelunt
THE MELOIDOGYNE RKN SYSTEM
Meloidogyne Root Knot Nematodes• Globally important agricultural pest species
• Enormous plant host range
• parasitise all main crop plants
• ~5% loss of world agriculture
JD Eisenback
RKN juveniles enter root tip
infected uninfectedSEM Meloidogyne female
JD Eisenback
THE MELOIDOGYNE RKN SYSTEM
Meloidogyne ReproductionWide variety of reproductive modes in a single genus
• Many species are mitotic parthenogens without chromosome pairs
Asexuals
• Other species are meiotic parthenogens• automixis
• Some species are obligatory outbreeding sexuals with males & females
• amphimixis
Sexuals
THE MELOIDOGYNE RKN SYSTEM
Meloidogyne ReproductionWide variety of reproductive modes in a single genus
MELOIDOGYNE HYBRIDIZATION
Hybrid Speciation
Once thought that hybrid speciation was rare and inconsequential in animals
Genome biology is revealing a very different view
MELOIDOGYNE HYBRIDIZATION
Hybrid Speciation in Meloidogyne?
Have the mitotic parthenogen root knot nematodes arisen by interspecific hybridization?
Is M. floridensis the parent of the asexuals?
M. floridensis is found within the phylogenetic diversity of asexual species
It reproduces sexually by automixis
Could it be a parent of the asexual lineages via interspecific hybridization?
MELOIDOGYNE HYBRIDIZATION GENOMICS
M.floridensis M. ???
M. incognitaM. javanica
M. arenaria
x
apomicts
parental species
automict
MELOIDOGYNE HYBRIDIZATION GENOMICS
Meloidogyne comparative genomics
We have sequenced M. floridensis genome and are able to compare to 2 other Meloidogyne genomes published by other groups
M.floridensis M. ???
M. incognitaM. javanica
M. arenaria
x
apomicts
parental species
automict
asexual, hybrid?
sexual, parental?
sexual, outgroup
100MB, 100x coverage, 15.3k protein coding loci
Is M. floridensis the parent of the asexuals?
1. look at the within-genome patterns of diversity to determine hybrid nature of genomes
!
2. look at phylogenetic relationships of all genes to study origins and parents
MELOIDOGYNE HYBRIDIZATION GENOMICS
1: Intra-genomic diversity
2: Phylogenomics
Investigated using whole genome sequences and 2 distinct approaches;
Extreme Hybrid Allelic Sequence Divergence1. INTRA-GENOMIC ANALYSES: ALLELIC SEQUENCE DIVERGENCE
1: Intra-genomic diversity look at the within-genome patterns of diversity to determine hybrid nature of genomes
A B A D CAlleles
Taxa
Recent
Ancient
Sexual parental species
Divergence between alleles of parental species
Divergence between hybrid species alleles
A C D
Ancestor of sexual parental
species
Hybridization event
Sexual parental species
hybrid apomict
hybrid apomict
mitotic
Extreme Hybrid Allelic Sequence Divergence1. INTRA-GENOMIC ANALYSES: ALLELIC SEQUENCE DIVERGENCE
‘Alleles’ (homeologues) may date to the divergence of the parental species which hybridized
A B A D CAlleles
Taxa
Recent
Ancient
Sexual parental species
Divergence between alleles of parental species
Divergence between hybrid species alleles
A C D
Ancestor of sexual parental
species
Hybridization event
Sexual parental species
hybrid apomict
hybrid apomict
mitotic
1. INTRA-GENOMIC ANALYSES
Divergence of protein-coding allelesLunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
Coding sequences from each of the three target genomes were compared to the set of genes from the same species The percent identity of the best matching (non-self) coding sequence was calculated, and is plotted as a frequency histogram
Both M. incognita and M. floridensis show evidence of presence of many duplicates, while M. hapla does not
Self identity comparisons
1. INTRA-GENOMIC ANALYSES
Divergence of protein-coding allelesLunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
Coding sequences from each of the three target genomes (M. hapla, M. incognita and M. floridensis) were compared to the set of genes from the same species
The percent identity of the best matching (non-self) coding sequence was calculated, and is plotted as a frequency histogram Both M. incognita and M. floridensis show evidence of presence of many duplicates, while M. hapla does not
Self identity comparisons
1. INTRA-GENOMIC ANALYSES
Divergence of protein-coding allelesLunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
Coding sequences from each of the three target genomes (M. hapla, M. incognita and M. floridensis) were compared to the set of genes from the same species
The percent identity of the best matching (non-self) coding sequence was calculated, and is plotted as a frequency histogram
Both M. incognita and M. floridensis show evidence of presence of many duplicates, while M. hapla does not
Self identity comparisons
1. INTRA-GENOMIC ANALYSES
Divergence of protein-coding allelesLunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
Coding sequences from each of the three target genomes (M. hapla, M. incognita and M. floridensis) were compared to the set of genes from the same species
The percent identity of the best matching (non-self) coding sequence was calculated, and is plotted as a frequency histogram
Both M. incognita and M. floridensis show evidence of presence of many duplicates, while M. hapla does not
This is exactly the pattern expected for hybrid genomes
Self identity comparisons
Is M. floridensis the parent of the asexuals?
!
look at phylogenetic relationships of all genes to study origins and parents
MELOIDOGYNE HYBRIDIZATION GENOMICS
1: Intra-genomic diversity2: Phylogenomics
2. PHYLOGENOMIC ANALYSES
Hybridization HypothesesLunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
There are very many ways species could hybridize, duplicate genes, lose genes
We have selected a broad range of possibilities informed by prior knowledge
We have tested their predictions phylogenetically
M. h
apla
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C Scenario 4
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(X+Y)+Z
D Scenario 5
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B Scenario 3
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A Scenario 1 & 2
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A
M. h
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C Scenario 4
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(X+Y)+Z
D Scenario 5
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B Scenario 3
M. h
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M. f
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M. i
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X Z+Z
A Scenario 1 & 2
X+Y
B
M. h
apla
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M. f
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X+Y Y+Z
C Scenario 4
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M. f
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(X+Y)+Z
D Scenario 5
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B Scenario 3M
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M. f
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M. i
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A Scenario 1 & 2
X+Y
C
M. h
apla
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M. f
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M. i
ncog
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C Scenario 4
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(X+Y)+Z
D Scenario 5
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B Scenario 3
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M. f
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M. i
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A Scenario 1 & 2
X+Y
D
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M. h
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C Scenario 4
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(X+Y)+Z
D Scenario 5
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B Scenario 3
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M. f
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A Scenario 1 & 2
X+Y
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C Scenario 4
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D Scenario 5
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B Scenario 3
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A Scenario 1 & 2
X+Y
M. h
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M. f
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C Scenario 4
M. h
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M. f
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M. i
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(X+Y)+Z
D Scenario 5
M. h
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M. f
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B Scenario 3
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M. f
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A Scenario 1 & 2
X+Y
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M. f
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C Scenario 4
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(X+Y)+Z
D Scenario 5M
. hap
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B Scenario 3
M. h
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. flo
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M. i
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A Scenario 1 & 2
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Hybridization hypothesesA B
C D
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C Scenario 4
M. h
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M. f
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(X+Y)+Z
D Scenario 5M
. hap
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X Z
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B Scenario 3
M. h
apla
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A Scenario 1 & 2
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(A) Whole genome duplication(s)
���22
M. h
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C Scenario 4
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(X+Y)+Z
D Scenario 5
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B Scenario 3
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M. f
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A Scenario 1 & 2
X+Y
(B) M. incognita is an
interspecific hybrid with M. floridensis as one
parent
M. h
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M. i
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C Scenario 4M
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D Scenario 5
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B Scenario 3
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M. f
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M. i
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A Scenario 1 & 2
X+Y
(C) M. incognita and M.
floridensis are independent hybrids sharing one parent
M. h
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M. f
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C Scenario 4
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(X+Y)+Z
D Scenario 5
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B Scenario 3
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A Scenario 1 & 2
X+Y
(D) M. floridensis is a hybrid
and M. incognita is a secondary hybrid
between M. floridensis and a 3rd parent
2. PHYLOGENOMIC ANALYSES
Testing by PhylogenomicsLunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
M. h
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C Scenario 4
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D Scenario 5
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B Scenario 3
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A Scenario 1 & 2
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B Scenario 3
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A Scenario 1 & 2
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B Scenario 3M
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A Scenario 1 & 2
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C
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C Scenario 4
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(X+Y)+Z
D Scenario 5
M. h
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B Scenario 3
M. h
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M. f
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M. i
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A Scenario 1 & 2
X+Y
D
• Coding sequences from 3 genomes were placed into orthologous groups (InParanoid)
• 4018 ortholog clusters included all 3 species • We retained those with a single copy in the
outgroup M. hapla • Phylogenies of relationships between Mi and
Mf gene copies (RAxML) • Trees were parsed and pooled to represent
frequencies of different relationships
���26
Each tree contains a single M. hapla sequence as outgroup (black square)
Grey square indicates relative
frequency of those
topologies
Trees are pooled within squares into different patterns of relationships
Grid squares represent different numbers of gene copies
2. PHYLOGENOMIC ANALYSES
Testing by PhylogenomicsLunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
M. h
apla
X Y Z
M. f
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M. i
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C Scenario 4
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(X+Y)+Z
D Scenario 5
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B Scenario 3
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A Scenario 1 & 2
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A
M. h
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M. f
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M. i
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C Scenario 4
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(X+Y)+Z
D Scenario 5
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B Scenario 3
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M. f
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M. i
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A Scenario 1 & 2
X+Y
B
M. h
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M. f
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M. i
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X+Y Y+Z
C Scenario 4
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M. f
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M. i
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(X+Y)+Z
D Scenario 5
M. h
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M. f
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M. i
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B Scenario 3M
. hap
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X Z
M. f
lorid
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M. i
ncog
nita
X Z+Z
A Scenario 1 & 2
X+Y
C
M. h
apla
X Y Z
M. f
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s
M. i
ncog
nita
X+Y Y+Z
C Scenario 4
M. h
apla
X Y Z
M. f
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M. i
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(X+Y)+Z
D Scenario 5
M. h
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M. f
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M. i
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B Scenario 3
M. h
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M. f
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A Scenario 1 & 2
X+Y
D
• We assess the fit of the tree topologies to our hypotheses
• Five out of seven cluster sets, and 95% of all trees, support hybrid origins for both M. floridensis and M. incognita • ie exclude hypotheses A and B
• Hypothesis C best explains 17 trees • Hypothesis D best explains 1335 trees
2. PHYLOGENOMIC ANALYSES
Testing by PhylogenomicsLunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
M. h
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M. f
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M. i
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C Scenario 4
M. h
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M. f
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(X+Y)+Z
D Scenario 5
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B Scenario 3
M. h
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M. f
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M. i
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A Scenario 1 & 2
X+Y
A
M. h
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M. f
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M. i
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X+Y Y+Z
C Scenario 4
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(X+Y)+Z
D Scenario 5
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M. i
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X X+Z
B Scenario 3
M. h
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M. f
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M. i
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A Scenario 1 & 2
X+Y
B
M. h
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M. f
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M. i
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X+Y Y+Z
C Scenario 4
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M. f
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M. i
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(X+Y)+Z
D Scenario 5
M. h
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B Scenario 3
M. h
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M. f
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M. i
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A Scenario 1 & 2
X+Y
C
M. floridensis is a parental species of “double hybrid” M. incognita with other parent unknownM
. hap
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C Scenario 4M
. hap
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(X+Y)+Z
D Scenario 5
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nita
X X+Z
B Scenario 3
M. h
apla
X Z
M. f
lorid
ensi
s
M. i
ncog
nita
X Z+Z
A Scenario 1 & 2
X+Y
Hypothesis D
MELOIDOGYNE COMPARATIVE GENOMICS
Meloidogyne hybrid species formation
• Suggestions that hybrid speciation may be common in Meloidogyne
• Do asexual agricultural pathogens have a single (hybrid) origin
• What are the common features of hybrid genome architecture? • Ongoing work...
COMPLEX HYBRID ORIGINS OF ROOT KNOT NEMATODES
Dave LuntEvolutionary Biology Group, University of Hull
http://www.slideshare.net/davelunt/presentations
davelunt.net
@davelunt
@EvoHull +EvoHull
+davelunt
http://www.github.com/davelunt
davelunt.net
@davelunt
@EvoHull +EvoHull
+davelunt
http://www.github.com/davelunt