Fig 1.
Map depicting in the extent of vernal pool regions throughout California (gray) and Southern Oregon and sampling localities (black dots) from which genetic data was generated for an analysis of phylogeographic structure and diversity for the species of Branchinecta lynchi.
Vernal pool region abbreviations are as follows: Carrizo (CZVP), Central Coast (CCVP), Klamath Mountains (KMVP), Livermore (LMVP), Northeastern Sacramento Valley (NESV), Northwestern Sacramento Valley (NWVP), San Joaquin Valley (SJVP), Santa Barbara (SBVP), Solano-Colusa (SCVP), Southeastern Sacramento Valley (SESV), Southern Sierra Foothills (SSFH), and Western Riverside (WRVP). B. lynchi are not known from the Santa Rosa (SRVP), Lake-Napa (LNVP), Modoc Plateau (MPVP) or San Diego (SDVP) vernal pool regions in historical or contemporary samples and thus no sample locations were evaluated from these locations for this study.
Table 1.
Description of samples used to estimate phylogenetic diversity with COI and 16S in Branchinecta lynchi across the species range.
Fig 2.
Putative isolated geographic regions that were tested for an analysis of molecular variance.
See Table 1 for abbreviations for vernal pool regions indicated in colors in panel D. Larger watersheds are Klamath River in black, Sacramento River in red, the San Joaquin River in Brown, the Central Coast watersheds in purple, the Sothern Sierra Foothills watersheds in light blue, and the Southern coast watersheds in grey. A) Model 1 tested whether larger watersheds best explain the population genetic structure populations of the vernal pool fairy shrimp treating the Southern Sierra Foothills vernal pool region as an independent watershed. B) Model 2 tested whether larger watersheds best explain the population genetic structure populations of the vernal pool fairy shrimp treating the Southern Sierra Foothills vernal pool region as belonging to the Sacramento River watershed. C) Model 3 tested whether larger watersheds best explain the population genetic structure populations of the vernal pool fairy shrimp treating the Southern Sierra Foothills vernal pool region as belonging to the San Joaquin River watershed. D) Model 4 tested whether individual vernal pool regions best explain the population genetic structure of Branchinecta lynchi. Starred values of Φst and Φct are significant at a p-value of 0.05 or less.
Fig 3.
Depicts the negative relationship between the age of the Branchinecta lynchi specimen and its success for amplification and sequencing for two mitochondrial genes (COI and 16S).
Fig 4.
Depicts the evolutionary relationship of COI haplotypes across the species range and the network of their relatedness.
Open circles in network are hypothesized but not sampled haplotypes. Abbreviations are as in Table 1. Asterisks on nodes of tree indicate that this group of haplotypes had a bootstrap support greater than 65% and/or Bayesian support of a posterior probability greater than 95 (see S1 and S2 Figs for all support values).
Table 2.
Estimated pairwise differentiation (Фst) from the COI gene among vernal pool regions.
Table 3.
Estimated molecular diversity indexes for Branchinecta lynchi for vernal pool regions.
Fig 5.
Depicts a significant pattern of isolation by distance across the species’ range between geographic distance in kilometers and genetic distance (corrected K2P; r = 0.278, p = 0.000).
Black dots are comparisons within a vernal pool region and grey circles are comparisons between vernal pool regions. Lines are for illustration purpose only to show the direction of the correlation of within vernal pool region (solid line) versus between vernal pool regions (dashed line).
Fig 6.
Depicts the patterns of isolation by distance within each vernal pool region between geographic distance in kilometers and genetic distance estimated with corrected K2P.
CZVP, SJVP and WRVP regions were not analyzed due to low sample size.