Genetic diversity and population parameters of sea otters, Enhydra lutris, before fur trade extirpation from 1741-1911

All existing sea otter, Enhydra lutris, populations have suffered at least one historic population bottleneck stemming from the fur trade extirpations of the eighteenth and nineteenth centuries. We examined genetic variation, gene flow, and population structure at five microsatellite loci in samples from five pre-fur trade populations throughout the sea otter's historical range: California, Oregon, Washington, Alaska, and Russia. We then compared those values to genetic diversity and population structure found within five modern sea otter populations throughout their current range: California, Prince William Sound, Amchitka Island, Southeast Alaska and Washington. We found twice the genetic diversity in the pre-fur trade populations when compared to modern sea otters, a level of diversity that was similar to levels that are found in other mammal populations that have not experienced population bottlenecks. Even with the significant loss in genetic diversity modern sea otters have retained historical structure. There was greater gene flow before extirpation than that found among modern sea otter populations but the difference was not statistically significant. The most dramatic effect of pre fur trade population extirpation was the loss of genetic diversity. For long term conservation of these populations increasing gene flow and the maintenance of remnant genetic diversity should be encouraged.     

Stress-related hormones and genetic diversity in sea otters (Enhydra lutris)

Sea otters ( Enhydra lutris ) once ranged throughout the coastal regions of the north Pacific, but were extirpated throughout their range during the fur trade of the 18th and 19th centuries, leaving only small, widely scattered, remnant populations. All extant sea otter populations are believed to have experienced a population bottleneck and thus have lost genetic variation. Populations that undergo severe population reduction and associated inbreeding may suffer from a general reduction in fitness termed inbreeding depression. Inbreeding depression may result in decreased testosterone levels in males, and reduced ability to respond to stressful stimuli associated with an increase in the stress-related adrenal glucocorticoid hormones, cortisol and corticosterone. We investigated correlations of testosterone, cortisol, and corticosterone with genetic diversity in sea otters from five populations. We found a significant negative correlation between genetic diversity and both mean population-level ( r ²= 0.27, P < 0.001) and individual-level ( r ²= 0.54, P < 0.001) corticosterone values, as well as a negative correlation between genetic diversity and cortisol at the individual level ( r ²= 0.17, P = 0.04). No relationship was found between genetic diversity and testosterone ( P = 0.57). The strength of the correlations, especially with corticosterone, suggests potential negative consequences for overall population health, particularly for populations with the lowest genetic diversity.     

Patterns of ancestry and genetic diversity in reintroduced populations of the slimy sculpin: implications for conservation

Reintroductions are a common approach for preserving intraspecific biodiversity in fragmented landscapes. However, they may exacerbate the reduction in genetic diversity initially caused by population fragmentation because the effective population size of reintroduced populations is often smaller and reintroduced populations also tend to be more geographically isolated than native populations. Mixing genetically divergent sources for reintroduction purposes is a practice intended to increase genetic diversity. We documented the outcome of reintroductions from three mixed sources on the ancestral composition and genetic variation of a North American fish, the slimy sculpin (Cottus cognatus). We used microsatellite markers to evaluate allelic richness and heterozygosity in the reintroduced populations relative to computer simulated expectations. Sculpins in reintroduced populations exhibited higher levels of heterozygosity and allelic richness than any single source, but only slightly higher than the single most genetically diverse source population. Simulations intended to mimic an ideal scenario for maximizing genetic variation in the reintroduced populations also predicted increases, but they were only moderately greater than the most variable source population. We found that a single source contributed more than the other two sources at most reintroduction sites. We urge caution when choosing whether to mix source populations in reintroduction programs. Genetic characteristics of candidate source populations should be evaluated prior to reintroduction if feasible. When combined with knowledge of the degree of genetic distinction among sources, simulations may allow the genetic diversity benefits of mixing populations to be weighed against the risks of outbreeding depression in reintroduced and nearby populations.     

Microsatellite and mitochondrial DNA variation defines island genetic reservoirs for reintroductions of an endangered Australian marsupial, <Emphasis Type="Italic">Perameles bougainville</Emphasis>

Natural populations of the endangered western barred bandicoot (Perameles bougainville) now exist on only two islands in Shark Bay, Western Australia. Our aim was to investigate genetic diversity in natural, reintroduced, and captive populations of the bandicoots and to assess the extent of divergence between the populations. The contemporary isolation of the natural populations has resulted in heterogeneity of allele frequency between the islands, which has acted to maintain a higher combined diversity than would be expected from either population on its own. These findings highlight how remnant island populations can act as genetic reservoirs to maximize diversity for reintroductions into a species former range. Although diversity is high between island populations, diversity within populations, based on six microsatellite loci, are amongst the lowest ever recorded for populations of marsupials. The mtDNA sequence data indicate that the two remaining natural populations show only minor divergence from each other, with the five haplotypes separated by just single base pairs. The reintroduced population and captive colonies show evidence for the loss of diversity related to genetic drift operating on small isolated populations.     

Archaeological mitogenomes illuminate the historical ecology of sea otters (Enhydra lutris) and the viability of reintroduction

Genetic analyses are an important contribution to wildlife reintroductions, particularly in the modern context of extirpations and ecological destruction. To address the complex historical ecology of the sea otter (Enhydra lutris) and its failed 1970s reintroduction to coastal Oregon, we compared mitochondrial genomes of pre-extirpation Oregon sea otters to extant and historical populations across the range. We sequenced, to our knowledge, the first complete ancient mitogenomes from archaeological Oregon sea otter dentine and historical sea otter dental calculus. Archaeological Oregon sea otters (n = 20) represent 10 haplotypes, which cluster with haplotypes from Alaska, Washington and British Columbia, and exhibit a clear division from California haplotypes. Our results suggest that extant northern populations are appropriate for future reintroduction efforts. This project demonstrates the feasibility of mitogenome capture and sequencing from non-human dental calculus and the diverse applications of ancient DNA analyses to pressing ecological and conservation topics and the management of at-risk/extirpated species.     

Evaluating otter reintroduction outcomes using genetic spatial capture–recapture modified for dendritic networks

Monitoring the demographics and genetics of reintroduced populations is critical to evaluating reintroduction success, but species ecology and the landscapes that they inhabit often present challenges for accurate assessments. If suitable habitats are restricted to hierarchical dendritic networks, such as river systems, animal movements are typically constrained and may violate assumptions of methods commonly used to estimate demographic parameters. Using genetic detection data collected via fecal sampling at latrines, we demonstrate applicability of the spatial capture–recapture (SCR) network distance function for estimating the size and density of a recently reintroduced North American river otter (Lontra canadensis) population in the Upper Rio Grande River dendritic network in the southwestern United States, and we also evaluated the genetic outcomes of using a small founder group (n = 33 otters) for reintroduction. Estimated population density was 0.23–0.28 otter/km, or 1 otter/3.57–4.35 km, with weak evidence of density increasing with northerly latitude (β = 0.33). Estimated population size was 83–104 total otters in 359 km of riverine dendritic network, which corresponded to average annual exponential population growth of 1.12–1.15/year since reintroduction. Growth was ≥40% lower than most reintroduced river otter populations and strong evidence of a founder effect existed 8–10 years post‐reintroduction, including 13–21% genetic diversity loss, 84%–87% genetic effective population size decline, and rapid divergence from the source population (F _ST accumulation = 0.06/generation). Consequently, genetic restoration via translocation of additional otters from other populations may be necessary to mitigate deleterious genetic effects in this small, isolated population. Combined with non‐invasive genetic sampling, the SCR network distance approach is likely widely applicable to demogenetic assessments of both reintroduced and established populations of multiple mustelid species that inhabit aquatic dendritic networks, many of which are regionally or globally imperiled and may warrant reintroduction or augmentation efforts.     

Influence of occupation history and habitat on Washington sea otter diet

Habitat characteristics are primary determinants of nearshore marine communities. However, biological drivers like predation can also be important for community composition. Sea otters (Enhydra lutris ssp.) are a salient example of a keystone species exerting top‐down control on ecosystem community structure. The translocation and subsequent population growth and range expansion of the northern sea otter (Enhydra lutris kenyoni) in Washington State over the last five decades has created a spatio‐temporal gradient in sea otter occupation time and density, and acts as a natural experiment to quantify how sea otter population status and habitat type influence sea otter diet. We collected focal observations of sea otters foraging at sites across the gradient in varying habitat types between 2010 and 2017. We quantified sea otter diet composition and diversity, and long‐term rates of energy gain across the gradient. We found that sea otter diet diversity was positively correlated with cumulative sea otter density, while rate of energy gain was negatively correlated with cumulative density. Additionally, we found that habitat type explained 1.77 times more variance in sea otter diet composition than sea otter cumulative density. Long‐term diet studies can provide a broader picture of sea otter population status in Washington State.     

Clinical pathology and assessment of pathogen exposure in southern and Alaskan sea otters

The southern sea otter (Enhydra lutris nereis) population in California (USA) and the Alaskan sea otter (E. lutris kenyoni) population in the Aleutian Islands (USA) chain have recently declined. In order to evaluate disease as a contributing factor to the declines, health assessments of these two sea otter populations were conducted by evaluating hematologic and/or serum biochemical values and exposure to six marine and terrestrial pathogens using blood collected during ongoing studies from 1995 through 2000. Samples from 72 free-ranging Alaskan, 78 free-ranging southern, and (for pathogen exposure only) 41 debilitated southern sea otters in rehabilitation facilities were evaluated and compared to investigate regional differences. Serum chemistry and hematology values did not indicate a specific disease process as a cause for the declines. Statistically significant differences were found between free-ranging adult southern and Alaskan population mean serum levels of creatinine kinase, alkaline phosphatase, alanine aminotransferase, aspartate aminotransferase, calcium, cholesterol, creatinine, glucose, phosphorous, total bilirubin, blood urea nitrogen, and sodium. These were likely due to varying parasite loads, contaminant exposures, and physiologic or nutrition statuses. No free-ranging sea otters had signs of disease at capture, and prevalences of exposure to calicivirus, Brucella spp., and Leptospira spp. were low. The high prevalence (35%) of antibodies to Toxoplasma gondii in free-ranging southern sea otters, lack of antibodies to this parasite in Alaskan sea otters, and the pathogen's propensity to cause mortality in southern sea otters suggests that this parasite may be important to sea otter population dynamics in California but not in Alaska. The evidence for exposure to pathogens of public health importance (e.g., Leptospira spp., T. gondii) in the southern sea otter population, and the na?veté of both populations to other pathogens (e.g., morbillivirus and Coccidiodes immitis) may have important implications for their management and recovery.     

中国水獭保护现状及珠江口水獭种群重建探讨

顶级捕食者在生态系统中发挥着重要作用，受到研究者们的广泛关注。水獭作为很多淡水生态系统的顶级捕食者，在我国却长期处于被忽视的状态。我国分布有3种水獭--欧亚水獭、亚洲小爪水獭和江獭，曾经遍布我国中东部和东北地区，包括珠江口地区。但在20世纪，3种水獭均经历了大规模的种群下降，甚至区域性灭绝。在全球13种水獭中，已有3种（海獭、北美水獭和欧亚水獭）通过种群复壮和重引入实现了种群重建，这为其它水獭物种的种群重建提供了重要参考和建议。同国内其它地区类似，珠江口地区的水獭种群在20世纪后期大量减少，目前只在少数几个地点还有确切的欧亚水獭分布记录，亚洲小爪水獭和江獭已无近期记录。在珠江口重建水獭种群具有重要的生态意义和社会价值。本文对重建珠江口水獭种群的相关问题进行了分析。     

Transmission of Toxoplasma: clues from the study of sea otters as sentinels of Toxoplasma gondii flow into the marine environment

Toxoplasma gondii affects a wide variety of hosts including threatened southern sea otters (Enhydra lutris nereis) which serve as sentinels for the detection of the parasite's transmission into marine ecosystems. Toxoplasmosis is a major cause of mortality and contributor to the slow rate of population recovery for southern sea otters in California. An updated seroprevalence analysis showed that 52% of 305 freshly dead, beachcast sea otters and 38% of 257 live sea otters sampled along the California coast from 1998 to 2004 were infected with T. gondii. Areas with high T. gondii exposure were predominantly sandy bays near urban centres with freshwater runoff. Genotypic characterisation of 15 new T. gondii isolates obtained from otters in 2004 identified only X alleles at B1 and SAG1. A total of 38/50 or 72% of all otter isolates so far examined have been infected with a Type X strain. Type X isolates were also obtained from a Pacific harbor seal (Phoca vitulina) and California sea lion (Zalophus californianus). Molecular analysis using the C8 RAPD marker showed that the X isolates were more genetically heterogeneous than archetypal Type I, II and III genotypes of T. gondii. The origin and transmission of the Type X T. gondii genotype are not yet clear. Sea otters do not prey on known intermediate hosts for T. gondii and vertical transmission appears to play a minor role in maintaining infection in the populations. Therefore, the most likely source of infection is by infectious, environmentally resistant oocysts that are shed in the feces of felids and transported via freshwater runoff into the marine ecosystem. As nearshore predators, otters serve as sentinels of protozoal pathogen flow into the marine environment since they share the same environment and consume some of the same foods as humans. Investigation into the processes promoting T. gondii infections in sea otters will provide a better understanding of terrestrial parasite flow and the emergence of disease at the interface between wildlife, domestic animals and humans.     

AN ESTIMATION OF CARRYING CAPACITY FOR SEA OTTERS ALONG THE CALIFORNIA COAST

Carrying capacity (K) for the California sea otter ( Enhydra lutris nereis ) was estimated as a product of the density of sea otters at equilibrium within a portion of their existing range and the total area of available habitat. Equilibrium densities were determined using the number of sea otters observed during spring surveys in 1994, 1995, and 1996 in each of three habitat types where sea otters currently exist. Potential sea otter habitat was defined as from the California coastline to the 40-m isobath and classified as rocky, sandy, or mixed habitat according to the amount of kelp and rocky substrate in the area. The amount of habitat available to sea otters in California was estimated using a Geographic Information Systems (GIS) program. The estimated mean number of sea otters that could be supported by the marine environment to a depth of 40 m in California was 15,941 (95% CI 13,538–18,577). The GIS-based approach incorporated detailed bathymetric contours, produced repeatable and accurate estimates, and served as an innovative method of measuring sea otter habitat. We believe the approach described in this paper represents the best available information on how a sea otter population at equilibrium would be distributed along the California coast.     

How do reproductive skew and founder group size affect genetic diversity in reintroduced populations?

Reduced genetic diversity can result in short-term decreases in fitness and reduced adaptive potential, which may lead to an increased extinction risk. Therefore, maintaining genetic variation is important for the short- and long-term success of reintroduced populations. Here, we evaluate how founder group size and variance in male reproductive success influence the long-term maintenance of genetic diversity after reintroduction. We used microsatellite data to quantify the loss of heterozygosity and allelic diversity in the founder groups from three reintroductions of tuatara ( Sphenodon ), the sole living representatives of the reptilian order Rhynchocephalia. We then estimated the maintenance of genetic diversity over 400 years (∼10 generations) using population viability analyses. Reproduction of tuatara is highly skewed, with as few as 30% of males mating across years. Predicted losses of heterozygosity over 10 generations were low (1–14%), and populations founded with more animals retained a greater proportion of the heterozygosity and allelic diversity of their source populations and founder groups. Greater male reproductive skew led to greater predicted losses of genetic diversity over 10 generations, but only accelerated the loss of genetic diversity at small population size (<250 animals). A reduction in reproductive skew at low density may facilitate the maintenance of genetic diversity in small reintroduced populations. If reproductive skew is high and density-independent, larger founder groups could be released to achieve genetic goals for management.     

Reductions in the dietary niche of southern sea otters (Enhydra lutris nereis) from the Holocene to the Anthropocene

The sea otter (Enhydra lutris) is a marine mammal hunted to near extinction during the 1800s. Despite their well‐known modern importance as a keystone species, we know little about historical sea otter ecology. Here, we characterize the ecological niche of ancient southern sea otters (E. lutris nereis) using δ¹³C analysis and δ¹⁵N analysis of bones recovered from archaeological sites spanning ~7,000 to 350 years before present (N = 112 individuals) at five regions along the coast of California. These data are compared with previously published data on modern animals (N = 165) and potential modern prey items. In addition, we analyze the δ¹⁵N of individual amino acids for 23 individuals to test for differences in sea otter trophic ecology through time. After correcting for tissue‐specific and temporal isotopic effects, we employ nonparametric statistics and Bayesian niche models to quantify differences among ancient and modern animals. We find ancient otters occupied a larger isotopic niche than nearly all modern localities; likely reflecting broader habitat and prey use in prefur trade populations. In addition, ancient sea otters at the most southerly sites occupied an isotopic niche that was more than twice as large as ancient otters from northerly regions. This likely reflects greater invertebrate prey diversity in southern California relative to northern California. Thus, we suggest the potential dietary niche of sea otters in southern California could be larger than in central and northern California. At two sites, Año Nuevo and Monterey Bay, ancient otters had significantly higher δ¹⁵N values than modern populations. Amino acid δ¹⁵N data indicated this resulted from shifting baseline isotope values, rather than a change in sea otter trophic ecology. Our results help in better understanding the contemporary ecological role of sea otters and exemplify the strength of combing zooarchaeological and biological information to provide baseline data for conservation efforts.     

Development of polymorphic microsatellite loci for North American river otters (Lontra canadensis) and amplification in related Mustelids

In order to complement ecological research on native and reintroduced populations of the North American river otter (Lontra canadensis), we developed 10 polymorphic microsatellite loci that would permit us to evaluate population genetic structure and conduct fecal DNA analyses. The number of alleles per locus ranged from 3 to 14 and observed heterozygosity ranged from 0.23 to 0.68. Preliminary screening revealed that primers were polymorphic in a subset of other Mustelids.     

POTENTIAL IMPACT OF OIL SPILLS ON CALIFORNIA SEA OTTERS: IMPLICATIONS OF THE EXXON VALDEZ SPILL IN ALASKA

Based on the survival of sea otters held at rehabilitation centers during the 1989 Exxon Valdez oil spill in Alaska, we built two models of otter mortality. One was based on the relationship between mortality and distance from spill origin, the other was based on the relationship between mortality and time from the spill origin. These models are simplistic and are meant as first steps in arriving at realistic risk estimates and in providing a conceptual framework for relating oil spills and sea otter mortality. Using the distance model, we simulated the impact of an Exxon Valdez event occurring at different locations along the California coast. A spill at the Monterey Peninsula had the greatest impact, exposing 90% of the California sea otter population to oil and killing at least 50% of the individuals. The time model was used to predict the mortality of otters exposed to oil of various ages and for various periods of time. It suggested that efforts to rehabilitate otters should be discontinued 20-30 d after a spill. The limitations of the data available from the Exxon Valdez spill emphasize the importance of being prepared to conduct appropriate research during the next oil spill in sea otter habitat.     

River otter population size estimation using noninvasive latrine surveys

Across much of North America, river otter (Lontra canadensis) populations were extirpated or greatly reduced by the early 20th century. More recently, reintroductions have resulted in restored populations and the recommencement of managed trapping. Perhaps the best example of these river otter reintroductions occurred in Missouri, regarded as one of the most successful carnivore recovery programs in history. However, abundance estimates for river otter populations are difficult to obtain and often contentious when used to underpin management activities. We assessed the value of latrine site monitoring as a mechanism for quantifying river otter abundance. Analyses of fecal DNA to identify individual animals may result in an improved population estimate and have been used for a variety of mammal species. We optimized laboratory protocols, redesigned existing microsatellite primers, and calculated genotyping error rates to enhance genotyping success for a large quantity of river otter scat samples. We also developed a method for molecular sexing. We then extracted DNA from 1,421 scat samples and anal sac secretions (anal jelly) collected during latrine site counts along 22–34-km stretches representing 8–77% of 8 rivers in southern Missouri in 2009. Error rates were low for the redesigned microsatellites. We obtained genotypes at 7–10 microsatellite loci for 24% of samples, observing highest success for anal jelly samples (71%) and lowest for fresh samples (collected within 1 day of defecation). We identified 63 otters (41 M, 22 F) in the 8 rivers, ranging from 2 to 14 otters per river. Analyses using program CAPWIRE resulted in population estimates similar to the minimum genotyping estimate. Density estimates averaged 0.24 otters/km. We used linear regression to develop and contrast models predicting population size based on latrine site and scat count indices, which are easily collected in the field. Population size was best predicted by a combination of scats per latrine and latrines per kilometer. Our results provide methodological approaches to guide wildlife managers seeking to initiate similar river otter fecal genotyping studies, as well as to estimate and monitor river otter population sizes. © 2011 The Wildlife Society.     

Novel polymorphic microsatellite loci for a new target species,the sea cucumber Holothuria mammata

With traditional finfish fisheries declining and pushing transition to new invertebrates target species, sea cucumbers have been heavily explored, suffering global overexploitation and worldwide depletion of their stocks.Nowadays, holothurians from the Mediterranean Sea and NE Atlantic Ocean are being exported to Asian markets. The scarce knowledge about their biology, population dynamics, ecology and genetics, is promoting defective management of their fisheries.We report the development of 9 novel polymorphic microsatellites markers for Holothuria mammata and characterized them by testing in three different sample locations. All nine microsatellites revealed high polymorphism and diversity, with high number of alleles, ranged from 11 to 22 and expected heterozygosity, between 0.52 and 0.92. Significant genetic differentiation was found between populations.These microsatellites are providing valuable information which could be applied to fisheries management including, identification of stocks, assessment of their genetic diversity, estimation of gene flow and monitoring the fishery effects on exploited populations.     

KILLER WHALES AND MARINE MAMMAL TRENDS IN THE NORTH PACIFIC—A RE-EXAMINATION OF EVIDENCE FOR SEQUENTIAL MEGAFAUNA COLLAPSE AND THE PREY-SWITCHING HYPOTHESIS

Springer et al . (2003) contend that sequential declines occurred in North Pacific populations of harbor and fur seals, Steller sea lions, and sea otters. They hypothesize that these were due to increased predation by killer whales, when industrial whaling's removal of large whales as a supposed primary food source precipitated a prey switch. Using a regional approach, we reexamined whale catch data, killer whale predation observations, and the current biomass and trends of potential prey, and found little support for the prey-switching hypothesis. Large whale biomass in the Bering Sea did not decline as much as suggested by Springer et al ., and much of the reduction occurred 50–100 yr ago, well before the declines of pinnipeds and sea otters began; thus, the need to switch prey starting in the 1970s is doubtful. With the sole exception that the sea otter decline followed the decline of pinnipeds, the reported declines were not in fact sequential. Given this, it is unlikely that a sequential megafaunal collapse from whales to sea otters occurred. The spatial and temporal patterns of pinniped and sea otter population trends are more complex than Springer et al . suggest, and are often inconsistent with their hypothesis. Populations remained stable or increased in many areas, despite extensive historical whaling and high killer whale abundance. Furthermore, observed killer whale predation has largely involved pinnipeds and small cetaceans; there is little evidence that large whales were ever a major prey item in high latitudes. Small cetaceans (ignored by Springer et al .) were likely abundant throughout the period. Overall, we suggest that the Springer et al . hypothesis represents a misleading and simplistic view of events and trophic relationships within this complex marine ecosystem.     

Decline and recovery in otter Lutra lutra populations in Italy

• 1 Changes in otter Lutra lutra distribution in Italy were examined by analysing geographical, historical and survey data.
• 2 As in other European countries, otters declined sharply in Italy during the late 1970s and throughout the 1980s. Between 1985 and 2004 the species became extinct, except for some reintroductions, in northern and most of central Italy while the species appears to have substantially recovered in its southern range. This recovery of the otter population is apparently not due to increased research effort, but reflects a real expansion of range.
• 3 Differences in the degree of range reduction during the second half of the 20th century and in the availability of suitable habitats are probably the major factors that have determined the two opposite trends shown by otter populations in the last 20 years.
• 4 Better knowledge of otter status and distribution is needed for effective conservation management. We suggest that a national survey of the Italian otter population that employs genetic approaches should represent a first step of the national action plan for otter conservation.

     

Genetic Diversity and Divergence among Bighorn Sheep from Reintroduced Herds in Washington and Idaho

Bighorn sheep (Ovis canadensis) populations in the western United States have undergone widespread declines and extirpations since the late nineteenth century as a consequence of introduced diseases, competition with livestock, and unregulated hunting. Washington, Idaho, USA, and British Columbia, Canada were historically thought to be occupied by 2 bighorn lineages or subspecies: Rocky Mountain (O. c. canadensis) and California (O. c. californiana). The putative California lineage was completely extirpated in the United States, and reintroductions to reestablish populations were sourced directly or indirectly from a single region in southern British Columbia. Restoration efforts have attempted to maintain the diversity and divergence of these 2 lineages, sometimes referred to as subspecies although taxonomic classifications have changed over time. In this study we describe genetic variation in a subset of native and reintroduced herds of California and Rocky Mountain bighorn sheep. We examined genetic diversity and divergence between bighorn sheep herds using 15 microsatellite loci, including 4 loci linked to genes involved in immune function. We analyzed 504 samples from reintroduced herds in Washington (n = 10 California herds, n = 4 Rocky Mountain herds) and Idaho (n = 5 California), and source herds in Oregon (n = 1 Rocky Mountain) and British Columbia (n = 5 California, 1 Rocky Mountain). Genetic structure reflected known reintroduction history, and geographic proximity also was associated with decreased genetic divergence. Herds in Washington and Idaho sourced from California bighorn sheep were less genetically diverse than those sourced from Rocky Mountain herds. Also, levels of relatedness within and across California herds were higher than in Rocky Mountain herds and similar to what would be expected for full and half siblings. Lower diversity and higher relatedness among California herds is a concern for long-term fitness and likely related to past population bottlenecks, fewer source populations, and management history, such as entirely sourcing California herds from British Columbia. Genetic divergence of neutral loci between California and Rocky Mountain herds was greater than that of adaptive loci, potentially indicating that balancing selection has maintained similar genetic diversity across lineages in loci associated with immune and other adaptive functions. Thus, we recommend future reintroductions and augmentations should continue to use source populations from the appropriate California or Rocky Mountain lineage to avoid potential outbreeding depression and maintain possible adaptive differences. This could be accomplished by obtaining sheep from ≥1 source within the genetic lineage, while avoiding sourcing from admixed herds. Future work encompassing a broader geographic sampling of populations and a greater portion of the genome is necessary to better evaluate the degree to which contemporary divergence between lineages is associated with recent founder effects and genetic isolation or evolutionary adaptation. © 2021 The Wildlife Society