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8 J. L. METCALF ET AL. 0.02 contemporary blue lineage were sampled from the Yampa and Colorado River drainages (one individual in each drainage). Of the seven museum samples that grouped with green lineage, five were sampled from the Colorado and Gunnison basins west of the Conti- nental Divide and two were sampled from Twin Lakes in the Arkansas River basin east of the Continental Divide. Comparison of historical and modern distribution of distinct lineages An analysis of molecular variance (AMOVA) revealed the amount of genetic variation distributed among drain- ages declined significantly since historical times (Fig. 6), highlighting the change in distribution of trout over the last century. Historically, the per cent of sequence varia- tion distributed by drainage was 64 %; by contrast, 95% (one- tailed) of values from modern data (subsampled to an equally small sample size as the museum data) ran- ged from 6 to 61% with a mean of 30 %. These results suggest several long- standing biogeographical barriers to gene flow were breached towards the end of the 19th century. The modern distribution of lineages shows some sim- ilarities and some important differences with the histor- ical phylogeography. The historical and modern ranges Fig. 5 Phylogenetic inference for the extant lineages of cutthroat trout in the arki Southern Rocky Mountains based on 430 by of mitochondrial DNA sequence data. The maximum - likelihood tree lc. lewisi shown was generated using PhyML. Branches were collapsed to a polytomy in cases where branching order conflicted with results from analyses using Baye- n Sian approaches in BEAST. Approximate likelihood -ratio test for branch support and Bayesian posterior probabilities are shown for all branches (only BPPs for the analysis incorporating a coalescent tree prior are shown). The sizes of trian- gles are proportional to the diversity present in each clade. O. mykiss are similar for the Rio Grande cutthroat trout (shown in orange in Figs 2 and 4). For the purple lineage, the only modern representative is currently restricted to a single stream within the Arkansas River basin (Bear Creek); by contrast, all historical samples were restricted to streams in the South Platte drainage. Because the museum samples from the Arkansas River basin were clearly divergent from the purple lineage, these results suggest that the lineage currently restricted to Bear Creek was originally native to the South Platte basin. The other two extant mtDNA lineages (green and blue) are both widely distributed today across multiple basins on both slopes of the Continental Divide. The blue line- age fish were historically restricted to one or two drain- age basins on the western slope of the Continental Divide. Today, they have been sampled from multiple localities in the Arkansas, South Platte, San Juan, Gunn- ison, Colorado and Yampa River basins (Table S5). The green lineage trout were sampled from three drainages in 1889, the Colorado, Gunnison and Arkansas River. Today, they are present in the Colorado, Gunnison, Arkansas and in the South Platte basin as well (Table S5). Discussion The diversity and distribution of cutthroat trout have changed dramatically over the last 150 years in the © 2012 Blackwell Publishing Ltd