Levels Of Population Structure Research Articles

Genetic Characterization of the Savannah and Pee Dee River Populations of Robust Redhorse (Moxostoma robustum) with Conservation Implications

Robust Redhorse (Moxostoma robustum) is a deep-dwelling catostomid that lives in southeastern rivers of the United States. After being lost to science for about 100 years, M. robustum was rediscovered in the 1980s by the Georgia DNR and is a federal species of special concern. Our goal was to genetically characterize populations of M. robustum in the Savannah and Pee Dee rivers based on genetic diversity and population structure using a suite of ten microsatellites. Substantial levels of population structure were detected between rivers (RST = 0.308), with high genetic diversity (0.81–0.87) and low inbreeding in both systems. Long-term estimates of effective population sizes were very high for both systems, but contemporary estimates were substantially lower, with the Pee Dee River estimate being of concern from a conservation standpoint. Their long life span and overlapping generations result in a high potential for across-year-class spawning and are likely contributing to the maintenance of high genet...

Assessing the Impact of Population Stratification on Association Studies of Rare Variation

Aims: The study of rare variants, which can potentially explain a great proportion of heritability, has emerged as an important topic in human gene mapping of complex diseases. Although several statistical methods have been developed to increase the power to detect disease-related rare variants, none of these methods address an important issue that often arises in genetic studies: false positives due to population stratification. Using simulations, we investigated the impact of population stratification on false-positive rates of rare-variant association tests. Methods: We simulated a series of case-control studies assuming various sample sizes and levels of population structure. Using such data, we examined the impact of population stratification on rare-variant collapsing and burden tests of rare variation. We further evaluated the ability of 2 existing methods (principal component analysis and genomic control) to correct for stratification in such rare-variant studies. Results: We found that population stratification can have a significant influence on studies of rare variants especially when the sample size is large and the population is severely stratified. Our results showed that principal component analysis performed quite well in most situations, while genomic control often yielded conservative results. Conclusions: Our results imply that researchers need to carefully match cases and controls on ancestry in order to avoid false positives caused by population structure in studies of rare variants, particularly if genome-wide data are not available.

Genetic structuring of the common shrew,Sorex araneus(Soricomorpha: Soricidae) in the Polish Sudetes may suggest ways of northwards colonization

An effect of geographical barriers on the level of population structuring and ways of northwards colonization in the common shrew Sorex araneus was investigated by contrasting gene flow inferred by one Y-linked and eight autosomal microsatellites. A total of 102 shrews trapped at eight localities separated by mountain ridges of the Śnieżnik Massif (East Sudetes, Poland) were studied. The genetic structure of populations was estimated using the standard analysis of molecular variance based on F-statistic, as well as two clustering methods implemented in Structure and Geneland. In pair-wise population comparisons both FST and RST were estimated. A Mantel-test was used to investigate the patterns and causes of structuring. No significant correlation between genetic differentiation and geographical distance was found for autosomal loci and for the Y-linked locus. Significant genetic structuring was found in four out of six pairs of populations. Studying autosomal loci we found nonsignificant correlations between pair-wise matrices of FST and RST and the presence of the barrier. On the other hand, for the Y-linked locus these correlations were significant, both for FST and RST, suggesting reduced gene flow between populations for males. Patterns of genetic structuring in the common shrew of the Massif of Śnieżnik may suggest two possible ways of northwards colonization, which promoted genetic distinction of shrews migrating different routes.

Chromosomal and morphological divergences in Atlantic populations of the frillfin goby Bathygobius soporator (Gobiidae, Perciformes)

Evidence of population fragmentation and speciation processes has been reported for several species of marine fish, including small cryptobenthics forms of Atlantic. Four populations of the frillfin goby Bathygobius soporator, which cover a wide geographical area of the Atlantic coast in North/Northeast Brazil, were cytogenetically analyzed and their morphological patterns compared. Continental populations of this species (denominated MA, RN, and BA) exhibited divergences in morphological and chromosomal characteristics compatible with interpopulation differentiation. However, specimens from Rocas Atoll (RA) displayed notable divergences in these parameters, corroborating molecular data that suggest they are a different species. Furthermore, the RN population showed intrinsic chromosomal markers, revealing a certain level of population structuring. Chromosomal and morphological patterns found confirm the biodiversity of B. soporator, substantiating an evolutionary scenario of population divergences and adaptation to new habitats.

Population structure and marker–trait association analysis of the US peanut (Arachis hypogaea L.) mini-core collection

Peanut (Arachis hypogaea L.) is one of the most important oilseed and nutritional crops in the world. To efficiently utilize the germplasm collection, a peanut mini-core containing 112 accessions was established in the United States. To determine the population structure and its impact on marker-trait association, this mini-core collection was assessed by genotyping 94 accessions with 81 SSR markers and two functional SNP markers from fatty acid desaturase 2 (FAD2). Seed quality traits (including oil content, fatty acid composition, flavonoids, and resveratrol) were obtained through nuclear magnetic resonance (NMR), gas chromatography (GC), and high-performance liquid chromatography (HPLC) analysis. Genetic diversity and population structure analysis identified four major subpopulations that are related to four botanical varieties. Model comparison with different levels of population structure and kinship control was conducted for each trait and association analyses with the selected models verified that the functional SNP from the FAD2A gene is significantly associated with oleic acid (C18:1), linoleic acid (C18:2), and oleic-to-linoleic (O/L) ratio across this diverse collection. Even though the allele distribution of FAD2A was structured among the four subpopulations, the effect of FAD2A gene remained significant after controlling population structure and had a likelihood-ratio-based R ( 2 ) (R ( LR ) ( 2 ) ) value of 0.05 (oleic acid), 0.09 (linoleic acid), and 0.07 (O/L ratio) because the FAD2A alleles were not completely fixed within subpopulations. Our genetic analysis demonstrated that this peanut mini-core panel is suitable for association mapping. Phenotypic characterization for seed quality traits and association testing of the functional SNP from FAD2A gene provided information for further breeding and genetic research.

Barriers acting on the genetic structure of a highly aerial seabird: The magnificent frigatebird

The sometimes-distant association between dispersal movements and mating strategies may govern seabird ecology. Despite their large dispersal capability, pelagic seabirds are subject to the influence of physical and non-physical barriers that may limit the magnitude of realized effective dispersal and gene flow. The Magnificent Frigatebird (Fregata magnificens) is a widespread, tropical, pelagic, sequentially monogamous seabird capable to breach physical barriers, such as land masses. Nevertheless, Mexican frigatebirds have shown movement preferences by sex (female migration and high male site fidelity), which, along with the complex female mate choice behavior, may promote breeding isolation. In order to ascertain if levels of population structure are influenced by physical or non-physical barriers, we analyzed mitochondrial DNA variation of adult Magnificent Frigatebirds breeding in the main nesting colonies in Mexico, three in the eastern Pacific Ocean and one in the Caribbean Sea. Control region sequences revealed significant genetic structure between Pacific and Caribbean frigatebirds (AMOVA, ΦSC = 0.105, P < 0.0001), but none among Pacific breeding colonies (non-significant pairwise ΦST). Whereas the C-haplotype was shared by Pacific and Caribbean frigatebirds, the T-haplotype was absent in the Caribbean. Genetic differentiation between ocean basins and available evidence of Mexican frigatebird movements suggest that in spite of the capability of frigatebirds to breach physical barriers, movement preferences by sex and mate selection acting in a large inter-oceanic scale are the prime behaviors promoting population structure, which is highly consequential for their conservation.

Genetic variation and population structure of Sudanese populations as indicated by 15 Identifiler sequence-tagged repeat (STR) loci

BackgroundThere is substantial ethnic, cultural and linguistic diversity among the people living in east Africa, Sudan and the Nile Valley. The region around the Nile Valley has a long history of succession of different groups, coupled with demographic and migration events, potentially leading to genetic structure among humans in the region.ResultWe report the genotypes of the 15 Identifiler microsatellite markers for 498 individuals from 18 Sudanese populations representing different ethnic and linguistic groups. The combined power of exclusion (PE) was 0.9999981, and the combined match probability was 1 in 7.4 × 1017. The genotype data from the Sudanese populations was combined with previously published genotype data from Egypt, Somalia and the Karamoja population from Uganda. The Somali population was found to be genetically distinct from the other northeast African populations. Individuals from northern Sudan clustered together with those from Egypt, and individuals from southern Sudan clustered with those from the Karamoja population. The similarity of the Nubian and Egyptian populations suggest that migration, potentially bidirectional, occurred along the Nile river Valley, which is consistent with the historical evidence for long-term interactions between Egypt and Nubia.ConclusionWe show that despite the levels of population structure in Sudan, standard forensic summary statistics are robust tools for personal identification and parentage analysis in Sudan. Although some patterns of population structure can be revealed with 15 microsatellites, a much larger set of genetic markers is needed to detect fine-scale population structure in east Africa and the Nile Valley.

Genetic population structure in horse chestnut (Aesculus hippocastanum L.): effects of human‐mediated expansion across Europe

AbstractThe geographical distribution of existing populations of horse chestnut (Aesculus hippocastanum L.) in Europe is determined by past demographic events during the Quaternary. In the present study we evaluate the imprints that northward expansions originated from common ancestry at southern Europe may have left on the present patterns of genetic variation for horse chestnut across the continent. Genetic diversity and levels of population structure in a European south–north gradient, ranging from the Balkans to the Scandinavian Peninsula, were determined with Amplified Fragment Length Polymorphism (AFLP) markers in 159 loci. A family of rarefaction techniques for the estimation of gene diversity was used to exclude potential confounding effects as a result of the unequal sample sizes. The results indicate that northern populations are not more genetically depleted than southern populations, thus suggesting that diversity for this species is not correlated with latitudinal distribution. Detailed hypotheses based on prediction models for different historical events associated with human‐mediated spread of cultivation are examined for a better understanding of the current genetic patterns of regional differentiation.

Migration patterns counteract seasonal isolation of Squalius torgalensis, a critically endangered freshwater fish inhabiting a typical Circum-Mediterranean small drainage

Freshwater species with small distribution ranges are vulnerable to extinction, especially when they exhibit small effective population sizes. Squalius torgalensis, Cyprinidae, is an endemic critically endangered fish species from southwestern Portugal, confined to the intermittent streams of the Mira drainage. Assessment of genetic diversity and population structure levels was conducted through the analysis of both mitochondrial (cytochrome b) and nine nuclear microsatellite markers. Remarkable low levels of genetic diversity for both markers were observed (He < 0.38, π < 0.001). These results may be related with the restricted distribution range and dispersion patterns of the species together with demographic fluctuations associated with the intermittent features of the river system. Population structure analyses suggest the existence of two incipient divergent populations; one comprising the tributaries located upstream and the other comprising downstream tributaries of the Mira River. Data also supports the occurrence of high gene flow mainly from downstream to upstream, failing to reflect isolation of populations due to seasonal drought. Obtained results should be incorporated in future management plans for the species. These should be centred around the current connection between populations and on the maintenance of suitable habitat patches, not only for reproduction, but also for summer refuges.

Lack of spatial genetic variation in the edible crab (Cancer pagurus) in the Kattegat–Skagerrak area

Abstract Ungfors, A., McKeown, N. J., Shaw, P. W., and André, C. 2009. Lack of spatial genetic variation in the edible crab (Cancer pagurus) in the Kattegat–Skagerrak area. – ICES Journal of Marine Science, 66: 462–469. The stock structure of the edible crab (Cancer pagurus L.) in the Kattegat and Skagerrak was investigated using eight microsatellite DNA loci. Replicate samples, collected 4–6 years apart, were derived from the Kattegat (Grove Bank, 57°N) and the Skagerrak (Lunneviken, 59°N), plus a geographical outgroup sample from the Norwegian Sea (Midsund, 62°N). Genetic differentiation among samples, estimated as global FST = 0.002, was significant (p = 0.03) when the statistical test was based on allele frequencies, but not when based on genotype frequencies. Moreover, all single- and multilocus pairwise tests between samples were non-significant. An analysis of molecular variance, AMOVA, did not reveal significant differentiation between spatial (Kattegat vs. Skagerrak) or temporal (2001/2002 vs. 2006/2007) groups of samples. Power analysis suggested that the loci and sample sizes employed conferred a power of &gt;90% of detecting even low (true FST = 0.002) levels of population structure. Low spatial and temporal genetic structure might be explained by either or both of (i) high levels of contemporary gene flow in the area attributable to adult migration or larval dispersal or both factors taken together, and (ii) patterns of historical gene flow persisting among recently founded large populations.

Significant population structure and asymmetric gene flow patterns amidst expanding populations of Clinus cottoides (Perciformes, Clinidae): application of molecular data to marine conservation planning in South Africa

Clinus cottoides is a fish endemic to the coast of South Africa, predominantly inhabiting rock pools. All South African clinids are viviparous, but probably breed throughout the year; as such, their dispersal may be limited, unlike species with pelagic larval stages. We analysed 343 fish from 14 localities on the west, south and east coasts using two mitochondrial genes and the second intron of the S7 ribosomal gene. Mitochondrial DNA analyses recovered significant genetic differentiation between fish populations from the east coast and other sampling locations, with a second break found between Gansbaai and Cape Agulhas on the south coast. Nuclear DNA recovered shallower, but significant, levels of population structure. Coalescent analyses suggested remarkably asymmetrical gene flow between sampling locations, suggesting that the cold Atlantic Benguela Current and Indian Ocean Agulhas counter-current play important roles in facilitating dispersal. There was no gene flow between the east coast and the other sites, suggesting that these populations are effectively isolated. Divergence times between them were estimated to at least 68 000 years. Neutrality tests and mismatch distributions suggest recent population expansions, with the exception of peripheral western and eastern populations (possibly a consequence of environmental extremes at the edge of the species distribution). Analyses of the current South African marine protected areas network show that it is not connected and that De Hoop, one of South Africa's largest marine reserves, appears to be an important source population of recruits to both the south and southwest coasts.

Community Resources and Strategies for Association Mapping in Sorghum

Association mapping is a powerful strategy for identifying genes underlying quantitative traits in plants. We have assembled and characterized genetic and phenotypic diversity of a sorghum [Sorghum bicolor (L.) Moench] panel suitable for association mapping, comprised of 377 accessions representing all major cultivated races (tropical lines from diverse geographic and climatic regions), and important U.S. breeding lines and their progenitors. Accessions were phenotyped for eight traits, and levels of population structure and familial relatedness were assessed with 47 simple sequence repeat (SSR) loci. The panel exhibited substantial morphological variation and little genotypic differentiation was observed between the converted tropical and breeding lines. The phenotypic and genotypic data were used to evaluate the performance of several association models in controlling for spurious associations. Our analysis indicated that association models that accounted for both population structure and kinship performed better than those that did not. In addition, we found that the optimal number of subpopulations used to correct for population structure was trait dependent. Although augmentation of the genotypic data with additional SSR loci may be necessary, the association models, genotypic data, and germplasm panel described here provide a starting point for sorghum researchers to begin association studies of traits and markers or candidate genes of interest.

POPULATION DIFFERENTIATION DECREASES WITH DEPTH IN DEEP-SEA BIVALVES

The deep sea is the largest ecosystem on Earth. Recent exploration has revealed that it supports a highly diverse and endemic benthic invertebrate fauna, yet the evolutionary processes that generate this remarkable species richness are virtually unknown. Environmental heterogeneity, topographic complexity, and morphological divergence all tend to decrease with depth, suggesting that the potential for population differentiation may decrease with depth. To test this hypothesis, we use mitochondrial DNA (16S rRNA gene) to examine patterns of population differentiation in four species of protobranch bivalves (Nuculoma similis, Deminucula atacellana, Malletia abyssorum, and Ledella ultima) distributed along a depth gradient in the western North Atlantic. We sequenced 268 individuals from formalin-fixed samples and found 45 haplotypes. The level of sequence divergence among haplotypes within species was similar, but shifted from between populations at bathyal depths to within populations at abyssal depths. Levels of population structure as measured by phiST were considerably greater in the upper bathyal species (N. similis = 0.755 and D. atacellana = 0.931; 530-3834 m) than in the lower bathyal/abyssal species (M. abyssorum = 0.071 and L. ultima = 0.045; 2864-4970 m). Pairwise genetic distances among the samples within each species also decreased with depth. Population trees (UPGMA) based on modified coancestry coefficients and nested clade analysis both indicated strong population-level divergence in the two upper bathyal species but little for the deeper species. The population genetic structure in these protobranch bivalves parallels depth-related morphological divergence observed in deep-sea gastropods. The higher level of genetic and morphological divergence, coupled with the strong biotic and abiotic heterogeneity at bathyal depths, suggests this region may be an active area of species formation. We suggest that the steep, topographically complex, and dynamic bathyal zone, which stretches as a narrow band along continental margins, plays a more important role in the evolutionary radiation of the deep-sea fauna than the much more extensive abyss.

POPULATION DIFFERENTIATION DECREASES WITH DEPTH IN DEEP-SEA BIVALVES

The deep sea is the largest ecosystem on Earth. Recent exploration has revealed that it supports a highly diverse and endemic benthic invertebrate fauna, yet the evolutionary processes that generate this remarkable species richness are virtually unknown. Environmental heterogeneity, topographic complexity, and morphological divergence all tend to decrease with depth, suggesting that the potential for population differentiation may decrease with depth. To test this hypothesis, we use mitochondrial DNA (16S rRNA gene) to examine patterns of population differentiation in four species of protobranch bivalves (Nuculoma similis, Deminucula atacellana, Malletia abyssorum, and Ledella ultima) distributed along a depth gradient in the western North Atlantic. We sequenced 268 individuals from formalin-fixed samples and found 45 haplotypes. The level of sequence divergence among haplotypes within species was similar, but shifted from between populations at bathyal depths to within populations at abyssal depths. Levels of population structure as measured by ΦST were considerably greater in the upper bathyal species (N. similis = 0.755 and D. atacellana = 0.931; 530–3834 m) than in the lower bathyal/abyssal species (M. abyssorum = 0.071 and L. ultima = 0.045; 2864–4970 m). Pairwise genetic distances among the samples within each species also decreased with depth. Population trees (UPGMA) based on modified coancestry coefficients and nested clade analysis both indicated strong population-level divergence in the two upper bathyal species but little for the deeper species. The population genetic structure in these protobranch bivalves parallels depth-related morphological divergence observed in deep-sea gastropods. The higher level of genetic and morphological divergence, coupled with the strong biotic and abiotic heterogeneity at bathyal depths, suggests this region may be an active area of species formation. We suggest that the steep, topographically complex, and dynamic bathyal zone, which stretches as a narrow band along continental margins, plays a more important role in the evolutionary radiation of the deep-sea fauna than the much more extensive abyss.

High genetic homogeneity of an intertidal marine invertebrate along 8000 km of the Atlantic coast of the Americas

Phallusia nigra is a cosmopolitan solitary ascidian with a distinct niger-blue tunic that is considered to be an easy diagnostic feature, even in the field. The wide geographic distribution of this species may have been a result of the overconfidence of taxonomists and ecologists in the assignment of unknown specimens to this species, based on this simple diagnostic character. Indeed, there seems to be a correlation between cosmopolitanism and the presence of few, but very conspicuous diagnostic characters in benthic invertebrate species. Almost invariably, genetic studies have demonstrated that the cosmopolitanism of those species is artificial and that, rather, they are made up of groups of morphologically very similar, but genetically distinct, species. Thus, we decided to verify the specific status of Western Atlantic populations of P. nigra, from Miami (USA) to São Paulo (southeastern Brazil) by estimating genetic variation and population structure levels along the entire range of this ascidian in the Western Atlantic. The analysis of 10 allozyme systems shows high levels of mean heterozygosity ( H=0.28) so that P. nigra has genetic variation levels more related with other invertebrates than to their, phylogenetically closer, chordate relatives (that show lower levels of heterozygosity). The genetic structure of the population was relatively high ( F ST=0.083) for conspecific populations, but much lower than what would be expected if they belonged to different species. High levels of gene identity also indicate that the Western Atlantic population of P. nigra constitutes a single species. This result suggests an extremely high dispersal capability of the larvae of this ascidian or a relatively recent range expansion of its populations. Since this species is commonly found in harbors, the anthropogenic transport (p.e., in ballast water) may have contributed for the observed genetic homogeneity.

Extinction-colonization dynamics structure genetic variation of spotted sunfish (Lepomis punctatus) in the Florida Everglades.

The population genetics of aquatic animals in the Florida Everglades may be strongly influenced by extinction and colonization dynamics. We combined analyses of allozyme and microsatellite loci to test the hypothesis that two levels of population structure are present for spotted sunfish (Pisces: Centrarchidae: Lepomis punctatus) inhabiting the Everglades. We hypothesized that annual cycles of marsh dry-down increase local-scale genetic variation through a process of local extinction and colonization; we hypothesized that barriers to gene flow by levee/canal systems create a second, regional level of genetic variation. In 1996 and 1997, we sampled spotted sunfish from 11 Everglades sites that were distributed in three regions separated by levees. We documented patterns of genetic variation at 7 polymorphic allozyme loci and 5 polymorphic microsatellite loci. Most genetic variation was present among local populations, according to both types of genetic markers. Furthermore, samples from marsh sites were heterogeneous, while those from canals were not. These data supported our hypothesis that dry-down events and local population dynamics in the marsh have a significant effect on population genetic structure of spotted sunfish. We found no support for our hypothesis that water-management structures superimpose a second level of genetic structure on this species, possibly because canals obscure historical structure by facilitating gene flow or because the complete canal system has been in place for fewer than 20 generations of this species. Our data suggests a continent-island (canal-marsh) structure of populations with high gene flow among regions and recurrent mixing in marshes from canal and creek habitats.

HYBRIDIZATION AND POPULATION SUBDIVISION WITHIN AND BETWEEN ROSS'S GEESE AND LESSER SNOW GEESE: A MOLECULAR PERSPECTIVE

Abstract We reanalyzed Quinn's (1992) mtDNA control region data set including new sequences from nine Lesser Snow Geese (Chen caerulescens caerulescens) and 10 Ross's Geese (Chen rossi) and found the same divergent lineages that Quinn (1992) attributed to vicariant separation of Lesser Snow Goose populations during the Pleistocene. However, peculiar patterns of mtDNA control region sequence variation, including a multimodal mismatch distribution of mtDNA sequences with two levels of population structuring and the sharing of two divergent haplotype lineages, are consistent with two hybridization episodes in Chen geese. Comparisons of mtDNA variation with historical and allozyme data sets compiled by Cooke et al. (1988) are consistent with the hypothesis that sharing of two mtDNA haplotype lineages between Ross's Goose and Lesser Snow Goose resulted from hybridization (Avise et al. 1992). Furthermore, population structure found within one haplotype cluster is consistent with Cooke et al.‘s (1988) hypothesis...

Corralling of larvae in the deep sea

Large numbers of small individuals (pediveligers and juveniles &lt;5 mm) are routinely recorded in size–frequency distributions of mussel samples collected from deep-sea chemosynthetic environments. If recruitment of invertebrates to deep-sea hydrothermal vent sites were via long-distance dispersal, as is typically assumed, one would expect recruitment ‘events’ recorded in size–frequency distributions to be difficult to detect, due to loss of larvae in an open system over large distances. If one imposes mesoscale oceanographic phenomena that minimize dilution of larvae (such as eddies shed from hydrothermal vent plumes) and episodic spawning, expression of this mesoscale corralling at the level of population structure would likely be limited to discrete records of recruitment events encountered serendipitously during haphazard sampling in space and time. The ubiquity of large numbers of post-larvae in mussel samples from a number of disparate sites is likely not serendipitous, but instead may reflect the importance of local sources and sinks of propagules in maintenance of mussel populations.

Conservation genetics of the endangered Shenandoah salamander (Plethodon shenandoah, Plethodontidae)

AbstractThe Shenandoah salamander (Plethodon shenandoah) is restricted to three isolated talus outcrops in Shenandoah National Park, VA, USA and has one of the smallest ranges of any tetrapod vertebrate. This species was listed as endangered under the US Endangered Species Act in 1989 over concern that direct competition with the red‐backed salamander (Plethodon cinereus), successional habitat changes, and human impacts may cause its decline and possible extinction. We address two issues herein: (1) whether extensive introgression (through long‐term hybridization) is present between the two species and threatens the survival of P. shenandoah, and (2) the level of population structure within P. shenandoah. We provide evidence from mtDNA haplotypes that shows no genetic differentiation among the three isolates of P. shenandoah, suggesting that their fragmentation is a geologically recent event, and/or that the isolates are still connected by occasional gene flow. There is also no evidence for extensive introgression of alleles in either direction between P. cinereus and P. shenandoah, which suggests that P. shenandoah may not be in danger of being genetically swamped out through hybridization with P. cinereus.

Geographic heterogeneity in natural selection on an MHC locus in sockeye salmon.

Balancing selection maintains high levels of polymorphism and heterozygosity in genes of the MHC (major histocompatibility complex) of vertebrate organisms, and promotes long evolutionary persistence of individual alleles and strongly differentiated allelic lineages. In this study, genetic variation at the MHC class II DAB-beta1 locus was examined in 31 populations of sockeye salmon (Oncorhynchus nerka) inhabiting the Fraser River drainage of British Columbia, Canada. Twenty-five percent of variation at the locus was partitioned among sockeye populations, as compared with 5% at neutral genetic markers. Geographic heterogeneity of balancing selection was detected among four regions in the Fraser River drainage and among lake systems within regions. High levels of beta1 allelic diversity and heterozygosity, as well as distributions of alleles and allelic lineages that were more even than expected for a neutral locus, indicated the presence of balancing selection in populations throughout much of the interior Fraser drainage. However, proximate populations in the upper Fraser region, and four of six populations from the lower Fraser drainage, exhibited much lower levels of genetic diversity and had beta1 allele frequency distributions in conformance with those expected for a neutral locus, or a locus under directional selection. Pair-wise FST values for beta1 averaged 0.19 and tended to exceed the corresponding values estimated for neutral loci at all levels of population structure, although they were lower among populations experiencing balancing selection than among other populations. The apparent heterogeneity in selection resulted in strong genetic differentiation between geographically proximate populations with and without detectable levels of balancing selection, in stark contrast to observations at neutral loci. The strong partitioning and complex structure of beta1 diversity within and among sockeye populations on a small geographic scale illustrates the value of incorporating adaptive variation into conservation planning for the species.