PATTERNS OF REPRODUCTION,GENETIC DIVERSITY,AND GENETIC DIFFERENTIATION IN CALIFORNIA POPULATIONS OF THE GENICULATE CORALLINE ALGA LITHOTHRIX ASPERGILLUM (RHODOPHYTA)1

The reproductive composition and genetic diversity of populations of the red seaweed Lithothrix aspergillum Gray (O. Corallinales) were studied at three southern California sites (Shaw's Cove and Treasure Island, Laguna Beach; Indian Rock, Santa Catalina Island) and at a fourth site (Bodega Bay) located in northern California. Sexually reproducing populations were confined to southern California. Diploid individuals were numerically dominant over haploid (gametophytic) individuals at all sites. Intertidal and subtidal subpopulations from Shaw's Cove differed in their reproductive profiles. Most intertidal specimens found on emersed surfaces were densely branched, turf-forming, and bore tetrasporangial (68.6%), carposporangial (11.4%), or spermatangial (5.7%) conceptacles, reflecting a sexual life history; none produced asexual bispores. In contrast, 74.3% of the larger, loosely branched subtidal specimens bore bisporangial conceptacles indicative of asexual reproduction. Nearly 70% of the Indian Rock thalli showed no evidence of conceptacle formation. Only asexual, diploid bispore-producing thalli were obtained from the Bodega Bay site. Genetic diversity (mean number of alleles per locus, percent of polymorphic loci, and average expected heterozygosity) of diploid L. aspergillum populations varied with life-history characteristics and geographic location. A total of 30 alleles was inferred from zymograms of 16 loci examined by starch-gel electrophoresis; of these loci, 11 were polymorphic. The genetic diversity of sexual, diploid populations of L. aspergillum (alleles per locus [A/L] = 1.4-1.5; percent polymorphic loci [%P] = 37.5-50.0) was relatively high compared with other red seaweeds. Lowest diversity (A/L = 1.0; %P = 0.0) occurred in the exclusively asexual Bodega Bay population which consisted of genetic clones. All sexual L. aspergillum populations deviated significantly from Hardy-Wein-berg expectations due to lower than expected heterozygosity. Genetic differentiation (Wright's F_statistic [F_ST]; Nei's Genetic Distance [D]) among sexually reproducing southern California populations was low (F_ST= 0.030) on a local scale (ca. 5 km), suggesting high levels of gene flow, but high genetic differention (F_ST= 0.390 and 0.406) occurred among southern California populations separated by ca. 70 km. Very high genetic differentiation (F_ST= 0.583–0.683) was obtained between northern and southern California populations separated by 700–760 km. Our genetic and reproductive data suggest that the L. aspergillum population from Bodega Bay is sustained by perennation, vegetative propagation, or asexual reproduction by bispores and may represent an isolated remnant or a population established by a founder event.     

Barn owls (<Emphasis Type="Italic">Tyto alba</Emphasis>) in western North America: phylogeographic structure,connectivity, and genetic diversity

The barn owl (Tyto alba) is a non-migratory species widely distributed across much of North America in areas with extensive old-field and grassland habitat and without extensive winter snow cover. We investigated the genetic diversity and phylogeographic patterns of barn owl populations in western North America, ranging from British Columbia (BC) to southern California, and one eastern population from Pennsylvania. We also determined the genetic distinctiveness of a population off the coast of southern California, Santa Barbara Island, as management plans to control the local owl population are being considered to decrease predation rate on the now threatened Scripps’s Murrelet (Synthliboramphus scrippsi). Using 8 polymorphic microsatellite markers (N = 126) and ND2 mitochondrial sequences (N = 37), we found little to no genetic structure among all sampled regions, with the exception of Santa Barbara Island. The BC mainland population, despite its northwestern geographically peripheral location and ongoing habitat degradation, is not genetically depauperate. However, individuals from Vancouver Island, likewise a peripheral population in BC, exhibited the lowest genetic diversity of all sampled locations. The low global F_ST value (0.028) estimated from our study suggests that old-field agricultural habitats are well connected in North America. Since the BC population has declined by about 50 % within the last three decades, it is vital to focus on preserving the remaining barn owl habitats in BC to allow successful establishment from neighbouring populations. Additionally, our microsatellite data revealed that the population on Santa Barbara Island showed genetic divergence from its continental counterpart. Mitochondrial data, however, demonstrated that this island population is not a monophyletic lineage containing unique haplotypes, and hence cannot be designated as an Evolutionarily Significant Unit.     

Genetic evidence for the persistence of the critically endangered Sierra Nevada red fox in California

California is home to both the native state-threatened Sierra Nevada red fox (Vulpes vulpes necator), which historically inhabited high elevations of the Sierra Nevada and Cascade mountains, and to multiple low-elevation red fox populations thought to be of exotic origin. During the past few decades the lowland populations have dramatically expanded their distribution, and possibly moved into the historic range of the native high-elevation fox. To determine whether the native red fox persists in its historic range in California, we compared mitochondrial cytochrome-b haplotypes of the only currently-known high-elevation population (n = 9 individuals) to samples from 3 modern lowland populations (n = 35) and historic (1911–1941) high-elevation (n = 22) and lowland (n = 7) populations. We found no significant population differentiation among the modern and historic high-elevation populations (average pairwise F _ST = 0.06), but these populations differed substantially from all modern and historic lowland populations (average pairwise F _ST = 0.52). Among lowland populations, the historic and modern Sacramento Valley populations were not significantly differentiated from one another (F _ST = −0.06), but differed significantly from recently founded populations in the San Francisco Bay region and in southern California (average pairwise F _ST = 0.42). Analysis of molecular variance indicated that 3 population groupings (mountain, Sacramento Valley, and other lowland regions) explained 45% of molecular variance (F _CT = 0.45) whereas only 4.5% of the variance was partitioned among populations within these groupings (F _SC = 0.08). These findings provide strong evidence that the native Sierra Nevada red fox has persisted in northern California. However, all nine samples from this population had the same haplotype, suggesting that several historic haplotypes may have become lost. Unidentified barriers have apparently prevented gene flow from the Sacramento Valley population to other eastern or southern populations in California. Future studies involving nuclear markers are needed to assess the origin of the Sierra Nevada red fox and to quantify levels of nuclear gene flow.     

Phenotypic variation among populations of Atherinops affinis(Atherinopsidae) with insights from a geometric morphometric analysis

Morphological character variation was examined in Atherinops affinis , a temperate marine silverside with a broad geographic range and presumed limited powers of dispersal. Populations of this species were sampled from three California mainland sites, one Channel Island site and one site in the upper Gulf of California. A geometric morphometric analysis yielded higher resolution in the assessment of phenotypic divergence among the four Pacific coast populations than either body measurement or meristic analysis, and it showed that most of the shape variation among these populations occurs in the head region and body depth of the fish. All three analyses supported the hypothesis that populations of A. affinis from central and southern California coastal waters and from Santa Catalina Island are morphologically distinct from each other; the Santa Catalina Island population was found to be the most divergent. On the basis of meristic characters alone, the population of A. affinis from the upper Gulf of California was different from A. affinis populations along the Pacific coast of California. The analyses revealed variation in several morphological characters, e.g . body depth and meristics, known to vary in association with environmental conditions. Given that A. affinis appears to have low among‐population genetic variation, this species may be phenotypically plastic in response to the environmental conditions of the habitat of each population.     

Comparison of Four Mendelian Loci of the California Sea Hare (Aplysia californica) from Populations of the Coast of California and the Sea of Cortez

Aplysia californica is a species widely used in neurobiology, and specimens are collected from a wide range of places along its distribution range. A. californica is endemic to the coast of California and the Gulf of California. On the west coast, this is an unusual distribution range relative to other benthic species from that region. Four polymorphic nuclear Mendelian markers were identified (three single-copy nuclear DNA loci and one microsatellite) for an initial survey of genetic variation of wild populations. F _ST values not significantly different from 0 (overall F _ST= 0.0148) suggest there was no geographic genetic population subdivision in 177 individuals examined. Received December 3, 1999; accepted March 3, 2000.     

First report of the Asian seaweed <Emphasis Type="Italic">Sargassum filicinum</Emphasis> Harvey (Fucales) in California,USA

We report the occurrence of the brown seaweed Sargassum filicinum Harvey in southern California. Sargassum filicinum is native to Japan and Korea. It is monoecious, a trait that increases its chance of establishment. In October 2003, Sargassum filicinum was collected in Long Beach Harbor. In April 2006, we discovered three populations of this species on the leeward west end of Santa Catalina Island. Many of the individuals were large, reproductive and senescent; a few were small, young but precociously reproductive. We compared the sequences of the mitochondrial cox3 gene for 6 individuals from the 3 sites at Catalina with 3 samples from 3 sites in the Seto Inland Sea, Japan region. The 9 sequences (469 bp in length) were identical. Sargassum filicinum may have been introduced through shipping to Long Beach; it may have spread to Catalina via pleasure boats from the mainland.     

Population structure of loggerhead shrikes in the California Channel Islands

The loggerhead shrike (Lanius ludovicianus), a songbird that hunts like a small raptor, maintains breeding populations on seven of the eight California Channel Islands. One of the two subspecies, L. l. anthonyi, was described as having breeding populations on six of the islands while a second subspecies, L. l. mearnsi, was described as being endemic to San Clemente Island. Previous genetic studies have demonstrated that the San Clemente Island loggerhead shrike is well differentiated genetically from both L. l. anthonyi and mainland populations, despite the fact that birds from outside the population are regular visitors to the island. Those studies, however, did not include a comparison between San Clemente Island shrikes and the breeding population on Santa Catalina Island, the closest island to San Clemente. Here we use mitochondrial control region sequences and nuclear microsatellites to investigate the population structure of loggerhead shrikes in the Channel Islands. We confirm the genetic distinctiveness of the San Clemente Island loggerhead shrike and, using Bayesian clustering analysis, demonstrate the presence and infer the source of the nonbreeding visitors. Our results indicate that Channel Island loggerhead shrikes comprise three distinct genetic clusters that inhabit: (i) San Clemente Island, (ii) Santa Catalina Island and (iii) the Northern Channel Islands and nearby mainland; they do not support a recent suggestion that all Channel Island loggerhead shrikes should be managed as a single entity.     

The population genetics of nonmigratory Allen’s Hummingbird (Selasphorus sasin sedentarius) following a recent mainland colonization

Allen''s Hummingbird comprises two subspecies, one migratory (Selasphorus sasin sasin) and one nonmigratory (S. s. sedentarius). The nonmigratory subspecies, previously endemic to the California Channel Islands, apparently colonized the California mainland on the Palos Verdes Peninsula some time before 1970 and now breeds throughout coastal southern California. We sequenced and compared populations of mainland nonmigratory Allen''s Hummingbird to Channel Island populations from Santa Catalina, San Clemente, and Santa Cruz Island. We found no evidence of founder effects on the mainland population. Values of nucleotide diversity on the mainland were higher than on the Channel Islands. There were low levels of divergence between the Channel Islands and the mainland, and Santa Cruz Island was the most genetically distinct. Ecological niche models showed that rainfall and temperature variables on the Channel Islands are similar in the Los Angeles basin and predicted continued expansion of nonmigratory Allen''s Hummingbird north along the coast and inland. We also reviewed previous genetic studies of vertebrate species found on the Channel Islands and mainland and showed that broad conclusions regarding island–mainland patterns remain elusive. Challenges include the idiosyncratic nature of colonization itself as well as the lack of a comprehensive approach that incorporates similar markers and sampling strategies across taxa, which, within the context of a comparative study of island–mainland relationships, may lead to inconsistent results.     

Genetic Divergence of an Avian Endemic on the Californian Channel Islands

The Californian Channel Islands are near–shore islands with high levels of endemism, but extensive habitat loss has contributed to the decline or extinction of several endemic taxa. A key parameter for understanding patterns of endemism and demography in island populations is the magnitude of inter–island dispersal. This paper estimates the extent of migration and genetic differentiation in three extant and two extinct populations of Channel Island song sparrows (Melospiza melodia graminea). Inter–island differentiation was substantial (G''''_ST: 0.14–0.37), with San Miguel Island having the highest genetic divergence and lowest migration rates. Santa Rosa and Santa Cruz Island populations were less diverged with higher migration rates. Genetic signals of past population declines were detected in all of the extant populations. The Channel Island populations were significantly diverged from mainland populations of M. m. heermanni (G''''_ST: 0.30–0.64). Ten mtDNA haplotypes were recovered across the extant and extinct Channel Island population samples. Two of the ten haplotypes were shared between the Northern and Southern Channel Islands, with one of these haplotypes being detected on the Californian mainland. Our results suggest that there is little contemporary migration between islands, consistent with early explanations of avian biogeography in the Channel Islands, and that song sparrow populations on the northern Channel Islands are demographically independent.     

Contrasting patterns of morphological and neutral genetic divergence among geographically proximate populations of sockeye salmon Oncorhynchus nerka in Lake Aleknagik,Alaska

Levels of differentiation in morphological traits (age at maturity, body length at age, egg mass and body depth) and spawning time were examined in sockeye salmon Oncorhynchus nerka from three geographically proximate but physically distinct creeks in Lake Aleknagik, Alaska. Happy Creek fish had significantly greater values for most measured morphological traits, and Eagle Creek fish spawned significantly later than fish in the other creeks. Phenotypic differentiation between creeks, measured as P_ST, was then compared with microsatellite marker differentiation between creeks, measured as F_ST. No correlations were apparent between P_ST and F_ST values, and P_ST values were generally significantly larger than zero (P_ST= 0·0018–0·31) whereas F_ST values were not (F_ST=?0·0004 to 0·0016). The insignificant pair‐wise F_ST values between creek samples indicated that gene flow occurs between creeks, assuming the creek populations have reached migration–drift equilibrium. However, the strong homing behaviour of sockeye salmon precludes a scenario in which fish from the three creeks constitute a single population that segregates by body size. Rather, significant phenotypic differentiation suggests that strong divergent selection occurs on the phenotypic traits despite the homogenizing effects of gene flow.     

Genetic diversity and seed production in Santa Lucia fir (Abies bracteata), a relict of the Miocene Broadleaved Evergreen Forest

Santa Lucia fir (Abies bracteata), is a unique fir, the sole member of the subgenus Pseudotorreya. It is a relict of the Miocene broadleaved evergreen sclerophyll forest, and is now restricted to a highly fragmented range in the Santa Lucia Mountains of central coastal California. Expected heterozygosity for 30 isozyme loci in 18 enzyme systems, averaged over six populations that spanned the species’ north–south range, was only 0.036. Despite a fragmented range and isolated populations, differentiation (F _ST) was only 0.080 for mature trees, and the number of migrants per generation (Nm) was 2.88 or 3.83, depending on the method of estimation. F _ST for embryos was lower, 0.025, and Nm correspondingly higher, 9.75. Nei’s genetic distances were small and unrelated to geographic distances between populations. The proportion of full seeds per cone was only 0.082–0.488, depending on population, which suggests a high incidence of selfing followed by embryo abortion. However, the level of accumulated inbreeding, F _IS, in mature trees was low, only 0.049. By contrast, F _IS for embryos was 0.388, which indicates a high proportion of selfed progeny, in agreement with the low seed yields. The difference in inbreeding coefficients between seed trees and their progeny suggest that most inbreds are eliminated before maturity and, therefore, seed production, already low, overestimates the true potential for regeneration of these populations. These results have implications for conservation.     

Evidence for interannual variation in genetic structure of Dungeness crab (Cancer magister) along the California Current System

Using a combination of population‐ and individual‐based analytical approaches, we provide a comprehensive examination of genetic connectivity of Dungeness crab (Cancer magister) along ~1,200 km of the California Current System (CCS). We sampled individuals at 33 sites in 2012 to establish a baseline of genetic diversity and hierarchal population genetic structure and then assessed interannual variability in our estimates by sampling again in 2014. Genetic diversity showed little variation among sites or across years. In 2012, we observed weak genetic differentiation among sites (F_ST range = ?0.005–0.014) following a pattern of isolation by distance (IBD) and significantly high relatedness among individuals within nine sampling sites. In 2014, pairwise F_ST estimates were lower (F_ST range = ?0.014–0.007), there was no spatial autocorrelation, and fewer sites had significant evidence of relatedness. Based on these findings, we propose that interannual variation in the physical oceanographic conditions of the CCS influences larval recruitment and thus gene flow, contributing to interannual variation in population genetic structure. Estimates of effective population size (N_e) were large in both 2012 and 2014. Together, our results suggest that Dungeness crab in the CCS may constitute a single evolutionary population, although geographically limited dispersal results in an ephemeral signal of IBD. Furthermore, our findings demonstrate that populations of marine organisms may be susceptible to temporal changes in population genetic structure over short time periods; thus, interannual variability in population genetic measures should be considered.     

Dictyota cyanoloma (Dictyotales,Phaeophyceae), a Newly Introduced Brown Algal Species in California

Here, we report for the first time the presence of Dictyota cyanoloma in southern California. Dictyota cyanoloma is conspicuous in harbors and bays by its distinctive bright blue‐iridescent margins. This species was originally described from Europe, but subsequent studies have revealed that it represented an introduction from Australia. The current distribution of D. cyanoloma comprises southern Australia and the North East Atlantic, including the Mediterranean Sea and the Macaronesian islands. The presence of D. cyanoloma in southern California is supported by molecular cox1 and psbA gene sequences. A reconstruction of the invasive history based on nine polymorphic microsatellite markers reveals a close affinity of the Californian specimens with European populations. Dictyota cyanoloma in the United States appears to be (so far) restricted to the Californian coast from San Diego Bay in the south to Santa Catalina Island and Long Beach Harbor in the north. A correlative species distribution model suggests gradually declining habitat suitability north of the Southern Californian Bight and high suitability in Baja California, including the Gulf of California. Finally, its widespread abundance in bays and harbors suggests shipping is a likely transport mechanism.     

Low mtDNA variation and shallow population structure of the Chinese pomfret Pampus chinensis along the China coast

In the present study, population genetic structure and genetic diversity of the Chinese pomfret Pampus chinensis, along the China coast were investigated and compared with that from Indonesia using mitochondrial DNA cytochrome b gene sequences. A total of 28 variable sites (including 18 singleton sites and 10 parsimony information sites) were observed and 23 haplotypes were defined in 330 individuals from 11 localities. The haplotype diversity (H_D) of the populations ranged from 0·540 to 0·828, the nucleotide diversity (π) ranged from 0·081 to 0·295%. Pairwise F_ST statistics showed that significant genetic divergence occurred among populations from different geographical regions. The high dispersal capabilities, geographic segregation and ocean currents may be responsible for the present population genetic structure in this species. In addition, a population expansion event during the late Pleistocene period was inferred. The time of population expansion was estimated to occur about 117 000–169 000 years ago.     

Exclusion of introduced deer increases size and seed production success in an island‐endemic plant species

The presence of extra‐local invaders, such as the southern California mule deer (Odocoileus hemionus) on Santa Catalina Island, may contribute to more selective and insidious effects within the unique ecosystems that have evolved in their absence. Studies at the species level may detect effects not noticed in broader, community level vegetation monitoring or help tease apart differences in the level of effect among the various ecological components of an invaded system. In this initial study, we measured the impacts of herbivory by mule deer, a species native to analogous habitats on the adjacent mainland, on size and seed production success for Crocanthemum greenei (island rush‐rose), a federally listed sub‐shrub that is not present on mainland California. We found deer exclusion resulted in an overall increase in stem measurement of 18.8 cm. Exclosure populations exhibited complete seed production success, whereas control populations showed significantly reduced success and exhibited complete failure within 58% of populations. These results show that the introduced mule deer on Santa Catalina Island are negatively affecting a federally threatened plant species. This strongly implies that the current deer management strategy is insufficient, if one of its goals is biodiversity and endemic species conservation.     

Population genetic structure of annual and perennial populations of Zostera marina L. along the Pacific coast of Baja California and the Gulf of California

The Baja California peninsula represents a biogeographical boundary contributing to regional differentiation among populations of marine animals. We investigated the genetic characteristics of perennial and annual populations of the marine angiosperm, Zostera marina, along the Pacific coast of Baja California and in the Gulf of California, respectively. Populations of Z. marina from five coastal lagoons along the Pacific coast and four sites in the Gulf of California were studied using nine microsatellite loci. Analyses of variance revealed significant interregional differentiation, but no subregional differentiation. Significant spatial differentiation, assessed using θ_ST values, was observed among all populations within the two regions. Z. marina populations along the Pacific coast are separated by more than 220 km and had the greatest θ_ST (0.13–0.28) values, suggesting restricted gene flow. In contrast, lower but still significant genetic differentiation was observed among populations within the Gulf of California (θ_ST = 0.04–0.18), even though populations are separated by more than 250 km. This suggests higher levels of gene flow among Gulf of California populations relative to Pacific coast populations. Direction of gene flow was predominantly southward among Pacific coast populations, whereas no dominant polarity in the Gulf of California populations was observed. The test for isolation by distance (IBD) showed a significant correlation between genetic and geographical distances in Gulf of California populations, but not in Pacific coast populations, perhaps because of shifts in currents during El Niño Southern Oscillation (ENSO) events along the Pacific coast.     

Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction‐site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small N_e (range = 2.1–89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome‐wide divergence. Nonetheless, outlier tests identified 3.6–6.6% of loci as high F_ST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high F_ST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small N_e in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential.     

Microsatellite Markers Reveal Strong Genetic Structure in the Endemic Chilean Dolphin

Understanding genetic differentiation and speciation processes in marine species with high dispersal capabilities is challenging. The Chilean dolphin, Cephalorhynchus eutropia, is the only endemic cetacean of Chile and is found in two different coastal habitats: a northern habitat with exposed coastlines, bays and estuaries from Valparaíso (33°02′S) to Chiloé (42°00′S), and a southern habitat with highly fragmented inshore coastline, channels and fjords between Chiloé and Navarino Island (55°14′S). With the aim of evaluating the potential existence of conservation units for this species, we analyzed the genetic diversity and population structure of the Chilean dolphin along its entire range. We genotyped 21 dinucleotide microsatellites for 53 skin samples collected between 1998 and 2012 (swab: n = 8, biopsy: n = 38, entanglement n = 7). Bayesian clustering and spatial model analyses identified two genetically distinct populations corresponding to the northern and southern habitats. Genetic diversity levels were similar in the two populations (He: 0.42 v/s 0.45 for southern and northern populations, respectively), while effective size population was higher in the southern area (Ne: 101 v/s 39). Genetic differentiation between these two populations was high and significant (F_ST = 0.15 and R_ST = 0.19), indicating little or no current gene flow. Because of the absence of evident geographical barriers between the northern and southern populations, we propose that genetic differentiation may reflect ecological adaptation to the different habitat conditions and resource uses. Therefore, the two genetic populations of this endemic and Near Threatened species should be considered as different conservation units with independent management strategies.     

Inter and intra‐population phenotypic and genotypic structuring in the European whitefish Coregonus lavaretus,a rare freshwater fish in Scotland

This study revealed between‐lake genetic structuring between Coregonus lavaretus collected from the only two native populations of this species in Scotland, U.K. (Lochs Eck and Lomond) evidenced by the existence of private alleles (12 in Lomond and four in Eck) and significant genetic differentiation (F_ST = 0·056) across 10 microsatellite markers. Juvenile C. lavaretus originating from eggs collected from the two lakes and reared in a common‐garden experiment showed clear phenotypic differences in trophic morphology (i.e. head and body shape) between these populations indicating that these characteristics were, at least partly, inherited. Microsatellite analysis of adults collected from different geographic regions within Loch Lomond revealed detectable and statistically significant but relatively weak genetic structuring (F_ST = 0·001–0·024) and evidence of private alleles related to the basin structure of the lake. Within‐lake genetic divergence patterns suggest three possibilities for this observed pattern: (1) differential selection pressures causing divergence into separate gene pools, (2) a collapse of two formerly divergent gene pools and (3) a stable state maintained by balancing selection forces resulting from spatial variation in selection and lake heterogeneity. Small estimates of effective population sizes for the populations in both lakes suggest that the capacity of both populations to adapt to future environmental change may be limited.