Whitefish Biology, Distribution, and Fisheries in the Yukon and Kuskokwim River Drainages in Alaska

330 Pages·2012·8.18 MB·English

by  Bill Spearman

U.S. Fish & Wildlife Service
Whitefish Biology, Distribution, and Fisheries
in the Yukon and Kuskokwim River Drainages
in Alaska: a Synthesis of Available Information
Alaska Fisheries Data Series Number 2012-4

Fairbanks Fish and Wildlife Field Office
Fairbanks, Alaska
May 2012
The Alaska Region Fisheries Program of the U.S. Fish and Wildlife Service conducts
fisheries monitoring and population assessment studies throughout many areas of
Alaska. Dedicated professional staff located in Anchorage, Fairbanks, and Kenai
Fish and Wildlife Offices and the Anchorage Conservation Genetics Laboratory serve
as the core of the Program’s fisheries management study efforts. Administrative and
technical support is provided by staff in the Anchorage Regional Office. Our program
works closely with the Alaska Department of Fish and Game and other partners to
conserve and restore Alaska’s fish populations and aquatic habitats. Our fisheries
studies occur throughout the 16 National Wildlife Refuges in Alaska as well as off-
Refuges to address issues of interjurisdictional fisheries and aquatic habitat
conservation. Additional information about the Fisheries Program and work
conducted by our field offices can be obtained at:

http://alaska.fws.gov/fisheries/index.htm
The Alaska Region Fisheries Program reports its study findings through the Alaska
Fisheries Data Series (AFDS) or in recognized peer-reviewed journals. The AFDS
was established to provide timely dissemination of data to fishery managers and
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archive detailed study designs and results for the benefit of future investigations.
Publication in the AFDS does not preclude further reporting of study results through
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Cover: Six common whitefish species in the Yukon and Kuskokwim River drainages
in Alaska (photo credit: R.J. Brown, USFWS).
Disclaimer: The use of trade names of commercial products in this report does not
constitute endorsement or recommendation for use by the federal government.
Alaska Fisheries Data Series Number 2012-4
U.S. Fish and Wildlife Service

Whitefish Biology, Distribution, and Fisheries in the
Yukon and Kuskokwim River Drainages in Alaska:
a Synthesis of Available Information

Randy J. Brown1, Caroline Brown2, Nicole M. Braem2,
William K. Carter III1, Nicole Legere1, and Lisa Slayton2
Abstract
Whitefish species in Alaska are subject to intensive subsistence fisheries
everywhere they occur, commercial fisheries in certain places, and limited sport
fisheries. Our understanding of whitefish biology comes primarily from studies
of the same or similar species in other places, although some biological studies
have taken place locally. Whitefish fisheries in the Yukon and Kuskokwim River
drainages in Alaska have been documented in numerous anthropological and
social science publications and in subsistence harvest surveys, but usually without
species distinctions. Scientific sampling work since the 1960s has been
reasonably effective at describing the species that are present and their
distributions within the two drainages, but our understanding of populations,
migrations, and demographic distribution among habitats is poor. We are just
beginning to understand that major spawning migrations into upstream reaches of
the drainage occur each summer and fall, juvenile and non-spawning fish
dominate the lower reaches of both rivers and the coastal areas, and mature and
spawning fish dominate the upper reaches. A small number of whitefish
spawning areas have been identified in gravel substrate reaches of main-stem and
tributary rivers in both turbid and clear water. Genetics work with whitefish
species has focused more on taxonomy and biogeography issues than for
management applications. With two exceptions in the entire Yukon and
Kuskokwim River drainages, population abundance data are absent. Our ability
to protect essential habitats for whitefish populations is growing with the
improved understanding of their spawning destinations and life histories. Our
ability to monitor whitefish population trends and to make effective harvest
regulations, however, is very limited at this point.
In the following manuscript we provide an overview of the whitefish and
whitefish fisheries in the Yukon and Kuskokwim River drainages in Alaska. The
geography and aquatic habitat qualities of the two drainages are explored in
detail. The taxonomy of whitefish species present in the drainage is discussed.
We introduce a selection of important biological qualities of whitefish species, as

1 U.S. Fish and Wildlife Service, Fairbanks Fish and Wildlife Field Office
2 Alaska Department of Fish and Game, Subsistence Division
Randy J. Brown can be contacted by e-mail at <[email protected]>.

Caroline Brown can be contacted by e-mail at <[email protected]>.
Alaska Fisheries Data Series Number 2012-4
U.S. Fish and Wildlife Service

documented in the literature. The nature of the many fisheries on whitefish
species is described based on individual community studies and regional harvest
surveys. Threats to whitefish populations, as identified in two meetings of
delegates from a wide range of experience with whitefish harvest, research, and
management, are critically examined. These include threats that may arise from
overharvest of fishery resources, from habitat destruction that may occur during
development activities, and from natural environmental changes. We then review
the current state of knowledge of whitefish populations, distribution, and life
history within the study area. Information that would improve our ability to
protect essential habitats, monitor the abundance of whitefish populations, obtain
harvest estimates, and establish reasonable and effective harvest regulations are
identified. Finally, a general approach to research of whitefish populations is
outlined and a number of specific research concepts and project ideas are
recommended for the four species we thought most likely to be impacted by
human activities.
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Table of Contents
Abstract ...................................................................................................................................... i
Table of Contents ..................................................................................................................... iii
List of Tables ........................................................................................................................... vi
List of Figures ......................................................................................................................... vii
List of Appendices ................................................................................................................... xi
Introduction ............................................................................................................................... 1
Study Area ................................................................................................................................ 4
Methods..................................................................................................................................... 9
Taxonomy ............................................................................................................................... 10
Biology and Life History ........................................................................................................ 13
Spawning season ................................................................................................................. 15
Fecundity and egg biology .................................................................................................. 17
Spawning areas ................................................................................................................... 18
Maturity and spawning readiness........................................................................................ 20
Minimum length at maturity ............................................................................................... 24
Aging, minimum age at maturity, and longevity ................................................................ 26
Spawning frequency............................................................................................................ 31
Food preferences ................................................................................................................. 33
Fisheries (Subsistence, Commercial, Sport) ........................................................................... 36
Potential Threats and Concerns .............................................................................................. 39
Harvest and fishery related issues ....................................................................................... 40
Development issues ............................................................................................................ 48
Minerals mining .............................................................................................................. 48
Streambed gravel mining ................................................................................................ 49
Logging ........................................................................................................................... 50
Roads............................................................................................................................... 51
Contaminants and hazardous material spills ................................................................... 52
Dams and water control .................................................................................................. 54
Development conclusion ................................................................................................. 55
Natural environmental issues .............................................................................................. 57
Climate change................................................................................................................ 57
Beaver dams .................................................................................................................... 62
Yukon River Main-Stem Habitat Region ............................................................................... 66
Whitefish species, distribution, and biology ....................................................................... 66
Fisheries .............................................................................................................................. 80
Culture and language ...................................................................................................... 81
Harvest and use ............................................................................................................... 82
Potential threats and concerns ............................................................................................. 86
Overfishing ..................................................................................................................... 86
Development issues ........................................................................................................ 87
Innoko River Habitat Region .................................................................................................. 89
Whitefish species, distribution, and biology ....................................................................... 91
Fisheries .............................................................................................................................. 93
Culture and language ...................................................................................................... 94
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Harvest and use ............................................................................................................... 95
Potential threats and concerns ............................................................................................. 98
Overfishing ..................................................................................................................... 98
Development issues ........................................................................................................ 98
Koyukuk River Habitat Region ............................................................................................ 100
Whitefish species, distribution, and biology ..................................................................... 100
Fisheries ............................................................................................................................ 104
Culture and language .................................................................................................... 105
Harvest and use ............................................................................................................. 105
Potential threats and concerns ........................................................................................... 108
Overfishing ................................................................................................................... 108
Development ................................................................................................................. 108
Nowitna River Habitat Region.............................................................................................. 111
Whitefish species, distribution, and biology ..................................................................... 113
Fisheries ............................................................................................................................ 117
Culture and language .................................................................................................... 117
Harvest and use ............................................................................................................. 118
Potential threats and concerns ........................................................................................... 119
Overfishing ................................................................................................................... 119
Development ................................................................................................................. 119
Tanana River Habitat Region................................................................................................ 121
Whitefish species, distribution, and biology ..................................................................... 124
Fisheries ............................................................................................................................ 132
Culture and language .................................................................................................... 133
Harvest and use ............................................................................................................. 134
Potential threats and concerns ........................................................................................... 137
Overfishing ................................................................................................................... 137
Development ................................................................................................................. 139
Upper Yukon River Habitat Region ..................................................................................... 144
Whitefish species, distribution, and biology ..................................................................... 150
Fisheries ............................................................................................................................ 162
Culture and language .................................................................................................... 163
Harvest and use ............................................................................................................. 164
Local issues and concerns ............................................................................................. 167
Potential threats and concerns ........................................................................................... 168
Overfishing ................................................................................................................... 168
Development issues ...................................................................................................... 169
Kuskokwim River Habitat Region ........................................................................................ 172
Whitefish species, distribution, and biology ..................................................................... 174
Fisheries ............................................................................................................................ 183
Culture and language .................................................................................................... 185
Lower Kuskokwim........................................................................................................ 186
Central Kuskokwim ...................................................................................................... 188
Upper Kuskokwim ........................................................................................................ 190
Potential threats and concerns ........................................................................................... 193
Overfishing ................................................................................................................... 193
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Development ................................................................................................................. 194
Coastal Habitat Region ......................................................................................................... 198
Whitefish species, distribution, and biology ..................................................................... 201
Fisheries ............................................................................................................................ 205
Southern coastal area .................................................................................................... 205
Culture and language ................................................................................................ 205
Harvest and use ......................................................................................................... 205
Material technology .................................................................................................. 208
Northern coastal area .................................................................................................... 209
Culture and language ................................................................................................ 209
Harvest and use ......................................................................................................... 209
Local issues and concerns ......................................................................................... 210
Possible threats and concerns............................................................................................ 212
Overfishing ................................................................................................................... 212
Development issues ...................................................................................................... 214
Research Recommendations ................................................................................................. 216
Inconnu ............................................................................................................................. 217
Broad whitefish ................................................................................................................. 220
Humpback whitefish ......................................................................................................... 223
Bering cisco ...................................................................................................................... 226
Acknowledgements ............................................................................................................... 231
References ............................................................................................................................. 232
Appendices A1 Through A7 ................................................................................................. 287
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List of Tables
Table 1. Native freshwater and anadromous fish species present in the Yukon and
Kuskokwim River drainages ......................................................................................... 2
Table 2. Select life history qualities of the six common whitefish species in the Yukon and
Kuskokwim River drainages in Alaska....................................................................... 13
Table 3. Citation list for biological data presented in Table 2. ............................................... 15
Table 4. An order-of-magnitude scale estimate of annual whitefish subsistence harvests in
interior Alaska communities ....................................................................................... 37
Table 5. Estimated sport fishery harvest of inconnu in the Yukon and Kuskokwim drainages
..................................................................................................................................... 38
Table 6. Deg Xinag and Holikachuk terminology for whitefish species ................................ 82
Table 7. Estimated harvest of whitefish species in Emmonak................................................ 83
Table 8. Estimated harvest of whitefish species in kg (pounds below) by GASH communities
..................................................................................................................................... 84
Table 9. Estimated harvest of whitefish species by residents of middle Yukon River
communities ................................................................................................................ 85
Table 10. Estimated number and weight of whitefish harvested in Shageluk ........................ 97
Table 11. Common, Linnaean, Koyukon, and Inupiaq names for whitefish species
encountered by residents of the Koyukuk River in interior Alaska .......................... 105
Table 12. Estimated harvest of whitefish species in Koyukuk River communities .............. 107
Table 13. Length data for mature male and female inconnu from populations in the Yukon
River drainage. .......................................................................................................... 154
Table 14. Terms for whitefish species in the Yukon Flats region ........................................ 163
Table 15. Estimated harvest of whitefish species in Yukon Flats communities ................... 165
Table 16. Terms for whitefish in the Kuskokwim River main stem. .................................... 185
Table 17. Estimated harvest of whitefish species by lower Kuskokwim River communities
................................................................................................................................... 186
Table 18. Estimated harvest of whitefish species in Kwethluk and Akiachak ..................... 187
Table 19. Estimated harvest of whitefish in Aniak and Chuathbaluk ................................... 190
Table 20. Terms for whitefish species in the Yukon Kuskokwim Delta. ............................. 206
Table 21. Timing of whitefish harvests in Yukon Kuskokwim Delta communities ............ 207
Table 22. English, Linnaean, and common Iñupiaq terms for whitefish species in the northern
coastal area. ............................................................................................................... 209
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List of Figures
Figure 1. The Yukon and Kuskokwim River drainages in Alaska and Yukon Territory. ........ 5
Figure 2. Photographs of the Kanuti lake district in the upper Koyukuk River drainage and in
the Yukon Kuskokwim Delta lake district. ................................................................... 7
Figure 3. Two examples of upland lakes: Helpmejack Lake in the upper Koyukuk River
drainage and unnamed lakes in the recently burned foothills of the White Mountain in
the southern Yukon Flats .............................................................................................. 7
Figure 4. We recognize six common whitefish species in the Yukon and Kuskokwim River
drainages in Alaska ..................................................................................................... 11
Figure 5. Hybrid whitefish forms from the Yukon River drainage in Alaska ........................ 12
Figure 6. Residual or atretic eggs in a gravid female Bering cisco and pearl tubercles on a
humpback whitefish preparing to spawn. ................................................................... 21
Figure 7. Gonadosomatic indices for female whitefish sampled throughout the summer in the
upper Yukon River ...................................................................................................... 22
Figure 8. Egg skeins of female inconnu preparing to spawn become very enlarged in the late
summer and fall while those of female inconnu that are not preparing to spawn
remain small. ............................................................................................................... 23
Figure 9. Gonadosomatic index values from broad whitefish harvested in the Selawik River
delta in September plotted against age and length ...................................................... 23
Figure 10. Microscopic image of a transverse sectioned otoliths illustrating how annuli are
counted and the occurrence of capping in older fish. ................................................. 27
Figure 11. Transverse sectioned otolith images from some of the oldest individual whitefish
observed in Alaska ...................................................................................................... 30
Figure 12. Mouthparts of whitefish species are good indicators of their primary feeding
strategies ..................................................................................................................... 34
Figure 13. Gill rakers are also good indicators of primary feeding strategies of whitefish
species ......................................................................................................................... 35
Figure 14. An aerial image of the Bear Creek mine in the Hogatza River drainage, Yukon
River basin .................................................................................................................. 49
Figure 15. Streambed gravel mining with dragline dredges is a common practice in the
Yukon and Kuskokwim River drainages .................................................................... 50
Figure 16. Airboat and all-terrain vehicle trails across the Tanana River flats south of
Fairbanks ..................................................................................................................... 51
Figure 17. Images of the Trans-Alaska Pipeline shooting incident near Livengood, Alaska,
and a leaking fuel oil tank in Eagle, Alaska ................................................................ 53
Figure 18. Aerial images of two common types of industrial fuel spills ................................ 53
Figure 19. The hydroelectric dam on the Yukon River at the community of Whitehorse,
Yukon Territory, and a fish ladder completed in 1959 to facilitate fish migration past
the dam. ....................................................................................................................... 56
Figure 20. Two dams within the Tanana River drainage ........................................................ 56
Figure 21. A drying lake in Minto Flats, Tanana River drainage. .......................................... 58
Figure 22. A lake system in the northern Yukon Flats with a stable connection to the
Christian River and a drying lake in the southern Yukon Flats that no longer
maintains a stream connection to Birch Creek ........................................................... 61
Figure 23. Sediment flows following natural environmental events ...................................... 63
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Figure 24. A beaver dam across American Creek, a small stream in the upper Yukon River
drainage in Alaska, and another that appears to be blocking fish passage across an
floodplain oxbow ........................................................................................................ 63
Figure 25. The Yukon River main-stem habitat region including major tributaries and
communities. ............................................................................................................... 67
Figure 26. The Yukon River delta illustrating the layout of the major distributaries and
landforms. ................................................................................................................... 67
Figure 27. A remote, radio receiving station located high on a bluff along the Yukon River 71
Figure 28. Ten years of cumulative CPUE data at Rapids, a sampling site approximately
1,176 km (731 miles) from the Yukon River mouth .................................................. 73
Figure 29. Catch per day of inconnu and Bering cisco during 10 summers of sampling at
Rapids revealing annual spawning migration timing .................................................. 75
Figure 30. Catch per day of broad whitefish and humpback whitefish during 10 summers of
sampling at Rapids revealing annual spawning migration timing .............................. 76
Figure 31. Length distributions of female and male Bering cisco sampled from the spawning
migration at Rapids and the commercial fishery at the mouth of the Yukon River ... 78
Figure 32. Age distributions of female and male Bering cisco sampled from the spawning
migration at Rapids and the commercial fishery at the mouth of the Yukon River ... 79
Figure 33. Gonadosomatic indices of mature Bering cisco preparing to spawn and from the
commercial fishery at the mouth of the Yukon River................................................. 80
Figure 34. The Innoko River habitat region in western interior Alaska ................................. 90
Figure 35. Looking upstream at the confluence of the Innoko and Iditarod rivers in the
Innoko River flats ....................................................................................................... 91
Figure 36. Looking downstream into the inconnu spawning reach in the upper Innoko River
..................................................................................................................................... 92
Figure 37. Raymond Dutchman of Shageluk maps important habitat and harvest sites for
non-salmon fish species with Caroline Brown ........................................................... 94
Figure 38. Lucy Hamilton of Shageluk making a net while visiting with a neighbor. ........... 96
Figure 39. A Shageluk family checks a whitefish trap in front of a fish fence. ..................... 96
Figure 40. Set net by Shagleuk in 2004. ................................................................................. 97
Figure 41. Heavily mined streambeds in Colorado and Ophir Creek valleys in the upper
Innoko River drainage................................................................................................. 99
Figure 42. The Koyukuk River habitat region in interior Alaska ......................................... 101
Figure 43. Late September view of spawning habitat for inconnu and other whitefish species
on the Alatna River. .................................................................................................. 103
Figure 44. Sithylemenkat Lake, an upland lake in the Kanuti River drainage ..................... 104
Figure 45. The Nowitna River habitat region in western interior Alaska ............................. 112
Figure 46. Looking upstream at inconnu spawning habitat in the Sulukna River and the
DIDSON sonar station located downstream ............................................................. 115
Figure 47. Length and age distributions of mature male and female inconnu from the Sulukna
River spawning population ....................................................................................... 116
Figure 48. Caroline Brown maps traditional fishing sites with Martha Wright ................... 117
Figure 49. Mouth of the Nowitna River................................................................................ 118
Figure 50. The Tanana River habitat region in interior Alaska ............................................ 121
Figure 51. Characteristic images of the lower Tanana River, downstream from the Nenana
River, and the braided reach between the Chena and Delta River mouths ............... 123
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