10.5061/DRYAD.1538F
Gladieux, Pierre
University of California, Berkeley
Wilson, Benjamin A.
Stanford University
Perraudeau, Fanny
University of California, Berkeley
Montoya, Liliam A.
University of California, Berkeley
Kowbel, David
University of California, Berkeley
Hann-Soden, Christopher
University of California, Berkeley
Fischer, Monika
University of California, Berkeley
Sylvain, Iman
University of California, Berkeley
Jacobson, David J.
University of California, Berkeley
Taylor, John W.
University of California, Berkeley
Data from: Genomic sequencing reveals historical, demographic and
selective factors associated with the diversification of the
fire-associated fungus Neurospora discreta
Dryad
dataset
2015
Neurospora discreta Phylogenetic Species 6 (PS6)
Neurospora discreta Phylogenetic Species 4 Group B (PS4B)
Neurospora discreta Phylogenetic Species 4 Group A (PS4A)
resequencing
Neurospora discreta (Morphological and Biological species)
selective sweeps
Ascomycete
Neurospora discreta
2015-10-08T16:16:38Z
2015-10-08T16:16:38Z
en
https://doi.org/10.1111/mec.13417
4682557820 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Delineating microbial populations, discovering ecologically relevant
phenotypes and identifying migrants, hybrids or admixed individuals have
long proved notoriously difficult, thereby limiting our understanding of
the evolutionary forces at play during the diversification of microbial
species. However, recent advances in sequencing and computational methods
have enabled an unbiased approach whereby incipient species and the
genetic correlates of speciation can be identified by examining patterns
of genomic variation within and between lineages. We present here a
population genomic study of a phylogenetic species in the Neurospora
discreta species complex, based on the resequencing of full genomes (~37
Mb) for 52 fungal isolates from nine sites in three continents. Population
structure analyses revealed two distinct lineages in South–East Asia, and
three lineages in North America/Europe with a broad longitudinal and
latitudinal range and limited admixture between lineages. Genome scans for
selective sweeps and comparisons of the genomic landscapes of diversity
and recombination provided no support for a role of selection at linked
sites on genomic heterogeneity in levels of divergence between lineages.
However, demographic inference indicated that the observed genomic
heterogeneity in divergence was generated by varying rates of gene flow
between lineages following a period of isolation. Many putative cases of
exchange of genetic material between phylogenetically divergent fungal
lineages have been discovered, and our work highlights the quantitative
importance of genetic exchanges between more closely related taxa to the
evolution of fungal genomes. Our study also supports the role of
allopatric isolation as a driver of diversification in saprobic microbes.
SNPs for full set of non-redundant sequencesThis file contains SNPs for
the 41 isolates of taxa PS4A, PS4B and PS6. Initially the dataset was
comprised of 52 isolates, but after genome sequencing a "clone
correction" was carried out, i.e. only one representative of groups
of genome with genetic distance below 0.1 were kept in the dataset. The
file used for clone correction has also been deposited on
Dryad.PS4_HiQ.vcfSNPs for non-redundant European and North-American
sequencesThis file contains SNPs for the European and North American
isolates of PS4B. SNP-calling was performed independently for this set of
sequences, for the full set of sequences and for the full set of non
redundant sequences.PS4BUSEU_HiQ.vcfComplete genomic sequences for the
full set of non-redundant sequencesGenomic sequences were constructed
using the genomic sequence of the reference genome and a table of
SNPs.PS4_complete_genomic_sequences.phySNPs used to identify redundant
sequencesThis files contains the SNPs that were used to identify redundant
sequences. It is based on the file containing "SNPs for non-redundant
European and North-American sequences", with missing data removed. It
was analysed using DNADIST&NEIGHBOR programs in the PHYLIP
Package, and a single representative of each clonal complex was kept in
the dataset "SNPs for non-redundant European and North-American
sequences" (clonal complex identified as groups of individuals with
genetic distance <0.1)PS4BUSEU_HiQ_woNs.phyMating types and
Reproductive successReproductive success of 239 crosses (478 matings).
Columns represent the 16 mat A strains, and rows represent the 15 mat a
strains, with isolates numbers along the row and column headings of the
matrix. Numbers within matrix cells indicate the reproductive success
ratings (see below) of the two reciprocal matings of the cross between the
corresponding isolates (mat a isolate as the perithecial parent/mat A
isolate as the perithecial parent). The matrix cells have been shaded in
proportion to the reproductive success of the best mating (see Figure 5B
in the corresponding publication). Additional row and column headings
indicate the lineage designation (see Figure 1). Isolates P581 and TX8127
are tester strains of N. discreta sensu stricto. Categories of
reproductive success, corresponding to different stages in reproductive
development, from the development of perithecia, to the formation of black
ascospores were scored as follows: 0 & 1 if sterile, no perithecia
produced; & barren perithecia, no ostiole developed; 2 if
perithecia developed ostioles, but no spores; 3 & 4 if <1%
black ascospores ; & 1-15% black ascospores; 5 if 15-50% black
ascospores; 6 if > 50% black
ascospores.Compatibility_and_matingtypes.xlsxNeighbor-joining tree
constructed based on a matrix F84 distance computed using the full set of
sequencesNeighbor-joining tree based on F84 distance (DNADIST, PHYLIP
Package). Computations were performed on the full set of SNPs and this
analysis was used to identify redundant (i.e. nearly identical, or clonal)
genomic sequences.PS4_F84_NJ_for_figure.outtreeMaximum likelihood
genealogy representing the relationships among non-redundant genomic
sequences.Analyses were based on full genomic sequences (i.e. including
both variant and invariant sites).RAxML_tree
USA
Papua New Guinea
Côte d'Ivoire
Thailand
Switzerland
Spain