Population structure analyses
For STRUCTURE analysis, a thinned version of the VCF file was generated
with vcftools 0.1.15 (–thin 500) (Danecek et al., 2011), containing
11,447 similarly-spaced SNPs, while including only L. cidristrains. Structure was run on this dataset five times for K values
ranging from 1 to 7, with 10,000 burn-in and 100,000 replications for
each run, using admixture model, infer alpha, lambda =1, fpriormean =1,
unifprioralpha 1, and alpha max 10. The structure-selector website was
employed to obtain the optimal K values
(http://lmme.qdio.ac.cn/StructureSelector/) (Li and Liu, 2018) according
to the Evanno method (Evanno et al., 2005). The results for each K were
plotted using CLUMPAK (Kopelman et al., 2015) and visualized using a
structure plot (http://omicsspeaks.com/strplot2/ ) (Ramasamy et
al., 2014). In addition, we performed clustering analyses of the same
samples by using SMARTPCA without outlier removal (Patterson et al.,
2006). For fineSTRUCTURE analysis (Lawson et al., 2012), a VCF file that
included all SNPs among L. cidri strains was phased using BEAGLE
3.0.4 (Browning and Browning, 2007). Since we lacked a L. cidrirecombination map, we used a constant recombination rate between
consecutive SNPs based on the average recombination rate of L.
kluyveri (0.4 cM kbp-1, (Brion et al., 2017)). All
versus all chromosomal painting was performed with Chromopainter V2, and
the output was further analyzed with fineSTRUCTURE (-x 100000 -y 100000
-z 1000). Plotting of the ancestry matrix was done using fineSTRUCTURE R
scripts.