10.5061/DRYAD.H5G60
Morgan-Richards, Mary
Massey University
Hills, Simon F. K.
Massey University
Biggs, Patrick J.
Massey University
Trewick, Steven A.
Massey University
Data from: Sticky genomes: using NGS evidence to test hybrid speciation
hypotheses
Dryad
dataset
2016
Hybrid speciation
Acanthoxyla geisovii
Holocene
Clitarchus hookeri
Stick insect
2016-12-16T16:24:55Z
2016-12-16T16:24:55Z
en
https://doi.org/10.1371/journal.pone.0154911
1551236123 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Hypotheses of hybrid origin are common. Here we use next generation
sequencing to test a hybrid hypothesis for a non-model insect with a large
genome. We compared a putative hybrid triploid stick insect species
(Acanthoxyla geisovii) with its putative paternal diploid taxon
(Clitarchus hookeri), a relationship that provides clear predictions for
the relative genetic diversity within each genome. The parental taxon is
expected to have comparatively low allelic diversity that is nested within
the diversity of the hybrid daughter genome. The scale of genome
sequencing required was conveniently achieved by extracting mRNA and
sequencing cDNA to examine expressed allelic diversity. This allowed us to
test hybrid-progenitor relationships among non-model organisms with large
genomes and different ploidy levels. Examination of thousands of
independent loci avoids potential problems produced by the silencing of
parts of one or other of the parental genomes, a phenomenon sometimes
associated with the process of stabilisation of a hybrid genome.
Transcript assembles were assessed for evidence of paralogs and/or
alternative splice variants before proceeding. Comparison of transcript
assemblies was not an appropriate measure of genetic variability, but by
mapping reads back to clusters derived from each species we determined
levels of allelic diversity. We found greater cDNA sequence diversity
among alleles in the putative hybrid species (Acanthoxyla geisovii) than
the non-hybrid. The allelic diversity within the putative paternal species
(Clitachus hookeri) nested within the hybrid-daughter genome, supports the
current view of a hybrid-progenitor relationship for these stick insect
species. Next generation sequencing technology provides opportunities for
testing evolutionary hypotheses with non-model organisms, including, as
here, genomes that are large due to polyploidy
contigs from Clitarchus hookeriA fasta file listing the longest contigs
from Clitarchus hookeri used in the analysis.longestContigs_Cl.facontigs
from Acanthoxyla geisoviiA fasta file listing the longest contigs from
Acanthoxyla geisovii used in the analysis.longestContigs_Ac.faIllumina
Fastq files from Acanthoxyla geisoviA compressed file for the Illumina
short read sequences from the Acanthoxyla geisovii used in the
analysis.Ag_sequence.fq.zipIllumina Fastq files from Clitarchus hookeriA
compressed file for the Illumina short read sequences from the Clitarchus
hookeri used in the analysis.Ch_sequence.fq.zip
New Zealand