Genetic stock identification of Atlantic salmon (Salmo salar) populations in the southern part of the European range

Griffiths, Andrew M; Machado-Schiaffino, Gonzalo; Dillane, Eileen; Coughlan, Jamie; Horreo, Jose L; Bowkett, Andrew E; Minting, Peter; Toms, Simon; Roche, Willie; Gargan, Paddy; McGinnity, Philip; Cross, Tom; Bright, Dylan; Garcia-Vazquez, Eva; Stevens, Jamie R

doi:10.1186/1471-2156-11-31

Table 5 Estimated proportion (with standard deviation) of the simulated single-population mixtures that is apportioned back to the correct baseline sample using ONCOR.

From: Genetic stock identification of Atlantic salmon (Salmo salar) populations in the southern part of the European range

Catchment	Sample Code	Sample Size	a) Sample Allocation (10 loci)	b) Sample Allocation (12 loci)	c) Catchment Allocation	d) Pooled Catchment Allocation	e) Regional Allocation
ANNAN	ANN.Bk	30	0.5791 (0.0612)	0.5541 (0.0531)	0.5908 (0.0558)		0.7673 (0.0454)
	ANN.Ev	35	0.2918 (0.0558)	0.3317 (0.0635)	0.4073 (0.0593)	0.5682 (0.0706)	0.8931 (0.0303)
	ANN.Whi	31	0.2939 (0.0535)	0.3210 (0.0636)	0.4062 (0.0611)		0.7882 (0.0497)
AULNE	AULNE	39	0.3475 (0.0597)	0.4081 (0.0621)	0.4081 (0.0621)	0.3932 (0.0645)	0.8717 (0.0347)
AVON	AVON.Brd	23	0.7956 (0.0509)	0.8068 (0.0418)	0.9590 (0.0258)	0.9830 (0.0163)	0.9993 (0.0023)
	AVON.Bug	20	0.6040 (0.0666)	0.6657 (0.0541)	0.9042 (0.0325)		0.9935 (0.0072)
AWE	AWE.Bra	35	0.9551 (0.0210)	0.9673 (0.0192)	0.9703 (0.0189)		0.9751 (0.0152)
	AWE.Cla	35	0.9203 (0.0293)	0.9553 (0.0202)	0.9575 (0.0195)	0.9516 (0.0223)	0.9619 (0.0178)
	AWE.Mai	35	0.8611 (0.0393)	0.8929 (0.0314)	0.8953 (0.0306)		0.9127 (0.0353)
AYR	AYR.Gle	30	0.4368 (0.0639)	0.4197 (0.0609)	0.9756 (0.0164)		0.9786 (0.0124)
	AYR.How	30	0.3265 (0.0616)	0.4122 (0.0590)	0.7047 (0.0620)	0.9524 (0.0227)	0.7748 (0.0551)
	AYR.Lug	68	0.7924 (0.0523)	0.8418 (0.0490)	0.9173 (0.0327)		0.9381 (0.0248)
BARROW	BAR.Bal	40	0.5409 (0.0530)	0.5224 (0.0600)	0.5224 (0.0600)	0.4629 (0.0617)	0.7475 (0.0463)
BLAVET	BLAVET	49	0.3544 (0.0640)	0.5474 (0.0601)	0.5474 (0.0601)	0.5415 (0.0649)	0.9445 (0.0245)
BLACKWATER	ROAG.Tar	33	0.4980 (0.0580)	0.5202 (0.0616)	0.5202 (0.0616)	0.4621 (0.0547)	0.7290 (0.0486)
BOYNE	BOY.Dee	36	0.7222 (0.0575)	0.7764 (0.0492)	0.8785 (0.0389)		0.9070 (0.0294)
	BOY.Moy	35	0.6724 (0.0592)	0.7129 (0.0528)	0.8041 (0.0424)	0.9169 (0.0305)	0.8372 (0.0434)
	BOY.Ska	35	0.5359 (0.0552)	0.6703 (0.0596)	0.7859 (0.0478)		0.8135 0.0417)
CAMAL	CAM.Del	30	0.4496 (0.0693)	0.5280 (0.0611)	0.5735 (0.0610)		0.8119 (0.0496)
	CAM.Gam	30	0.5369 (0.0638)	0.6511 (0.0559)	0.6977 (0.0562)	0.7511 (0.0495)	0.8668 (0.0405)
	CAM.Ken	30	0.3952 (0.0570)	0.4270 (0.0613)	0.5024 (0.0612)		0.8318 (0.0492)
CARES	CARES02	72	0.6363 (0.0615)	0.6855 (0.0547)	0.6866 (0.0548)	0.7858 (0.0525)	0.9831 (0.0120)
	CAR.Cas	24	0.9140 (0.0361)	0.9113 (0.0316)	0.9692 (0.0239)		0.9981 (0.0038)
CLYDE	CLY.Boc	30	0.4885 (0.0571)	0.5693 (0.0579)	0.5712 (0.0576)	0.7160 (0.0505)	0.6497 (0.0552)
	CLY.Cal	25	0.7475 (0.0494)	0.7987 (0.0460)	0.8014 (0.0460)		0.8456 (0.0395)
CORK BLACKWATER	COR.Awn	35	0.3076 (0.0596)	0.3599 (0.0577)	0.6915 (0.0516)		0.7493 (0.0441)
	COR.Cly	35	0.3581 (0.0629)	0.3624 (0.0599)	0.6443 (0.0521)	0.7640 (0.0468)	0.7193 (0.0585)
	COR.Gle	35	0.2661 (0.0574)	0.3763 (0.0596)	0.5453 (0.0553)		0.5836 (0.0591)
CREE	CREE.Whi	39	0.4748 (0.0641)	0.5826 (0.0603)	0.5826 (0.0603)	0.5111 (0.0612)	0.6371 (0.0589)
CREED	CREED.All	36	0.6212 (0.0545)	0.6257 (0.0551)	0.6257 (0.0551)	0.5744 (0.0575)	0.7530 (0.0592)
DART	DAR.Pos	84	0.9141 (0.0328)	0.9423 (0.0287)	0.9423 (0.0287)	0.9375 (0.0260)	0.9793 (0.0159)
DEE	DEE.Abb	24	0.4976 (0.0582)	0.5313 (0.0521)	0.5701 (0.0511)	0.7180 (0.0526)	0.7101 (0.0484)
	DEE.Cer	39	0.6529 (0.0536)	0.6540 (0.0598)	0.6593 (0.0595)		0.7393 (0.0569)
DERWENT	DERW.Dash	25	0.0444 (0.0301)	0.0916 (0.0399)	0.2118 (0.0583)		0.4926 (0.0613)
	DERW.Mar	30	0.2230 (0.0506)	0.2617 (0.0571)	0.4020 (0.0610)	0.6065 (0.0651)	0.6299 (0.0616)
	DERW.New	32	0.4599 (0.0579)	0.4550 (0.0563)	0.5733 (0.0642)		0.6801 (0.0572)
DOON	DOON.Muc	30	0.6977 (0.0479)	0.6867 (0.0564)	0.7515 (0.0460)		0.7861 (0.0464)
	DOON.Nes	27	0.5924 (0.0575)	0.5767 (0.0580)	0.7433 (0.0481)	0.7978 (0.0435)	0.7612 (0.0444)
	DOON.Ske	29	0.2733 (0.0548)	0.3583 (0.0594)	0.4359 (0.0607)		0.5441 (0.0578)
EDEN	EDEN.Dac	30	0.5034 (0.0631)	0.5582 (0.0543)	0.7146 (0.0496)		0.9642 (0.0178)
	EDEN.Sca	31	0.5468 (0.0564)	0.4726 (0.0554)	0.5167 (0.0553)	0.7984 (0.0592)	0.8917 (0.0378)
	EDEN.Swin	30	0.4540 (0.0631)	0.5860 (0.0619)	0.7200 (0.0570)		0.9156 (0.0299)
ELLE	ELLE	50	0.3690 (0.0685)	0.4589 (0.0623)	0.4589 (0.0623)	0.4562 (0.0718)	0.9604 (0.0205)
ELORN	ELORN	49	0.5774 (0.0654)	0.6068 (0.0592)	0.6068 (0.0592)	0.6152 (0.0627)	0.9809 (0.0124)
EO	EO	46	0.9593 (0.0219)	0.9704 (0.0168)	0.9704 (0.0168)	0.9714 (0.0205)	0.9897 (0.0093)
ESK (Border)	ESKB.Boy	30	0.1651 (0.0531)	0.2192 (0.0477)	0.3084 (0.0581)		0.7579 (0.0506)
	ESKB.Ewe	30	0.1758 (0.0525)	0.1523 (0.0476)	0.2305 (0.0525)	0.5600 (0.0703)	0.7846 (0.0449)
	ESKB.Lid	35	0.6293 (0.0581)	0.6615 (0.0481)	0.6958 (0.0476)		0.9187 (0.0296)
EWE	EWE.Gru	26	0.3999 (0.0619)	0.4459 (0.0618)	0.4479 (0.0615)	0.6913 (0.0500)	0.8044 (0.0454)
	EWE.Kem	23	0.6749 (0.0537)	0.7443 (0.0471)	0.7510 (0.0475)		0.8560 (0.0358)
EXE	EXE.Dan	43	0.7485 (0.0528)	0.7621 (0.0487)	0.9266 (0.0282)		0.9808 (0.0138)
	EXE.Sher	31	0.3760 (0.0632)	0.4859 (0.0655)	0.7901 (0.0454)	0.9017 (0.0330)	0.9325 (0.0296)
	EXE.Sim	68	0.7348 (0.0576)	0.8304 (0.0443)	0.8720 (0.0393)		0.9513 (0.0254)
FLEET	FLE.Big	21	0.2120 (0.0499)	0.3837 (0.0589)	0.4322 (0.0593)	0.7521 (0.0532)	0.5670 (0.0615)
	FLE.Lit	26	0.7316 (0.0547)	0.7677 (0.0489)	0.8106 (0.0429)		0.8337 (0.0401)
FOWEY	FOW.Mar	20	0.5447 (0.0565)	0.6016 (0.0536)	0.6146 (0.0554)	0.6367 (0.0534)	0.8273 (0.0389)
	FOW.Tre	36	0.5255 (0.0570)	0.5423 (0.0548)	0.5448 (0.0539)		0.8574 (0.0412)
GRUINARD	GRU.Abh	27	0.1807 (0.0537)	0.2700 (0.0559)	0.2859 (0.0560)	0.6262 (0.0591)	0.6265 (0.0613)
	GRU.Ghi	27	0.5741 (0.0587)	0.5889 (0.0543)	0.6450 (0.0512)		0.7815 (0.0503)
ITCHEN	ITC.Bis	53	0.9215 (0.0381)	0.9644 (0.0232)	0.9644 (0.0232)	0.9608 (0.0222)	0.9975 (0.0047)
KENT	KENT.SpA	41	0.5339 (0.0607)	0.5975 (0.0638)	0.6246 (0.0634)	0.5048 (0.0669)	0.8821 (0.0344)
	KENT.Sto	20	0.0645 (0.0337)	0.0499 (0.0297)	0.2331 (0.0518)		0.7921 (0.0495)
LAUNE	LAU.Cot	47	0.5335 (0.0556)	0.6026 (0.0621)	0.6026 (0.0621)	0.5624 (0.0591)	0.7022 (0.0539)
LAXFORD	LAX.Ach	32	0.6540 (0.0598)	0.6882 (0.0572)	0.7423 (0.0553)		0.8579 (0.0420)
	LAX.Mai	30	0.2647 (0.0529)	0.3172 (0.0517)	0.3582 (0.0539)	0.8735 (0.0375)	0.6014 (0.0685)
	LAX.Thu	32	0.9983 (0.0039)	0.9978 (0.0045)	0.9978 (0.0045)		0.9986 (0.0035)
LEUGER	LEUGER	48	0.5531 (0.0588)	0.6086 (0.0652)	0.6086 (0.0652)	0.6205 (0.0666)	0.9235 (0.0287)
LOCH LOCHY	LOC.loc	46	0.5521 (0.0623)	0.6493 (0.0584)	0.6621 (0.0559)	0.7290 (0.0508)	0.7789 (0.0491)
	LOC.lun	26	0.4907 (0.0656)	0.4937 (0.0694)	0.6243 (0.0645)		0.7567 (0.0525)
LOCH	LOM.End	25	0.7578 (0.0490)	0.8568 (0.0397)	0.9377 (0.0239)	0.9631 (0.0192)	0.9478 (0.0240)
LOMOND	LOM.Fru	51	0.9356 (0.0262)	0.9613 (0.0184)	0.9639 (0.0182)		0.9712 (0.0169)
LUNE	LUNE.Birk	29	0.2499 (0.0577)	0.3227 (0.0517)	0.4072 (0.0622)		0.7938 (0.0471)
	LUNE.Cha	28	0.3762 (0.0573)	0.3617 (0.0677)	0.4067 (0.0650)	0.6959 (0.0593)	0.8240 (0.0396)
	LUNE.Ger	30	0.5511 (0.0525)	0.6270 (0.0512)	0.7186 (0.0568)		0.9407 (0.0276)
MOY	MOY.TriL	42	0.6995 (0.0537)	0.7281 (0.0564)	0.7281 (0.0564)	0.6681 (0.0511)	0.8209 (0.0461)
NARCEA	NARCEA02	40	0.5757 (0.0666)	0.6291 (0.0568)	0.6291 (0.0568)	0.5309 (0.0561)	0.9872 (0.0107)
NITH	NITH.RC	30	0.2519 (0.0578)	0.2875 (0.0613)	0.3588 (0.0656)		0.8590 (0.0347)
	NITH.NM	30	0.1596 (0.0478)	0.1928 (0.0521)	0.2553 (0.0558)	0.4859 (0.0658)	0.7314 (0.0608)
	NITH.NSC	30	0.6190 (0.0596)	0.6766 (0.0491)	0.6994 (0.0469)		0.9542 (0.0229)
RIBBLE	RIB.Bro	28	0.3664 (0.0503)	0.3255 (0.0517)	0.4399 (0.0593)		0.6874 (0.0577)
	RIB.Cra	29	0.5675 (0.0550)	0.5534 (0.0580)	0.7010 (0.0498)	0.7816 (0.0478)	0.9421 (0.0273)
	RIB.Ham	31	0.5400 (0.0624)	0.5979 (0.0623)	0.7223 (0.0484)		0.9008 (0.0355)
SCORFF	SCORFF	47	0.4018 (0.0710)	0.5002 (0.0710)	0.5002 (0.0710)	0.5077 (0.0700)	0.9778 (0.0137)
SEE	SEE	49	0.5916 (0.0623)	0.6705 (0.0633)	0.6705 (0.0633)	0.6607 (0.0613)	0.9613 (0.0177)
SELLA	SELLA.Pig	34	0.6253 (0.0576)	0.6967 (0.0538)	0.7406 (0.0510)	0.6630 (0.0643)	0.9934 (0.0088)
	SELLA02	48	0.3433 (0.0736)	0.4001 (0.0568)	0.4048 (0.0561)		0.9727 (0.0155)
SELUNE	SELUNE	50	0.5384 (0.0547)	0.6437 (0.0526)	0.6437 (0.0526)	0.6398 (0.0546)	0.9437 (0.0261)
SEVERN	SEV.CinA	22	0.5538 (0.0624)	0.5591 (0.0635)	0.5591 (0.0635)	0.4827 (0.0640)	0.9147 (0.0307)
SUIR	SUIR.Clo	28	0.2048 (0.0562)	0.1644 (0.0404)	0.2490 (0.0529)	0.5407 (0.0611)	0.5215 (0.0596)
	SUIR.MCb	20	0.2218 (0.0554)	0.2102 (0.0415)	0.6235 (0.0579)		0.8203 (0.0491)
TAMAR	TAM.Gat	33	0.3341 (0.0546)	0.3357 (0.0572)	0.5546 (0.0558)		0.8327 (0.0455)
	TAM.Ott	33	0.4564 (0.0619)	0.4843 (0.0534)	0.6979 (0.0541)	0.8110 (0.0544)	0.8377 (0.0409)
	TAM.Tre	30	0.6582 (0.0589)	0.6171 (0.0598)	0.7382 (0.0477)		0.8688 (0.0381)
TAW	TAW.Bra	25	0.5186 (0.0537)	0.6695 (0.0580)	0.6897 (0.0562)	0.5992 (0.0635)	0.9141 (0.0299)
	TAW.Twi	32	0.3199 (0.0651)	0.4196 (0.0648)	0.4226 (0.0655)		0.8506 (0.0408)
TEIFI	TEIFI.Cle	27	0.2314 (0.0515)	0.2581 (0.0529)	0.4018 (0.0586)		0.6037 (0.0577)
	TEIFI.Egn	24	0.3088 (0.0575)	0.4052 (0.0556)	0.6015 (0.0559)	0.6292 (0.0653)	0.8136 (0.0523)
	TEIFI.Lam	27	0.2229 (0.0485)	0.2310 (0.0557)	0.4185 (0.0600)		0.7051 (0.0566)
TEST	TEST	49	0.8644 (0.0432)	0.9642 (0.0240)	0.9642 (0.0240)	0.9676 (0.0232)	0.9962 (0.0060)
TORRIDGE	TOR.Eoak	21	0.2131 (0.0599)	0.3046 (0.0559)	0.3064 (0.0558)	0.8098 (0.0417)	0.7273 (0.0613)
	TOR.Woak	29	0.9248 (0.0274)	0.9362 (0.0237)	0.9384 (0.0234)		0.9765 (0.0162)
ULLA	ULLA	46	0.9350 (0.0308)	0.9641 (0.0195)	0.9641 (0.0195)	0.9610 (0.0245)	0.9996 (0.0018)
USK	USK.Bra	29	0.1643 (0.0497)	0.2160 (0.0544)	0.6023 (0.0651)		0.8644 (0.0357)
	USK.Gir	30	0.1840 (0.0467)	0.2293 (0.0501)	0.6600 (0.0558)	0.7371 (0.0609)	0.8865 (0.0412)
	USK.Grw	29	0.3297 (0.0646)	0.2726 (0.0531)	0.6865 (0.0629)		0.9321 (0.0276)
WYE	WYE.Lly(Wye)	30	0.4398 (0.0621)	0.4951 (0.0573)	0.7486 (0.0578)		0.9671 (0.0206)
	WYE.Edw	30	0.2290 (0.0517)	0.3178 (0.0664)	0.5506 (0.0666)	0.7413 (0.0622)	0.9389 (0.0274)
	WYE.Gar.	27	0.1242 (0.0497)	0.1532 (0.0521)	0.3548 (0.0624)		0.9280 (0.0304)
Mean			0.5029	0.5470	0.6366	0.7006	0.8441

The table shows: a) correct apportionment to individual sample sites within catchments with 10 loci (i.e. SSspG7 and Ssa197 removed); b) correct apportionment to individual sample sites within catchments with 12 loci; c) the sum of the apportionment to all samples in a catchment; d) the apportionment to catchment when all samples from within a catchment are pooled (i.e. the pool and allocate method); and e) the sum of apportionment to all samples in a reporting region. In the case of the individual sample simulations, a 108-sample baseline was used. One-hundred fish were used in the mixture sample, with 100 simulations of the mixture and baseline samples; an apportionment score of 1 = 100% correct. Individual samples are identified by tributary name; see Additional File 1 for details of latitude and longitude, collection date and individual sample size.

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