DOI: 10.5061/dryad.ttdz08kxx
title: Contrasting demographic histories revealed in two invasive populations of the dry rot fungus Serpula lacrymans

description: Globalization and international trade have impacted organisms around the
 world leading to a considerable number of species establishing in new
 geographic areas. Many organisms have taken advantage of human-made
 environments, including buildings. One such species is the dry rot fungus
 Serpula lacrymans, which is the most aggressive wood-decay fungus in
 indoor environments in temperate regions. Using population genomic
 analyses of 36 full genome sequenced isolates, we demonstrated that
 European and Japanese isolates are highly divergent and the populations
 split 3,000 - 19,000 generations ago, probably predating human influence.
 Approximately 250 generations ago, the European population went through a
 tight bottleneck, likely corresponding to the fungus colonization of the
 built environment in Europe. The demographic history of these populations,
 probably lead to low adaptive potential. Only two loci under selection
 were identified using a Fst outlier approach, and selective sweep analyses
 identified three loci with extended haplotype homozygosity. The selective
 sweep analyses found signals in genes possibly related to decay of various
 substrates in Japan and in genes involved DNA replication and protein
 modification in Europe. Our results suggest that the dry rot fungus
 independently established in indoor environments in Europe and Japan and
 that invasive species can potentially establish large populations in new
 habitats based on a few colonizing individuals.
description: Full genome sequences from Illumina from 36 isolates
 of Serpula lacrymans were analyzed in parallel using two pipelines: (1)
 the first pipeline trimmed the data using TrimGalore
 version 0.3.3, aligned using Bowtie2
 (Langmead & Salzberg), and SAMtools (Li
 <i>et al.</i> 2009) to include only reads that mapped
 concordantly and only once to remove PCR duplicates. Variants were called
 for each alignment using HaplotypeCaller, combined into a common variant
 file with GenotypeGVCFs and further quality filtered with
 VariantFiltration
 (QD&lt;2.0||FS&gt;60.0||MQ&lt;40.0||MQRankSum&lt;
 -12.5||ReadPosRankSum&lt; -8.0) in Genome Analysis Tool Kit (GATK)
 (McKenna <i>et al.</i> 2010; Van der Auwera <i>et
 al.</i> 2013). (2) The second pipeline trimmed the sequences using
 Trimmomatic
 (Bolger <i>et al.</i> 2014), mapped the reads
 using BWAmem (Li
 2013), filtered using SAMtools,
 called variants using BCFtools call
 and filtered with BCFtools view.
 For both pipelines, the sequence data were mapped to the monokaryotic
 <i>S. lacrymans</i> isolate S7.3, version 2 (Eastwood
 <i>et al.</i> 2011). Repetitive regions of the <i>S.
 lacrymans</i> v. 2 genome were annotated using the REPET package
 v.2.5 (Flutre <i>et al.</i> 2011), following the procedure
 outlined in (Sipos <i>et al.</i> 2017). Regions annotated as
 transposable element-derived were filtered from the SNP data set using
 BEDtools
 (Quinlan & Hall 2010). A combined data set using only SNPs called
 by both pipelines resulted in 419,196 high quality SNPs for the 36
 isolates included in this analysis.
description: The file is in vcf format, and gziped.