Gene flow and inbreeding depression inferred from fine-scale genetic structure in an endangered heterostylous perennial, Primula sieboldii

We estimated the gene dispersal distance and the magnitude of inbreeding depression from the fine-scale genetic structure in the endangered heterostylous perennial Primula sieboldii. We indirectly estimated the neighbourhood size (Nb) and the standard deviation of gene dispersal distance (sigma(g)) from the detected genetic structure by using 10 microsatellite markers. We also estimated the fitness reduction in mating among neighbouring individuals caused by biparental inbreeding according to the genetic structure. We found clear fine-scale genetic structure (a significantly positive kinship coefficient within 42.3 m), and the indirect estimates of sigma(g) and Nb were 15.7 m and 50.9, respectively. These indirect estimates were similar to the direct estimates (18.4 m and 44.0). The slightly larger indirect estimate of Nb may reflect that inbreeding depression and genetic structure or rare long-distance dispersal that were overlooked in the direct estimate have elongated the long-term average of gene dispersal distance. P. sieboldii is also likely to suffer about 19% fitness reduction in progenies from mating among individuals 5 m apart. Our results suggest that biparental inbreeding and genetic structure can affect the range of gene dispersal and seed reproductive success in P. sieboldii.     

Fine-scale genetic structure and gene dispersal inferences in 10 neotropical tree species

The extent of gene dispersal is a fundamental factor of the population and evolutionary dynamics of tropical tree species, but directly monitoring seed and pollen movement is a difficult task. However, indirect estimates of historical gene dispersal can be obtained from the fine-scale spatial genetic structure of populations at drift-dispersal equilibrium. Using an approach that is based on the slope of the regression of pairwise kinship coefficients on spatial distance and estimates of the effective population density, we compare indirect gene dispersal estimates of sympatric populations of 10 tropical tree species. We re-analysed 26 data sets consisting of mapped allozyme, SSR (simple sequence repeat), RAPD (random amplified polymorphic DNA) or AFLP (amplified fragment length polymorphism) genotypes from two rainforest sites in French Guiana. Gene dispersal estimates were obtained for at least one marker in each species, although the estimation procedure failed under insufficient marker polymorphism, limited sample size, or inappropriate sampling area. Estimates generally suffered low precision and were affected by assumptions regarding the effective population density. Averaging estimates over data sets, the extent of gene dispersal ranged from 150 m to 1200 m according to species. Smaller gene dispersal estimates were obtained in species with heavy diaspores, which are presumably not well dispersed, and in populations with high local adult density. We suggest that limited seed dispersal could indirectly limit effective pollen dispersal by creating higher local tree densities, thereby increasing the positive correlation between pollen and seed dispersal distances. We discuss the potential and limitations of our indirect estimation procedure and suggest guidelines for future studies.     

Increased inbreeding and strong kinship structure in Taxus baccata estimated from both AFLP and SSR data

Habitat fragmentation can have severe genetic consequences for trees, such as increased inbreeding and decreased effective population size. In effect, local populations suffer from reduction of genetic variation, and thus loss of adaptive capacity, which consequently increases their risk of extinction. In Europe, Taxus baccata is among a number of tree species experiencing strong habitat fragmentation. However, there is little empirical data on the population genetic consequences of fragmentation for this species. This study aimed to characterize local genetic structure in two natural remnants of English yew in Poland based on both amplified fragment length polymorphism (AFLP) and microsatellite (SSR) markers. We introduced a Bayesian approach that estimates the average inbreeding coefficient using AFLP (dominant) markers. Results showed that, in spite of high dispersal potential (bird-mediated seed dispersal and wind-mediated pollen dispersal), English yew populations show strong kinship structure, with a spatial extent of 50–100 m, depending on the population. The estimated inbreeding levels ranged from 0.016 to 0.063, depending on the population and marker used. Several patterns were evident: (1) AFLP markers showed stronger kinship structure than SSRs; (2) AFLP markers provided higher inbreeding estimates than SSRs; and (3) kinship structure and inbreeding were more pronounced in denser populations regardless of the marker used. Our results suggest that, because both kinship structure and (bi-parental) inbreeding exist in populations of English yew, gene dispersal can be fairly limited in this species. Furthermore, at a local scale, gene dispersal intensity can be more limited in a dense population.     

Fine-scale genetic structure of the common Primula elatior (Primulaceae) at an early stage of population fragmentation

Many rare species are threatened by habitat fragmentation; however, less is known about effects of fragmentation on common species, despite their potential role in ecosystem productivity and functioning. We identified key factors and processes influencing gene flow in a large population of Primula elatior, a common distylous perennial herb, at an early stage of the fragmentation process, i.e., when fragmentation is taking place. Using 19 allozyme loci, we investigated genetic variation and fine-scale spatial genetic structure (SGS) at seedling and adult life stages in relation to fragmentation history (recent bottlenecks), selection, clonal propagation, sexual reproduction (seed and pollen dispersal, distyly), and patchy structure (patch size, plant density, and morph ratio). The main factors contributing to the strong SGS are seed and (to a lesser extent) pollen dispersal, through a spatial Wahlund effect and biparental inbreeding. Significant differences in allele frequencies between seedlings and adults indicate a temporal Wahlund effect. Patch plant density and biased morph ratio also affect the genetic patterns. Our results show that if P. elatior populations evolve into patchworks of small, isolated remnants, genetic erosion, reduced gene flow, and increased inbreeding can be expected, suggesting that such common plant species might require large population sizes to remain viable.     

Limiting inbreeding in disjunct and isolated populations of a woody shrub

Pollen movements and mating patterns are key features that influence population genetic structure. When gene flow is low, small populations are prone to increased genetic drift and inbreeding, but naturally disjunct species may have features that reduce inbreeding and contribute to their persistence despite genetic isolation. Using microsatellite loci, we investigated outcrossing levels, family mating parameters, pollen dispersal, and spatial genetic structure in three populations of Hakea oldfieldii, a fire‐sensitive shrub with naturally disjunct, isolated populations prone to reduction in size and extinction following fires. We mapped and genotyped a sample of 102 plants from a large population, and all plants from two smaller populations (28 and 20 individuals), and genotyped 158–210 progeny from each population. We found high outcrossing despite the possibility of geitonogamous pollination, small amounts of biparental inbreeding, a limited number of successful pollen parents within populations, and significant correlated paternity. The number of pollen parents for each seed parent was moderate. There was low but significant spatial genetic structure up to 10 m around plants, but the majority of successful pollen came from outside this area including substantial proportions from distant plants within populations. Seed production varied among seven populations investigated but was not correlated with census population size. We suggest there may be a mechanism to prevent self‐pollination in H. oldfieldii and that high outcrossing and pollen dispersal within populations would promote genetic diversity among the relatively small amount of seed stored in the canopy. These features of the mating system would contribute to the persistence of genetically isolated populations prone to fluctuations in size.     

Mating patterns of black oak Quercus velutina (Fagaceae) in a Missouri oak-hickory forest

Wind-pollinated forest trees usually have high outcrossing rates, but allogamy does not necessarily translate into high pollen movement. The goal of this study was to determine the outcrossing rates, pollen pool genetic structure, and the size of the effective pollination neighborhood in a population of black oak, Quercus velutina, in a Missouri oak-hickory forest. Based on 6 allozyme loci, 12 maternal trees, and 439 progenies sampled along a transect of 1300 m, we found complete outcrossing (t(m) = 1.000, P < 0.001) and small amounts of biparental inbreeding. Using a TwoGener analysis of the pollen gene pool, we found significant structure across maternal plants (Phi(FT) = 0.078, P < 0.001), which when corrected for adult inbreeding translates into Phi(FT) = 0.066 that corresponds to an effective number of pollen donors of 7.5 individuals. Assuming a bivariate normal distribution and an adult density of 16.25 trees ha(-1), we estimated that the effective pollination neighborhood area had a radius of 41.9 m. Even assuming that our estimates may be conservative, these findings join a growing body of evidence that suggest that the local neighborhood of wind-pollinated forest tree populations may be relatively small creating opportunities for local selection and genetic drift.     

SPATIAL GENETIC STRUCTURE OF CLONAL AND SEXUAL REPRODUCTION IN POPULATIONS OF ADENOPHORA GRANDIFLORA (CAMPANULACEAE)

The spatial distribution of clonal versus sexual reproduction in plant populations should generally have differing effects on the levels of biparental inbreeding and the apparent selfing rate, produced via mating by proximity through limited pollen dispersal. We used allozyme loci, join-count statistics, and Moran's spatial autocorrelation statistics to separate the spatial genetic structure caused by clonal reproduction from that maintained in sexually reproduced individuals in two populations of Adenophora grandiflora, a perennial herb. Join-count statistics showed that there were statistically significant clustering of clonal genotypes within distances less than 4 m. Both the entire populations and the sets of sexually reproduced individuals exhibited significant spatial autocorrelation at less than about 12 m, and the sexually reproduced individuals are substantially structured in an isolation-by-distance manner, consistent with a neighborhood size of about 50.     

Impact of selective logging on inbreeding and gene dispersal in an Amazonian tree population of Carapa guianensis Aubl

Selective logging may impact patterns of genetic diversity within populations of harvested forest tree species by increasing distances separating conspecific trees, and modifying physical and biotic features of the forest habitat. We measured levels of gene diversity, inbreeding, pollen dispersal and spatial genetic structure (SGS) of an Amazonian insect-pollinated Carapa guianensis population before and after commercial selective logging. Similar levels of gene diversity and allelic richness were found before and after logging in both the adult and the seed generations. Pre- and post-harvest outcrossing rates were high, and not significantly different from one another. We found no significant levels of biparental inbreeding either before or after logging. Low levels of pollen pool differentiation were found, and the pre- vs. post-harvest difference was not significant. Pollen dispersal distance estimates averaged between 75 m and 265 m before logging, and between 76 m and 268 m after logging, depending on the value of tree density and the dispersal model used. There were weak and similar levels of differentiation of allele frequencies in the adults and in the pollen pool, before and after logging occurred, as well as weak and similar pre- and post-harvest levels of SGS among adult trees. The large neighbourhood sizes estimated suggest high historical levels of gene flow. Overall our results indicate that there is no clear short-term genetic impact of selective logging on this population of C. guianensis.     

Limited pollen dispersal and biparental inbreeding in Symphonia globulifera in French Guiana

In this paper, we report a study of the mating system and gene flow of Symphonia globulifera, a hermaphroditic, mainly bird-pollinated tree species with a large geographic distribution in the tropical Americas and Africa. Using three microsatellites, we analysed 534 seeds of 28 open pollinated families and 164 adults at the experimental site 'Paracou' in French Guiana. We observed, compared to other tropical tree species, relatively high values for the effective number of alleles. Significant spatial genetic structure was detected, with trees at distances up to 150 m more genetically similar than expected at random. We estimated parameters of the mating system and gene flow by using the mixed mating model and the TwoGener approach. The estimated multilocus outcrossing rate, tm, was 0.920. A significant level of biparental inbreeding and a high proportion of full-sibs were estimated for the 28 seed arrays. We estimated mean pollen dispersal distances between 27 and 53 m according to the dispersal models used. Although the adult population density of S. globulifera in Paracou was relatively high, the joint estimation of pollen dispersal and density of reproductive trees gave effective density estimates of 1.6 and 1.3 trees/ha. The parameters of the mating system and gene flow are discussed in the context of spatial genetic and demographic structures, flowering phenology and pollinator composition and behaviour.     

Restricted mating dispersal and strong breeding group structure in a mid-sized marsupial mammal (Petrogale penicillata)

Ecological genetic studies have demonstrated that spatial patterns of mating dispersal, the dispersal of gametes through mating behaviour, can facilitate inbreeding avoidance and strongly influence the structure of populations, particularly in highly philopatric species. Elements of breeding group dynamics, such as strong structuring and sex-biased dispersal among groups, can also minimize inbreeding and positively influence levels of genetic diversity within populations. Rock-wallabies are highly philopatric mid-sized mammals whose strong dependence on rocky terrain has resulted in series of discreet, small colonies in the landscape. Populations show no signs of inbreeding and maintain high levels of genetic diversity despite strong patterns of limited gene flow within and among colonies. We used this species to investigate the importance of mating dispersal and breeding group structure to inbreeding avoidance within a 'small' population. We examined the spatial patterns of mating dispersal, the extent of kinship within breeding groups, and the degree of relatedness among brush-tailed rock-wallaby breeding pairs within a colony in southeast Queensland. Parentage data revealed remarkably restricted mating dispersal and strong breeding group structuring for a mid-sized mammal. Breeding groups showed significant levels of female kinship with evidence of male dispersal among groups. We found no evidence for inbreeding avoidance through mate choice; however, anecdotal data suggest the importance of life history traits to inbreeding avoidance between first-degree relatives. We suggest that the restricted pattern of mating dispersal and strong breeding group structuring facilitates inbreeding avoidance within colonies. These results provide insight into the population structure and maintenance of genetic diversity within colonies of the threatened brush-tailed rock-wallaby.     

Experimental dissection of inbreeding and its adaptive significance in a flowering plant, Aquilegia canadensis (Ranunculaceae)

Inbreeding is a major component of the mating system in populations of many plants and animals, particularly hermaphroditic species. In flowering plants, inbreeding can occur through self-pollination within flowers (autogamy), self-pollination between flowers on the same plant (geitonogamy), or cross-pollination between closely related individuals (biparental inbreeding). We performed a floral emasculation experiment in 10 populations of Aquilegia canadensis (Ranunculaceae) and used allozyme markers to estimate the relative contribution of each mode of inbreeding to the mating system. We also examined how these modes of inbreeding were influenced by aspects of population structure and floral morphology and display predicted to affect the mating system. All populations engaged in substantial inbreeding. On average, only 25% of seed was produced by outcrossing (range among populations = 9-37%), which correlated positively with both population size (r = +0.61) and density (r = +0.64). Inbreeding occurred through autogamy and biparental inbreeding, and the relative contribution of each was highly variable among populations. Estimates of geitonogamy were not significantly greater than zero in any population. We detected substantial biparental inbreeding (mean = 14% of seeds, range = 4-24%) by estimating apparent selfing in emasculated plants with no opportunity for true selfing. This mode of inbreeding correlated negatively with population size (r = -0.87) and positively with canopy cover (r = +0.90), suggesting that population characteristics that increase outcross pollen transfer reduce biparental inbreeding. Autogamy was the largest component of the mating system in all populations (mean = 58%, range = 37-84%) and, as expected, was lowest in populations with the most herkogamous flowers (r = -0.59). Although autogamy provides reproductive assurance in natural populations of A. canadensis, it discounts ovules from making superior outcrossed seed. Hence, high autogamy in these populations seems disadvantageous, and therefore it is difficult to explain the extensive variation in herkogamy observed both among and especially within populations.     

Local genetic population structure in an endangered plant species, Silene tatarica (Caryophyllaceae)

Genetic substructuring in plant populations may evolve as a consequence of sampling events that occur when the population is founded or regenerated, or if gene dispersal by pollen and seeds is restricted within a population. Silene tatarica is an endangered, perennial plant species growing along periodically disturbed riverbanks in northern Finland. We investigated the mechanism behind the microspatial genetic structure of S. tatarica in four subpopulations using amplified fragment length polymorphism markers. Spatial autocorrelation revealed clear spatial genetic structure in each subpopulation, even though the pattern diminished in older subpopulations. Parentage analysis in an isolated island subpopulation indicated a very low level of selfing and avoidance of breeding between close relatives. The mean estimated pollen dispersal distance (24.10 m; SD = 10.5) was significantly longer and the mean seed dispersal distance (9.07 m; SD = 9.23) was considerably shorter than the mean distance between the individuals (19.20 m; SD = 13.80). The estimated indirect and direct estimates of neighbourhood sizes in this subpopulation were very similar, 32.1 and 37.6, respectively. Our results suggested that the local spatial genetic structure in S. tatarica was attributed merely to the isolation-by-distance process rather than founder effect, and despite free pollen movement across population, restricted seed dispersal maintains local genetic structure in this species.     

Fine-scale spatial genetic structure of the distylous Primula veris in fragmented habitats

In Flanders (northern Belgium), the distylous self-incompatible perennial herb Primula veris is common, but mainly occurs in fragmented habitats. Distyly, which favours disassortative mating, is characterized in P. veris by two genetically determined floral morph types (pin or thrum). Using 18 polymorphic loci, we investigated fine-scale spatial genetic structure (SGS) and spatial distribution of the morphs within four populations from two regions that differ in degree of habitat fragmentation. We studied the contributions made by sexual reproduction and clonal propagation and compared the SGS patterns between pin and thrum morph types. Clonal growth was very restricted to a few individuals and to short distances. One population showed a non-random spatial distribution of the morphs. Pin and thrum individuals differed in SGS patterns at a small scale, suggesting intrapin biparental inbreeding, also related to high plant densities. This may be explained by partial self-compatibility of the pin morph combined with restricted seed dispersal and pollinator behaviour. There is an indication of more pronounced SGS when populations occur in highly fragmented habitats. From our findings, we may hypothesize disruption of the gene flow processes if these large populations evolve into patchworks of small remnants, but also a possible risk for long-term population survival if higher intrapin biparental inbreeding leads to inbreeding depression. Our study emphasizes the need for investigating the interactions between the heterostylous breeding system, population demographic and genetic structure for understanding population dynamics in fragmented habitats and for developing sustainable conservation strategies.     

Contemporary pollen and seed dispersal in a Prunus mahaleb population: patterns in distance and direction

Pollination and seed dispersal determine the spatial pattern of gene flow in plant populations and, for those species relying on pollinators and frugivores as dispersal vectors, animal activity plays a key role in determining this spatial pattern. For these plant species, reported dispersal patterns are dominated by short-distance movements with a significant amount of immigration. However, the contribution of seed and pollen to the overall contemporary gene immigration is still poorly documented for most plant populations. In this study we investigated pollination and seed dispersal at two spatial scales in a local population of Prunus mahaleb (L.), a species pollinated by insects and dispersed by frugivorous vertebrates. First, we dissected the relative contribution of pollen and seed dispersal to gene immigration from other parts of the metapopulation. We found high levels of gene immigration (18.50%), due to frequent long distance seed dispersal events. Second, we assessed the distance and directionality for pollen and seed dispersal events within the local population. Pollen and seed movement patterns were non-random, with skewed distance distributions: pollen tended moved up to 548 m along an axis approaching the N-S direction, and seeds were dispersed up to 990 m, frequently along the SW and SE axes. Animal-mediated dispersal contributed significantly towards gene immigration into the local population and had a markedly nonrandom pattern within the local population. Our data suggest that animals can impose distinct spatial signatures in contemporary gene flow, with the potential to induce significant genetic structure at a local level.     

Influence of cryptic population structure on observed mating patterns in the wild progenitor of maize (Zea mays ssp. parviglumis)

Indirect two-generation analysis of pollen flow has proven to be an effective alternative to exhaustive paternity analysis in numerous plant populations. In this investigation, the method is extended to an annual wild maize species, Zea mays ssp. parviglumis (Poaceae). Our analysis of mating system in parviglumis revealed high levels of outcrossing and higher biparental inbreeding than typically observed in grasses. Pollen dispersal analysis suggested low levels of long-distance dispersal. Given previous evidence for intrapopulation genetic structure in parviglumis populations, we explored the impact of cryptic population structure on estimates of mating system and pollen flow. Subpopulations inferred through spatially explicit Bayesian assignment showed markedly different values for both mating system parameters and pollen flow than the entire population. Finally, a novel method of pollen haplotype assignment revealed nonrandom mating consistent with intrapopulation structure. These results indicate parviglumis could be particularly susceptible to habitat fragmentation currently occurring throughout Mexico due to recent changes in land use.     

THE RELATIONSHIP BETWEEN CROSS SUCCESS AND SPATIAL PROXIMITY OF EUCALYPTUS GLOBULUS SSP. GLOBULUS PARENTS

The genetic structure of Eucalyptus globulus forest was examined using progeny vigor as an indirect measure of parental relatedness. Seven trees were crossed with pollen from trees: 0 m (seifing); 21 m (nearest flowering neighbors), 250 m, 500 m, 1 km, 10 km, and 100 km away from the female. Only selfing depressed seed set. Growth of the 21 m progenies was intermediate to selfing and the longer distance pollinations, suggesting tight family clusters occur due to limited seed dispersal. Under this structure biparental inbreeding may be common, however, the cumulative impact of inbreeding seems negligible as relatedness did not appear to decline with distance between mates beyond 50 m.     

Effect of the landscape matrix on gene flow in a coastal amphibian metapopulation

Functional connectivity is crucial for the persistence of a metapopulation, because migration among subpopulations enables recolonization and counteracts genetic drift, which is especially important in small subpopulations. We studied the degree and drivers of connectivity among occupied patches of a coastal dune metapopulation of the Natterjack Toad (Epidalea calamita Laurenti), on the basis of microsatellite variation. As spatial landscape heterogeneity is expected to influence dispersal and genetic structure, we analyzed which landscape features affect functional connectivity and to what extent. Sixty different landscape resistance scenarios as well as the isolation-by-distance model were compared using two landscape genetics approaches. We identified three subpopulations with unidirectional levels of gene flow among the two most geographically separated subpopulations, while inferred gene flow into the geographically intermediate subpopulation was limited. Urbanization and vegetation height negatively affected connectivity. Low estimates of genetic diversity and effective population size indicate that conservation measures in the smallest and most isolated subpopulation are required.     

Inbreeding depresses short and long distance dispersal in three congeneric spiders

Dispersal is one of the most important precopulatory inbreeding avoidance mechanisms and subject to landscape related selection pressures. In small populations, inbreeding within and between populations may strongly affect population dynamics if it reduces fitness and gene‐flow. While inbreeding avoidance is generally considered to be a key evolutionary driver of dispersal, potential effects of inbreeding on the dispersal process, are poorly known. Here, I document how inbreeding within a population, so by mating among relatives, affects the survivorship and the dispersal behaviour of three congeneric spider Erigone species (Araneae: Linyphiidae) that differ in habitat preference and regional rarity. The three species were chosen as a model because they allow the assessment of both long and short distance dispersal motivation (respectively ballooning and rappelling) under laboratory conditions. Inbreeding reduced both long and short distance dispersal modes in the three congeneric species. Because survival was depressed after inbreeding, with a tendency of reduced survival loss in the rare and highly stenotopic species, energetic constraints are likely to be the underlying mechanism. Inbreeding consequently depresses silk‐related dispersal in three related spiders. This may induce an inbreeding depression vortex with important consequences for range expansion and metapopulation dynamics of aerially dispersing species from highly fragmented landscapes.     

Experimental analysis of biparental inbreeding in a self-fertilizing plant

Abstract.— Localized dispersal and mating may genetically structure plant populations, resulting in matings among related individuals. This biparental inbreeding has significant consequences for the evolution of mating systems, yet is difficult to estimate in natural populations. We estimated biparental inbreeding in two populations of the largely self-fertilizing plant Aquilegia canadensis using standard inference as well as a novel experiment comparing apparent selfing between plants that were randomly relocated within populations to experimental control plants. Using two allozyme markers, biparental inbreeding ( b ) inferred from the difference between single-locus and multilocus estimates of selfing ( b = s_s – s_m ) was low. Less than 3% of matings involved close relatives (mean b = 0.029). In contrast, randomly relocating plants greatly reduced apparent selfing (mean s_s = 0.674) compared to control plants that had been dug up and replanted in their original locations ( s_s = 0.953, P = 0.002). Based on this difference in s_s , we estimated that approximately 30% of all matings involved close relatives (mean b = 0.279, 95% CL = 0.072–0.428). Inference from s_s – s_m underestimated b in these populations by more than an order of magnitude. Biparental inbreeding is thought to influence the evolution of self-fertilization primarily through reducing the genetic cost of outcrossing. This is unlikely to be of much significance in A. canadensis because inbreeding depression (a major cost of selfing) is much stronger than the cost of outcrossing. However, biparental inbreeding combined with strong inbreeding depression may influence selection on dispersal.