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Hybrid origins of M. floridensis

Hybrid origins of M. floridensis

10minute talk at "Evolutionary biology of Caenorhabditis and other nematodes" 2014

Dave Lunt

June 15, 2014
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  1. Dave Lunt
    @davelunt
    speakerdeck.com/davelunt
    slides available
    Georgios Koutsovoulos
    Mark Blaxter
    Sujai Kumar
    Comparative genomics of
    root knot nematodes:
    Tales of sex, hybridisation
    and adaptation
    Evolutionary Biology Group, University of Hull
    Institute of Evolutionary Biology, University of Edinburgh

    View Slide

  2. THE MELOIDOGYNE RKN SYSTEM
    Meloidogyne Reproduction
    • Mitotic parthenogens (apomixis) without
    chromosome pairs. Ancient asexuals?
    Asexuals- meiosis absent
    • Meiotic parthenogens (automixis)
    • Obligatory outbreeding sexuals with
    males & females (amphimixis)
    Sexuals- meiosis present
    Wide variety of reproductive modes in a single genus

    View Slide

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

    View Slide

  4. MELOIDOGYNE HYBRIDISATION
    Hybrid Speciation in Meloidogyne?
    Some previous work has
    suggested interspecific
    hybridisation may be involved
    with Meloidogyne asexual
    species
    Heliconius butterflies
    Lake Malawi cichlids
    Root knot nematodes?

    View Slide

  5. 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
    apomict
    apomict
    automict

    View Slide

  6. MELOIDOGYNE HYBRIDISATION GENOMICS
    Meloidogyne comparative genomics
    We have sequenced M. floridensis
    genome and compare to 2 other
    published Meloidogyne genomes
    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

  7. 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

  8. 1. INTRA-GENOMIC ANALYSES
    Divergence of protein-coding alleles
    Lunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
    Coding sequences from each species
    were compared to loci in the same
    species!
    The percent identity of the best match
    was plotted
    Self identity comparisons
    Both M. incognita and M.
    floridensis show
    evidence of presence of
    many duplicates, while
    M. hapla does not

    View Slide

  9. 1. INTRA-GENOMIC ANALYSES
    Divergence of protein-coding alleles
    Lunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
    Self identity comparisons
    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

    View Slide

  10. 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

  11. 11
    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
    Hybridisation hypotheses
    A B
    C D
    We have selected a broad range of possibilities
    informed by prior knowledge!
    We have tested their predictions phylogenetically

    View Slide

  12. 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

  13. 13
    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

  14. 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

  15. 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

  16. 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
    • Recover all genes from 3 genomes!
    • CDS orthologues determined by InParanoid!
    • 4018 ortholog clusters included all 3 species!
    • Retained those with a single copy in the outgroup M. hapla !
    • ML Phylogenies of relationships
    between Mi and Mf gene copies!
    • Trees parsed and pooled to represent
    frequencies of different relationships

    View Slide

  17. 17
    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

  18. 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

  19. 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
    Conclusion:

    View Slide

  20. MELOIDOGYNE COMPARATIVE GENOMICS
    1. Ongoing Work
    • 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
    Meloidogyne breeding system and genome
    evolution

    View Slide

  21. MELOIDOGYNE COMPARATIVE GENOMICS
    2. Wild speculation
    Happy to discuss in the bar…!
    • ancient asexuality!
    • reproductive mode transitions!
    • adaptation through transgressive segregation!
    • the ‘hybrid threat’!
    • distinguishing single/multiple origins of apomicts!
    • contagious asexuality
    Dave Lunt
    Evolutionary Biology Group, University of Hull
    [email protected] davelunt.net
    speakerdeck.com/davelunt
    slides available

    View Slide

  22. Dave Lunt
    @davelunt
    speakerdeck.com/davelunt
    slides available
    Georgios Koutsovoulos
    Mark Blaxter
    Sujai Kumar
    Comparative genomics of
    root knot nematodes:
    Tales of sex, hybridisation
    and adaptation
    Evolutionary Biology Group, University of Hull
    Institute of Evolutionary Biology, University of Edinburgh
    [email protected] davelunt.net

    View Slide