The effect of reintroductions on the genetic variability in Eurasian lynx populations: the cases of Bohemian–Bavarian and Vosges–Palatinian populations

Over the past ~40 years, several attempts were made to reintroduce Eurasian lynx to suitable habitat within their former distribution range in Western Europe. In general, limited numbers of individuals have been released to establish new populations. To evaluate the effects of reintroductions on the genetic status of lynx populations we used 12 microsatellite loci to study lynx populations in the Bohemian–Bavarian and Vosges–Palatinian forests. Compared with autochthonous lynx populations, these two reintroduced populations displayed reduced genetic diversity, particularly the Vosges–Palatinian population. Our genetic data provide further evidence to support the status of ‘endangered’ and ‘critically endangered’ for the Bohemian–Bavarian and Vosges–Palatinian populations, respectively. Regarding conservation management, we highlight the need to limit poaching, and advocate additional translocations to bolster genetic variability.     

Genetic guidelines for the conservation of the endangered polyploid Centaurea borjae (Asteraceae)

Appropriate management of species of conservation concern requires designing strategies that should include genetic information as small population size and restricted geographic range can reduce genetic variation. We used AFLPs to investigate genetic variation within and among populations of the endangered narrow endemic Centaurea borjae, and found no evidence for genetic impoverishment despite its <40 km range and potential for vegetative propagation. Genetic variation was comparable to other plants with similar life history (88 % occurring within populations) and potential clone mates were less frequent than expected. Nonetheless, populations separated by few hundred meters showed signs of significant genetic differentiation suggesting low gene flow between them. Our results suggested that the three geographically closer populations located at the center of the range might be treated as a single management unit, while the remaining ones could be considered independent units. We found evidence of fine-scale spatial genetic structure up to 80 m indicating that the collection of germplasm for ex-situ conservation should focus on individuals separated >80 m to maximize genetic variation.     

From connectivity to isolation: genetic consequences of population fragmentation in capercaillie across Europe

The capercaillie inhabits a continuous range in large parts of the Palearctic boreal forest, but is patchily distributed in temperate Europe. An ongoing population decline, largely related to human land use changes, has been most pronounced in central and western Europe, where some local populations have become extinct. In this study, we document the genetic differentiation of capercaillie populations at different stages along a gradient of spatial structuring from high connectivity (continuous range in the boreal forest) to a metapopulation systems (Alps) and recent (central Europe) and historic (Pyrenees) isolation. Four hundred and sixty individuals from 14 sample sites were genotyped at 10 polymorphic microsatellite loci to assess genetic structure and variation of capercaillie populations across its European range. As expected, differentiation was least pronounced within the continuous range in the boreal forest. Within the metapopulation system of the Alps, differentiation was less than among the isolated populations of central Europe (Black Forest, Fichtelgebirge, Thuringia, Vosges). In the long-isolated population of the Pyrenees, and the recently isolated populations of central Europe, genetic diversity was significantly reduced compared with the Alps and boreal forest. Our results agree with the concept of a gradual increase in genetic differentiation from connectivity to isolation, and from recent to historic isolation. Anthropogenic habitat deterioration and fragmentation thus not only leads to range contractions and extinctions, but may also have significant genetic and evolutionary consequences for surviving populations. To maintain high levels of genetic variation in species in fragmented habitats, conservation should aim at securing connectivity between spatially distinct populations.     

Conservation genetics of the endangered terrestrial orchid Liparis japonica in Northeast China based on AFLP markers

Levels of genetic diversity and population genetic structure of the rare, endangered terrestrial orchid Liparis japonica were examined for eight natural populations (n = 185) in Northeast China using six AFLP primer pairs, where this species has experienced severe habitat loss and fragmentation. Based on 406 DNA bands, a high level of genetic diversity was found at the species level with the PPB of 85.47 %, while the genetic diversity at the population level was low (PPB = 47.48 %). A significantly high degree of population differentiation was found with 42.69 % variation existed among populations as measured by AMOVA, indicating potential restricted gene flow. The genetic distances between populations were independent of the corresponding geographic distances, and the genetic relationship of individuals had no significant correlation with their spatial distribution. The restricted gene flow might be impacted by reduced population size, habitat destruction and fragmentation. The results in this study suggested that habitat protection and keeping a stable environment are critical for the conservation of L. japonica species.     

Genetic differentiation of the Western Capercaillie highlights the importance of South-eastern Europe for understanding the species phylogeography

The Western Capercaillie (Tetrao urogallus L.) is a grouse species of open boreal or high altitude forests of Eurasia. It is endangered throughout most mountain range habitat areas in Europe. Two major genetically identifiable lineages of Western Capercaillie have been described to date: the southern lineage at the species' southernmost range of distribution in Europe, and the boreal lineage. We address the question of genetic differentiation of capercaillie populations from the Rhodope and Rila Mountains in Bulgaria, across the Dinaric Mountains to the Slovenian Alps. The two lineages' contact zone and resulting conservation strategies in this so-far understudied area of distribution have not been previously determined. The results of analysis of mitochondrial DNA control region sequences of 319 samples from the studied populations show that Alpine populations were composed exclusively of boreal lineage; Dinaric populations of both, but predominantly (96%) of boreal lineage; and Rhodope-Rila populations predominantly (>90%) of southern lineage individuals. The Bulgarian mountains were identified as the core area of the southern lineage, and the Dinaric Mountains as the western contact zone between both lineages in the Balkans. Bulgarian populations appeared genetically distinct from Alpine and Dinaric populations and exhibited characteristics of a long-term stationary population, suggesting that they should be considered as a glacial relict and probably a distinct subspecies. Although all of the studied populations suffered a decline in the past, the significantly lower level of genetic diversity when compared with the neighbouring Alpine and Bulgarian populations suggests that the isolated Dinaric capercaillie is particularly vulnerable to continuing population decline. The results are discussed in the context of conservation of the species in the Balkans, its principal threats and legal protection status. Potential conservation strategies should consider the existence of the two lineages and their vulnerable Dinaric contact zone and support the specificities of the populations.     

Genetic diversity and population structure of the roughskin sculpin (<Emphasis Type="Italic">Trachidermus fasciatus</Emphasis> Heckel) inferred from microsatellite analyses: implications for its conservation and management

Identification of population units is crucial for management and monitoring programs, especially for endangered wild species. The roughskin sculpin (Trachidermus fasciatus Heckel) is a small catadromous fish and has been listed as a second class state protected aquatic animal since 1988 in China. To achieve sustainable conservation of this species, it is necessary to clarify the existing genetic structure both between and within populations. Here, population genetic structure among eight populations of T. fasciatus were analyzed by using 16 highly polymorphic microsatellites. High levels of genetic variation were observed in all populations. All pairwise F _ST estimates were significant after false discovery rate correction (overall average F _ST = 0.054). Furthermore, both STRUCTURE and discriminant analysis of principal components (DAPC) analysis showed that the eight populations were grouped into six clusters. BAYESASS analysis showed generally low recent and asymmetric migration among populations. All these results suggested significant genetic structure across populations. However, there was no isolation by distance relationship among populations, likely resulting from barriers to gene flow created by habitat fragmentation. Our results highlight the need for in situ conservation efforts for T. fasciatus across its entire distribution range, through maximizing habitat size and quality to preserve overall genetic diversity and evolutionary potential.     

Crossing the Rhine: a potential barrier to wildcat (<Emphasis Type="Italic">Felis silvestris silvestris</Emphasis>) movement?

The European wildcat (Felis silvestris silvestris) underwent a severe decline across Europe in the early twentieth century. Remaining populations are often very small and isolated, though there are indications that wildcat populations are currently expanding their range. However, linear landscape elements such as rivers and roads are thought to present barriers to dispersal, inhibiting gene flow and, thus, affecting the recolonization process. In this study, we investigated the fine-scale genetic structure of wildcats in the Upper Rhine Valley. We specifically analysed wildcats on both sides of the Rhine River by genotyping 55 individual wildcats, using 20 microsatellite loci. Genetic differentiation was weak and positive spatial autocorrelation was found up to a distance of 10 km (females: 5 km, males: 10 km) indicating substantial gene flow among sampling sites. High levels of gene flow, even across the Rhine River, indicated that the water body itself does not necessarily have a strong barrier effect, which is in contrast to other studies. Our findings could best be explained by the populations’ history, a local extinction east of the River Rhine and a current ongoing population expansion. Our study highlights that potential barriers, such as rivers, may have different effects in different local wildcat populations and that the history of the populations is important to interpret genetic results. As many wildcats still occur in isolated and patchy forest fragments, maintaining connectivity between populations is crucial to ensure their viability in the long term.     

Population genetics of the endangered Wattled Curassow (Crax globulosa,Cracidae, Aves) of the Colombian–Peruvian Amazon using DNA microsatellites and ND2 mitochondrial sequences

The Wattled Curassow (Crax globulosa, Cracidae, Aves) is a large bird living in the Western Amazon basin and a critically endangered species in the Colombian and in the Peruvian Amazon. We carried out the first population genetics analysis of this species employing six nuclear microsatellite markers and sequences of the mtND2 gene. The main results are as follows. (1) The levels of gene diversity were high for the overall population as well as for each of the three islands for both microsatellites and mtDNA. (2) A small amount of genetic differentiation among populations was found with both types of markers (F_ST = 0.027 for microsatellites and N_ST = 0.17 for mitochondrial sequences). (3) Using microsatellites, the Geneclass 2.0 software detected a low correct assignment of individuals to their respective populations. The Structure software only detected one gene pool for the entire area studied. These results are relevant for conservation efforts of this critically endangered species.     

Capercaillie in the Alps: genetic evidence of metapopulation structure and population decline

In the Alps, the capercaillie is distributed in a metapopulation pattern with local populations on mountain ranges separated by farmland valleys. Habitat deterioration, primarily related to human land use, resulted in population declines and range contractions became obvious. At the edge of a species' range, lower connectivity and less gene flow may render populations more susceptible to decline and extinction than in the core of the range. If this were true for the capercaillie in the Alps, edge populations should be subject to limited gene flow and should show genetic signs of a more severe population decline than core populations. To test this hypothesis, we used microsatellite DNA typing techniques. We assessed genetic variation within and among 18 local capercaillie populations across the Alps in relation to geographical distribution within the metapopulation system. All populations showed high levels of genetic variation in terms of average number of alleles, allelic richness and heterozygosity. Excess heterozygosity suggested a recent population decline, that was more pronounced in edge than core populations. We found high gene flow, but also significant differentiation among populations. Differentiation among edge populations was related to geographical distance, and appeared to be a recent process, most probably caused by reduced gene flow after population decline. In the core group, the high mountains of the central Alps seem to limit dispersal, and genetic drift was the most likely explanation for the observed differentiation among populations. We conclude that maintaining connectivity within the metapopulation system is vital for capercaillie conservation in the Alps.     

Landscape genetics of an endangered salt marsh endemic: Identifying population continuity and barriers to dispersal

Preserving the genetic diversity of endangered species is fundamental to their conservation and requires an understanding of genetic structure. In turn, identification of landscape features that impede gene flow can facilitate management to mitigate such obstacles and help with identifying isolated populations. We conducted a landscape genetic study of the endangered salt marsh harvest mouse (Reithrodontomys raviventris), a species endemic to the coastal marshes of the San Francisco Estuary of California. We collected and genotyped?>?500 samples from across the marshes of Suisun Bay which contain the largest remaining tracts of habitat for the species. Cluster analyses and a population tree identified three geographically discrete populations. Next, we conducted landscape genetic analyses at two scales (the entire study area and across the Northern Marshes) where we tested 65 univariate models of landscape features and used the best supported to test multivariable analyses. Our analysis of the entire study area indicated that open water and elevation (>?2 m) constrained gene flow. Analysis of the Northern Marshes, where low elevation marsh habitat is more continuous, indicated that geographic distance was the only significant predictor of genetic distance at this scale. The identification of a large, connected population across Northern Marshes achieves a number of recovery targets for this stronghold of the species. The identification of landscape features that act as barriers to dispersal enables the identification of isolated and vulnerable populations more broadly across the species range, thus aiding conservation prioritization.

     

Conservation in the southern edge of <Emphasis Type="Italic">Tetrao urogallus</Emphasis> distribution: Gene flow despite fragmentation in the stronghold of the Cantabrian capercaillie

The Cantabrian capercaillie (Tetrao urogallus cantabricus) is an endangered subspecies of the Western capercaillie, endemic of northern Spain, inhabiting the south-western limit of the species range. Assessing genetic variability and the factors that determine it is crucial in order to develop an effective conservation strategy. In this work, non-invasive samples were collected in some of the best preserved areas inhabited by Cantabrian capercaillie. Nine microsatellite loci and a sex-specific marker were analysed. We included five zones, separated by valleys with different levels of habitat modifications. No evidence of genetic clustering was found which suggests that fragmentation and development in the area do not act as barriers to gene flow. Nonetheless, significant differences among sampling zones were encountered in terms of their allelic frequencies (global F _ST = 0.035, p = 0.001). Pairwise F _ST comparisons showed differences between all sampling zones included, except between the two ones located in the South (Degaña and Alto Sil). These findings, along with the results of individual based genetic differences, indicate that gene flow among sampling zones might be at least slightly compromised, except between the two zones located in the South. Despite this, the sampling zones seem to exchange migrants at a rate that prevents genetic differentiation to the point of creating clusters. Our results show that the capercaillies in the study area constitute a single interbreeding group, which is an important piece of information that provides support to better understand the dynamics of this endangered subspecies.     

Inbreeding and strong population subdivision in an endangered salamander

Studies of genetic population structure and genetic diversity are often critical components of endangered species conservation and management plans. Genetic studies are thus particularly important for amphibians, which are in global decline. We studied genetic variation and population structure among 276 individuals from approximately half of the known localities of the endangered Sonora tiger salamander, Ambystoma mavortium stebbinsi, using ten microsatellite loci. Allelic diversity was generally low (2.7 alleles per locus per population) and overall observed heterozygosity (0.191) was significantly lower than expected (0.332). Most populations showed significant departures from Hardy–Weinberg equilibrium, which are likely due to inbreeding. In addition, evidence of recent bottlenecks was suggested by shifted allele frequency distributions in 5 of 16 populations, and ratios of allele number to allele size range (M) values lower than critical values in all populations. A high degree of genetic subdivision (θ = 0.133) was found over all populations, and nearly all pairwise population combinations were genetically subdivided. Thus, gene flow is limited even over small distances, perhaps because high desert grassland throughout the study area limits the efficacy of inter-pond movement of salamanders. Further, population sizes and gene flow of Sonora tiger salamanders are likely compromised by several contemporary ecological threats, including: frequent die-offs due to an infectious virus, introductions of non-native species, and continuing cattle grazing. Overall, these genetic data support the endangered status of the Sonora tiger salamander and suggest the subspecies exists in small, inbred populations.     

Genetic differentiation of an endangered capercaillie (<Emphasis Type="Italic">Tetrao urogallus</Emphasis>) population at the Southern edge of the species range

The low-latitude limits of species ranges are thought to be particularly important as long-term stores of genetic diversity and hot spots for speciation. The Iberian Peninsula, one of the main glacial refugia in Europe, houses the southern distribution limits of a number of boreal species. The capercaillie is one such species with a range extending northwards to cover most of Europe from Iberia to Scandinavia and East to Siberia. The Cantabrian Range, in North Spain, constitutes the contemporary south-western distribution limit of the species. In contrast to all other populations, which live in pure or mixed coniferous forests, the Cantabrian population is unique in inhabiting pure deciduous forests. We have assessed the existence of genetic differentiation between this and other European populations using microsatellite and mitochondrial DNA (mtDNA) extracted from capercaillie feathers. Samples were collected between 2001 and 2004 across most of the current distribution of the Cantabrian population. Mitochondrial DNA analysis showed that the Cantabrian birds form a distinct clade with respect to all the other European populations analysed, including the Alps, Black Forest, Scandinavia and Russia, which are all members of a discrete clade. Microsatellite DNA from Cantabrian birds reveals the lowest genetic variation within the species in Europe. The existence of birds from both mtDNA clades in the Pyrenees and evidence from microsatellite frequencies for two different groups, points to the existence of a Pyrenean contact zone between European and Cantabrian type birds. The ecological and genetic differences of the Cantabrian capercaillies qualify them as an Evolutionarily Significant Unit and support the idea of the importance of the rear edge for speciation. Implications for capercaillie taxonomy and conservation are discussed.     

High genetic diversity in isolated populations of Thesium ebracteatum at the edge of its distribution range

The aim of this study was to estimate the degree and distribution of genetic diversity within Central-European populations of Thesium ebracteatum—one of the most endangered plant species in Europe. By analyzing allozymes from 17 populations, we estimated the distribution of genetic diversity and suggest the most valuable populations for conservation. Analysis of molecular variance results showed the highest variance existed between populations (54 %), whereas the mean variance within populations was 46 %. A surprisingly low degree of variance (less than 1 %) was found between the six studied regions. We also observed no correlation between geographical and genetic distance, which supports the idea that individual populations are strongly isolated. T. ebracteatum undergoes extensive clonal growth and may survive for very long periods of time without generative reproduction. Consistent with this, we found a strong and significant relationship between genetic diversity and population size. All populations occupying an area greater than 300 m² showed high genetic diversity, whereas small populations contained less genetic diversity. Therefore, conservation priorities could generally be decided based on population size. Because this species is a weak competitor, existing localities should also be managed to prevent species loss from habitat degradation, by mowing or from time to time otherwise disturbing population areas to create open areas for growth.     

Isolation by distance and gene flow in the Eurasian badger (Meles meles) at both a local and broad scale

Eurasian badgers, Meles meles, have been shown to possess limited genetic population structure within Europe; however, field studies have detected high levels of philopatry, which are expected to increase population structure. Population structure will be a consequence of both contemporary dispersal and historical processes, each of which is expected to be evident at a different scale. Therefore, to gain a greater understanding of gene flow in the badger, we examined microsatellite diversity both among and within badger populations, focusing on populations from the British Isles and western Europe. We found that while populations differed in their allelic diversity, the British Isles displayed a similar degree of diversity to the rest of western Europe. The lower genetic diversity occurring in Ireland, Norway and Scotland was more likely to have resulted from founder effects rather than contemporary population density. While there was significant population structure (F ST = 0.19), divergence among populations was generally well explained by geographic distance (P < 0.0001) across the entire range studied of more than 3000 km. Transient effects from the Pleistocene appear to have been replaced by a strong pattern of genetic isolation by distance across western Europe, suggestive of colonization from a single refugium. Analysis of individuals within British populations through Mantel tests and spatial autocorrelation demonstrated that there was significant local population structure across 3-30 km, confirming that dispersal is indeed restricted. The isolation by distance observed among badger populations across western Europe is likely to be a consequence of this restricted local dispersal.     

AFLP and ISSR analysis reveals high genetic variation and inter-population differentiation in fragmented populations of the endangered Litsea szemaois (Lauraceae) from Southwest China

Litsea szemaois (Lauraceae) is an endemic and endangered species from the tropical rain forests of Xishuangbanna, southern Yunnan, SW China, but habitat fragmentation, especially exacerbated by rubber planting, has caused a decline in population size of the species. AFLP and ISSR were used to investigate the genetic diversity and population structure of eight populations from across its known distribution. Three AFLP and ten ISSR primer combinations produced a total of 203 and 77 unambiguous and repeatable bands respectively, of which 164 (80.8%) and 67 (87.0%) were polymorphic for the two markers. These two markers showed that Litsea szemaois exhibits comparatively high genetic diversity at species level (heterozygosity (hs) = 0.2109) relative to some other Lauraceae. Most of the genetic variation was partitioned within populations, but genetic differentiation between populations was significant and relatively high (Φ _st = 0.2420, θ^B = 0.1986) compared with other tropical plants. The genetic characteristics of L. szemaois may be related to its outbreeding system, insect pollination and fragmented distribution. Because L. szemaois is dioecious and slow to mature, ex situ conservation across its genetic diversity is unlikely to succeed, although seedlings grow well under cultivation. Thus, in situ conservation is very important for this endangered species, especially as only 133 adult individuals are known in the wild. In particular, the Nabanhe and Mandian populations should be given a high conservation priority due to their higher genetic diversity, larger population size and better field condition, but wider sampling is required across all populations to determine additional areas with significant genetic conservation value.     

Using genetic diversity and mating system parameters estimated from genetic markers to determine strategies for the conservation of <Emphasis Type="Italic">Araucaria angustifolia</Emphasis> (Bert.) O. Kuntze (Araucariaceae)

In order to understand the impacts of forest fragmentation on Araucaria angustifolia populations, we evaluated the genetic diversity and mating system using SSR markers and open-pollinated seeds from four populations of varying sizes and spatial isolation, in and around one of the best-conserved Araucaria Forest remnants in Southern Brazil. The four population types of A. angustifolia include: (1) a continuous forest; (2) a physically isolated cluster located 2 km from the continuous forest; (3) an open population in a field located between the cluster and continuous forest; and (4) a fragment on a private property located 5 km from the cluster. Approximately 28 seeds were collected from ten reproductive trees in each population. We found higher amounts of alleles (113) and exclusive alleles (25) in the continuous forest than in the other populations. The multilocus paternity correlation was significantly higher and effective number of pollen donors was significantly lower in the private population, decreasing the diversity and consequently the variance effective size of families sampled from that population. However, despite its isolation from the other studied fragments, the private population had the second highest number of alleles as well as unique alleles from the other populations. Therefore, strategies for A. angustifolia conservation should focus not only on larger populations, such as those found in protected areas, but also include smaller and isolated fragments on private properties as these populations are able to maintain high levels of genetic diversity and functional connectivity between isolated stands across a landscape.     

Conservation genetics of the annual hemiparasitic plant <Emphasis Type="Italic">Melampyrum sylvaticum</Emphasis> (Orobanchaceae) in the UK and Scandinavia

Melampyrum sylvaticum is an endangered annual hemiparasitic plant that is found in only 19 small and isolated populations in the United Kingdom (UK). To evaluate the genetic consequences of this patchy distribution we compared levels of diversity, inbreeding and differentiation from ten populations from the UK with eight relatively large populations from Sweden and Norway where the species is more continuously distributed. We demonstrate that in both the UK and Scandinavia, the species is highly inbreeding (global F _IS = 0.899). Levels of population differentiation were high (F’_ST = 0.892) and significantly higher amongst UK populations (F’_ST = 0.949) than Scandinavian populations (F’_ST = 0.762; P < 0.01). The isolated populations in the UK have, on average, lower genetic diversity (allelic richness, proportion of loci that are polymorphic, gene diversity) than Scandinavian populations, and this diversity difference is associated with the smaller census size and population area of UK populations. From a conservation perspective, the naturally inbreeding nature of the species may buffer the species against immediate effects of inbreeding depression, but the markedly lower levels of genetic diversity in UK populations may represent a genetic constraint to evolutionary change. In addition, the high levels of population differentiation suggest that gene flow among populations will not be effective at replenishing lost variation. We thus recommend supporting in situ conservation management with ex situ populations and human-mediated seed dispersal among selected populations in the UK.     

Use of a genetically informed population viability analysis to evaluate management options for Polish populations of endangered beetle <Emphasis Type="Italic">Cerambyx cerdo</Emphasis> L. (1758) (Coleoptera,Cerambycidae)

A paucity of genetic information and the drastic decline in population size of the beetle Cerambyx cerdo has made this species a high priority for research and conservation management. The state-listed beetle, a saproxylic insect associated with oaks, has a discontinuous range, with larger and more connected populations in southern Europe and small and isolated populations in the continent’s central and northern parts. Here, we used seven microsatellite loci and one DNA fragment of the mitochondrial gene COI to examine the population structure, genetic diversity, and contemporary gene flow between two Polish populations of the beetle. A population viability analysis summarizing collected genetic data as well as field records and species-specific information was performed to investigate the probability of the populations’ persistence over 20 years under different simulation scenarios. Genetic drift due to spatial isolation and bottleneck(s) is probably a major evolutionary force responsible for a low number of haplotypes and lower gene diversity in these populations as compared to the neighboring Czech populations. Despite a large geographic distance between the Polish populations, genetic differentiation between them was low, which could reflect shared ancestral polymorphism and stochasticity of retained alleles rather than the homogenizing effect of gene flow. Differences among probabilities of extinction over 20 years were detected between populations, and, in the worst-case scenarios, one population will disappear within four generations. Conservation efforts must focus on supplementation, habitat restoration, and post-release monitoring. The results of our study provided information that can be incorporated into future management actions to aid in the conservation of the beetle.     

Genetic structure and mating system of Manilkara huberi (Ducke) A. Chev., a heavily logged Amazonian timber species

In this work, we report on the population genetic structure of the endangered tree species Manilkara huberi, an Amazonian tree species intensely exploited due to the high density and resistance of its wood. We investigated the patterns of spatial distribution, genetic structure, and mating system using 7 microsatellite loci and here discuss the consequences for conservation and management of the species. To examine the population genetic structure, 481 adult trees and 810 seedlings were sampled from an area of 200 ha from a natural population in FLONA Tapajós, PA, Brazil. We found relatively high and consistent inbreeding levels (intrapopulation fixation index [f] 0.175 and 0.240) and a significant spatial genetic structure up to a radius of approximately 300 m, most likely due to a limited seed and pollen flow. The multilocus (tm) population outcrossing rate was high (0.995), suggesting that the species is predominantly allogamous with a pollen flow restricted to 47 m. These results suggest that M. huberi is spatially structured, consistent with a model of isolation by distance. Fragmentation may therefore cause the loss of subpopulations, suggesting that management programs for production and conservation should include large areas. The genetic data also revealed that for ex situ conservation, seeds should be collected from more than 175 maternal trees, in order to keep an effective population size of 500. Furthermore, as the species is widely distributed across the Amazon Forest, samples should include several populations in order to represent the highest genetic diversity possible. These results provide a blueprint to guide the production and conservation management policies of this valuable timber species.