Pollen and seed dispersal inferred from seedling genotypes: the Bayesian revolution has passed here too

Understanding precisely how plants disperse their seeds and pollen in their neighbourhood is a central question for both ecologists and evolutionary biologists because seed and pollen dispersal governs both the rate of spread of an expanding population and gene flow within and among populations. The concept of a 'dispersal kernel' has become extremely popular in dispersal ecology as a tool that summarizes how dispersal distributes individuals and genes in space and at a given scale. In this issue of Molecular Ecology, the study by Moran & Clark (2011) (M&C in the following) shows how genotypic and spatial data of established seedlings can be analysed in a Bayesian framework to estimate jointly the pollen and seed dispersal kernels and finally derive a parentage analysis from a full-probability approach. This approach applied to red oak shows important dispersal of seeds (138 m on average) and pollen (178 m on average). For seeds, this estimate contrasts with previous results from inverse modelling on seed trap data (9.3 m). This research gathers several methodological advances made in recent years in two research communities and could become a cornerstone for dispersal ecology.     

A direct regional scale estimate of transgene movement from genetically modified oilseed rape to its wild progenitors

One of the major environmental concerns over genetically modified (GM) crops relates to transgene movement into wild relatives. The pattern of hybridization ultimately affects the scale and rapidity of ecological change and the feasibility of containment. A new procedure for quantifying hybrid formation over large areas is described. Remote sensing was used to identify possible sites of sympatry between Brassica napus and its progenitor species across 15 000 km2 of south-east England in 1998. Two sympatric populations with B. rapa and one with B. oleracea were found over the entire survey area. Every newly recruited plant in these populations in 1999 was screened for hybrid status using flow cytometry and molecular analyses. One hybrid was observed from the 505 plants screened in the B. rapa populations but none of the nine B. oleracea recruits were hybrids. Measures to minimize gene flow are suggested, and a procedure for the post-release evaluation and containment of GM cultivars is proposed.     

Spatial vs. temporal effects on demographic and genetic structures: the roles of dispersal, masting and differential mortality on patterns of recruitment in Fagus sylvatica

Trees' long lifespan, long-distance dispersal abilities and high year-to-year variability in fecundity are thought to have pervasive consequences for the demographic and genetic structure of recruited seedlings. However, we still lack experimental studies quantifying the respective roles of spatial processes such as restricted seed and pollen dispersal and temporal processes such as mast seeding on patterns of regeneration. Dynamics of European beech (Fagus sylvatica) seedling recruitment was monitored in three plots from 2004 to 2006. Six polymorphic microsatellite genetic markers were used to characterize seedlings and their potential parents in a 7.2-ha stand. These seedlings were shown to result from 12 years of recruitment, with one predominant year of seedling recruitment in 2002 and several years without significant recruitment. Using a spatially explicit mating model based on parentage assignment, short average dispersal distances for seed (δ(s) = 10.9 m) and pollen (43.7 m < δ(p) <57.3 m) were found, but there was also a non-negligible immigration rate from outside the plot (m(s) = 20.5%; 71.6% < m(p) < 77.9%). Hierarchical analyses of seedling genetic structure showed that (i) most of the genetic variation was within plots; (ii) the genetic differentiation among seedling plots was significant (F(ST) = 2.6%) while (iii) there was no effect of year-to-year seed rain variation on genetic structure. In addition, no significant effect of genetic structure on mortality was detected. The consequences of these results for the prediction of population dynamics at ecological timescales are discussed.     

Regional gene flow and population structure of the wind-dispersed plant species Hypochaeris radicata (Asteraceae) in an agricultural landscape

Using microsatellites, we investigated population structure and gene flow of the short-lived, wind-dispersed plant species Hypochaeris radicata in a fragmented agricultural landscape where more than 99% of the nutrient-poor grasslands have disappeared over the last century. We sampled populations in the few remaining high density populations in conservation areas, as well as individuals that occurred, with lower densities, in linear landscape elements, at two spatial scales. In a re-inventory of the landscape, after 3 years, both extinctions and colonizations of populations were observed. Contrary to expectations, no differences in genetic diversity between high and low density populations were observed. Both types of populations had relatively high levels of diversity. Overall genetic differentiation (theta) was 0.04 and significantly different from zero (P < 0.01). A significant isolation-by-distance pattern was found when all populations were simultaneously analysed (r = 0.24, P = 0.013). Isolation by distance was (marginally) significant at the small scale (r = 0.32, P = 0.06), whereas nonsignificant at the large spatial scale (r = -0.05, P = 0.66). A maximization-of-explained-variance procedure resulted in a threshold distance of 3.5 km above which populations were effectively genetically isolated. An additional partial exclusion Bayesian-based assignment test showed that overall 32.3% of the individuals were assigned to their population of origin, 48% were assigned to another population in the area and 19.7% were not assigned. Together, these results suggest high levels of gene flow. Seed dispersal contributes to the observed gene flow up to several hundred metres, which is higher than previously modelled using aerodynamic models on seed dispersal of H. radicata. We discuss the consequences of these results for an evaluation of the probability of persistence of this species in the fragmented landscape.     

A pollen-dispersal experiment with transgenic oilseed rape. Estimation of the average pollen dispersal of an individual plant within a field

 In order to help establish a basis for the assessment of gene flow associated with the large-scale release of transgenic oilseed rape, we previously designed a method which makes it possible to retrieve the average pollen dispersal of a single plant from that of a large source plot. The ‘individual’ pollen distribution thus obtained is less dependent on the experimental design than pollen distributions usually published and could therefore be used to model the possible escape of a transgene from commercial transgenic crops. In this study we report on a field experiment set up to study the pollen dispersal from an herbicide-resistant transgenic variety of oilseed rape and to test the applicability of the method on the experimental data. Two techniques were used to determine the individual pollen dispersal, and their outcomes are compared. The results suggest that approximately half of the pollen produced by an individual plant fell within 3 m and that the probability of fertilisation afterwards decreased slowly along a negative exponential of the distance. Comparison with the global pollen distribution from the source plot indicates that pollen-dispersal distributions based on dispersal from whole plots instead of individual plants would have underestimated the proportion of pollen that was dispersed over average or long distances. Received: 20 September 1997 / Accepted: 28 October 1997     

Linking dispersal, immigration and scale in the neutral theory of biodiversity

In the classic spatially implicit formulation of Hubbell's neutral theory of biodiversity a local community receives immigrants from a metacommunity operating on a relatively slow timescale, and dispersal into the local community is governed by an immigration parameter m . A current problem with neutral theory is that m lacks a clear biological interpretation. Here, we derive analytical expressions that relate the immigration parameter m to the geometry of the plot defining the local community and the parameters of a dispersal kernel. Our results facilitate more rigorous and extensive tests of the neutral theory: we conduct a test of neutral theory by comparing estimates of m derived from fits to empirical species abundance distributions to those derived from dispersal kernels and find acceptable correspondence; and we generate a new prediction of neutral theory by investigating how the shapes of species abundance distributions change theoretically as the spatial scale of observation changes. We also discuss how our main analytical results can be used to assess the error in the mean-field approximations associated with spatially implicit formulations of neutral theory.     

Closing the gaps for animal seed dispersal: Separating the effects of habitat loss on dispersal distances and seed aggregation

Habitat loss can alter animal movements and disrupt animal seed dispersal mutualisms; however, its effects on spatial patterns of seed dispersal are not well understood. To explore the effects of habitat loss on seed dispersal distances and seed dispersion (aggregation), we created a spatially explicit, individual‐based model of an animal dispersing seeds (SEADS—Spatially Explicit Animal Dispersal of Seeds) in a theoretical landscape of 0%–90% habitat loss based on three animal traits: movement distance, gut retention time, and time between movements. Our model design had three objectives: to determine the effects of (1) animal traits and (2) habitat loss on seed dispersal distances and dispersion and (3) determine how animal traits could mitigate the negative effects of habitat loss on these variables. SEADS results revealed a complex interaction involving all animal traits and habitat loss on dispersal distances and dispersion, driven by a novel underlying mechanism of fragment entrapment. Unexpectedly, intermediate habitat loss could increase dispersal distances and dispersion relative to low and high habitat loss for some combinations of animal traits. At intermediate habitat loss, movement between patches was common, and increased dispersal distances and dispersion compared to continuous habitats because animals did not stop in spaces between fragments. However, movement between patches was reduced at higher habitat loss as animals became trapped in fragments, often near the parent plant, and dispersed seeds in aggregated patterns. As movement distance increased, low time between movements and high gut retention time combinations permitted more movement to adjacent patches than other combinations of animal traits. Because habitat loss affects movement in a nonlinear fashion under some conditions, future empirical tests would benefit from comparisons across landscapes with more than two levels of fragmentation.     

Large‐scale PVA modeling of insects in cultivated grasslands: The role of dispersal in mitigating the effects of management schedules under climate change

In many species, dispersal is decisive for survival in a changing climate. Simulation models for population dynamics under climate change thus need to account for this factor. Moreover, large numbers of species inhabiting agricultural landscapes are subject to disturbances induced by human land use. We included dispersal in the HiLEG model that we previously developed to study the interaction between climate change and agricultural land use in single populations. Here, the model was parameterized for the large marsh grasshopper (LMG) in cultivated grasslands of North Germany to analyze (1) the species development and dispersal success depending on the severity of climate change in subregions, (2) the additional effect of grassland cover on dispersal success, and (3) the role of dispersal in compensating for detrimental grassland mowing. Our model simulated population dynamics in 60‐year periods (2020–2079) on a fine temporal (daily) and high spatial (250 × 250 m²) scale in 107 subregions, altogether encompassing a range of different grassland cover, climate change projections, and mowing schedules. We show that climate change alone would allow the LMG to thrive and expand, while grassland cover played a minor role. Some mowing schedules that were harmful to the LMG nevertheless allowed the species to moderately expand its range. Especially under minor climate change, in many subregions dispersal allowed for mowing early in the year, which is economically beneficial for farmers. More severe climate change could facilitate LMG expansion to uninhabited regions but would require suitable mowing schedules along the path. These insights can be transferred to other species, given that the LMG is considered a representative of grassland communities. For more specific predictions on the dynamics of other species affected by climate change and land use, the publicly available HiLEG model can be easily adapted to the characteristics of their life cycle.     

The effects of species pool,dispersal and competition on the diversity–productivity relationship

Aim The diversity–productivity relationship is a controversial issue in ecology. Diversity is sometimes seen to increase with productivity but a unimodal relationship has often been reported. Competitive exclusion was cited initially to account for the decrease of diversity at high productivity. Subsequently, the roles of evolutionary history (species pool size) and dispersal rate have been acknowledged. We explore how the effects of species pool, dispersal and competition combine to produce different diversity–productivity relationships. Methods We use a series of simulations with a spatially explicit, individual‐based model. Following empirical expectations, we used four scenarios to characterize species pool size along the productivity gradient (uniformly low and high, linear increase and unimodal). Similarly, the dispersal rate varied along the productivity gradient (uniformly low and high, and unimodal). We considered both neutral communities and communities with competitive exclusion. Results and main conclusions Our model predicts that competitive interactions will result in unimodal diversity–productivity relationships. The model often predicts unimodal patterns in neutral communities as well, although the decline in richness at high productivity is less than in competing communities. A positive diversity–productivity relationship is simulated for neutral communities when the species pool size increases with productivity and the dispersal rate is high. This scenario is probably more widespread in nature than the others since positive diversity–productivity relationships have been observed more frequently than previously expected, especially in the tropics and for woody species. Our simulated effects of species pool, dispersal and competition on diversity patterns can be linked to empirical observations to uncover mechanisms behind the diversity–productivity relationship.     

Modelling single nucleotide effects in phosphoglucose isomerase on dispersal in the Glanville fritillary butterfly: coupling of ecological and evolutionary dynamics

Dispersal comprises a complex life-history syndrome that influences the demographic dynamics of especially those species that live in fragmented landscapes, the structure of which may in turn be expected to impose selection on dispersal. We have constructed an individual-based evolutionary sexual model of dispersal for species occurring as metapopulations in habitat patch networks. The model assumes correlated random walk dispersal with edge-mediated behaviour (habitat selection) and spatially correlated stochastic local dynamics. The model is parametrized with extensive data for the Glanville fritillary butterfly. Based on empirical results for a single nucleotide polymorphism (SNP) in the phosphoglucose isomerase (Pgi) gene, we assume that dispersal rate in the landscape matrix, fecundity and survival are affected by a locus with two alleles, A and C, individuals with the C allele being more mobile. The model was successfully tested with two independent empirical datasets on spatial variation in Pgi allele frequency. First, at the level of local populations, the frequency of the C allele is the highest in newly established isolated populations and the lowest in old isolated populations. Second, at the level of sub-networks with dissimilar numbers and connectivities of patches, the frequency of C increases with decreasing network size and hence with decreasing average metapopulation size. The frequency of C is the highest in landscapes where local extinction risk is high and where there are abundant opportunities to establish new populations. Our results indicate that the strength of the coupling of the ecological and evolutionary dynamics depends on the spatial scale and is asymmetric, demographic dynamics having a greater immediate impact on genetic dynamics than vice versa.     

Population structure and gene flow reversals in Atlantic salmon (Salmo salar) over contemporary and long-term temporal scales: effects of population size and life history

Metapopulation dynamics are increasingly invoked in management and conservation of endangered species. In this context, asymmetrical gene flow patterns can be density dependent, with migration occurring mainly from larger into smaller populations, which may depend on it for their persistence. Using genetic markers, such patterns have recently been documented for various organisms including salmonids, suggesting this may be a more general pattern. However, metapopulation theory does not restrict gene flow asymmetry to 'source-sink' structures, nor need these patterns be constant over longer evolutionary timescales. In anadromous salmonids, gene flow can be expected to be shaped by various selective pressures underlying homing and dispersal ('straying') behaviours. The relative importance of these selective forces will vary spatially and for populations of different census size. Furthermore, the consequences of life-history variation among populations for dispersal and hence gene flow remain poorly quantified. We examine population structure and connectivity in Atlantic salmon (Salmo salar L.) from Newfoundland and Labrador, a region where populations of this species are relatively pristine. Using genetic variation at 13 microsatellite loci from samples (N=1346) collected from a total of 20 rivers, we examine connectivity at several regional and temporal scales and test the hypothesis that the predominant direction of gene flow is from large into small populations. We reject this hypothesis and find that the directionality of migration is affected by the temporal scale over which gene flow is assessed. Whereas large populations tend to function as sources of dispersal over contemporary timescales, such patterns are often changed and even reversed over evolutionary, coalescent-derived timescales. These patterns of population structure furthermore vary between different regions and are compatible with demographic and life-history attributes. We find no evidence for sex-biased dispersal underlying gene flow asymmetry. Our findings caution against generalizations concerning the directionality of gene flow in Atlantic salmon and emphasize the need for detailed regional study, if such information is to be meaningfully applied in conservation and management of salmonids.     

Demographic and genetic connectivity: the role and consequences of reproduction,dispersal and recruitment in seagrasses

Accurate estimation of connectivity among populations is fundamental for determining the drivers of population resilience, genetic diversity, adaptation and speciation. However the separation and quantification of contemporary versus historical connectivity remains a major challenge. This review focuses on marine angiosperms, seagrasses, that are fundamental to the health and productivity of temperate and tropical coastal marine environments globally. Our objective is to understand better the role of sexual reproduction and recruitment in influencing demographic and genetic connectivity among seagrass populations through an integrated multidisciplinary assessment of our present ecological, genetic, and demographic understanding, with hydrodynamic modelling of transport. We investigate (i) the demographic consequences of sexual reproduction, dispersal and recruitment in seagrasses, (ii) contemporary transport of seagrass pollen, fruits and seed, and vegetative fragments with a focus on hydrodynamic and particle transport models, and (iii) contemporary genetic connectivity among seagrass meadows as inferred through the application of genetic markers. New approaches are reviewed, followed by a summary outlining future directions for research: integrating seascape genetic approaches; incorporating hydrodynamic modelling for dispersal of pollen, seeds and vegetative fragments; integrating studies across broader geographic ranges; and incorporating non‐equilibrium modelling. These approaches will lead to a more integrated understanding of the role of contemporary dispersal and recruitment in the persistence and evolution of seagrasses.     

Immigration history and gene dispersal: allozyme variation in Nordic populations of the red campion, Silene dioica (Caryophyllaceae)

Most of the Nordic region was ice-covered during the last (Weichselian) glaciation. During the postglacial period, plant and animal species recolonized the region from several directions and the geographic structuring of genetic variation within Nordic species may still contain a historic component that reflects patterns of postglacial immigration. The present investigation of 69 populations of Silene dioica represents the first large-scale allozyme study of a widespread herbaceous plant in the Nordic region. Although the frequencies of individual alleles showed a range of different geographic patterns, mapping of the axis scores from an ordination of variation at eight polymorphic loci revealed a division into two main geographic groups of populations. The broadly south-western and north-eastern distributions of these two groups of populations suggest that immigration into the region may have involved both eastern and southern geographic sources. However, the geographic boundaries between the two groups of populations are diffuse, and the relatively low between-population component of genetic diversity (G_ST = 16.4%) suggests a history of extensive gene dispersal by pollen.  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 77 , 23–34.     

Population structure and dispersal in a patchy landscape: nuclear and mitochondrial markers reveal area effects in the spider Theridion californicum (Araneae: Theridiidae)

Changes in land use have a major effect on patterns of biodiversity. However, few studies have examined the demographic and genetic shifts associated with a return to semi‐natural habitat following extended periods of human disturbance. Here we examine patterns of population structure in a spider restricted to the Pacific coastal strip of North America that exhibits an exuberant colour polymorphism. We use mitochondrial DNA and AFLP markers to examine genetic structure and estimate gene flow. The results show contrasting, gender‐specific patterns between these markers that suggest limited dispersal, combined with area effects most likely caused by expansion from refugial habitat patches following land‐management changes in a region of the San Francisco East Bay. Colour‐morph frequencies are not correlated with this complex genetic structure. Thus, unlike the classical area effects that were based on colour morphs, we demonstrate in T. californicum signals of historical contingency at neutral loci but not at the Colour locus, where traces of past events have been obliterated by balancing selection. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 600–620.     

Assessing lignocellulosic biomass production from crop residues in the European Union: Modelling,analysis of the current scenario and drivers of interannual variability

This study assesses crop residues in the EU from major crops using empirical models to predict crop residues from yield statistics; furthermore it analyses the inter‐annual variability of those estimates over the period 1998‐2015, identifying its main drivers across Europe. The models were constructed based on an exhaustive collection of experimental data from scientific papers for the crops: wheat, barley, rye, oats, triticale, rice, maize, sorghum, rapeseed, sunflower, soybean, potato and sugarbeet. We discuss the assumptions on the relationship between yield and the harvest index, adopted by previous studies, to interpret the experimental data, quantify the uncertainties of these models, and establish the premises to implement them at regional scale –i.e., NUTS level 3– within the EU. To cope this, we created a consolidated sub‐national statistical data along with an algorithm able to aggregate (figures are provided at country level) and disaggregate (production at 25 km grid is provided assupplementary material) estimates. The total lignocellulosic biomass production in the EU28 over the review period, according to our models, is 419 Mt, from which wheat is the major contributor (155 Mt). Our results show that maize and rapeseed are the two crops with the highest residue yield, respectively 8.9 and 8.6 t ha‐1. The spatial analysis revealed that these three crops, which, according to our results, are feedstocks highly suitable a priori for second generation biofuels in the EU and are unevenly distributed across Europe. Weather fluctuation was identified as the major driver in residue production from cereals, while, in the case of starch crops and oilseeds – which are predominant in northern Europe – corresponded to the marked production trend likely influenced by the agricultural policies and agro‐management over the review period. Our results, among others, could help to understand and quantify the ecological boundaries of the bioeconomy from agriculture.     

Dissimilarity of contemporary and historical gene flow in a wild carrot (Daucus carota) metapopulation under contrasting levels of human disturbance: implications for risk assessment and management of transgene introgression

Background and Aims

Transgene introgression from crops into wild relatives may increase the resistance of wild plants to herbicides, insects, etc. The chance of transgene introgression depends not only on the rate of hybridization and the establishment of hybrids in local wild populations, but also on the metapopulation dynamics of the wild relative. The aim of the study was to estimate gene flow in a metapopulation for assessing and managing the risks of transgene introgression.

Methods

Wild carrots (Daucus carota) were sampled from 12 patches in a metapopulation. Eleven microsatellites were used to genotype wild carrots. Genetic structure was estimated based on the F_ST statistic. Contemporary (over the last several generations) and historical (over many generations) gene flow was estimated with assignment and coalescent methods, respectively.

Key Results

The genetic structure in the wild carrot metapopulation was moderate (F_ST = 0·082) and most of the genetic variation resided within patches. A pattern of isolation by distance was detected, suggesting that most of the gene flow occurred between neighbouring patches (≤1 km). The mean contemporary gene flow was 5 times higher than the historical estimate, and the correlation between them was very low. Moreover, the contemporary gene flow in roadsides was twice that in a nature reserve, and the correlation between contemporary and historical estimates was much higher in the nature reserve. Mowing of roadsides may contribute to the increase in contemporary gene flow. Simulations demonstrated that the higher contemporary gene flow could accelerate the process of transgene introgression in the metapopulation.

Conclusions

Human disturbance such as mowing may alter gene flow patterns in wild populations, affecting the metapopulation dynamics of wild plants and the processes of transgene introgression in the metapopulation. The risk assessment and management of transgene introgression and the control of weeds need to take metapopulation dynamics into consideration.     

景观遗传学原理及其在生境片断化遗传效应研究中的应用

景观遗传学是近年来在景观生态学和种群遗传学之间形成的一个交叉领域,强调景观的组成、空间构型和环境梯度对基因流、种群遗传空间结构和局域种群适应的影响。景观遗传学尚未成为一门独立的学科,其理论基础主要来自分子遗传学、种群生物学和景观生态学。现代分子遗传标记技术、遥感和GIS支持下的景观分析和空间统计方法的综合运用是景观遗传学主要研究途径。系统介绍了景观遗传学的基础概念,关键科学问题,基本理论框架,及其与相邻研究领域的关系,综述了景观遗传学最为关注的现实课题——景观碎裂化的种群遗传效应的研究进展,主要涉及生境片断化的遗传效应、不同属性的物种响应、以及生境片断化过程的选择作用等方面。通过采取一种跨尺度的视角,景观遗传学研究显著深化了关于景观碎裂化对生物多样性影响的理解。     

No need for stepping stones: Direct,joint dispersal of the lichen‐forming fungus Mastodia tessellata (Ascomycota) and its photobiont explains their bipolar distribution

Aim

The hypotheses proposed to explain the high percentage of bipolar lichens in Antarctica have never been explicitly tested. We used the strictly bipolar, coastal lichenized fungus Mastodia tessellata (Verrucariaceae, Ascomycota) and its photobionts (Prasiola, Trebouxiophyceae, Chlorophyta) as model species to discern whether this extraordinary disjunction originated from vicariance or long‐distance dispersal.

Location

Coasts of Antarctica, Tierra del Fuego (Chile), Alaska (USA) and British Columbia (Canada).

Methods

Based on a comprehensive geographical (315 specimens and 16 populations from Antarctica, Tierra del Fuego and North America) and molecular sampling (three and four loci for the fungus and algae respectively), we implemented explicit Bayesian methods to compare alternative hypotheses of speciation and migration, and performed dating analyses for the fungal and algal partner, in order to infer the timing of the colonization events and the direction of gene flow among distant, disjunct areas.

Results

Mastodia tessellata comprises two fungal species which in turn associate with three photobiont lineages along the studied distribution range. Independent estimation of divergence ages for myco‐ and photobionts indicated a middle to latest Miocene species split in the Southern Hemisphere, and a late Miocene to Pleistocene acquisition of the bipolar distribution. Comparison of migration models and genetic diversity patterns suggested an austral origin for the bipolar species.

Main conclusions

The complex evolutionary history of Mastodia tessellata s.l. can be explained by a combination of vicariant and long‐distance dispersal mechanisms. We provide novel evidence of a pre‐Pleistocene long‐term evolution of lichens in Antarctica as well as for bipolar distributions shaped by Southern to Northern Hemisphere migratory routes without the need for stepping stones.