[email protected] davelunt.net Dr Dave Lunt invasive species ecological networks in forestry and agriculture biomonitoring bioinformatics metabarcoding genomics phylogenetics apomixis and breeding systems environmental DNA
BRIEFLY HOW DO THE EVOLUTIONARY FORCES DETERMINE THE SHAPE AND CONTENT OF OUR GENOMES? MUTATION, SELECTION, DRIFT, GENE FLOW, AND RECOMBINATION Evolutionary forces
HOST RANGE ~5% LOSS IN WORLD AGRICULTURE? ALL MAJOR CROPS SPECIES 6 den Akker SE, Jones JT. doi:10.1371/journal.pgen.1007160 M. incognita parasitises the majority of flowering plant diversity, red
TEMPERATURE >3±C, & IS POSSIBLY THE SINGLE MOST DAMAGING CROP PATHOGEN IN THE WORLD. IN ECUADOR, BASED ON A SURVEY OF 207 HORTICULTURAL CROPS, ESTIMATED LOSSES DUE TO M. INCOGNITA EXCEED 20%” 7 den Akker SE, Jones JT. doi:10.1371/journal.pgen.1007160 Trudgill and Blok 2001 Apomictic, polyphagous root-knot nematodes: exceptionally successful and damaging biotrophic root pathogens. doi:10.1146/annurev.phyto.39.1.53
Janssen et al 2017 Fig 7. Majority rule consensus tree based on 18S ribosomal rDNA sequences with karyology doi:10.1371/journal.pone.0172190 These are the tropical root-knot nematodes, causing major economic loss
(mitotic) ▸ mitotic parthenogenesis- apomixis ▸ no meiosis or exchange ▸ Sexual (meiotic) ▸ meiotic parthenogenesis- automixis ▸ outbreeding sexuality- amphimixis ▸ meiosis and genetic exchange 11 RKN juveniles SEX REFERS TO MEIOSIS NOT MATING
REPRODUCTIVE MODES IN SINGLE GENUS 18S structural alignment ML tree The genus has >6 losses of meiosis and many other transitions Janssen et al 2017 doi:10.1371/journal.pone.0172190, Lunt unpublished
REPRODUCTIVE MODES IN SINGLE GENUS 18S structural alignment ML tree Frequent reproductive mode changes gives opportunity to examine evolutionary genomics of meiosis Work ongoing
TEs LTRs transposons 500 million years of evolution 42 genomes 14 NEMATODE TRANSPOSABLE ELEMENTS FOLLOW PHYLOGENY THE GENOMIC TRANSPOSABLE ELEMENT LOAD IS EXPLAINED BY PHYLOGENY NOT BREEDING SYSTEM
BE DISTRACTED BY ‘TABLOID’ SCIENTIFIC SEX STORIES ASEXUAL ROOT-KNOT NEMATODES ARE EXCEPTIONALLY SUCCESSFUL, RAPIDLY ADAPTING, AND NOT SUFFERING FROM ACCUMULATION OF DELETERIOUS GENOMIC MUTATIONS
OF GRASS, TO GROW UPON A SPOT OF GROUND WHERE ONLY ONE GREW BEFORE, WOULD DESERVE BETTER OF MANKIND… THAN THE WHOLE RACE OF POLITICIANS PUT TOGETHER’ “GULLIVER’S TRAVELS” 1726, BY JONATHAN SWIFT
Hybridization, Ploidy, and Dynamic Genome Change. Genome Biol Evol. 2017;9: 2844–2861. doi:10.1093/gbe/evx201 WE HAVE SEQUENCED 19 NEW GENOMES Abad P, Gouzy J, Aury J-M, Castagnone-Sereno P, Danchin EGJ, Deleury E, et al. Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita. Nat Biotechnol. 2008;26: 909–915. doi:10.1038/ nbt.1482 Lunt DH. Genetic tests of ancient asexuality in root knot nematodes reveal recent hybrid origins. BMC Evol Biol. 2008;8: 194. doi:10.1186/1471-2148-8-194 Lunt DH, Kumar S, Koutsovoulos G, Blaxter ML. The complex hybrid origins of the root knot nematodes revealed through comparative genomics. PeerJ. PeerJ Inc.; 2014;2: e356. doi:10.7717/peerj.356 Blanc-Mathieu R, Perfus-Babeoch L, Aury J-M, Da Rocha M, Gouzy J, Sallet E, et al. Peculiar hybrid genomes of devastating plant pests promote plasticity in the absence of sex and meiosis [Internet]. bioRxiv. 2016. p. 046805. doi:10.1101/046805
CASTAGNONE- SERENO, BOB ROBBINS, PABLO CASTILLO & MANY MANY OTHERS data accession: PRJNA340324 Amir Szitenberg & Laura Salazar have carried out much of this work AMIR SZITENBERG, LAURA SALAZAR, VIVIAN BLOK, SOUMI JOSEPH, DOMINIK LAETSCH, VALERIE WILLIAMSON, MARK BLAXTER, DAVE LUNT THANKS images: Wikipedia, JD Eisenback, et al Szitenberg et al. Comparative Genomics of Apomictic Root-Knot Nematodes: Hybridization, Ploidy, and Dynamic Genome Change. Genome Biol Evol. 2017;9: 2844–2861. doi:10.1093/gbe/evx201
of Orthology Groups M. incognita M. javanica M. arenaria M. floridensis Copies per genome has mostly lost the divergent second genome copy 26 but M. floridensis is mostly homozygous
ML tree RAxML Single origin of 2 genome copies predating speciation Phylogeny in each genome copy A/B is identical M. incognita M. javanica M. arenaria M. floridensis B A 29
ML tree RAxML M. floridness is a sibling not a parent of the apomicts M. incognita M. javanica M. arenaria M. floridensis B A 30 No species contains 3 genomic copies, indicating a single hybridisation Mf Mf
RARE AND INCONSEQUENTIAL IN ANIMALS Heliconius Lake Malawi Polar and brown GENOME BIOLOGY IS REVEALING A VERY DIFFERENT VIEW HYBRID SPECIATION IN MELOIDOGYNE?
ASEXUAL SPECIES Heliconius butterflies Lake Malawi cichlids Root knot nematodes? HYBRID SPECIATION IN MELOIDOGYNE Lunt et al. 2014 The complex hybrid origins of the root knot nematodes revealed through comparative genomics. doi:10.7717/peerj.356 APOMICTS ARE VERY HETEROZYGOUS, VERY POLYPHAGOUS, VERY ADAPTABLE
phenotypic variation TRANSGRESSIVE SEGREGATION phenotype could be anything, including nematode host-range is greater than sum of parental variation Transgressive segregation is when the absolute values of traits in some hybrids exceed the trait variation shown by either parental lineage small big very small very big 33
some parts of genome are diploid copy A1 copy B copy A2 copy number 1 2 A1-A2 are ~100% identical to each other copy A copy B copy number 1 2 3% divergence in protein coding regions illustration of diversity at each diploid locus Some loci are diploid A,B, some triploid A1,A2,B illustration of diversity at each triploid locus
of diversity at each triploid locus not all loci are triploid, diploid loci add to read depth 100 peak many loci have read depth 100 some loci have read depth 200 A1 + A2 from high quality PacBio genome copy A1 copy B copy A2 copy number 1 2 sequence read depth A + B
IS EVIDENT RECIPROCAL EXCHANGE GENE CONVERSION A1 B A2 A1 B A2 Identical & no recombination detectable B A1 A2 or We do not observe this process This is frequent Szitenberg et al. Comparative Genomics of Apomictic Root-Knot Nematodes: Hybridization, Ploidy, and Dynamic Genome Change. Genome Biol Evol. 2017;9: 2844–2861. doi:10.1093/gbe/evx201
sex in the most devastating plant-parasitic nematodes. PLoS Genet. Public Library of Science; 2017;13: e1006777. Available: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006777 Figure S3 BOTH SZITENBERG ET AL AND BLANC-MATHIEU ET AL FIND A MIXTURE OF DIVERGENT AND INVARIANT SEQUENCE ON LONG CONTIGS Is this gene conversion? Chromosomes may be patchworks of the former A and B parental genomes
of Orthology Groups M. incognita M. javanica M. arenaria M. floridensis Copies per genome has mostly lost the divergent second genome copy 40 but M. floridensis is mostly homozygous
COPIES MIG APOMICTS ARE HYPOTRIPLOID A AND B DIVERGED BEFORE MIG SPECIES GENE CONVERSION IS A POWERFUL FORCE MIG ARE DIVERGENT DUE TO MUCH MORE THAN SIMPLE MUTATION NUCLEAR GENOME RESOLVES PHYLOGENY