Weak Genetic Structure Research Articles

Going west—invasion genetics of the alien raccoon dog Nyctereutes procynoides in Europe

The raccoon dog, a medium-sized carnivore, has long been recognised as a prominent example of an invasive alien species in Europe with a wide distribution, significant ecological impact and remarkable dynamics of spread at both national and continental scales. We conducted a study of genetic diversity of 73 individuals collected at 20 sites across North and Central Europe to (1) identify major phylogenetic lineages and (2) elucidate spatial patterns of population genetic structure. Reconstructed phylogenies reveal two major clades differing on average by Tamura–Nei corrected distance of 3.4% for a 599-bp segment of the mitochondrial control region corresponding to a coalescence time of approximately 457,800 years ago (95% CI, 223,300–773,900). Many expectations based on introduction history, such as the presence of signatures of repeated founder effects and subsequently rapid population expansion, were not confirmed by our demographic analyses, probably due to an insufficient amount of time since translocations. Nevertheless, global F ST = 13.9% and landscape approaches provided evidence for weak population genetic structure that followed a pattern of isolation by distance. Finally, we found no congruence between previously reported morphological differentiation and the sorting of mtDNA variation. We therefore conclude that an exceptional combination of factors including multiple translocations, secondary contact and admixture of divergent matrilineages, as well as natural processes of colonisation associated with a wide ecological tolerance, promoted the successful spread of the raccoon dog into Europe.

Low levels of genetic differentiation between Opuntia echios varieties on Santa Cruz (Galapagos)

Three processes play an important role in plant speciation: isolation, hybridization and polyploidization. Galapagos endemic Opuntia display putatively all of these processes. On this archipelago most islands are inhabited by a single Opuntia taxon. Santa Cruz, however, houses two morphologically distinct O. echios varieties (echios and gigantea). Morphological intermediates are found where these two geographically isolated varieties meet. Here we used ten microsatellite loci to reveal the population genetic structure of this system. In contrast to earlier studies, we found high genetic variability within localities. Genetic structuring was weak and no evidence for the existence of hybrids was found. The reasons for this weak genetic structure may include: the species’ hexaploid nature, high levels of gene flow, recent colonization, and the lack of geographic barriers. This first detailed genetic study on these threatened species will be important for further conservation planning.

High genetic diversity detected in the endemic Primula apennina Widmer (Primulaceae) using ISSR fingerprinting

Primula apennina Widmer is endemic to the North Apennines (Italy). ISSR were used to detect the genetic diversity within and among six populations representative of the species distribution range. High levels of genetic diversity were revealed both at population percentage of polymorphic band (PPB = 75.92%, H S = 0.204, H pop = 0.319) and at species level (PPB = 96.95%, H T = 0.242, H sp = 0.381). Nei gene diversity statistics (15.7%), Shannon diversity index (16.3%) and AMOVA (14%) detected a moderate level of interpopulation diversity. Principal coordinate and Bayesian analyses clustered the populations in three major groups along a geographic gradient. The correlation between genetic and geographic distances was positive (Mantel test, r = 0.232). All together, these analyses revealed a weak but significant spatial genetic structure in P. apennina, with gene flow acting as a homogenizing force that prevents a stronger differentiation of populations. Conservation measures are suggested based on the observed pattern of genetic variability.

Conserving the endangered Mexican fishing bat (Myotis vivesi): genetic variation indicates extensive gene flow among islands in the Gulf of California

The endangered Mexican fishing bat, Myotis vivesi, appears to have suffered widespread extinction and population decline on islands throughout the Gulf of California, largely due to predation by introduced cats and rats. To restore populations of fishing bats and other native species, conservation efforts have focused on eradicating introduced vertebrates from several Gulf islands. These efforts assume that individuals from existing populations will recolonize islands and that continued dispersal will help sustain vulnerable populations thereafter. However, the extent of inter-island dispersal in fishing bats is unknown. In this study we analyzed patterns of genetic variation to gauge the extent of gene flow and, thus, potential dispersal among islands. DNA was sampled from 257 fishing bats on 11 Gulf islands (separated by ca. 6–685 km of open water), and individuals were genotyped at six microsatellite loci and haplotyped at a 282 bp fragment of the mtDNA control region. With microsatellites, we found weak population genetic structure and a pattern of isolation by distance, while with mtDNA we found strong structure but no isolation by distance. Our results indicate that island subpopulations separated by large expanses of open water are nonetheless capable of maintaining high genetic diversity and high rates of gene flow. Unfortunately, little is known about the spatial patterns of dispersal or mating system of fishing bats, and these behavioral factors, in particular female philopatry, might reduce the probability of the species recolonizing Gulf islands.

Low Genetic Diversity in the Rare Madeiran Endemic Armeria maderensis (Plumbaginaceae)

The genetic diversity and possible geographic structure of the Madeiran endemic Armeria maderensis have been assessed with AFLP. Its scarce distribution (less than 3 km between the two most distant localities) and restricted habitat (vertical pastures on the highest elevations of Madeira), at least in part due to grazing by goats, suggest an assessment of its conservation status. Diversity estimates obtained for A. maderensis were evaluated through comparison with reference values of AFLP diversity for outcrossing plants and, in order to correct for phylogenetic constraints, with a widespread congener analyzed with the same AFLP markers. Our results reveal that low levels of genetic diversity and a weak intraspecific genetic structure underlie the restricted distribution of A. maderensis.

Multigenerational analysis of spatial structure in the terrestrial, food‐deceptive orchid Orchis mascula

Summary In long‐lived, terrestrial orchids, strong aggregation of adults and recruits within populations and pronounced spatial association between recruits and adults can be expected when seed dispersal is limited, probabilities of seed germination decrease with increasing distance from mother plants and/or not all mother plants contribute to future generations. When individuals are distributed evenly across life‐history stages, these processes can also be expected to result in a significant fine‐scale spatial genetic structure in recruits that will persist into the adult‐stage class. We combined detailed spatial genetic and point pattern analyses across different generations with parentage analyses to elucidate the role of the diverse processes that might determine spatial structure in Orchis mascula. Analyses of spatial point patterns showed a significant association between adults and recruits and similar clustering patterns for both. Weak, but highly significant spatial genetic structure was observed in adults and recruits, but no significant differences were observed across life stages, indicating that the spatial genetic structure present in recruits persists into the adult stage. Parentage analyses highlighted relatively short seed dispersal distances (median offspring‐recruitment distance: 1.55 and 1.70 m) and differential contribution of mother plants to future generations. Persistence of fine‐scale spatial genetic structure from seedlings into the adult stage class is consistent with the life history of O. mascula, whereas relatively large dispersal distances of both pollen and seeds compared to the fine‐scale clustering of adults and seedlings suggest overlapping seed shadows and mixing of genotypes within populations as the major factors explaining the observed weak spatial genetic structure. Nonetheless, comparison of the spatial association between recruits and adults with the genetic analysis of offspring‐parent distances suggests that the tight clustering of recruits around adults was probably caused by decreasing probabilities of seed germination with increasing distance from mother plants. Synthesis. This study shows that the approach presented here, which combines spatial genetic and spatial pattern analyses with parentage analyses, may be broadly applied to other plant species to elucidate the processes that determine spatial structure within their populations.

Life style and genetic variation in teleosts: the case of pelagic (Aphia minuta) and benthic (Gobius niger) gobies (Perciformes: Gobiidae)

The pattern of genetic variability of two species of Mediterranean gobiids was compared, with reference to their different life history traits (Aphia minuta paedomorphic and pelagic; Gobiusniger metamorphosed and benthic). The aim was to evaluate how different life histories can affect the genetic structure in these marine teleosts. The study was carried out on populations of both species sampled in the western Mediterranean and in the Adriatic Sea. Seven restriction endonucleases were used for the RFLP analysis of a mitochondrial DNA segment comprising the NADH dehydrogenase subunits 3, 4L and 4. The results highlighted two different patterns of genetic variation, a weak genetic structure in A. minuta and population subdivision in G. niger. These observations may be explained not only in terms of the different dispersal capabilities of these species, but also considering that A. minuta is an abbreviate iteroparous spawner while G. niger is a protracted iteroparous spawner. Because abbreviate iteroparity is a reproductive strategy selected in stable environments with high resource availability, Pliocene and Pleistocene climate oscillations may have represented factors that negatively influenced the reproductive success of A. minuta, producing demographic fluctuations and bottlenecks, as suggested by the mismatch distribution analysis. The weak genetic structure of A. minuta populations seems to be therefore due to a more recent re-colonization of the Mediterranean basin after a severe population decline, rather than to the high vagility of this pelagic goby.

Genetic variation in natural populations ofAnthurium sinuatumandA. pentaphyllumvar.pentaphyllum(Araceae) from north-east Brazil using AFLP molecular markers

Genetic variation was investigated using AFLP markers in 12 populations of Anthurium sinuatum and A. pentaphyllum var. pentaphyllum (Araceae) in north-east Brazil, Amazonia and the Brazilian Atlantic forest. Two unique genetic patterns characterized the populations of A. sinuatum as a group, but no correlation between genetic and geographical interpopulation distance was found; the Amazonian population was not separated from that in Ceará. The isolated Ceará brejo populations of A. sinuatum were genetically distinct, but genetic diversity levels were similar to populations elsewhere, with no evidence of genetic erosion. Anthurium pentaphyllum populations were significantly different from each other; Bayesian genetic structural analysis found no common genetic pattern, but revealed genetic clusters unique to subgroups and individual populations in the Atlantic forest and French Guiana. Anthurium pentaphyllum and A. sinuatum can be distinguished genetically, but individuals of both species formed intermediate genetic clusters that blurred their distinction. We suggest that genetic mixing of A. sinuatum and A. pentaphyllum has occurred in north-east Brazil, possibly connected with cycles of humid forest expansion. The weak genetic structure in A. sinuatum is consistent with the natural fragmentation of continuous forest areas, possibly during the Holocene. This study highlights the scientific importance of the highly threatened brejo forests for tropical American biogeography.

Does spatial aggregation of total nectar production lead to genetic structure?

Abstract Spatial aggregation of plants of high nectar production, receiving an enhanced pollinator service is known to occur in Echium vulgare . Moreover, an emanating effect of nectar production on pollinator visits may occur, i.e. many pollinator visits may be observed around high nectar patches. Consequently, gene flow within patches of plants of high nectar production and their close neighbours may result in genetic structure. In this study, we investigated whether aggregation of total nectar production (nectar production per flower×number of flowers) and its emanating effect resulted in genetic structure in a natural E. vulgare population. We compared the spatial structure of total nectar production, pollinator visits and microsatellite markers using spatial autocorrelation analysis. Increased geitonogamy, caused by longer boutlengths in plants of high nectar production may generate genetic structure. We estimated selfing rates of plants of the highest and lowest total nectar production. Spatial aggregation of total nectar production occurred on a relatively small scale up to 2.83 m. A significant emanating correlation between total nectar production and pollinator visits was observed on a relatively large scale up to a 4.24 m. Thus, around patches of high nectar production numbers of pollinator visits were relatively high, while few visits were observed around patches of low nectar production. Weak genetic structure was present on a small scale up to 2.20 m. This corresponded with the scale of aggregation of total nectar production. High gene flow around the patches of high nectar production seems to weaken genetic structure. This is supported by the relatively low selfing rates. The average selfing rate of the plants of highest nectar production was 8.8% and that of the plants of lowest nectar production 5.0%. Low gene flow within and around low nectar patches sustain a weak genetic structure or, conversely, may have caused it in the first instance. Results indicate the importance of spatial structure of nectar production for pollinator movement.

Effects of seed- and pollen-mediated gene dispersal on genetic structure among Quercus salicina saplings

We evaluated the effects of seed- and pollen-mediated gene dispersal on genetic structure among Quercus salicina saplings. Parentage analysis using 10 microsatellite markers indicated that the 111 adult trees located within a 11.56 ha plot in the Tatera Forest Reserve, Japan, included only one parent of 44.2% and both parents of 40.7% of the 226 saplings located in a 1-ha core plot at its center. Coancestry (F(ij)) estimates indicated that there was strong genetic structure among the saplings. The numbers of pairs of full- and half-siblings were high among neighboring saplings, suggesting that there was strong maternal half-sibling family structure among the saplings around their seed parents, probably generated by the spatially limited seed dispersal and the small extent of overlapping seed shadows owing to the low density of adults. The frequencies also suggest that the maternal half-sibling families are interspersed with full-siblings, produced by correlated mating, probably because pollination frequency depends on the distance between parents. The frequencies of pairs of half-siblings decreased as the distance between saplings increased, but did not fall to zero even at distances up to the 90-95 m class, suggesting that paternal half-siblings originating from correlated paternity were widely distributed owing to extensive pollen flow. We separately examined the genetic structure for maternal and paternal alleles in the saplings. Unsurprisingly, very strong genetic structure was detected for maternal alleles. However, weak (but significant) genetic structure was also detected for paternal alleles. Therefore, pollen dispersal may affect the extent of genetic structure as well as seed dispersal.

Genetic diversity in fragmented populations of the critically endangered spider orchid Caladenia huegelii: implications for conservation

The Orchidaceae is characterised by a diverse range of life histories, reproductive strategies and geographic distribution, reflected in a variety of patterns in the population genetic structure of different species. In this study, the genetic diversity and structure was assessed within and among remnant populations of the critically endangered sexually deceptive orchid, Caladenia huegelii. This species has experienced severe recent habitat loss in a landscape marked by ancient patterns of population fragmentation within the Southwest Australian Floristic Region, a global biodiversity hotspot. Using seven polymorphic microsatellite loci, high levels of within-population diversity (mean alleles/locus = 6.73; mean HE = 0.690), weak genetic structuring among 13 remnant populations (FST = 0.047) and a consistent deficit of heterozygotes from Hardy–Weinberg expectation were found across all populations (mean FIS = 0.22). Positive inbreeding coefficients are most likely due to Wahlund effects and/or inbreeding effects from highly correlated paternity and typically low fruit set. Indirect estimates of gene flow (Nm = 5.09 using FST; Nm = 3.12 using the private alleles method) among populations reflects a historical capacity for gene flow through long distance pollen dispersal by sexually deceived wasp pollinators and/or long range dispersal of dust-like orchid seed. However, current levels of gene flow may be impacted by habitat destruction, fragmentation and reduced population size. A genetically divergent population was identified, which should be a high priority for conservation managers. Very weak genetic differentiation indicates that the movement and mixing of seeds from different populations for reintroduction programs should result in minimal negative genetic effects.

Population genetic structure of the ascidian Styela rustica at Kongsfjorden, Svalbard, Arctic

The actual Arctic biota shows a strong affinity with that of the Boreal Atlantic and Pacific ones, as a result of an active recolonization process after the Quaternary glaciations. The geographic distribution of sessile species is usually linked to larvae dispersive capabilities which can be directly related with time spent in the plankton. Ascidians larvae are lecitothorphic and short-lived, which suggest that ascidians could be not efficient dispersers. However, the solitary ascidian Styela rustica (Linnaeus, 1767) (Tunicata, Ascidiacea) shows a wide distribution pattern from the North Atlantic to the Arctic that, together with the relatively recent colonization of the Arctic system could indicate that this species efficiently disperses and colonizes new habitats. In this study we used ISSR-PCR markers to study the genetic structure of five populations of the ascidian Styela rustica at Kongsfjorden, west Spitsbergen (Svalbard archipelago). We analyzed whether this species presents a low genetic structure, as can be expected due to the historical process of recent post glaciations colonization, or if there is genetic differentiation at a local scale, caused by short-lived larvae and limited dispersal potential. The genetic diversity in each population assessed using the marker diversity index (M) ranged from 0.288 to 0.324. Population HN, situated close to a fast retreating glacier, showed the lowest diversity. Processes associated with deglatiation (icebergs calving from the glacier that scour the benthos and the increment of inorganic particulate matter on the water column) would drive to reduced population sizes and explain the reduced genetic variability observed in the HN population with respect to the others in the fjord. This suggests a possible linkage with the global warming process. Although the weak genetic structure found among the studied populations could indicate a founder effect, the genetic landscape shape analysis together with a positive relationship between genetic and geographic distances also suggest possible current gene flow among populations in the fjord.

Trans‐Atlantic dispersal and large‐scale lack of genetic structure in the circumpolar, arctic‐alpine sedge Carex bigelowii s. l. (Cyperaceae)

Paradoxically, several of the ecologically most important plant groups in the Arctic are little understood in terms of taxonomy and biogeographic history. The circumpolar Carex bigelowii s. l. (Cyperaceae) is abundant in the Arctic and is one of the most complicated arctic plant groups. While its ecology and population genetics have been extensively studied, its taxonomy is largely unexplored. We analyzed the large-scale geographical structuring of amplified fragment length polymorphisms (AFLPs) covering most of the distribution range. We detected high levels of genetic variation, most (66%) within populations, and a fairly weak genetic structure. Only the Central Asian populations, referred to as C. orbicularis, were strongly divergent. For the remaining populations, Bayesian clustering separated three distinct clusters (one European, one amphi-Atlantic, and one broadly amphi-Beringian), probably reflecting different major glacial refugia and recent transoceanic dispersal. The isolated central European populations were most closely related to those from a larger distribution area in northern Europe. Differences in genetic diversity suggest that the Alpine and Tatra populations have experienced strong bottlenecks, whereas the Krkonoše population may have been part of a continuous distribution area during the cold stages of the Pleistocene. Finally, we discuss the relevance of our results for a uniform, range-wide taxonomic concept.

Genetic structure, migration, and patterns of allelic richness among coho salmon (Oncorhynchus kisutch) populations of the Oregon coast

Genotypic data from eight microsatellite loci are used to infer population structure, effective population size, migration rates, and patterns of allelic richness among wild and hatchery populations of Oregon coastal coho salmon ( Oncorhynchus kisutch ). Corroborating the results of a previous study, we found relatively weak genetic structure among coho from different river basins, although some geographically and ecologically defined clades are supported. Contemporary migration rates among basins appear to be high and asymmetrical. Hatchery populations tended to resemble the wild populations from which they were founded, but presented significantly lower levels of allelic richness. Allelic richness was also low in Oregon coastal lake populations and peaked in the central region of the evolutionarily significant unit among wild river populations. We suggest that the observed patterns may reflect both current source–sink dynamics and post-Pleistocene colonization events.

Genetic structure of the endangered perennial plant Eryngium alpinum (Apiaceae) in an alpine valley

We investigated the genetic structure of Eryngium alpinum (Apiaceae) in an Alpine valley where the plant occurs in patches of various sizes. In a conservation perspective, our goal was to determine whether the valley consists of one or several genetic units. Habitat fragmentation and previous observations of restricted pollen/seed dispersal suggested pronounced genetic structure, but gene dispersal often follows a leptokurtic distribution, which may lead to weak genetic structure. We used nine microsatellite loci and two nested sampling designs (50 × 50 m grid throughout the valley and 2 × 2 m grid in two 50 × 10 m quadrats). Within the overall valley, F-statistics and Bayesian approaches indicated high genetic homogeneity. This result might be explained by: (1) underestimation of long-distance pollen/seed dispersal by in situ experiments and (2) too recent fragmentation events to build up genetic structure. Spatial autocorrelation revealed isolation by distance on the overall valley but this pattern was much more pronounced in the 50 × 10 m quadrats sampled with a 2-m mesh. This was probably associated with limited primary seed dispersal, leading to the spatial clustering of half-sibs around maternal plants. We emphasize the interest of nested sampling designs and of combining several statistical tools. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 93, 667–677.

Weak genetic structuring indicates ongoing gene flow across White-ruffed Manakin (Corapipo altera) populations in a highly fragmented Costa Rica landscape

We explored the effects of recent forest fragmentation on fine-scale patterns of population structuring and genetic diversity in populations of White-ruffed Manakins (Corapipo altera) inhabiting premontane forest fragments of varying size in southwestern Costa Rica. Habitat fragmentation is a major conservation concern for avian populations worldwide, but studies of the genetic effects of fragmentation on Neotropical birds are limited. We sampled 159 manakins from nine forest fragments of varying size within an 18 km radius, and genotyped these birds at 13 microsatellite loci. Bayesian clustering methods revealed that birds from all fragments comprised a single genetic population, and an MCMC approach showed that the fragments were likely to be at migration-drift equilibrium. F-statistics showed only modest levels of differentiation between forest fragments. We calculated allelic diversity indices for each fragment but found no correlation between genetic diversity and fragment size. These results suggest that manakins may retain substantial connectivity via inter-fragment dispersal despite habitat fragmentation.

Diffusion of the Nearctic leafhopper Scaphoideus titanus Ball in Europe: a consequence of human trading activity

Scaphoideus titanus Ball is a Nearctic leafhopper that was introduced for the first time in Europe probably at the beginning of the 20th century. In Europe, this species is a specialist on cultivated grapevines and is of great economic importance as the vector of Flavescence dorée (FD), a Grapevine Yellows disease caused by Candidatus Phytoplasma vitis. The Random Amplified Polymorphic DNA (RAPD) technique was employed to obtain genetic information about the diffusion and the structure of S. titanus populations. Two American and 14 European populations were analysed. A total of 188 reproducible bands, obtained from three arbitrary primers, were considered to assess the amount and the pattern of genetic variation within and among leafhopper populations. American populations showed high levels of intra-population polymorphism and dissimilarity and appeared to be the most isolated of all the tested samples. The results confirm the historical role of American samples as the sources for the more recently founded European populations. RAPD analyses revealed a weak genetic structure of European samples that could probably be explained invoking the human role in their diffusion. The non-natural spreading of S. titanus across Europe is in fact attributable to the exchange of grapevine canes and grafts carrying eggs that the insect laid under the bark to overwinter.

Limits to gene flow in the slipper limpet Crepidula fornicata as revealed by microsatellite data and a larval dispersal model

Crepidula fornicata, one of the most invasive marine sessile invertebrates in Europe, has traits commonly associated with a weak population genetic structure (high population connectivity): wide environmental tolerance, high fecundity, and a long planktonic larval stage (21 d). In order to determine the scale at which effective dispersal occurs in this potentially highly dispersive species, we designed a hierarchical sampling protocol and analyzed genetic variation at 4 microsatellite loci in 17 populations from 6 French bays situated in the English Channel and at the entrance of the Eng- lish Channel (Iroise Sea). A strong regional pattern with populations clustered into 3 main groups (Iroise Sea, western and eastern English Channel) was revealed, as was significant isolation by dis- tance along the Channel coasts. Conversely, a high degree of genetic connectivity was observed within the study bays. These estimates of effective dispersal were in agreement with outputs of a 2D larval-dispersal model based on local hydrodynamic conditions, suggesting that connectivity between populations of C. fornicata is influenced by hydrodynamic feature. This study suggests the existence of barriers to gene flow of C. fornicata over moderate distances (ca. 100 km).

Comparative analysis of the within‐population genetic structure in wild cherry (Prunus avium L.) at the self‐incompatibility locus and nuclear microsatellites

Gametophytic self-incompatibility (SI) systems in plants exhibit high polymorphism at the SI controlling S-locus because individuals with rare alleles have a higher probability to successfully pollinate other plants than individuals with more frequent alleles. This process, referred to as frequency-dependent selection, is expected to shape number, frequency distribution, and spatial distribution of self-incompatibility alleles in natural populations. We investigated the genetic diversity and the spatial genetic structure within a Prunus avium population at two contrasting gene loci: nuclear microsatellites and the S-locus. The S-locus revealed a higher diversity (15 alleles) than the eight microsatellites (4-12 alleles). Although the frequency distribution of S-alleles differed significantly from the expected equal distribution, the S-locus showed a higher evenness than the microsatellites (Shannon's evenness index for the S-locus: E = 0.91; for the microsatellites: E = 0.48-0.83). Also, highly significant deviations from neutrality were found for the S-locus whereas only minor deviations were found for two of eight microsatellites. A comparison of the frequency distribution of S-alleles in three age-cohorts revealed no significant differences, suggesting that different levels of selection acting on the S-locus or on S-linked sites might also affect the distribution and dynamics of S-alleles. Autocorrelation analysis revealed a weak but significant spatial genetic structure for the multilocus average of the microsatellites and for the S-locus, but could not ascertain differences in the extent of spatial genetic structure between these locus types. An indirect estimate of gene dispersal, which was obtained to explain this spatial genetic pattern, indicated high levels of gene dispersal within our population (sigma(g) = 106 m). This high gene dispersal, which may be partly due to the self-incompatibility system itself, aids the effective gene flow of the microsatellites, thereby decreasing the contrast between the neutral microsatellites and the S-locus.

Microsatellite variation reveals weak genetic structure and retention of genetic variability in threatened Chinook salmon (Oncorhynchus tshawytscha) within a Snake River watershed

Pacific salmon (Oncorhynchus spp.) have been central to the development of management concepts associated with evolutionarily significant units (ESUs), yet there are still relatively few studies of genetic diversity within threatened and endangered ESUs for salmon or other species. We analyzed genetic variation at 10 microsatellite loci to evaluate spatial population structure and genetic variability in indigenous Chinook salmon (Oncorhynchus tshawytscha) across a large wilderness basin within a Snake River ESU. Despite dramatic 20th century declines in abundance, these populations retained robust levels of genetic variability. No significant genetic bottlenecks were found, although the bottleneck metric (M ratio) was significantly correlated with average population size and variability. Weak but significant genetic structure existed among tributaries despite evidence of high levels of gene flow, with the strongest genetic differentiation mirroring the physical segregation of fish from two sub-basins. Despite the more recent colonization of one sub-basin and differences between sub-basins in the natural level of fragmentation, gene diversity and genetic differentiation were similar between sub-basins. Various factors, such as the (unknown) genetic contribution of precocial males, genetic compensation, lack of hatchery influence, and high levels of current gene flow may have contributed to the persistence of genetic variability in this system in spite of historical declines. This unique study of indigenous Chinook salmon underscores the importance of maintaining natural populations in interconnected and complex habitats to minimize losses of genetic diversity within ESUs.