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10 1. L. METCALF ET AL. (a) —4000000 NumberofflshsWdad - 1000000 — soo 000 (b) ��: V 7— a Fig. 7 The effect of fish stocking on modern cutthroat trout dis- tribution. (A) Numbers of cutthroat trout stocked using two divergent lineages from different drainage basins (indicated by different colours) between 1899 and 1925. Colour schemes reflect new hypothesized historical distributions of native cut- throat trout lineages (see Figs 2 and 3). (B) Coloured circles represent genetic identification of cutthroat trout lineages in contemporary populations examined in this study (Table 54). Only populations without evidence of introgression between distinct clades of cutthroat trout are included. Colours corre- spond with those in the haplotype networks (Figs 2 and 4). Contemporary distribution of native Rio Grande trout can be found in Pritchard et al. (2009). stretch of a small stream (Bear Creek) within the Arkan- sas River basin above several natural barriers to upstream movement of fish. Historical records indicate that Bear Creek was originally fishless, but in 1882, an early homesteader had built a trout pond in the head- waters. With no state or federal hatcheries propagating native cutthroat trout at that time, fish would probably have been obtained from one of two private hatcheries both of which obtained their fish from a tributary of the South Platte drainage (Kennedy 2010). Ironically, while stocking contributed to the decline of native cutthroat trout throughout their range (Behnke 1992; Young 2009), it appears to have also inadvertently prevented the extinction of this unique lineage. Implications for taxonomy of Colorado's cutthroat trout Mitochondrial DNA sequence data support recognition of six divergent, native lineages of cutthroat trout Colo- rado. Although we acknowledge limitations inherent in using single gene trees to describe phylogeny, we did previously use clustering methods (Metcalf et al. 2007; Pritchard et al. 2009) to demonstrate nuclear support for extant lineages. Therefore, based on the historical and modern mitochondrial sequence data, we suggest a new working hypothesis for taxonomy of cutthroat trout in the Southern Rocky Mountains. In some cases, taxonomic inference is fairly straight- forward. The two haplotypes comprising the yellow lineage included the type specimen of O. c. macdonaldi, and thus most probably represents the Yellowfin cut- throat trout O. c. macdonaldi. Moreover, the lack of modern samples representing the O. c. macdonaldi clade confirmed reports from the early twentieth century documenting its extinction (Wiltzius 1985). Addition- ally, the phylogeography of the modern (see Pritchard et al. 2009) and historical data provide little doubt that O. c. virginalis, first described from the Rio Grande basin in 1853, is an evolutionarily distinct lineage. Finally, the native to the San Juan drainage does not fall into one of the four named lineages (Fig. 4A) and appears to have also gone extinct since historical times. This leaves three lineages for which taxonomy is less clear. The purple lineage was once restricted to the South Platte. Early taxonomists were clear that the designation O. c. stomias belonged to cutthroat trout native to the east side of the Continental Divide (Cope 1871; Jordan 1891; Cockerell 1908). With O. c. macdonaldi occupying the Arkansas River drainage, the name stomias reasonably falls to those fish of the South Platte drainage. Complicating the issue, however, is a misla- belling of locality information on O. c. stomias type specimens (suggested in Behnke 1976), which appear to have been collected near Santa Fe, New Mexico in 1855 —a belief confirmed by genetic data in this study (see results for ANSP 7825 and 7826) —and not in the Platte River. The error stems from mislabelled specimens many years later when the samples were designated O. c. stomias (Supporting Information). Therefore, it could also be argued that the name O. c. stomias is a diminutive, second name for Rio Grande cutthroat trout (O. c. virginalis), for which type specimens were collected in 1853 (Behnke 2002). We argue that the greenback cutthroat trout has been held as the native to the South Platte and Front Range of Colorado for over a century, and thus, the lineage native to the South Platte should keep the designation O. c. stomias. Indeed, as the first person to use the name greenback cutthroat trout to describe O. c. stomias, David Starr Jordan wrote that he 'adopted the name stomias for trout of the Platte' (Jordan 1891). This leaves two lineages (blue and green) for which there is a need for taxonomic resolution and perhaps 2012 Blackwell Publishing Ltd —4000000 NumberofflshsWdad - 1000000 — soo 000 (b) ��: V 7— a Fig. 7 The effect of fish stocking on modern cutthroat trout dis- tribution. (A) Numbers of cutthroat trout stocked using two divergent lineages from different drainage basins (indicated by different colours) between 1899 and 1925. Colour schemes reflect new hypothesized historical distributions of native cut- throat trout lineages (see Figs 2 and 3). (B) Coloured circles represent genetic identification of cutthroat trout lineages in contemporary populations examined in this study (Table 54). Only populations without evidence of introgression between distinct clades of cutthroat trout are included. Colours corre- spond with those in the haplotype networks (Figs 2 and 4). Contemporary distribution of native Rio Grande trout can be found in Pritchard et al. (2009). stretch of a small stream (Bear Creek) within the Arkan- sas River basin above several natural barriers to upstream movement of fish. Historical records indicate that Bear Creek was originally fishless, but in 1882, an early homesteader had built a trout pond in the head- waters. With no state or federal hatcheries propagating native cutthroat trout at that time, fish would probably have been obtained from one of two private hatcheries both of which obtained their fish from a tributary of the South Platte drainage (Kennedy 2010). Ironically, while stocking contributed to the decline of native cutthroat trout throughout their range (Behnke 1992; Young 2009), it appears to have also inadvertently prevented the extinction of this unique lineage. Implications for taxonomy of Colorado's cutthroat trout Mitochondrial DNA sequence data support recognition of six divergent, native lineages of cutthroat trout Colo- rado. Although we acknowledge limitations inherent in using single gene trees to describe phylogeny, we did previously use clustering methods (Metcalf et al. 2007; Pritchard et al. 2009) to demonstrate nuclear support for extant lineages. Therefore, based on the historical and modern mitochondrial sequence data, we suggest a new working hypothesis for taxonomy of cutthroat trout in the Southern Rocky Mountains. In some cases, taxonomic inference is fairly straight- forward. The two haplotypes comprising the yellow lineage included the type specimen of O. c. macdonaldi, and thus most probably represents the Yellowfin cut- throat trout O. c. macdonaldi. Moreover, the lack of modern samples representing the O. c. macdonaldi clade confirmed reports from the early twentieth century documenting its extinction (Wiltzius 1985). Addition- ally, the phylogeography of the modern (see Pritchard et al. 2009) and historical data provide little doubt that O. c. virginalis, first described from the Rio Grande basin in 1853, is an evolutionarily distinct lineage. Finally, the native to the San Juan drainage does not fall into one of the four named lineages (Fig. 4A) and appears to have also gone extinct since historical times. This leaves three lineages for which taxonomy is less clear. The purple lineage was once restricted to the South Platte. Early taxonomists were clear that the designation O. c. stomias belonged to cutthroat trout native to the east side of the Continental Divide (Cope 1871; Jordan 1891; Cockerell 1908). With O. c. macdonaldi occupying the Arkansas River drainage, the name stomias reasonably falls to those fish of the South Platte drainage. Complicating the issue, however, is a misla- belling of locality information on O. c. stomias type specimens (suggested in Behnke 1976), which appear to have been collected near Santa Fe, New Mexico in 1855 —a belief confirmed by genetic data in this study (see results for ANSP 7825 and 7826) —and not in the Platte River. The error stems from mislabelled specimens many years later when the samples were designated O. c. stomias (Supporting Information). Therefore, it could also be argued that the name O. c. stomias is a diminutive, second name for Rio Grande cutthroat trout (O. c. virginalis), for which type specimens were collected in 1853 (Behnke 2002). We argue that the greenback cutthroat trout has been held as the native to the South Platte and Front Range of Colorado for over a century, and thus, the lineage native to the South Platte should keep the designation O. c. stomias. Indeed, as the first person to use the name greenback cutthroat trout to describe O. c. stomias, David Starr Jordan wrote that he 'adopted the name stomias for trout of the Platte' (Jordan 1891). This leaves two lineages (blue and green) for which there is a need for taxonomic resolution and perhaps 2012 Blackwell Publishing Ltd