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4 J. L. METCALF ET AL. p d 800 v 700 -State and federal stocking p Private stocking H 600 to Cutthroat trout 'a y 500 Rainbow trout p Brook trout 2 400 H E 300 w " — 0 i— zoo i 100 o z o 1840 1860 1880 1900 1920 1940 1960 Fig. 3 Cumulative numbers (in millions of fish) of cutthroat trout, rainbow trout and brook trout stocked in Colorado waters from 1885 to 1953 by state and federal agencies. Private interests also stocked fish around the state, but their efforts were generally smaller in scale, and much less well docu- mented. Dates of museum collections used in this study are indicated by arrowheads. stocked throughout the state. Production of native cut- throat trout by federal fish biologists began in 1899 at the Grand Mesa Lakes region of the Gunnison River basin in Colorado. By 1909, that effort alone produced 29 000 000 trout in 798 lots that were stocked into lakes and streams of all major drainages on both the Pacific and Atlantic slopes in the state of Colorado. Stocking of Gunnison River basin trout across the state continued until 1931. In 1903, a second source of native cutthroat trout, also from the western slope of the Continental Divide (Trappers Lake), was brought into the hatchery system and propagated until 1938. For the period 1914- 1925 when the stocking data were most complete, over 26 000 000 fish were stocked in 989 different lots to tributaries of all major drainages across the state. By contrast, cutthroat trout native to the east slope of the Continental Divide (O. c. stomias) were rarely used for large -scale hatchery broodstock. Importantly, many cutthroat trout were stocked into habitats that were originally fishless, usually above waterfalls that served as barriers to upstream movement of fish (Fausch et al. 2009). Therefore, the signal of the native phylogeogra- phy may have been erased by extirpation of native populations coupled with widespread stocking of wes- tern slope cutthroat trout in high alpine lakes and streams on both slopes of the Continental Divide. The stocking records suggest that the cutthroat trout lin- eages that are widespread today may be descendents of ancestors derived from two major drainages —the Gunnison and the Yampa —of Colorado's western slope. The absence of commensurate large -scale hatchery production of native cutthroat trout (O. c. stomias and O. c. macdonaldi) east of the Continental Divide in Colorado meant that similar reservoirs of genetic diversity may not have been available to buffer native trout declines in the Arkansas and South Platte basins. In this study, we use DNA recovered from 19th century museum specimens of cutthroat trout to test three hypotheses about the native diversity and distri- bution of cutthroat trout in the Southern Rocky Moun- tains and how it has changed in recent times. First, we test the prevailing view that cutthroat trout diversity includes four divergent and distinct lineages within Colorado corresponding to the four named subspecies (1-11). Also in line with prevailing view, we test that divergent lineages were largely confined to major drain- age basins: O. c. pleuriticus to the San Juan, Gunnison, Colorado, Yampa and Green River drainages west of the Continental Divide; O. c. stomias to the Arkansas and South Platte east of the Continental Divide; O. c. macdonaldi was restricted to a pair of lakes in the upper Arkansas Basin; and O. c. virginalis to waters in the Rio Grande River drainage basin east of the Conti- nental Divide (H2). Finally, based on the historical stocking data, we test that the current distribution of cutthroat trout subspecies differs markedly from the historical distribution, with trout native to the western slope of the Continental Divide becoming widespread beyond their native range (1-13). Methods Museum specimen tissue collection, DNA extraction and sequence generation Skin, gill, muscle and bone were sampled from cut- throat trout specimens stored in ethanol and housed at the California Academy of Sciences, Smithsonian Museum of Natural History, the Academy of Natural Sciences in Philadelphia and the Museum of Compara- tive Zoology at Harvard University (Table Sl). Because intensive propagation and stocking of native trout began in earnest with state and federally operated hatcheries as early as 1885, with efforts expanding considerably in the very early years in the first decade of twentieth century, we focused our efforts on securing samples collected prior to the first decade of twentieth century. We note that a low -level of propagation and movement of trout by private interests probably began by the 1870s. We sampled specimens collected between the years 1857 and 1889 across seven drainage basins in Colorado and New Mexico: South Platte, Arkansas, Rio Grande, San Juan, Gunnison, Colorado and Yampa River drainage basins (Table 1). Collection locality details and notes were recorded (Table S1). As some museum specimens were collected after fish stocking activities initiated, albeit at a scale much lower than in the 20th century, some uncertainty in their native status © 2012 Blackwell Publishing Ltd