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Molecular Ecology (2012) doi: 10.1111/mec.12028
<br />Historical stocking data and 19th century DNA reveal
<br />human - induced changes to native diversity and
<br />distribution of cutthroat trout
<br />J. L. METCALF, *j S. LOVE STOWELL,- C. M. KENNEDY,$ K. B. ROGERS,§ D. MCDONALD,¶
<br />J. EPP, ** K. KEEPERS,* A. COOPER, j J. J. AUSTIN j and A. P. MARTIN*
<br />*Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA, jAustralian Centre for
<br />Ancient DNA, University of Adelaide, Adelaide, SA 5005, Australia, JU.S. Fish and Wildlife Service, Colorado Fish and
<br />Wildlife Conservation Office, Estes Park, CO 80517, USA, §Aquatic Research Group, Colorado Parks and Wildlife, Steamboat
<br />Springs, CO 80477, USA, ¶Department of Chemistry & Biochemistry and Biofrontiers Institute, University of Colorado,
<br />Boulder, CO, USA, * *Pisces Molecular, LLC, Boulder, CO 80301, USA
<br />Abstract
<br />Many species are threatened with extinction and efforts are underway worldwide to
<br />restore imperilled species to their native ranges. Restoration requires knowledge of
<br />species' historical diversity and distribution. For some species, many populations were
<br />extirpated or individuals moved beyond their native range before native diversity and
<br />distribution were documented, resulting in a lack of accurate information for establish-
<br />ing restoration goals. Moreover, traditional taxonomic assessments often failed to accu-
<br />rately capture phylogenetic diversity. We illustrate a general approach for estimating
<br />regional native diversity and distribution for cutthroat trout in the Southern Rocky
<br />Mountains. We assembled a large archive of historical records documenting human -
<br />mediated change in the distribution of cutthroat trout (Oncorhynchus clarkii) and com-
<br />bined these data with phylogenetic analysis of 19th century samples from museums
<br />collected prior to trout stocking activities and contemporary DNA samples. Our study
<br />of the trout in the Southern Rocky Mountains uncovered six divergent lineages, two of
<br />which went extinct, probably in the early 20th century. A third lineage, previously
<br />declared extinct, was discovered surviving in a single stream outside of its native
<br />range. Comparison of the historical and modern distributions with stocking records
<br />revealed that the current distribution of trout largely reflects intensive stocking early
<br />in the late 19th and early 20th century from two phylogenetically and geographically
<br />distinct sources. Our documentation of recent extinctions, undescribed lineages, errors
<br />in taxonomy and dramatic range changes induced by human movement of fish under-
<br />scores the importance of the historical record when developing and implementing con-
<br />servation plans for threatened and endangered species.
<br />Keywords: ancient DNA, conservation genetics, greenback cutthroat trout, historical records,
<br />Oncorhynchus clarkii, phylogeography
<br />Received 16 December 2011; revision received 30 July 2012; accepted 3 August 2012
<br />Correspondence: Jessica L. Metcalf, Fax: 720 224 5522;
<br />E -mail: jessicalmetcalf @gmail.com and Andrew P. Martin,
<br />Fax: 303 325 1790; E -mail: am @colorado.edu
<br />© 2012 Blackwell Publishing Ltd
<br />Introduction
<br />The diversity and distribution of many taxa have
<br />changed dramatically over the last couple of centuries
<br />largely in response to human activities. Extirpation
<br />of populations has resulted in cases in which the con-
<br />temporary range underestimates the historical range
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