Table 2

Summary of generalized linear model results. Each row corresponds to a single model using multiple explanatory variables. Significant values are indicated in bold. Quasibinomial and negative-binomial error distributions were used and results are given after calculating type-II analysis-of-variance using a F test (Quasibinomial family) or a likelihood ratio test (negative-binomial family).

Explanatory variables


Upstream parameters

AFLP parameters

AFLP diagnostics




Species

No. of sba

CG cont

No. of peaks per profile

Peak length

Homoplasy per peak

Response variables

Distribution

(Df = 2)

(Df = 1)

(Df = 2)

(Df = 1)

(Df = 1)

(Df = 1)


In silico analyses

Peak length distributionb

Quasibinomial

F1,1349 = 2.09e-12,

P = 1

F1,1349 = 967.20,

P < 0.001

No. of peaks per profile

Negative binomial

χ2 = 1574.87,

P < 0.001

χ2 = 1869.47,

P < 0.001

χ2 = 275.24,

P < 0.001

Homoplasy rate H

Quasibinomial

F2,278 = 0.98,

P = 0.38

F2,278 = 0.72,

P = 0.49

F1,278 = 576.26,

P < 0.001

No. of CFc

Negative binomial

χ2 = 19.90,

P < 0.001

χ2 = 2.99,

P = 0.22

χ2 = 25.32,

P < 0.001

χ2 = 37.92,

P < 0.001

No. of CFc in peaks with more than 10 fragments

Negative binomial

χ2 = 6.96,

P = 0.03

χ2 = 0.90,

P = 0.64

χ2 = 0.87,

P = 0.35

χ2 = 2.74,

P = 0.10

Empirical analyses

Fluorescence intensity

Negative binomial

χ2 = 22.33,

P < 0.001

χ2 = 2.39,

P = 0.12


a Total number of selective bases added for the 2 primers.

b Peak length distribution is expressed in relative frequencies.

c "CF" corresponds to comigrating fragments within a peak.

Paris et al. BMC Genomics 2010 11:287   doi:10.1186/1471-2164-11-287

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