UEA Rebellion2014: nematode sex, hybridisation and adaptation

Transcript

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 davelunt@gmail.com davelunt.net @EvoHull

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

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

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?

5. COMPARATIVE GENOMICS OF ROOT KNOT NEMATODES WHAT’S IN A GENOME

   & WHY? Evolutionary Forces: Selection! Mutation! Drift! Gene Flow! Recombination

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

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

8. THE GENUS MELOIDOGYNE: ROOT KNOT NEMATODES Globally important agricultural pathogens!

   Extreme polyphagy and rapid adaptation! Hyper-diverse breeding systems! Ancient asexuals?

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

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

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?

12. THE MELOIDOGYNE RKN SYSTEM Meloidogyne Reproduction Wide variety of reproductive

    modes in a single genus

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

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

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

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

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

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

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

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

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

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

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

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

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?!

26. MELOIDOGYNE HYBRIDISATION Hybrid Speciation Once thought that hybrid speciation was

    rare and inconsequential in animals! Genome biology is revealing a very different view

27. MELOIDOGYNE HYBRIDISATION Hybrid Speciation in Meloidogyne? Have the mitotic parthenogen

    root knot nematodes arisen by interspecific hybridisation?

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

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

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;

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

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

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

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

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

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

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

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

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

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

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)

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

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

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

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

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

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

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

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...

50. Ongoing work ! ! (and wild speculation)

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

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

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

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

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?

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?

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?

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’

59. Conclusions RKN are not ancient asexuals despite showing some of

    the classic signatures instead some are interspecific hybrids

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

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

62. COMPARATIVE GENOMICS OF ROOT KNOT NEMATODES github.com/davelunt speakerdeck.com/davelunt Slides available

    davelunt.net @davelunt davelunt@gmail.com +davelunt Dave Lunt Evolutionary ! Biology Group! University of Hull @EvoHull EvoHull.org Remember to mention jobs