Biases underlying species detection using fluorescent amplified-fragment length polymorphisms yielded from roots

Table 3 Detection success of amplicons yielded from species mixtures containing identified and undetermined plant species

cpDNA	Fragment size (bp)	Species	Soil source^a	Detection rate
cpDNA	Fragment size (bp)	Species	Soil source^a	4.5 ng μL⁻¹ DNA	25 ng μL⁻¹ DNA	45.5 ng μL⁻¹ DNA
trnT-trnL intergenic spacer	531	Undetermined	1, 2	0/6	1/6	5/6
trnT-trnL intergenic spacer	637	Undetermined	1	0/3	2/3	3/3
trnT-trnL intergenic spacer	679	Undetermined	2	0/3	6/6	3/3
trnT-trnL intergenic spacer	881	Undetermined	1, 2	0/6	6/6	6/6
trnT-trnL intergenic spacer	1,154	Melilotus officinalis	n/a	0/6	6/6	6/6

cpDNA	Fragment size (bp)	Species	Soil source^a	Detection rate
cpDNA	Fragment size (bp)	Species	Soil source^a	0.09 ngμL⁻¹ DNA	0.5 ng μL⁻¹ DNA	0.9 ng μL⁻¹ DNA
trnL intron	320	Undetermined	1	0/3	2/2	3/3
trnL intron	490	Undetermined	1	3/3	2/2	3/3
trnL intron	504	Undetermined	3	3/3	0/3	3/3
trnL intron	508	Undetermined	1	3/3	2/2	3/3
trnL intron	512	Undetermined	3	3/3	3/3	3/3
trnL intron	522	Undetermined	1	3/3	2/2	3/3
trnL intron	560	Undetermined	1, 3	6/6	5/5	6/6
trnL intron	584	Undetermined	3	0/3	0/3	3/3
trnL intron	604	Undetermined	3	3/3	3/3	3/3
trnL intron	696	Populus tremuloides	n/a	0/6	5/5	6/6
trnL-trnF intergenic spacer	179	Undetermined	5	3/3	3/3	3/3
trnL-trnF intergenic spacer	300	Undetermined	4	3/3	3/3	3/3
trnL-trnF intergenic spacer	324	Undetermined	4	3/3	3/3	3/3
trnL-trnF intergenic spacer	387	Undetermined	4, 5	6/6	6/6	6/6
trnL-trnF intergenic spacer	391	Undetermined	4	3/3	3/3	3/3
trnL-trnF intergenic spacer	394	Bromus inermis ^b	n/a	3/3	6/6	9/9
trnL-trnF intergenic spacer	402	Undetermined	4	3/3	3/3	3/3
trnL-trnF intergenic spacer	432	Undetermined	4	3/3	3/3	3/3
trnL-trnF intergenic spacer	443	Bromus inermis ^b	n/a	3/3	6/6	9/9
trnL-trnF intergenic spacer	460	Undetermined	4, 5	6/6	3/3	6/6

DNA was extracted from leaves of an identified species and mixed in varied proportions with DNA extracted from unidentified roots in soil. Numerator is number of successful detections; denominator is number of trials. See text for description of soil source.
^aRoots from individual soil samples yielded fragments of different sizes; the genomic material yielding these fragments occurred in an unknown proportion, which comprised the DNA template.
^bThis species yielded fragments of different sizes.

ISSN: 1746-4811