Table 1.

Genetic diversity (π), private alleles, total nucleotide sites examined and percentage of polymorphic sites in Death Valley pupfishes and additional pupfish outgroups for comparison (EW = extinct in the wild based on IUCN designation or unpublished observations). (The number of individuals sequenced in each population is indicated (electronic supplementary material, appendix S1).)

species/subspecies	location	genetic diversity	private alleles	total sites	%polymorphic
Cyprinodon diabolis (n = 4)	Devils Hole	0.0009	1019	1 017 310	0.0938
C. nevadensis mionectes (n = 8)	Point-of-Rocks	0.0023	1572	1 229 973	0.2348
C. nevadensis mionectes (n = 1)	Big Spring	0.0006	272	403 729	0.0577
C. nevadensis pectoralis (n = 7)	Indian Spring	0.0001	21	141 445	0.0099
C. nevadensis amargosae (n = 7)	Amargosa River	0.002	1008	1 261 354	0.1954
C. nevadensis shoshone (n = 5)	Shoshone Spring	0.0013	539	874 517	0.1337
C. nevadensis nevadensis (n = 7)	Saratoga Spring	0.0021	1360	1 314 878	0.2135
C. salinus salinus (n = 2)	Salt Creek	0.0009	1244	1 184 303	0.0888
C. salinus milleri (n = 1)	Cottonball Marsh	0.0004	264	367 191	0.0400
all Death Valley species	Death Valley	0.0036	10 224	1 140 524	0.7117
C. artifrons (n = 1)	coastal Cancun, Mexico	0.0034	3212	1 185 394	0.3354
C. variegatus (n = 1)	coastal San Salvador, Bahamas	0.0039	9900	1 311 769	0.3862
C. alvarezi (n = 1)	captive colony—EW	0.0011	2211	965 072	0.1149
C. maya (n = 1)	captive colony—EW	0.0027	657	964 452	0.2722
C. veronicae (n = 1)	captive colony—EW	0.0015	5160	1241 190	0.1491