Sequence alignment for the mitchondrial ND4 gene

Nexus file containing the sequence alignment for the mitochondrial ND4 haplotypes presented in this study. Sequence labels are field tag identifiers for individual, field-collected specimens. Georeference points for each specimen are available upon request to J. Q. Richmond ([email protected]). Nucleotide positions 1-1341 encode the NADH4 gene; 1342 - 1411 encodes tHIS; 1412-1476 encodes tSER; and 1477-1486 partially encides tLEU. Gene assignments were based on an alignment with the full mitochondrial genome sequence of Plestiodon egregius

Patterns of richness by data type of California freshwater species.

<p>Maps show the number of native freshwater species when summarized by: (A) observational data recorded after 1980; (B) observational data recorded before 1980 or observations of extirpated populations; and (C) data that includes range maps, historical range maps, modeled habitat, professional judgment, critical habitat designations, and management area designations. Spatial data with an unknown observation date or unknown type are not included in any panel. The black lines on the maps represent the major hydrologic regions in the study area.</p

Taxonomic grouping and conservation status of freshwater taxa native to California.

<p>Percentage of freshwater species by taxonomic groups that are considered vulnerable (at risk of extinction) in California watersheds, “Insects and other invertebrates” includes the classes Arachnida, Branchiopoda, Insecta and Polychaeta.</p

Taxonomic grouping and conservation rank of freshwater taxa endemic to study area.

<p>Percentage of freshwater endemic species by taxonomic groups that are considered vulnerable (at risk of extinction) in California watersheds. “Insects and other invertebrates” includes the classes Arachnida, Branchiopoda, Insecta and Polychaeta.</p

Study area.

<p>The extent of the study area in California and the major hydrologic regions it contains. Inset shows the location of California in North America. Shaded relief is from “The National Map” by the U.S. Geological Survey.</p

Location of hotspots.

<p>Comparison of the location of hotspot watersheds (top 5% by richness) for A) listed species with all non-listed species, and B) vulnerable but non-listed species.</p

Patterns of richness and vulnerability of freshwater species endemic to California, watersheds.

<p>Maps of (A) the number of endemic freshwater species in each HUC12 watershed (includes current, historic, range and modeled data). The range of endemic species richness is shown in quintiles, therefore the darkest blue is the top 20% of species richness, the lightest blue the lowest 20%.; (; (B) percentage of endemic species considered vulnerable in each HUC12 watershed; and (C) percentage of endemic species in each HUC12 watershed that are listed as endangered or threatened under state or federal ESA lists. Maps in panels B and C share the legend on the right of the figure. The black lines on the maps represent the major hydrologic regions in the study area.</p

Patterns of freshwater species richness by taxonomic group.

<p>Maps show richness of: (A) fishes; (B) herpetofauna; (C) birds; (D) mollusks/crustaceans; (E) insects and other invertebrates; (F) plants.</p

Patterns of richness and vulnerability of freshwater species native to California watersheds.

<p>Maps of (A) the number of native freshwater species in each HUC12 watershed (includes current, historic, range and modeled data). The range of species richness is shown in quintiles, therefore the darkest blue is the top 20% of species richness, the lightest blue the lowest 20%.; (B) percentage of species in each HUC12 watershed that are ranked as vulnerable; and (C) percentage of species in each HUC12 watershed that are listed as endangered or threatened under state or federal ESA lists. Maps in panels B and C share the legend on the right of the figure. The black lines on the maps represent the major hydrologic regions in the study area.</p

Sources and criteria used to rank taxa.

<p>A taxon was classified as listed, vulnerable or apparently secure if one of the criteria conditions were met. For example, if a taxon is classified as endangered on the federal ESA list, we designated the taxon as “listed” in our database. Alternatively, if a taxon was classified as EN (endangered) in Moyle et al. 2011, we classified the taxon as “vulnerable” in our database.</p><p>Sources and criteria used to rank taxa.</p