Enhanced cross-species utility of conserved microsatellite markers in shorebirds

BMC Genomics

Table 1 Generalised linear models for a) amplification success and b) polymorphism of conserved microsatellite loci

a) Amplification success¹						b) Polymorphism²
	Error	Residual	B	t	P		Error	Residual	B	t	P
	df *	deviance*					df *	deviance*
Maximal model	39	57.29				Maximal model	12	24.97
- Interactions	49	62.32				- Microsatellite retained	13	24.97
- Repeat length	50	62.32				- Primer type⁵	14	25.46
- Unique/multiple hits	51	62.70				- H_o in source species⁶	17	26.91
- Microsatellite motif³	52	63.55				- No. of mismatches⁷	18	27.60
- No of mismatches⁴	53	67.65				- E-value	19	30.15
Minimal adequate model						Minimal adequate model
E-value	53	67.65	-0.02	-2.58	0.013	Repeat length	19	30.15	0.02	2.22	0.039
						Microsatellite motif³	19	30.15	-1.00	-2.15	0.045
						Microsatellite interrupted⁸	19	30.15	-1.02	-2.09	0.051

*model descriptives are given for models after removal of explanatory variables
¹based on tests in three charadriiform species: Kentish plover Charadrius alexandrinus, whiskered auklet Aethia pygmaea and ruff Philomachus pugnax
²based on proportion of species in which a microsatellite locus was found to be polymorphic when tested in four individuals
³dinucleotide or tetranucleotide repeat motif of microsatellite
⁴total number of mismatches between chicken and charadriiform sequence for both primer sequences combined
⁵Gga-consensus primer or standard primer design
⁶observed heterozygosity for source species given in original publication of the microsatellite sequence
⁷number of mismatches in primer sequence between charadriiform sequence and chicken homologue
⁸microsatellite sequence interrupted by non-motif base insertions (imperfect) or not (perfect)

ISSN: 1471-2164