davelunt@gmail.com davelunt.net Dr Dave Lunt invasive species ecological networks in forestry and agriculture biomonitoring bioinformatics metabarcoding genomics phylogenetics apomixis and breeding systems environmental DNA
CASTAGNONE- SERENO, BOB ROBBINS, PABLO CASTILLO & MANY MANY OTHERS @davelunt davelunt@gmail.com 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
TEs LTRs transposons 500 million years of evolution 42 genomes 13 NEMATODE TRANSPOSABLE ELEMENTS FOLLOW PHYLOGENY THE GENOMIC TRANSPOSABLE ELEMENT LOAD IS EXPLAINED BY PHYLOGENY NOT BREEDING SYSTEM
REPRODUCTIVE MODES IN SINGLE GENUS Janssen et al 2017 Fig 7. Majority rule consensus tree based on 18S ribosomal rDNA sequences with karyology doi:10.1371/journal.pone.0172190
REPRODUCTIVE MODES IN SINGLE GENUS Janssen et al 2017 Fig 7. Majority rule consensus tree based on 18S ribosomal rDNA sequences with karyology doi:10.1371/journal.pone.0172190 THE GENUS HAS >6 TRANSITIONS TO MITOTIC PARTHENOGENESIS LOSS OF SEX/MEIOSIS FACULTATIVE MEIOTIC PARTHENOGENESIS (AUTOMIXIS) AND SEXUALITY (AMPHIMIXIS)
DAMAGE: THE TROPICAL APOMICTS Janssen et al 2017 Fig 7. Majority rule consensus tree based on 18S ribosomal rDNA sequences with karyology doi:10.1371/journal.pone.0172190
DAMAGE: THE TROPICAL APOMICTS Janssen et al 2017 Fig 7. Majority rule consensus tree based on 18S ribosomal rDNA sequences with karyology doi:10.1371/journal.pone.0172190
DAMAGE: THE TROPICAL APOMICTS Janssen et al 2017 Fig 7. Majority rule consensus tree based on 18S ribosomal rDNA sequences with karyology doi:10.1371/journal.pone.0172190
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
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 THE MELOIDOGYNE INCOGNITA GROUP THE MIG OUTGROUP
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 THE MELOIDOGYNE INCOGNITA GROUP THE MIG OUTGROUP We have genome sequenced 19 new genomes
UNDERSTANDING THE COMPLEXITY WILL INFORM BIOLOGY AND CONTROL Lunt et al. 2014 The complex hybrid origins of the root knot nematodes revealed through comparative genomics. doi:10.7717/peerj.356
REGIONS Number of Orthology Groups M. incognita M. javanica M. arenaria M. floridensis Copies per genome has mostly lost the divergent second genome copy 33
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 colours are different species not reproductive system B A 34
M. arenaria M. javanica Libya USA French West Indies Ivory Coast USA Morocco French West Indies USA ROOT-KNOT NEMATODES LIKELY SPREAD WITH MODERN AGRICULTURE
RARE AND INCONSEQUENTIAL IN ANIMALS Heliconius Lake Malawi Polar and brown GENOME BIOLOGY IS REVEALING A VERY DIFFERENT VIEW HYBRID SPECIATION IN MELOIDOGYNE?
BE INVOLVED WITH 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
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 40
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
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
KNOWN? By Mason Masteka - originally posted to Flickr as End of Summer Tomatoes, CC BY-SA 2.0, https://commons.wikimedia.org/w/index.php?curid=11444911
Dave Lunt EVOHULL: EVOLUTIONARY AND ENVIRONMENTAL GENOMICS UNIVERSITY OF HULL, UK @davelunt davelunt@gmail.com davelunt.net By Mason Masteka - originally posted to Flickr as End of Summer Tomatoes, CC BY-SA 2.0, https://commons.wikimedia.org/w/index.php?curid=11444911