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 sequences
This 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.vcf
SNPs for non-redundant European and North-American sequences
This 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.vcf
Complete genomic sequences for the full set of non-redundant sequences
Genomic sequences were constructed using the genomic sequence of the reference genome and a table of SNPs.
PS4_complete_genomic_sequences.phy
SNPs used to identify redundant sequences
This 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.phy
Mating types and Reproductive success
Reproductive 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.xlsx
Neighbor-joining tree constructed based on a matrix F84 distance computed using the full set of sequences
Neighbor-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.outtree
Maximum 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