U.S. Dept Commerce/NOAA/NMFS/NWFSC/Publications Tech Memo-15: Status Review for Oregon's Umpqua River Sea-Run Cutthroat Trout DISCUSSION
In this section, we address the two key questions raised at the start of this status review: Do North and South Umpqua River sea-run cutthroat trout represent a species as defined by the ESA and NMFS policy? and, if so, is the species threatened or endangered? We begin by summarizing evidence developed in the status review on the two criteria that must be met for a population to be considered an ESU, and hence a species under the ESA: reproductive isolation and contribution to ecological / genetic diversity.
Reproductive Isolation
Relationship Between Different Life-History Forms 

A recurrent issue throughout this status review has been the relationship of the various life-history forms of cutthroat trout. Across their range, cutthroat trout are well known to occur in two life-history forms: anadromous and resident. A third, lesser known form, termed river migrating or potamodromous, has been described in the Willamette and Rogue Rivers. There is also evidence that potamodromous cutthroat trout occur in the Umpqua River system.
Figure 9. Some possible interactions of three cutthroat trout life-history forms
A key question in this status review is, Are these alternative life-history forms of O. clarki reproductively isolated within the Umpqua River, or are they part of the same gene pool? According to NMFS policy on this issue, anadromous and nonanadromous forms can be considered separately under the ESA if they are reproductively isolated, but they should be considered together if they are not. Figure 9 shows some possible relationships between forms of O. clarki in the Umpqua River that range from panmixia to complete reproductive isolation. In the latter case, the different forms represent distinct gene pools; in the former, the forms represent polymorphisms within a single gene pool. Between these extremes are a range of intermediate scenarios in which there is partial reproductive isolation (but also partial gene flow) between the three forms. 

Both resident and anadromous life-history forms have been identified in other species of salmonids (e.g., Arctic char, brown trout, rainbow trout Atlantic salmon, and sockeye salmon), In these species, it has generally been found that although alternative life-history forms may be genetically distinct within a local area, they are more similar to one another than they are to their respective forms outside of the local area.

There have been no comparable studies for O. clarki. However, there are a number of factors related to life-history traits of cutthroat trout that suggest that the opportunities for genetic exchange between anadromous and nonanadromous forms may be greater than is generally believed to be the case for other Oncorhynchus species: 1) Sea-run cutthroat trout do not always die after spawning (as do Pacific salmon), and it is generally believed that the incidence of repeat spawning in anadromous cutthroat trout is higher than in steelhead. 2) Unlike species of Pacific salmon and steelhead, sea-run cutthroat trout do not overwinter at sea; rather, it is believed that they return to fresh water each year after only a few months, or even weeks, at sea. 3) It is thought that some cutthroat trout that have gone to sea and returned may spend an entire year (or more) in fresh water before migrating to sea again. 4) A cutthroat trout may spend as much as 5 years in fresh water before migrating to the sea. 5) Evidence suggests that the different life-history forms of O. clarki utilize similar spawning habitat. 6) The potamodromous form may provide a link that retards divergence between anadromous and resident fish.

Returning to an evaluation of the three scenarios depicted in Figure 9, we concluded that the various life-history features discussed above suggest it is unlikely that there is complete reproductive isolation between anadromous, resident, and potamodromous forms of cutthroat trout in the Umpqua River. However, based on information available from studies on anadromous / nonanadromous forms in other species (see section Genetic Studies on Life-History Forms in Other Species), there is also little reason to believe that matings among the three forms are completely random. Therefore we conclude that partial gene flow between the life-history forms is the most likely scenario. The extent of the reproductive overlap is unknown but could be substantial. Therefore, at least until better information is developed, the resident, potamodromous, and anadromous forms should be considered together under the ESA. The following discussion considers all forms of Umpqua River O. clarki as a unit.
Reproductive Isolation of Umpqua River O. clarki
There are no genetic or tagging data directly relevant to this issue. However, data for anadromous cutthroat trout from Puget Sound and coastal Oregon suggest some genetic structuring at the level of local populations and strong isolation of some geographic areas. Spawning sites of presumed anadromous O. clarki in the North Umpqua River are a considerable distance from the ocean (240 km or more), suggesting the possibility for strong isolation. Resident forms of O. clarki in the Umpqua River also probably have little contact at present with conspecifics from outside the Basin . Furthermore, temperature data from the Umpqua River estuary suggest that the lower part of the mainstem is too warm during much of the summer for cutthroat trout, and may act as an isolating mechanism. Therefore, we concluded that available evidence supports the hypothesis that Umpqua River O. clarki as a group satisfy the first criterion to be an ESU: substantial reproductive isolation from other conspecific populations.
Ecological and Genetic Diversity
The second criterion to be considered an ESU is that Umpqua River cutthroat trout contribute substantially to ecological/genetic diversity of the biological species. Evidence in support of this criterion includes a lengthy freshwater migration for the anadromous form, possible adaptations for dealing with high water temperatures, distinctive run times, and distinctive physical and environmental features of the Umpqua River drainage.
Physical and Environmental Features of the Umpqua River Basin
The mainstem Umpqua River and its two major tributaries, the North and South Umpqua Rivers, form one of the longest coastal basins in Oregon, approximately 340 km in length, with a drainage area of over 12,200 km2. The North Umpqua River has historically had lower water-temperatures and larger summer water flows than most other Oregon coastal rivers because it begins farther inland and flows for a greater distance at a higher elevation than the other rivers. Because of these factors, the North Umpqua River contained a large and diverse salmonid population. The South Umpqua River also begins at a high elevation, but rapidly descends; it has always had higher water temperatures and a lower summer flow than the North Umpqua River.

Beginning in the mid-1950s, summer water temperatures and the frequency of winter flooding increased in the Umpqua River watershed due in part to removal of riparian cover and to other poor forestry practices in the basin . Summer water temperatures were often above the preferred limit for cutthroat trout in portions of the river. In recent years, the riparian forest canopy has begun to recover in the North Umpqua River watershed, but maximum water temperatures are still higher than those preferred by cutthroat trout and other salmonids.
Distance of Freshwater Migration
Anadromous cutthroat trout that spawn in the upper tributaries of the North and South Umpqua Rivers migrate farther inland (240 to 280 km) than do cutthroat trout from most other rivers in North America. In most medium-sized coastal streams such as the Nestucca, Siletz, or Naselle Rivers, sea-run cutthroat trout spawn within 90 km of the coast; even in the Rogue River, Tomasson (1978) concluded that only rarely, if at all, do anadromous trout migrate above RKm 104. Only in the Columbia, Fraser, and perhaps the Skeena Rivers are cutthroat trout reported to migrate distances comparable to that in the Umpqua River (P. Trotter, see footnote 1)
Run Times and Water Temperatures
A bimodal peak of run times is not unique to sea-run cutthroat trout from the Umpqua River, but historically the timing of each of the peaks at Winchester Dam occurred earlier than in other streams. Early returning cutthroat trout (July through November) are characteristic of large river systems, but the combination of the late- July and mid-October peaks counted passing Winchester Dam in the 1940s and early 1950s appeared to be earlier than in other river systems.

The cause of the earlier run-timing of Umpqua River sea-run cutthroat trout is not known, but it has been suggested that high summer water-temperatures may be a factor. The petitioners argue that 1) Umpqua River cutthroat trout have unique physiological adaptations to withstand the high summer temperatures in the river, and 2) their unique timing of adult migration can be attributed to high water- temperatures that block upstream passage at certain times of the year. Thus, the petitioners argue both that cutthroat trout in the Umpqua River are adapted to the elevated water temperatures now common in the river, and have evolved behavioral mechanisms to avoid lethally high river temperatures found at certain times of the year.

Due to cool water and consistently high summer flows originating in the upper North Umpqua River watershed, the Umpqua River did not historically experience as high water temperatures as did other coastal streams in Oregon. Since the extensive clear-cut logging that occurred in the Basin during the mid-1950s, maximum summer water temperatures in certain sections of the Umpqua River Basin have exceeded the preferred, and even lethal, temperatures for cutthroat trout. By the mid-1970s, the stream canopy had begun to recover, and water temperatures, although still high, were no longer increasing.

Thus, it is unclear whether elevated water temperatures have played an important role in promoting adaptations of cutthroat trout within the Umpqua River Basin. The occurrence of unusually high water-temperatures in the upper Basin appears to be a relatively recent phenomenon that is unlikely to have substantially affected the evolutionary history of the population. Water temperature data for the upper Basin also do not support the hypothesis that the bimodal peak in run times of Umpqua River sea-run cutthroat trout is caused by inhospitably warm water in the period between the runs. Maximum water temperatures at Winchester Dam during September (the time between peak runs) was consistently lower than in July or August over the period 1946-1992 (Fig. 5). Finally, Alsea River hatchery fish released below Winchester Dam in the 1960s and early 1970s apparently were able to return to the dam as adults in spite of some of the highest maximum water temperatures recorded in the Basin.

Water temperature may, however, be a significant factor affecting cutthroat trout in other parts of the Umpqua River Basin. In contrast to its northern counterpart, the South Umpqua River historically experienced high summer water temperatures (Roth 1937, FCO and GCO 1946, Lauman et al. 1972), which are believed to be caused by lower overall elevation, little or no spring/summer snow pack, less-porous soils, and less heavily forested riverine habitat. Unfortunately, virtually no biological information is available on cutthroat trout in the South Umpqua River, so we have no way of directly evaluating the importance of possible adaptations to elevated water temperatures.

As noted above, elevated water temperatures in the lower river may act as an isolating mechanism for Umpqua River cutthroat trout. It is also possible that the bimodal peak of run times at Winchester Dam may be caused in part by a thermal block in the lower river during part of the summer. However, insufficient data are available to determine whether this is the case.
Effects of Artificial Propagation
Counts of adult (presumably sea-run) cutthroat trout crossing Winchester Dam show that the number of fish declined to nearly zero in the mid 1950s, increased dramatically from about 1961 to 1975, and rapidly declined again after about 1976. The period of increase coincided almost exactly with releases of sea-run cutthroat trout from the Alsea River Hatchery into the Umpqua River below Winchester Dam. Although other explanations are possible, the most parsimonious is that the increases during 1961-75 represented predominantly Alsea River hatchery fish straying to areas above Winchester Dam. Alsea River fish have a slightly later run- timing than the Umpqua River fish, and a shift toward later run-timing can be detected in fish returning to Winchester Dam after 1960 (Fig. 6). There is also evidence of a shift back toward the original run timing after cessation of the hatchery program.

Although the pattern of abundance and tag-recovery data during the period of supplementation indicate that Alsea River hatchery fish returned as adults to Winchester Dam in some numbers, it is apparent that 15 years of hatchery releases did not result in a viable, self-sustaining population of naturally spawning fish. One explanation for this result is that Alsea River Hatchery fish are poorly adapted to conditions in the North Umpqua River. If true, this would support the concept of an ESU in the Umpqua River. Alternative explanations are that 1) the effects of hatchery rearing, rather than poor adaptation, are responsible for the lack of long- term survival of Alsea River fish, or 2) the declines following the end of the hatchery program merely reflect deteriorating conditions for sea-run cutthroat trout in the North Umpqua River.

A key unresolved issue is, What do the few remaining anadromous fish in the North Umpqua River represent: remnants of the original Umpqua River gene pool, descendants of the Alsea River hatchery fish, or a mixed lineage? The run-timing shift suggested that an indigenous component may remain in spite of the extensive stocking history, but the evidence is far from conclusive.

Extensive releases of Alsea River hatchery fish have also occurred near the Umpqua River estuary in the Smith River from 1975 to the present, and in Scholfield Creek from 1983 to the present (Table 1, Fig. 7). Approximately 12,000 hatchery fish per year have been released into the Smith River and 4,000 into Scholfield Creek. These fish are released as smolts and as legal-sized catchable trout prior to or during the trout fishing season (ODFW 1993a). It is believed by ODFW (D. Loomis, see footnote 2) that the majority of these fish are caught by anglers, but no data are available to confirm this hypothesis. There is also no information on the possible impact of these fish (or the fishery for them) on natural sea-run cutthroat trout from the North or South Umpqua Rivers. However, considering the life history of sea-run cutthroat trout, their susceptibility to angling (Pauley et al. 1989), and their extensive utilization of estuaries, the impact of these releases could be substantial.

In summary, scientific information regarding the geographic extent of the ESU that contains Umpqua River cutthroat trout is inconclusive. The relationship of the existing population to the original population and the introduced hatchery fish is uncertain. Several features of the Umpqua River Basin suggest the possibility for evolutionarily important adaptations in O. clarki, but there is little direct evidence on this issue. The Biological Review Team was equally divided on the question whether there is sufficient scientific information for the presumption of an ESU of cutthroat trout within the Umpqua River Basin.
The Threshold Question
The precarious status of the remaining sea-run fish in the Umpqua River is not in question. However, we were unable to determine if the ESU is limited to the Umpqua River. Furthermore, as discussed above, we believe that it is important to consider resident and potamodromous fish along with sea-run fish in the listing determination. Data on riverine-migrating fish within the Umpqua River are very limited, and the total information we were able to develop on abundance of resident O. clarki in the Umpqua River drainage amounted to a list of lakes and tributaries believed to contain cutthroat trout. It is reasonable to presume that widespread habitat degradation in the Umpqua River Basin has reduced the abundance of resident and riverine-migrating fish below historical levels (perhaps substantially below), but we have no direct information on this issue. For these reasons, a formal threshold determination for an ESU containing anadromous, resident, and riverine- migrating cutthroat trout is problematical at this time.

A complicating factor in the threshold determination is the evaluation of the evolutionary significance of the anadromous life-history form to O. clarki as a whole. On the issue of anadromy/nonanadromy, the NMFS "species definition" paper (Waples 1991, p. 16) has this to say:
If substantial gene flow occurs or has recently occurred between the two forms, they represent polymorphisms within a single population and should be considered as a unit for purposes of the Act. In determining whether such a population unit is an ESU, the anadromous and nonanadromous traits should be considered in the same manner as other population characteristics.... The important questions are whether the traits have a genetic basis and whether they help to make the population unit "distinct" from other populations. For example, an anadromous/nonanadromous unit might be considered an ESU if other ecologically comparable populations of the species harbored only the nonanadromous form. In this case, if the population unit is considered to be an ESU solely or primarily on the basis of the anadromous trait, then the potential loss of anadromy should be a legitimate ESA concern. A key question would be whether the nonanadromous form was likely to give rise to the anadromous form after the latter had gone locally extinct. Therefore, an anadromous / nonanadromous population unit could be listed based on a threat to one of the life-history traits, if the trait were genetically based and loss of the trait would compromise the "distinctness" of the population. 
Thus, even if the resident form were determined to be healthy, risk of loss of the anadromous form still would be an ESA concern if the trait has a genetic basis and it contributes substantially to ecological/genetic diversity. Unfortunately, there is no direct information about the genetic basis for anadromy in cutthroat trout, either in the Umpqua River or anywhere else.
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