RNA sequencing describes both population structure and plasticity-selection dynamics in a non-model fish

BMC Genomics

Table 1 Population genetic results for microsatellites, neutral SNPs, and overall SNPs in two populations of Sacramento splittail (Pogonichthys macrolepidotus)

Dataset	Statistic	Central Valley	San Pablo
Microsatellites (n = 528 and 191; 19 markers)	Pairwise F_ST	0.04262 (0.0296–0.0589)
	H_O	0.605	0.652
	H_S	0.622	0.653
	F_IS	0.0266 (0.0054–0.0542)	0.00177 (−0.0171–0.0193)
	Population-specific F_ST	0.06475 (0.02951–0.1067)	0.01959 (− 0.009956–0.04752)
Neutral SNPs (n = 16 per population; 69,951 SNPs)	Pairwise F_ST	0.0263 (0.0257–0.027)
	H_O	0.273	0.279
	H_S	0.261	0.264
	F_IS	−0.0489 (− 0.0515 - -0.0466)	−0.0541 (− 0.0565–0.0517)
	Population-specific F_ST	0.0324 (0.0302–0.0348)	0.0170 (0.01504–0.0190)
Overall SNPs (n = 16 per population; 420,626 SNPs)	Pairwise F_ST	0.0230 (0.0227–0.0233)
	H_O	0.253	0.264
	H_S	0.287	0.290
	F_IS	0.120 (0.118–0.121)	0.091 (0.0893–0.0924)
	Population-specific F_ST	0.03359 (0.03274–0.03450)	0.02213 (0.02121–0.02290)

The Central Valley population (n = 191) represents a larger, less salinity-tolerant group than the San Pablo population (n = 191). Neutral and overall single nucleotide polymorphisms (SNPs) were generated with raw RNA sequencing data of 32 fish (n = 16 per population). There were a total of 420,626 overall SNPs and 69,951 neutral SNPs after filtering. Pairwise F_ST represents Weir & Cockerham’s pairwise F_ST, H_O represents observed heterozygosity, H_S represents gene diversity (sometimes referred to as expected heterozygosity), F_IS refers to the inbreeding coefficient, and population-specific F_ST refers to a coalescent approach to F_ST. 95% confidence intervals are provided where possible in parentheses, based on 1000 bootstrapping iterations

ISSN: 1471-2164