DOI: 10.5061/dryad.1538f
title: Data from: Genomic sequencing reveals historical, demographic and selective factors associated with the diversification of the fire-associated fungus Neurospora discreta

description: 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.
description: 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 &lt;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 &lt;1% black ascospores ; & 1-15% black ascospores; 5 if 15-50% black ascospores; 6 if &gt; 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