Historical stocking data and 19th century DNA reveal human-induced changes to native diversity and distribution of cutthroat trout

Mol Ecol. 2012 Nov;21(21):5194-207. doi: 10.1111/mec.12028. Epub 2012 Sep 24.


Many species are threatened with extinction and efforts are underway worldwide to restore imperilled species to their native ranges. Restoration requires knowledge of species' historical diversity and distribution. For some species, many populations were extirpated or individuals moved beyond their native range before native diversity and distribution were documented, resulting in a lack of accurate information for establishing restoration goals. Moreover, traditional taxonomic assessments often failed to accurately capture phylogenetic diversity. We illustrate a general approach for estimating regional native diversity and distribution for cutthroat trout in the Southern Rocky Mountains. We assembled a large archive of historical records documenting human-mediated change in the distribution of cutthroat trout (Oncorhynchus clarkii) and combined these data with phylogenetic analysis of 19th century samples from museums collected prior to trout stocking activities and contemporary DNA samples. Our study of the trout in the Southern Rocky Mountains uncovered six divergent lineages, two of which went extinct, probably in the early 20th century. A third lineage, previously declared extinct, was discovered surviving in a single stream outside of its native range. Comparison of the historical and modern distributions with stocking records revealed that the current distribution of trout largely reflects intensive stocking early in the late 19th and early 20th century from two phylogenetically and geographically distinct sources. Our documentation of recent extinctions, undescribed lineages, errors in taxonomy and dramatic range changes induced by human movement of fish underscores the importance of the historical record when developing and implementing conservation plans for threatened and endangered species.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Conservation of Natural Resources
  • DNA, Mitochondrial / genetics
  • Genetics, Population*
  • Humans
  • Molecular Sequence Data
  • Oncorhynchus / genetics*
  • Phylogeny*
  • Phylogeography
  • Sequence Analysis, DNA
  • Southwestern United States


  • DNA, Mitochondrial

Associated data

  • GENBANK/JX195488
  • GENBANK/JX195489
  • GENBANK/JX195490
  • GENBANK/JX195491
  • GENBANK/JX195492
  • GENBANK/JX195493
  • GENBANK/JX195494
  • GENBANK/JX195495
  • GENBANK/JX195496
  • GENBANK/JX195497