Population genetics of Formica aquilonia wood ants in Scotland: the effects of long-term forest fragmentation and recent reforestation

Formica aquilonia wood ants are forest specialists which play a key role in the ecology of forests in Europe. Many of the Scottish populations at the edge of the species distribution range occur in highly fragmented landscapes. We used ten microsatellite loci to study the genetic diversity and structure of populations from two contrasting regions (Inverpolly and the Trossachs) to set the Scottish populations in the context of conspecific populations in mainland Europe. Historically, both study regions have experienced extreme habitat loss and fragmentation over several centuries. Inverpolly has remained fragmented whereas large scale reforestation over the last century has greatly increased the forested area in the Trossachs. Despite the long history of fragmentation, genetic diversity in the Scottish populations was greater than in the populations in mainland Europe. Genetic diversity was similar in the two Scottish regions and no evidence of inbreeding was detected. However, the populations in Inverpolly showed more evidence of genetic bottlenecks, possibly due to more frequent stochastic events such as moorland fires. The ant populations in individual forests were genetically distinct and we detected no contemporary gene flow between forests. The most intensively studied forest where non-native conifer plantations now occupy the matrix between the remaining ancient woodland fragments showed evidence that admixture and gene flow between nests was reducing the past differentiation. This may reflect a dynamic response to the reconnection of previously isolated populations in forest fragments by recent reforestation.     

Limited effect of anthropogenic habitat fragmentation on molecular diversity in a rain forest skink, Gnypetoscincus queenslandiae

To examine the effects of recent habitat fragmentation, we assayed genetic diversity in a rain forest endemic lizard, the prickly forest skink (Gnypetoscincus queenslandiae), from seven forest fragments and five sites in continuous forest on the Atherton tableland of northeastern Queensland, Australia. The rain forest in this region was fragmented by logging and clearing for dairy farms in the early 1900s and most forest fragments studied have been isolated for 50-80 years or nine to 12 skink generations. We genotyped 411 individuals at nine microsatellite DNA loci and found fewer alleles per locus in prickly forest skinks from small rain forest fragments and a lower ratio of allele number to allele size range in forest fragments than in continuous forest, indicative of a decrease in effective population size. In contrast, and as expected for populations with small neighbourhood sizes, neither heterozygosity nor variance in allele size differed between fragments and sites in continuous forests. Considering measures of among population differentiation, there was no increase in FST among fragments and a significant isolation by distance pattern was identified across all 12 sites. However, the relationship between genetic (FST) and geographical distance was significantly stronger for continuous forest sites than for fragments, consistent with disruption of gene flow among the latter. The observed changes in genetic diversity within and among populations are small, but in the direction predicted by the theory of genetic erosion in recently fragmented populations. The results also illustrate the inherent difficulty in detecting genetic consequences of recent habitat fragmentation, even in genetically variable species, and especially when effective population size and dispersal rates are low.     

Endangered species in small habitat patches can possess high genetic diversity: the case of the Tana River red colobus and mangabey

We used mtDNA sequence data from the Tana River red colobus and mangabey to determine how their population genetic structure was influenced by dispersal and habitat fragmentation. The colobus and mangabey are critically endangered primates endemic to gallery forests in eastern Kenya. The forests are a Pliocene–Pleistocene refugium that has recently undergone significant habitat loss and fragmentation due to human activities. We expected both primates to exhibit low levels of genetic diversity due to elevated genetic drift in their small populations, and to show a strong correspondence between genetic and geographic distance due to disruption of gene flow between forests by habitat fragmentation. Additionally, because mangabey females are philopatric, we expected their mtDNA variation to be homogeneous within forest patches but to be heterogeneous between patches. In contrast, colobus have a female-biased dispersal and so we expected their mtDNA variation to be homogeneous within and between forest patches. We found high levels of haplotype and nucleotide diversity as well as high levels of sequence divergence between haplotype groups in both species. The red colobus had significantly higher genetic variation than the mangabey did. Most of the genetic variation in both primates was found within forest fragments. Although both species showed strong inter-forest patch genetic structure we found no correspondence between genetic and geographic distances for the two primates. We attributed the high genetic diversity to recent high effective population size, and high sequence divergence and strong genetic structures to long-term habitat changes in the landscape.     

Remnants fragments preserve genetic diversity of the old forest lichen <Emphasis Type="Italic">Lobaria pulmonaria</Emphasis> in a fragmented Mediterranean mountain forest

Fragmentation represents a serious threat to biodiversity worldwide, however its effects on epiphytic organisms is still poorly understood. We study the effect of habitat fragmentation on the genetic population structure and diversity of the red-listed epiphytic lichen, Lobaria pulmonaria, in a Mediterranean forest landscape. We tested the relative importance of forest patch quality, matrix surrounding fragments and connectivity on the genetic variation within populations and the differentiation among them. A total of 855 thalli were sampled in 44 plots (400 m²) of 31 suitable forest fragments (beeches and oaks), in the Sierra de Ayllón in central Spain. Variables related to landscape attributes of the remnant forest patches such as size and connectivity and also the nature of the matrix or tree species had no significant effects on the genetic diversity of L. pulmonaria. Values of genetic diversity (Nei’s) were only affected by habitat quality estimated as the age patches. Most of the variation (76%) in all populations was observed at the smallest sampled unit (plots). Using multiple regression analysis, we found that habitat quality is more important in explaining the genetic structure of the L. pulmonaria populations than spatial distance. The relatively high level of genetic diversity of the species in old forest patches regardless of patch size indicates that habitat quality in a highly structured forest stand determines the population size and distribution pattern of this species and its associated lichen community. Thus, conservation programmes of Mediterranean mountain forests have to prioritize area and habitat quality of old forest patches.     

Historical habitat connectivity affects current genetic structure in a grassland species

Many recent studies have explored the effects of present and past landscape structure on species distribution and diversity. However, we know little about the effects of past landscape structure on distribution of genetic diversity within and between populations of a single species. Here we describe the relationship between present and past landscape structure (landscape connectivity and habitat size estimated from historical maps) and current genetic structure in a perennial herb, Succisa pratensis. We used allozymes as co‐dominant markers to estimate genetic diversity and deviation from Hardy–Weinberg equilibrium in 31 populations distributed within a 5 km² agricultural landscape. The results showed that current genetic diversity of populations was related to habitat suitability, habitat age, habitat size and habitat connectivity in the past. The effects of habitat age and past connectivity on genetic diversity were in most cases also significant after taking the current landscape structure into account. Moreover, current genetic similarity between populations was affected by past connectivity after accounting for current landscape structure. In both cases, the oldest time layer (1850) was the most informative. Most populations showed heterozygote excess, indicating disequilibrium due to recent gene flow or selection against homozygotes. These results suggest that habitat age and past connectivity are important determinants of distribution of genetic diversity between populations at a scale of a few kilometres. Landscape history may significantly contribute to our understanding of distribution of current genetic structure within species and the genetic structure may be used to better understand landscape history, even at a small scale.     

Functional connectivity and genetic diversity of Eulaema atleticana (Apidae,Euglossina) in the Brazilian Atlantic Forest Corridor: assessment of gene flow

The mobility and dispersal of organisms affect population genetics and dynamics, and consequently affect persistence and the risk of extinction. Thus, it is important to understand how organisms move in the fragmented landscapes in order to manage populations and predict the effects of habitat changes on species persistence. This study evaluated the functional connectivity of an orchid bee (Eulaema atleticana Nemésio, 2009) with a high fidelity to forest habitats in the Brazilian Atlantic Forest Corridor by analyzing genetic diversity, spatial genetic structure, and gene flow estimated from microsatellite and mitochondrial markers. Genetic diversity was not correlated with area of the forest fragments, or with forest isolation. At the mosaic scale, Eulaema atleticana showed no significant or low genetic differentiation, indicating genetic homogeneity among forest fragments. A previous field study indicated that Eulaema atleticana was one of the most sensitive Euglossina bees to forest fragmentation but the present molecular analyses demonstrates that current gene flow is sufficient to maintain genetic variability at the mosaic scale.     

Recent habitat fragmentation caused by major roads leads to reduction of gene flow and loss of genetic variability in ground beetles

Although habitat fragmentation is suspected to jeopardize the long-term survival of many species, few data are available on its impact on the genetic variability of invertebrates. We assess the genetic population structure of the flightless ground beetle Carabus violaceus L., 1758 in a Swiss forest, which is divided into several fragments by a highway and two main roads. Eight samples were collected from different forest fragments and analysed at six microsatellite loci. The largest genetic differentiation was observed between samples separated by roads and in particular by the highway. The number of roads between sites explained 44% of the variance in pairwise F(ST) estimates, whereas the age of the road and the geographical distance between locations were not significant factors. Furthermore, a comparison of allelic richness showed that the genetic variability in a small forest fragment isolated by the highway was significantly lower than in the rest of the study area. These findings strongly support the hypothesis that large roads are absolute barriers to gene flow in C. violaceus, which may lead to a loss of genetic variability in fragmented populations.     

Conservation of long-lived perennial forest herbs in an urban context: <Emphasis Type="Italic">Primula elatior</Emphasis> as study case

Urban forests are generally fragmented in small isolated remnants, embedded in an inhospitable human-used matrix, and incur strong anthropogenic pressures (recreational activities, artificialization, pollution and eutrophication). These lead to particularly high constraints even for common forest herbs, whose genetic response may depend on life-history traits and population demographic status. This study investigated genetic variation and structure for 20 allozyme loci in 14 populations of Primula elatior, a self-incompatible long-lived perennial herb, occurring in forest fragments of Brussels urban zone (Belgium), in relation to population size and young plants recruitment rate. Urban populations of P. elatior were not genetically depauperate, but the small populations showed reduced allelic richness. Small populations showing high recruitment rates—and therefore potential rejuvenation—revealed lower genetic diversity (H _o and H _e) than those with low or no recruitment. No such pattern was observed for the large populations. There was a significant genetic differentiation among populations within forest fragments (F _SC = 0.052, P < 0.001), but not between fragments (F _CT = 0.002, P > 0.10). These findings suggest restricted gene flow among populations within fragments and local processes (genetic drift, inbreeding) affecting small populations, strengthened when there is recruitment. Urban forest populations of long-lived perennial herbs can be of conservation value. However, restoration of small populations by increasing population size through regeneration by seedling recruitment may lead to negative genetic consequences. Additional management, aiming to restore gene flow among populations, may need to be applied to compensate the loss of genetic diversity and to reduce inbreeding.     

Multi-annual density fluctuations and habitat size enhance genetic variability in two northern voles

In order to gain a better understanding of the consequences of population density cycles and landscape structure for the genetic composition in time and space of vole populations, we analyzed the multiannual genetic structure of the two numerically dominant, sympatric small rodent species of northernmost Fennoscandia. Red voles Myodes rutilus and grey-sided voles M. rufocanus were trapped in the subarctic birch forest along three fjords over five years. Along each fjord, there were four or five altitudinal transects each with five trapping stations. Spring and fall population densities were estimated from mark–recapture data. Grey-sided voles exhibited higher amplitude density fluctuations than red voles. Polymorphism at eight or nine microsatellite loci, determined in 1228 voles, was used to estimate local genetic diversity and differentiation among samples. Genetic diversity was higher in grey-sided voles than in red voles. Spring densities had no effect on local genetic diversity or on differentiation. The amplitude of density fluctuations and the extent of favorable habitat (sub-arctic birch forest) surrounding each site had a positive effect on genetic diversity, and the amplitude of density fluctuations had a negative effect on differentiation in red voles, for which fluctuating populations were compared with more stable populations. The harmonic mean of densities, reflecting average population sizes, had a negative effect on genetic diversity in red voles, but a positive effect in grey-sided voles, for which only fluctuating populations were compared. No other effects were significant for grey-sided voles. A temporal assignment test showed that the spatial structure was more stable in time for populations with more stable population dynamics. Altogether our results suggest that high amplitude density fluctuations lead to more gene flow and higher genetic diversity in vole populations.     

Weak genetic structuring indicates ongoing gene flow across White-ruffed Manakin (<Emphasis Type="Italic">Corapipo altera</Emphasis>) 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.     

Genetic Variation in Fragmented Forest Stands of the Andean Oak Quercus humboldtii Bonpl. (Fagaceae)1

Quercus humboldtii is a montane forest dominant species in Colombia, which has experienced significant habitat loss. Using three microsatellite loci, we compared the genetic diversity of adults and seedlings in fragments of small and large size. Results show high genetic diversity, comparable to other temperate oak species (H_o= 0.813, H_e= 0.780, and f=?0.044). However, allelic richness reduction in seedlings of the most fragmented part of the landscape, suggested restricted gene flow and risk of future genetic bottlenecks, if larger tracts of forest disappear.     

Habitat loss and fragmentation reduce effective gene flow by disrupting seed dispersal in a neotropical palm

Habitat loss and fragmentation often reduce gene flow and genetic diversity in plants by disrupting the movement of pollen and seed. However, direct comparisons of the contributions of pollen vs. seed dispersal to genetic variation in fragmented landscapes are lacking. To address this knowledge gap, we partitioned the genetic diversity contributed by male gametes from pollen sources and female gametes from seed sources within established seedlings of the palm Oenocarpus bataua in forest fragments and continuous forest in northwest Ecuador. This approach allowed us to quantify the separate contributions of each of these two dispersal processes to genetic variation. Compared to continuous forest, fragments had stronger spatial genetic structure, especially among female gametes, and reduced effective population sizes. We found that within and among fragments, allelic diversity was lower and genetic structure higher for female gametes than for male gametes. Moreover, female gametic allelic diversity in fragments decreased with decreasing surrounding forest cover, while male gametic allelic diversity did not. These results indicate that limited seed dispersal within and among fragments restricts genetic diversity and strengthens genetic structure in this system. Although pollen movement may also be impacted by habitat loss and fragmentation, it nonetheless serves to promote gene flow and diversity within and among fragments. Pollen and seed dispersal play distinctive roles in determining patterns of genetic variation in fragmented landscapes, and maintaining the integrity of both dispersal processes will be critical to managing and conserving genetic variation in the face of continuing habitat loss and fragmentation in tropical landscapes.     

Gene flow among native bush rat,Rattus fuscipes (Rodentia: Muridae), populations in the fragmented subtropical forests of south‐east Queensland

Abstract Many natural populations in areas of continuous habitat exhibit some form of local genetic structure. Anthropogenic habitat fragmentation can also strongly influence the dynamics of gene flow between populations. We used eight microsatellite markers to investigate the population genetic structure of an abundant forest species, the Australian bush rat (Rattus fuscipes), in the subtropical forests of south‐east Queensland. Five sites were sampled, allowing pairwise comparisons within continuous habitat and across clearings. Weak, but significant population differentiation and a significant pattern of isolation by distance was detected over the small scale (<10 km) of this study. Fine‐scale analysis at a single site (<1 km) showed a significant correlation between individual female genetic distance and geographical distance, but no similar pattern among male individuals. There was no evidence of increased population differentiation across clearings relative to comparisons within continuous forest. This was attributed to dispersal within corridors of remnant and revegetated habitat between the forested areas. We concluded that an inherently restricted dispersal ability, female philopatry and natural habitat heterogeneity play an important part in the development of genetic structure among populations of R. fuscipes. It is important to understand the relationship between landscape features and the pattern of gene flow among continuous populations, as this allows us to predict the impact of fragmentation on natural populations.     

Evidence for demographic bottlenecks and limited gene flow leading to low genetic diversity in a rare thistle

European calcareous grasslands have decreased dramatically in area and number during the last two centuries. As a result, many populations of calcareous grassland species are confined to small and isolated fragments, where their long-term survival is to some extent uncertain. Recently, several restoration projects have been initiated to enlarge the current grassland area in order to maintain the exceptionally high species richness. However, from a genetic point of view, the success of these restoration measures is not necessarily guaranteed, as strong historical decreases in population size and limited gene flow may have led to low genetic diversity through genetic bottlenecks and drift. In this study, we investigated genetic diversity and structure of 16 populations of the calcareous grassland specialist Cirsium acaule in a severely fragmented landscape in south-western Belgium. The overall distribution of this species in the study area was significantly and positively related to patch area, suggesting that small patches do not allow survival of this species. Both allelic richness and genetic diversity were significantly and positively related to population size. Estimation of observed and expected gene diversity provided evidence for population bottlenecks in the history of not less than 31% of all sampled populations. Reconstruction of the historical land use showed that patch area decline in populations that went through a recent bottleneck was significantly larger than that in populations that showed no evidence of a bottleneck. Assignment analyses showed low migration rates, suggesting that replenishment of lost alleles through gene flow is highly unlikely. Overall, our results indicate that in the absence of gene flow strong decreases in calcareous grassland area may have long-lasting effects on genetic diversity of plant populations and may hamper the success of restoration projects that simply aim at restoring initial habitat conditions or enlarging population fragments, as indicated by the fact that none of the recently restored areas has been occupied by C. acaule.     

The conservation-refugium value of small and disturbed Brazilian Atlantic forest fragments for the endemic ovoviviparous cockroach Monastria biguttata (Insecta: Dictyoptera, Blaberidae, Blaberinae)

The Brazilian Atlantic forest is a biodiversity hotspot and harbors many endemic species showing peculiar and unique traits. However, it has been reduced to less than 8% of its original surface and is distributed in scattered fragments, the great majority of which are smaller than 20 hectares and very disturbed, making it worth asking about their value for conservation. In this paper we assess the refugium value of small fragments to the conservation of one of the endemics of the Atlantic forest, the ovoviviparous cockroach Monastria biguttata. Our results showed that this species was ubiquitous in large and small forest fragments, but never present in plantations or pastures. The population age structure and sex ratio were balanced in every fragment, and total population size in the smallest fragments was at least several hundreds of individuals. Colony size, sex ratio, age structure, and density per piece of dead tree trunk indicated that populations from small fragments were not unbalanced or at risk of extinction. According to the analysis of resource availability, small fragments can provide suitable habitat for this species. In this situation, even very small forest fragments have a high refugium value for some endemic insect species. Considering their number in the landscape, these fragments should be considered with more attention in strategies of biodiversity conservation.     

A comparison of the population genetic structure of parasitic Viscum album from two landscapes differing in degree of fragmentation

Parasite populations do not necessarily conform to expected patterns of genetic diversity and structure. Parasitic plants may be more vulnerable to the negative consequences of landscape fragmentation because of their specialized life history strategies and dependence on host plants, which are themselves susceptible to genetic erosion and reduced fitness following habitat change. We used AFLP genetic markers to investigate the effects of habitat fragmentation on genetic diversity and structure within and among populations of hemiparasitic Viscum album. Comparing populations from two landscapes differing in the amount of forest fragmentation allowed us to directly quantify habitat fragmentation effects. Populations from both landscapes exhibited significant isolation-by-distance and sex ratios biased towards females. The less severely fragmented landscape had larger and less isolated populations, resulting in lower levels of population genetic structure (F _ST = 0.05 vs. 0.09) and inbreeding (F _IS = 0.13 vs. 0.27). Genetic differentiation between host-tree subpopulations was also higher in the more fragmented landscape. We found no significant differences in within-population gene diversity, percentage of polymorphic loci, or molecular variance between the two regions, nor did we find relationships between genetic diversity measures and germination success. Our results indicate that increasing habitat fragmentation negatively affects population genetic structure and levels of inbreeding in V. album, with the degree of isolation among populations exerting a stronger influence than forest patch size.     

Genetic effects of chronic habitat fragmentation on tree species: the case of Sorbus aucuparia in a deforested Scottish landscape

Sustainable forest restoration and management practices require a thorough understanding of the influence that habitat fragmentation has on the processes shaping genetic variation and its distribution in tree populations. We quantified genetic variation at isozyme markers and chloroplast DNA (cpDNA), analysed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in severely fragmented populations of Sorbus aucuparia (Rosaceae) in a single catchment (Moffat) in southern Scotland. Remnants maintain surprisingly high levels of gene diversity (HE) for isozymes (HE = 0.195) and cpDNA markers (HE = 0.490). Estimates are very similar to those from non-fragmented populations in continental Europe, even though the latter were sampled over a much larger spatial scale. Overall, no genetic bottleneck or departures from random mating were detected in the Moffat fragments. However, genetic differentiation among remnants was detected for both types of marker (isozymes Theta n = 0.043, cpDNA Theta c = 0.131; G-test, P-value < 0.001). In this self-incompatible, insect-pollinated, bird-dispersed tree species, the estimated ratio of pollen flow to seed flow between fragments is close to 1 (r = 1.36). Reduced pollen-mediated gene flow is a likely consequence of habitat fragmentation, but effective seed dispersal by birds is probably helping to maintain high levels of genetic diversity within remnants and reduce genetic differentiation between them.     

Landscape genomic signatures indicate reduced gene flow and forest‐associated adaptive divergence in an endangered neotropical turtle

Human‐induced transformations of ecosystems usually result in fragmented populations subject to increased extinction risk. Fragmentation is also often associated with novel environmental heterogeneity, which in combination with restricted gene flow may increase the opportunity for local adaptation. To manage at‐risk populations in these landscapes, it is important to understand how gene flow is changing, and how populations respond to habitat loss. We conducted a landscape genomics analysis using Restriction‐site Associated DNA sequencing to investigate the evolutionary response of the critically endangered Dahl's Toad‐headed turtle (Mesoclemmys dahli) to severe habitat modification. The species has lost almost all of its natural habitat in the southwestern part of its range and about 70% in the northeast. Based on least cost path analysis across different resistance surfaces for 3,211 SNPs, we found that the landscape matrix is restricting gene flow, causing the fragmentation of the species into at least six populations. Genome scans and allele‐environment association analyses indicate that the population fragments in the deforested grasslands of the southwest are adaptively different from those in the more forested northeast. Populations in areas with no forest had low levels of adaptive genetic diversity and the fixation of ancestrally‐polymorphic SNPs, consistent with directional selection in this novel environment. Our results suggest that this forest‐stream specialist is adapting to pond‐grassland conditions, but it is also suffering from negative consequences of habitat loss, including genetic erosion, isolation, small effective population sizes, and inbreeding. We recommend gene flow restoration via genetic rescue to counteract these threats, and provide guidance for this strategy.     

Dispersal of the orchid bee <Emphasis Type="Italic">Euglossa imperialis</Emphasis> over degraded habitat and intact forest

Fragmentation of habitat can decrease resource availability and restrict movement among geographic areas. Persistence in fragmented landscapes depends on the maintenance of connectivity among populations, without which genetic diversity may decrease and lead to population declines. Bees are particularly vulnerable to the negative effects of low genetic diversity so it is important to understand patterns of dispersal for native bees living in fragmented areas. I used population genetic techniques to characterize patterns of genetic diversity and dispersal for the orchid bee Euglossa imperialis within and among forest fragments in southern Costa Rica, in which the furthest two fragments were 226 km from one another. In addition, I compared results of population genetic analyses conducted with all bees sampled, and results from analyses conducted with a reduced dataset containing only one individual per full sibling family from each site. For both datasets genetic diversity was low within forest fragments, with expected heterozygosity averaging 0.28 for the full dataset and 0.29 for the dataset containing only one full sibling per site. I found no evidence that deforested areas restricted dispersal; pairwise estimates of genetic differentiation \(F_{\text{ST}}^{\prime }\) among forest fragments averaged 0.01 for the full dataset, and 0 for the dataset containing only one full sibling per site. Genetic distance among sites within forest fragments was significantly correlated to geographic distance for the full dataset, but there was no significant correlation for the dataset that contained only one individual from each full sibling family. This suggests that family structure can drive results of analyses of genetic structure, although reductions in sample sizes following removal of full siblings may have reduced power to detect genetic structure. Despite no evidence for restricted dispersal, the low genetic diversity found suggests that E. imperialis may be an important candidate for future conservation monitoring.     

Fragmentation reduces regional‐scale spatial genetic structure in a wind‐pollinated tree because genetic barriers are removed

Gene flow strongly influences the regional genetic structuring of plant populations. Seed and pollen dispersal patterns can respond differently to the increased isolation resulting from habitat fragmentation, with unpredictable consequences for gene flow and population structuring. In a recently fragmented landscape we compared the pre‐ and post‐fragmentation genetic structure of populations of a tree species where pollen and seed dispersal respond differentially to forest fragmentation generated by flooding. Castanopsis sclerophylla is wind‐pollinated, with seeds that are dispersed by gravity and rodents. Using microsatellites, we found no significant difference in genetic diversity between pre‐ and post‐fragmentation cohorts. Significant genetic structure was observed in pre‐fragmentation cohorts, due to an unknown genetic barrier that had isolated one small population. Among post‐fragmentation cohorts this genetic barrier had disappeared and genetic structure was significantly weakened. The strengths of genetic structuring were at a similar level in both cohorts, suggesting that overall gene flow of C. sclerophylla has been unchanged by fragmentation at the regional scale. Fragmentation has blocked seed dispersal among habitats, but this appears to have been compensated for by enhanced pollen dispersal, as indicated by the disappearance of a genetic barrier, probably as a result of increased wind speeds and easier pollen movement over water. Extensive pollen flow can counteract some negative effects of fragmentation and assist the long‐term persistence of small remnant populations.