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                  <text>C O L O R A D O

P A R K S

&amp;

W I L D L I F E

Native Cutthroat Trout
SEPTEMBER 2018

Rediscovery of the San Juan River basin’s native trout

© GRANT WILCOX/CPW

Nine years ago, the Greenback Cutthroat Trout Recovery Team commissioned a collaborative study by researchers
from the University of Colorado, along with state, and federal biologists to examine Cutthroat Trout specimens
collected in the late 1800s and housed in our nations most prestigious museums. The goal of that study was to
establish what the native range of these fish
was prior to European settlement. While
these trout look similar to each other in
outward appearance, inspection of their DNA
revealed that six discrete lineages historically
called Colorado home – essentially one in
each major drainage basin. Four lineages are
still found on the landscape today: two that
comprise Colorado River Cutthroat Trout
west of the Continental Divide, Greenback
Cutthroat Trout in the South Platte River
drainage, and Rio Grande Cutthroat Trout in
their namesake river basin. The authors

©KEVIN ROGERS/CPW

Distinct lineages of Cutthroat Trout evolved in six
major drainage basins in Colorado

Specimen collected from the San Juan River by C. E. Aiken
in 1874 (now at the National Museum of Natural History
in Washington D. C.)

reported that the remaining two lineages were thought
to be extinct: the Yellowfin Cutthroat Trout historically
found in the headwaters of the Arkansas River, and one
native to the San Juan River that was only known from
two specimens collected near Pagosa Springs during
the Wheeler Survey in 1874 while mapping the
territories in what is now the American southwest.

After learning that a previously unknown lineage of Cutthroat Trout was native to the San Juan basin, we launched an
intensive search to determine if any relict populations remained tucked away in the corners of the rugged San Juan
Mountains of southwest Colorado.

COLORADO PARKS &amp; WILDLIFE • 317 W. Prospect Rd., Fort Collins, CO 80526 • (970) 472-4432 • cpw.state.co.us

�Approach

©KEVIN ROGERS/CPW

Armed with new genetic markers with which to identify this San Juan lineage trout, we gathered tissue samples (fin
clips) from all known cutthroat trout populations in southwest Colorado. We isolated DNA and sequenced a specific
mitochondrial gene to identify any candidate fish that might have the same marker as those found in the museum
specimens. We then examined their
nuclear DNA to determine if any
Present day San Juan lineage trout from a small stream in the
hybridization had occurred with
headwaters of the San Juan River
Rainbow Trout or other subspecies of
Cutthroat Trout, or if they appeared
to be pure.

Results

•

•
•

Surveyed the 20 waters thought to
contain pure Cutthroat Trout in the
San Juan River basin
Eight of those waters harbored
populations containing the same
mitochondrial DNA marker found
in the two museum specimens
collected in 1874
Examination of nuclear DNA also
suggests they are a unique lineage
No evidence of hybridization with
Rainbow Trout or other nonnative
Cutthroat Trout lineages was detected

Colorado River (Blue)
Cu9hroat Trout

•

South Pla9e
San Juan
Colorado River (Green)
Rio Grande
Rainbow Trout

DNA tree comparing relatedness of Colorado’s native Cutthroat
Trout lineages (from map figure) to each other and Rainbow
Trout. Longer branches represent more distant relationships

Management implications
This represents an exciting conservation success story, and is testimony to the effectiveness of our recovery strategies
for preserving native trout diversity. Though genetic tools to distinguish these fish were not available until recently,
biologists recognized that hidden diversity was likely still out there, and protected populations accordingly. Our
conservation efforts will now focus on replicating these populations and securing them from invasion by nonnative
trout so that future generations can enjoy this rare piece of Colorado’s legacy.

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