What are the consequences of combining nuclear and mitochondrial data for phylogenetic analysis? Lessons from Plethodonsalamanders and 13 other vertebrate clades

Table 5 Genes used in the phylogenetic analysis of Plethodon.

Type of locus	Locus	Length	Variable characters	Parsimony-informative characters	Best-fitting model	Partitions	Number of taxa sampled	Data source
Nuclear introns	GAPD	659	221	92	GTR + Γ	none	48	this study
	ILF3	281	56	34	HKY	none	40	this study
	Mlc2a	257	79	39	GTR + Γ	none	55	this study
	RPL12	463	159	90	HKY + Γ	none	48	this study
	RHO	224	57	43	HKY + I	none	62	this study
	TPI	1938	569	211	GTR + Γ	intron/exon	29	[56]
Nuclear exons	RAG-1	1467	358	248	GTR + I + Γ	codon	60	[56]
	BDNF	707	67	29	GTR + Γ	codon	14	[60]
	POMC	481	98	41	GTR + Γ	codon	15	[60]
Mitochondrial genes	Cyt-b	649	369	313	GTR + I + Γ	codon	66	[56]
	ND4	686	409	364	GTR + I + Γ	codon	65	[56]
	ND2	1107	741	635	GTR + I + Γ	codon, tRNA-TRP	52	[55]

ISSN: 2730-7182