The relative contributions of seed and pollen dispersal to gene flow and genetic diversity in seedlings of a tropical palm

Effective dispersal patterns in prairie plant species across human-modified landscapes

Effective dispersal among plant populations is dependent on vector behaviour, landscape features and availability of adequate habitats. To capture landscape feature effects on dispersal, studies must be conducted at scales reflecting single-generation dispersal events (mesoscale). Many studies are conducted at large scales where genetic differentiation is due to dispersal occurring over multiple generations, making it difficult to interpret the effects of specific landscape features on vector behaviour. Genetic structure at the mesoscale may be determined by ecological and evolutionary processes, such as the consequences of vector behaviour on patterns of gene flow. We used chloroplast haplotypes and nuclear genome SNP surveys to identify landscape features influencing seed and pollen dispersal at a mesoscale within the Rogue River Valley in southern Oregon. We evaluated biotic and abiotic vector behaviour by contrasting two annual species with differing dispersal mechanisms; Achyrachaena mollis (Asteraceae) is a self-pollinating and anemochoric species, and Plectritis congesta (Caprifoliaceae) is biotically pollinated with barochoric seeds. Using landscape genetics methods, we identified features of the study region that conduct or restrict dispersal. We found chloroplast haplotypes were indicative of historic patterns of gene flow prior to human modification of landscapes. Seed dispersal of A. mollis was best supported by models of isolation by distance, while seed-driven gene flow of P. congesta was determined by the distribution of preserved natural spaces and quality habitat. Nuclear genetic structure was driven by both pollen and seed dispersal, and both species responded to contemporary landscape changes, such as urban and agricultural conversion, and habitat availability.

Leaf gene expression trajectories during the growing season are consistent between sites and years in American beech

Transcriptomics provides a versatile tool for ecological monitoring. Here, through genome-guided profiling of transcripts mapping to 33 042 gene models, expression differences can be discerned among multi-year and seasonal leaf samples collected from American beech trees at two latitudinally separated sites. Despite a bottleneck due to post-Columbian deforestation, the single nucleotide polymorphism-based population genetic background analysis has yielded sufficient variation to account for differences between populations and among individuals. Our expression analyses during spring-summer and summer-autumn transitions for two consecutive years involved 4197 differentially expressed protein coding genes. Using Populus orthologues we reconstructed a protein-protein interactome representing leaf physiological states of trees during the seasonal transitions. Gene set enrichment analysis revealed gene ontology terms that highlight molecular functions and biological processes possibly influenced by abiotic forcings such as recovery from drought and response to excess precipitation. Further, based on 324 co-regulated transcripts, we focused on a subset of GO terms that could be putatively attributed to late spring phenological shifts. Our conservative results indicate that extended transcriptome-based monitoring of forests can capture diverse ranges of responses including air quality, chronic disease, as well as herbivore outbreaks that require activation and/or downregulation of genes collectively tuning reaction norms maintaining the survival of long living trees such as the American beech.

Examining the spatiotemporal variation of genetic diversity and genetic rarity in the natural plant recolonization of human-altered areas

The spatiotemporal genetic variation at early plant life stages may substantially affect the natural recolonization of human-altered areas, which is crucial to understand plant and habitat conservation. In animal-dispersed plants, dispersers’ behavior may critically drive the distribution of genetic variation. Here, we examine how genetic rarity is spatially and temporally structured in seedlings of a keystone pioneer palm (Chamaerops humilis) and how the variation of genetic rarity could ultimately affect plant recruitment. We intensively monitored the seed rain mediated by two medium-sized carnivores during two consecutive seasons in a Mediterranean human-altered area. We genotyped 143 out of 309 detected seedlings using 12 microsatellite markers. We found that seedlings emerging from carnivore-dispersed seeds showed moderate to high levels of genetic diversity and no evidence of inbreeding. We found inflated kinship among seedlings that emerged from seeds within a single carnivore fecal sample, but a dilution of such FSGS at larger spatial scales (e.g. latrine). Seedlings showed a significant genetic sub-structure and the sibling relationships varied depending on the spatial scale. Rare genotypes arrived slightly later throughout the dispersal season and tended to be spatially isolated. However, genetic rarity was not a significant predictor by itself which indicates that, at least, its influence on seedling survival was smaller than other spatiotemporal factors. Our results suggest strong C. humilis resilience to genetic bottlenecks due to human disturbances. We highlight the study of plant-animal interactions from a genetic perspective since it provides crucial information for plant conservation and the recovery of genetic plant resilience.

Differential ability of three bee species to move genes via pollen

Since the release of genetically engineered (GE) crops, there has been increased concern about the introduction of GE genes into non-GE fields of a crop and their spread to feral or wild cross-compatible relatives. More recently, attention has been given to the differential impact of distinct pollinators on gene flow, with the goal of developing isolation distances associated with specific managed pollinators. To examine the differential impact of bee species on gene movement, we quantified the relationship between the probability of getting a GE seed in a pod, and the order in which a flower was visited, or the cumulative distance traveled by a bee in a foraging bout. We refer to these relationships as 'seed curves' and compare these seeds curves among three bee species. The experiments used Medicago sativa L. plants carrying three copies of the glyphosate resistance (GR) allele as pollen donors (M. sativa is a tetraploid), such that each pollen grain carried the GR allele, and conventional plants as pollen recipients. Different foraging metrics, including the number of GR seeds produced over a foraging bout, were also quantified and contrasted among bee species. The lowest number of GR seeds set per foraging bout, and the GR seeds set at the shortest distances, were produced following leafcutting bee visits. In contrast, GR seeds were found at the longest distances following bumble bee visits. Values for honey bees were intermediate. The ranking of bee species based on seed curves correlated well with field-based gene flow estimates. Thus, differential seed curves of bee species, which describe patterns of seed production within foraging bouts, translated into distinct abilities of bee species to move genes at a landscape level. Bee behavior at a local scale (foraging bout) helps predict gene flow and the spread of GE genes at the landscape scale.

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.

Environmental factors have a major effect in shaping the gene expression of Siberian larch in the Altai Mountains of China

The differentiation of gene expression is an important link between genotype and phenotype and has important contributions to species adaptation and ecosystem evolution. As a major component of the world's forests, boreal forests play an important role in regulating the global climate, and the phenology of tree species has been and is undergoing changes during global warming. Here, to understand the impact of global warming on gene expression in boreal forest species, we used PacBio and Illumina sequencing methods to study the transcriptome of natural populations of Siberian larch (Larix sibirica Ledeb.) from the Altai Mountains in Xinjiang, China. We found that populations in this area had low genetic differentiation, but individuals were genetically clustered together when they had close geographic distance. Environmental factors, especially temperature, dominated differential gene expression of Siberian larch, while the contribution of genetic variation is relatively small. We speculate that Siberian larch adapts to changes in temperature and precipitation by altering its own gene expression. These results not only predict the tolerance of boreal forests to higher temperatures in the future, but also inform forest management strategies under global climate change.

Long-Distance Pollen Dispersal in Urban Green Roof and Ground-Level Habitats

Long-distance pollen dispersal is critical for gene flow in plant populations, yet pollen dispersal patterns in urban habitats such as green roofs have not been extensively studied. Pollen dispersal patterns typically are assessed either by fitting non-linear models to the relationship between the degree of pollen dispersal and distance to the pollen source (i.e., curve fitting), or by fitting probability density functions (PDFs) to pollen dispersal probability histograms (i.e., PDF fitting). Studies using curve fitting typically report exponential decay patterns in pollen dispersal. However, PDF fitting typically produces more fat-tailed distributions, suggesting the exponential decay may not be the best fitting model. Because the two approaches may yield conflicting results, we used both approaches to examine pollen dispersal patterns in the wind-pollinated Amaranthus tuberculatus and the insect-pollinated Solanum lycopersicum at two green roof and two ground-level sites in the New York (NY, United States) metropolitan area. For the curve fitting analyses, the exponential decay and inverse power curves provided good fits to pollen dispersal patterns across both green roof and ground-level sites for both species. Similar patterns were observed with the PDF fitting analyses, where the exponential or inverse Gaussian were the top PDF at most sites for both species. While the curve fitting results are consistent with other studies, the results differ from most studies using PDF fitting, where long-distance pollen dispersal is more common than we observed. These results highlight the need for further research to compare curve and PDF fitting for predicting pollen dispersal patterns. And, critically, while long-distance pollen dispersal may be an important component of overall pollen dispersal for A. tuberculatus and S. lycopersicum in both urban green roof and ground-level sites, our results suggest it potentially may occur to a lesser extent compared with plants in less-urban areas.

Small mammal personalities generate context dependence in the seed dispersal mutualism

Mutualisms are foundational components of ecosystems with the capacity to generate biodiversity through adaptation and coevolution and give rise to essential services such as pollination and seed dispersal. To understand how mutualistic interactions shape communities and ecosystems, we must identify the mechanisms that underlie their functioning. One mechanism that may drive mutualisms to vary in space and time is the unique behavioral types, or personalities, of the individuals involved. Here, our goal was to examine interindividual variation in the seed dispersal mutualism and identify the role that different personalities play. In a field experiment, we observed individual deer mice (Peromyscus maniculatus) with known personality traits predating and dispersing seeds in a natural environment and classified all observed interactions made by individuals as either positive or negative. We then scored mice on a continuum from antagonistic to mutualistic and found that within a population of scatter hoarders, some individuals are more mutualistic than others and that one factor driving this distinction is animal personality. Through this empirical work, we provide a conceptual advancement to the study of mutualism by integrating it with the study of intraspecific behavioral variation. These findings indicate that animal personality is a previously overlooked mechanism generating context dependence in plant–animal interactions and suggest that behavioral diversity may have important consequences for the functioning of mutualisms.

Forest cover at landscape scales increases male and female gametic diversity of palm seedlings

Genetic diversity shapes the evolutionary potential of plant populations. For outcrossing plants, genetic diversity is influenced by effective population size and by dispersal, first of paternal gametes through pollen, and then of paternal and maternal gametes through seeds. Forest loss often reduces genetic diversity, but the degree to which it differentially impacts the paternal and maternal contributions to genetic diversity and the spatial scale at which these impacts are most pronounced are poorly understood. To address these questions, we genotyped 504 seedlings of the animal-dispersed palm Oenocarpus bataua collected from 29 widely distributed sites across Ecuador and decomposed the contribution of paternal and maternal gametes to overall genetic diversity. The amount of forest cover at a landscape scale (>10 km radius) had an equally significant positive association with both male and female gametic diversity. In addition, there was a significant positive association between forest cover and effective population size. Stronger fine-scale spatial genetic structure for female versus male gametes was observed at sites with low forest cover, but this did not scale up to differences in male versus female gametic diversity. These findings show that reductions in forest cover at spatial scales much larger than those typically evaluated in ecological studies lead to significant, and equivalent, decreases of diversity in both male and female gametes, and that this association between landscape level forest loss and genetic diversity may be driven directly by reductions in effective population size of O. bataua, rather than by indirect disruptions to local dispersal processes.

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.

Life history, climate and biogeography interactively affect worldwide genetic diversity of plant and animal populations

Understanding how biological and environmental factors interactively shape the global distribution of plant and animal genetic diversity is fundamental to biodiversity conservation. Genetic diversity measured in local populations (GDP) is correspondingly assumed representative for population fitness and eco-evolutionary dynamics. For 8356 populations across the globe, we report that plants systematically display much lower GDP than animals, and that life history traits shape GDP patterns both directly (animal longevity and size), and indirectly by mediating core-periphery patterns (animal fecundity and plant dispersal). Particularly in some plant groups, peripheral populations can sustain similar GDP as core populations, emphasizing their potential conservation value. We further find surprisingly weak support for general latitudinal GDP trends. Finally, contemporary rather than past climate contributes to the spatial distribution of GDP, suggesting that contemporary environmental changes affect global patterns of GDP. Our findings generate new perspectives for the conservation of genetic resources at worldwide and taxonomic-wide scales.

Landscape Genetics of Plants: Challenges and Opportunities

Dispersal is one of the most important but least understood processes in plant ecology and evolutionary biology. Dispersal of seeds maintains and establishes populations, and pollen and seed dispersal are responsible for gene flow within and among populations. Traditional views of dispersal and gene flow assume models that are governed solely by geographic distance and do not account for variation in dispersal vector behavior in response to heterogenous landscapes. Landscape genetics integrates population genetics with Geographic Information Systems (GIS) to evaluate the effects of landscape features on gene flow patterns (effective dispersal). Surprisingly, relatively few landscape genetic studies have been conducted on plants. Plants present advantages because their populations are stationary, allowing more reliable estimates of the effects of landscape features on effective dispersal rates. On the other hand, plant dispersal is intrinsically complex because it depends on the habitat preferences of the plant and its pollen and seed dispersal vectors. We discuss strategies to assess the separate contributions of pollen and seed movement to effective dispersal and to delineate the effects of plant habitat quality from those of landscape features that affect vector behavior. Preliminary analyses of seed dispersal for three species indicate that isolation by landscape resistance is a better predictor of the rates and patterns of dispersal than geographic distance. Rates of effective dispersal are lower in areas of high plant habitat quality, which may be due to the effects of the shape of the dispersal kernel or to movement behaviors of biotic vectors. Landscape genetic studies in plants have the potential to provide novel insights into the process of gene flow among populations and to improve our understanding of the behavior of biotic and abiotic dispersal vectors in response to heterogeneous landscapes.

Multiscale spatial genetic structure within and between populations of wild cherry trees in nuclear genotypes and chloroplast haplotypes

Spatial genetic structure (SGS) of plants mainly depends on the effective population size and gene dispersal. Maternally inherited loci are expected to have higher genetic differentiation between populations and more intensive SGS within populations than biparentally inherited loci because of smaller effective population sizes and fewer opportunities of gene dispersal in the maternally inherited loci. We investigated biparentally inherited nuclear genotypes and maternally inherited chloroplast haplotypes of microsatellites in 17 tree populations of three wild cherry species under different conditions of tree distribution and seed dispersal. As expected, interpopulation genetic differentiation was 6-9 times higher in chloroplast haplotypes than in nuclear genotypes. This difference indicated that pollen flow 4-7 times exceeded seed flow between populations. However, no difference between nuclear and chloroplast loci was detected in within-population SGS intensity due to their substantial variation among the populations. The SGS intensity tended to increase as trees became more aggregated, suggesting that tree aggregation biased pollen and seed dispersal distances toward shorter. The loss of effective seed dispersers, Asian black bears, did not affect the SGS intensity probably because of mitigation of the bear loss by other vertebrate dispersers and too few tree generations after the bear loss to alter SGS. The findings suggest that SGS is more variable in smaller spatial scales due to various ecological factors in local populations.