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UEA Rebellion2014: nematode sex, hybridisation and adaptation

Dave Lunt
March 04, 2014

UEA Rebellion2014: nematode sex, hybridisation and adaptation

Plenary to UEA CEEC Rebellion 2014 "Comparative Genomics of Root Knot Nematodes: tales of sex, hybridisation and adaptation"

Dave Lunt

March 04, 2014
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  1. TALES OF SEX,
    HYBRIDISATION &
    ADAPTATION
    Dave Lunt
    Evolutionary Biology Group, University of Hull
    COMPARATIVE GENOMICS OF
    ROOT KNOT NEMATODES
    @davelunt
    speakerdeck.com/davelunt
    slides available
    [email protected] davelunt.net
    @EvoHull

    View Slide

  2. Dave Lunt
    Evolutionary Biology Group, University of Hull
    COMPARATIVE GENOMICS OF
    ROOT KNOT NEMATODES
    Institute of Evolutionary Biology, University of Edinburgh
    Georgios Koutsovoulos
    Mark Blaxter
    Sujai Kumar

    View Slide

  3. COMPARATIVE GENOMICS OF
    ROOT KNOT NEMATODES
    Acknowledgements
    Africa Gómez, Richard Ennos, Amir Szitenberg,
    Karim Gharbi, Chris Mitchell, Steve Moss, Tom
    Powers, Janete Brito, Etienne Danchin, Marian
    Thomson & GenePool
    Funding
    NERC, BBSRC, Yorkshire Agricultural Society,
    Nuffield Foundation, University of Hull,
    University of Edinburgh

    View Slide

  4. COMPARATIVE GENOMICS OF ROOT KNOT NEMATODES
    WHAT’S IN A
    GENOME & WHY?
    mostly transposons,
    repeats, & sequences
    of incertae sedis
    For many eukaryotes:
    but why?

    View Slide

  5. COMPARATIVE GENOMICS OF ROOT KNOT NEMATODES
    WHAT’S IN A
    GENOME & WHY?
    Evolutionary Forces:
    Selection!
    Mutation!
    Drift!
    Gene Flow!
    Recombination

    View Slide

  6. COMPARATIVE GENOMICS OF ROOT KNOT NEMATODES
    Studying
    Recombination
    Study its effects in genomic regions with
    reduced recombination!
    • sex chromosomes !
    • inversions!
    Study its action in species that have lost
    meiotic recombination!
    • asexuals
    A B C D E F
    sexual
    asexual
    origin of
    asexuality
    asexual

    View Slide

  7. COMPARATIVE GENOMICS OF ROOT KNOT NEMATODES
    Studying
    Recombination
    Mitotic reproduction has consequences
    for the genome!
    • decay of sex-specific genes!
    • extreme Allelic Sequence Divergence!
    • loss of mutational effects of
    recombination
    A B C D E F
    sexual
    asexual
    origin of
    asexuality
    asexual

    View Slide

  8. THE GENUS
    MELOIDOGYNE:
    ROOT KNOT
    NEMATODES
    Globally important agricultural pathogens!
    Extreme polyphagy and rapid adaptation!
    Hyper-diverse breeding systems!
    Ancient asexuals?

    View Slide

  9. THE MELOIDOGYNE RKN SYSTEM
    Meloidogyne Root Knot Nematodes
    • Globally important agricultural pest species!
    • ~5% loss of world agriculture!
    • Enormous plant host range!
    • parasitise all main crop plants
    JD Eisenback
    RKN
    juveniles
    enter root tip
    infected uninfected
    SEM Meloidogyne female
    JD Eisenback

    View Slide

  10. THE MELOIDOGYNE RKN SYSTEM
    Meloidogyne Reproduction
    Wide 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

    View Slide

  11. THE MELOIDOGYNE RKN SYSTEM
    Meloidogyne Reproduction
    Wide variety of reproductive modes in a
    single genus
    • Many species are mitotic parthenogens
    without chromosome pairs
    • Incapable of meiosis!
    • Could be ‘ancient’ asexuals!
    • 17 million years without meiosis?

    View Slide

  12. THE MELOIDOGYNE RKN SYSTEM
    Meloidogyne Reproduction
    Wide variety of reproductive modes in a single genus

    View Slide

  13. MELOIDOGYNE REPRODUCTION
    Are RKN Ancient Asexuals?
    Investigations based on multi-species
    gene sequencing and phylogenetics: !
    •testing for changes in molecular evolution
    pattern of sex-specific loci!
    •testing for extreme allelic sequence
    divergence
    Lunt DH 2008 BMC Evolutionary Biology 8:194

    View Slide

  14. RECOMBINATION AND ASEXUALITY
    Extreme Allelic Sequence Divergence
    "If we suppose an ameiotic form evolving
    for a very long period of time we might
    imagine its two chromosome sets
    becoming completely unlike, so that it
    could no longer be considered as a
    diploid either in a genetical or cytological
    sense."!
    Sometimes called Meselson effect, similar to paralogous loci
    A B C D E F
    sexual
    asexual
    origin of
    asexuality
    asexual
    MJD White ‘Animal Cytology and Evolution’ 1st ed 1945, p283

    View Slide

  15. RECOMBINATION AND ASEXUALITY
    loss of meiosis
    A B C D E F
    Extreme Asexual ASD
    alleles
    taxon
    Recent
    Ancient
    1 2 3
    asexual sexual
    asexual
    Redrawn after Birky 1996
    Divergence between
    alleles of sexual species
    Divergence between
    asexual species ‘alleles’
    alleles
    by
    recom
    bination
    m
    eiosis
    hom
    ogenizes

    View Slide

  16. THE SIGNATURES OF ANCIENT ASEXUALITY
    Extreme allelic sequence divergence
    Allelic Sequence Divergence levels are
    much greater in asexuals Meloidogyne
    than sexual Meloidogyne
    Pi (nucleotide diversity)
    Sexual Asexual apomicts
    |
    Species Max intraspecific
    substitutions
    Substitutions to
    closest relative
    M. incognita 15 0 M. javanica
    M. javanica 16 0 M. incognita
    RNA polymerase II
    Dystrophin
    Species Max intraspecific
    substitutions
    Substitutions to
    closest relative
    M. javanica 30 0 M. arenaria
    M. arenaria 32 0 M. javanica
    M.javanica
    M.javanica
    M.javanica
    M.arenaria
    M.javanica
    M.javanica
    M.javanica
    M.incognita

    View Slide

  17. THE SIGNATURES OF ANCIENT ASEXUALITY
    Extreme allelic sequence divergence
    ASD can be very large within asexual
    individuals
    Pi (nucleotide
    Sex Asexual
    |
    Species Max intraspecific
    substitutions
    Substitutions to closest
    relative
    M. incognita 15 0 M. javanica
    M. javanica 16 0 M. incognita
    RNA polymerase II
    Dystrophin
    Species Max intraspecific
    substitutions
    Substitutions to closest
    relative
    M. javanica 30 0 M. arenaria
    M. arenaria 32 0 M. javanica
    M.javanica
    M.javanica
    M.javanica
    M.arenaria
    M.javanica
    M.javanica
    M.javanica
    M.incognita
    Yet identical alleles can be found
    between different species

    View Slide

  18. THE SIGNATURES OF ANCIENT ASEXUALITY
    Extreme allelic sequence divergence
    Lunt DH 2008 BMC Evolutionary Biology 8:194
    Pi (nucleotide
    Sex Asexual
    |
    Species Max intraspecific
    substitutions
    Substitutions to closest
    relative
    M. incognita 15 0 M. javanica
    M. javanica 16 0 M. incognita
    RNA polymerase II
    Dystrophin
    Species Max intraspecific
    substitutions
    Substitutions to closest
    relative
    M. javanica 30 0 M. arenaria
    M. arenaria 32 0 M. javanica
    M.javanica
    M.javanica
    M.javanica
    M.arenaria
    M.javanica
    M.javanica
    M.javanica
    M.incognita
    This allele sharing is not predicted by
    ancient asexuality, and suggests
    interspecific hybridization

    View Slide

  19. RECOMBINATION AND ASEXUALITY
    loss of meiosis
    A B C D E F
    Extreme Asexual ASD
    alleles
    taxon
    Recent
    Ancient
    1 2 3
    asexual sexual
    asexual
    Redrawn after Birky 1996
    Divergence between
    alleles of sexual species
    Divergence between
    asexual species ‘alleles’
    alleles
    by
    recom
    bination
    m
    eiosis
    hom
    ogenises

    View Slide

  20. RECOMBINATION AND ASEXUALITY
    A B A D C
    Extreme Hybrid ASD
    Alleles
    Taxa
    Recent
    Ancient
    Sexual
    parental
    species
    Redrawn after Birky 1996
    Divergence between
    alleles of parental species
    Divergence between
    hybrid species alleles
    m
    eiosis
    hom
    ogenises
    alleles
    by
    recom
    bination
    A C D
    Ancestor of
    sexual parental
    species
    Hybridization
    event
    meiosis homogenises alleles
    Sexual
    parental
    species
    hybrid
    apomict
    hybrid
    apomict
    mitotic

    View Slide

  21. TESTING ANCIENT ASEXUALITY
    Sex Specific Loci
    Electron microscope images from
    Ward lab, http://
    www.mcb.arizona.edu/wardlab/
    • Nematodes have amoeboid (crawling) sperm!
    • msp genes only expressed in sperm and
    spermatocytes!
    • Structural protein of sperm!
    • Prediction: msp gene should show signatures
    of loss of function (pseudogenization) in
    asexuals
    Major Sperm Protein

    View Slide

  22. msp intron diversity in asexuals
    14
    Mutations are not
    randomly distributed but
    cluster within the intron,
    exactly as for functional
    genes
    Selection on this gene cannot have been abandoned anciently

    View Slide

  23. msp intron diversity in asexuals
    14
    ML models of evolution
    are identical on sexual
    and asexual branches of
    tree
    Selection on this gene cannot have been abandoned anciently

    View Slide

  24. MELOIDOGYNE REPRODUCTION
    Previous Single Gene Sequencing
    I can reject ancient asexuality on basis
    of interspecific allele sharing and identical
    molecular evolution of sperm protein
    genes!
    Data suggests interspecific hybrid origins
    Lunt DH 2008 BMC Evolutionary Biology 8:194

    View Slide

  25. Hybrid Speciation
    Developing methods for investigating the hybrid
    status of species using genomics!
    How has hybridisation influenced Meloidogyne
    species?!
    How do hybrid genomes behave?!

    View Slide

  26. MELOIDOGYNE HYBRIDISATION
    Hybrid Speciation
    Once thought that hybrid
    speciation was rare and
    inconsequential in animals!
    Genome biology is revealing a
    very different view

    View Slide

  27. MELOIDOGYNE HYBRIDISATION
    Hybrid Speciation in Meloidogyne?
    Have the mitotic parthenogen
    root knot nematodes arisen by
    interspecific hybridisation?

    View Slide

  28. 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 hybridisation?
    MELOIDOGYNE HYBRIDISATION GENOMICS
    M.floridensis M. ???
    M. incognita
    M. javanica
    M. arenaria
    x
    apomicts
    parental species
    automict

    View Slide

  29. MELOIDOGYNE HYBRIDISATION 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. incognita
    M. javanica
    M. arenaria
    x
    apomicts
    parental species
    automict
    asexual, hybrid?
    sexual, parental?
    sexual, outgroup
    100MB, 100x coverage, 15.3k protein coding loci

    View Slide

  30. 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 HYBRIDISATION GENOMICS
    1: Intra-genomic diversity
    2: Phylogenomics
    Investigated using whole genome
    sequences and 2 distinct approaches;

    View Slide

  31. Extreme Hybrid Allelic Sequence Divergence
    1. 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 C
    Alleles
    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

    View Slide

  32. Extreme Hybrid Allelic Sequence Divergence
    1. INTRA-GENOMIC ANALYSES: ALLELIC SEQUENCE DIVERGENCE
    ‘Alleles’ (homeologues) may date to the divergence of the parental species
    which hybridized
    A B A D C
    Alleles
    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

    View Slide

  33. 1. INTRA-GENOMIC ANALYSES
    Divergence of protein-coding alleles
    Lunt 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

    View Slide

  34. 1. INTRA-GENOMIC ANALYSES
    Divergence of protein-coding alleles
    Lunt 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

    View Slide

  35. 1. INTRA-GENOMIC ANALYSES
    Divergence of protein-coding alleles
    Lunt 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

    View Slide

  36. 1. INTRA-GENOMIC ANALYSES
    Divergence of protein-coding alleles
    Lunt 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

    View Slide

  37. COMPARATIVE GENOMICS
    M. floridensis Genome Size
    Lunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
    • Assembly size is not haploid genome
    size for hybrid species!
    • Divergence (4-8%) between
    homeologous (hybrid) copies will
    preclude assembly!
    • Our assembly of 100Mb is ~2x
    50-54Mb genome size of M. hapla
    1: Intra-genomic diversity
    2: Phylogenomics

    View Slide

  38. Is M. floridensis the parent of the asexuals?
    !
    look at phylogenetic relationships of all
    genes to study origins and parents
    MELOIDOGYNE HYBRIDISATION GENOMICS
    1: Intra-genomic diversity
    2: Phylogenomics

    View Slide

  39. Hybridisation Hypotheses
    Lunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
    There are very many ways species could
    hybridise, duplicate genes, lose genes!
    We have selected a broad range of
    possibilities informed by prior knowledge!
    We have tested their predictions
    phylogenetically
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    A Scenario 1 & 2
    A
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    A Scenario 1 & 2
    B
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y Y+Z
    C Scenario 4
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    A Scenario 1 & 2
    C
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y Y+Z
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y
    (X+Y)+Z
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    X+Y
    D
    2. PHYLOGENOMIC ANALYSES

    View Slide

  40. !42
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y Y+Z
    C Scenario 4
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y
    (X+Y)+Z
    D Scenario 5
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    Z
    M. incognita
    Z+Z
    1 & 2
    X+Y
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y Y+Z
    C Scenario 4
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y
    (X+Y)+Z
    D Scenario 5
    Z
    M. incognita
    +Z
    X+Y
    M. hapla
    X Y
    M. floridensis
    X+Y
    C Scenario 4
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    A Scenario 1 & 2
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y Y+Z
    C Scenario 4
    M. hapla
    D
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    A Scenario 1 & 2
    Hybridization hypotheses
    A B
    C D

    View Slide

  41. M. hapla
    X
    M. floridensis
    X
    B Scenario
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    A Scenario 1 & 2
    (A)"
    Whole genome
    duplication(s)

    View Slide

  42. !44
    M. hapla
    X
    M. floridensis
    X+Y
    C Scena
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    M. incognita
    Z
    (B)!
    M. incognita is an
    interspecific hybrid with
    M. floridensis as one
    parent

    View Slide

  43. M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y Y+Z
    C Scenario 4
    M. hapla
    X Y
    M. florid
    X+Y
    D Scenario
    X+Y
    (C)!
    M. incognita and M.
    floridensis are
    independent hybrids
    sharing one parent

    View Slide

  44. Z
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y
    (X+Y)+Z
    X+Y
    (D)!
    M. floridensis is a hybrid
    and M. incognita is a
    secondary hybrid
    between M. floridensis and
    a 3rd parent

    View Slide

  45. 2. PHYLOGENOMIC ANALYSES
    Testing by Phylogenomics
    Lunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
    M. hapla
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    A Scenario 1 & 2
    A
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    A Scenario 1 & 2
    B
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y Y+Z
    C Scenario 4
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y
    (X+Y)+Z
    D Scenario 5
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    A Scenario 1 & 2
    X+Y
    C
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y Y+Z
    C Scenario 4
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y
    (X+Y)+Z
    D Scenario 5
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    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

    View Slide

  46. !48
    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

    View Slide

  47. 2. PHYLOGENOMIC ANALYSES
    Testing by Phylogenomics
    Lunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
    M. hapla
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    A Scenario 1 & 2
    A
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    A Scenario 1 & 2
    B
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y Y+Z
    C Scenario 4
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y
    (X+Y)+Z
    D Scenario 5
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    A Scenario 1 & 2
    X+Y
    C
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y Y+Z
    C Scenario 4
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y
    (X+Y)+Z
    D Scenario 5
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    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

    View Slide

  48. 2. PHYLOGENOMIC ANALYSES
    Testing by Phylogenomics
    Lunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y Y+Z
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y
    (X+Y)+Z
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    X+Y
    A
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y Y+Z
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y
    (X+Y)+Z
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    X+Y
    B
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y Y+Z
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y
    (X+Y)+Z
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X X+Z
    M. hapla
    X Z
    M. floridensis
    M. incognita
    X Z+Z
    X+Y
    C
    M. floridensis is a parental species
    of “double hybrid” M. incognita
    with other parent unknown
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y Y+Z
    C Scenario 4
    M. hapla
    X Y Z
    M. floridensis
    M. incognita
    X+Y
    (X+Y)+Z
    D Scenario 5
    X Z
    M. floridensis
    M. incognita
    X X+Z
    B Scenario 3
    X+Y
    Hypothesis D

    View Slide

  49. 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...

    View Slide

  50. Ongoing work !
    !
    (and wild speculation)

    View Slide

  51. MELOIDOGYNE COMPARATIVE GENOMICS
    Ongoing Work
    • ~20 genomes in a phylogenetic design!
    • Testing effect of recombination &
    breeding system on genome change!
    • hybrids, inbred, outbred, loss of meiosis, TEs,
    mutational patterns, gene families
    Current NERC grant on Meloidogyne breeding
    system and genome evolution

    View Slide

  52. COMPARATIVE GENOMICS AND MOLECULAR EVOLUTION
    Phylogenetic models of genome change

    View Slide

  53. COMPARATIVE GENOMICS AND MOLECULAR EVOLUTION
    Phylogenetic models of genome change

    View Slide

  54. COMPARATIVE GENOMICS AND MOLECULAR EVOLUTION
    Phylogenetic models of genome change
    Sexual
    Sexual
    Sexual
    Asexual
    Species
    What
    happens
    here?
    Understanding the
    mutational and selective
    changes in replicated
    phylogenetic design

    View Slide

  55. COMPARATIVE GENOMICS AND MOLECULAR EVOLUTION
    Phylogenetic models of genome change
    Understanding the mutational and selective changes in
    replicated phylogenetic design
    Do transposons increase
    or decrease with loss of
    recombination?

    View Slide

  56. COMPARATIVE GENOMICS AND MOLECULAR EVOLUTION
    Phylogenetic models of genome change
    Understanding the mutational and selective changes in
    replicated phylogenetic design
    What mechanisms
    promote variation in
    obligatory inbreeding
    versus outbreeding
    species?

    View Slide

  57. COMPARATIVE GENOMICS AND MOLECULAR EVOLUTION
    Phylogenetic models of genome change
    Understanding the mutational and selective changes in
    replicated phylogenetic design
    How does gene
    duplication and origin of
    new genes change without
    crossing over?

    View Slide

  58. ADAPTATION TO THE AGRICULTURAL ENVIRONMENT
    Transgressive segregation
    Transgressive segregation is when the absolute values
    of traits in some hybrids exceed the trait variation
    shown by either parental lineage
    Hybrid
    Parent 1 Parent 2
    Arrows represent ‘phenotypic range’

    View Slide

  59. Conclusions
    RKN are not ancient asexuals
    despite showing some of the
    classic signatures
    instead some are interspecific hybrids

    View Slide

  60. Conclusions
    M. floridensis is a hybrid and a
    parent of the double-hybrid
    M. incognita
    genomic tests for hybrids, whether
    recent or ancient, can be sensitive
    and powerful

    View Slide

  61. Conclusions
    Root knot nematodes are
    amazingly successful and have
    adapted to agriculture very
    rapidly
    hybridisation and transgressive
    segregation may be involved in this rapid
    adaptation

    View Slide

  62. COMPARATIVE GENOMICS OF
    ROOT KNOT NEMATODES
    github.com/davelunt
    speakerdeck.com/davelunt
    Slides available
    davelunt.net
    @davelunt
    [email protected]
    +davelunt
    Dave Lunt
    Evolutionary !
    Biology Group!
    University of Hull
    @EvoHull
    EvoHull.org
    Remember to mention jobs

    View Slide