NMπ-improved re-implementation of NM+, a software for estimating gene dispersal and mating patterns

Impacts of Flowering Density on Pollen Dispersal and Gametic Diversity Are Scale Dependent

AbstractPollen dispersal is a key evolutionary and ecological process, but the degree to which variation in the density of concurrently flowering conspecific plants (i.e., coflowering density) shapes pollination patterns remains understudied. We monitored coflowering density and corresponding pollination patterns of the insect-pollinated palm Oenocarpus bataua in northwestern Ecuador and found that the influence of coflowering density on these patterns was scale dependent: high neighborhood densities were associated with reductions in pollen dispersal distance and gametic diversity of progeny arrays, whereas we observed the opposite pattern at the landscape scale. In addition, neighborhood coflowering density also impacted forward pollen dispersal kernel parameters, suggesting that low neighborhood densities encourage pollen movement and may promote gene flow and genetic diversity. Our work reveals how coflowering density at different spatial scales influences pollen movement, which in turn informs our broader understanding of the mechanisms underlying patterns of genetic diversity and gene flow within populations of plants.

Mating and fitness consequences of variation in male allocation in a wind-pollinated plant

In hermaphrodites, the allocation of resources to each sex function can influence fitness through mating success. A prediction that arises from sex allocation theory is that in wind-pollinated plants, male fitness should increase linearly with investment of resources into male function but there have been few empirical tests of this prediction. In a field experiment, we experimentally manipulated allocation to male function in Ambrosia artemisiifolia (common ragweed) and measured mating success in contrasting phenotypes using genetic markers. We investigated the effects of morphological traits and flowering phenology on male siring success, and on the diversity of mates. Our results provide evidence for a linear relation between allocation to male function, mating, and fitness. We find earlier onset of male flowering time increases reproductive success, whereas later flowering increases the probability of mating with diverse individuals. Our study is among the first empirical tests of the prediction of linear male fitness returns in wind-pollinated plants and emphasizes the importance of a large investment into male function by wind-pollinated plants and mating consequences of temporal variation in sex allocation.

Guidelines for genetic monitoring of translocated plant populations

Plant translocation is a useful tool for implementing assisted gene flow in recovery plans of critically endangered plant species. Although it helps to restore genetically viable populations, it is not devoid of genetic risks, such as poor adaptation of transplants and outbreeding depression in the hybrid progeny, which may have negative consequences in terms of demographic growth and plant fitness. Hence, a follow-up genetic monitoring should evaluate whether the translocated populations are genetically viable and self-sustaining in the short and long term. The causes of failure to adjust management responses also need to be identified. Molecular markers and fitness-related quantitative traits can be used to determine whether a plant translocation enhanced genetic diversity, increased fitness, and improved the probability of long-term survival. We devised guidelines and illustrated them with studies from the literature to help practitioners determine the appropriate genetic survey methods so that management practices can better integrate evolutionary processes. These guidelines include methods for sampling and for assessing changes in genetic diversity and differentiation, contemporary gene flow, mode of local recruitment, admixture level, the effects of genetic rescue, inbreeding or outbreeding depression and local adaptation on plant fitness, and long-term genetic changes.

Population structure and the influence of microenvironment and genetic similarity on individual growth at Alaskan white spruce treelines

Knowledge on the adaptation of trees to rapid environmental changes is essential to preserve forests and their ecosystem services under climate change. Treeline populations are particularly suitable for studying adaptation processes in trees, as environmental stress together with reduced gene flow can enhance local adaptation. We investigated white spruce (Picea glauca) populations in Alaska on one moisture-limited and two cold-limited treeline sites with a paired plot design of one forest and one treeline population each, resulting in six plots. Additionally, one forest plot in the middle of the distribution range complements the study design. We combined spatial, climatic and dendrochronological data with neutral genetic marker of 2203 trees to investigate population genetic structure and drivers of tree growth. We used several individual-based approaches including random slope mixed-effects models to test the influence of genetic similarity and microenvironment on growth performance. A high degree of genetic diversity was found within each of the seven plots associated with high rates of gene flow. We discovered a low genetic differentiation between the three sites which was better explained by geographic distances than by environmental differences, indicating genetic drift as the main driver of population differentiation. Our findings indicated that microenvironmental features had an overall larger influence on growth performances than genetic similarity among individuals. The effects of climate on growth differed between sites but were smaller than the effect of tree size. Overall, our results suggest that the high genetic diversity of white spruce may result in a wider range of phenotypes which enhances the efficiency of selection when the species is facing rapid climatic changes. In addition, the large intra-individual variability in growth responses may indicate the high phenotypic plasticity of white spruce which can buffer short-term environmental changes and, thus, allow enduring the present changing climate conditions.

Directional seed and pollen dispersal and their separate effects on anisotropy of fine-scale spatial genetic structure among seedlings in a dioecious, wind-pollinated, and wind-dispersed tree species, Cercidiphyllum japonicum

Prevailing directions of seed and pollen dispersal may induce anisotropy of the fine-scale spatial genetic structure (FSGS), particularly in wind-dispersed and wind-pollinated species. To examine the separate effects of directional seed and pollen dispersal on FSGS, we conducted a population genetics study for a dioecious, wind-pollinated, and wind-dispersed tree species, Cercidiphyllum japonicum Sieb. et Zucc, based on genotypes at five microsatellite loci of 281 adults of a population distributed over a ca. 80 ha along a stream and 755 current-year seedlings. A neighborhood model approach with exponential-power-von Mises functions indicated shorter seed dispersal (mean = 69.1 m) and much longer pollen dispersal (mean = 870.6 m), effects of dispersal directions on the frequencies of seed and pollen dispersal, and the directions with most frequent seed and pollen dispersal (prevailing directions). Furthermore, the distance of effective seed dispersal within the population was estimated to depend on the dispersal direction and be longest at the direction near the prevailing direction. Therefore, patterns of seed and pollen dispersal may be affected by effective wind directions during the period of respective dispersals. Isotropic FSGS and spatial sibling structure analyses indicated a significant FSGS among the seedlings generated by the limited seed dispersal, but anisotropic analysis for the seedlings indicated that the strength of the FSGS varied with directions between individuals and was weakest at a direction near the directions of the most frequent and longest seed dispersal but far from the prevailing direction of pollen dispersal. These results suggest that frequent and long-distance seed dispersal around the prevailing direction weakens the FSGS around the prevailing direction. Therefore, spatially limited but directional seed dispersal would determine the existence and direction of FSGS among the seedlings.

Sex-specific spatial variation in fitness in the highly dimorphic Leucadendron rubrum

Sexual dimorphism in plants may emerge as a result of sex-specific selection on traits enhancing access to nutritive resources and/or to sexual partners. Here we investigated sex-specific differences in selection of sexually dimorphic traits and in the spatial distribution of effective fecundity (our fitness proxy) in a highly dimorphic dioecious wind-pollinated shrub, Leucadendron rubrum. In particular, we tested for the effect of density on male and female effective fecundity. We used spatial and genotypic data of parent and offspring cohorts to jointly estimate individual male and female effective fecundity on the one hand and pollen and seed dispersal kernels on the other hand. This methodology was adapted to the case of dioecious species. Explicitly modelling dispersal avoids the confounding effects of heterogeneous spatial distribution of mates and sampled seedlings on the estimation of effective fecundity. We also estimated selection gradients on plant traits while modelling sex-specific spatial autocorrelation in fecundity. Males exhibited spatial autocorrelation in effective fecundity at a smaller scale than females. A higher local density of plants was associated with lower effective fecundity in males but was not related to female effective fecundity. These results suggest sex-specific sensitivities to environmental heterogeneity in L. rubrum. Despite these sexual differences, we found directional selection for wider canopies and smaller leaves in both sexes, and no sexually antagonistic selection on strongly dimorphic traits in L. rubrum. Many empirical studies in animals similarly failed to detect sexually antagonistic selection in species expressing strong sexual dimorphism, and we discuss reasons explaining this common pattern.

Identification of determinants of pollen donor fecundity using the hierarchical neighborhood model

Individual differences in male reproductive success drive genetic drift and natural selection, altering genetic variation and phenotypic trait distributions in future generations. Therefore, identifying the determinants of reproductive success is important for understanding the ecology and evolution of plants. Here, based on the spatially explicit mating model (the neighborhood model), we develop a hierarchical probability model that links co-dominant genotypes of offspring and candidate parents with phenotypic determinants of male reproductive success. The model accounts for pollen dispersal, genotyping errors as well as individual variation in selfing, pollen immigration, and differentiation of immigrant pollen pools. Unlike the classic neighborhood model approach, our approach is specially designed to account for excessive variation (overdispersion) in male fecundity. We implemented a Bayesian estimation method (the Windows computer program available at: https://www.ukw.edu.pl/pracownicy/plik/igor_chybicki/1806/) that, among others, allows for selecting phenotypic variables important for male fecundity and assessing the fraction of variance in fecundity (R² ) explained by selected variables. Simulations showed that our method outperforms both the classic neighborhood model and the two-step approach, where fecundities and the effects of phenotypic variables are estimated separately. The analysis of two data examples showed that in wind-pollinated trees, male fecundity depends on both the amount of produced pollen and the ability to pollen spread. However, despite that the tree size was positively correlated with male fecundity, it explained only a fraction of the total variance in fecundity, indicating the presence of additional factors. Finally, case studies highlighted the importance of accounting for pollen dispersal in the estimation of fecundity determinants.

Fine-scale spatial genetic structure, mating, and gene dispersal patterns in Parkia biglobosa populations with different levels of habitat fragmentation

PREMISE

A good understanding of genetic variation and gene dispersal in tree populations is crucial for their sustainable management, particularly in a context of rapid environmental changes. West African Sudanian savannahs are being fragmented and degraded, partly due to expansion of crop cultivation and monocultures that reduce tree density and may impact pollinators. The population dynamics of important indigenous trees could also be affected. We investigated the influence of habitat fragmentation on patterns of genetic diversity and gene dispersal of a key Sudanian agroforestry tree species, Parkia biglobosa.

METHODS

Using 10 highly polymorphic nuclear microsatellites, we genotyped 2475 samples from reproductive trees, seedlings, and embryos in four tree populations presenting different levels of habitat fragmentation.

RESULTS

Parkia biglobosa presented similar high genetic diversity across the four populations studied. Genetic diversity and inbreeding were similar between adults and embryo cohorts. In all four populations, the selfing rate was less than 1%. The effective number of pollen donors per tree was high (N_EP ~ 18-22), as was the pollen immigration rate (from 34 to 74%). Pollen dispersal was characterized by a fat-tailed distribution with mean estimates exceeding 200 m. In three populations, stem diameter had a pronounced effect on male reproductive success. Here, the highest male reproductive success was observed in trees with a diameter at breast height between 60 and 75 cm.

CONCLUSIONS

At the scale analyzed, fragmentation does not seem to pose limitations to gene flow in any of the sites investigated, regardless of the landscape configuration associated with the different tree stands. The study provides useful insights on the reproductive biology of an important tree species in the West African savannahs.

Individual reproductive success in Norway spruce natural populations depends on growth rate, age and sensitivity to temperature

Quantifying the individual reproductive success and understanding its determinants is a central issue in evolutionary research for the major consequences that the transmission of genetic variation from parents to offspring has on the adaptive potential of populations. Here, we propose to distil the myriad of information embedded in tree-ring time series into a set of tree-ring-based phenotypic traits to be investigated as potential drivers of reproductive success in forest trees. By using a cross-disciplinary approach that combines parentage analysis and a thorough dendrophenotypic characterisation of putative parents, we assessed sex-specific relationships between such dendrophenotypic traits (i.e., age, growth rate and parameters describing sensitivity to climate and to extreme climatic events) and reproductive success in Norway spruce. We applied a full probability method for reconstructing parent-offspring relationships between 604 seedlings and 518 adult trees sampled within five populations from southern and central Europe. We found that individual female and male reproductive success was positively associated with tree growth rate and age. Female reproductive success was also positively influenced by the correlation between growth and the mean temperature of the previous vegetative season. Overall, our results showed that Norway spruce individuals with the highest fitness are those who are able to keep high-growth rates despite potential growth limitations caused by reproductive costs and climatic limiting conditions. Identifying such functional links between the individual ecophysiological behaviour and its evolutionary gain would increase our understanding on how natural selection shapes the genetic composition of forest tree populations over time.

The future of parentage analysis: From microsatellites to SNPs and beyond

Parentage analysis is a cornerstone of molecular ecology that has delivered fundamental insights into behaviour, ecology and evolution. Microsatellite markers have long been the king of parentage, their hypervariable nature conferring sufficient power to correctly assign offspring to parents. However, microsatellite markers have seen a sharp decline in use with the rise of next-generation sequencing technologies, especially in the study of population genetics and local adaptation. The time is ripe to review the current state of parentage analysis and see how it stands to be affected by the emergence of next-generation sequencing approaches. We find that single nucleotide polymorphisms (SNPs), the typical next-generation sequencing marker, remain underutilized in parentage analysis but are gaining momentum, with 58 SNP-based parentage analyses published thus far. Many of these papers, particularly the earlier ones, compare the power of SNPs and microsatellites in a parentage context. In virtually every case, SNPs are at least as powerful as microsatellite markers. As few as 100-500 SNPs are sufficient to resolve parentage completely in most situations. We also provide an overview of the analytical programs that are commonly used and compatible with SNP data. As the next-generation parentage enterprise grows, a reliance on likelihood and Bayesian approaches, as opposed to strict exclusion, will become increasingly important. We discuss some of the caveats surrounding the use of next-generation sequencing data for parentage analysis and conclude that the future is bright for this important realm of molecular ecology.

Seed and pollen gene dispersal in Taxus baccata, a dioecious conifer in the face of strong population fragmentation

Background and Aims

Dispersal is crucial due to its direct impact on dynamics of a species' distribution as well as having a role in shaping adaptive potential through gene flow. In plants forming scarce and small populations, knowledge about the dispersal process is required to assess the potential for colonizing new habitats and connectivity of present and future populations. This study aimed to assess dispersal potential in Taxus baccata, a dioecious gymnosperm tree with a wide but highly fragmented distribution.

Methods

Seed and pollen dispersal kernels were estimated directly in the framework of the spatially explicit mating model, where genealogies of naturally established seedlings were reconstructed with the help of microsatellite markers. In this way, six differently shaped dispersal functions were compared.

Key Results

Seed dispersal followed a leptokurtic distribution, with the Exponential-Power, the Power-law and Weibull being almost equally best-fitting models. The pollen dispersal kernel appeared to be more fat-tailed than the seed dispersal kernel, and the Lognormal and the Exponential-Power function showed the best fit. The rate of seed immigration from the background sources was not significantly different from the rate of pollen immigration (13.1 % vs. 19.7 %) and immigration rates were in agreement with or below maximum predictions based on the estimated dispersal kernels. Based on the multimodel approach, 95 % of seeds travel <109 m, while 95 % of pollen travels <704 m from the source.

Conclusions

The results showed that, at a local spatial scale, yew seeds travel shorter distances than pollen, facilitating a rapid development of a kinship structure. At the landscape level, however, although yew exhibits some potential to colonize new habitats through seed dispersal, genetic connectivity between different yew remnants is strongly limited. Taking into account strong population fragmentation, the study suggests that gene dispersal may be a limiting factor of the adaptability of the species.