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Introduction

BACKGROUND

Maine was once the home of abundant populations of wild Atlantic salmon (Salmo solar), but they have been declining since at least the middle of the nineteenth century (Baum 1997). Despite conservation efforts over the past 130 years or so, populations in Maine have continued to decline, and now they are seriously depleted in all the rivers that still retain natural runs. Only about 1,000 adults returned to Maine streams to spawn in 2000. The declines led to the listing of Atlantic salmon in eight Maine rivers (Cove Brook, Dennys, Ducktrap, East Machias, Machias, Narraguagus, Pleasant, and Sheepscot) as endangered under the federal Endangered Species Act (ESA) by the Fish and Wildlife Service (FWS) and the National Marine Fisheries Service (NMFS) (Figure 1). Those eight rivers together had only around 100 returning adults in 2000.

No one disputes the general seriousness of the declines, but many people in Maine claim that the populations are not wild and, therefore, oppose the ESA listing.1 They argue that the fish are derived mainly from hatchery

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The term wild is used by the committee to mean populations of salmon that have been maintained by natural spawning for at least two full generations. The committee agrees with Baum (1997) that pristine salmon populations—populations that have always been wild with no human influences on their genetic makeup—almost surely



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Genetic Status of Atlantic Salmon in Maine: Interim Report from the Committee on Atlantic Salmon in Maine 1 Introduction BACKGROUND Maine was once the home of abundant populations of wild Atlantic salmon (Salmo solar), but they have been declining since at least the middle of the nineteenth century (Baum 1997). Despite conservation efforts over the past 130 years or so, populations in Maine have continued to decline, and now they are seriously depleted in all the rivers that still retain natural runs. Only about 1,000 adults returned to Maine streams to spawn in 2000. The declines led to the listing of Atlantic salmon in eight Maine rivers (Cove Brook, Dennys, Ducktrap, East Machias, Machias, Narraguagus, Pleasant, and Sheepscot) as endangered under the federal Endangered Species Act (ESA) by the Fish and Wildlife Service (FWS) and the National Marine Fisheries Service (NMFS) (Figure 1). Those eight rivers together had only around 100 returning adults in 2000. No one disputes the general seriousness of the declines, but many people in Maine claim that the populations are not wild and, therefore, oppose the ESA listing.1 They argue that the fish are derived mainly from hatchery 1   The term wild is used by the committee to mean populations of salmon that have been maintained by natural spawning for at least two full generations. The committee agrees with Baum (1997) that pristine salmon populations—populations that have always been wild with no human influences on their genetic makeup—almost surely

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Genetic Status of Atlantic Salmon in Maine: Interim Report from the Committee on Atlantic Salmon in Maine FIGURE 1 USA Atlantic salmon rivers with active restoration/recovery programs in New England. *The eight DPS rivers in Maine listed as endangered under the ESA are (5) Dennys, (6) East Machias, (7) Machias, (8) Pleasant, (9) Narraguagus, (11a) Cove Brook, (12) Ducktrap, and (13) Sheepscot. Source: E.Baum, Atlantic Salmon Unlimited, unpublished material, 2001. Printed with permission of the author.     do not exist in Maine. The term natural is used for salmon populations that are derived from parents’ reproduction in streams rather than stocking.

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Genetic Status of Atlantic Salmon in Maine: Interim Report from the Committee on Atlantic Salmon in Maine stocking and aquaculture escapes. If so, then appropriate measures to increase the number of salmon in Maine’s rivers could be quite different from appropriate measures to increase wild salmon runs in those rivers. The controversy led Congress to mandate a study of Atlantic salmon in Maine by the National Research Council (NRC), including an interim report in time to help any recovery efforts (see Appendix A for committee’s statement of task). This is the interim report. The NRC’s Committee on Atlantic Salmon in Maine hopes it will help to inform any future salmon-recovery efforts, whether they are undertaken under the ESA or otherwise, because if the populations are genetically indistinguishable, then it would be hard to justify recovery programs that treat the populations in different drainages separately, whereas if they are distinguishable, then such programs might be justifiable. The report focuses on the genetic characteristics of the wild populations in Maine, especially in the listed rivers. THE LISTING OF SALMON UNDER THE ENDANGERED SPECIES ACT The ESA of 1973 as amended, most recently by Public Law 100–478 in 1988, defines species as including “any subspecies of fish or wildlife or plants, and any distinct population segment of any species o[f] vertebrate fish or wildlife which interbreeds when mature” (Section 3{15}). The salmon in the eight Maine rivers—including “all naturally reproducing wild populations and those river-specific hatchery populations of Atlantic salmon having historical, river-specific characteristics found north of and including tributaries of the lower Kennebec River to, but not including, the mouth of the St. Croix River at the U.S.-Canada border”—were listed as an endangered distinct population segment (DPS) by FWS and NMFS (“the Services”) on November 17, 2000 (DOI and DOC 2000). The science that underlies the ESA; the concept of species, including subspecies and DPSs; and the meaning of “endangered” under the ESA are discussed in considerable detail in two earlier NRC reports (NRC 1995, 1996). In this interim report, the committee focuses only on the genetic makeup of natural populations of salmon in Maine and whether they are distinct from salmon populations elsewhere and from each other. The committee’s final report will address broader issues, such as factors contributing to the decline of Maine’s salmon populations and options for helping them to recover.

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Genetic Status of Atlantic Salmon in Maine: Interim Report from the Committee on Atlantic Salmon in Maine THE PRESENT STUDY AND REPORT ORGANIZATION For this study, the committee met twice in Maine. At its first meeting in Bangor on June 12–14, 2001, the committee heard presentations from representatives of the state government of Maine, including Governor Angus King; from the Services; from the Atlantic Salmon Commission; and from a variety of industry, academic, environmental, and other private organizations and individuals. At its second meeting on September 20–22, 2001, members of the committee visited an Atlantic salmon farm and two blueberry farms in Washington County, a weir on the Pleasant River, and the federal hatchery at Craig Brook. The committee received additional briefings in Bangor. A complete list of the presenters and facilities visited is in Appendix B. The committee also considered an array of published literature and reports. Section 2 of the report briefly reviews the biology and evolution of Atlantic salmon in Maine. Section 3 describes the current state of Atlantic salmon in Maine, including their stocking history and the aquaculture escapements that are relevant to the question of wild- population genetic makeup. Section 4 provides a description of the available data on genetic makeup and analyses of these data. Section 5 discusses data quality and related issues. Finally, Section 6 presents the committee’s conclusion that the wild salmon populations in Maine are genetically distinct from salmon in Canada and elsewhere; furthermore, there is divergence even among populations within Maine. This pattern and degree of genetic variation among populations is consistent with the patterns observed in wild salmon populations elsewhere.