SRX5211168 I03-270-EPS+ SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215482 SAMN10689876 I03-270-EPS+ WGS GENOMIC RANDOM NextSeq 500 SRX5211169 S02.13-270-EPS+ SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215484 SAMN10689878 S02.13-270-EPS+ WGS GENOMIC RANDOM NextSeq 500 SRX5211170 R11-276-EPS- SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215483 SAMN10689871 R11-276-EPS- WGS GENOMIC RANDOM NextSeq 500 SRX5211171 R09-267-EPS+ SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215485 SAMN10689858 R09-267-EPS+ WGS GENOMIC RANDOM NextSeq 500 SRX5211172 Q08-313-EPS- SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215486 SAMN10689850 Q08-313-EPS- WGS GENOMIC RANDOM NextSeq 500 SRX5211173 P09.5-279-EPS- SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215487 SAMN10689867 P09.5-279-EPS- WGS GENOMIC RANDOM NextSeq 500 SRX5211174 M10-313-EPS+ SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215488 SAMN10689849 M10-313-EPS+ WGS GENOMIC RANDOM NextSeq 500 SRX5211175 P09.3-279-EPS- SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215490 SAMN10689866 P09.3-279-EPS- WGS GENOMIC RANDOM NextSeq 500 SRX5211176 P06-267-EPS- SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215489 SAMN10689857 P06-267-EPS- WGS GENOMIC RANDOM NextSeq 500 SRX5211177 O12-267-EPS+ SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215491 SAMN10689856 O12-267-EPS+ WGS GENOMIC RANDOM NextSeq 500 SRX5211178 N10-270-EPS+ SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215492 SAMN10689877 N10-270-EPS+ WGS GENOMIC RANDOM NextSeq 500 SRX5211179 D09-313-EPS- SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215494 SAMN10689848 D09-313-EPS- WGS GENOMIC RANDOM NextSeq 500 SRX5211180 D01-270-EPS+ SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215493 SAMN10689874 D01-270-EPS+ WGS GENOMIC RANDOM NextSeq 500 SRX5211181 B13.18-279-EPS- SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215496 SAMN10689860 B13.18-279-EPS- WGS GENOMIC RANDOM NextSeq 500 SRX5211182 B13.16-279-EPS- SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215495 SAMN10689859 B13.16-279-EPS- WGS GENOMIC RANDOM NextSeq 500 SRX5211183 C13-270-EPS+ SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215497 SAMN10689873 C13-270-EPS+ WGS GENOMIC RANDOM NextSeq 500 SRX5211184 B13.20-279-EPS- SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215498 SAMN10689861 B13.20-279-EPS- WGS GENOMIC RANDOM NextSeq 500 SRX5211185 A1022.3-3 SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215499 SAMN10690217 A1022.3-3 WGS GENOMIC RANDOM NextSeq 500 SRX5211186 A1022.3-2 SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215500 SAMN10690216 A1022.3-2 WGS GENOMIC RANDOM NextSeq 500 SRX5211187 A13.4-267-EPS- SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215501 SAMN10689852 A13.4-267-EPS- WGS GENOMIC RANDOM NextSeq 500 SRX5211188 A13.1-267-EPS- SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215502 SAMN10689851 A13.1-267-EPS- WGS GENOMIC RANDOM NextSeq 500 SRX5211189 F02-279-EPS- SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215503 SAMN10689862 F02-279-EPS- WGS GENOMIC RANDOM NextSeq 500 SRX5211190 F05-267-EPS- SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215504 SAMN10689854 F05-267-EPS- WGS GENOMIC RANDOM NextSeq 500 SRX5211191 P09.4-279-EPS+ SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215505 SAMN10689865 P09.4-279-EPS+ WGS GENOMIC RANDOM NextSeq 500 SRX5211192 S02.19-270-EPS- SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215506 SAMN10689880 S02.19-270-EPS- WGS GENOMIC RANDOM NextSeq 500 SRX5211193 T06.21-270-EPS- SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215509 SAMN10689883 T06.21-270-EPS- WGS GENOMIC RANDOM NextSeq 500 SRX5211194 T06.22-270-EPS- SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215507 SAMN10689881 T06.22-270-EPS- WGS GENOMIC RANDOM NextSeq 500 SRX5211195 T06.23-270-EPS- SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215508 SAMN10689882 T06.23-270-EPS- WGS GENOMIC RANDOM NextSeq 500 SRX5211196 T09-270-EPS- SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215510 SAMN10689884 T09-270-EPS- WGS GENOMIC RANDOM NextSeq 500 SRX5211197 T10.21-279-EPS+ SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215512 SAMN10689868 T10.21-279-EPS+ WGS GENOMIC RANDOM NextSeq 500 SRX5211198 T10.22-279-EPS+ SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215511 SAMN10689869 T10.22-279-EPS+ WGS GENOMIC RANDOM NextSeq 500 SRX5211199 T11-276-EPS+ SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215513 SAMN10689872 T11-276-EPS+ WGS GENOMIC RANDOM NextSeq 500 SRX5211200 A1022.1-2 SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215514 SAMN10690210 A1022.1-2 WGS GENOMIC RANDOM NextSeq 500 SRX5211201 A1022.1-3 SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215515 SAMN10690211 A1022.1-3 WGS GENOMIC RANDOM NextSeq 500 SRX5211202 A1022.2-1 SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215516 SAMN10690212 A1022.2-1 WGS GENOMIC RANDOM NextSeq 500 SRX5211203 A1022.2-2 SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215517 SAMN10690213 A1022.2-2 WGS GENOMIC RANDOM NextSeq 500 SRX5211204 A1021.3-1 SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215519 SAMN10690224 A1021.3-1 WGS GENOMIC RANDOM NextSeq 500 SRX5211205 A1021.3-2 SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215518 SAMN10690225 A1021.3-2 WGS GENOMIC RANDOM NextSeq 500 SRX5211206 A1021.3-3 SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215520 SAMN10690226 A1021.3-3 WGS GENOMIC RANDOM NextSeq 500 SRX5211207 A1022.1-1 SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215521 SAMN10690209 A1022.1-1 WGS GENOMIC RANDOM NextSeq 500 SRX5211208 H11.12-279-EPS+ SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215522 SAMN10689863 H11.12-279-EPS+ WGS GENOMIC RANDOM NextSeq 500 SRX5211209 H11.26-279-EPS+ SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215523 SAMN10689864 H11.26-279-EPS+ WGS GENOMIC RANDOM NextSeq 500 SRX5211210 F06-276-EPS+ SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215524 SAMN10689870 F06-276-EPS+ WGS GENOMIC RANDOM NextSeq 500 SRX5211211 H01-267-EPS+ SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215525 SAMN10689855 H01-267-EPS+ WGS GENOMIC RANDOM NextSeq 500 SRX5211212 A1022.2-3 SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215526 SAMN10690214 A1022.2-3 WGS GENOMIC RANDOM NextSeq 500 SRX5211213 A1022.3-1 SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215527 SAMN10690215 A1022.3-1 WGS GENOMIC RANDOM NextSeq 500 SRX5211214 D11-267-EPS- SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215530 SAMN10689853 D11-267-EPS- WGS GENOMIC RANDOM NextSeq 500 SRX5211215 E07-270-EPS+ SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215528 SAMN10689875 E07-270-EPS+ WGS GENOMIC RANDOM NextSeq 500 SRX5211216 A1021.2-2 SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215529 SAMN10690222 A1021.2-2 WGS GENOMIC RANDOM NextSeq 500 SRX5211217 A1021.2-3 SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215531 SAMN10690223 A1021.2-3 WGS GENOMIC RANDOM NextSeq 500 SRX5211218 A1021.1-3 SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215532 SAMN10690220 A1021.1-3 WGS GENOMIC RANDOM NextSeq 500 SRX5211219 A1021.2-1 SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215533 SAMN10690221 A1021.2-1 WGS GENOMIC RANDOM NextSeq 500 SRX5211220 A1021.1-1 SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215534 SAMN10690218 A1021.1-1 WGS GENOMIC RANDOM NextSeq 500 SRX5211221 A1021.1-2 SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215535 SAMN10690219 A1021.1-2 WGS GENOMIC RANDOM NextSeq 500 SRX5211222 A09.1-313-EPS+ SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215536 SAMN10689728 A09.1-313-EPS+ WGS GENOMIC RANDOM NextSeq 500 SRX5211223 A09.3-313-EPS+ SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215537 SAMN10689847 A09.3-313-EPS+ WGS GENOMIC RANDOM NextSeq 500 SRX5211224 A01-270-EPS- SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215538 SAMN10689879 A01-270-EPS- WGS GENOMIC RANDOM NextSeq 500 SRX5211225 A06-313-EPS+ SRP176381 PRJNA512862 For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9 2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150 2 PE reads. SRS4215539 SAMN10689705 A06-313-EPS+ WGS GENOMIC RANDOM NextSeq 500