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C HAPTER 5:

Caribou and Reindeer (Rangifer tarandus) Genetic Variation and Herd Structure in Northern Alaska

by

Matthew A. Cronin

1

and John C. Patton

2

1

LGL Alaska Research Associates

,

Inc.

1101 East 76

th

Avenue, Suite B Anchorage, Alaska 99518

2

Department of Fisheries and Wildlife Texas A&M University

College Station, Texas 77843

for

BP EXPLORATION (ALASKA) INC.

Environmental Studies Group P.O. Box 196612

Anchorage, Alaska 99519-6612

LGL Report P587

September 2002

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Table of Contents

Table of Contents...5-2 List of Figures ...5-3 List of Tables ...5-3 List of Appendices ...5-3 Abstract...5-4 Introduction...5-5 Herds, Segments, and Subspecies ...5-5 Review of Caribou and Reindeer Genetics...5-7 Objectives...5-8 Business Rationale ...5-9 Methods ...5-10 Assessment of Movements Among Herds...5-10 Genetic Analysis ...5-10 Data Analysis ...5-11 Results...5-12

Interaction Between Adjacent Caribou Herds and Herd Segments in Arctic

Alaskan Herds...5-12 Segments ...5-14 Genetic Analysis ...5-15 Segments ...5-15 Microsatellite Variation in Caribou and Reindeer...5-15 Microsatellite Allele Frequency Differentiation – Arctic Alaskan Caribou Herds ...5-16 Microsatellite Allele Frequency Differentiation – North American and Eurasian

Caribou and Reindeer ...5-17

Genetic Variation – mtDNA Cytochrome b Gene...5-19

Discussion ...5-20

Acknowledgements...5-22

Literature Cited ...5-22

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List of Figures

Figure 1. Central Arctic Caribou Herd estimates for developed (Western Segment) and undeveloped (Eastern Segment) areas of the central arctic slope of

Alaska, 1992–1997...5-30 Figure 2. Dendrogram of the relationship among caribou and reindeer herds based on

7 microsatellite loci constructed with the UPGMA method ...5-31 Figure 3. Dendrogram of the relationships among caribou and reindeer herds based on

19 microsatellite loci constructed with the UPGMA method ...5-32 Figure 4. Consensus UPGMA dendrogram of cytochrome b mtDNA haplotype sequences,

showing bootstrap values ...5-33

List of Tables

Table 1. Census counts of the number of caribou and calves/100 cows in the Central Arctic Herd including ranges with oilfield development (Western Segment), ranges

without oilfields (Eastern Segment), and the entire herd, 1992–2000 ...5-34 Table 2. Allele frequencies for 7 microsatellite loci in caribou and reindeer ...5-35 Table 3. Information on microsatellite loci analyzed in reindeer and caribou ...5-39 Table 4. Measures of genetic variation of caribou and reindeer herds for 7 and 19

microsatellite loci. N = sample size, A = average number of alleles/locus,

H

o

= observed individual heterozygosity, H

e

= expected individual heterozygosity,

and P = percent polymorphic loci ...5-41 Table 5. F

st

and Nm (number of migrants) estimates for caribou and reindeer herds ...5-42 Table 6. Genetic distances between caribou and reindeer herds for 7 microsatellite loci...5-43 Table 7. Genetic distances between caribou and reindeer herds for 19 microsatellite loci...5-44 Table 8. Relatedness indices (standard deviation) of individual caribou based on 7

microsatellite loci within and between Alaskan Arctic herds ...5-45 Table 9. Mitochondrial DNA cytochrome b haplotypes in caribou and reindeer ...5-46

List of Appendices

Appendix A. Mitochondrial DNA cytochrome b sequences for caribou and reindeer ...5-47

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Abstract

The concept of “herds” is central to caribou biology and management, but it is not rigorously or consistently defined. In Alaska, herds are defined by their calving ranges, but they are defined by other criteria elsewhere. Other groups, herd segments and subspecies, are also of concern to wildlife managers, but are also not well defined. Regardless, negative impacts of Alaska’s North Slope oilfields on caribou herds and segments have been hypothesized without rigorous and consistent definition of these units. We reviewed literature on caribou movements and analyzed genetic variation in caribou to better define herds, herd segments, and subspecies. Observations of caribou movements indicate that herds often mix on fall and winter ranges, while fidelity of cows to calving areas is relatively high. Movements of bulls have not been quantified as much as movements of cows, but bulls probably move more extensively than cows. There is also considerable movement of caribou between herd segments.

Genetic variation at 7–19 microsatellite DNA loci and the cytochrome b gene of mitochondrial DNA was quantified in the four arctic Alaskan caribou herds (Porcupine River, Western Arctic, Central Arctic, and Teshekpuk Lake caribou herds). The Central Arctic, Western Arctic, and Porcupine River caribou herds in Alaska have similar microsatellite allele frequencies and share mtDNA haplotypes. Measures of genetic differentiation were low (F

st

<0.008), indicating these herds comprise one interbreeding population. A small sample size from the Teshekpuk Lake Caribou Herd precluded comparison of microsatellite allele frequencies with the other herds, but caribou of all four herds share mtDNA haplotypes. The arctic Alaska herds can be considered geographic management units, defined by calving area, while the population as a whole consists of animals from different calving herds with overlapping fall and winter ranges. These herds are temporally and spatially dynamic. Across a larger geographic range, caribou herds in northern and eastern Canada are genetically differentiated from the arctic Alaskan herds.

Reindeer were introduced to Alaska from Siberia, Russia 110 years ago. Traditional knowledge of the native people indicates that reindeer have frequently escaped and joined wild caribou herds, and wildlife biologists have concerns that interbreeding may reduce the fitness of caribou herds. We compared microsatellite and mtDNA variation in herds of domestic reindeer from Alaska, Scandinavia, and Siberia, Russia with the arctic Alaskan caribou herds. Genetic distances between reindeer in Alaska and Russia are relatively low, probably reflecting common ancestry prior to the introduction of reindeer to Alaska. In contrast, genetic distances between wild caribou and domestic reindeer in Alaska are high, indicating limited gene flow between them. However, microsatellite allele and mtDNA haplotype distributions suggest that limited introgressive hybridization from reindeer to caribou occurred over the last 110 years. Genetic distances between the major groups are: 0.23 among three Alaskan reindeer herds, 0.24 between Russian and Alaskan reindeer, 0.16 between two Alaskan caribou herds, 0.31 between Alaskan caribou and Alaskan reindeer, and 0.38 between Russian reindeer and Norwegian reindeer. Natural selection has probably limited the genetic influence of reindeer on the arctic Alaskan caribou herds.

Key words: caribou, genetic variation, herds, microsatellite DNA, mitochondrial DNA, Rangifer

tarandus, reindeer.

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Introduction

Herds, Segments, and Subspecies

Caribou (Rangifer tarandus) occur in groups called herds. However, there is not consistent use of the term “herd” in the research and management literature. The dictionary (Webster 1988) defines a herd as (1) a congregation of gregarious wild animals, and (2) a number of animals of one kind kept together under human control. In Alaska, caribou herds are defined as the animals sharing a calving area, which is consistent with the first definition. However, wild herds are not static entities, and the composition of a congregation of caribou may change as herd members migrate between seasonal ranges, breed, and raise calves. Reindeer herds are defined by owner or geographic range, consistent with either definition, depending on if they are under human control or not.

In Alaska, caribou herds are defined as groups with distinct calving ranges, although fall, winter, and spring ranges of different herds may overlap (Skoog 1968; Bergerud et al. 1984; Cronin et al. 1998b).

Herds with distinct calving ranges and overlapping winter ranges also occur in northern Québec, Canada, while in other parts of Québec herds may be isolated year round or overlap during different seasons (R.

Courtois, Québec Wildlife and Parks, Earth and Wildlife Service, pers. comm.). In the Yukon Territory, Canada, groups with a common winter range are considered herds (Zittlau et al. 2000).

For science-based management of caribou, it is desirable to have a consistent definition of herd. The question, “What is a caribou herd?” was explicitly asked at a meeting of caribou experts in Fairbanks, Alaska in 1989, in which the extent of mixing and interaction of herds were discussed (Burns 1990). No definitive answer was found, but assessment of the movements, distribution, and genetic relationships among herds to clarify their identity was endorsed by several of the experts. Similar research needs were identified in a review of caribou research on the North Slope of Alaska (WMI 1991). Since the 1989 meeting, radio telemetry and genetic studies have provided data that can contribute to the issue of herd identity.

In arctic Alaska, there are four caribou herds: the Western Arctic Herd (WAH), the Central Arctic Herd (CAH), the Teshekpuk Lake Caribou Herd (TCH), and the Porcupine River Caribou Herd (PCH).

These herds are distinguished by distinct calving areas, although fall and winter ranges may overlap.

Because breeding occurs in the fall the herds are not independent interbreeding groups (i.e., populations) and each arctic herd can therefore be considered a subpopulation of one large population (Skoog 1968).

Whitten and Cameron (1983) also noted that caribou herds in Alaska constitute one interbreeding population. This concept is reinforced when one considers that most of the evidence for calving ground fidelity is from marked females. Movements of males have not been well quantified and are likely more extensive than females. This could serve to increase the genetic interchange (and interdependence) among herds.

Herd identification has been complicated by the subdivision of the CAH on Alaska’s North Slope into

“segments” on the east and west sides of the Sagavanirktok River (Cameron 1994, 1995; BLM 1998).

The segments have been used to assess oilfield impacts because the western segment uses range adjacent

to and within the oilfields while the eastern segment uses range in less developed areas. In essence, the

segments have been used as “reference” (i.e., undeveloped eastern segment) and “impact” (oilfield

developed western segment) units for impact assessment (Cameron et al. 2002). However, the segments

suffer the same status as herds in that there is frequent movement between them, and demographic

parameters do not necessarily differ between them (Cronin et al. 1997, 2000, 2001b). It is therefore

important to ask: What is a herd segment?

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The relationship between wild caribou (R. t. granti) and domestic reindeer (R. t. tarandus) in Alaska was also raised at the 1989 caribou meeting (Burns 1990) and in earlier research (Klein 1980). Domestic reindeer were imported from Siberia, Russia, to western Alaska in the 1890s and there have been frequent interactions with wild caribou and the potential for hybridization between the forms (Klein 1980; Røed and Whitten 1986; Burns 1990; Cronin et al. 1995b). There were many reindeer in Alaska, including the North Slope, in the early 1900s that were lost from human control, and thought to have joined wild caribou herds (e.g., Bown 2000). The extent of interbreeding between reindeer and caribou was unknown, and this issue was discussed at length at the 1989 meeting (Burns 1990). Because of concerns that interbreeding with reindeer could decrease the fitness of wild caribou herds, and because wild caribou may have genetic variation of use to domestic reindeer breeders, this issue is not entirely academic.

BPXA’s recognition of the importance of biodiversity conservation, including genetic diversity, is relevant to concerns about crossbreeding between reindeer and wild caribou. Alaskan barren ground caribou (R. t. granti) and Eurasian reindeer (R. t. tarandus) are considered subspecies. Several other subspecies of caribou are recognized including woodland caribou (R. t. caribou) across the boreal zone of Canada, Peary caribou (R. t. pearyi) on the Canadian Arctic Islands, and migratory caribou (R. t.

groenlandicus) in northwestern Canada and Greenland (Bergerud 2000). Most Eurasian reindeer are R. t.

tarandus, but those on Svalbard Island are R. t. platyrhynchus. Management issues related to caribou subspecies include the listing of woodland caribou in northern Idaho and Washington under the Endangered Species Act (ESA) (Federal Register 2000) and the slaughter and removal of introduced reindeer from Hagemeister Island by the U.S. Fish and Wildlife Service in the 1990s (Stimmelmeyer and Renecker 1998).

This leads to the question: What is a subspecies? This question has been addressed by taxonomists frequently over the last few decades and there is still no consensus. However, there is general agreement that the best approach to identify subspecies is to use the same methods and assumptions as at higher taxonomic levels, and to base classification on phylogenetic (i.e., genetic) relationships (reviewed by Avise and Ball 1990; Cronin 1997).

Exactly what constitutes a herd, a herd segment, or a subspecies is important to wildlife managers.

This is because management objectives are identified for specific units, including herds, populations, or in some cases involving the ESA, subspecies (Cronin 1997). In Alaska, caribou herds (or populations of other species) are the units of management. Members of a herd (or population) will share habitats, ranges, weather conditions, exposure to predators and hunters, and will be characterized by common recruitment, mortality, immigration/emigration, and other parameters. Managers in Alaska have identified herds by calving range, perhaps because that is the most important part of their year-round range in which recruitment of new members to the herd occurs. However, herds may not be equivalent to populations in the classical sense (defined below). One reason for this is because caribou migrate between seasonal ranges and herds may mix during part of the year. This phenomenon is similar to that of migratory salmon (Oncorhynchus), in which the “stock” (i.e., population) is identified by the watershed in which spawning occurs even though stocks may mix over most of their life history in the ocean. The primary difference is that salmon stocks are defined as interbreeding groups on spawning grounds, while caribou herds in Alaska are defined by calving range without regard for breeding relationships.

If we consider the standard biological unit of a population, we see that caribou herds may not be equivalent to populations. The classical definition of a population has been given by various authors:

• Local Population – The community of potentially interbreeding individuals at a given locality (Mayr 1963).

• Population – A collective group of organisms of the same species occupying a particular

space (Odum 1971).

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• Population – A set of organisms belonging to the same species and occupying a clearly delimited area at the same time (Wilson 1980).

• Population – A group of conspecific organisms that occupy a more or less well defined geographic region and exhibit reproductive continuity from generation to generation; it is generally presumed that ecological and reproductive interactions are more frequent among these individuals than between them and members of other populations of the same species (Futuyma 1986).

Interbreeding and occurrence in the one location are key components to these definitions of a population.

There is no definition of the term “herd segment,” other than its use to identify groups of animals of the CAH on the east and west sides of the Sagavanirktok River (Cameron 1994, 1995; Cronin et al. 1997;

BLM 1998; Cronin et al. 2000, 2001b; Wolfe 2000; Cameron et al. 2002).

Subspecies, which may be considered synonymous with “geographic race,” is a subjective and arbitrary term (Wilson and Brown 1953; Futuyma 1986; Vanzolini 1992; Cronin 1997). However, subspecies can be listed under the ESA so this is not a trivial issue. The following definitions of subspecies have been suggested:

• “An aggregate of phenotypically similar populations of a species inhabiting a geographic subdivision of the range of the species and differing taxonomically from other populations of the species” (Mayr 1963).

• “Subspecies are groups of actually or potentially interbreeding populations, phylogenetically distinguishable from, but reproductively compatible with, other such groups. Importantly, the evidence for phylogenetic distinction must normally come from the concordant distributions of multiple, independent, genetically based traits” (Avise and Ball 1990).

Here, the distinguishing criteria are taxonomic, or phylogenetic, differences. We will address these criteria when assessing the relationships of caribou and reindeer.

Review of Caribou and Reindeer Genetics

Genetic analyses have become widespread in assessments of fish and wildlife population structure and subspecies status. This includes fish and wildlife on Alaska’s North Slope: grizzly bear (Ursus arctos; Cronin et al. 1999), spectacled eiders (Somateria fisheri; Scribner et al. 2001), bowhead whales (Balaena mysticetus; Shelden et al. 2001), polar bears (Ursus maritimus; Cronin et al. 1991; Paetkau et al.

1999), and broad whitefish (Coregonus nasus; Patton et al. 1997). There has also been research on the genetics of caribou and reindeer on the North Slope and other areas. The genetic relationships among caribou and reindeer herds has been previously assessed with genetic markers, including serum transferrin and other proteins (Storset et al. 1978; Baccus et al. 1983; Røed & Whitten 1986; Røed et al. 1991), maternally-inherited mitochondrial DNA (mtDNA; Cronin 1992; Cronin et al. 1995b; Gravlund et al.

1998), nuclear genes (Olsaker & Røed 1990; Cronin et al. 1995b), and microsatellite DNA (Engel et al.

1996; Wilson et al. 1997; Røed & Midthjell 1998; Zittlau et al. 2000). These studies have shown that caribou and reindeer generally have high levels of genetic variation and differentiation among herds.

Small sample sizes in previous comparisons precluded conclusions about the relationships among the

arctic Alaskan caribou herds (Cronin et al. 1995b).

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There is considerable natural variation in phenotypic traits among herds of caribou and reindeer. For example, both sexes of Rangifer have antlers, but the frequency of antlered and antlerless females varies considerably among herds (Reimers 1993; Cronin et al. 1996). Other morphological (e.g., body size, proportions, and coloration) and physiological (e.g., timing of reproduction and parturition) traits also vary among herds (Klein 1980; Klein et al. 1987; Bergerud 2000). The environmental and genetic components of these phenotypic differences have not been quantified, although they are probably due in part to natural selection and local adaptations in wild herds, and artificial (human) selection in domestic herds.

Domestic reindeer occur in either confined herds or free-ranging herds. In western Alaska, for example, reindeer occur on large unfenced ranges where they sometimes mix with wild caribou.

Evidence of reindeer influence in the wild caribou herds is frequently noted by native hunters, and biologists had concerns that interbreeding could reduce the fitness of wild herds (Klein 1980; Burns 1990). Reindeer are smaller in size, less wary of predators, use different foraging habits, have a breeding season that begins 2–4 weeks earlier in the fall, and have a lower propensity to migrate than caribou.

These characteristics could result in relatively low fitness of reindeer that join wild caribou herds and limit successful interbreeding. In Alaska, there has been deliberate crossbreeding of caribou and domestic reindeer, resulting in increased calf weights, perhaps through heterosis. However, the desirable traits selected previously in domestic stock, such as docility, may be compromised (Klein 1980).

Although there has been ample opportunity for interbreeding, there has apparently been little genetic influence of reindeer on wild caribou in Alaska (Klein 1980). Cronin et al. (1995b) assessed genetic differentiation of domestic reindeer and wild caribou in Alaska at two nuclear loci (k-casein and a DQA locus of the Major Histocompatability Complex), and the D-loop of mtDNA. Most alleles for each locus occurred in both caribou and reindeer, although allele frequencies indicated that gene flow between caribou and reindeer in Alaska is limited. This is consistent with data for serum transferrin (Røed and Whitten 1986). However, it is necessary to compare the introduced Alaskan reindeer with the Russian reindeer source herds for a thorough assessment of genetic differentiation, and these comparisons were not included in previous studies. Comparison of Russian reindeer with the Alaskan reindeer and caribou will allow a more thorough assessment of the potential impacts of hybridization, genetic drift, and selection on the genetic makeup of the Alaskan reindeer and caribou herds after more than 100 years of coexistence.

In this study, we assessed the extent of movements and genetic differentiation among caribou herds and their potential effect on herd numbers. We also assessed the potential influence of domestic reindeer on the North Slope caribou herds. There are two primary ways to assess the extent of movement among herds: direct measures with radio telemetry, and indirect measures with genetic data (Slatkin 1987).

Marking animals and documenting movements with radio collars allows quantification of movements of a limited number of animals over short time scales. Genetic data provides a long-term picture of the relationships among herds. Over time, if there is limited movement and interbreeding between herds, genetic differentiation may occur. Conversely, if there is considerable movement among herds, gene flow will prevent genetic differentiation from occurring. The extent of genetic differentiation can be quantified, and the extent of gene flow inferred, with analysis of protein and DNA variation (e.g., Røed and Whitten 1986; Cronin et al. 1995b, 2001a).

Objectives

Our specific objectives in this study are to:

1. Quantify genetic differentiation of caribou herds.

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2. Assess the extent of inter-herd exchange and range overlap for the arctic Alaska herds with analysis of movement and telemetry data.

3. Quantify the genetic differentiation of Alaskan caribou and reindeer, and assess the potential for genetic introgression between them.

Business Rationale

It is frequently hypothesized that the Alaskan North Slope oilfields have a negative impact on the Central Arctic Herd, particularly the western segment of the herd that ranges within the oilfield (Dau and Cameron 1986; Cameron et al. 1992, 1995; Cameron 1995; Nelleman and Cameron 1996, 1998; Wolfe 2000; Cameron et al. 2002; Griffith et al. 2002). However, there is no rigorous and consistent definition of what constitutes a herd or herd segment. In this report, we analyze the issue of herd and herd segment identity.

Why is it important to define caribou herds and segments? If the issue is simply taxonomy (i.e., classification) and the grouping of caribou into herds is a function of basic science, it need not concern resource managers. However, taxonomy is one of the foundations of biological science, and without proper classification, both science and management can be compromised. Specifically, it is important to define herds and herd segments because it has been hypothesized that development of Alaska’s North Slope oilfields have caused the following negative impacts on the Central Arctic Herd (CAH) as a whole, and on the western segment of the CAH in particular:

• Caribou are displaced from oilfield infrastructure during the calving period.

• Caribou are displaced from the oilfields during the post-calving period.

• Displacement may lead to loss of habitat and nutritional deficiencies in cows.

• Nutritional deficiencies may result in reduced production of calves.

Reduced calf production may result in a decline in the number of animals in the western segment and in the entire herd.

There are equivocal data to support the first of these hypotheses. Some cows with calves may distance themselves >1 km from oilfield roads with traffic for a few weeks around the calving period (Dau and Cameron 1986; Cameron et al. 1992). However, more recent data show frequent use of habitats close to roads by calving caribou in the Milne Point area (Haskell 2001; Noel and Demarchi 2002) so further assessment is justified. It also has been suggested that the calving area of the western segment of the CAH has “shifted” south of the Kuparuk oilfield. However, the number of caribou calving in the oilfield areas has not necessarily declined, and the “shift” may simply be a range expansion, as the herd has grown five-fold since the oilfields were first developed.

There is a considerable body of data that do not support the other hypotheses, including the final, italicized hypothesis, which is the one of primary management interest. Caribou use oilfield habitats extensively during the post-calving period (Pollard et al. 1996a, 1996b; Noel et al. 1998; Cronin et al.

1998a 1998b. There do not appear to be nutritional or reproductive problems with cows in the oilfields, as the calf/cow ratios are frequently higher in the oilfields than in less developed areas (Cronin et al.

1998b, 2000). Most importantly, the herd has grown over the period of oilfield development, and the

numbers of animals in the oilfield areas (i.e., western segment) are frequently greater than the numbers in

less developed areas (i.e., eastern segment; Table 1; Figure 1; Cronin et al. 1997, 2000, 2001b). It was

explicitly stated in these studies that movements between the segments and herds could explain the

changes in numbers, and that this was a viable alternative to invoking oilfield impacts. These papers, and

the others documenting frequent use of the oilfield habitats, have been ignored in recent reviews of the

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oilfield/caribou issues by government and university biologists (Wolfe 2000; Cameron et al. 2002;

Griffith et al. 2002).

In this report, our primary consideration is the identification of the units (i.e., the herd, or segment of the herd) that are thought to be impacted by the oilfields. In particular, we note it is important to consider factors such as emigration/immigration to avoid incorrect conclusions about oilfield impacts on herd numbers (Bergerud et al. 1984; Cronin et al. 1997, 1998b, 2000). Emigration/immigration may have little effect on population dynamics in some cases (e.g., the Nelchina Caribou Herd in southcentral Alaska;

Van Ballenbergh 1985), but the importance of emigration/immigration on wildlife populations is potentially significant (e.g., Rosenberry et al. 1999).

The potential negative impact of reindeer on the Arctic caribou herds has also been hypothesized (Klein 1980). This could occur if reindeer interbreed with caribou and the hybrid progeny have lower fitness than the caribou. Large numbers of reindeer escaped from domestic herds on the North Slope during the first half of the 20

th

century and it is widely believed by local North Slope residents that they interbred with wild caribou. Because many escaped reindeer were on the North Slope, it is of interest to assess the extent of interbreeding with caribou and potential effects on fitness.

Methods

Assessment of Movements Among Herds

We assessed herd movements and radio-telemetry data for the arctic Alaskan caribou herds from published papers and unpublished agency and industry reports. The goal was to use existing information to assess the frequency with which caribou of the CAH, TCH, PCH, and WAH move among calving ranges and other seasonal ranges. Our literature search targeted studies of the four caribou herds conducted by management agencies, university researchers, industry, and private consultants. Documents were located in our files, the wildlife literature, interviews with biologists, the Internet, and the database at the ARLIS library in Anchorage.

Genetic Analysis

We used 19 microsatellite DNA markers from cattle gene maps, as in other studies of genetic variation in cervids (Engel et al. 1996; Talbot et al. 1996; Slate et al. 1998; Cronin et al. 2001a). These include 7 microsatellite DNA loci previously used on caribou and reindeer (Cronin et al. In Press), and an additional 12 microsatellite DNA loci that were developed in cattle and tested on caribou and reindeer. In addition, DNA sequence variation was assessed for the cytochrome b gene of mitochondrial DNA (mtDNA). The combination of biparentally-inherited microsatellites and maternally-inherited mtDNA has been useful in other studies of North Slope fish and wildlife (Patton et al. 1997; Cronin et al. 1999;

Scribner et al. 2001).

Blood and muscle samples were obtained from 19 herds of caribou and reindeer (Table 2). Caribou

(R. t. granti) samples from arctic Alaska included the Teshekpuk Lake, Central Arctic, Western Arctic,

and Porcupine River herds. The CAH and PCH samples were obtained from previous studies (Gerhart et

al. 1996; Allaye-Chan 1991) with the assistance of R. White and K. Gerhart (University of Alaska,

Fairbanks). The herd of origin of these samples was identified by the labels on the samples (B. Pierson,

U.S. Geological Survey, pers. comm.). The TCH samples were obtained from C. George (North Slope

Borough) and the WAH samples were obtained from the Alaska Department of Fish and Game and the

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U.S. Fish and Wildlife Service. Caribou samples were also obtained from Canada, including Newfoundland, Labrador, Alberta (R. t. caribou), the Northwest Territories (NWT), Nunavut (Victoria Island and Baffin Island) (R. t. pearyi or R. t. groenlandicus). Reindeer (R. t. tarandus) samples included domestic animals from Alaska (Hagemeister Island, Tom Gray’s Seward Peninsula herd, and Nunivak Island), Russia (Wrangel Island, Pevek, and Severoevensk), and Scandinavia (Sweden and Norway).

Samples from Svalbard Island represent a separate subspecies of reindeer (R. t. platyrhynchus).

DNA was extracted from tissues with standard methods (Cronin et al. 1995b). Genotypes at 7 microsatellite loci were determined with the Polymerase Chain Reaction (PCR) using primers developed in cattle (Table 3). These loci have been identified on the following chromosomes on cattle gene maps (Fries et al. 1993; Barendse et al. 1994; Bishop et al. 1994; Slate et al. 1998): chromosome 1 (BMC6438, BMS574, URB014), chromosome 2 (TGLA44), chromosome 4 (BMS1788), chromosome 5 (BMC1009, IGF-1, BMS1315), chromosome 6 (k-CSN), chromosome 7 (CRFA, BMS1247), chromosome 11 (ILSTS028) chromosome 15 (BM848), chromosome 17 (ILSTS023), chromosome 19 (BMS745), chromosome 23 (BMS468), chromosome 24 (BMS2270), chromosome 28 (IRBP), and chromosome 27 (CSSM036). There is conservation of microsatellite loci between bovids and cervids (Talbot et al. 1996;

Slate et al. 1998), although we do not know if these loci occur on homologous chromosomes in both families.

PCR reactions (15 µl) contained 5-50 ng DNA in 10 mM Tris-Cl, pH 8.3, 50 mM KCI, 2.5 mM MgCl

2

, 0.2 mM of each dNTP, 2 µM of each of the two primers and 1.25 Units of AmpliTaq DNA polymerase (Perkin Elmer, Norwalk, CT, USA). Reactions were heated to 95°C for 5 min followed by 38 cycles of amplification. Each cycle consisted of denaturation for 45 s at 95°C, annealing for 30 s at the temperatures shown in Table 3, and extension for 1 min at 70°C. A cocktail of all 7 PCR products was run simultaneously using the 400HD Rox standard (ABI, Foster City, CA) on gels formed with Long Ranger Singel packs (BioWhittaker Molecular Applications, Rockland, ME) on an ABI 377 autosequencer. Genotypes were determined and data tables created using ABI Genescan 3.1 and Genotyper 1.1.1 software packages.

The mtDNA cytochrome b gene was amplified and sequenced with the methods described by Cronin et al. (1999). Ninety-three samples from the same reindeer and caribou herds analyzed for microsatellites were sequenced.

The lab work and data analysis was done in collaboration with genetics labs of the U.S. Department of Agriculture (U.S.D.A.) in Miles City, Montana and Texas A & M University, Department of Fisheries and Wildlife Science.

Data Analysis

We focused our analysis on the arctic Alaskan caribou herds (CAH, WAH, TCH, PCH), but included comparisons with other herds from North America and Eurasia. We quantified genetic variation within herds, including the average number of alleles per locus, observed heterozygosity, and expected heterozygosity with the BIOSYS computer program (Swofford and Selander 1981). We used the GENEPOP program (Raymond and Roussett 1995) to test among loci for linkage disequilibrium, among genotypes for Hardy-Weinberg equilibrium, and differentiation of allele frequencies among herds with pair-wise tests of heterogeneity.

We also quantified genetic differentiation among herds with estimates of F

st

(standardized variance of allele frequencies; Wright 1965), relatedness indices (r

xy

; Goodnight and Queller 1999, Cronin et al.

1999), and genetic distances (chord distance; Cavalli-Sforza and Edwards 1967). F

st

is a measure of allele

frequency differences, and was calculated between herds using the GENEPOP program. The relatedness

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index, r

xy

, is a measure of sharing of alleles that are identical by descent, weighted by allele frequency, and was calculated between animals within and between herds with the Kinship program (Goodnight and Queller 1999). The mean r

xy

within or between herds indicates the average level of relatedness between individuals. We calculated genetic distances with the BIOSYS program, and subjected them to cluster analysis to construct dendrograms with the unweighted pair-group-method based on arithmetic averages (UPGMA; Sneath and Sokal 1973). F

st

is related to the effective number of migrants between populations (Nm, effective population size X migration rate) as F

st

= 1/(1 + 4Nm). For an estimate of the extent of migration between herds over time, we calculated Nm = (1-F

st

)/(4 F

st

).

The mtDNA sequences were analyzed with the MEGA version 2.0 computer program (Kumar et al.

2001). Jukes and Cantor (1969) distances of nucleotide substitutions between haplotypes were calculated for the entire sequence, and for synonymous (ds) and nonsynonymous (dn) substitutions. The ds/dn ratios were tested for evidence of selection on the DNA sequences. A consensus UPGMA dendrogram showing the relationships of the Rangifer mtDNA haplotypes was constructed with the Jukes-Cantor genetic distances, using moose (Alces alces) as an outgroup. The bootstrap option, with 500 replications, was used to estimate reliability measures for the nodes of the dendrogram.

Results

Interaction Between Adjacent Caribou Herds and Herd Segments in Arctic Alaskan Herds Because the arctic Alaskan caribou herds have overlapping ranges, it is reasonable to expect that animals will sometimes change herds. That is, caribou may migrate to calving ranges different from the one in which they were born. Because herds are usually counted on summer ranges, the magnitude of this change is important for assessment of the impact of immigration/emigration on the number of animals in a herd. The literature provides some relevant anecdotal and quantitative data on this issue.

The ranges of the four arctic Alaskan caribou herds often overlap, particularly during winter. In the late 1950s as many as 150,000 caribou from the WAH were reported to winter in the region between the Colville and Canning rivers, which is currently within the range of the CAH (Carruthers et al. 1987).

During the 1980s, the number of caribou in the CAH range varied seasonally as the result of fall and winter influxes of WAH animals in some years (Sopuck and Jakimchuk 1986; Carruthers and Jakimchuk 1986; Carruthers et al. 1987). For example, during the winter of 1983, approximately 20,000 WAH caribou were in the range of the CAH (Carruthers et al. 1984), and some WAH animals wintered as far east as the Sagavanirktok River (Cameron et al. 1986). The CAH and PCH have also occurred together on winter (Carruthers et al. 1987) and summer (Fancy et al. 1989) ranges. There were 7,000–10,000 CAH caribou mixed with the PCH over more than 140 km of range in July 1987 and July 1988 (Fancy et al. 1989). Whitten and Cameron (1983) found that 10%–41% of their collared CAH caribou migrated to the ranges of other herds throughout the year. In addition, telemetry data show that bulls of the WAH and PCH may mix with the CAH during the fall (Hicks 1997).

In his historical review of caribou in Alaska, Skoog (1968) noted that, “Interchanges of animals

between regions have been common.” and “An intermingling and interchange of animals between

adjacent herds occurs sporadically.” Interchange has occurred when herds mixed during winter, and large

exchanges occurred when herds reached large numbers (Skoog 1968). Specifically, Skoog reported that

there was a shift of animals from the PCH westward, and from the “arctic herd” (i.e., presumably the

WAH) eastward to the “Central Brooks Range” herd in the late 1910s. In addition, Skoog noted that the

PCH split in the 1920s with one part comprising the “Central Brooks Range” herd. In the late 1940s,

animals from the “Central Brooks Range” herd shifted westward and no longer formed a separate herd

(Skoog 1968). In the 1970s, caribou from the “arctic herd” (presumably the WAH) and the PCH

(13)

occupied the area around Prudhoe Bay in June and July (Hemming 1971; Luick 1974). Gavin (1973) and Child (1973) noted that a small population stayed in the Prudhoe Bay region all year. It is important to note that these accounts were made before the recognition of the extant CAH as a separate herd of about 5000 caribou in 1979 (Cameron and Whitten 1979). More recently, Sopuck and Jakimchuk (1986) suggested that the CAH’s high rate of population increase might be due in part to an ingress of animals from adjacent herds, particularly the WAH.

The occurrence of WAH caribou within the range of the CAH has led to suggestions that the extant CAH is a “remnant” herd that split off from the large WAH (Skoog 1968; Carruthers 1983; Carruthers et al. 1984; Bergerud et al. 1984). Hemming (1971) and Roseneau et al. (1974) also concluded that a

“remnant herd” hypothesis was particularly compelling because the CAH was “discovered” in the mid- 1970s when the WAH was declining dramatically in numbers and range size. Bergerud et al. (1984) predicted that, if the CAH and WAH continue to grow they would probably merge into a single herd again.

It appears from these observations that the CAH range was colonized in the period between 1910 and the 1940s, was vacated for a few decades, and recolonized in the 1970s. The animals using this range came from the adjacent herds, and distributions are dynamic. Such large-scale shifts of arctic tundra caribou to and from ranges they have occupied for several decades may be due to density-dependant forage depletion and overgrazing or other factors (Messier et al. 1988; Messier 1991; Cronin et al. 1995a;

Ferguson et al. 2001). Range shifts have the potential to affect the number of animals in a herd, and even result in the designation of new herds (i.e., the CAH).

Quantitative evidence of movement of caribou among arctic Alaskan herds comes primarily from radio-collared animals. Actual locations of radio-collared caribou were provided by only one source, the website run by the non-profit Arctic Borderlands Ecological Knowledge Society (ABEKS 2001). This website shows selected agency locations of a small number of satellite collared caribou of the PCH from 1997 to 2001, but is not an original data source. Government reports and papers sporadically describe movements of caribou in the four herds, although not actual location data. These reports of telemetry results are consistent with the general observations that herds frequently mix. Radio-collared animals indicated there were 7000–10,000 CAH caribou mixed with the PCH in July 1987 and July 1988 and the two herds occurred together over more than 140 km of range (Fancy et al. 1989). Whitten and Cameron (1983) radio-collared 160 caribou bulls and cows of the CAH (between the Canning and Itkillik rivers) between 1975 and 1978 and found that 10%–41% of them migrated to the ranges of other herds throughout the year. Other telemetry and aerial survey data for the CAH shows that mixing of the CAH with the WAH, PCH and TCH during the winter is common, as is mixing of animals from the CAH and PCH in July (Abbott 1992, Hicks 1997). In addition, telemetry data show that bulls of the WAH and PCH may mix with the CAH during the fall (Hicks 1997).

Although there is a high degree of overlap between herds on the winter and fall ranges, radio-

telemetry data indicate that cows have high fidelity to their calving areas and, to a lesser extent, post-

calving areas. Abbott (1992) reports that despite the high amount of winter range overlap between herds,

there have been “very few (less than 1% of radio-collared caribou) documented cases of radio-collared

caribou changing herds.” Prior to 1990, however, little effort was made to locate WAH radio-collared

cows except in their recognized calving areas, and effort in searching other areas has been irregular since

then (Hicks 1997). Cameron et al. (1986) also report that between 1979 and 1985, none of more than 200

radio-collared female caribou from the WAH, TCH, and PCH were found within the summer range of the

CAH. In contrast, Fancy et al. (1989) report that the “CAH has not been censused since 1983 because of

overlap between the eastern portion of the CAH and the PCH in early July each year.” and that “An

estimated 10,000 caribou from the CAH had aggregated with the PCH” in July 1989. It should be noted

that caribou are on post-calving, not calving, ranges in July.

(14)

The rate of inter-herd movement between the PCH and CAH in the 1970s and 1980s ranged from 1%

to 9%, based on radio-collar data (Whitten and Cameron 1983; Cameron et al. 1986; Whitten et al. 1992).

Cameron et al. (1986) found an overall summer range fidelity of 91% for radio-collared caribou of the CAH and that 1 of 7 unaccounted for animals was a confirmed emigrant to another arctic herd. Whitten and Cameron (1983) collared 160 caribou in the CAH range in spring 1975 and 1978. They observed that 92% of the caribou were relocated repeatedly within this region through 1979. They also observed at least 6 different cows that were marked in the CAH range were subsequently with either the PCH or the WAH. Whitten and Cameron (1983) stated that: “While Alaskan caribou occur in separate herds, interchange is sufficiently frequent that all caribou in the state constitute a single breeding population….

To our knowledge this is the first fully documented report of inter-herd movements in Alaska.”

Telemetry of the TCH also shows herd interchange. From 1990 through 1993, Philo et al. (1993) studied 12 TCH cows equipped with satellite radio collars. These cows had variable movements between years, and moved greater distances than previously reported for TCH animals. The calving locations of 5 of the cows were determined; 1 was in an area where herd affiliation was unclear and the other 4 calved with the TCH. Of 3 satellite-collared cows from the TCH monitored in the spring of 1995, 1 calved within the TCH calving grounds, the other 2 spent the spring on the WAH calving grounds, and 1 was observed to calve among the WAH caribou (Hicks 1997). Of 9 satellite-collared TCH cows monitored in 1996, 1 was observed to calve with the WAH, and the other 8 calved within the TCH calving grounds (Hicks 1997).

In summary, the arctic Alaskan herds share common ancestry, overlap on non-calving ranges, and exchange individuals at varying rates. Previous assessments that the herds are parts of a larger breeding population are supported by these observations (Skoog 1968; Whitten and Cameron 1983).

Segments

The CAH has putative “segments” with different calving areas: one east and one west of the Sagavanirktok River (Cameron 1994, 1995; BLM 1998; Wolfe 2000). Radio-telemetry data of individuals moving between two segments of the herd, east and west of the Sagavanirktok River, shows that CAH caribou tend to return to the same segment each summer (Lawhead and Curatolo 1984;

Cameron and Smith 1988). However, some interchange occurs between years and within the same year.

Of 27 collared cows, 7 (25.9%) spent the summer of 1983 in a different segment than the summer of 1982 (Lawhead and Curatolo 1984). Wolfe (2000) reported an exchange rate of 18% (10 of 55) radio-collared cows (which produced a calf in >1 year) between the segments over a 15-year (1980–1995) time interval.

Interchange within the same year was lower than between years, with 4 out of 34 (11.8%) collared cows switching segments within a year (Lawhead and Curatolo 1984).

It is also possible that the eastern segment of the CAH may overlap with the PCH in the summer.

Recall that the CAH was not censused from 1983–1989 because of overlap between the eastern portion of the CAH and the PCH in early July each year (Fancy et al. 1989). If this degree of overlap occurred in other years, it could explain the occasional increases (e.g., 1995) in the eastern segment of the CAH (Figure 1, Table 1).

Regarding the PCH, our review indicates that there are “segments” of this herd on winter ranges. The satellite telemetry data show two distinct wintering areas: one in Alaska, and one in the Yukon Territory (ABEKS 2001). Despite the concerns about the segments of the CAH, there have been no issues raised about the differing impacts on these herd segments of the PCH.

These data show that the CAH herd segments are not independent units, but are aggregations in

different parts of a summer range. Cronin et al. (1997, 2000) showed that the changes in numbers

(15)

between the eastern and western segments of the CAH could be explained by inter-segment movements.

The western segment of the herd has been considered as impacted by the oilfields while the eastern segment of the herd has not. Between 1992 and 1995, the CAH declined from 23,444 to 18,093 animals, with most of the decline occurring in the western (oilfield) range. It was speculated that this was due to oilfield impacts (Rinehart 1995; USFWS 2001). In early 1997, Cronin et al. (1997) suggested that the changes in numbers probably reflected population density effects or movement of animals between areas, not oilfield impacts on calf production. This hypothesis was supported by censuses later in 1997 and in 2000 when the herd increased, with most of the increase in the western range (Cronin et al. 2000, 2001b).

As indicated in Table 1 and Figure 1, the numbers of caribou in the eastern (undeveloped) and western (oilfield) ranges fluctuate without a declining pattern in the western range, as one would expect if there were oilfield impacts. Cronin et al. (1997, 2000) contend that the most likely explanation for this pattern was that animals move between the eastern and western ranges. As described above, the telemetry data showing 12%–26% movement between segments, and frequent overlap of the eastern segment with the PCH in summer, support this idea (Cronin et al. 1997).

Genetic Analysis

Segments

Although we obtained hair samples from the Alaska Department of Fish and Game (S. Arthur, pers.

comm.) from calves captured on east and west sides of the Sagavanirktok River during a study of body weights in 2001, the amount of DNA extracted from the hairs was not adequate for our analyses.

Comparison of the genetic characteristics from the eastern and western segments is not possible with these samples at this time. Analyses with the ability to amplify small amounts of DNA may be tried in the future on these samples.

Microsatellite Variation in Caribou and Reindeer

We analyzed all 19 microsatellite loci for 14 herds (258 animals) and 7 loci for 19 herds (308 animals, Table 2). The WAH, NWT, Baffin Island, Victoria Island, and Svalbard Island herds (50 animals) were analyzed for 7 loci, but not for the 12 additional loci. These samples, and others collected in 2001–2002 from the TCH and other Alaskan herds, will be analyzed in the future for all 19 loci.

In our samples of caribou and reindeer there is 1 allele at 2 loci (ITLS028, BMS1315), 2 alleles at 2 loci (BMC1009, k-CSN), 4 alleles at 3 loci (BMS574, CSSM036, URB014), 5 alleles at 2 loci (IGF-1, IRBP), 8 alleles at 1 locus (BM6438), 9 alleles at 1 locus (BMS468), 10 alleles at 2 loci (BMS745, BMS1247) 13 alleles at 1 locus (ILSTS023), 14 alleles at 1 locus (TGLA44), 16 alleles at 1 locus (CRFA), 17 alleles at 1 locus (BMS2270), and 19 alleles at 2 loci (BM848, BMS1788, Table 2). Most alleles differed by multiples of 2 nucleotides in length suggesting these microsatellites contain dinucleotide repeats. In three cases, there are alleles that differ by 1 nucleotide (CSSM036 alleles 158, 159, 160; BMS745 alleles 103, 104, 105; and TGLA44 alleles 146, 147, 148).

Most alleles occurred across herds and geographic regions, but several alleles were restricted to one

region. For the 7 loci analyzed in all 19 herds there were several alleles observed only in Alaskan

caribou: alleles 246, 248, and 262 for locus BM6438; alleles 359, 379, 383, 389, and 401 for locus

BM848; and alleles, 253, 257, 259, and 263 for locus CRFA. All but 2 of these alleles were rare

(frequency <0.05; Table 2). In addition, allele 355 for locus BM848 was restricted to the Norwegian

herd, allele 188 for locus k-CSN was restricted to the Labrador and Newfoundland herds, and allele 361

for locus BM848 was restricted to the Victoria Island herd.

(16)

For the additional 12 loci analyzed in 14 herds, there were also several alleles observed only in Alaskan caribou: allele 162 for locus CSSM036; allele 113 for locus BMS745; alleles 147, 150, 152, and 154 for locus TGLA44; alleles 93, 97, 99, and 143 for locus BMS1788; alleles 125 and 133 for locus BMS1247; alleles 140 and 166 for locus BMS468; alleles 147, 164, 166, 180, 182, and 186 for locus ILSTS023; alleles 110 and 112 for locus URB014; alleles 176, 178, 180, and 182, for locus BMS2270;

and alleles 204, 206, and 208 for locus BMS2270. All but 2 of these alleles were rare (frequency <0.05;

Table 2). Allele 123 for locus BMS574, alleles125 and 127 for locus BMS1788, and allele 127 for locus BMS1247 were restricted to Alaskan reindeer. Allele 115 for locus BMS574, allele 104 for locus BMS745, allele 162 for locus TGLA44, and allele 129 for locus BMS1788 were restricted to Russian reindeer. Allele 132 for locus TGLA44 and allele 202 for locus BMS2270 were restricted to Labrador caribou. Allele 200 for locus BMS2270 was restricted to Albertan caribou, and allele 139 for locus BMS1247 was restricted to Norwegian reindeer.

There is considerable genetic variation at the 7 loci analyzed in all of the herds except the Svalbard Island reindeer (Table 4). Excluding Svalbard Island, the percent polymorphic loci ranged from 71% to 100%, the average number of alleles per locus ranged from 2.0 to 6.6, and observed heterozygosity ranged from 0.333 to 0.500. The Alaskan caribou had the highest number of alleles/locus (>6) and relatively high-observed heterozygosities (0.417–0.480). The Alaskan reindeer and Russian reindeer had fewer alleles, but levels of heterozygosity (0.333–0.496) similar to the Alaskan caribou. The Svalbard Island herd had a relatively low level of variation for all measures, and was fixed for 1 allele for 5 of the 7 loci. When comparing the measures of variation, it is important to note that there is a positive relationship between sample size and the number of alleles detected (R

2

= 0.75, P = 0.000002), which may explain the relatively high number of alleles in the Alaskan caribou herds. The numbers of alleles in herds with small sample sizes are probably underestimates and there may be other rare alleles that we did not detect. The measures of variation for the herds analyzed for all 19 loci are comparable to those for the 7 loci (Table 4).

For the 7 loci analyzed in all herds, 6 tests showed significant deviations from Hardy-Weinberg equilibrium (P <0.05): the BM6438 locus for the Severoevensk herd; the CRFA locus for the WAH; and the BM848 locus for the CAH, Tom Gray, Nunivak Island, and Severoevensk herds. In all these cases, there were fewer observed heterozygotes than expected. All other herd/locus tests for these 7 loci were in Hardy-Weinberg equilibrium. For the additional 12 loci analyzed in 14 herds, there were 8 tests with significant deviations from Hardy-Weinberg equilibrium (P <0.05): the CSSMO36 locus for the CAH, Severoevensk, and Norwegian herds; the BMS 468 locus for the CAH and Labrador herds; the ILSTS023 locus for the Labrador and Newfoundland herds; and the BMS2270 locus for the Newfoundland herd.

Tests of linkage disequilibrium between the 7 loci analyzed for all 19 herds showed a significant relationship between only the CRFA and IRBP loci (P = 0.0207). The BMC1009 and IGF-1 loci had a relationship that was close to the 0.05 level of significance (P = 0.0610). These loci are on the same chromosome (5) in the cattle genome and this linkage may also occur in Rangifer genome. For the additional 12 loci analyzed in 14 herds, there were significant relationships between the BMS468 (bovine chromosome 23) and the ILSTS023 (bovine chromosome 17) loci (P = 0.0444), and between the BMS468 (bovine chromosome 23) and the BMS2270 (bovine chromosome 24) loci (P = 0.0113).

Microsatellite Allele Frequency Differentiation – Arctic Alaskan Caribou Herds

We conducted pair-wise tests of heterogeneity between the three Alaskan caribou herds with adequate

sample sizes (CAH, PCH, WAH). Of the 19 loci analyzed, there were significant (P <0.05) differences in

allele frequencies between the CAH and PCH for 4 of 19 (21%) loci: CSSM036, BMS745, BMS1247,

and URBO14. The WAH was only analyzed for 7 loci. Comparisons of the PCH and the WAH for these

7 loci resulted in 1 significant difference in allele frequency (for the IGF-1 locus) of 7 pair-wise

(17)

comparisons (14%). There were zero significant tests of 7 pair-wise comparisons of the CAH and WAH.

Overall, 15% (5 of 33) of the pair-wise tests of heterogeneity showed significant differences between the caribou herds (Table 5).

F

st

values are relatively low, and Nm values are relatively high between the Alaskan caribou herds, indicating there are similar allele frequencies among the PCH, CAH, and WAH (Table 5). The relationship between the CAH and PCH is particularly close, as indicated by the lowest F

st

(0.0005) and highest Nm (499) values in Table 5. The estimates of Nm (from 32 to 499; Table 5) among the arctic Alaskan caribou herds indicate that over time, there are tens to hundreds of caribou moving between herds each generation. It is important to recognize that such movement (and interbreeding) does not necessarily occur each year, but may be episodic over longer time periods. The close relationship of the Alaskan caribou herds is also reflected in the 7-locus and 19-locus microsatellite genetic distances (Tables 6 and 7) and UPGMA dendrograms, in which the WAH, CAH, and PCH cluster together (Figures 2 and 3).

The relatedness indices (r

xy

) for 7 microsatellite loci (Table 8) also reflect genetic similarity of the CAH, WAH, and PCH. For scale of comparison, an r

xy

of 1.0 is expected for identical twins, an r

xy

of 0.5 is expected for parent-offspring or sibling pairs, and an r

xy

of 0.0 is expected for unrelated individuals (i.e., sharing no alleles that are identical by descent). Negative numbers are essentially zero, and occur because of the weighting of allele sharing by the allele frequency. The average relatedness of animals is actually higher between the PCH and CAH (0.1057) than within either herd (0.08). The high standard deviations of r

xy

indicate each of these herds is comprised of related and unrelated animals, but the overall relatedness of animals within a herd is not greater than that between herds. The r

xy

within the WAH, and between the WAH and the PCH and CAH, are negative numbers close to zero. The WAH also appears to have animals that, on average, are as closely related to those of the other two herds as they are to herd- mates. The r

xy

values indicate that, on average, animals in the PCH, CAH, and WAH are not more closely related to other herd members than they are to animals in the other herds. This reflects the similar allele frequencies, common ancestry, and gene flow among these herds. The r

xy

values for the other caribou and reindeer herds reveal higher levels of relatedness than for the Alaskan caribou herds. This may reflect smaller population sizes, lack of gene flow with other herds, fewer alleles, and higher allele sharing among individuals of these herds. The low level of allelic variation in the Svalbard Island herd resulted in a very high r

xy

(0.95, Table 8).

Microsatellite Allele Frequency Differentiation – North American and Eurasian Caribou and Reindeer

The Alaskan reindeer herds came from Siberian stock and have been subdivided in different areas in Alaska over the last century. Our most numerous Russian samples (from Severoevensk), and possibly the original stock brought to Alaska from Siberia, came from the same region near Magadan (see R. White’s comments on page 14 of Burns 1990).

The tests of heterogeneity indicate the following significant differences in allele frequency between the three Alaskan reindeer herds for the microsatellite loci: 5 of 19 loci (26%) Hagemeister Island and Tom Gray herds for the BMS745, BMS1788, BMS1247, BMS468, and BMS2270 loci; 4 of 19 loci (21%) Hagemeister and Nunivak herds for the BMS745, BMS1247, BMS468, and BMS2270 loci; and 3 of 19 loci (15%) Tom Gray and Nunivak Island herds for the BMS1788, ILST023, and BMS2270 loci.

Overall, 21% (12 of 57) of the pair-wise tests of heterogeneity showed significant differences between the

Alaskan reindeer herds (Table 5). The F

st

estimates (for the 7 loci analyzed in all herds) between the

Alaskan reindeer herds are relatively low and of the same magnitude as the values between the Alaskan

caribou herds. The F

st

values between the Alaskan reindeer herds considering all 19 loci are higher, and

probably reflect the lack of gene flow among these herds that are isolated from one another (Table 5).

(18)

There is more differentiation of allele frequencies between the Russian and Alaskan reindeer than among the Alaskan reindeer herds. Comparison of the Alaskan and Russian reindeer for the microsatellite loci showed the following significant differences: 9 of 19 loci (47%) between the Severoevensk and Hagemeister Island herds for the IGF-1, CRFA, BM848, IRBP, TGLA44, BMS1788, BMS1247, ILSTO23, and URB014 loci; 8 of 19 loci (42%) between the Severoevensk and Tom Gray herds for the IGF-1, CRFA, BM848, IRBP, BMS745, TGLA44, ILSTO23, and BMS2270 loci; and 7 of 19 loci (37%) between the Nunivak Island and Severoevensk herds for the IGF-1, CRFA, IRBP, BMS745, BMS1788, BMS468, and BMS2270 loci. Overall, 42% (24 of 57) of the pair-wise tests of heterogeneity showed significant differences between the Alaskan and Russian reindeer herds. This is twice as high as the proportion of significant tests among the Alaskan reindeer herds. In addition, the F

st

estimates between the Russian and Alaskan reindeer herds (average 0.0572 for 19 loci) were higher than the F

st

estimates among the Alaskan reindeer herds (average 0.0427 for 19 loci, Table 5). This divergence of the Alaskan and Russian reindeer may be due to genetic drift over the last 100 years of separation, although we are not sure the Russian and Alaskan reindeer originated from the same stock. Despite this measurable differentiation of allele frequencies, the Alaskan and Russian reindeer are closely related compared to other reindeer and caribou herds as indicated by their relatively low genetic distances (Tables 6 and 7) and clustering together in the dendrograms (Figures 2 and 3).

Various measures indicate that the Alaskan caribou and Alaskan reindeer are genetically differentiated. The F

st

estimates are relatively high, (7 loci F

st

= 0.0630, 19 loci F

st

= 0.0537, Table 5), as are the average genetic distances (19 loci D = 0.3072, 7 loci D = 0.3277). The pair-wise tests of heterogeneity between the Alaskan caribou and Alaskan reindeer revealed a large number of significant differences: CAH-Hagemeister 13/19 loci (68%), CAH-Tom Gray herd 9/19 loci (47%), CAH-Nunivak 7/19 loci (37%), PCH-Hagemeister 11/19 loci (58%), PCH-Tom Gray herd 11/19 loci (58%), PCH- Nunivak 8/19 loci (42%), WAH-Hagemeister 4/7 loci (57%), WAH-Tom Gray herd 4/7 loci (57%), and WAH-Nunivak 3/7 loci (43%). Overall, 52% (70 of 135) of the pair-wise comparisons of Alaskan caribou and Alaskan reindeer were significantly different (Table 5). It is interesting to note that the proportion of the tests of heterogeneity that are significantly different (and F

st

values) are highest between Alaskan caribou and reindeer (52%), followed by Alaskan and Russian reindeer (42%), Alaskan reindeer herds (21%), and Alaskan caribou herds (15%).

The F

st

, genetic distances, tests of heterogeneity, and the dendrograms (Figures 2 and 3), indicate the microsatellite allele frequencies in Alaskan reindeer and caribou are differentiated. However, the allele distributions suggest some gene flow may have occurred between caribou and reindeer. Cases in which an allele is common in one group and rare in the other (i.e., Alaskan/Russian reindeer or Alaskan caribou) may indicate introgressive hybridization (i.e., movement of alleles from one subspecies to another through hybridization) in the Alaskan herds. Possible gene flow from reindeer to caribou may be indicated by allele 371 at the BM848 locus, allele 137 at the IRBP locus, allele 270 at the BMC1009 locus, allele 258 at the BM6438 locus, and allele 136 at the TGLA44 locus. There were two cases where gene flow from caribou to reindeer may be indicated: allele 375 at the BM848 locus, and allele 138 at the TGLA44 locus.

When we consider caribou and reindeer herds across their Eurasian and North American ranges, the

genetic distances (Tables 6 and 7) and the UPGMA dendrogram resulting from them (Figures 2 and 3)

show several important divisions. First, the three arctic Alaskan caribou herds cluster together within a

larger cluster containing the arctic Canadian caribou herds (Victoria Island and Baffin Island). Second,

the eastern Canadian caribou (Newfoundland and Labrador) are separate from the other caribou. Third,

the Alaskan reindeer and Russian reindeer occur in a cluster, separate from North American caribou and

Scandinavian reindeer. Fourth, the Russian and Norwegian reindeer occur on separate clusters. The

means of the pair-wise herd genetic distances (D) reflect these clusters: between Alaskan caribou herds

19 loci D = 0.159, 7 loci D = 0.1823; between Alaskan reindeer herds 19 loci D = 0.2137, 7 loci D =

(19)

0.1863; between Alaskan reindeer and Russian reindeer herds 19 loci D = 0.2437, 7 loci D = 0.2383;

between Alaskan reindeer and Alaskan caribou herds 19 loci D = 0.3072, 7 loci D = 0.3277; between Alaskan caribou and Russian reindeer herds 19 loci D = 0.2915, 7 loci D = 0.3553; and between Russian and Norwegian reindeer herds 19 loci D = 0.381, 7 loci D = 0.427.

Genetic Variation – mtDNA Cytochrome b Gene

We obtained 1194 nucleotides of DNA sequence for the cytochrome b gene of mtDNA from 95 animals (Appendix A). There are 44 Rangifer haplotypes distributed among the samples plus the moose outgroup (Table 9). The average Jukes-Cantor distance between the Rangifer haplotypes is 0.008 nucleotide substitutions/site (SE = 0.001). A previous analysis of restriction fragment length polymorphisms showed mtDNA sequence divergences <0.014 nucleotide substitutions/site among North American caribou haplotypes (Cronin 1992). The average distance between the 44 Rangifer haplotypes and the moose sequence is 0.140 nucleotide substitutions/site. Cronin (1991) reported a distance of 0.0955 nucleotide substitutions/site between moose and caribou mtDNA haplotypes. Estimates of synonymous (ds = 0.029, SE = 0.005) and nonsynonymous (dn = 0.001, SE = 0.000) substitutions/site between the Rangifer haplotypes are significantly different (Z = 5.9812, P = 1.2 X 10

-9

). The ds > dn suggests that purifying selection has removed deleterious nonsynonymous substitutions during the evolution of the Rangifer cytochrome b sequences.

There are two ways to assess mtDNA differentiation: comparison of haplotype frequencies among herds (as with the microsatellite loci), and phylogenetic analysis of DNA sequences (Cronin 1993). A phylogenetic analysis of the cytochrome b mtDNA haplotypes (Figure 4) results in several well-defined clusters as indicated by the high bootstrap values in the UPGMA dendrogram. However, there is little geographic structure to the dendrogram, with haplotypes from diverse locations co-occurring in clusters.

An exception is the cluster containing haplotypes A, B, C, and D from eastern Canada (Newfoundland and Labrador). Unique mtDNA haplotypes in this region were identified previously (Cronin 1992). The relationships among the herds are consistent with earlier work showing that caribou subspecies are not monophyletic mtDNA lineages (Cronin 1992).

Although the numbers of samples analyzed do not allow statistical comparisons of mtDNA haplotype frequencies, the distribution of haplotypes (Table 9, Figure 4) shows the following important patterns:

1. The four arctic Alaskan caribou herds have the most variation, with 25 haplotypes shared among them. Samples sizes are not adequate for statistical testing of haplotype frequencies among the herds (N = TCH 3, WAH 13, PCH 21, and CAH 19), although the following distribution is noteworthy: the PCH and CAH share 7 mtDNA haplotypes, 4 of them exclusively (P, S, Y, MM); the PCH and WAH share 3 haplotypes; the CAH and WAH share 4 haplotypes; the CAH and TCH share 1 haplotype; and the TCH and WAH share 1 haplotype. These haplotypes do not occur in other caribou herds outside Alaska.

One CAH caribou (sample CAH10) shared haplotype X with Alaskan reindeer and Russian reindeer (see point 7 below).

2. The Alaskan reindeer and Russian reindeer share 2 haplotypes (haplotypes X and DD), and collectively have 6 unique haplotypes.

3. The Labrador and Newfoundland herds each have 2 different haplotypes that are in a separate cluster in Figure 4. The Labrador herd has an additional haplotype (J) in a different cluster.

4. The Svalbard Island herd has a single haplotype not observed elsewhere.

References

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