Table 2. Summary of the tested scenarios for SSRseq genotyping.

Species	SSRseq development strategy	Candidate loci	Screened loci	Number of loci in a single multiplexed PCR	Sequencing Plateform	Total number of individuals sequenced	Number of individual analyzed for this study	Number of repeated individuals	Sequenced locia	Mean (cv)sequences/ loci/ individual	Reliable loci genotypedb	Overall success rate
S. salar	Previously developed loci	81	–	23	Ion Torrent PGM i316	960	66	66	20	161 (61%)	9	39%
				23	Illumina MiSeq - 1/2 nano PE	192	96	96	20	70 (41%)	10	43%
S. salar	Previously developed loci	15c	–	15	Illumina MiSeq - 1/2 nano PE	192	96	96	13	99 (65%)	7	47%
Quercus sp.	Primer redesign around previously developped loci	462	60	60	Illumina MiSeq - 1/3 V2 PE	380	46	46	53	260 (32%)	40	67%
Alosa sp.	De novo	2,872	60	28	Illumina MiSeq - 1 nano SE	382	156	156	25	95 (58%)	21	75%
				28	Illumina MiSeq - 2 nano SE	382	156	156	26	198 (58%)	24	86%
				28	Illumina MiSeq - 3 nano SE	382	156	156	26	267 (58%)	24	86%
A. ostoyae	De novo	1,806	60	51	Illumina MiSeq - 1/2 V2 PE	384	384	96	48	243 (83%)	38	75%
M. variegatipes	De novo	8,937	60	54	Illumina MiSeq - 1/4 V2 PE	182	91	91	49	176 (45%)	39	72%

Notes.

^aLoci showing substantial evidence for minimum sequencing success (at least 20 sequences in at least 50% of the individuals).

^bReliable loci (less than 50% of missing data among individuals and less than 6% of genotyping error based on comparison of repeated genotyping).

^cRoutinely genotyped using optimized multiplexed PCR and capillary-based sequencer. FDSTools analysis using two parameter sets: stutterfinder -s:-1:50, +1:10 allelefinder -m 15 -n 20; and stuttermark -s:-1:70, +1:10 allelefinder -m 10 -n 20. For each marker, four parameter combination were used (two strategies and two parameters set) and for each strategy, the best parameter set was used for a given locus.